|
1
|
Ye J, Boileau RM, Parchem RJ, Judson-Torres RL, Blelloch R. The miR-290 and miR-302 clusters are essential for reprogramming of fibroblasts to induced pluripotent stem cells. Stem Cells 2025; 43:sxae080. [PMID: 40037390 PMCID: PMC11879289 DOI: 10.1093/stmcls/sxae080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Accepted: 10/24/2024] [Indexed: 03/06/2025]
Abstract
The miR-290 and miR-302 clusters of microRNAs are highly expressed in naïve and primed pluripotent stem cells, respectively. Ectopic expression of the embryonic stem cell (ESC)-specific cell cycle regulating family of microRNAs arising from these two clusters dramatically enhances the reprogramming of both mouse and human somatic cells to induced pluripotency. Here, we used genetic knockouts to dissect the requirement for the miR-290 and miR-302 clusters during the reprogramming of mouse fibroblasts into induced pluripotent stem cells (iPSCs) with retrovirally introduced Oct4, Sox2, and Klf4. Knockout of either cluster alone did not negatively impact the efficiency of reprogramming. Resulting cells appeared identical to their ESC microRNA cluster knockout counterparts. In contrast, the combined loss of both clusters blocked the formation of iPSCs. While rare double knockout clones could be isolated, they showed a dramatically reduced proliferation rate, a persistent inability to fully silence the exogenously introduced pluripotency factors, and a transcriptome distinct from individual miR-290 or miR-302 mutant ESC and iPSCs. Taken together, our data show that miR-290 and miR-302 are essential yet interchangeable in reprogramming to the induced pluripotent state.
Collapse
Affiliation(s)
- Julia Ye
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California at San Francisco, San Francisco, CA 94143, United States
- Center for Reproductive Sciences, University of California at San Francisco, San Francisco, CA 94143, United States
- Department of Urology, University of California at San Francisco, San Francisco, CA 94143, United States
| | - Ryan M Boileau
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California at San Francisco, San Francisco, CA 94143, United States
- Center for Reproductive Sciences, University of California at San Francisco, San Francisco, CA 94143, United States
- Department of Urology, University of California at San Francisco, San Francisco, CA 94143, United States
| | - Ronald J Parchem
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Robert L Judson-Torres
- Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT 84112, United States
- Department of Dermatology, The University of Utah, Salt Lake City, UT 84112, United States
| | - Robert Blelloch
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California at San Francisco, San Francisco, CA 94143, United States
- Center for Reproductive Sciences, University of California at San Francisco, San Francisco, CA 94143, United States
- Department of Urology, University of California at San Francisco, San Francisco, CA 94143, United States
| |
Collapse
|
|
2
|
Brown T, Mishra K, Elewa A, Iarovenko S, Subramanian E, Araus AJ, Petzold A, Fromm B, Friedländer MR, Rikk L, Suzuki M, Suzuki KIT, Hayashi T, Toyoda A, Oliveira CR, Osipova E, Leigh ND, Yun MH, Simon A. Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration. CELL GENOMICS 2025; 5:100761. [PMID: 39874962 PMCID: PMC11872487 DOI: 10.1016/j.xgen.2025.100761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 12/04/2024] [Accepted: 01/03/2025] [Indexed: 01/30/2025]
Abstract
Newts have large genomes harboring many repeat elements. How these elements shape the genome and relate to newts' unique regeneration ability remains unknown. We present here the chromosome-scale assembly of the 20.3 Gb genome of the Iberian ribbed newt, Pleurodeles waltl, with a hitherto unprecedented contiguity and completeness among giant genomes. Utilizing this assembly, we demonstrate conserved synteny as well as genetic rearrangements, such as in the major histocompatibility complex locus. We provide evidence suggesting that intronic repeat elements drive newt-specific circular RNA (circRNA) biogenesis and show their regeneration-specific expression. We also present a comprehensive in-depth annotation and chromosomal mapping of microRNAs, highlighting genomic expansion profiles as well as a distinct regulatory pattern in the regenerating limb. These data reveal links between repeat elements, non-coding RNAs, and adult regeneration and provide key resources for addressing developmental, regenerative, and evolutionary principles.
Collapse
Affiliation(s)
- Thomas Brown
- DRESDEN-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01307 Dresden, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Ketan Mishra
- Department of Cell and Molecular Biology, Karolinska Institute, 171 65 Stockholm, Sweden
| | - Ahmed Elewa
- Department of Biology, Augsburg University, Minneapolis, MN 55454, USA
| | - Svetlana Iarovenko
- CRTD Center for Regenerative Therapies Dresden, Technische Universität Dresden, 01307 Dresden, Germany
| | - Elaiyaraja Subramanian
- Department of Cell and Molecular Biology, Karolinska Institute, 171 65 Stockholm, Sweden
| | - Alberto Joven Araus
- Department of Cell and Molecular Biology, Karolinska Institute, 171 65 Stockholm, Sweden
| | - Andreas Petzold
- DRESDEN-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01307 Dresden, Germany
| | - Bastian Fromm
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, 9006 Tromsø, Norway
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 114 18 Stockholm, Sweden
| | - Lennart Rikk
- Molecular Medicine and Gene Therapy, Wallenberg Centre for Molecular Medicine, Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
| | - Miyuki Suzuki
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ken-Ichi T Suzuki
- Emerging Model Organisms Facility, Trans-scale Biology Center, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Toshinori Hayashi
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8511, Japan; Amphibian Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8511, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan
| | - Catarina R Oliveira
- CRTD Center for Regenerative Therapies Dresden, Technische Universität Dresden, 01307 Dresden, Germany
| | - Ekaterina Osipova
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany
| | - Nicholas D Leigh
- Molecular Medicine and Gene Therapy, Wallenberg Centre for Molecular Medicine, Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden.
| | - Maximina H Yun
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; CRTD Center for Regenerative Therapies Dresden, Technische Universität Dresden, 01307 Dresden, Germany; Physics of Life Excellence Cluster Dresden, 01307 Dresden, Germany.
| | - András Simon
- Department of Cell and Molecular Biology, Karolinska Institute, 171 65 Stockholm, Sweden.
| |
Collapse
|
|
3
|
Loehr AR, Timmerman DM, Liu M, Gillis AJM, Matthews M, Bloom JC, Nicholls PK, Page DC, Miller AD, Looijenga LHJ, Weiss RS. Analysis of a mouse germ cell tumor model establishes pluripotency-associated miRNAs as conserved serum biomarkers for germ cell cancer detection. Sci Rep 2025; 15:4452. [PMID: 39910147 PMCID: PMC11799207 DOI: 10.1038/s41598-025-88554-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 01/29/2025] [Indexed: 02/07/2025] Open
Abstract
Malignant testicular germ cells tumors (TGCTs) are the most common solid cancers in young men. Current TGCT diagnostics include conventional serum protein markers, but these lack the sensitivity and specificity to serve as accurate markers across all TGCT subtypes. MicroRNAs (miRNAs) are small non-coding regulatory RNAs and informative biomarkers for several diseases. In humans, miRNAs of the miR-371-373 cluster are detectable in the serum of patients with malignant TGCTs and outperform existing serum protein markers for both initial diagnosis and subsequent disease monitoring. We previously developed a genetically engineered mouse model featuring malignant mixed TGCTs consisting of pluripotent embryonal carcinoma (EC) and differentiated teratoma that, like the corresponding human malignancies, originate in utero and are highly chemosensitive. Here, we report that miRNAs in the mouse miR-290-295 cluster, homologs of the human miR-371-373 cluster, were detectable in serum from mice with malignant TGCTs but not from tumor-free control mice or mice with benign teratomas. miR-291-293 were expressed and secreted specifically by pluripotent EC cells, and expression was lost following differentiation induced by the drug thioridazine. Notably, miR-291-293 levels were significantly higher in the serum of pregnant dams carrying tumor-bearing fetuses compared to that of control dams. These findings reveal that expression of the miR-290-295 and miR-371-373 clusters in mice and humans, respectively, is a conserved feature of malignant TGCTs, further validating the mouse model as representative of the human disease. These data also highlight the potential of serum miR-371-373 assays to improve patient outcomes through early TGCT detection, possibly even prenatally.
Collapse
Affiliation(s)
- Amanda R Loehr
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | | | - Michelle Liu
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Ad J M Gillis
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Melia Matthews
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | | | | | - David C Page
- Whitehead Institute, Cambridge, MA, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew D Miller
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Leendert H J Looijenga
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
- Department of Pathology, University Medical Center, Utrecht, The Netherlands.
| | - Robert S Weiss
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA.
| |
Collapse
|
|
4
|
Yao M, Zhang L, Teng X, Lei Y, Xing X, Ren T, Pan Y, Zhang L, Li Z, Lin J, Zheng Y, Xing L, Zhou J, Wu C. Transcriptomic profiling of Dip2a in the neural differentiation of mouse embryonic stem cells. Comput Struct Biotechnol J 2024; 23:700-710. [PMID: 38292475 PMCID: PMC10825174 DOI: 10.1016/j.csbj.2023.12.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 02/01/2024] Open
Abstract
Introduction The disconnected-interacting protein 2 homolog A (DIP2A), a member of disconnected-interacting 2 protein family, has been shown to be involved in human nervous system-related mental illness. This protein is highly expressed in the nervous system of mouse. Mutation of mouse DIP2A causes defects in spine morphology and synaptic transmission, autism-like behaviors, and defective social novelty [5], [27], indicating that DIP2A is critical to the maintenance of neural development. However, the role of DIP2A in neural differentiation has yet to be investigated. Objective To determine the role of DIP2A in neural differentiation, a neural differentiation model was established using mouse embryonic stem cells (mESCs) and studied by using gene-knockout technology and RNA-sequencing-based transcriptome analysis. Results We found that DIP2A is not required for mESCs pluripotency maintenance, but loss of DIP2A causes the neural differentiation abnormalities in both N2B27 and KSR medium. Functional knockout of Dip2a gene also decreased proliferation of mESCs by perturbation of the cell cycle and profoundly inhibited the expression of a large number of neural development-associated genes which mainly enriched in spinal cord development and postsynapse assembly. Conclusions The results of this report demonstrate that DIP2A plays an essential role in regulating differentiation of mESCs towards the neural fate.
Collapse
Affiliation(s)
- Mingze Yao
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Lei Zhang
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
- Center of Reproductive Medicine, Children's Hospital of Shanxi and Women Health Center of Shanxi, Taiyuan 030006, China
| | - Xiaojuan Teng
- Dermatology Hospital, Southern Medical University, Guangzhou 510000, China
| | - Yu Lei
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Xiaoyu Xing
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Tinglin Ren
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Yuanqing Pan
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Liwen Zhang
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Zhengfeng Li
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510000, China
| | - Jingxia Lin
- Dermatology Hospital, Southern Medical University, Guangzhou 510000, China
| | - Yaowu Zheng
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Li Xing
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Jiajian Zhou
- Dermatology Hospital, Southern Medical University, Guangzhou 510000, China
| | - Changxin Wu
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| |
Collapse
|
|
5
|
Liu W, Zhang Q, Guo S, Wang H. The role of microRNAs regulation of endoplasmic reticulum stress in ischemia-reperfusion injury: A review. Int J Biol Macromol 2024; 283:137566. [PMID: 39542287 DOI: 10.1016/j.ijbiomac.2024.137566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Revised: 11/06/2024] [Accepted: 11/10/2024] [Indexed: 11/17/2024]
Abstract
The endoplasmic reticulum (ER) is an important organelle in eukaryotic cells, responsible for a range of biological functions such as the secretion, modification and folding of proteins, maintaining Ca2+ homeostasis and the synthesis of steroids/lipids, secreted proteins and membrane proteins. When cells are affected by internal or external factors, including abnormal energy metabolism, disrupted Ca2+ balance, altered glycosylation, drug toxicity, and so on, the unfolded or misfolded proteins accumulate in the ER, leading to the unfolded protein response (UPR) and ER stress. The abnormal ER stress has been reported to be involved in various pathological processes. MicroRNAs (miRNAs) are non-coding RNAs with the length of approximately 19-25 nucleotides. They control the expression of multiple genes through posttranscriptional gene silencing in eukaryotes or some viruses. Increasing evidence indicates that miRNAs are involved in various cellular functions and biological processes, such as cell proliferation and differentiation, growth and development, and metabolic homeostasis. Hence, miRNAs participate in multiple pathological processes. Recently, many studies have shown that miRNAs play an important role by regulating ER stress in ischemia-reperfusion (I/R) injury, but the relevant mechanisms are not fully understood. In this review, we reviewed the current understanding of ER stress, as well as the biogenesis and function of miRNAs, and focused on the role of miRNAs regulation of ER stress in I/R injury, with the aim of providing new targets for the treatment of I/R injury.
Collapse
Affiliation(s)
- Wanying Liu
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Qi Zhang
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Shiyun Guo
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Honggang Wang
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan 475004, China.
| |
Collapse
|
|
6
|
Zhang Q, Zhang Y, Guo S, Wang X, Wang H. Hydrogen sulfide plays an important role by regulating microRNA in different ischemia-reperfusion injury. Biochem Pharmacol 2024; 229:116503. [PMID: 39179120 DOI: 10.1016/j.bcp.2024.116503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/28/2024] [Accepted: 08/20/2024] [Indexed: 08/26/2024]
Abstract
MicroRNAs (miRNAs) are the short endogenous non-coding RNAs that regulate the expression of the target gene at posttranscriptional level through degrading or inhibiting the specific target messenger RNAs (mRNAs). MiRNAs regulate the expression of approximately one-third of protein coding genes, and in most cases inhibit gene expression. MiRNAs have been reported to regulate various biological processes, such as cell proliferation, apoptosis and differentiation. Therefore, miRNAs participate in multiple diseases, including ischemia-reperfusion (I/R) injury. Hydrogen sulfide (H2S) was once considered as a colorless, toxic and harmful gas with foul smelling. However, in recent years, it has been discovered that it is the third gas signaling molecule after carbon monoxide (CO) and nitric oxide (NO), with multiple important biological functions. Increasing evidence indicates that H2S plays a vital role in I/R injury through regulating miRNA, however, the mechanism has not been fully understood. In this review, we summarized the current knowledge about the role of H2S in I/R injury by regulating miRNAs, and analyzed its mechanism in detail.
Collapse
Affiliation(s)
- Qi Zhang
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Yanting Zhang
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Shiyun Guo
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Xiao Wang
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Honggang Wang
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan 475004, China.
| |
Collapse
|
|
7
|
Ye J, Boileau RM, Parchem RJ, Judson-Torres RL, Blelloch R. The miR-290 and miR-302 clusters are essential for reprogramming of fibroblasts to induced pluripotent stem cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.02.610895. [PMID: 39282363 PMCID: PMC11398367 DOI: 10.1101/2024.09.02.610895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2024]
Abstract
The miR-290 and miR-302 clusters of microRNAs are highly expressed in naïve and primed pluripotent stem cells, respectively. Ectopic expression of the embryonic stem cell-specific cell cycle regulating (ESCC) family of microRNAs arising from these two clusters dramatically enhances the reprogramming of both mouse and human somatic cells to induced pluripotency. Here, we used genetic knockouts to dissect the requirement for the miR-290 and miR-302 clusters during the reprogramming of mouse fibroblasts into induced pluripotent stem cells (iPSCs) with retrovirally introduced Oct4, Sox2, and Klf4. Knockout of either cluster alone did not negatively impact the efficiency of reprogramming. Resulting cells appeared identical to their embryonic stem cell microRNA cluster knockout counterparts. In contrast, the combined loss of both clusters blocked the formation of iPSCs. While rare double knockout clones could be isolated, they showed a dramatically reduced proliferation rate, a persistent inability to fully silence the exogenously introduced pluripotency factors, and a transcriptome distinct from individual miR-290 or miR-302 mutant ESC and iPSCs. Taken together, our data show that miR-290 and miR-302 are essential yet interchangeable in reprogramming to the induced pluripotent state. Impact Statement The process by which somatic cell reprogramming yields induced pluripotent stem cells (iPSCs) is incompletely understood. MicroRNAs from the miR-290 and miR-302 clusters have been shown to greatly increase reprogramming efficiency, but their requirement in the process has not been studied. Here, we examine this requirement by genetically removing the miRNA clusters in somatic cells. We discover that somatic cells lacking either, but not both, of these miRNA clusters can form iPSC cells. This work thus provides new important insight into mechanisms underlying reprogramming to pluripotency.
Collapse
Affiliation(s)
- Julia Ye
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, California, 94143, USA
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, California, 94143, USA
- Department of Urology, University of California, San Francisco, San Francisco, California, 94143, USA
| | - Ryan M. Boileau
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, California, 94143, USA
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, California, 94143, USA
- Department of Urology, University of California, San Francisco, San Francisco, California, 94143, USA
| | - Ronald J. Parchem
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Robert L. Judson-Torres
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Dermatology, University of Utah, Salt Lake City, UT 84112, USA
| | - Robert Blelloch
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, California, 94143, USA
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, California, 94143, USA
- Department of Urology, University of California, San Francisco, San Francisco, California, 94143, USA
| |
Collapse
|
|
8
|
Abulsoud AI, Elshaer SS, Rizk NI, Khaled R, Abdelfatah AM, Aboelyazed AM, Waseem AM, Bashier D, Mohammed OA, Elballal MS, Mageed SSA, Elrebehy MA, Zaki MB, Elesawy AE, El-Dakroury WA, Abdel-Reheim MA, Saber S, Doghish AS. Unraveling the miRNA Puzzle in Atherosclerosis: Revolutionizing Diagnosis, Prognosis, and Therapeutic Approaches. Curr Atheroscler Rep 2024; 26:395-410. [PMID: 38869707 DOI: 10.1007/s11883-024-01216-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2024] [Indexed: 06/14/2024]
Abstract
PURPOSE OF REVIEW To eradicate atherosclerotic diseases, novel biomarkers, and future therapy targets must reveal the burden of early atherosclerosis (AS), which occurs before life-threatening unstable plaques form. The chemical and biological features of microRNAs (miRNAs) make them interesting biomarkers for numerous diseases. We summarized the latest research on miRNA regulatory mechanisms in AS progression studies, which may help us use miRNAs as biomarkers and treatments for difficult-to-treat diseases. RECENT FINDINGS Recent research has demonstrated that miRNAs have a regulatory function in the observed changes in gene and protein expression during atherogenesis, the process that leads to atherosclerosis. Several miRNAs play a role in the development of atherosclerosis, and these miRNAs could potentially serve as non-invasive biomarkers for atherosclerosis in various regions of the body. These miRNAs have the potential to serve as biomarkers and targets for early treatment of atherosclerosis. The start and development of AS require different miRNAs. It reviews new research on miRNAs affecting endothelium, vascular smooth muscle, vascular inflammation, lipid retention, and cholesterol metabolism in AS. A miRNA gene expression profile circulates with AS everywhere. AS therapies include lipid metabolism, inflammation reduction, and oxidative stress inhibition. Clinical use of miRNAs requires tremendous progress. We think tiny miRNAs can enable personalized treatment.
Collapse
Affiliation(s)
- Ahmed I Abulsoud
- Biochemistry Department, Faculty of Pharmacy, Heliopolis University, Cairo, 11785, Egypt
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, Cairo, 11231, Egypt
| | - Shereen Saeid Elshaer
- Biochemistry Department, Faculty of Pharmacy, Heliopolis University, Cairo, 11785, Egypt
- Department of Biochemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Nasr City, Cairo, 11823, Egypt
| | - Nehal I Rizk
- Biochemistry Department, Faculty of Pharmacy, Heliopolis University, Cairo, 11785, Egypt
| | - Reem Khaled
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo, 11829, Egypt
| | - Amr M Abdelfatah
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Badr University in Cairo, Badr City, Cairo, 11829, Egypt
| | - Ahmed M Aboelyazed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo, 11829, Egypt
| | - Aly M Waseem
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Badr University in Cairo, Badr City, Cairo, 11829, Egypt
| | | | - Osama A Mohammed
- Department of Pharmacology, College of Medicine, University of Bisha, 61922, Bisha, Saudi Arabia
| | - Mohammed S Elballal
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo, 11829, Egypt
| | - Sherif S Abdel Mageed
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo, 11829, Egypt
| | - Mahmoud A Elrebehy
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo, 11829, Egypt
| | - Mohamed Bakr Zaki
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Biochemistry, 32897, Menoufia, Egypt
| | - Ahmed E Elesawy
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo, 11829, Egypt
| | - Walaa A El-Dakroury
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo, 11829, Egypt
| | - Mustafa Ahmed Abdel-Reheim
- Department of Pharmaceutical Sciences, College of Pharmacy, Shaqra University, 11961, Shaqra, Saudi Arabia.
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Beni-Suef University, Beni Suef, 62521, Egypt.
| | - Sameh Saber
- Department of Pharmacology, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa, 11152, Egypt
| | - Ahmed S Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo, 11829, Egypt.
- Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, Cairo, 11231, Egypt.
| |
Collapse
|
|
9
|
Liu Q, Pepin RM, Novak MK, Maschhoff KR, Worner K, Hu W. AGO1 controls protein folding in mouse embryonic stem cell fate decisions. Dev Cell 2024; 59:979-990.e5. [PMID: 38458189 DOI: 10.1016/j.devcel.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/27/2023] [Accepted: 02/12/2024] [Indexed: 03/10/2024]
Abstract
Argonaute (AGO) proteins are evolutionarily conserved RNA-binding proteins that control gene expression through the small RNAs they interact with. Whether AGOs have regulatory roles independent of RNAs, however, is unknown. Here, we show that AGO1 controls cell fate decisions through facilitating protein folding. We found that in mouse embryonic stem cells (mESCs), while AGO2 facilitates differentiation via the microRNA (miRNA) pathway, AGO1 controls stemness independently of its binding to small RNAs. We determined that AGO1 specifically interacts with HOP, a co-chaperone for the HSP70 and HSP90 chaperones, and enhances the folding of a set of HOP client proteins with intrinsically disordered regions. This AGO1-mediated facilitation of protein folding is important for maintaining stemness in mESCs. Our results demonstrate divergent functions between AGO1 and AGO2 in controlling cellular states and identify an RNA-independent function of AGO1 in controlling gene expression and cell fate decisions.
Collapse
Affiliation(s)
- Qiuying Liu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Rachel M Pepin
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Mariah K Novak
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Katharine R Maschhoff
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Kailey Worner
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Wenqian Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA.
| |
Collapse
|
|
10
|
Shi Y, Yang W, Lin H, Han L, Cai AJ, Saraf R, Lei Y, Zhang C. Identification of RNA-based cell-type markers for stem-cell manufacturing systems with a statistical scoring function. GENE REPORTS 2024; 34:101869. [PMID: 38351912 PMCID: PMC10861185 DOI: 10.1016/j.genrep.2023.101869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Cell-type biomarkers are useful in stem-cell manufacturing to monitor cell purity, quantity, and quality. However, the study on cell-type markers, specifically for stem cell manufacture, is limited. Emerging questions include which RNA transcripts can serve as biomarkers during stem cell culture and how to discover these biomarkers efficiently and precisely. We developed a scoring function system to identify RNA biomarkers with RNA-seq data for systems that have a limited number of cell types. We applied the method to two data sets, one for extracellular RNAs (ex-RNAs) and the other for intracellular microRNAs (miRNAs). The first data set has RNA-seq data of ex-RNAs from cell culture media for six different types of cells, including human embryonic stem cells. To get the RNA-seq data from intracellular miRNAs, we cultured three types of cells: human embryonic stem cells (H9), neural stem cells (NSC), hESC-derived endothelial cells (EC) and conducted small RNA-seq to their intracellular miRNAs. Using these data, we identified a set of ex-RNAs/smRNAs as candidates of biomarkers for different types of cells for cell manufacture. The validity of these findings was confirmed by the utilization of additional data sets and experimental procedures. We also used deep-learning-based prediction methods and simulated data to validate these discovered biomarkers.
Collapse
Affiliation(s)
- Yu Shi
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Weilong Yang
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Haishuang Lin
- Department of Chemical and Biomolecular Engineering, University of Nebraska, Lincoln, NE, USA
| | - Li Han
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Alyssa J. Cai
- Newark Academy, 91 W S Orange Ave, Livingston, NJ, USA
| | - Ravi Saraf
- Department of Chemical and Biomolecular Engineering, University of Nebraska, Lincoln, NE, USA
| | - Yuguo Lei
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Chi Zhang
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| |
Collapse
|
|
11
|
Bryant CJ, McCool MA, Rosado González G, Abriola L, Surovtseva Y, Baserga S. Discovery of novel microRNA mimic repressors of ribosome biogenesis. Nucleic Acids Res 2024; 52:1988-2011. [PMID: 38197221 PMCID: PMC10899765 DOI: 10.1093/nar/gkad1235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 12/03/2023] [Accepted: 12/16/2023] [Indexed: 01/11/2024] Open
Abstract
While microRNAs and other non-coding RNAs are the next frontier of novel regulators of mammalian ribosome biogenesis (RB), a systematic exploration of microRNA-mediated RB regulation has not yet been undertaken. We carried out a high-content screen in MCF10A cells for changes in nucleolar number using a library of 2603 mature human microRNA mimics. Following a secondary screen for nucleolar rRNA biogenesis inhibition, we identified 72 novel microRNA negative regulators of RB after stringent hit calling. Hits included 27 well-conserved microRNAs present in MirGeneDB, and were enriched for mRNA targets encoding proteins with nucleolar localization or functions in cell cycle regulation. Rigorous selection and validation of a subset of 15 microRNA hits unexpectedly revealed that most of them caused dysregulated pre-rRNA processing, elucidating a novel role for microRNAs in RB regulation. Almost all hits impaired global protein synthesis and upregulated CDKN1A (p21) levels, while causing diverse effects on RNA Polymerase 1 (RNAP1) transcription and TP53 protein levels. We provide evidence that the MIR-28 siblings, hsa-miR-28-5p and hsa-miR-708-5p, potently target the ribosomal protein mRNA RPS28 via tandem primate-specific 3' UTR binding sites, causing a severe pre-18S pre-rRNA processing defect. Our work illuminates novel microRNA attenuators of RB, forging a promising new path for microRNA mimic chemotherapeutics.
Collapse
Affiliation(s)
- Carson J Bryant
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Mason A McCool
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, 06520, USA
| | | | - Laura Abriola
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, 06516, USA
| | - Yulia V Surovtseva
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, 06516, USA
| | - Susan J Baserga
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, 06520, USA
| |
Collapse
|
|
12
|
Liao L, Yao Z, Kong J, Zhang X, Li H, Chen W, Xie Q. Exploring the role of miRNAs in early chicken embryonic development and their significance. Poult Sci 2023; 102:103105. [PMID: 37852050 PMCID: PMC10587638 DOI: 10.1016/j.psj.2023.103105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 08/10/2023] [Accepted: 09/07/2023] [Indexed: 10/20/2023] Open
Abstract
In the early stages of embryonic development, a precise and strictly controlled hierarchy of gene expression is essential to ensure proper development of all cell types and organs. To better understand this gene control process, we constructed a small RNA library from 1- to 5-day-old chick embryos, and identified 2,459 miRNAs including 827 existing, 695 known, and 937 novel miRNAs with bioinformatic analysis. There was absolute high expression of a number of miRNAs in each stage, including gga-miR-363-3p (Em1d), gga-miR-26a-5p (Em2d and Em3d), gga-miR-10a-5p (Em4d), and gga-miR-199-5p (Em5d). We evaluated enriched miRNA profiles, identifying VEGF, Insulin, ErbB, MAPK, Hedgehog, TLR and Hippo signaling pathways as primary regulatory mechanisms enabling complex morphogenetic transformations within tight temporal constraints. Pathway analysis revealed miRNAs as pivotal nodes of interaction, coordinating cascades of gene expression critical for cell fate determination, proliferation, migration, and differentiation across germ layers and developing organ systems. Weighted Gene Co-Expression Network Analysis (WGCNA) generated hub miRNAs whose modular connections spanned regulatory networks, including: gga-miR-181a-3p (blue module), coordinating immunegenesis and myogenesis; gga-miR-126-3p (brown module), regulating vasculogenesis and angiogenesis; gga-miR-302c-5p (turquoise module), enabling pluripotency and self-renew; and gga-miR-429-3p (yellow module), modulating neurogenesis and osteogenesis. The findings of this study extend the knowledge of miRNA expression in early embryonic development of chickens, providing insights into the intricate gene control process that helps ensure proper development.
Collapse
Affiliation(s)
- Liqin Liao
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, China; Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou 510642, Guangdong, China
| | - Ziqi Yao
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jie Kong
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, China
| | - Xinheng Zhang
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, China; Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou 510642, Guangdong, China
| | - Hongxin Li
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China; Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou 510642, Guangdong, China
| | - Weiguo Chen
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, China
| | - Qingmei Xie
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China; South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, China; Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou 510642, Guangdong, China.
| |
Collapse
|
|
13
|
Bryant CJ, McCool MA, Rosado-González GT, Abriola L, Surovtseva YV, Baserga SJ. Discovery of novel microRNA mimic repressors of ribosome biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.17.526327. [PMID: 36824951 PMCID: PMC9949135 DOI: 10.1101/2023.02.17.526327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
While microRNAs and other non-coding RNAs are the next frontier of novel regulators of mammalian ribosome biogenesis (RB), a systematic exploration of microRNA-mediated RB regulation has not yet been undertaken. We carried out a high-content screen in MCF10A cells for changes in nucleolar number using a library of 2,603 mature human microRNA mimics. Following a secondary screen for nucleolar rRNA biogenesis inhibition, we identified 72 novel microRNA negative regulators of RB after stringent hit calling. Hits included 27 well-conserved microRNAs present in MirGeneDB, and were enriched for mRNA targets encoding proteins with nucleolar localization or functions in cell cycle regulation. Rigorous selection and validation of a subset of 15 microRNA hits unexpectedly revealed that most of them caused dysregulated pre-rRNA processing, elucidating a novel role for microRNAs in RB regulation. Almost all hits impaired global protein synthesis and upregulated CDKN1A ( p21 ) levels, while causing diverse effects on RNA Polymerase 1 (RNAP1) transcription and TP53 protein levels. We discovered that the MIR-28 siblings, hsa-miR-28-5p and hsa-miR-708-5p, directly and potently target the ribosomal protein mRNA RPS28 via tandem primate-specific 3' UTR binding sites, causing a severe pre-18S pre-rRNA processing defect. Our work illuminates novel microRNA attenuators of RB, forging a promising new path for microRNA mimic chemotherapeutics.
Collapse
|
|
14
|
Bailey S, Ferraresso M, Alonso-Crisostomo L, Ward D, Smith S, Nicholson JC, Saini H, Enright AJ, Scarpini CG, Coleman N, Murray MJ. Targeting oncogenic microRNAs from the miR-371~373 and miR-302/367 clusters in malignant germ cell tumours causes growth inhibition through cell cycle disruption. Br J Cancer 2023; 129:1451-1461. [PMID: 37789102 PMCID: PMC10628203 DOI: 10.1038/s41416-023-02453-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 09/13/2023] [Accepted: 09/21/2023] [Indexed: 10/05/2023] Open
Abstract
BACKGROUND MiR-371~373 and miR-302/367 cluster over-expression occurs in all malignant germ cell tumours (GCTs), regardless of age (paediatric/adult), site (gonadal/extragonadal), or subtype [seminoma, yolk sac tumour (YST), embryonal carcinoma (EC)]. Six of eight microRNAs from these clusters contain the seed sequence 'AAGUGC', determining mRNA targeting. Here we sought to identify the significance of these observations by targeting these microRNAs functionally. METHODS We targeted miR-371~373 and/or miR-302/367 clusters in malignant GCT cell lines, using CRISPR-Cas9, gapmer primary miR-302/367 transcript inhibition, and peptide nucleic acid (PNA) or locked nucleic acid (LNA)-DNA inhibition targeting miR-302a-d-3p, and undertook relevant functional assays. RESULTS MiR-302/367 cluster microRNAs made the largest contribution to AAGUGC seed abundance in malignant GCT cells, regardless of subtype (seminoma/YST/EC). Following the unsuccessful use of CRISPR-Cas9, gapmer, and PNA systems, LNA-DNA-based targeting resulted in growth inhibition in seminoma and YST cells. This was associated with the de-repression of multiple mRNAs targeted by AAGUGC seed-containing microRNAs, with pathway analysis confirming predominant disruption of Rho-GTPase signalling, vesicle organisation/transport, and cell cycle regulation, findings corroborated in clinical samples. Further LNA-DNA inhibitor studies confirmed direct cell cycle effects, with an increase of cells in G0/G1-phase and a decrease in S-phase. CONCLUSION Targeting of specific miR-371~373 and miR-302/367 microRNAs in malignant GCTs demonstrated their functional significance, with growth inhibition mediated through cell cycle disruption.
Collapse
Affiliation(s)
- Shivani Bailey
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
- Department of Paediatric Haematology and Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Marta Ferraresso
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | | | - Dawn Ward
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Stephen Smith
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - James C Nicholson
- Department of Paediatric Haematology and Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Harpreet Saini
- EMBL-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Anton J Enright
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Cinzia G Scarpini
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Nicholas Coleman
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK.
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK.
| | - Matthew J Murray
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK.
- Department of Paediatric Haematology and Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK.
| |
Collapse
|
|
15
|
Moradi S, Guenther S, Soori S, Sharifi-Zarchi A, Kuenne C, Khoddami V, Tavakol P, Kreutzer S, Braun T, Baharvand H. Time-resolved Small-RNA Sequencing Identifies MicroRNAs Critical for Formation of Embryonic Stem Cells from the Inner Cell Mass of Mouse Embryos. Stem Cell Rev Rep 2023; 19:2361-2377. [PMID: 37402099 DOI: 10.1007/s12015-023-10582-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2023] [Indexed: 07/05/2023]
Abstract
Cells of the inner cell mass (ICM) acquire a unique ability for unlimited self-renewal during transition into embryonic stem cells (ESCs) in vitro, while preserving their natural multi-lineage differentiation potential. Several different pathways have been identified to play roles in ESC formation but the function of non-coding RNAs in this process is poorly understood. Here, we describe several microRNAs (miRNAs) that are crucial for efficient generation of mouse ESCs from ICMs. Using small-RNA sequencing, we characterize dynamic changes in miRNA expression profiles during outgrowth of ICMs in a high-resolution, time-course dependent manner. We report several waves of miRNA transcription during ESC formation, to which miRNAs from the imprinted Dlk1-Dio3 locus contribute extensively. In silico analyses followed by functional investigations reveal that Dlk1-Dio3 locus-embedded miRNAs (miR-541-5p, miR-410-3p, and miR-381-3p), miR-183-5p, and miR-302b-3p promote, while miR-212-5p and let-7d-3p inhibit ESC formation. Collectively, these findings offer new mechanistic insights into the role of miRNAs during ESC derivation.
Collapse
Affiliation(s)
- Sharif Moradi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Stefan Guenther
- Department of Cardiac Development and Remodelling, Max-Planck Institute for Heart and Lung Research, Ludwigstr. 43, 61231, Bad Nauheim, Germany
| | - Samira Soori
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Ali Sharifi-Zarchi
- Computer Engineering Department, Sharif University of Technology, Tehran, Iran
| | - Carsten Kuenne
- Department of Cardiac Development and Remodelling, Max-Planck Institute for Heart and Lung Research, Ludwigstr. 43, 61231, Bad Nauheim, Germany
| | - Vahid Khoddami
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Pouya Tavakol
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Susanne Kreutzer
- Department of Cardiac Development and Remodelling, Max-Planck Institute for Heart and Lung Research, Ludwigstr. 43, 61231, Bad Nauheim, Germany
| | - Thomas Braun
- Department of Cardiac Development and Remodelling, Max-Planck Institute for Heart and Lung Research, Ludwigstr. 43, 61231, Bad Nauheim, Germany.
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
- Department of Developmental Biology, School of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran.
| |
Collapse
|
|
16
|
Loehr AR, Timmerman DM, Liu M, Gillis AJ, Matthews M, Bloom JC, Nicholls PK, Page DC, Miller AD, Looijenga LH, Weiss RS. Analysis of a mouse germ cell tumor model establishes pluripotency-associated miRNAs as conserved serum biomarkers for germ cell cancer detection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.09.556995. [PMID: 37745561 PMCID: PMC10515752 DOI: 10.1101/2023.09.09.556995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Malignant testicular germ cells tumors (TGCTs) are the most common solid cancers in young men. Current TGCT diagnostics include conventional serum protein markers, but these lack the sensitivity and specificity to serve as accurate markers across all TGCT subtypes. MicroRNAs (miRNAs) are small non-coding regulatory RNAs and informative biomarkers for several diseases. In humans, miRNAs of the miR-371-373 cluster are detectable in the serum of patients with malignant TGCTs and outperform existing serum protein markers for both initial diagnosis and subsequent disease monitoring. We previously developed a genetically engineered mouse model featuring malignant mixed TGCTs consisting of pluripotent embryonal carcinoma (EC) and differentiated teratoma that, like the corresponding human malignancies, originate in utero and are highly chemosensitive. Here, we report that miRNAs in the mouse miR-290-295 cluster, homologs of the human miR-371-373 cluster, were detectable in serum from mice with malignant TGCTs but not from tumor-free control mice or mice with benign teratomas. miR-291-293 were expressed and secreted specifically by pluripotent EC cells, and expression was lost following differentiation induced by the drug thioridazine. Notably, miR-291-293 levels were significantly higher in the serum of pregnant dams carrying tumor-bearing fetuses compared to that of control dams. These findings reveal that expression of the miR-290-295 and miR-371-373 clusters in mice and humans, respectively, is a conserved feature of malignant TGCTs, further validating the mouse model as representative of the human disease. These data also highlight the potential of serum miR-371-373 assays to improve patient outcomes through early TGCT detection, possibly even prenatally.
Collapse
Affiliation(s)
- Amanda R. Loehr
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY
| | | | - Michelle Liu
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY
| | - Ad J.M. Gillis
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Melia Matthews
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY
| | | | | | - David C. Page
- Whitehead Institute, Cambridge, MA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA
| | - Andrew D. Miller
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY
| | | | - Robert S. Weiss
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY
| |
Collapse
|
|
17
|
Reid KM, Sanchez-Nieto JM, Terrasse S, Faccenda D, Pernaute B, Campanella M, Rodriguez TA, Cobb BS. MicroRNAs Regulate Ca 2+ Homeostasis in Murine Embryonic Stem Cells. Cells 2023; 12:1957. [PMID: 37566036 PMCID: PMC10417630 DOI: 10.3390/cells12151957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/23/2023] [Accepted: 07/24/2023] [Indexed: 08/12/2023] Open
Abstract
MicroRNAs (miRNAs) are important regulators of embryonic stem cell (ESC) biology, and their study has identified key regulatory mechanisms. To find novel pathways regulated by miRNAs in ESCs, we undertook a bioinformatics analysis of gene pathways differently expressed in the absence of miRNAs due to the deletion of Dicer, which encodes an RNase that is essential for the synthesis of miRNAs. One pathway that stood out was Ca2+ signaling. Interestingly, we found that Dicer-/- ESCs had no difference in basal cytoplasmic Ca2+ levels but were hyperresponsive when Ca2+ import into the endoplasmic reticulum (ER) was blocked by thapsigargin. Remarkably, the increased Ca2+ response to thapsigargin in ESCs resulted in almost no increase in apoptosis and no differences in stress response pathways, despite the importance of miRNAs in the stress response of other cell types. The increased Ca2+ response in Dicer-/- ESCs was also observed during purinergic receptor activation, demonstrating a physiological role for the miRNA regulation of Ca2+ signaling pathways. In examining the mechanism of increased Ca2+ responsiveness to thapsigargin, neither store-operated Ca2+ entry nor Ca2+ clearance mechanisms from the cytoplasm appeared to be involved. Rather, it appeared to involve an increase in the expression of one isoform of the IP3 receptors (Itpr2). miRNA regulation of Itpr2 expression primarily appeared to be indirect, with transcriptional regulation playing a major role. Therefore, the miRNA regulation of Itpr2 expression offers a unique mechanism to regulate Ca2+ signaling pathways in the physiology of pluripotent stem cells.
Collapse
Affiliation(s)
- Kimberley M. Reid
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, 4 Royal College Street, London NW1 0TU, UK; (K.M.R.)
| | - Juan Miguel Sanchez-Nieto
- National Heart and Lung Institute, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK (T.A.R.)
| | - Sandra Terrasse
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, 4 Royal College Street, London NW1 0TU, UK; (K.M.R.)
| | - Danilo Faccenda
- Department of Clinical, Pharmaceutical and Biological Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK;
- Centre for Clinical Pharmacology and Precision Medicine, William Harvey Research Institute, Queen Mary University of London, London E1 4NS, UK;
| | - Barbara Pernaute
- National Heart and Lung Institute, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK (T.A.R.)
| | - Michelangelo Campanella
- Centre for Clinical Pharmacology and Precision Medicine, William Harvey Research Institute, Queen Mary University of London, London E1 4NS, UK;
- University College London Consortium for Mitochondrial Research, London WC1E 6BT, UK
- Institute Gustave Roussy, 94800 Villejuif, France
- Department of Biomedical Sciences, University of Padua, 35122 Padua, Italy
| | - Tristan A. Rodriguez
- National Heart and Lung Institute, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK (T.A.R.)
| | - Bradley S. Cobb
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, 4 Royal College Street, London NW1 0TU, UK; (K.M.R.)
| |
Collapse
|
|
18
|
Maraghechi P, Aponte MTS, Ecker A, Lázár B, Tóth R, Szabadi NT, Gócza E. Pluripotency-Associated microRNAs in Early Vertebrate Embryos and Stem Cells. Genes (Basel) 2023; 14:1434. [PMID: 37510338 PMCID: PMC10379376 DOI: 10.3390/genes14071434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
MicroRNAs (miRNAs), small non-coding RNA molecules, regulate a wide range of critical biological processes, such as proliferation, cell cycle progression, differentiation, survival, and apoptosis, in many cell types. The regulatory functions of miRNAs in embryogenesis and stem cell properties have been extensively investigated since the early years of miRNA discovery. In this review, we will compare and discuss the impact of stem-cell-specific miRNA clusters on the maintenance and regulation of early embryonic development, pluripotency, and self-renewal of embryonic stem cells, particularly in vertebrates.
Collapse
Affiliation(s)
- Pouneh Maraghechi
- Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences; Agrobiotechnology and Precision Breeding for Food Security National Laboratory, Szent-Györgyi Albert str. 4, 2100 Gödöllő, Hungary
| | - Maria Teresa Salinas Aponte
- Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences; Agrobiotechnology and Precision Breeding for Food Security National Laboratory, Szent-Györgyi Albert str. 4, 2100 Gödöllő, Hungary
| | - András Ecker
- Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences; Agrobiotechnology and Precision Breeding for Food Security National Laboratory, Szent-Györgyi Albert str. 4, 2100 Gödöllő, Hungary
| | - Bence Lázár
- Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences; Agrobiotechnology and Precision Breeding for Food Security National Laboratory, Szent-Györgyi Albert str. 4, 2100 Gödöllő, Hungary
- National Centre for Biodiversity and Gene Conservation, Institute for Farm Animal Gene Conservation (NBGK-HGI), Isaszegi str. 200, 2100 Gödöllő, Hungary
| | - Roland Tóth
- Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences; Agrobiotechnology and Precision Breeding for Food Security National Laboratory, Szent-Györgyi Albert str. 4, 2100 Gödöllő, Hungary
| | - Nikolett Tokodyné Szabadi
- Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences; Agrobiotechnology and Precision Breeding for Food Security National Laboratory, Szent-Györgyi Albert str. 4, 2100 Gödöllő, Hungary
| | - Elen Gócza
- Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences; Agrobiotechnology and Precision Breeding for Food Security National Laboratory, Szent-Györgyi Albert str. 4, 2100 Gödöllő, Hungary
| |
Collapse
|
|
19
|
PRDM16, Negatively Regulated by miR-372-3p, Suppresses Cell Proliferation and Invasion in Prostate Cancer. Andrologia 2023. [DOI: 10.1155/2023/9821829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
Abstract
Prostate cancer (PCa) is one of the most prevalent malignant tumors. The alternation of microRNA (miRNA) expression is associated with prostate cancer progression, whereas its way to influence progression of prostate cancer remains elusive. The expression levels of PRDM16 mRNA and miR-372-3p in PCa cell lines were analyzed using qRT-PCR. The protein expression of PRDM16 in PCa cell lines was also analyzed using western blot. CCK-8, wound healing, and Transwell assays were applied to examine cell proliferation, migration, and invasion in prostate cancer cells, respectively. Dual-luciferase reporter assay was utilized to validate the interaction between miR-372-3p and PRDM16. In the present study, markedly decreased PRDM16 mRNA and protein expression levels were observed in prostate cancer cells. PRDM16 overexpression hampered cellular proliferation, migration, and invasion, while silencing PRDM16 had the opposite effect. Moreover, miR-372-3p could target the regulation expression of PRDM16. Rescue experiments demonstrated that upregulating miR-372-3p conspicuously restored the inhibitory effect of increased PRDM16 on cell proliferation, migration, and invasion in PCa. Overall, our study clarifies the biological role of miR-372-3p/PRDM16 axis in prostate cancer progression, which may be effective biomarkers for clinical treatment of prostate cancer.
Collapse
|
|
20
|
Non-Coding RNAs as Biomarkers for Embryo Quality and Pregnancy Outcomes: A Systematic Review and Meta-Analysis. Int J Mol Sci 2023; 24:ijms24065751. [PMID: 36982824 PMCID: PMC10052053 DOI: 10.3390/ijms24065751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
Despite advances in in vitro fertilization (IVF), there is still a lack of non-invasive and reliable biomarkers for selecting embryos with the highest developmental and implantation potential. Recently, small non-coding RNAs (sncRNAs) have been identified in biological fluids, and extracellular sncRNAs are explored as diagnostic biomarkers in the prediction of IVF outcomes. To determine the predictive role of sncRNAs in embryo quality and IVF outcomes, a systematic review and meta-analysis was performed. Articles were retrieved from PubMed, EMBASE, and Web of Science from 1990 to 31 July 2022. Eighteen studies that met the selection criteria were analyzed. In total, 22 and 47 different sncRNAs were found to be dysregulated in follicular fluid (FF) and embryo spent culture medium (SCM), respectively. MiR-663b, miR-454 and miR-320a in FF and miR-20a in SCM showed consistent dysregulation in two different studies. The meta-analysis indicated the potential predictive performance of sncRNAs as non-invasive biomarkers, with a pooled area under curve (AUC) value of 0.81 (95% CI 0.78, 0.844), a sensitivity of 0.79 (95% CI 0.72, 0.85), a specificity of 0.67 (95% CI 0.52, 0.79) and a diagnostic odds ratio (DOR) of 8 (95% CI 5, 12). Significant heterogeneity was identified among studies in sensitivity (I2 = 46.11%) and specificity (I2 = 89.73%). This study demonstrates that sncRNAs may distinguish embryos with higher developmental and implantation potentials. They can be promising non-invasive biomarkers for embryo selection in ART. However, the significant heterogeneity among studies highlights the demand for prospective multicenter studies with optimized methods and adequate sample sizes in the future.
Collapse
|
|
21
|
Keuls RA, Oh YS, Patel I, Parchem RJ. Post-transcriptional regulation in cranial neural crest cells expands developmental potential. Proc Natl Acad Sci U S A 2023; 120:e2212578120. [PMID: 36724256 PMCID: PMC9963983 DOI: 10.1073/pnas.2212578120] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 12/20/2022] [Indexed: 02/03/2023] Open
Abstract
Developmental potential is progressively restricted after germ layer specification during gastrulation. However, cranial neural crest cells challenge this paradigm, as they develop from anterior ectoderm, yet give rise to both ectodermal derivatives of the peripheral nervous system and ectomesenchymal bone and cartilage. How cranial neural crest cells differentiate into multiple lineages is poorly understood. Here, we demonstrate that cranial neural crest cells possess a transient state of increased chromatin accessibility. We profile the spatiotemporal emergence of premigratory neural crest and find evidence of lineage bias toward either a neuronal or ectomesenchymal fate, with each expressing distinct factors from earlier stages of development. We identify the miR-302 miRNA family to be highly expressed in cranial neural crest cells and genetic deletion leads to precocious specification of the ectomesenchymal lineage. Loss of mir-302 results in reduced chromatin accessibility in the neuronal progenitor lineage of neural crest and a reduction in peripheral neuron differentiation. Mechanistically, we find that mir-302 directly targets Sox9 to slow the timing of ectomesenchymal neural crest specification and represses multiple genes involved in chromatin condensation to promote accessibility required for neuronal differentiation. Our findings reveal a posttranscriptional mechanism governed by miRNAs to expand developmental potential of cranial neural crest.
Collapse
Affiliation(s)
- Rachel A. Keuls
- Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX77030
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX77030
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX77030
- Department of Neuroscience, Baylor College of Medicine, Houston, TX77030
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX77030
| | - Young Sun Oh
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX77030
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX77030
- Department of Neuroscience, Baylor College of Medicine, Houston, TX77030
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX77030
| | - Ivanshi Patel
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX77030
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX77030
- Department of Neuroscience, Baylor College of Medicine, Houston, TX77030
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX77030
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX77030
| | - Ronald J. Parchem
- Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX77030
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX77030
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX77030
- Department of Neuroscience, Baylor College of Medicine, Houston, TX77030
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX77030
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX77030
| |
Collapse
|
|
22
|
Deng M, Wang X, Xiong Z, Tang P. Control of RNA degradation in cell fate decision. Front Cell Dev Biol 2023; 11:1164546. [PMID: 37025171 PMCID: PMC10070868 DOI: 10.3389/fcell.2023.1164546] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/03/2023] [Indexed: 04/08/2023] Open
Abstract
Cell fate is shaped by a unique gene expression program, which reflects the concerted action of multilayered precise regulation. Substantial research attention has been paid to the contribution of RNA biogenesis to cell fate decisions. However, increasing evidence shows that RNA degradation, well known for its function in RNA processing and the surveillance of aberrant transcripts, is broadly engaged in cell fate decisions, such as maternal-to-zygotic transition (MZT), stem cell differentiation, or somatic cell reprogramming. In this review, we first look at the diverse RNA degradation pathways in the cytoplasm and nucleus. Then, we summarize how selective transcript clearance is regulated and integrated into the gene expression regulation network for the establishment, maintenance, and exit from a special cellular state.
Collapse
Affiliation(s)
- Mingqiang Deng
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiwei Wang
- Guangzhou Laboratory, Guangzhou, Guangdong, China
| | - Zhi Xiong
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou, China
| | - Peng Tang
- Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- *Correspondence: Peng Tang,
| |
Collapse
|
|
23
|
Machado HC, Bispo S, Dallagiovanna B. miR-6087 Might Regulate Cell Cycle–Related mRNAs During Cardiomyogenesis of hESCs. Bioinform Biol Insights 2023; 17:11779322231161918. [PMID: 37020502 PMCID: PMC10069004 DOI: 10.1177/11779322231161918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/16/2023] [Indexed: 04/03/2023] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that act as negative regulators of gene expression at the post-transcriptional level, promoting mRNA degradation or translation repression. Despite the well-described presence of miRNAs in various human tissues, there is still a lack of information about the relationship between miRNAs and the translation regulation in human embryonic stem cells (hESCs) during cardiomyogenesis. Here, we investigate RNA-seq data from hESCs, focusing on distinct stages of cardiomyogenesis and searching for polysome-bound miRNAs that could be involved in translational regulation. We identify miR-6087 as a differentially expressed miRNA at latest steps of cardiomyocyte differentiation. We analyzed the coexpression pattern between the differentially expressed mRNAs and miR-6087, evaluating whether they are predicted targets of the miRNA. We arranged the genes into an interaction network and identified BLM, RFC4, RFC3, and CCNA2 as key genes of the network. A post hoc analysis of the key genes suggests that miR-6087 could act as a regulator of the cell cycle in hESC during cardiomyogenesis.
Collapse
Affiliation(s)
- Hellen Cristine Machado
- Laboratory of Basic Stem-Cell Biology,
Instituto Carlos Chagas – FIOCRUZ-PR, Curitiba, Brazil
| | - Saloe Bispo
- Laboratory of Molecular and Systems
Biology of Trypanosomatids, Instituto Carlos Chagas – FIOCRUZ-PR, Curitiba,
Brazil
| | - Bruno Dallagiovanna
- Laboratory of Basic Stem-Cell Biology,
Instituto Carlos Chagas – FIOCRUZ-PR, Curitiba, Brazil
- Bruno Dallagiovanna, Laboratory of Basic
Stem-Cell Biology, Instituto Carlos Chagas – FIOCRUZ-PR, Rua Professor Algacyr
Munhoz Mader, 3775, Curitiba 81350-010, Brazil.
| |
Collapse
|
|
24
|
Radmand F, Baseri M, Farsadbakhsh M, Azimi A, Dizaj SM, Sharifi S. A Novel Perspective on Tissue Engineering Potentials of Periodontal Ligament Stem Cells. Open Dent J 2022. [DOI: 10.2174/18742106-v16-e221006-2021-216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
It is challenging to completely and predictably regenerate the missing periodontal tissues caused by the trauma or disease. To regenerate the periodontium, there is a need to consider several aspects that co-occur with periodontal development. This study provides an overview of the most up-to-date investigations on the characteristics and immunomodulatory features of Periodontal Ligament Stem Cells (PDLSCs) and the recent interventions performed using these cells, focusing on cell survival, proliferation, and differentiation. Keeping in mind the relationship between age and potency of PDLSCs, this work also demonstrates the necessity of establishing dental-derived stem cell banks for tissue regeneration applications. The data were collected from Pubmed and Google Scholar databases with the keywords of periodontal ligament stem cells, tissue engineering, characteristics, and stem cell therapy. The results showed the presence of wide-ranging research reports supporting the usability of PDLSCs for periodontal reconstruction. However, a better understanding of self-restoration for adequate regulation of adult stem cell growth is needed for various applied purposes.
Collapse
|
|
25
|
Pektaş SD, Kara M, Doğan G, Pektaş MB, Baloğlu MC, Sadi G. Differential Expression and in Silico Functional Analysis of Plasma MicroRNAs in the Pathogenesis of Non-segmental Vitiligo. Indian J Dermatol 2022; 67:705-714. [PMID: 36998849 PMCID: PMC10043660 DOI: 10.4103/ijd.ijd_383_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023] Open
Abstract
Vitiligo is a disease characterized by acquired depigmentation, white macules, and patches on the skin due to the dysfunction of epidermal melanocytes. In this study, we attempt to profile the microRNA (miRNA) expression patterns and predict the potential targets, assessing the biological functions of differentially expressed miRNAs in the blood of generalized vitiligo patients. Peripheral blood samples were taken from all participants, and the expression levels of 89 identified miRNAs were analyzed with real-time quantitative polymerase chain reaction (PCR). The results indicated significant upregulation of six miRNAs and downregulation of 19 miRNAs in the plasma of vitiligo patients. The top three upregulated miRNAs were hsa-miR-451a, hsa-miR-25-3p, and hsa-miR-19a-3p, and the top three downregulated miRNAs were hsa-miR-146a-5p, hsa-miR-940, and hsa-miR-142-3p. Moreover, the miRNA expression profiles of patients with Type 3 and Type 4 phototypes were substantially different in such a way that the patients with Type 3 phototype would be more prone to the emergence of melanoma and cancer. While significant variations in the expression patterns of miRNAs in male and female vitiligo patients were demonstrated, miR-let-7i-5p, miR-19a-3p, miR-25-3p, and miR-451a were commonly upregulated, and miR-142-3p and miR-146a-5p were commonly repressed in both sexes. This study may shed light on the roles of differentially expressed miRNAs in vitiligo patients by examining the miRNA expression patterns and the combined effects of miRNA and their predicted targets.
Collapse
Affiliation(s)
- Suzan Demir Pektaş
- Department of Dermatology, Faculty of Medicine, Muğla Sıtkı Koçman University, Mugla, Turkey
| | - Murat Kara
- Department of Dermatology, Faculty of Medicine, Muğla Sıtkı Koçman University, Mugla, Turkey
| | - Gürsoy Doğan
- Department of Dermatology, Faculty of Medicine, Muğla Sıtkı Koçman University, Mugla, Turkey
| | - Mehmet Bilgehan Pektaş
- Department of Pharmacology, Faculty of Medicine, Afyonkarahisar Health Sciences University, Kastamonu, Turkey
| | - Mehmet Cengiz Baloğlu
- Department of Genetics and Bioengineering, Engineering Faculty, Kastamonu University, Kastamonu, Turkey
| | - Gökhan Sadi
- Department of Biology, K. Ö. Science Faculty, Karamanoğlu Mehmetbey University, Karaman, Turkey
| |
Collapse
|
|
26
|
Schaefer M, Nabih A, Spies D, Hermes V, Bodak M, Wischnewski H, Stalder P, Ngondo RP, Liechti LA, Sajic T, Aebersold R, Gatfield D, Ciaudo C. Global and precise identification of functional
miRNA
targets in
mESCs
by integrative analysis. EMBO Rep 2022; 23:e54762. [PMID: 35899551 PMCID: PMC9442311 DOI: 10.15252/embr.202254762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 06/27/2022] [Accepted: 06/30/2022] [Indexed: 12/03/2022] Open
Abstract
MicroRNA (miRNA) loaded Argonaute (AGO) complexes regulate gene expression via direct base pairing with their mRNA targets. Previous works suggest that up to 60% of mammalian transcripts might be subject to miRNA‐mediated regulation, but it remains largely unknown which fraction of these interactions are functional in a specific cellular context. Here, we integrate transcriptome data from a set of miRNA‐depleted mouse embryonic stem cell (mESC) lines with published miRNA interaction predictions and AGO‐binding profiles. Using this integrative approach, combined with molecular validation data, we present evidence that < 10% of expressed genes are functionally and directly regulated by miRNAs in mESCs. In addition, analyses of the stem cell‐specific miR‐290‐295 cluster target genes identify TFAP4 as an important transcription factor for early development. The extensive datasets developed in this study will support the development of improved predictive models for miRNA‐mRNA functional interactions.
Collapse
Affiliation(s)
- Moritz Schaefer
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
- Life Science Zurich Graduate School University of Zürich Zurich Switzerland
| | - Amena Nabih
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
- Life Science Zurich Graduate School University of Zürich Zurich Switzerland
| | - Daniel Spies
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
- Life Science Zurich Graduate School University of Zürich Zurich Switzerland
| | - Victoria Hermes
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
| | - Maxime Bodak
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
- Life Science Zurich Graduate School University of Zürich Zurich Switzerland
| | - Harry Wischnewski
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
| | - Patrick Stalder
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
- Life Science Zurich Graduate School University of Zürich Zurich Switzerland
| | - Richard Patryk Ngondo
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
| | - Luz Angelica Liechti
- Center for Integrative Genomics (CIG) University of Lausanne Lausanne Switzerland
| | - Tatjana Sajic
- Swiss Federal Institute of Technology Zurich, IMSB Zürich Switzerland
| | - Ruedi Aebersold
- Swiss Federal Institute of Technology Zurich, IMSB Zürich Switzerland
| | - David Gatfield
- Center for Integrative Genomics (CIG) University of Lausanne Lausanne Switzerland
| | - Constance Ciaudo
- Swiss Federal Institute of Technology Zurich IMHS, Chair of RNAi and Genome Integrity Zurich Switzerland
| |
Collapse
|
|
27
|
Ayaz G, Yan H, Malik N, Huang J. An Updated View of the Roles of p53 in Embryonic Stem Cells. Stem Cells 2022; 40:883-891. [PMID: 35904997 PMCID: PMC9585900 DOI: 10.1093/stmcls/sxac051] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 07/14/2022] [Indexed: 11/12/2022]
Abstract
The TP53 gene is unarguably one of the most studied human genes. Its encoded protein, p53, is a tumor suppressor and is often called the "guardian of the genome" due to its pivotal role in maintaining genome stability. Historically, most studies of p53 have focused on its roles in somatic cells and tissues, but in the last two decades, its functions in embryonic stem cells (ESCs) and induced pluripotent stem cells have attracted increasing attention. Recent studies have identified p53 as a critical regulator of pluripotency, self-renewal, differentiation, proliferation, and genome stability in mouse and human embryonic stem cells. In this article, we systematically review the studies on the functions of p53 in ESCs, provide an updated overview, attempt to reconcile controversial results described in the literature, and discuss the relevance of these cellular functions of p53 to its roles in tumor suppression.
Collapse
Affiliation(s)
- Gamze Ayaz
- Cancer and Stem Cell Epigenetics, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hualong Yan
- Cancer and Stem Cell Epigenetics, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Navdeep Malik
- Cancer and Stem Cell Epigenetics, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jing Huang
- Cancer and Stem Cell Epigenetics, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
|
28
|
Yin G, Yan C, Hao J, Zhang C, Wang P, Zhao C, Cai S, Meng B, Zhang A, Li L. PRDM16, negatively regulated by miR-372-3p, suppresses cell proliferation and invasion in prostate cancer. Andrologia 2022:e14529. [PMID: 35858224 DOI: 10.1111/and.14529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/27/2022] [Accepted: 06/26/2022] [Indexed: 11/26/2022] Open
Abstract
Prostate cancer (PCa) is one of the most prevalent malignant tumours. The alternation of microRNAs (miRNAs) expression is associated with prostate cancer progression, whereas its way to influence progression of prostate cancer remains elusive. The expression levels of PRDM16 mRNA and miR-372-3p in PCa cell lines were analysed using qRT-PCR. The protein expression of PRDM16 in PCa cell lines was also analysed using Western blot. CCK-8, wound healing and Transwell assays were applied to examine cell proliferation, migration, and invasion in prostate cancer cells, respectively. Dual-luciferase reporter assay was utilised to validate the interaction between miR-372-3p and PRDM16. In the present study, markedly decreased PRDM16 mRNA and protein expression levels were observed in prostate cancer cells. PRDM16 overexpression hampered cellular proliferation, migration, and invasion, while silencing PRDM16 had the opposite effect. Moreover, miR-372-3p could target the regulation expression of PRDM16. Rescue experiments demonstrated that upregulating miR-372-3p conspicuously restored the inhibitory effect of increased PRDM16 on cell proliferation, migration, and invasion in PCa. Overall, our study clarifies the biological role of miR-372-3p/PRDM16 axis in prostate cancer progression, which may be effective biomarkers for clinical treatment of prostate cancer.
Collapse
Affiliation(s)
- Guangwei Yin
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Chengquan Yan
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Jing Hao
- Office of Academic Affairs, North China University of Science and Technology, Tangshan, Hebei Province, China
| | - Chunying Zhang
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Pengfei Wang
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Chaofei Zhao
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Shengyong Cai
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Bin Meng
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Aili Zhang
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Lin Li
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| |
Collapse
|
|
29
|
G1/S restriction point coordinates phasic gene expression and cell differentiation. Nat Commun 2022; 13:3696. [PMID: 35760790 PMCID: PMC9237072 DOI: 10.1038/s41467-022-31101-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 05/31/2022] [Indexed: 01/19/2023] Open
Abstract
Pluripotent embryonic stem cells have a unique cell cycle structure with a suppressed G1/S restriction point and little differential expression across the cell cycle phases. Here, we evaluate the link between G1/S restriction point activation, phasic gene expression, and cellular differentiation. Expression analysis reveals a gain in phasic gene expression across lineages between embryonic days E7.5 and E9.5. Genetic manipulation of the G1/S restriction point regulators miR-302 and P27 respectively accelerates or delays the onset of phasic gene expression in mouse embryos. Loss of miR-302-mediated p21 or p27 suppression expedites embryonic stem cell differentiation, while a constitutive Cyclin E mutant blocks it. Together, these findings uncover a causal relationship between emergence of the G1/S restriction point with a gain in phasic gene expression and cellular differentiation.
Collapse
|
|
30
|
Highly sensitive and non-disruptive detection of residual undifferentiated cells by measuring miRNAs in culture supernatant. Sci Rep 2022; 12:10351. [PMID: 35725891 PMCID: PMC9209417 DOI: 10.1038/s41598-022-14273-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/03/2022] [Indexed: 11/10/2022] Open
Abstract
The clinical usage of induced pluripotent stem cell (iPSC)-derived regenerative medicine products is limited by the possibility of residual undifferentiated cells forming tumours after transplantation. Most of the existing quality control tests involve crushing of cells. As a result, the cells to be transplanted cannot be directly tested, thereby increasing the cost of transplantation. Therefore, we tested a highly sensitive and non-disruptive quality-testing method that involves measuring microRNAs (miRNAs) in culture supernatants released by cells. By measuring miR-302b in the culture supernatant, residual iPSCs were detected with higher sensitivity than by measuring LIN28 (Lin-28 Homolog A) in the cells. To use this method, we also monitored the progression of differentiation. Our novel highly sensitive and non-disruptive method for detecting residual undifferentiated cells will contribute to reducing the manufacturing cost of iPSC-derived products and improving the safety of transplantation.
Collapse
|
|
31
|
Mazloom AR, Xu H, Reig-Palou J, Vasileva A, Román AC, Mulero-Navarro S, Lemischka IR, Sevilla A. Esrrb Regulates Specific Feed-Forward Loops to Transit From Pluripotency Into Early Stages of Differentiation. Front Cell Dev Biol 2022; 10:820255. [PMID: 35652095 PMCID: PMC9149258 DOI: 10.3389/fcell.2022.820255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/24/2022] [Indexed: 01/15/2023] Open
Abstract
Characterization of pluripotent states, in which cells can both self-renew or differentiate, with the irreversible loss of pluripotency, are important research areas in developmental biology. Although microRNAs (miRNAs) have been shown to play a relevant role in cellular differentiation, the role of miRNAs integrated into gene regulatory networks and its dynamic changes during these early stages of embryonic stem cell (ESC) differentiation remain elusive. Here we describe the dynamic transcriptional regulatory circuitry of stem cells that incorporate protein-coding and miRNA genes based on miRNA array expression and quantitative sequencing of short transcripts upon the downregulation of the Estrogen Related Receptor Beta (Esrrb). The data reveals how Esrrb, a key stem cell transcription factor, regulates a specific stem cell miRNA expression program and integrates dynamic changes of feed-forward loops contributing to the early stages of cell differentiation upon its downregulation. Together these findings provide new insights on the architecture of the combined transcriptional post-transcriptional regulatory network in embryonic stem cells.
Collapse
Affiliation(s)
- Amin R. Mazloom
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Huilei Xu
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jaume Reig-Palou
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Ana Vasileva
- Center for Radiological Research, Columbia University, New York, NY, United States
| | - Angel-Carlos Román
- Department of Biochemistry, Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain
| | - Sonia Mulero-Navarro
- Department of Biochemistry, Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain
| | - Ihor R. Lemischka
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ana Sevilla
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
- *Correspondence: Ana Sevilla,
| |
Collapse
|
|
32
|
Zhang Z, Chen W, Tiemessen DM, Oosterwijk E, Kouwer PHJ. A Temperature-Based Easy-Separable (TempEasy) 3D Hydrogel Coculture System. Adv Healthc Mater 2022; 11:e2102389. [PMID: 35029325 PMCID: PMC11469334 DOI: 10.1002/adhm.202102389] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/10/2021] [Indexed: 12/13/2022]
Abstract
Interactions between different cell types are crucial for their behavior in tissues, but are rarely considered in 3D in vitro cell culture experiments. One reason is that such coculture experiments are sometimes difficult to perform in 3D or require specialized equipment or know-how. Here, a new 3D cell coculture system is introduced, TempEasy, which is readily applied in any cell culture lab. The matrix material is based on polyisocyanide hydrogels, which closely resemble the mechanical characteristics of the natural extracellular matrix. Gels with different gelation temperatures, seeded with different cells, are placed on top of each other to form an indirect coculture. Cooling reverses gelation, allowing cell harvesting from each layer separately, which benefits downstream analysis. To demonstrate the potential of TempEasy , human adipose stem cells (hADSCs) with vaginal epithelial fibroblasts are cocultured. The analysis of a 7-day coculture shows that hADSCs promote cell-cell interaction of fibroblasts, while fibroblasts promote proliferation and differentiation of hADSCs. TempEasy provides a straightforward operational platform for indirect cocultures of cells of different lineages in well-defined microenvironments.
Collapse
Affiliation(s)
- Zhaobao Zhang
- Institute for Molecules and MaterialsRadboud University NijmegenHeyendaalseweg 135Nijmegen6525 AJThe Netherlands
| | - Wen Chen
- Institute for Molecules and MaterialsRadboud University NijmegenHeyendaalseweg 135Nijmegen6525 AJThe Netherlands
| | - Dorien M. Tiemessen
- Department of UrologyRadboud Institute for Molecular Life SciencesRadboud University Medical CenterGeert Grooteplein Zuid 28Nijmegen6525 GAThe Netherlands
| | - Egbert Oosterwijk
- Department of UrologyRadboud Institute for Molecular Life SciencesRadboud University Medical CenterGeert Grooteplein Zuid 28Nijmegen6525 GAThe Netherlands
| | - Paul H. J. Kouwer
- Institute for Molecules and MaterialsRadboud University NijmegenHeyendaalseweg 135Nijmegen6525 AJThe Netherlands
| |
Collapse
|
|
33
|
Chrysanthou S, Flores JC, Dawlaty MM. Tet1 Suppresses p21 to Ensure Proper Cell Cycle Progression in Embryonic Stem Cells. Cells 2022; 11:1366. [PMID: 35456045 PMCID: PMC9025953 DOI: 10.3390/cells11081366] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 12/19/2022] Open
Abstract
Ten eleven translocation 1 (Tet1) is a DNA dioxygenase that promotes DNA demethylation by oxidizing 5-methylcytosine. It can also partner with chromatin-activating and repressive complexes to regulate gene expressions independent of its enzymatic activity. Tet1 is highly expressed in embryonic stem cells (ESCs) and regulates pluripotency and differentiation. However, its roles in ESC cell cycle progression and proliferation have not been investigated. Using a series of Tet1 catalytic mutant (Tet1m/m), knockout (Tet1-/-) and wild type (Tet1+/+) mouse ESCs (mESCs), we identified a non-catalytic role of Tet1 in the proper cell cycle progression and proliferation of mESCs. Tet1-/-, but not Tet1m/m, mESCs exhibited a significant reduction in proliferation and delayed progression through G1. We found that the cyclin-dependent kinase inhibitor p21/Cdkn1a was uniquely upregulated in Tet1-/- mESCs and its knockdown corrected the slow proliferation and delayed G1 progression. Mechanistically, we found that p21 was a direct target of Tet1. Tet1 occupancy at the p21 promoter overlapped with the repressive histone mark H3K27me3 as well as with the H3K27 trimethyl transferase PRC2 component Ezh2. A loss of Tet1, but not loss of its catalytic activity, significantly reduced the enrichment of Ezh2 and H3K27 trimethylation at the p21 promoter without affecting the DNA methylation levels. We also found that the proliferation defects of Tet1-/- mESCs were independent of their differentiation defects. Together, these findings established a non-catalytic role for Tet1 in suppressing p21 in mESCs to ensure a rapid G1-to-S progression, which is a key hallmark of ESC proliferation. It also established Tet1 as an epigenetic regulator of ESC proliferation in addition to its previously defined roles in ESC pluripotency and differentiation.
Collapse
Affiliation(s)
- Stephanie Chrysanthou
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461, USA; (S.C.); (J.C.F.)
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461, USA
- Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
| | - Julio C. Flores
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461, USA; (S.C.); (J.C.F.)
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461, USA
- Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
| | - Meelad M. Dawlaty
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461, USA; (S.C.); (J.C.F.)
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461, USA
- Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
| |
Collapse
|
|
34
|
Rallabandi R, Sharp B, Cruz C, Wang Q, Locsin A, Driscoll CB, Lee E, Nelson T, Devaux P. miRNA-mediated control of exogenous OCT4 during mesenchymal-epithelial transition increases measles vector reprogramming efficiency. Mol Ther Methods Clin Dev 2022; 24:48-61. [PMID: 34977272 PMCID: PMC8683617 DOI: 10.1016/j.omtm.2021.11.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/27/2021] [Indexed: 12/14/2022]
Abstract
OCT4 is a key mediator of induced pluripotent stem cell (iPSC) reprogramming, but the mechanistic insights into the role of exogenous OCT4 and timelines that initiate pluripotency remain to be resolved. Here, using measles reprogramming vectors, we present microRNA (miRNA) targeting of exogenous OCT4 to shut down its expression during the mesenchymal to the epithelial transition phase of reprogramming. We showed that exogenous OCT4 is required only for the initiation of reprogramming and is dispensable for the maturation stage. However, the continuous expression of SOX2, KLF4, and c-MYC is necessary for the maturation stage of the iPSC. Additionally, we demonstrate a novel application of miRNA targeting in a viral vector to contextually control the vector/transgene, ultimately leading to an improved reprogramming efficiency. This novel approach could be applied to other systems for improving the efficiency of vector-induced processes.
Collapse
Affiliation(s)
- Ramya Rallabandi
- Virology and Gene Therapy Graduate Track, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55905, USA
- Regenerative Sciences PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Brenna Sharp
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Conrad Cruz
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Qi Wang
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Alexis Locsin
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Christopher B. Driscoll
- Virology and Gene Therapy Graduate Track, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Ella Lee
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Tim Nelson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester MN 55905, USA
| | - Patricia Devaux
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Virology and Gene Therapy Graduate Track, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55905, USA
- Regenerative Sciences PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55905, USA
| |
Collapse
|
|
35
|
Vardapour R, Kehl T, Kneitz S, Ludwig N, Meese E, Lenhof HP, Gessler M. The DGCR8 E518K mutation found in Wilms tumors leads to a partial miRNA processing defect that alters gene expression patterns and biological processes. Carcinogenesis 2021; 43:82-93. [PMID: 34919667 DOI: 10.1093/carcin/bgab110] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 11/01/2021] [Accepted: 11/25/2021] [Indexed: 11/14/2022] Open
Abstract
Wilms tumor (WT) is the most common renal tumor in childhood. We and others have previously identified oncogenic driver mutations affecting the microprocessor genes DROSHA and DGCR8 that lead to altered miRNA expression patterns. In the case of DGCR8, a single recurrent hotspot mutation (E518K) was found in the RNA binding domain. To functionally assess this mutation in vitro, we generated mouse Dgcr8-KO embryonic stem cell (mESC) lines with an inducible expression of wild-type or mutant DGCR8, mirroring the hemizygous mutant expression seen in WT. RNA-seq analysis revealed significant differences of miRNA expression profiles in DGCR8-E518K compared to DGCR8-wild-type mESCs. The E518K mutation only led to a partial rescue of the reported miRNA processing defect in Dgcr8-KO, with selectively reduced expression of numerous canonical miRNAs. Nevertheless, DGCR8-E518K retained significant activity given its ability to still process many miRNAs. Subsequent to altered miRNA levels, the expression of mRNA targets was likewise changed. Functional assays showed that DGCR8-E518K cells still have a partial proliferation and differentiation defect but were able to rescue critical biological processes in embryoid body development. The stem cell program could be shut down and all three germ layers were formed. These findings suggest that the E518K mutation leads to a partial reduction of microprocessor activity and altered specificity with selective impairment only in certain developmental contexts, apparently including nephrogenesis.
Collapse
Affiliation(s)
- Romina Vardapour
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, Wuerzburg University, 97074 Wuerzburg, Germany
| | - Tim Kehl
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany
| | - Susanne Kneitz
- Theodor-Boveri-Institute/Biocenter, Physiological Chemistry, Wuerzburg University, 97074 Wuerzburg, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany
| | - Manfred Gessler
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, Wuerzburg University, 97074 Wuerzburg, Germany.,Comprehensive Cancer Center Mainfranken, 97078 Wuerzburg, Germany
| |
Collapse
|
|
36
|
Wigton EJ, Mikami Y, McMonigle RJ, Castellanos CA, Wade-Vallance AK, Zhou SK, Kageyama R, Litterman A, Roy S, Kitamura D, Dykhuizen EC, Allen CD, Hu H, O’Shea JJ, Ansel KM. MicroRNA-directed pathway discovery elucidates an miR-221/222-mediated regulatory circuit in class switch recombination. J Exp Med 2021; 218:e20201422. [PMID: 34586363 PMCID: PMC8485858 DOI: 10.1084/jem.20201422] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 02/12/2021] [Accepted: 09/09/2021] [Indexed: 01/02/2023] Open
Abstract
MicroRNAs (miRNAs, miRs) regulate cell fate decisions by post-transcriptionally tuning networks of mRNA targets. We used miRNA-directed pathway discovery to reveal a regulatory circuit that influences Ig class switch recombination (CSR). We developed a system to deplete mature, activated B cells of miRNAs, and performed a rescue screen that identified the miR-221/222 family as a positive regulator of CSR. Endogenous miR-221/222 regulated B cell CSR to IgE and IgG1 in vitro, and miR-221/222-deficient mice exhibited defective IgE production in allergic airway challenge and polyclonal B cell activation models in vivo. We combined comparative Ago2-HITS-CLIP and gene expression analyses to identify mRNAs bound and regulated by miR-221/222 in primary B cells. Interrogation of these putative direct targets uncovered functionally relevant downstream genes. Genetic depletion or pharmacological inhibition of Foxp1 and Arid1a confirmed their roles as key modulators of CSR to IgE and IgG1.
Collapse
Affiliation(s)
- Eric J. Wigton
- Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA
| | - Yohei Mikami
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Rockville, MD
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Ryan J. McMonigle
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL
| | - Carlos A. Castellanos
- Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA
| | - Adam K. Wade-Vallance
- Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA
| | - Simon K. Zhou
- Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA
| | - Robin Kageyama
- Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA
| | - Adam Litterman
- Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA
| | - Suparna Roy
- Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA
- Department of Dermatology, University of California, San Francisco, San Francisco, CA
| | - Daisuke Kitamura
- Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Emily C. Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN
| | - Christopher D.C. Allen
- Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA
| | - Hui Hu
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL
| | - John J. O’Shea
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Rockville, MD
| | - K. Mark Ansel
- Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA
| |
Collapse
|
|
37
|
Hunkler HJ, Groß S, Thum T, Bär C. Non-coding RNAs: key regulators of reprogramming, pluripotency, and cardiac cell specification with therapeutic perspective for heart regeneration. Cardiovasc Res 2021; 118:3071-3084. [PMID: 34718448 PMCID: PMC9732524 DOI: 10.1093/cvr/cvab335] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/27/2021] [Indexed: 01/01/2023] Open
Abstract
Myocardial infarction causes a massive loss of cardiomyocytes (CMs), which can lead to heart failure accompanied by fibrosis, stiffening of the heart, and loss of function. Heart failure causes high mortality rates and is a huge socioeconomic burden, which, based on diets and lifestyle in the developed world, is expected to increase further in the next years. At present, the only curative treatment for heart failure is heart transplantation associated with a number of limitations such as donor organ availability and transplant rejection among others. Thus, the development of cellular reprogramming and defined differentiation protocols provide exciting new possibilities for cell therapy approaches and which opened up a new era in regenerative medicine. Consequently, tremendous research efforts were undertaken to gain a detailed molecular understanding of the reprogramming processes and the in vitro differentiation of pluripotent stem cells into functional CMs for transplantation into the patient's injured heart. In the last decade, non-coding RNAs, particularly microRNAs, long non-coding RNAs, and circular RNAs emerged as critical regulators of gene expression that were shown to fine-tune cellular processes both on the transcriptional and the post-transcriptional level. Unsurprisingly, also cellular reprogramming, pluripotency, and cardiac differentiation and maturation are regulated by non-coding RNAs. In here, we review the current knowledge on non-coding RNAs in these processes and highlight how their modulation may enhance the quality and quantity of stem cells and their derivatives for safe and efficient clinical application in patients with heart failure. In addition, we summarize the clinical cell therapy efforts undertaken thus far.
Collapse
Affiliation(s)
- Hannah J Hunkler
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Sonja Groß
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Thomas Thum
- Corresponding authors. Tel: +49 511 532 5272; fax: +49 511 532 5274, E-mail: (T.T.); Tel: +49 511 532 2883; fax: +49 511 532 5274, E-mail: (C.B.)
| | - Christian Bär
- Corresponding authors. Tel: +49 511 532 5272; fax: +49 511 532 5274, E-mail: (T.T.); Tel: +49 511 532 2883; fax: +49 511 532 5274, E-mail: (C.B.)
| |
Collapse
|
|
38
|
CHD8 safeguards early neuroectoderm differentiation in human ESCs and protects from apoptosis during neurogenesis. Cell Death Dis 2021; 12:981. [PMID: 34686651 PMCID: PMC8536677 DOI: 10.1038/s41419-021-04292-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 10/01/2021] [Accepted: 10/08/2021] [Indexed: 12/24/2022]
Abstract
The chromatin remodeler CHD8, which belongs to the ATP-dependent chromatin remodelers CHD family, is one of the most high-risk mutated genes in autism spectrum disorders. However, the role of CHD8 in neural differentiation and the mechanism of CHD8 in autism remains unclear, despite there are a few studies based on the CHD8 haploinsufficient models. Here, we generate the CHD8 knockout human ESCs by CRISPR/Cas9 technology and characterize the effect of loss-of-function of CHD8 on pluripotency maintenance and lineage determination by utilizing efficient directed differentiation protocols. The results show loss-of-function of CHD8 does not affect human ESC maintenance although having slight effect on proliferation and cell cycle. Interestingly, CHD8 depletion results in defective neuroectoderm differentiation, along with severe cell death in neural progenitor stage. Transcriptome analysis also indicates CHD8 does not alter the expression of pluripotent genes in ESC stage, but in neural progenitor cells depletion of CHD8 induces the abnormal expression of the apoptosis genes and suppresses neuroectoderm-related genes. These results provide the evidence that CHD8 plays an essential role in the pluripotency exit and neuroectoderm differentiation as well as the regulation of apoptosis during neurogenesis.
Collapse
|
|
39
|
Li R, Qu H, Wang S, Chater JM, Wang X, Cui Y, Yu L, Zhou R, Jia Q, Traband R, Wang M, Xie W, Yuan D, Zhu J, Zhong WD, Jia Z. CancerMIRNome: an interactive analysis and visualization database for miRNome profiles of human cancer. Nucleic Acids Res 2021; 50:D1139-D1146. [PMID: 34500460 PMCID: PMC8728249 DOI: 10.1093/nar/gkab784] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/22/2021] [Accepted: 08/30/2021] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs), which play critical roles in gene regulatory networks, have emerged as promising diagnostic and prognostic biomarkers for human cancer. In particular, circulating miRNAs that are secreted into circulation exist in remarkably stable forms, and have enormous potential to be leveraged as non-invasive biomarkers for early cancer detection. Novel and user-friendly tools are desperately needed to facilitate data mining of the vast amount of miRNA expression data from The Cancer Genome Atlas (TCGA) and large-scale circulating miRNA profiling studies. To fill this void, we developed CancerMIRNome, a comprehensive database for the interactive analysis and visualization of miRNA expression profiles based on 10 554 samples from 33 TCGA projects and 28 633 samples from 40 public circulating miRNome datasets. A series of cutting-edge bioinformatics tools and machine learning algorithms have been packaged in CancerMIRNome, allowing for the pan-cancer analysis of a miRNA of interest across multiple cancer types and the comprehensive analysis of miRNome profiles to identify dysregulated miRNAs and develop diagnostic or prognostic signatures. The data analysis and visualization modules will greatly facilitate the exploit of the valuable resources and promote translational application of miRNA biomarkers in cancer. The CancerMIRNome database is publicly available at http://bioinfo.jialab-ucr.org/CancerMIRNome.
Collapse
Affiliation(s)
- Ruidong Li
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA.,Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, CA, USA
| | - Han Qu
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Shibo Wang
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - John M Chater
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Xuesong Wang
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA.,Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, CA, USA
| | - Yanru Cui
- College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Lei Yu
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA.,Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, CA, USA
| | - Rui Zhou
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Qiong Jia
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA.,Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, CA, USA
| | - Ryan Traband
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Meiyue Wang
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Weibo Xie
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Dongbo Yuan
- Department of Urology, Guizhou Provincial People's Hospital, Guizhou, China
| | - Jianguo Zhu
- Department of Urology, Guizhou Provincial People's Hospital, Guizhou, China
| | - Wei-De Zhong
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China.,Urology Key Laboratory of Guangdong Province, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China.,Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
| | - Zhenyu Jia
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA.,Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, CA, USA
| |
Collapse
|
|
40
|
Afshari A, Yaghobi R, Rezaei G. Inter-regulatory role of microRNAs in interaction between viruses and stem cells. World J Stem Cells 2021; 13:985-1004. [PMID: 34567421 PMCID: PMC8422934 DOI: 10.4252/wjsc.v13.i8.985] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/11/2021] [Accepted: 07/13/2021] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are well known for post-transcriptional regulatory ability over specific mRNA targets. miRNAs exhibit temporal or tissue-specific expression patterns and regulate the cell and tissue developmental pathways. They also have determinative roles in production and differentiation of multiple lineages of stem cells and might have therapeutic advantages. miRNAs are a part of some viruses’ regulatory machinery, not a byproduct. The trace of miRNAs was detected in the genomes of viruses and regulation of cell reprograming and viral pathogenesis. Combination of inter-regulatory systems has been detected for miRNAs during viral infections in stem cells. Contraction between viruses and stem cells may be helpful in therapeutic tactics, pathogenesis, controlling viral infections and defining stem cell developmental strategies that is programmed by miRNAs as a tool. Therefore, in this review we intended to study the inter-regulatory role of miRNAs in the interaction between viruses and stem cells and tried to explain the advantages of miRNA regulatory potentials, which make a new landscape for future studies.
Collapse
Affiliation(s)
- Afsoon Afshari
- Shiraz Nephro-Urology Research Center, Shiraz University of Medical Sciences, Shiraz 7193711351, Iran
| | - Ramin Yaghobi
- Shiraz Transplant Research Center, Shiraz University of Medical Sciences, Shiraz 7193711351, Iran
| | - Ghazal Rezaei
- Shiraz Transplant Research Center, Shiraz University of Medical Sciences, Shiraz 7193711351, Iran
| |
Collapse
|
|
41
|
Bär C, Chatterjee S, Falcão Pires I, Rodrigues P, Sluijter JPG, Boon RA, Nevado RM, Andrés V, Sansonetti M, de Windt L, Ciccarelli M, Hamdani N, Heymans S, Figuinha Videira R, Tocchetti CG, Giacca M, Zacchigna S, Engelhardt S, Dimmeler S, Madonna R, Thum T. Non-coding RNAs: update on mechanisms and therapeutic targets from the ESC Working Groups of Myocardial Function and Cellular Biology of the Heart. Cardiovasc Res 2021; 116:1805-1819. [PMID: 32638021 DOI: 10.1093/cvr/cvaa195] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/15/2020] [Accepted: 06/30/2020] [Indexed: 02/06/2023] Open
Abstract
Vast parts of mammalian genomes are actively transcribed, predominantly giving rise to non-coding RNA (ncRNA) transcripts including microRNAs, long ncRNAs, and circular RNAs among others. Contrary to previous opinions that most of these RNAs are non-functional molecules, they are now recognized as critical regulators of many physiological and pathological processes including those of the cardiovascular system. The discovery of functional ncRNAs has opened up new research avenues aiming at understanding ncRNA-related disease mechanisms as well as exploiting them as novel therapeutics in cardiovascular therapy. In this review, we give an update on the current progress in ncRNA research, particularly focusing on cardiovascular physiological and disease processes, which are under current investigation at the ESC Working Groups of Myocardial Function and Cellular Biology of the Heart. This includes a range of topics such as extracellular vesicle-mediated communication, neurohormonal regulation, inflammation, cardiac remodelling, cardio-oncology as well as cardiac development and regeneration, collectively highlighting the wide-spread involvement and importance of ncRNAs in the cardiovascular system.
Collapse
Affiliation(s)
- Christian Bär
- Institute for Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany.,REBIRTH Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
| | - Shambhabi Chatterjee
- Institute for Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany.,REBIRTH Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
| | - Inês Falcão Pires
- Cardiovascular Research and Development Center, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Patrícia Rodrigues
- Cardiovascular Research and Development Center, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Joost P G Sluijter
- Experimental Cardiology Laboratory, UMC Utrecht Regenerative Medicine Center, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Reinier A Boon
- Department of Physiology, Amsterdam Cardiovascular Sciences (ACS), Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands.,Institute for Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University, Frankfurt am Main, Germany.,Partner site Rhein/Main, German Center for Cardiovascular Research (DZHK), Frankfurt am Main, Germany
| | - Rosa M Nevado
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Spain
| | - Vicente Andrés
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Spain
| | - Marida Sansonetti
- Institute for Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany.,REBIRTH Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany.,Department of Molecular Genetics, Faculty of Science and Engineering, Maastricht University, Maastricht, The Netherlands.,Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Leon de Windt
- Department of Molecular Genetics, Faculty of Science and Engineering, Maastricht University, Maastricht, The Netherlands.,Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Michele Ciccarelli
- Department of Medicine, Surgery and Dentistry, University of Salerno, Italy
| | - Nazha Hamdani
- Department of Molecular and Experimental Cardiology, Ruhr University Bochum, Bochum, Germany.,Department of Cardiology, St. Josef-Hospital, Ruhr University Bochum, Bochum, Germany
| | - Stephane Heymans
- Department of Cardiology, Maastricht University Medical Centre, University Hospital Maastricht, The Netherlands.,Center for Heart Failure Research, Cardiovascular Research Institute Maastricht (CARIM), University Hospital Maastricht, The Netherlands
| | - Raquel Figuinha Videira
- Cardiovascular Research and Development Center, Faculty of Medicine, University of Porto, Porto, Portugal.,Department of Molecular Genetics, Faculty of Science and Engineering, Maastricht University, Maastricht, The Netherlands.,Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Carlo G Tocchetti
- Department of Translational Medical Sciences and Interdepartmental Center of Clinical and Translational Research (CIRCET), Federico II University, Naples, Italy
| | - Mauro Giacca
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy.,School of Cardiovascular Medicine & Sciences, King's College London, London, UK.,Department of Medicine, Surgery and Health Sciences, University of Trieste, Italy
| | - Serena Zacchigna
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy.,Department of Medicine, Surgery and Health Sciences, University of Trieste, Italy
| | - Stefan Engelhardt
- Institute of Pharmacology and Toxicology, Technische Universität München, Biedersteiner Str. 29, Munich 80802, Germany.,DZHK (German Center for Cardiovascular Research), Partner site Munich Heart Alliance, Biedersteiner Str. 29, Munich 80802, Germany
| | - Stefanie Dimmeler
- Institute for Cardiovascular Regeneration, Goethe University, Germany.,German Center for Cardiovascular Research (DZHK), Frankfurt, Germany.,Cardio-Pulmonary Institute (CPI), Frankfurt, Germany
| | - Rosalinda Madonna
- Institute of Cardiology, University of Pisa, Pisa, Italy.,Department of Internal Medicine, University of Texas Medical School, Houston, TX, USA
| | - Thomas Thum
- Institute for Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany.,REBIRTH Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
| |
Collapse
|
|
42
|
Divisato G, Piscitelli S, Elia M, Cascone E, Parisi S. MicroRNAs and Stem-like Properties: The Complex Regulation Underlying Stemness Maintenance and Cancer Development. Biomolecules 2021; 11:biom11081074. [PMID: 34439740 PMCID: PMC8393604 DOI: 10.3390/biom11081074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/13/2021] [Accepted: 07/19/2021] [Indexed: 12/12/2022] Open
Abstract
Embryonic stem cells (ESCs) have the extraordinary properties to indefinitely proliferate and self-renew in culture to produce different cell progeny through differentiation. This latter process recapitulates embryonic development and requires rounds of the epithelial-mesenchymal transition (EMT). EMT is characterized by the loss of the epithelial features and the acquisition of the typical phenotype of the mesenchymal cells. In pathological conditions, EMT can confer stemness or stem-like phenotypes, playing a role in the tumorigenic process. Cancer stem cells (CSCs) represent a subpopulation, found in the tumor tissues, with stem-like properties such as uncontrolled proliferation, self-renewal, and ability to differentiate into different cell types. ESCs and CSCs share numerous features (pluripotency, self-renewal, expression of stemness genes, and acquisition of epithelial-mesenchymal features), and most of them are under the control of microRNAs (miRNAs). These small molecules have relevant roles during both embryogenesis and cancer development. The aim of this review was to recapitulate molecular mechanisms shared by ESCs and CSCs, with a special focus on the recently identified classes of microRNAs (noncanonical miRNAs, mirtrons, isomiRs, and competitive endogenous miRNAs) and their complex functions during embryogenesis and cancer development.
Collapse
|
|
43
|
microRNA regulation of pluripotent state transition. Essays Biochem 2021; 64:947-954. [PMID: 33034348 DOI: 10.1042/ebc20200028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/09/2020] [Accepted: 09/11/2020] [Indexed: 01/02/2023]
Abstract
microRNAs (miRNAs) play essential roles in mouse embryonic stem cells (ESCs) and early embryo development. The exact mechanism by which miRNAs regulate cell fate transition during embryo development is still not clear. Recent studies have identified and captured various pluripotent stem cells (PSCs) that share similar characteristics with cells from different stages of pre- and post-implantation embryos. These PSCs provide valuable models to understand miRNA functions in early mammalian development. In this short review, we will summarize recent work towards understanding the function and mechanism of miRNAs in regulating the transition or conversion between different pluripotent states. In addition, we will highlight unresolved questions and key future directions related to miRNAs in pluripotent state transition. Studies in these areas will further our understanding of miRNA functions in early embryo development, and may lead to practical means to control human PSCs for clinical applications in regenerative medicine.
Collapse
|
|
44
|
Hawke DC, Ahmed DB, Watson AJ, Betts DH. Murine Blastocysts Release Mature MicroRNAs Into Culture Media That Reflect Developmental Status. Front Genet 2021; 12:655882. [PMID: 34122510 PMCID: PMC8193861 DOI: 10.3389/fgene.2021.655882] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/12/2021] [Indexed: 01/01/2023] Open
Abstract
Extracellular microRNA (miRNA) sequences derived from the pre-implantation embryo have attracted interest for their possible contributions to the ongoing embryonic-uterine milieu, as well as their potential for use as accessible biomarkers indicative of embryonic health. Spent culture media microdroplets used to culture late-stage E4.0 murine blastocysts were screened for 641 mature miRNA sequences using a reverse transcription-quantitative polymerase chain reaction-based array. We report here 39 miRNAs exclusively detected in the conditioned media, including the implantation-relevant miR-126a-3p, miR-101a, miR-143, and miR-320, in addition to members of the highly expressed embryonic miR-125 and miR-290 families. Based on these results, an miRNA panel was assembled comprising five members of the miR-290 family (miR-291-295) and five conserved sequences with significance to the embryonic secretome (miR-20a, miR-30c, miR-142-3p, miR-191, and miR-320). Panel profiling of developing embryo cohort lysates and accompanying conditioned media microdroplets revealed extensive similarities in relative quantities of miRNAs and, as a biomarker proof of concept, enabled distinction between media conditioned with differently staged embryos (zygote, 4-cell, and blastocyst). When used to assess media conditioned with embryos of varying degrees of degeneration, the panel revealed increases in all extracellular panel sequences, suggesting cell death is an influential and identifiable factor detectable by this assessment. In situ hybridization of three panel sequences (miR-30c, miR-294, and miR-295) in late-stage blastocysts revealed primarily inner cell mass expression with a significant presence of miR-294 throughout the blastocyst cavity. Furthermore, extracellular miR-290 sequences responded significantly to high centrifugal force, suggesting a substantial fraction of these sequences may exist within a vesicle such as an exosome, microvesicle, or apoptotic bleb. Together, these results support the use of extracellular miRNA to assess embryonic health and enable development of a non-invasive viability diagnostic tool for clinical use.
Collapse
Affiliation(s)
- David Connor Hawke
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Department of Obstetrics and Gynecology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Children's Health Research Institute-LHRI, London, ON, Canada
| | - Danyal Baber Ahmed
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Department of Obstetrics and Gynecology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Children's Health Research Institute-LHRI, London, ON, Canada
| | - Andrew John Watson
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Department of Obstetrics and Gynecology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Children's Health Research Institute-LHRI, London, ON, Canada
| | - Dean Harvey Betts
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Department of Obstetrics and Gynecology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Children's Health Research Institute-LHRI, London, ON, Canada
| |
Collapse
|
|
45
|
Fasoulakis Z, Daskalakis G, Diakosavvas M, Papapanagiotou I, Theodora M, Bourazan A, Alatzidou D, Pagkalos A, Kontomanolis EN. MicroRNAs Determining Carcinogenesis by Regulating Oncogenes and Tumor Suppressor Genes During Cell Cycle. Microrna 2021; 9:82-92. [PMID: 31538910 PMCID: PMC7366009 DOI: 10.2174/2211536608666190919161849] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 05/21/2019] [Accepted: 08/03/2019] [Indexed: 02/06/2023]
Abstract
AIM To provide a review considering microRNAs regulating oncogenes and tumor suppressor genes during the different stages of cell cycle, controlling carcinogenesis. METHODS The role of microRNAs involved as oncogenes' and tumor suppressor genes' regulators in cancer was searched in the relevant available literature in MEDLINE, including terms such as "microRNA", "oncogenes", "tumor suppressor genes", "metastasis", "cancer" and others. RESULTS MicroRNAs determine the expression levels of multiple cell cycle regulators, such as cyclins, cyclin dependent kinases and other major cell cycle activators including retinoblastoma 1 (RB- 1) and p53, resulting in alteration and promotion/inhibition of the cell cycle. CONCLUSION MicroRNAs are proven to have a key role in cancer pathophysiology by altering the expression profile of different regulator proteins during cell division cycle and DNA replication. Thus, by acting as oncogenes and tumor suppressor genes, they can either promote or inhibit cancer development and formation, revealing their innovative role as biomarkers and therapeutic tools.
Collapse
Affiliation(s)
- Zacharias Fasoulakis
- Department of Obstetrics and Gynecology, Democritus University of Thrace, Alexandroupolis, Greece
| | - George Daskalakis
- 1st Department of Obstetrics and Gynecology, National and Kapodistrian University of Athens, Athens, Greece
| | - Michail Diakosavvas
- 1st Department of Obstetrics and Gynecology, National and Kapodistrian University of Athens, Athens, Greece
| | - Ioannis Papapanagiotou
- 1st Department of Obstetrics and Gynecology, National and Kapodistrian University of Athens, Athens, Greece
| | - Marianna Theodora
- 1st Department of Obstetrics and Gynecology, National and Kapodistrian University of Athens, Athens, Greece
| | - Arzou Bourazan
- Department of Obstetrics and Gynecology, Democritus University of Thrace, Alexandroupolis, Greece
| | - Dimitra Alatzidou
- Department of Obstetrics and Gynecology, Democritus University of Thrace, Alexandroupolis, Greece
| | - Athanasios Pagkalos
- Department of Obstetrics and Gynecology, General Hospital of Xanthi, Thrace, Greece
| | - Emmanuel N Kontomanolis
- Department of Obstetrics and Gynecology, Democritus University of Thrace, Alexandroupolis, Greece
| |
Collapse
|
|
46
|
Wu X, Tong R, Chen X, Jiang X, He X, Ma L. The miR-302s/367 Cluster Inhibits the Proliferation and Apoptosis in Sheep Fetal Fibroblasts via the Cell Cycle and PI3K-Akt Pathways. Mamm Genome 2021; 32:183-194. [PMID: 33956176 DOI: 10.1007/s00335-021-09873-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 04/26/2021] [Indexed: 01/15/2023]
Abstract
The miR-302s/367 family has the ability to induce mouse and human somatic cell reprogramming into induced pluripotent stem cells (iPSCs), inhibit the proliferation of several types of cancer cells, and even cause cancer cell apoptosis. However, the functions of the miR-302s/367 family in other mammals have not been explored. In the present study, the effects of miR-302s/367 on reprogramming, proliferation, and apoptosis in sheep fetal fibroblasts (SFFs) were evaluated by the delivery of a plasmid vector containing synthetic precursor miRNAs into cells, followed by the induction of mature miR-302s/367 expression. The results showed that miR-302s/367 could not reprogram SFFs into iPSCs; however, they could inhibit both the proliferation and apoptosis of SFFs by targeting CDK2, E2F1, E2F2, and PTEN in the cell cycle and PI3K-Akt pathways. Based on our findings, a novel mechanism was proposed in which the miR-302s/367 family functions in both the proliferation and apoptosis of somatic cells in mammals, suggesting that caution is needed when using miR-302s/367 as therapeutic agent.
Collapse
Affiliation(s)
- Xian Wu
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, Inner Mongolia, China
| | - Ruiying Tong
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, Inner Mongolia, China
| | - Xiuli Chen
- School of Biological Science and Technology, Baotou Teachers' College, Baotou, Inner Mongolia, China
| | - Xinying Jiang
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, Inner Mongolia, China
| | - Xiaoying He
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, Inner Mongolia, China
| | - Libing Ma
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, Inner Mongolia, China.
| |
Collapse
|
|
47
|
Abstract
Hundreds of microRNAs (miRNAs) are expressed in distinct spatial and temporal patterns during embryonic and postnatal mouse development. The loss of all miRNAs through the deletion of critical miRNA biogenesis factors results in early lethality. The function of each miRNA stems from their cumulative negative regulation of multiple mRNA targets expressed in a particular cell type. During development, miRNAs often coordinate the timing and direction of cell fate transitions. In adults, miRNAs frequently contribute to organismal fitness through homeostatic roles in physiology. Here, we review how the recent dissection of miRNA-knockout phenotypes in mice as well as advances related to their targets, dosage, and interactions have collectively informed our understanding of the roles of miRNAs in mammalian development and adaptive responses.
Collapse
|
|
48
|
Ter Huurne M, Stunnenberg HG. G1-phase progression in pluripotent stem cells. Cell Mol Life Sci 2021; 78:4507-4519. [PMID: 33884444 PMCID: PMC8195903 DOI: 10.1007/s00018-021-03797-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/19/2021] [Accepted: 02/19/2021] [Indexed: 11/10/2022]
Abstract
During early embryonic development both the rapid increase in cell number and the expression of genes that control developmental decisions are tightly regulated. Accumulating evidence has indicated that these two seemingly independent processes are mechanistically intertwined. The picture that emerges from studies on the cell cycle of embryonic stem cells is one in which proteins that promote cell cycle progression prevent differentiation and vice versa. Here, we review which transcription factors and signalling pathways play a role in both maintenance of pluripotency as well as cell cycle progression. We will not only describe the mechanism behind their function but also discuss the role of these regulators in different states of mouse pluripotency. Finally, we elaborate on how canonical cell cycle regulators impact on the molecular networks that control the maintenance of pluripotency and lineage specification.
Collapse
Affiliation(s)
- Menno Ter Huurne
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525GA, Nijmegen, The Netherlands
- Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Rd, Parkville, Melbourne, VIC, 3052, Australia
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525GA, Nijmegen, The Netherlands.
- Princess Maxima Centre for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands.
| |
Collapse
|
|
49
|
Maali A, Maroufi F, Sadeghi F, Atashi A, Kouchaki R, Moghadami M, Azad M. Induced pluripotent stem cell technology: trends in molecular biology, from genetics to epigenetics. Epigenomics 2021; 13:631-647. [PMID: 33823614 DOI: 10.2217/epi-2020-0409] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Induced pluripotent stem cell (iPSC) technology, based on autologous cells' reprogramming to the embryonic state, is a new approach in regenerative medicine. Current advances in iPSC technology have opened up new avenues for multiple applications, from basic research to clinical therapy. Thus, conducting iPSC trials have attracted increasing attention and requires an extensive understanding of the molecular basis of iPSCs. Since iPSC reprogramming is based on the methods inducing the expression of specific genes involved in pluripotency states, it can be concluded that iPSC reprogramming is strongly influenced by epigenetics. In this study, we reviewed the molecular basis of reprogramming, including the reprogramming factors (OCT4, SOX2, KLF4, c-MYC, NANOG, ESRRB, LIN28 as well as their regulatory networks), applied vectors (retroviral vectors, adenoviral vectors, Sendaiviral vectors, episomal plasmids, piggyBac, simple vectors, etc.) and epigenetic modifications (miRNAs, histones and DNA methylation states) to provide a comprehensive guide for reprogramming studies.
Collapse
Affiliation(s)
- Amirhosein Maali
- Student Research Committee, Pasteur Institute of Iran, Tehran, Iran.,Department of Medical Biotechnology, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Faezeh Maroufi
- Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Farzin Sadeghi
- Cellular & Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Amir Atashi
- Stem Cells & Tissue Engineering Research Center, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Reza Kouchaki
- Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mona Moghadami
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Mehdi Azad
- Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| |
Collapse
|
|
50
|
Tordonato C, Marzi MJ, Giangreco G, Freddi S, Bonetti P, Tosoni D, Di Fiore PP, Nicassio F. miR-146 connects stem cell identity with metabolism and pharmacological resistance in breast cancer. J Cell Biol 2021; 220:211945. [PMID: 33819341 PMCID: PMC8025236 DOI: 10.1083/jcb.202009053] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/26/2021] [Accepted: 03/01/2021] [Indexed: 02/07/2023] Open
Abstract
Although ectopic overexpression of miRNAs can influence mammary normal and cancer stem cells (SCs/CSCs), their physiological relevance remains uncertain. Here, we show that miR-146 is relevant for SC/CSC activity. MiR-146a/b expression is high in SCs/CSCs from human/mouse primary mammary tissues, correlates with the basal-like breast cancer subtype, which typically has a high CSC content, and specifically distinguishes cells with SC/CSC identity. Loss of miR-146 reduces SC/CSC self-renewal in vitro and compromises patient-derived xenograft tumor growth in vivo, decreasing the number of tumor-initiating cells, thus supporting its pro-oncogenic function. Transcriptional analysis in mammary SC-like cells revealed that miR-146 has pleiotropic effects, reducing adaptive response mechanisms and activating the exit from quiescent state, through a complex network of finely regulated miRNA targets related to quiescence, transcription, and one-carbon pool metabolism. Consistent with these findings, SCs/CSCs display innate resistance to anti-folate chemotherapies either in vitro or in vivo that can be reversed by miR-146 depletion, unmasking a “hidden vulnerability” exploitable for the development of anti-CSC therapies.
Collapse
Affiliation(s)
- Chiara Tordonato
- European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-Oncology, Università Degli Studi di Milano, Milano, Italy
| | - Matteo Jacopo Marzi
- Center for Genomic Science of Istituto Italiano di Tecnologia at European School of Molecular Medicine, Istituto Italiano di Tecnologia, Milan, Italy
| | - Giovanni Giangreco
- European Institute of Oncology IRCCS, Milan, Italy.,Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK
| | | | - Paola Bonetti
- Center for Genomic Science of Istituto Italiano di Tecnologia at European School of Molecular Medicine, Istituto Italiano di Tecnologia, Milan, Italy
| | | | - Pier Paolo Di Fiore
- European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-Oncology, Università Degli Studi di Milano, Milano, Italy
| | - Francesco Nicassio
- Center for Genomic Science of Istituto Italiano di Tecnologia at European School of Molecular Medicine, Istituto Italiano di Tecnologia, Milan, Italy
| |
Collapse
|