1
|
El-Magied MHA, Fawzy A, Mostafa MM, Elnaggar GN, Moselhy SS, Elhady MM. Alterations in expression of miRNA 497 and long non-coding RNAS (XIST-TSIX) and its significant role in colorectal cancer prediction. Sci Rep 2025; 15:7387. [PMID: 40032945 DOI: 10.1038/s41598-025-90110-3] [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: 12/27/2024] [Accepted: 02/10/2025] [Indexed: 03/05/2025] Open
Abstract
Colorectal cancer (CRC) is a common type of malignancy in Western nations with high incidence related to different factors as genetic, foods and pollution. Long non-coding RNAs (LncRNAs) play a significant role in cellular processes, oncogensis and can be used as biomarkers for cancer progression. The rationale of this study was to quantify the expression levels of miRNA 497 and LncRNAs (XIST-TSIX) as a sensitive and accurate markers for CRC diagnosis and correlated with serum FOXK1, CA19.9 and CEA compared with normal subjects. This study was carried outon100 participants, they were divided into two equal groups: Group (1): Patients were diagnosed with CRC and Group (2): Normal subjects as control. Tumor size, type, TNM staging, differentiation, levels of FOXK1and, CEA, CA19.9 were evaluated in serum. The RNA was extracted from the tissue of CRC patients for quantification expression of miRNA 497 and LncRNAs (XIST and TSIX) using qRT-PCR. Data obtained showed that, the expression levels of tissue miRNA 497, XIST, TSIX in combination with serum FOXK1, CA19.9 and CEA are good confirmatory non-invasive markers for CRC diagnosis. Sensitivity and specificity tests showed higher AUC values of miRNA 497 + XIST + TSIX + FOXK1 significantly than those of CA19.9 + CAE. It was concluded that, a rigorous assessment of these parameters could facilitate the discovery of non-invasive biomarkers for the early detection and prognosis of CRC, ultimately enhancing the protocols for early treatment decision-making.
Collapse
Affiliation(s)
| | - Amal Fawzy
- Clinical Pathology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Marwa Mohsen Mostafa
- Cardiovascular Hospital, Ain Shams University Hospitals, Ain Shams University, Cairo, Egypt
| | - Ghada Nabil Elnaggar
- Clinical Pathology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Said Salama Moselhy
- Biochemistry Department, Faculty of Science, Ain Shams University, Cairo, Egypt.
| | | |
Collapse
|
2
|
Strati A, Adamopoulos C, Kotsantis I, Psyrri A, Lianidou E, Papavassiliou AG. Targeting the PD-1/PD-L1 Signaling Pathway for Cancer Therapy: Focus on Biomarkers. Int J Mol Sci 2025; 26:1235. [PMID: 39941003 PMCID: PMC11818137 DOI: 10.3390/ijms26031235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2024] [Revised: 01/26/2025] [Accepted: 01/29/2025] [Indexed: 02/16/2025] Open
Abstract
The PD1/PD-L1 axis plays an important immunosuppressive role during the T-cell-mediated immune response, which is essential for the physiological homeostasis of the immune system. The biology of the immunological microenvironment is extremely complex and crucial for the development of treatment strategies for immunotherapy. Characterization of the immunological, genomic or transcriptomic landscape of cancer patients could allow discrimination between responders and non-responders to anti-PD-1/PD-L1 therapy. Immune checkpoint inhibitor (ICI) therapy has shown remarkable efficacy in a variety of malignancies in landmark trials and has fundamentally changed cancer therapy. Current research focuses on strategies to maximize patient selection for therapy, clarify mechanisms of resistance, improve existing biomarkers, including PD-L1 expression and tumor mutational burden (TMB), and discover new biomarkers. In this review, we focus on the function of the PD-1/PD-L1 signaling pathway and discuss the immunological, genomic, epigenetic and transcriptomic landscape in cancer patients receiving anti-PD-1/PD-L1 therapy. Finally, we provide an overview of the clinical trials testing the efficacy of antibodies against PD-1/PD-L1.
Collapse
Affiliation(s)
- Areti Strati
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece;
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (C.A.); (A.G.P.)
| | - Christos Adamopoulos
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (C.A.); (A.G.P.)
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ioannis Kotsantis
- Department of Medical Oncology, Second Department of Internal Medicine, Attikon University General Hospital, Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - Amanda Psyrri
- Department of Medical Oncology, Second Department of Internal Medicine, Attikon University General Hospital, Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - Evi Lianidou
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece;
| | - Athanasios G. Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (C.A.); (A.G.P.)
| |
Collapse
|
3
|
Xin X, Dong L, Li J, Chen W, Qiu Y, Lian F, Wu H. Exploring lncRNA expression in follicular fluid exosomes of patients with obesity and polycystic ovary syndrome based on high-throughput sequencing technology. J Ovarian Res 2024; 17:220. [PMID: 39529075 PMCID: PMC11552169 DOI: 10.1186/s13048-024-01552-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 11/01/2024] [Indexed: 11/16/2024] Open
Abstract
BACKGROUND Infertility is a reproductive health problem that attracts worldwide attention. Polycystic ovary syndrome (PCOS) is a major cause of female infertility and patients with obesity and PCOS are particularly common in clinical practice. Long non-coding RNA (lncRNAs) are a functional core in cells that regulate gene expression, transcription, and chromatin modification processes, and participate in epigenetics, cell cycle, and cell differentiation. LncRNAs are assumed to play a role in the occurrence and development of PCOS; however, their specific mechanism of action remains to be elucidated. METHODS High-throughput sequencing technology has been used to sequence and analyze lncRNAs in exosomes from the follicular fluid of patients with obesity and PCOS and those who underwent assisted reproductive therapy owing to male factors. Specific expression profiles of patients with obesity and PCOS were obtained and functional information analysis combined with a literature review were performed to screen for differentially expressed lncRNAs, which were validated using real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR). RESULTS High-throughput sequencing analysis revealed that compared to normal patients with male infertility, patients with obesity and PCOS had a total of 20 lncRNAs with significant expression differences in follicular fluid exosomes. Among them, 17 lncRNAs were upregulated and three were downregulated. Functional analysis showed that differentially expressed genes were mainly enriched in "cell metabolism," "cell adhesion," and other aspects: related gene pathways mainly involved Huntington's disease, Parkinson's disease, spliceosomes, non-alcoholic fatty liver disease, and ribosomes. Verification of differentially expressed lncRNAs revealed that the expression of lncRNAs TPT1-AS1, PTOV1-AS1, PTPRG-AS1, and SNHG14 in follicular fluid exosomes was consistent with the sequencing results. CONCLUSION A preliminary differential expression profile of lncRNAs in exosomes of patients with obesity and PCOS was established by transcriptomic analysis of these individuals. Our bioinformatics analysis results may be applicable to further study of the impact mechanism involving obesity and PCOS. These differentially expressed lncRNAs maybe served as potential biomarkers for in-depth studies of the occurrence, development on Follicle quality and function for patients with PCOS in the future.
Collapse
Affiliation(s)
- Xin Xin
- First School of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, 250011, China
| | - Li Dong
- First School of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, 250011, China
| | - Jiaxi Li
- Shandong Wendeng Osteopathic Hospital, Wendeng, Shandong, 264400, China
| | - Wen Chen
- First School of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, 250011, China
| | - Yue Qiu
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250014, China
| | - Fang Lian
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250014, China.
| | - Haicui Wu
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250014, China.
| |
Collapse
|
4
|
Zhao S, Song C, Chen F, Li M. LncRNA XIST/miR-455-3p/HOXC4 axis promotes breast cancer development by activating TGF-β/SMAD signaling pathway. Funct Integr Genomics 2024; 24:159. [PMID: 39261346 DOI: 10.1007/s10142-024-01442-8] [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: 06/29/2024] [Revised: 08/16/2024] [Accepted: 09/03/2024] [Indexed: 09/13/2024]
Abstract
Breast cancer is the second primary cause of cancer death among women. Long non-coding RNA (lncRNA) X-inactive specific transcript (XIST) is a central regulator for X chromosome inactivation, and its abnormal expression is a primary feature of breast cancer. So far, the mechanism of XIST in breast cancer has not been fully elucidated. We attempted to illustrate the mechanism of XIST in breast cancer. The expressions of XIST, microRNA-455-3p (miR-455-3p) in breast cancer were measured using quantitative real-time PCR. The expressions of homeobox C4 (HOXC4) were assessed with immunohistochemical and Western blot. Also, the functions of XIST in breast cancer were assessed by Cell Counting Kit-8 analysis, colony formation assay, flow cytometry, Western blot, Transwell, and cell scratch assays. Meanwhile, the mechanism of XIST in breast cancer was validated using database analysis and dual-luciferase reporter assay. Furthermore, the function of XIST in breast cancer in vivo was estimated by tumor xenograft model, immunohistochemical assay, and hematoxylin-eosin staining. XIST and HOXC4 expressions were increased, but miR-455-3p expressions were decreased in breast cancer tissues and cells. Knocking down XIST restrained breast cancer cell proliferation, invasion, migration, epithelial-mesenchymal transformation (EMT), and induced cell cycle arrest at G0/G1. Meanwhile, XIST interacted with miR-455-3p, while miR-455-3p interacted with HOXC4. XIST knockdown repressed breast cancer cell proliferation, invasion, and EMT, while miR-455-3p inhibitor or HOXC4 overexpression abolished those impacts. HOXC4 overexpression also blocked the impacts of miR-455-3p mimic on breast cancer cell malignant behavior. In vivo experimental data further indicated that XIST knockdown repressed breast cancer cell tumorigenic ability, and decreased HOXC4 and p-SMAD3 (TGF-β/SMAD-related protein) expressions.XIST/miR-455-3p/HOXC4 facilitated breast cancer development by activating the TGF-β/SMAD pathway.
Collapse
Affiliation(s)
- Shanshan Zhao
- Department of Oncology, The Second Hospital of Dalian Medical University, No.467 Zhongshan Road, Shahekou District, Dalian City, Liaoning Province, China
| | - Chen Song
- Department of Oncology, The Second Hospital of Dalian Medical University, No.467 Zhongshan Road, Shahekou District, Dalian City, Liaoning Province, China
| | - Fengxi Chen
- Department of Oncology, The Second Hospital of Dalian Medical University, No.467 Zhongshan Road, Shahekou District, Dalian City, Liaoning Province, China
| | - Man Li
- Department of Oncology, The Second Hospital of Dalian Medical University, No.467 Zhongshan Road, Shahekou District, Dalian City, Liaoning Province, China.
| |
Collapse
|
5
|
Carman BL, Qin S, Predescu DN, Jana M, Cortese R, Aldred MA, Gozal D, Mokhlesi B, Predescu SA. Dysregulation of the Long Noncoding RNA X-Inactive-Specific Transcript Expression in Male Patients with Pulmonary Arterial Hypertension. THE AMERICAN JOURNAL OF PATHOLOGY 2024; 194:1592-1606. [PMID: 38705381 PMCID: PMC11284765 DOI: 10.1016/j.ajpath.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 03/10/2024] [Accepted: 04/09/2024] [Indexed: 05/07/2024]
Abstract
Pulmonary arterial hypertension (PAH) is a sex-biased disease with female sex as a significant risk factor. Increased expression of the long noncoding RNA X-inactive-specific transcript (Xist), as induced by an intersectin-1s protein fragment with proliferative potential (EHITSN), may explain the sexual dimorphism of female pulmonary artery endothelial cells (ECs) and at least in part, the imbalance sex/ratio of PAH. Xist is essential for X-chromosome inactivation and dosage compensation of X-linked genes. Herein, increased Xist expression was detected in a subset of ECs and lung tissue samples of male patients with PAH. The role of different Xist expression levels in ECs of male patients with PAH (ECPAH) was studied in several lines of male ECPAH in conjunction with molecular, biochemical, morphologic, and functional approaches. Male ECPAH showed on average 10.3-fold increase in high Xist versus low Xist, a significant association between Xist levels and their proliferative potential, and a heterogeneous methylation of the Xist/XIST antisense RNA (Tsix) locus. Interestingly, Xist up-regulation in male ECPAH decreased the expression of Krueppel-like factor 2 (Klf2), via EHITSN interaction with enhancer of zeste polycomb repressive complex 2 subunit (EZH2), the catalytic subunit of the polycomb repressive complex 2. Moreover, the studies demonstrate that EHITSN-triggered p38/ETS domain-containing protein Elk1/AP-1 transcription factor subunit (c-Fos) signaling is a pathologic mechanism central to ECPAH proliferation and the dynamic crosstalk with cell cycle regulatory proteins cyclin A1/cyclin D2 and Xist-EZH2-Klf2 interaction participate directly and differentially in establishing the proliferative profile of male ECPAH.
Collapse
Affiliation(s)
- Brandon L Carman
- Division of Pulmonary, Critical Care and Sleep Medicine, Rush University Medical Center, Chicago, Illinois
| | - Shanshan Qin
- Division of Pulmonary, Critical Care and Sleep Medicine, Rush University Medical Center, Chicago, Illinois
| | - Dan N Predescu
- Division of Pulmonary, Critical Care and Sleep Medicine, Rush University Medical Center, Chicago, Illinois
| | - Malabendu Jana
- Department of Neurological Science, Rush University Medical Center, Chicago, Illinois
| | - Rene Cortese
- Child Health Research Institute, University of Missouri, Columbia, Missouri
| | - Micheala A Aldred
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - David Gozal
- Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia
| | - Babak Mokhlesi
- Division of Pulmonary, Critical Care and Sleep Medicine, Rush University Medical Center, Chicago, Illinois
| | - Sanda A Predescu
- Division of Pulmonary, Critical Care and Sleep Medicine, Rush University Medical Center, Chicago, Illinois.
| |
Collapse
|
6
|
Leithy AAE, Bakr YM, Hassan NM, Dardeer KT, Assem M, Wahab AHAA. PTCSC3, XIST, GAS5, UCA1, and HIFAL: Five lncRNAs Emerging as Potential Prognostic Players in Egyptian Adult Acute Myeloid Leukemia (AML) Patients. Cancer Control 2024; 31:10732748241309044. [PMID: 39673539 DOI: 10.1177/10732748241309044] [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] [Indexed: 12/16/2024] Open
Abstract
BACKGROUND AND AIMS So far, long noncoding RNAs (lncRNAs) signatures in acute myeloid leukemia (AML) are poorly understood. The present study aims to explore the prognostic significance of eleven cancer-related lncRNAs in bone marrow (BM) samples from adult Egyptian AML patients. MATERIALS AND METHODS In this study, we analyzed eleven lncRNAs using the qRT-PCR assay in the bone marrow (BM) of 79 de novo AML adult patients before receiving any therapy. RESULTS Five lncRNAs out of 11 were aberrantly expressed, and two lncRNAs influenced significantly the patient's overall survival (OS). LncRNA-XIST was favorable when overexpressed (in univariate and multivariate analysis, P-value = .001). LncRNA-GAS5 adversely affected the OS (only in multivariate analysis P-value = .02). Two other lncRNAs (UCA1 and HIFAL) impacted complete remission induction (CR) significantly in univariate analysis (P-value = .046 for both). Furthermore, lncRNA-UCA1 affected CR significantly in multivariate COX regression analysis (P-value = .004). The 4 previously mentioned lncRNAs were among the 9 downregulated lncRNAs. Instead, the only 2 upregulated lncRNAs (SNHG15, MALAT1) did not significantly influence neither CR induction nor OS. LncRNA-PTCSC3, a fifth lncRNA, emerged as the only one that could predict relapse occurrence in an upfront original BM sample. CONCLUSION Two lncRNAs out of eleven (lncRNA-XIST and GAS5) impacted OS, and two other lncRNAs (UCA1 and HIFAL) affected CR in adult de novo AML patients. LncRNA-PTCSC3 predict relapse, however, further validation is still required.
Collapse
Affiliation(s)
- Asmaa A El Leithy
- College of Biotechnology, Misr University for Science and Technology (MUST), Giza, Egypt
| | - Yasser Mabrouk Bakr
- Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Naglaa M Hassan
- Clinical Pathology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | | | - Magda Assem
- Clinical Pathology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | | |
Collapse
|
7
|
Zhang Z, Xu L, Zhang L, Lu J, Peng Z, Guo X, Gao J. Transcriptomics profiling reveal the heterogeneity of white and brown adipocyte. J Bioenerg Biomembr 2023; 55:423-433. [PMID: 37906396 DOI: 10.1007/s10863-023-09990-7] [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: 07/03/2023] [Accepted: 10/14/2023] [Indexed: 11/02/2023]
Abstract
The marker genes associated with white adipocytes and brown adipocytes have been previously identified; however, these markers have not been updated in several years, and the differentiation process of preadipocytes remains relatively fixed. Consequently, there has been a lack of exploration into alternative differentiation schemes. In this particular study, we present a transcriptional signature specific to brown adipocytes and white adipocytes. Notably, our findings reveal that ZNF497, ZIC1, ZFY, UTY, USP9Y, TXLNGY, TTTY14, TNNT3, TNNT2, TNNT1, TNNI1, TNNC1, TDRD15, SOX11, SLN, SFRP2, PRKY, PAX3KLHL40, PAX3, INKA2-AS1, SOX11, and TDRD15 exhibit high expression levels in brown adipocytes. XIST, HOXA10, PCAT19, HOXA7, PLSCR3, and AVPR1A exhibited high expression levels in white adipocytes, suggesting their potential as novel marker genes for the transition from white to brown adipocytes. Furthermore, our analysis revealed the coordinated activation of several pathways, including the PPAR signaling pathway, focal adhesion, retrograde endocannabinoid signaling, oxidative phosphorylation, PI3K-Akt signaling pathway, and thermogenesis pathways, in brown adipocytes. Moreover, in contrast to prevailing culture techniques, we conducted a comparative analysis of the differentiation protocols for white preadipocytes and brown preadipocytes, revealing that the differentiation outcome remained unaffected by the diverse culture schemes employed. However, the expression levels of certain marker genes in both adipocyte types were found to be altered. This investigation not only identified potential novel marker genes for adipocytes but also examined the impact of different differentiation methods on preadipocyte maturation. Consequently, these findings offer significant insights for further research on the differentiation processes of diverse adipocyte subtypes.
Collapse
Affiliation(s)
- Zhongxiao Zhang
- Department of Pediatrics, Tongren Hospital, Hongqiao International Institute of Medicine, Shanghai Jiao Tong University School of Medicine, No.1111, XianXia Road, Shanghai, 200336, China
| | - Liling Xu
- Department of Pediatrics, Tongren Hospital, Hongqiao International Institute of Medicine, Shanghai Jiao Tong University School of Medicine, No.1111, XianXia Road, Shanghai, 200336, China
| | - Ling Zhang
- Department of Pediatrics, Tongren Hospital, Hongqiao International Institute of Medicine, Shanghai Jiao Tong University School of Medicine, No.1111, XianXia Road, Shanghai, 200336, China
| | | | - Zhou Peng
- Department of Pediatrics, Tongren Hospital, Hongqiao International Institute of Medicine, Shanghai Jiao Tong University School of Medicine, No.1111, XianXia Road, Shanghai, 200336, China
| | - Xirong Guo
- Department of Pediatrics, Tongren Hospital, Hongqiao International Institute of Medicine, Shanghai Jiao Tong University School of Medicine, No.1111, XianXia Road, Shanghai, 200336, China.
| | - Jianfang Gao
- Department of Pediatrics, Tongren Hospital, Hongqiao International Institute of Medicine, Shanghai Jiao Tong University School of Medicine, No.1111, XianXia Road, Shanghai, 200336, China.
| |
Collapse
|
8
|
Mathias C, Kozak VN, Magno JM, Baal SCS, dos Santos VHA, Ribeiro EMDSF, Gradia DF, Castro MAA, Carvalho de Oliveira J. PD-1/PD-L1 Inhibitors Response in Triple-Negative Breast Cancer: Can Long Noncoding RNAs Be Associated? Cancers (Basel) 2023; 15:4682. [PMID: 37835376 PMCID: PMC10572024 DOI: 10.3390/cancers15194682] [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] [Received: 08/09/2023] [Revised: 08/25/2023] [Accepted: 08/25/2023] [Indexed: 10/15/2023] Open
Abstract
As immune checkpoint inhibitors (ICI) emerge as a paradigm-shifting treatment option for patients with advanced or metastatic cancer, there is a growing demand for biomarkers that can distinguish which patients are likely to benefit. In the case of triple-negative breast cancer (TNBC), characterized by a lack of therapeutic targets, pembrolizumab approval for high-risk early-stage disease occurred regardless of PD-L1 status, which keeps the condition in a biomarker limbus. In this review, we highlight the participation of long non-coding RNAs (lncRNAs) in the regulation of the PD-1/PD-L1 pathway, as well as in the definition of prognostic immune-related signatures in many types of tumors, aiming to shed light on molecules that deserve further investigation for a potential role as biomarkers. We also conducted a bioinformatic analysis to investigate lncRNAs already investigated in PD-1/PDL-1 pathways in other cancer types, considering the TNBC molecular context. In this sense, from the generated data, we evidence here two lncRNAs, UCA1 and HCP5, which have not yet been identified in the context of the tumoral immune response in breast cancer. These candidates can be further explored to verify their use as biomarkers for ICI response. In this article, we present an updated review regarding the use of lncRNA as biomarkers of response to ICI, highlighting the versatility of using these molecules.
Collapse
Affiliation(s)
- Carolina Mathias
- Post-Graduation Program in Genetics, Department of Genetics, Federal University of Parana, Curitiba 81530-980, Brazil; (C.M.)
| | - Vanessa Nascimento Kozak
- Post-Graduation Program in Genetics, Department of Genetics, Federal University of Parana, Curitiba 81530-980, Brazil; (C.M.)
| | - Jessica Maria Magno
- Post-Graduation Program in Bioinformatics, Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba 81520-260, Brazil (V.H.A.d.S.)
| | - Suelen Cristina Soares Baal
- Post-Graduation Program in Genetics, Department of Genetics, Federal University of Parana, Curitiba 81530-980, Brazil; (C.M.)
| | - Victor Henrique Apolonio dos Santos
- Post-Graduation Program in Bioinformatics, Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba 81520-260, Brazil (V.H.A.d.S.)
| | | | - Daniela Fiori Gradia
- Post-Graduation Program in Genetics, Department of Genetics, Federal University of Parana, Curitiba 81530-980, Brazil; (C.M.)
| | - Mauro Antonio Alves Castro
- Post-Graduation Program in Bioinformatics, Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba 81520-260, Brazil (V.H.A.d.S.)
| | - Jaqueline Carvalho de Oliveira
- Post-Graduation Program in Genetics, Department of Genetics, Federal University of Parana, Curitiba 81530-980, Brazil; (C.M.)
| |
Collapse
|
9
|
Lv J, Liu Y, Tang J, Xiao H, Hu R, Wang G, Niu D, Shao PL, Yang J, Jin Z, Xu Z, Zhang B. A Novel Cell Membrane-Associated RNA Extraction Method and Its Application in the Discovery of Breast Cancer Markers. Anal Chem 2023; 95:11706-11713. [PMID: 37459193 DOI: 10.1021/acs.analchem.3c01689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Cell membrane-associated RNA (mem-RNA) has been demonstrated to be cell-specific and disease-related and are considered as potential biomarkers for disease diagnostics, drug delivery, and cell screening. However, there is still a lack of methods specifically designed to extract mem-RNA from cells, limiting the discovery and applications of mem-RNA. In this study, we propose the first all-in-one solution for high-purity mem-RNA isolation based on two types of magnetic nanoparticles, named MREMB (Membrane-associated RNA Extraction based on Magnetic Beads), which achieved ten times enrichment of cell membrane components and over 90% recovery rate of RNA extraction. To demonstrate MREMB's potential in clinical research, we extracted and sequenced mem-RNA of typical breast cancer MCF-7, MDA-MB-231, and SKBR-3 cell lines and non-neoplastic breast epithelial cell MCF-10A. Compared to total RNA, sequencing results revealed that membrane/secreted protein-encoding mRNAs and long noncoding RNAs (lncRNAs) were enriched in the mem-RNA, some of which were significantly overexpressed in the three cancer cell lines, including extracellular matrix-related genes COL5A1 and lncRNA TALAM1. The results indicated that MREMB could enrich membrane/secreted protein-coding RNA and amplify the expression differences of related RNAs between cancer and non-neoplastic cells, promising for cancer biomarker discovery.
Collapse
Affiliation(s)
- Jiahui Lv
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ying Liu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jiahu Tang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hongjun Xiao
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruibin Hu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Guanghui Wang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Dan Niu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Pan-Lin Shao
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jingkai Yang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ziqi Jin
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ziyi Xu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Bo Zhang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| |
Collapse
|
10
|
Jaiswal A, Kaushik N, Choi EH, Kaushik NK. Functional impact of non-coding RNAs in high-grade breast carcinoma: Moving from resistance to clinical applications: A comprehensive review. Biochim Biophys Acta Rev Cancer 2023; 1878:188915. [PMID: 37196783 DOI: 10.1016/j.bbcan.2023.188915] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 04/08/2023] [Accepted: 05/12/2023] [Indexed: 05/19/2023]
Abstract
Despite the recent advances in cancer therapy, triple-negative breast cancers (TNBCs) are the most relapsing cancer sub-type. It is partly due to their propensity to develop resistance against the available therapies. An intricate network of regulatory molecules in cellular mechanisms leads to the development of resistance in tumors. Non-coding RNAs (ncRNAs) have gained widespread attention as critical regulators of cancer hallmarks. Existing research suggests that aberrant expression of ncRNAs modulates the oncogenic or tumor suppressive signaling. This can mitigate the responsiveness of efficacious anti-tumor interventions. This review presents a systematic overview of biogenesis and down streaming molecular mechanism of the subgroups of ncRNAs. Furthermore, it explains ncRNA-based strategies and challenges to target the chemo-, radio-, and immunoresistance in TNBCs from a clinical standpoint.
Collapse
Affiliation(s)
- Apurva Jaiswal
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Neha Kaushik
- Department of Biotechnology, College of Engineering, The University of Suwon, Suwon 18323, Republic of Korea.
| | - Eun Ha Choi
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea.
| | - Nagendra Kumar Kaushik
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea.
| |
Collapse
|
11
|
Biyu H, GuangWen T, Ming Z, Lixin G, Mengshan L. A lncRNA-disease association prediction model based on the two-step PU learning and fully connected neural networks. Heliyon 2023; 9:e17726. [PMID: 37539215 PMCID: PMC10395133 DOI: 10.1016/j.heliyon.2023.e17726] [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: 03/09/2023] [Revised: 06/13/2023] [Accepted: 06/26/2023] [Indexed: 08/05/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been shown to play a regulatory role in various processes of human diseases. However, lncRNA experiments are inefficient, time-consuming and highly subjective, so that the number of experimentally verified associations between lncRNA and diseases is limited. In the era of big data, numerous machine learning methods have been proposed to predict the potential association between lncRNA and diseases, but the characteristics of the associated data were seldom explored. In these methods, negative samples are randomly selected for model training and the model is prone to learn the potential positive association error, thus affecting the prediction accuracy. In this paper, we proposed a cyclic optimization model of predicting lncRNA-disease associations (COPTLDA in short). In COPTLDA, the two-step training strategy is adopted to search for the samples with the greater probability of being negative examples from unlabeled samples and the determined samples are treated as negative samples, which are combined together with known positive samples to train the model. The searching and training steps are repeated until the best model is obtained as the final prediction model. In order to evaluate the performance of the model, 30% of the known positive samples are used to calculate the model accuracy and 10% of positive samples are used to calculate the recall rate of the model. The sampling strategy used in this paper can improve the accuracy and the AUC value reaches 0.9348. The results of case studies showed that the model could predict the potential associations between lncRNA and malignant tumors such as colorectal cancer, gastric cancer, and breast cancer. The predicted top 20 associated lncRNAs included 10 colorectal cancer lncRNAs, 2 gastric cancer lncRNAs, and 8 breast cancer lncRNAs.
Collapse
Affiliation(s)
| | | | | | | | - Li Mengshan
- Corresponding author. Gannan Normal University, China.
| |
Collapse
|
12
|
Elgohary S, El Tayebi HM. Inflammasomes in breast cancer: the ignition spark of progression and resistance? Expert Rev Mol Med 2023; 25:e22. [PMID: 37337426 DOI: 10.1017/erm.2023.14] [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] [Indexed: 06/21/2023]
Abstract
Inflammation and immune evasion are major key players in breast cancer (BC) progression. Recently, the FDA approved the use of anti-programmed death-ligand 1 antibody (anti-PD-L1) and phosphoinositide 3-kinase (PI3K) inhibitors against aggressive BC. Despite the paradigm shift in BC treatments, patients still suffer from resistance, recurrence and serious immune-related adverse events. These obstacles require unravelling of the hidden molecular contributors for such therapy failure hence yielding therapeutics that are at least as efficient yet safer. Inflammasome pathway is activated when the pattern recognition receptor senses danger signals (danger-associated molecular patterns) from damagedRdying cells or pathogen-associated molecular patterns found in microbes, leading to secretion of the active pro-inflammatory cytokines interleukin-1β (IL-1β) and interleukin-18 (IL-18). It has been shown throughout numerous studies that inflammasome pathway enhanced invasion, metastasis, provoked BC progression and therapy resistance. Additionally, inflammasomes upregulated the proliferative index ki67 and enhanced PD-L1 expression leading to immunotherapy resistance. IL-1β contributed to significant decrease in oestrogen receptor levels and promoted BC chemo-resistance. High levels of IL-18 in sera of BC patients were associated with worst prognosis. Stimulation of purinergic receptors and modulation of adipokines in obese subjects activated inflammasomes that evoked radiotherapy resistance and BC progression. The micro RNA miR-223-3p attenuated the inflammasome over-expression leading to lowered tumour volume and lessened angiogenesis in BC. This review sheds the light on the molecular pathways of inflammasomes and their impacts in distinct BC subtypes. In addition, it highlights novel strategies in treatment and prevention of BC.
Collapse
Affiliation(s)
- Sawsan Elgohary
- Clinical Pharmacology and Pharmacogenomics Research Group, Department of Pharmacology and Toxicology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Hend M El Tayebi
- Clinical Pharmacology and Pharmacogenomics Research Group, Department of Pharmacology and Toxicology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| |
Collapse
|
13
|
Fonseca-Montaño MA, Vázquez-Santillán KI, Hidalgo-Miranda A. The current advances of lncRNAs in breast cancer immunobiology research. Front Immunol 2023; 14:1194300. [PMID: 37342324 PMCID: PMC10277570 DOI: 10.3389/fimmu.2023.1194300] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 05/24/2023] [Indexed: 06/22/2023] Open
Abstract
Breast cancer is the most frequently diagnosed malignancy and the leading cause of cancer-related death in women worldwide. Breast cancer development and progression are mainly associated with tumor-intrinsic alterations in diverse genes and signaling pathways and with tumor-extrinsic dysregulations linked to the tumor immune microenvironment. Significantly, abnormal expression of lncRNAs affects the tumor immune microenvironment characteristics and modulates the behavior of different cancer types, including breast cancer. In this review, we provide the current advances about the role of lncRNAs as tumor-intrinsic and tumor-extrinsic modulators of the antitumoral immune response and the immune microenvironment in breast cancer, as well as lncRNAs which are potential biomarkers of tumor immune microenvironment and clinicopathological characteristics in patients, suggesting that lncRNAs are potential targets for immunotherapy in breast cancer.
Collapse
Affiliation(s)
- Marco Antonio Fonseca-Montaño
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
- Programa de Doctorado, Posgrado en Ciencias Biológicas, Unidad de Posgrado, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | | | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| |
Collapse
|
14
|
Fonseca-Montaño MA, Cisneros-Villanueva M, Coales I, Hidalgo-Miranda A. LINC00426 is a potential immune phenotype-related biomarker and an overall survival predictor in PAM50 luminal B breast cancer. Front Genet 2023; 14:1034569. [PMID: 37260772 PMCID: PMC10228735 DOI: 10.3389/fgene.2023.1034569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 05/03/2023] [Indexed: 06/02/2023] Open
Abstract
Background: Breast cancer (BRCA) represents the most frequent diagnosed malignancy in women worldwide. Despite treatment advances, BRCAs eventually develop resistance to targeted therapies, resulting in poor prognosis. The identification of new biomarkers, like immune-related long non-coding RNAs (lncRNAs), could contribute to the clinical management of BRCA patients. In this report, we evaluated the LINC00426 expression in PAM50 BRCA subtypes from two clinical independent cohorts (BRCA-TCGA and GEO-GSE96058 datasets). Methods and results: Using Cox regression models and Kaplan-Meier survival analyses, we identified that LINC00426 expression was a consistent overall survival (OS) predictor in luminal B (LB) BRCA patients. Subsequently, differential gene expression and gene set enrichment analyses identified that LINC00426 expression was associated with different immune-related and cancer-related pathways and processes in LB BRCA. Additionally, the LINC00426 expression was correlated with the infiltration level of diverse immune cell populations, alongside immune checkpoint and cytolytic activity-related gene expression. Conclusion: This evidence suggests that LINC00426 is a potential biomarker of immune phenotype and an OS predictor in PAM50 LB BRCA.
Collapse
Affiliation(s)
- Marco Antonio Fonseca-Montaño
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
- Programa de Doctorado, Posgrado en Ciencias Biológicas, Unidad de Posgrado, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Mireya Cisneros-Villanueva
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Isabelle Coales
- Centre for Host Microbiome Interactions, King’s College London, London, United Kingdom
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| |
Collapse
|
15
|
HIRAYAMA AIRI, ISHIGAKI HIROTAKA, TAKAHASHI KATSUNORI, MIURA YUSUKE, KIKUCHI HARUHISA, KUBOHARA YUZURU. Dictyostelium Differentiation-inducing Factor Derivatives Reduce the Glycosylation of PD-L1 in MDA-MB-231 Human Breast Cancer Cells. JUNTENDO IJI ZASSHI = JUNTENDO MEDICAL JOURNAL 2023; 69:105-115. [PMID: 38854456 PMCID: PMC11153063 DOI: 10.14789/jmj.jmj22-0039-oa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 12/02/2022] [Indexed: 06/11/2024]
Abstract
Objectives Triple-negative breast cancer (TNBC) is a metastatic and intractable cancer with limited treatment options. Refractory cancer cells often express the immune checkpoint molecules programmed death-ligand 1 (PD-L1) and PD-L2, which inhibit the anticancer effects of T cells. Differentiation-inducing factors, originally found in Dictyostelium discoideum, and their derivatives possess strong antiproliferative activity, at least in part by reducing cyclin D1 expression in various cancer cells, but their effects on PD-L1/PD-L2 have not been examined. In this study, we investigate the effects of six DIF compounds (DIFs) on the expression of PD-L1/PD-L2 and cyclin D1/D3 in MDA-MB-231 cells, a model TNBC cell line. Methods MDA-MB-231 cells were incubated for 5 or 15 h with or without DIFs, and the mRNA expression of cyclin D1, PD-L1, and PD-L2 were assessed by quantitative polymerase chain reaction (qPCR). Whereas, MDA-MD-231 cells were incubated for 12 or 24 h with or without DIFs, and the protein expression of cyclins D1 and D3, PD-L1, and PD-L2 were assessed by Western blotting. Results As expected, some DIFs strongly reduced cyclin D1/D3 protein expression in MDA-MB-231 cells. Contrary to our expectation, DIFs had little effect on PD-L1 mRNA expression or increased it transiently. However, some DIFs partially reduced glycosylated PD-L1 and increased non-glycosylated PD-L1 in MDA-MB-231 cells. The level of PD-L2 was very low in these cells. Conclusions Since PD-L1 glycosylation plays an important role in preventing T cells from attacking cancer cells, such DIFs may promote T cell attack on cancer cells in vivo.
Collapse
Affiliation(s)
| | | | | | | | | | - YUZURU KUBOHARA
- Corresponding author: Yuzuru Kubohara, Laboratory of Health and Life Science, Graduate School of Health and Sports Science, Juntendo University, Inzai City, Chiba 270-1695, Japan, TEL: +81-476-98-1001 FAX: +81-476-98-1011 E-mail:
| |
Collapse
|
16
|
Pan X, Li C, Feng J. The role of LncRNAs in tumor immunotherapy. Cancer Cell Int 2023; 23:30. [PMID: 36810034 PMCID: PMC9942365 DOI: 10.1186/s12935-023-02872-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/13/2023] [Indexed: 02/23/2023] Open
Abstract
Cancer immunotherapy is a major breakthrough in the history of tumor therapy in the last decade. Immune checkpoint inhibitors blocking CTLA-4/B7 or PD-1/PD-L1 pathways have greatly prolonged the survival of patients with different cancers. Long non-coding RNAs (lncRNAs) are abnormally expressed in tumors and play an important role in tumor immunotherapy through immune regulation and immunotherapy resistance. In this review, we summarized the mechanisms of lncRNAs in regulating gene expression and well-studied immune checkpoint pathways. The crucial regulatory function of immune-related lncRNAs in cancer immunotherapy was also described. Further understanding of the underlying mechanisms of these lncRNAs is of great importance to the development of taking lncRNAs as novel biomarkers and therapeutic targets for immunotherapy.
Collapse
Affiliation(s)
- Xuan Pan
- Department of Medical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, People's Republic of China.
| | - Chenchen Li
- grid.89957.3a0000 0000 9255 8984Department of Medical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, People’s Republic of China
| | - Jifeng Feng
- Department of Medical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, People's Republic of China.
| |
Collapse
|
17
|
Pourramezan Z, Attar FA, Yusefpour M, Azizi M, Oloomi M. Circulating LncRNAs landscape as potential biomarkers in breast cancer. Cancer Rep (Hoboken) 2023; 6:e1722. [PMID: 36274054 PMCID: PMC9940007 DOI: 10.1002/cnr2.1722] [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: 09/27/2021] [Revised: 07/01/2022] [Accepted: 09/07/2022] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND In Iran, the delay in diagnosis and treatment of breast cancer results in low survival rates. AIM It is essential to characterize new therapeutic targets and prognostic breast cancer biomarkers. The rising evidence suggested that long non-coding RNAs (lncRNAs) expression levels are deregulated in human cancers and can use as biomarkers for the rapid diagnosis of breast cancer. METHODS In the present study, a quantitative real-time polymerase chain reaction (qRT-PCR) technique was used to measure 20 oncogenic and tumor suppressor lncRNAs expression levels in whole blood samples of female breast cancer patients and healthy women. Receiver operating characteristic curve (ROC) was used to assess the diagnostic value of each selected lncRNA as a biomarker. RESULTS The results revealed that some circulating lncRNAs (MEG3, NBAT1, NKILA, GAS5, EPB41L4A-AS2, Z38, and BC040587) were significantly down-regulated in breast cancer patients compared to healthy women. In contrast, other circulating lncRNAs (H19, SPRY4-IT1, XIST, UCA1, AC026904.1, CCAT1, CCAT2, ITGB2-AS, and AK058003) were significantly up-regulated in breast cancer patients compared to controls. It was shown that the expression levels of NKILA, and NBAT1 lncRNAs were related to tumor size, and BC040587 expression level related to age, node metastasis, tumor size, and grade (p < .05). The association between H19 and SPRY4-IT1 lncRNAs with HER-2 was confirmed statistically (p < .05). ROC curves illustrated that the blood levels of SPRY4-IT1, XIST, and H19 lncRNAs have excellent potential in discriminating breast cancer from the healthy controls, showing an AUC of 1.0 (95% CI 1.0-1.0, p = .00), 0.898 (95% CI 0.815-0.981, p = .00), and 0.848 (95% CI 0.701-0.995, p = .01), respectively. CONCLUSION In conclusion, the expression levels of circulating H19 and SPRY4-IT1 lncRNAs in breast cancer patients could consider as the prognostic biomarkers and therapeutic targets in breast cancer, because of their excellent power in discriminating breast cancer from healthy individuals and the significant correlation of H19, and SPRY4-IT1 lncRNAs with clinicopathological traits. We also suggest the possible application of BC040587 lncRNA as a diagnostic and prognostic indicator to assess tumor progression in case of verification in larger patients' cohorts.
Collapse
Affiliation(s)
| | | | - Maryam Yusefpour
- Department of Molecular BiologyPasteur Institute of IranTehranIran
| | - Masoumeh Azizi
- Department of Molecular MedicineBiotechnology Research Center, Pasteur Institute of IranTehranIran
| | - Mana Oloomi
- Department of Molecular BiologyPasteur Institute of IranTehranIran
| |
Collapse
|
18
|
Lin L, Chen R, Zhu Y, Xie W, Jing H, Chen L, Zou M. SCCPMD: Probability matrix decomposition method subject to corrected similarity constraints for inferring long non-coding RNA-disease associations. Front Microbiol 2023; 13:1093615. [PMID: 36713213 PMCID: PMC9874942 DOI: 10.3389/fmicb.2022.1093615] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 11/30/2022] [Indexed: 01/13/2023] Open
Abstract
Accumulating evidence has demonstrated various associations of long non-coding RNAs (lncRNAs) with human diseases, such as abnormal expression due to microbial influences that cause disease. Gaining a deeper understanding of lncRNA-disease associations is essential for disease diagnosis, treatment, and prevention. In recent years, many matrix decomposition methods have also been used to predict potential lncRNA-disease associations. However, these methods do not consider the use of microbe-disease association information to enrich disease similarity, and also do not make more use of similarity information in the decomposition process. To address these issues, we here propose a correction-based similarity-constrained probability matrix decomposition method (SCCPMD) to predict lncRNA-disease associations. The microbe-disease associations are first used to enrich the disease semantic similarity matrix, and then the logistic function is used to correct the lncRNA and disease similarity matrix, and then these two corrected similarity matrices are added to the probability matrix decomposition as constraints to finally predict the potential lncRNA-disease associations. The experimental results show that SCCPMD outperforms the five advanced comparison algorithms. In addition, SCCPMD demonstrated excellent prediction performance in a case study for breast cancer, lung cancer, and renal cell carcinoma, with prediction accuracy reaching 80, 100, and 100%, respectively. Therefore, SCCPMD shows excellent predictive performance in identifying unknown lncRNA-disease associations.
Collapse
Affiliation(s)
- Lieqing Lin
- Center of Campus Network & Modern Educational Technology, Guangdong University of Technology, Guangzhou, China
| | - Ruibin Chen
- School of Computer, Guangdong University of Technology, Guangzhou, China
| | - Yinting Zhu
- School of Computer, Guangdong University of Technology, Guangzhou, China
| | - Weijie Xie
- School of Computer, Guangdong University of Technology, Guangzhou, China
| | - Huaiguo Jing
- Sports Department, Guangdong University of Technology, Guangzhou, China
| | - Langcheng Chen
- Center of Campus Network & Modern Educational Technology, Guangdong University of Technology, Guangzhou, China
| | - Minqing Zou
- Department of Experiment Teaching, Guangdong University of Technology, Guangzhou, China
| |
Collapse
|
19
|
Lindemann A, Brandes F, Borrmann M, Meidert AS, Kirchner B, Steinlein OK, Schelling G, Pfaffl MW, Reithmair M. Anesthetic‑specific lncRNA and mRNA profile changes in blood during colorectal cancer resection: A prospective, matched‑case pilot study. Oncol Rep 2022; 49:28. [PMID: 36562401 PMCID: PMC9813548 DOI: 10.3892/or.2022.8465] [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: 07/22/2022] [Accepted: 11/03/2022] [Indexed: 12/23/2022] Open
Abstract
Prometastatic and antitumor effects of different anesthetics have been previously analyzed in several studies with conflicting results. Thus, the underlying perioperative molecular mechanisms mediated by anesthetics potentially affecting tumor phenotype and metastasis remain unclear. It was hypothesized that anesthetic‑specific long non‑coding RNA (lncRNA) expression changes are induced in the blood circulation and play a crucial role in tumor outcome. In the present study, high‑throughput sequencing and quantitative PCR were performed in order to identify lncRNA and mRNA expression changes affected by two therapeutic regimes, total intravenous anesthesia (TIVA) and volatile anesthetic gas (VAG) in patients undergoing colorectal cancer (CRC) resection. Total blood RNA was isolated prior to and following resection and characterized using RNA sequencing. mRNA‑lncRNA interactions and their roles in cancer‑related signaling of differentially expressed lncRNAs were identified using bioinformatics analyses. The comparison of these two time points revealed 35 differentially expressed lncRNAs in the TIVA‑group, and 25 in the VAG‑group, whereas eight were shared by both groups. Two lncRNAs in the TIVA‑group, and 23 in the VAG‑group of in silico identified target‑mRNAs were confirmed as differentially regulated in the NGS dataset of the present study. Pathway analysis was performed and cancer relevant canonical pathways for TIVA were identified. Target‑mRNA analysis of VAG revealed a markedly worsened immunological response against cancer. In this proof‑of‑concept study, anesthesic‑specific expression changes in lncRNA and mRNA profiles in blood were successfully identified. Moreover, the data of the present study provide the first evidence that anesthesia‑induced lncRNA pattern changes may contribute further in the observed differences in CRC outcome following tumor resection.
Collapse
Affiliation(s)
- Anja Lindemann
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, 80336 Munich, Germany
| | - Florian Brandes
- Department of Anesthesiology, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Melanie Borrmann
- Department of Anesthesiology, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Agnes S. Meidert
- Department of Anesthesiology, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Benedikt Kirchner
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Ortrud K. Steinlein
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, 80336 Munich, Germany
| | - Gustav Schelling
- Department of Anesthesiology, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Michael W. Pfaffl
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Marlene Reithmair
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, 80336 Munich, Germany,Correspondence to: Dr Marlene Reithmair, Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Goethestraße 29, 80336 Munich, Germany, E-mail:
| |
Collapse
|
20
|
Database Mining Detected a Cuproptosis-Related Prognostic Signature and a Related Regulatory Axis in Breast Cancer. DISEASE MARKERS 2022; 2022:9004830. [PMID: 36312586 PMCID: PMC9605827 DOI: 10.1155/2022/9004830] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/07/2022] [Indexed: 11/24/2022]
Abstract
Background Breast cancer is the frequent cause of disease burden related to cancer among women. It affects one in 20 women globally and up to one in eight women in high-income countries. Cuproptosis is a copper-induced modality of mitochondrial cell death that is involved in tumor proliferation and metastasis. Methods To construct a prognostic cuproptosis-related signature, LASSO Cox regression analysis was employed. Additionally, ceRNA was developed with an aim of exploring the possible lncRNA-miRNA-mRNA regulatory axis in breast cancer. Results The expression of FDX1, DLD, DLAT, LIAS, LIPT1, GLS MTF1, and PDHA1 was downregulated, while CDKN2A expression level was elevated in breast cancer in contrast with normal tissue. We furthermore reviewed the genetic mutation landscape of genes linked to cuproptosis in breast cancer. Prognosis analysis revealed poor OS and RFS rates in breast cancer patients with elevated levels of CDKN2A and PDHA1 and low levels of MTF1, DLD, LIPT1, and FDX1. We then constructed a cuproptosis-related signature with six genes (DKN2A, MTF1, PDHA1, DLD, LIPT1, and FDX1) for breast cancer, which predicted the OS rate with an accuracy that ranged from medium to high. Further analysis demonstrated a significant correlation between the cuproptosis-related prognostic signature and pTNM stage, MSI score, drug sensitivity, TMB score, and immune cell infiltration. Moreover, we identified the lncRNA XIST/miR-92b-3p/MTF1 regulatory axis for breast cancer. Conclusion Multiomics approaches were used to create a cuproptosis-related signature with six genes (DKN2A, MTF1, PDHA1, DLD, LIPT1, and FDX1) for breast cancer. We discovered the lncRNA XIST/miR-92b-3p/MTF1 regulatory axis for breast cancer, which has not yet been investigated previously.
Collapse
|
21
|
Kumar S, Chatterjee M, Ghosh P, Ganguly KK, Basu M, Ghosh MK. Targeting PD-1/PD-L1 in cancer immunotherapy: an effective strategy for treatment of triple-negative breast cancer (TNBC) patients. Genes Dis 2022. [DOI: 10.1016/j.gendis.2022.07.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022] Open
|
22
|
Najafi S, Khatami SH, Khorsand M, Jamali Z, Shabaninejad Z, Moazamfard M, Majidpoor J, Aghaei Zarch SM, Movahedpour A. Long non-coding RNAs (lncRNAs); roles in tumorigenesis and potentials as biomarkers in cancer diagnosis. Exp Cell Res 2022; 418:113294. [PMID: 35870535 DOI: 10.1016/j.yexcr.2022.113294] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/11/2022] [Accepted: 07/16/2022] [Indexed: 12/15/2022]
Abstract
New research has indicated that long non-coding RNAs (lncRNAs) play critical roles in a broad range of biological processes, including the pathogenesis of many complex human diseases, including cancer. The detailed regulation mechanisms of many lncRNAs in cancer initiation and progression have yet to be discovered, even though a few of lncRNAs' functions in cancer have been characterized. In the present study, we summarize recent advances in the mechanisms and functions of lncRNAs in cancer. We focused on the roles of newly-identified lncRNAs as oncogenes and tumor suppressors, as well as the potential pathways these molecules could play. The paper also discusses their potential uses as biomarkers for the diagnosis and prognosis of cancer.
Collapse
Affiliation(s)
- Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Seyyed Hossein Khatami
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Marjan Khorsand
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zeinab Jamali
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Shabaninejad
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Jamal Majidpoor
- Department of Anatomy, Faculty of Medicine, Infectious Disease Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Seyed Mohsen Aghaei Zarch
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | |
Collapse
|
23
|
Eldesouki S, Samara KA, Qadri R, Obaideen AA, Otour AH, Habbal O, Bm Ahmed S. XIST in Brain Cancer. Clin Chim Acta 2022; 531:283-290. [PMID: 35483442 DOI: 10.1016/j.cca.2022.04.993] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 11/16/2022]
Abstract
Long non-coding RNAs (lncRNAs) make up the majority of the human genome. They are a group of small RNA molecules that do not code for any proteins but play a primary role in regulating a variety of physiological and pathological processes. X-inactive specific transcript (XIST), one of the first lncRNAs to be discovered, is chiefly responsible for X chromosome inactivation: an evolutionary process of dosage compensation between the sex chromosomes of males and females. Recent studies show that XIST plays a pathophysiological role in the development and prognosis of brain tumors, a heterogeneous group of neoplasms that cause significant morbidity and mortality. In this review, we explore recent advancements in the role of XIST in migration, proliferation, angiogenesis, chemoresistance, and evasion of apoptosis in different types of brain tumors, with particular emphasis on gliomas.
Collapse
Affiliation(s)
| | - Kamel A Samara
- College of Medicine, University of Sharjah, Sharjah, UAE
| | - Rama Qadri
- College of Medicine, University of Sharjah, Sharjah, UAE
| | | | - Ahmad H Otour
- College of Medicine, University of Sharjah, Sharjah, UAE
| | - Omar Habbal
- College of Medicine, University of Sharjah, Sharjah, UAE
| | - Samrein Bm Ahmed
- College of Medicine, University of Sharjah, Sharjah, UAE; College of Health and Wellbeing and Life sciences, Department of Biosciences and chemistry, Sheffield Hallam University, UK
| |
Collapse
|
24
|
Li J, Che L, Xu C, Lu D, Xu Y, Liu M, Chai W. XIST/miR-34a-5p/PDL1 axis regulated the development of lung cancer cells and the immune function of CD8+ T cells. J Recept Signal Transduct Res 2022; 42:469-478. [PMID: 35067156 DOI: 10.1080/10799893.2021.2019274] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Jing Li
- Respiratory Department, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, PR China
| | - Liyan Che
- Respiratory Department, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, PR China
| | - Chang Xu
- Emergency Dpartment, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, PR China
| | - Dongdong Lu
- Respiratory Department, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, PR China
| | - Yan Xu
- Respiratory Department, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, PR China
| | - Mengru Liu
- Respiratory Department, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, PR China
| | - Wenshu Chai
- Respiratory Department, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, PR China
| |
Collapse
|
25
|
Wu C, Fang S, Zhang H, Li X, Du Y, Zhang Y, Lin X, Wang L, Ma X, Xue Y, Guan M. Long noncoding RNA XIST regulates brown preadipocytes differentiation and combats high-fat diet induced obesity by targeting C/EBPα. Mol Med 2022; 28:6. [PMID: 35062859 PMCID: PMC8781062 DOI: 10.1186/s10020-022-00434-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/05/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Activation of brown adipose tissue (BAT) increases energy expenditure, which makes it an attractive therapeutic strategy for obesity. LncRNAs play an important role in adipocyte differentiation and regulation. Here we assessed the effect of lncRNA XIST on brown preadipocytes differentiation and metabolic regulation. METHODS XIST expression levels were detected in human perirenal (peri-N) and subcutaneous adipose tissues (sub-Q), brown preadipocytes and 3T3-L1 preadipocytes. XIST overexpression and knockdown experiments were performed in brown preadipocytes. XIST overexpression mouse model was established by plasmid injection through tail vein. RESULTS In human adipose tissues, XIST expression was significantly higher in female than in male individuals. In vitro, XIST expression was significantly up-regulated during brown adipocyte differentiation. XIST knockdown inhibited differentiation of brown preadipocytes, while overexpression of XIST promotes brown preadipocytes to fully differentiation. RNA Binding Protein Immunoprecipitation (RIP) experiment revealed that XIST could directly bind to C/EBPα. In vivo, XIST overexpression prevents high-fat diet induced obesity and improves metabolic dysorder in male mice. CONCLUSION Our results suggest that XIST combats obesity through BAT activation at least partly by combination with transcription factor C/EBPα.
Collapse
Affiliation(s)
- Chunyan Wu
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510515, China
| | - Shu Fang
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Huijian Zhang
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Xiaoqiang Li
- Department of Plastic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Yuejun Du
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Yudan Zhang
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Xiaochun Lin
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Ling Wang
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Xiaoqin Ma
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Yaoming Xue
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Meiping Guan
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| |
Collapse
|
26
|
Selem NA, Youness RA, Gad MZ. What is beyond LncRNAs in breast cancer: A special focus on colon cancer-associated Transcript-1 (CCAT-1). Noncoding RNA Res 2021; 6:174-186. [PMID: 34938928 PMCID: PMC8666458 DOI: 10.1016/j.ncrna.2021.11.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/28/2021] [Accepted: 11/29/2021] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (LncRNAs) play a vital role in the process of malignant transformation. In breast cancer (BC), lncRNAs field is currently under intensive investigations. Yet, the role of lncRNAs as promising diagnostic and/or prognostic biomarkers and as therapeutic target/tool among BC patients still needs a special focus from the biomedical scientists. In BC, triple negative breast cancer patients (TNBC) are the unlucky group as they are always represented with the worst prognosis and the highest mortality rates. For that reason, a special focus on TNBC and associated lncRNAs was addressed in this review. Colon cancer-associated transcript 1 (CCAT-1) is a newly discovered oncogenic lncRNA that has been emerged as a vital biomarker for diagnosis, prognosis and therapeutic interventions in multiple malignancies and showed differential expression among TNBC patients. In this review, the authors shed the light onto the general role of lncRNAs in BC and the specific functional activities, molecular mechanisms, competing endogenous ncRNA role of CCAT-1 in TNBC.
Collapse
Affiliation(s)
- Noha A. Selem
- Biochemistry Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Egypt
| | - Rana A. Youness
- Molecular Genetics Research Team (MGRT), Pharmaceutical Biology Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Egypt
- School of Life and Medical Sciences, University of Hertfordshire Hosted By Global Academic Foundation, New Administrative Capital, 11586, Cairo, Egypt
| | - Mohamed Z. Gad
- Biochemistry Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Egypt
| |
Collapse
|
27
|
Tang SJ, You GR, Chang JT, Cheng AJ. Systematic Analysis and Identification of Dysregulated Panel lncRNAs Contributing to Poor Prognosis in Head-Neck Cancer. Front Oncol 2021; 11:731752. [PMID: 34733782 PMCID: PMC8558550 DOI: 10.3389/fonc.2021.731752] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 10/04/2021] [Indexed: 12/22/2022] Open
Abstract
Head and neck cancer (HNC) is one of the most prevalent cancers worldwide, accounting for approximately 5% of all cancers. While the underlying molecules and their pathogenetic mechanisms in HNC have yet to be well elucidated, recent studies have shown that dysregulation of lncRNAs may disrupt the homeostasis of various biological pathways. However, the understanding of lncRNAs in HNC is still limited by the lack of expression profiling. In the present study, we employed a systematic strategy to identify a panel of lncRNA associated with HNC. A cancer-related lncRNA profile PCR array was screened to explore potential molecules specific for HNC. A total of 55 lncRNAs were found to be dysregulated in HNC cells when compared to normal keratinocytes. Further analysis of the prognostic significance using The Cancer Genome Atlas (TCGA) database revealed 15 lncRNAs highly correlated with overall survival in HNC patients. Additionally, clinical sample expression analysis of the TCGA-HNSC cohort revealed 16 highly dysregulated lncRNAs in HNC, resulting in a combined 31-lncRNA signature panel that could predict prognosis. Validation of these molecules confirmed the considerable level of altered expressions in HNC cells, with XIST, HOXA11-AS, TSIX, MALAT1, WT1-AS, and IPW being the most prominently dysregulated. We further selected a molecule from our panel (XIST) to confirm the validity of these lncRNAs in the regulation of cancer aggressiveness. Gene ontology (GO) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analyses demonstrated that XIST participated in various cancer-related functions, including cell proliferation and metastasis. XIST silencing with the RNAi technique substantially reduced invasion and migration in several HNC cell lines. Thus, our study defined a 31-lncRNA panel as prognostic signatures in HNC. These perspective results provide a knowledge foundation for further application of these molecules in precision medicine.
Collapse
Affiliation(s)
- Shang-Ju Tang
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Change Gung University, Taoyuan, Taiwan
| | - Guo-Rong You
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Joseph T. Chang
- Department of Radiation Oncology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Medical School, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ann-Joy Cheng
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Change Gung University, Taoyuan, Taiwan
- Department of Radiation Oncology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| |
Collapse
|
28
|
Jiang W, Pan S, Chen X, Wang ZW, Zhu X. The role of lncRNAs and circRNAs in the PD-1/PD-L1 pathway in cancer immunotherapy. Mol Cancer 2021; 20:116. [PMID: 34496886 PMCID: PMC8424797 DOI: 10.1186/s12943-021-01406-7] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/08/2021] [Indexed: 12/15/2022] Open
Abstract
Cancer immunotherapy has recently shown promising antitumor effects in various types of tumors. Among all immune checkpoints, the PD-1/PD-L1 pathway plays an important role in the immune evasion of tumor cells, making it a potent target in antitumor immunity. Accordingly, antibodies targeting the PD-1/PD-L1 pathway have been developed to attack tumor cells; however, resistance to immune therapy remains to be solved. Hence, identification of the underlying modulators of the PD-1/PD-L1 pathway is of significant importance to understand the mechanisms of antitumor immunotherapy. Long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) have been identified to regulate the PD-1/PD-L1 pathway, leading to participation in the immune response and immunotherapy. Therefore, this review focuses on the functions of lncRNAs and circRNAs in regulation of the PD-1/PD-L1 axis in tumorigenesis and tumor progression. We hope this review will stimulate research to supply more precise and effective cancer immune checkpoint therapies for a large number of tumors.
Collapse
Affiliation(s)
- Wenxiao Jiang
- Departmant of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, No. 109 Xueyuan Xi Road, Wenzhou, 325027 Zhejiang China
| | - Shuya Pan
- Departmant of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, No. 109 Xueyuan Xi Road, Wenzhou, 325027 Zhejiang China
| | - Xin Chen
- Departmant of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, No. 109 Xueyuan Xi Road, Wenzhou, 325027 Zhejiang China
| | - Zhi-wei Wang
- Departmant of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, No. 109 Xueyuan Xi Road, Wenzhou, 325027 Zhejiang China
| | - Xueqiong Zhu
- Departmant of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, No. 109 Xueyuan Xi Road, Wenzhou, 325027 Zhejiang China
| |
Collapse
|
29
|
Samir A, Tawab RA, El Tayebi HM. Long non-coding RNAs XIST and MALAT1 hijack the PD-L1 regulatory signaling pathway in breast cancer subtypes. Oncol Lett 2021; 22:593. [PMID: 34149904 PMCID: PMC8200942 DOI: 10.3892/ol.2021.12854] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 01/14/2021] [Indexed: 02/06/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have attracted widespread attention as potential biological and pathological regulators. lncRNAs are involved in several biological processes in cancer. Triple negative breast cancer (TNBC) is characterized by strong heterogeneity and aggressiveness. At present, the implication of microRNAs (miRs) and lncRNAs in immunotherapy has been poorly studied. Nevertheless, the blockade of immune checkpoints, particularly that of the programmed cell-death protein-1/programmed cell-death ligand-1 (PD-L1) axis, is considered as a principle approach in breast cancer (BC) therapy. The present study aimed to investigate the interaction between immune-modulatory upstream signaling pathways of the PD-L1 transcript that could enhance personalized targeted therapy. MDA-MB-231 cells were transfected with miR-182-5p mimics followed by RNA extraction and cDNA synthesis using a reverse transcription kit, and the expression levels of the target genes were assessed by reverse transcription-quantitative PCR. Furthermore, the expression levels of target genes were measured in tissues derived from 41 patients with BC, including patients with luminal BC and TNBC, as well as their adjacent lymph nodes. The results revealed that the expression levels of miR-182-5p, PD-L1 and metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) were upregulated in MDA-MB-231 cells and BC tissues. However, X-inactive specific transcript (XIST) expression was downregulated in cancer tissues and TNBC cells. Following co-transfection of cells with small interfering RNAs specific for each target gene and miR-182-5p antagomirs, the effect of miR-182-5p was abolished in the presence of lncRNAs. Therefore, the results of the present study indicated that although miR-182-5p exhibited an oncogenic effect, XIST exerted a dominant effect on the regulation of the PD-L1 signaling pathway via the inhibition of the oncogenic function of MALAT1.
Collapse
Affiliation(s)
- Amany Samir
- Molecular Pharmacology Research Group, Department of Pharmacology and Toxicology, German University in Cairo, Cairo 11835, Egypt
| | - Reda Abdel Tawab
- Department of General Surgery, Ain Shams University, Cairo 11772, Egypt
| | - Hend M. El Tayebi
- Molecular Pharmacology Research Group, Department of Pharmacology and Toxicology, German University in Cairo, Cairo 11835, Egypt
| |
Collapse
|
30
|
Hamed MM, Handoussa H, Hussein NH, Eissa RA, Abdel-Aal LK, El Tayebi HM. Oleuropin controls miR-194/XIST/PD-L1 loop in triple negative breast cancer: New role of nutri-epigenetics in immune-oncology. Life Sci 2021; 277:119353. [PMID: 33798547 DOI: 10.1016/j.lfs.2021.119353] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/07/2021] [Accepted: 03/12/2021] [Indexed: 12/27/2022]
Abstract
Oleuropein, the main secoiridoid glucoside found in Olea europaea L., has attracted scientific community as a potential anticancer agent. Immunotherapy and RNA interference revolutionized cancer treatment. Success of PD-L1/PD-1 antibodies encouraged the investigation of PD-1/PD-L1 regulation by non-coding RNAs. This study aimed to verify the cytotoxic effect of oleuropein on MDA-MB-231 cell line and to unravel novel ceRNA interaction between miR-194-5p and XIST in breast cancer and their immunomodulatory effect on PD-L1 expression to propose a promising prophylactic and preventive role of Oleuropin in diet. For the first time, miR-194/Lnc-RNA XIST/PD-L1 triad was investigated in breast cancer, where miR-194 and PD-L1 levels were significantly upregulated in 21 BC-biopsies, yet XIST was downregulated. Ectopic expression of miR-194 enhanced cell function and viability with concomitant increase in PD-L1 expression yet XIST expression decreased, in contrast to miR-194 antagomirs that yielded opposite results. XIST knock-out elevated miR194-5p and PD-L1 levels. miR-194-5p mimics and XIST siRNAs co-transfection induced PD-L1 expression, while miR-194-5p mimics and TSIX siRNAs co-transfection showed opposite effect. Oleuropein showed anti-carcinogenic impact by decreasing miR-194 and PD-L1 levels while increasing XIST level. In conclusion, our study highlighted novel ceRNA interaction controlling PD-L1 expression in BC. Oleuropein is a promising nutraceutical for cancer therapy. Therefore, oleuropin represents a new nutri-epigenetic in immune-oncology that controls miR-194/XIST/PD-L1 loop in triple negative breast cancer.
Collapse
Affiliation(s)
- Marwa M Hamed
- The Molecular Pharmacology Research Group, Department of Pharmacology, Toxicology and Clinical Pharmacy, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Heba Handoussa
- Department of Pharmaceutical Biology, German University in Cairo, Cairo, Egypt
| | - Nada H Hussein
- The Molecular Pharmacology Research Group, Department of Pharmacology, Toxicology and Clinical Pharmacy, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Reda A Eissa
- Department of Surgery, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Lobna K Abdel-Aal
- Department of Pharmacology and Toxicology, German University in Cairo, Cairo, Egypt
| | - Hend M El Tayebi
- The Molecular Pharmacology Research Group, Department of Pharmacology, Toxicology and Clinical Pharmacy, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt.
| |
Collapse
|
31
|
Kozłowska J, Kolenda T, Poter P, Sobocińska J, Guglas K, Stasiak M, Bliźniak R, Teresiak A, Lamperska K. Long Intergenic Non-Coding RNAs in HNSCC: From "Junk DNA" to Important Prognostic Factor. Cancers (Basel) 2021; 13:2949. [PMID: 34204634 PMCID: PMC8231241 DOI: 10.3390/cancers13122949] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 12/24/2022] Open
Abstract
Head and neck squamous cell carcinoma is one of the most common and fatal cancers worldwide. Even a multimodal approach consisting of standard chemo- and radiotherapy along with surgical resection is only effective in approximately 50% of the cases. The rest of the patients develop a relapse of the disease and acquire resistance to treatment. Especially this group of individuals needs novel, personalized, targeted therapy. The first step to discovering such solutions is to investigate the tumor microenvironment, thus understanding the role and mechanism of the function of coding and non-coding sequences of the human genome. In recent years, RNA molecules gained great interest when the complex character of their impact on our biology allowed them to come out of the shadows of the "junk DNA" label. Furthermore, long non-coding RNAs (lncRNA), specifically the intergenic subgroup (lincRNA), are one of the most aberrantly expressed in several malignancies, which makes them particularly promising future diagnostic biomarkers and therapeutic targets. This review contains characteristics of known and validated lincRNAs in HNSCC, such as XIST, MALAT, HOTAIR, HOTTIP, lincRNA-p21, LINC02487, LINC02195, LINC00668, LINC00519, LINC00511, LINC00460, LINC00312, and LINC00052, with a description of their prognostic abilities. Even though much work remains to be done, lincRNAs are important factors in cancer biology that will become valuable biomarkers of tumor stage, outcome prognosis, and contribution to personalized medicine.
Collapse
Affiliation(s)
- Joanna Kozłowska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (T.K.); (J.S.); (K.G.); (M.S.); (R.B.); (A.T.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
| | - Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (T.K.); (J.S.); (K.G.); (M.S.); (R.B.); (A.T.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
| | - Paulina Poter
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
- Department of Oncologic Pathology and Prophylaxis, Poznan University of Medical Sciences, Greater Poland Cancer Centere, Garbary 15, 61-866 Poznan, Poland
- Department of Pathology, Pomeranian Medical University, Rybacka 1, 70-204 Szczecin, Poland
| | - Joanna Sobocińska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (T.K.); (J.S.); (K.G.); (M.S.); (R.B.); (A.T.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
| | - Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (T.K.); (J.S.); (K.G.); (M.S.); (R.B.); (A.T.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, ul. Zwirki 61 and ul. Wigury, 02-091 Warsaw, Poland
| | - Maciej Stasiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (T.K.); (J.S.); (K.G.); (M.S.); (R.B.); (A.T.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
| | - Renata Bliźniak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (T.K.); (J.S.); (K.G.); (M.S.); (R.B.); (A.T.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (T.K.); (J.S.); (K.G.); (M.S.); (R.B.); (A.T.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
| | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (T.K.); (J.S.); (K.G.); (M.S.); (R.B.); (A.T.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
| |
Collapse
|
32
|
Wang W, Min L, Qiu X, Wu X, Liu C, Ma J, Zhang D, Zhu L. Biological Function of Long Non-coding RNA (LncRNA) Xist. Front Cell Dev Biol 2021; 9:645647. [PMID: 34178980 PMCID: PMC8222981 DOI: 10.3389/fcell.2021.645647] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/12/2021] [Indexed: 12/24/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) regulate gene expression in a variety of ways at epigenetic, chromatin remodeling, transcriptional, and translational levels. Accumulating evidence suggests that lncRNA X-inactive specific transcript (lncRNA Xist) serves as an important regulator of cell growth and development. Despites its original roles in X-chromosome dosage compensation, lncRNA Xist also participates in the development of tumor and other human diseases by functioning as a competing endogenous RNA (ceRNA). In this review, we comprehensively summarized recent progress in understanding the cellular functions of lncRNA Xist in mammalian cells and discussed current knowledge regarding the ceRNA network of lncRNA Xist in various diseases. Long non-coding RNAs (lncRNAs) are transcripts that are more than 200 nt in length and without an apparent protein-coding capacity (Furlan and Rougeulle, 2016; Maduro et al., 2016). These RNAs are believed to be transcribed by the approximately 98-99% non-coding regions of the human genome (Derrien et al., 2012; Fu, 2014; Montalbano et al., 2017; Slack and Chinnaiyan, 2019), as well as a large variety of genomic regions, such as exonic, tronic, and intergenic regions. Hence, lncRNAs are also divided into eight categories: Intergenic lncRNAs, Intronic lncRNAs, Enhancer lncRNAs, Promoter lncRNAs, Natural antisense/sense lncRNAs, Small nucleolar RNA-ended lncRNAs (sno-lncRNAs), Bidirectional lncRNAs, and non-poly(A) lncRNAs (Ma et al., 2013; Devaux et al., 2015; St Laurent et al., 2015; Chen, 2016; Quinn and Chang, 2016; Richard and Eichhorn, 2018; Connerty et al., 2020). A range of evidence has suggested that lncRNAs function as key regulators in crucial cellular functions, including proliferation, differentiation, apoptosis, migration, and invasion, by regulating the expression level of target genes via epigenomic, transcriptional, or post-transcriptional approaches (Cao et al., 2018). Moreover, lncRNAs detected in body fluids were also believed to serve as potential biomarkers for the diagnosis, prognosis, and monitoring of disease progression, and act as novel and potential drug targets for therapeutic exploitation in human disease (Jiang W. et al., 2018; Zhou et al., 2019a). Long non-coding RNA X-inactive specific transcript (lncRNA Xist) are a set of 15,000-20,000 nt sequences localized in the X chromosome inactivation center (XIC) of chromosome Xq13.2 (Brown et al., 1992; Debrand et al., 1998; Kay, 1998; Lee et al., 2013; da Rocha and Heard, 2017; Yang Z. et al., 2018; Brockdorff, 2019). Previous studies have indicated that lncRNA Xist regulate X chromosome inactivation (XCI), resulting in the inheritable silencing of one of the X-chromosomes during female cell development. Also, it serves a vital regulatory function in the whole spectrum of human disease (notably cancer) and can be used as a novel diagnostic and prognostic biomarker and as a potential therapeutic target for human disease in the clinic (Liu et al., 2018b; Deng et al., 2019; Dinescu et al., 2019; Mutzel and Schulz, 2020; Patrat et al., 2020; Wang et al., 2020a). In particular, lncRNA Xist have been demonstrated to be involved in the development of multiple types of tumors including brain tumor, Leukemia, lung cancer, breast cancer, and liver cancer, with the prominent examples outlined in Table 1. It was also believed that lncRNA Xist (Chaligne and Heard, 2014; Yang Z. et al., 2018) contributed to other diseases, such as pulmonary fibrosis, inflammation, neuropathic pain, cardiomyocyte hypertrophy, and osteoarthritis chondrocytes, and more specific details can be found in Table 2. This review summarizes the current knowledge on the regulatory mechanisms of lncRNA Xist on both chromosome dosage compensation and pathogenesis (especially cancer) processes, with a focus on the regulatory network of lncRNA Xist in human disease.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Dongyi Zhang
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, China
| | - Lingyun Zhu
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, China
| |
Collapse
|
33
|
Hu M, Li Y, Lu Y, Wang M, Li Y, Wang C, Li Q, Zhao H. The regulation of immune checkpoints by the hypoxic tumor microenvironment. PeerJ 2021; 9:e11306. [PMID: 34012727 PMCID: PMC8109006 DOI: 10.7717/peerj.11306] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/29/2021] [Indexed: 12/14/2022] Open
Abstract
The tumor microenvironment (TME) influences the occurrence and progression of tumors, and hypoxia is an important characteristic of the TME. The expression of programmed death 1 (PD1)/programmed death-ligand 1 (PDL1), cytotoxic T-lymphocyte-associated antigen 4 (CTLA4), and other immune checkpoints in hypoxic malignant tumors is often significantly increased, and is associated with poor prognosis. The application of immune checkpoint inhibitors (ICIs) for treating lung cancer, urothelial carcinoma, and gynecological tumors has achieved encouraging efficacy; however, the rate of efficacy of ICI single-drug treatment is only about 20%. In the present review, we discuss the possible mechanisms by which the hypoxic TME regulates immune checkpoints. By activating hypoxia-inducible factor-1α (HIF-1α), regulating the adenosine (Ado)-A2aR pathway, regulating the glycolytic pathway, and driving epithelial-mesenchymal transition (EMT) and other biological pathways, hypoxia regulates the expression levels of CTLA4, PD1, PDL1, CD47, lymphocyte activation gene 3 (LAG3), T-cell immunoglobulin and mucin domain 3 (TIM3), and other immune checkpoints, which interfere with the immune effector cell anti-tumor response and provide convenient conditions for tumors to escape immune surveillance. The combination of HIF-1α inhibitors, Ado-inhibiting tumor immune microenvironment regulatory drugs, and other drugs with ICIs has good efficacy in both preclinical studies and phase I-II clinical studies. Exploring the effects of TME hypoxia on the expression of immune checkpoints and the function of infiltrating immune cells has greatly clarified the relationship between the hypoxic TME and immune escape, which is of great significance for the development of new drugs and the search for predictive markers of the efficacy of immunotherapy for treating malignant tumors. In the future, combination therapy with hypoxia pathway inhibitors and ICIs may be an effective anti-tumor treatment strategy.
Collapse
Affiliation(s)
- Min Hu
- Department of Biochemistry & Molecular Biology, Basic Medical College, Shanxi Medical University, Taiyuan, Shanxi Province, China.,Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yongfu Li
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Department of Oncology, The Second Affiliated Hospital of Hainan Medical University, Haikou, Hainan Province, China
| | - Yuting Lu
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Miao Wang
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yingrui Li
- Department of Biochemistry & Molecular Biology, Basic Medical College, Shanxi Medical University, Taiyuan, Shanxi Province, China.,Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Chaoying Wang
- Department of Oncology, The Second Affiliated Hospital of Hainan Medical University, Haikou, Hainan Province, China
| | - Qin Li
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Hong Zhao
- Department of Biochemistry & Molecular Biology, Basic Medical College, Shanxi Medical University, Taiyuan, Shanxi Province, China
| |
Collapse
|
34
|
Falahati Z, Mohseni-Dargah M, Mirfakhraie R. Emerging Roles of Long Non-coding RNAs in Uterine Leiomyoma Pathogenesis: a Review. Reprod Sci 2021; 29:1086-1101. [PMID: 33844188 DOI: 10.1007/s43032-021-00571-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/01/2021] [Indexed: 01/19/2023]
Abstract
Uterine leiomyoma (UL), as the most prevalent type of women's health disorders, is a benign tumor that originates from the smooth muscle cell layer of the uterus. A great number of associated complications are observed including infertility, miscarriage, bleeding, pain, dysmenorrhea, menorrhagia, and dyspareunia. Although the etiology of UL is largely undefined, environmental and genetic factors are witnessed to engage in the UL development. As long non-coding RNAs (lncRNAs) are involved in various types of cellular functions, in recent years, a great deal of attention has been drawn to them and their possible roles in UL pathogenesis. Moreover, they have illustrated their potential to be promising candidates for UL treatment. In this review paper, firstly, an overview of UL pathogenesis is presented. Then, the regulation of lncRNAs in UL and their possible mechanisms in cancer development are reviewed. Eventually, therapeutic approaches targeting lncRNAs in various cancers and UL are explored.
Collapse
Affiliation(s)
- Zahra Falahati
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, Iran
| | - Masoud Mohseni-Dargah
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- School of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, Australia
| | - Reza Mirfakhraie
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Koodakyar St., Velenjak Ave, Chamran Highway, Tehran, Iran.
- Genomic Research Centre, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
35
|
Association between HOX Transcript Antisense RNA Single-Nucleotide Variants and Recurrent Implantation Failure. Int J Mol Sci 2021; 22:ijms22063021. [PMID: 33809601 PMCID: PMC8002254 DOI: 10.3390/ijms22063021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 12/26/2022] Open
Abstract
Recurrent implantation failure (RIF) refers to the occurrence of more than two failed in vitro fertilization–embryo transfers (IVF-ETs) in the same individual. RIF can occur for many reasons, including embryo characteristics, immunological factors, and coagulation factors. Genetics can also contribute to RIF, with some single-nucleotide variants (SNVs) reported to be associated with RIF occurrence. We examined SNVs in a long non-coding RNA, homeobox (HOX) transcript antisense RNA (HOTAIR), which is known to affect cancer development. HOTAIR regulates epigenetic outcomes through histone modifications and chromatin remodeling. We recruited 155 female RIF patients and 330 healthy controls, and genotyped HOTAIR SNVs, including rs4759314, rs920778, rs7958904, and rs1899663, in all participants. Differences in these SNVs were compared between the patient and control groups. We identified significant differences in the occurrence of heterozygous genotypes and the dominant expression model for the rs1899663 and rs7958904 SNVs between RIF patients and control subjects. These HOTAIR variants were associated with serum hemoglobin (Hgb), luteinizing hormone (LH), total cholesterol (T. chol), and blood urea nitrogen (BUN) levels, as assessed by analysis of variance (ANOVA). We analyzed the four HOTAIR SNVs and found significant differences in haplotype patterns between RIF patients and healthy controls. The results of this study showed that HOTAIR is not only associated with the development of cancer but also with pregnancy-associated diseases. This study represents the first report showing that HOTAIR is correlated with RIF.
Collapse
|
36
|
Samir A, El Khodiry AA, ElTayebi HM. From Whole Blood to Isolated Pro-Metastasis Immune Cells: An Ex Vivo Approach to Isolate and Manipulate Immune Cells Contributing to Tumor Metastasis. Methods Mol Biol 2021; 2294:209-218. [PMID: 33742404 DOI: 10.1007/978-1-0716-1350-4_15] [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] [Indexed: 11/25/2022]
Abstract
Immune evasion hallmark has grabbed wide attention in cancer progression on the clinical level. Accordingly, innate and adaptive immune cells isolation and manipulation is essential in order to assess their activity and role in the tumor microenvironment (TME). This could open a gate toward a personalized therapy by a simple aspiration of blood sample from patients. Here, we describe the isolation of peripheral blood mononuclear cells (PBMCs) using Ficoll plus media in order to achieve the highest yield of immune cells that can be further processed and used in isolation of specific immune cells such as macrophages and cytotoxic T cells (CD8+ cells). Among the highly metastatic macrophages are the M2. This protocol describes the optimized techniques to isolate monocytes from whole blood, differentiate them into M2. This is followed by genetic and epigenetic (using synthetic nucleotides of noncoding RNAs) manipulation of these isolated immune cells in a tumor culture media, in addition to measurement of released cytokines using specific ELISA kit. In the last decade, new groups of noncoding RNAs have been emerged which are microRNAs and long noncoding RNAs. First, they were known as "junk DNA" with unknown regulatory functions. Despite the limited knowledge of these molecules, basic expression profiling is proving to be clinically relevant to cancer diagnosis, metastasis, and prognosis. Here, we describe methods used in molecular biology to assess the epigenetic expression of ncRNAs and their impact on other messenger RNA transcripts in M2 macrophages that could serve as future biomarkers in the context of tumor biology and metastasis or could open a gate in the treatment of cancer.
Collapse
Affiliation(s)
- Amany Samir
- Molecular Pharmacology Research Group, Department of Pharmacology and Toxicology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Aya Aly El Khodiry
- Molecular Pharmacology Research Group, Department of Pharmacology and Toxicology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Hend M ElTayebi
- Molecular Pharmacology Research Group, Department of Pharmacology and Toxicology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt.
| |
Collapse
|
37
|
Atwa SM, Handoussa H, Hosny KM, Odenthal M, El Tayebi HM. Pivotal role of long non-coding ribonucleic acid-X-inactive specific transcript in regulating immune checkpoint programmed death ligand 1 through a shared pathway between miR-194-5p and miR-155-5p in hepatocellular carcinoma. World J Hepatol 2020; 12:1211-1227. [PMID: 33442449 PMCID: PMC7772730 DOI: 10.4254/wjh.v12.i12.1211] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/30/2020] [Accepted: 10/29/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Anti-programmed death therapy has thrust immunotherapy into the spotlight. However, such therapy has a modest response in hepatocellular carcinoma (HCC). Epigenetic immunomodulation is a suggestive combinatorial therapy with immune checkpoint blockade. Non-coding ribonucleic acid (ncRNA) driven regulation is a major mechanism of epigenetic modulation. Given the wide range of ncRNAs that co-opt in programmed cell-death protein 1 (PD-1)/programmed death ligand 1 (PD-L1) regulation, and based on the literature, we hypothesized that miR-155-5p, miR-194-5p and long non-coding RNAs (lncRNAs) X-inactive specific transcript (XIST) and MALAT-1 are involved in a regulatory upstream pathway for PD-1/PD-L1. Recently, nutraceutical therapeutics in cancers have received increasing attention. Thus, it is interesting to study the impact of oleuropein on the respective study key players. AIM To explore potential upstream regulatory ncRNAs for the immune checkpoint PD-1/PD-L1. METHODS Bioinformatics tools including microrna.org and lnCeDB software were adopted to detect targeting of miR-155-5p, miR-194-5p and lncRNAs XIST and MALAT-1 to PD-L1 mRNA, respectively. In addition, Diana tool was used to predict targeting of both aforementioned miRNAs to lncRNAs XIST and MALAT-1. HCC and normal tissue samples were collected for scanning of PD-L1, XIST and MALAT-1 expression. To study the interaction among miR-155-5p, miR-194-5p, lncRNAs XIST and MALAT-1, as well as PD-L1 mRNA, a series of transfections of the Huh-7 cell line was carried out. RESULTS Bioinformatics software predicted that miR-155-5p and miR-194-5p can target PD-L1, MALAT-1 and XIST. MALAT-1 and XIST were predicted to target PD-L1 mRNA. PD-L1 and XIST were significantly upregulated in 23 HCC biopsies compared to healthy controls; however, MALAT-1 was barely detected. MiR-194 induced expression elevated the expression of PD-L1, XIST and MALAT-1. However, overexpression of miR-155-5p induced the upregulation of PD-L1 and XIST, while it had a negative impact on MALAT-1 expression. Knockdown of XIST did have an impact on PD-L1 expression; however, following knockdown of the negative regulator of X-inactive specific transcript (TSIX), PD-L1 expression was elevated, and abolished MALAT-1 activity. Upon co-transfection of miR-194-5p with siMALAT-1, PD-L1 expression was elevated. Co-transfection of miR-194-5p with siXIST did not have an impact on PD-L1 expression. Upon co-transfection of miR-194 with siTSIX, PD-L1 expression was upregulated. Interestingly, the same PD-L1 expression pattern was observed following miR-155-5p co-transfections. Oleuropein treatment of Huh-7 cells reduced the expression profile of PD-L1, XIST, and miR-155-5p, upregulated the expression of miR-194-5p and had no significant impact on the MALAT-1 expression profile. CONCLUSION This study reported a novel finding revealing that opposing acting miRNAs in HCC, have the same impact on PD-1/PD-L1 immune checkpoint by sharing a common signaling pathway.
Collapse
Affiliation(s)
- Sara M Atwa
- Pharmaceutical Biology Department, German University in Cairo, Cairo 11865, Egypt
| | - Heba Handoussa
- Pharmaceutical Biology Department, German University in Cairo, Cairo 11865, Egypt
| | - Karim M Hosny
- Department of General Surgery, Faculty of Medicine, Cairo University, Cairo 11562, Egypt
| | - Margarete Odenthal
- Institute for Pathology, University Hospital Cologne, Cologne 50924, Germany
| | - Hend M El Tayebi
- Molecular Pharmacology Research Group, Department of Pharmacology and Toxicology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt.
| |
Collapse
|
38
|
Barsoum FS, Awad AS, Hussein NH, Eissa RA, El Tayebi HM. MALAT-1: LncRNA ruling miR-182/PIG-C/mesothelin triad in triple negative breast cancer. Pathol Res Pract 2020; 216:153274. [PMID: 33171372 DOI: 10.1016/j.prp.2020.153274] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023]
Abstract
Breast cancer (BC) remains a major health problem, despite the remarkable advances in cancer research setting. BC is the most common cancer affecting women worldwide. In the context of triple negative breast cancer (TNBC) treatment, major obstacles include late diagnoses and detrimental side effects of chemotherapy and radiotherapy. Research effort was rewarded with the discovery of mesothelin (MSLN), an oncogenic Glycosyl-Phosphatidyl-Inositol (GPI) anchored protein, over-expressed in TNBC. GPI pathway is a post-translational modification that attaches proteins to cellular membrane. MSLN targeted therapy succeeded in early clinical trials, nevertheless, to date, the epigenetic regulation of MSLN and GPI pathway by non-coding RNAs (nc-RNAs) in BC remains an untouched area. Accordingly, our aim is to investigate-for the first time- the impact of simultaneous targeting of MSLN and its associated GPI pathway member, PIG-C, by non-coding-RNAs. Expression profiling of PIG-C, MSLN in BC was performed. Using bioinformatics tools, MALAT-1 and miR-182 were found to target MSLN and PIG-C. MDA-MB-231 cells were transfected with synthetic nc-RNAs. Expression profiling of MSLN, miR-182 and MALAT-1 showed a dramatic over-expression in BC samples. MiR-182 ectopic expression and MALAT-1 silencing increased MSLN and PIG-C transcript levels. However, miR-182 inhibition and miR-182/si-MALAT-1 co-transfection lowered MSLN and PIG-C levels. Finally, si-PIG-C decreased MSLN and PIG-C levels. To conclude, our investigation unravels a new axis in TNBC, where miR-182 can manipulate MSLN and PIG-C. Meanwhile, MALAT-1 is the culprit lncRNA in this novel axis, possibly a sponge for miR-182. Altogether, this sheds light on new targets for BC immune-therapy.
Collapse
Affiliation(s)
- Farida S Barsoum
- Molecular Pharmacology Research Group, Department of Pharmacology and Toxicology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Egypt
| | - Amany S Awad
- Molecular Pharmacology Research Group, Department of Pharmacology and Toxicology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Egypt
| | - Nada H Hussein
- Molecular Pharmacology Research Group, Department of Pharmacology and Toxicology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Egypt
| | - Reda A Eissa
- Department of Surgery, Ain Shams University, Egypt
| | - Hend M El Tayebi
- Molecular Pharmacology Research Group, Department of Pharmacology and Toxicology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Egypt.
| |
Collapse
|
39
|
Shen C, Yang C, Xia B, You M. Long non-coding RNAs: Emerging regulators for chemo/immunotherapy resistance in cancer stem cells. Cancer Lett 2020; 500:244-252. [PMID: 33242560 DOI: 10.1016/j.canlet.2020.11.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/03/2020] [Accepted: 11/11/2020] [Indexed: 02/06/2023]
Abstract
Cancer stem cells (CSCs) are a small subpopulation of tumor cells critical for tumor development. Their unique abilities, such as self-renewal, have resulted in tumor resistance to various cancer treatments, including traditional chemotherapy and latest immunotherapy. CSCs-targeting therapy is a promising treatment to overcome the therapeutic resistances to different tumors. However, despite their significance, the regulatory mechanism generating therapy-resistant CSCs is still obscure. Long non-coding RNAs (lncRNAs) are key regulators in various biological processes, including cell proliferation, apoptosis, migration, and invasion. Recent studies have revealed that lncRNAs play an important role in the therapeutic resistance of CSCs. Here we summarize the latest studies on the regulatory role of lncRNAs in sustaining the stemness of CSCs, and discuss the associated mechanisms behind these behavior changes in CSCs-related chemo- and immune-resistance. Future research implications are also discussed, shedding light on the potential CSCs-targeted strategies to break through the resistance of current therapies.
Collapse
Affiliation(s)
- Chongyang Shen
- Basic Medicine School, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China; Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Anhui, 230038, China
| | - Chuan Yang
- Department of Respiratory and Critical Care Medicine, Clinical Research Center for Respiratory Disease, West China Hospital, Sichuan University, Chengdu, 610041, China; Laboratory of Pulmonary Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, Sichuan University, Chengdu, 610041, China
| | - Bing Xia
- Department of Radiation Oncology, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Hangzhou Cancer Hospital, Hangzhou, 310002, China
| | - Mingliang You
- Hangzhou Cancer Institute, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Hangzhou Cancer Hospital, Hangzhou, 310002, China.
| |
Collapse
|
40
|
Peng L, Jiang J, Tang B, Nice EC, Zhang YY, Xie N. Managing therapeutic resistance in breast cancer: from the lncRNAs perspective. Theranostics 2020; 10:10360-10377. [PMID: 32929354 PMCID: PMC7482807 DOI: 10.7150/thno.49922] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/04/2020] [Indexed: 02/05/2023] Open
Abstract
Breast cancer (BC) is the most common female malignancy and the second leading cause of cancer-related death worldwide. In spite of significant advances in clinical management, the mortality of BC continues to increase due to the frequent occurrence of treatment resistance. Intensive studies have been conducted to elucidate the molecular mechanisms underlying BC therapeutic resistance, including increased drug efflux, altered drug targets, activated bypass signaling pathways, maintenance of cancer stemness, and deregulated immune response. Emerging evidence suggests that long noncoding RNAs (lncRNAs) are intimately involved in BC therapy resistance through multiple modes of action. Therefore, an in-depth understanding of the implication of lncRNAs in resistance to clinical therapies may improve the clinical outcome of BC patients. Here, we highlight the role and underlying mechanisms of lncRNAs in regulating BC treatment resistance with an emphasis on lncRNAs-mediated resistance in different clinical scenarios, and discuss the potential of lncRNAs as novel biomarkers or therapeutic targets to improve BC therapy response.
Collapse
Affiliation(s)
- Liyuan Peng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China
| | - Jingwen Jiang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China
| | - Bo Tang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Edouard C. Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Yuan-Yuan Zhang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, P.R. China
| | - Na Xie
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China
| |
Collapse
|
41
|
Li W, Chen Y, Nie X. Regulatory Mechanisms of lncRNAs and Their Target Gene Signaling Pathways in Laryngeal Squamous Cell Carcinoma. Front Pharmacol 2020; 11:1140. [PMID: 32848755 PMCID: PMC7397781 DOI: 10.3389/fphar.2020.01140] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/13/2020] [Indexed: 12/24/2022] Open
Abstract
Laryngeal squamous cell carcinoma (LSCC) is a common malignant tumor that occurs in the head and neck. People living in areas with serious air pollution and those who smoke and drink for a long time belong to high-risk groups. Although great progress has been made in chemotherapy, radiotherapy, and molecular targeted therapy in recent years, the prognosis of patients is still not good. The proliferation, invasion, and apoptosis of LSCC are controlled by many factors, which are the key factors influencing the prognosis of patients. Previous researches have demonstrated that long noncoding RNAs (lncRNAs) can be used as oncogenes or tumor suppressor genes in the occurrence and development of cancer and regulate cancer through various ways including epigenetic regulation and post-transcriptional regulation. The characteristics and roles of lncRNAs in LSCC, however, are not clear. In this review, we will discuss the role and function of lncRNAs in the proliferation, invasion, and apoptosis of LSCC and analyze the relationship between lncRNAs and lncRNA-regulated signaling pathways in LSCC pathological process. The difficulties faced by the related research of LSCC are discussed. It provides reference ideas for the molecular mechanism research of LSCC targeting lncRNA and its signaling pathways, the development of clinical prevention and therapeutic drug and individualized treatment, thereby improving the quality of life of patients.
Collapse
Affiliation(s)
- Wei Li
- College of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Yu Chen
- College of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Xuqiang Nie
- College of Pharmacy, Zunyi Medical University, Zunyi, China
- Joint International Research Laboratory of Ethnomedicine of Chinese Ministry of Education, College of Pharmacy, Zunyi Medical University, Zunyi, China
| |
Collapse
|