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Jang SJ, Atyeo N, Mietzsch M, Chae MY, McKenna R, Toth Z, Papp B. Genome-Wide Transcriptional Roles of KSHV Viral Interferon Regulatory Factors in Oral Epithelial Cells. Viruses 2024; 16:846. [PMID: 38932139 PMCID: PMC11209080 DOI: 10.3390/v16060846] [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: 04/23/2024] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
The viral interferon regulatory factors (vIRFs) of KSHV are known to dysregulate cell signaling pathways to promote viral oncogenesis and to block antiviral immune responses to facilitate infection. However, it remains unknown to what extent each vIRF plays a role in gene regulation. To address this, we performed a comparative analysis of the protein structures and gene regulation of the four vIRFs. Our structure prediction analysis revealed that despite their low amino acid sequence similarity, vIRFs exhibit high structural homology in both their DNA-binding domain (DBD) and IRF association domain. However, despite this shared structural homology, we demonstrate that each vIRF regulates a distinct set of KSHV gene promoters and human genes in epithelial cells. We also found that the DBD of vIRF1 is essential in regulating the expression of its target genes. We propose that the structurally similar vIRFs evolved to possess specialized transcriptional functions to regulate specific genes.
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Affiliation(s)
- Seung Jin Jang
- Department of Oral Biology, University of Florida College of Dentistry, 1395 Center Drive, Gainesville, FL 32610, USA
| | - Natalie Atyeo
- Department of Oral Biology, University of Florida College of Dentistry, 1395 Center Drive, Gainesville, FL 32610, USA
| | - Mario Mietzsch
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, 1200 Newell Drive, Gainesville, FL 32610, USA
| | - Min Y. Chae
- Department of Oral Biology, University of Florida College of Dentistry, 1395 Center Drive, Gainesville, FL 32610, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, 1200 Newell Drive, Gainesville, FL 32610, USA
| | - Zsolt Toth
- Department of Oral Biology, University of Florida College of Dentistry, 1395 Center Drive, Gainesville, FL 32610, USA
- UF Genetics Institute, Gainesville, FL 32610, USA
- UF Health Cancer Center, Gainesville, FL 32610, USA
| | - Bernadett Papp
- Department of Oral Biology, University of Florida College of Dentistry, 1395 Center Drive, Gainesville, FL 32610, USA
- UF Genetics Institute, Gainesville, FL 32610, USA
- UF Health Cancer Center, Gainesville, FL 32610, USA
- UF Center for Orphaned Autoimmune Disorders, Gainesville, FL 32610, USA
- UF Informatics Institute, Gainesville, FL 32610, USA
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2
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Zorc M, Dolinar M, Dovč P. A Single-Cell Transcriptome of Bovine Milk Somatic Cells. Genes (Basel) 2024; 15:349. [PMID: 38540408 PMCID: PMC10970057 DOI: 10.3390/genes15030349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/04/2024] [Accepted: 03/06/2024] [Indexed: 06/14/2024] Open
Abstract
The production of milk by dairy cows far exceeds the nutritional needs of the calf and is vital for the economical use of dairy cattle. High milk yield is a unique production trait that can be effectively enhanced through traditional selection methods. The process of lactation in cows serves as an excellent model for studying the biological aspects of lactation with the aim of exploring the mechanistic base of this complex trait at the cellular level. In this study, we analyzed the milk transcriptome at the single-cell level by conducting scRNA-seq analysis on milk samples from two Holstein Friesian cows at mid-lactation (75 and 93 days) using the 10× Chromium platform. Cells were pelleted and fat was removed from milk by centrifugation. The cell suspension from each cow was loaded on separate channels, resulting in the recovery of 9313 and 14,544 cells. Library samples were loaded onto two lanes of the NovaSeq 6000 (Illumina) instrument. After filtering at the cell and gene levels, a total of 7988 and 13,973 cells remained, respectively. We were able to reconstruct different cell types (milk-producing cells, progenitor cells, macrophages, monocytes, dendritic cells, T cells, B cells, mast cells, and neutrophils) in bovine milk. Our findings provide a valuable resource for identifying regulatory elements associated with various functions of the mammary gland such as lactation, tissue renewal, native immunity, protein and fat synthesis, and hormonal response.
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Affiliation(s)
| | | | - Peter Dovč
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia; (M.Z.); (M.D.)
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3
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Hu XT, Wu XF, Sui LM, Ao LQ, Pu CX, Yuan M, Xing W, Xu X. The GRHL3-regulated long non-coding RNA lnc-DC modulates keratinocytes differentiation by interacting with IGF2BP2 and up-regulating ZNF750. J Dermatol Sci 2024; 113:93-102. [PMID: 38383230 DOI: 10.1016/j.jdermsci.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 01/18/2024] [Accepted: 02/09/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND Aberrant keratinocytes differentiation has been demonstrated to be associated with a number of skin diseases. The roles of lncRNAs in keratinocytes differentiation remain to be largely unknown. OBJECTIVE Here we aim to investigate the role of lnc-DC in regulating epidermal keratinocytes differentiation. METHODS Expression of lnc-DC in the skin was queried in AnnoLnc and verified by FISH. The lncRNA expression profiles during keratinocytes differentiation were reanalyzed and verified by qPCR and FISH. Gene knock-down and over-expression were used to explore the role of lnc-DC in keratinocytes differentiation. The downstream target of lnc-DC was screened by whole transcriptome sequencing. CUT&RUN assay and siRNAs transfection was used to reveal the regulatory effect of GRHL3 on lnc-DC. The mechanism of lnc-DC regulating ZNF750 was revealed by RIP assay and RNA stability assay. RESULTS Lnc-DC was biasedly expressed in skin and up-regulated during epidermal keratinocytes differentiation. Knockdown lnc-DC repressed epidermal keratinocytes differentiation while over-express lnc-DC showed the opposite effect. GRHL3, a well-known transcription factor regulating keratinocytes differentiation, could bind to the promoter of lnc-DC and regulate its expression. By whole transcriptome sequencing, we identified that ZNF750 was a downstream target of lnc-DC during keratinocytes differentiation. Mechanistically, lnc-DC interacted with RNA binding protein IGF2BP2 to stabilize ZNF750 mRNA and up- regulated its downstream targets TINCR and KLF4. CONCLUSION Our study revealed the novel role of GRHL3/lnc-DC/ZNF750 axis in regulating epidermal keratinocytes differentiation, which may provide new therapeutic targets of aberrant keratinocytes differentiation related skin diseases.
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Affiliation(s)
- Xue-Ting Hu
- Department of Stem Cell & Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hosptial, Army Medical University, Chongqing, China; Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Army Medical University, Chongqing, China
| | - Xiao-Feng Wu
- Department of Stem Cell & Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hosptial, Army Medical University, Chongqing, China
| | - Lu-Min Sui
- Department of Stem Cell & Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hosptial, Army Medical University, Chongqing, China
| | - Luo-Quan Ao
- Department of Stem Cell & Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hosptial, Army Medical University, Chongqing, China
| | - Cheng-Xiu Pu
- Department of Stem Cell & Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hosptial, Army Medical University, Chongqing, China
| | - Mu Yuan
- Department of Stem Cell & Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hosptial, Army Medical University, Chongqing, China
| | - Wei Xing
- Department of Stem Cell & Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hosptial, Army Medical University, Chongqing, China.
| | - Xiang Xu
- Department of Stem Cell & Regenerative Medicine, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hosptial, Army Medical University, Chongqing, China; Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Army Medical University, Chongqing, China.
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4
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Murray MJ, Bradley E, Ng Y, Thomas O, Patel K, Angus C, Atkinson C, Reeves MB. In silico interrogation of the miRNAome of infected hematopoietic cells to predict processes important for human cytomegalovirus latent infection. J Biol Chem 2023; 299:104727. [PMID: 37080390 PMCID: PMC10206818 DOI: 10.1016/j.jbc.2023.104727] [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: 04/03/2022] [Revised: 04/14/2023] [Accepted: 04/16/2023] [Indexed: 04/22/2023] Open
Abstract
Human cytomegalovirus (HCMV) latency in CD34+ progenitor cells is the outcome of a complex and continued interaction of virus and host that is initiated during very early stages of infection and reflects pro- and anti-viral activity. We hypothesized that a key event during early infection could involve changes to host miRNAs, allowing for rapid modulation of the host proteome. Here, we identify 72 significantly upregulated miRNAs and three that were downregulated by 6hpi of infection of CD34+ cells which were then subject to multiple in silico analyses to identify potential genes and pathways important for viral infection. The analyses focused on the upregulated miRNAs and were used to predict potential gene hubs or common mRNA targets of multiple miRNAs. Constitutive deletion of one target, the transcriptional regulator JDP2, resulted in a defect in latent infection of myeloid cells; interestingly, transient knockdown in differentiated dendritic cells resulted in increased viral lytic IE gene expression, arguing for subtle differences in the role of JDP2 during latency establishment and reactivation of HCMV. Finally, in silico predictions identified clusters of genes with related functions (such as calcium signaling, ubiquitination, and chromatin modification), suggesting potential importance in latency and reactivation. Consistent with this hypothesis, we demonstrate that viral IE gene expression is sensitive to calcium channel inhibition in reactivating dendritic cells. In conclusion, we demonstrate HCMV alters the miRNAome rapidly upon infection and that in silico interrogation of these changes reveals new insight into mechanisms controlling viral gene expression during HCMV latency and, intriguingly, reactivation.
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Affiliation(s)
- M J Murray
- Institute of Immunity & Transplantation, Division of Infection & Immunity, Royal Free Campus, UCL, London, United Kingdom.
| | - E Bradley
- Institute of Immunity & Transplantation, Division of Infection & Immunity, Royal Free Campus, UCL, London, United Kingdom
| | - Y Ng
- Institute of Immunity & Transplantation, Division of Infection & Immunity, Royal Free Campus, UCL, London, United Kingdom
| | - O Thomas
- Institute of Immunity & Transplantation, Division of Infection & Immunity, Royal Free Campus, UCL, London, United Kingdom
| | - K Patel
- Institute of Immunity & Transplantation, Division of Infection & Immunity, Royal Free Campus, UCL, London, United Kingdom
| | - C Angus
- Institute of Immunity & Transplantation, Division of Infection & Immunity, Royal Free Campus, UCL, London, United Kingdom
| | - C Atkinson
- Institute of Immunity & Transplantation, Division of Infection & Immunity, Royal Free Campus, UCL, London, United Kingdom
| | - M B Reeves
- Institute of Immunity & Transplantation, Division of Infection & Immunity, Royal Free Campus, UCL, London, United Kingdom.
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5
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Zhang Y, He Q. The role of SELENBP1 and its epigenetic regulation in carcinogenic progression. Front Genet 2022; 13:1027726. [PMID: 36386843 PMCID: PMC9663989 DOI: 10.3389/fgene.2022.1027726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/10/2022] [Indexed: 01/24/2023] Open
Abstract
The initiation and progression of cancer is modulated through diverse genetic and epigenetic modifications. The epigenetic machinery regulates gene expression through intertwined DNA methylation, histone modifications, and miRNAs without affecting their genome sequences. SELENBP1 belongs to selenium-binding proteins and functions as a tumor suppressor. Its expression is significantly downregulated and correlates with carcinogenic progression and poor survival in various cancers. The role of SELENBP1 in carcinogenesis has not been fully elucidated, and its epigenetic regulation remains poorly understood. In this review, we summarize recent findings on the function and regulatory mechanisms of SELENBP1 during carcinogenic progression, with an emphasis on epigenetic mechanisms. We also discuss the potential cancer treatment targeting epigenetic modification of SELENBP1, either alone or in combination with selenium-containing compounds or dietary selenium.
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6
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Genetic Variants in Epidermal Differentiation Complex Genes as Predictive Biomarkers for Atopic Eczema, Allergic Sensitization, and Eczema-Associated Asthma in a 6-Year Follow-Up Case-Control Study in Children. J Clin Med 2022; 11:jcm11164865. [PMID: 36013110 PMCID: PMC9410399 DOI: 10.3390/jcm11164865] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/04/2022] [Accepted: 08/16/2022] [Indexed: 11/29/2022] Open
Abstract
Atopic eczema is the most common chronic inflammatory skin disease of early childhood and is often the first manifestation of atopic march. Therefore, one challenge is to identify the risk factors associated with atopic eczema that may also be predictors of atopic disease progression. The aim of this study was to investigate the association of SNPs in hornerin (HRNR) and filaggrin-2 (FLG2) genes with childhood atopic eczema, as well as other atopic phenotypes. Genotyping for HRNR and FLG2 was performed in 188 children younger than 2 years of age, previously screened for the FLG null mutations, and followed at yearly intervals until the age of 6. We demonstrated that risk variants of HRNR rs877776[C] and FLG2 rs12568784[T] were associated with atopic eczema, allergic sensitization, and susceptibility to the complex phenotype—asthma plus eczema. These effects seem to be supplementary to the well-known associations for FLG mutations and may be modulated by gene–gene interactions. Additionally, in children with eczema, these genetic variants may also be considered, along with FLG mutations, as predictive biomarkers for eczema-associated asthma. In conclusion, our results indicate that genetic variants in the epidermal differentiation complex gene could contribute to the pathogenesis of atopic eczema and progression to subsequent allergic disease.
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7
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Guerber L, Pangou E, Sumara I. Ubiquitin Binding Protein 2-Like (UBAP2L): is it so NICE After All? Front Cell Dev Biol 2022; 10:931115. [PMID: 35794863 PMCID: PMC9250975 DOI: 10.3389/fcell.2022.931115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/01/2022] [Indexed: 12/30/2022] Open
Abstract
Ubiquitin Binding Protein 2-like (UBAP2L, also known as NICE-4) is a ubiquitin- and RNA-binding protein, highly conserved in metazoans. Despite its abundance, its functions have only recently started to be characterized. Several studies have demonstrated the crucial involvement of UBAP2L in various cellular processes such as cell cycle regulation, stem cell activity and stress-response signaling. In addition, UBAP2L has recently emerged as a master regulator of growth and proliferation in several human cancers, where it is suggested to display oncogenic properties. Given that this versatile protein is involved in the regulation of multiple and distinct cellular pathways, actively contributing to the maintenance of cell homeostasis and survival, UBAP2L might represent a good candidate for future therapeutic studies. In this review, we discuss the current knowledge and latest advances on elucidating UBAP2L cellular functions, with an aim to highlight the importance of targeting UBAP2L for future therapies.
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Affiliation(s)
- Lucile Guerber
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Centre National de la Recherche Scientifique UMR 7104, Strasbourg, France
- Institut National de la Santé et de la Recherche Médicale U964, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Evanthia Pangou
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Centre National de la Recherche Scientifique UMR 7104, Strasbourg, France
- Institut National de la Santé et de la Recherche Médicale U964, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Izabela Sumara
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Centre National de la Recherche Scientifique UMR 7104, Strasbourg, France
- Institut National de la Santé et de la Recherche Médicale U964, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
- *Correspondence: Izabela Sumara,
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8
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Jadeja SD, Tobin DJ. Autoantigen Discovery in the Hair Loss Disorder, Alopecia Areata: Implication of Post-Translational Modifications. Front Immunol 2022; 13:890027. [PMID: 35720384 PMCID: PMC9205194 DOI: 10.3389/fimmu.2022.890027] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 04/21/2022] [Indexed: 12/24/2022] Open
Abstract
Alopecia areata (AA) is a chronic, multifactorial, polygenic, and heterogeneous disorder affecting growing hair follicles in susceptible individuals, which results in a non-scarring and reversible hair loss with a highly unpredictable course. Despite very considerable research effort, the nature of the precipitating factor(s) responsible for initiating AA in any given hair follicle remains unclear, due largely to significant gaps in our knowledge of the precise sequence of the etiopathogenic events in this dermatosis. However, disease-related changes in the immune-competence of the lower growing hair follicle, together with an active immune response (humoral and cellular) to hair follicle-associated antigens, are key associated phenomena. Confirmation of the hair follicle antigen(s) implicated in AA disease onset has remained stubbornly elusive. While it may be considered somewhat philosophical by some, it is also unclear whether immune-mediated hair loss in AA results from a) an ectopic (i.e., in an abnormal location) immune response to native (unmodified) self-antigens expressed by the healthy hair follicle, b) a normal immune response against modified self-antigens (or neoantigens), or c) a normal immune response against self-antigens (modified/non-modified) that were not previously visible to the immune system (because they were conformationally-hidden or sequestered) but become exposed and presentable in an MHC-I/-II molecule-restricted manner. While some candidate hair follicle antigen target(s) in AA are beginning to emerge, with a potential role for trichohyalin, it is not yet clear whether this represents the initial and immunodominant antigenic focus in AA or is simply one of an expanding repertoire of exposed hair follicle tissue damage-associated antigens that are secondary to the disease. Confirmation of autoantigen identity is essential for our understanding of AA etiopathogenesis, and consequently for developing a more informed therapeutic strategy. Major strides have been made in autoantigen discovery in other autoimmune conditions. In particular, some of these conditions may provide insights into how post-translational modifications (e.g., citrullination, deamidation, etc.) of hair follicle-restricted proteins may increase their antigenicity and so help drive the anti-hair follicle immune attack in AA.
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Affiliation(s)
- Shahnawaz D. Jadeja
- The Charles Institute of Dermatology, School of Medicine, University College Dublin, Dublin, Ireland
| | - Desmond J. Tobin
- The Charles Institute of Dermatology, School of Medicine, University College Dublin, Dublin, Ireland
- The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
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9
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Skin biological responses to urban pollution in an ex vivo model. Toxicol Lett 2021; 348:85-96. [PMID: 34044057 DOI: 10.1016/j.toxlet.2021.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 04/20/2021] [Accepted: 05/21/2021] [Indexed: 12/15/2022]
Abstract
The skin epidermis is continuously exposed to external aggressions, including environmental pollution. The cosmetic industry must be able to offer dedicated products to fight the effects of pollutants on the skin. We set up an experimental model that exposed skin explants maintained in culture to a pollutant mixture. This mixture P representing urban pollution was designed on the basis of the French organization 'Air Parif' database. A chamber, called Pollubox®, was built to allow a controlled nebulization of P on the cultured human skin explants. We investigated ultrastructural morphology by transmission electron microscopy of high pressure frozen skin explants. A global transcriptomic analysis indicated that the pollutant mixture was able to induce relevant xenobiotic and antioxidant responses. Modulated detoxifying genes were further investigated by laser micro-dissection coupled to qPCR, and immunochemistry. Both approaches showed that P exposure correlated with overexpression of detoxifying genes and provoked skin physiological alterations down to the stratum basale. The model developed herein might be an efficient tool to study the effects of pollutants on skin as well as a powerful testing method to evaluate the efficacy of cosmetic products against pollution.
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10
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Du L, Wu Y, Han X, Wang C, Li A, Huang G. NICE-3-knockdown induces cell cycle arrest and autophagy in lung adenocarcinoma cells via the AKT/mTORC1 signaling pathway. Exp Ther Med 2021; 21:625. [PMID: 33936282 PMCID: PMC8082604 DOI: 10.3892/etm.2021.10057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/22/2021] [Indexed: 12/21/2022] Open
Abstract
The NICE-3 protein serves an oncogenic role in hepatocellular carcinoma, but its role in lung adenocarcinoma (LUAD) remains unknown. The aim of the present study was to investigate the potential role and underlying mechanisms of NICE-3 in LUAD. In the present study, NICE-3 expression in LUAD tissues and its association with patient prognosis were analyzed using datasets from The Cancer Genome Atlas and Gene Express Omnibus. After NICE-3-knockdown with small interfering RNA in LUAD cells, cell proliferation was measured by cell counting, cell cycle was examined by flow cytometry, cell invasion and migration were detected by Transwell assays and autophagic markers LC3 and p62, as well as phosphorylation of S6K and AKT, were determined by western blotting. The results of public database analysis demonstrated that compared with normal lung tissues, NICE-3 expression was increased in LUAD tissues, where high expression levels were associated with a poor prognosis. The results of in vitro experimentation in LUAD cells indicated that NICE-3-knockdown inhibited proliferation, cell cycle, migration and invasion, but enhanced autophagy. Notably, NICE-3-knockdown inhibited AKT/mTORC1 signaling. The present results suggested that NICE-3 may serve an oncogenic role in LUAD via the AKT/mTORC1 signaling pathway and may therefore be a potential therapeutic target for LUAD.
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Affiliation(s)
- Longxia Du
- Laboratory of Respiratory Diseases, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001, P.R. China
| | - Youru Wu
- Laboratory of Respiratory Diseases, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001, P.R. China
| | - Xiaodan Han
- Laboratory of Respiratory Diseases, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001, P.R. China
| | - Chen Wang
- Laboratory of Respiratory Diseases, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001, P.R. China
| | - Aili Li
- Laboratory of Respiratory Diseases, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001, P.R. China
| | - Guojin Huang
- Laboratory of Respiratory Diseases, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001, P.R. China.,Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, Guilin Medical University, Guilin, Guangxi 541001, P.R. China
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11
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Pisani C, Onori A, Gabanella F, Di Certo MG, Passananti C, Corbi N. Identification of protein/mRNA network involving the PSORS1 locus gene CCHCR1 and the PSORS4 locus gene HAX1. Exp Cell Res 2021; 399:112471. [PMID: 33417922 DOI: 10.1016/j.yexcr.2021.112471] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 12/22/2020] [Accepted: 12/30/2020] [Indexed: 01/22/2023]
Abstract
CCHCR1 (Coiled-Coil alpha-Helical Rod 1), maps to chromosomal region 6p21.3, within the major psoriasis susceptibility locus PSORS1. CCHCR1 itself is a plausible psoriasis candidate gene, however its role in psoriasis pathogenesis remains unclear. We previously demonstrated that CCHCR1 protein acts as a cytoplasmic docking site for RNA polymerase II core subunit 3 (RPB3) in cycling cells, suggesting a role for CCHCR1 in vesicular trafficking between cellular compartments. Here, we report a novel interaction between CCHCR1 and the RNA binding protein HAX1. HAX1 maps to chromosomal region 1q21.3 within the PSORS4 locus and is over-expressed in psoriasis. Both CCHCR1 and HAX1 share subcellular co-localization with mitochondria, nuclei and cytoplasmic vesicles as P-bodies. By a series of ribonucleoprotein immunoprecipitation (RIP) assays, we isolated a pool of mRNAs complexed with HAX1 and/or CCHCR1 proteins. Among the mRNAs complexed with both CCHCR1 and HAX1 proteins, there are Vimentin mRNA, previously described to be bound by HAX1, and CAMP/LL37 mRNA, whose gene product is over-expressed in psoriasis.
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Affiliation(s)
- Cinzia Pisani
- CNR-Institute of Molecular Biology and Pathology, Department of Molecular Medicine, Sapienza University of Rome, Italy.
| | - Annalisa Onori
- CNR-Institute of Molecular Biology and Pathology, Department of Molecular Medicine, Sapienza University of Rome, Italy.
| | - Francesca Gabanella
- CNR-Institute of Molecular Biology and Pathology, Department of Molecular Medicine, Sapienza University of Rome, Italy; CNR-Institute of Biochemistry and Cell Biology, Department of Sense Organs, Sapienza University of Rome, Italy.
| | - Maria Grazia Di Certo
- CNR-Institute of Biochemistry and Cell Biology, Department of Sense Organs, Sapienza University of Rome, Italy.
| | - Claudio Passananti
- CNR-Institute of Molecular Biology and Pathology, Department of Molecular Medicine, Sapienza University of Rome, Italy.
| | - Nicoletta Corbi
- CNR-Institute of Molecular Biology and Pathology, Department of Molecular Medicine, Sapienza University of Rome, Italy.
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12
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Bhatt T, Bhosale A, Bajantri B, Mathapathi MS, Rizvi A, Scita G, Majumdar A, Jamora C. Sustained Secretion of the Antimicrobial Peptide S100A7 Is Dependent on the Downregulation of Caspase-8. Cell Rep 2020; 29:2546-2555.e4. [PMID: 31775025 DOI: 10.1016/j.celrep.2019.10.090] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 08/02/2019] [Accepted: 10/22/2019] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial peptides (AMPs) are the body's natural innate immune defense against a spectrum of pathogens and can also modulate cell proliferation, chemotaxis, angiogenesis, wound healing, and immune cell activity. Harnessing these diverse functions for prophylactic use is contingent upon understanding the regulatory mechanisms governing their unconventional secretion from cells. Analysis of the secretion of S100A7 (Psoriasin), an abundant AMP stored in differentiated keratinocytes of the skin, has revealed an unexpected biphasic secretory response to bacterial exposure. The core components regulating S100A7 secretion are NFκB/p38MAPK, caspase-1, and interleukin (IL)-1α. The initial activation of this core machinery is mediated by Toll-like receptor signaling, whereas the chronic response is mediated by Caspase-8 downregulation. Interestingly, there is a concomitant downregulation of Caspase-8 in inflammatory skin diseases wherein S100A7 is constitutively released. These results highlight the potential of targeting these components to control the release of AMPs from the skin in both homeostatic and disease conditions.
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Affiliation(s)
- Tanay Bhatt
- IFOM-inStem Joint Research Laboratory, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, Karnataka 560065, India; National Centre for Biological Sciences (TIFR), Bangalore, Karnataka 560065, India
| | - Aishwarya Bhosale
- IFOM-inStem Joint Research Laboratory, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, Karnataka 560065, India
| | - Bhavya Bajantri
- IFOM-inStem Joint Research Laboratory, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, Karnataka 560065, India
| | | | - Abrar Rizvi
- IFOM, FIRC Institute of Molecular Oncology, 20139 Milan, Italy; Department of Oncology and Hemato-oncology, School of Medicine, University of Milan, 20122 Milan, Italy
| | - Giorgio Scita
- IFOM, FIRC Institute of Molecular Oncology, 20139 Milan, Italy; Department of Oncology and Hemato-oncology, School of Medicine, University of Milan, 20122 Milan, Italy
| | | | - Colin Jamora
- IFOM-inStem Joint Research Laboratory, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, Karnataka 560065, India.
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13
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Saraswati S, Lietman CD, Li B, Mathew S, Zent R, Young PP. Small proline-rich repeat 3 is a novel coordinator of PDGFRβ and integrin β1 crosstalk to augment proliferation and matrix synthesis by cardiac fibroblasts. FASEB J 2020; 34:7885-7904. [PMID: 32297675 PMCID: PMC7302973 DOI: 10.1096/fj.201902815r] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 03/04/2020] [Accepted: 03/26/2020] [Indexed: 12/16/2022]
Abstract
Nearly 6 million Americans suffer from heart failure. Increased fibrosis contributes to functional decline of the heart that leads to heart failure. Previously, we identified a mechanosensitive protein, small proline‐rich repeat 3 (SPRR3), in vascular smooth muscle cells of atheromas. In this study, we demonstrate SPRR3 expression in cardiac fibroblasts which is induced in activated fibroblasts following pressure‐induced heart failure. Sprr3 deletion in mice showed preserved cardiac function and reduced interstitial fibrosis in vivo and reduced fibroblast proliferation and collagen expression in vitro. SPRR3 loss resulted in reduced activation of Akt, FAK, ERK, and p38 signaling pathways, which are coordinately regulated by integrins and growth factors. SPRR3 deletion did not impede integrin‐associated functions including cell adhesion, migration, or contraction. SPRR3 loss resulted in reduced activation of PDGFRβ in fibroblasts. This was not due to the reduced PDGFRβ expression levels or decreased binding of the PDGF ligand to PDGFRβ. SPRR3 facilitated the association of integrin β1 with PDGFRβ and subsequently fibroblast proliferation, suggesting a role in PDGFRβ‐Integrin synergy. We postulate that SPRR3 may function as a conduit for the coordinated activation of PDGFRβ by integrin β1, leading to augmentation of fibroblast proliferation and matrix synthesis downstream of biomechanical and growth factor signals.
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Affiliation(s)
- Sarika Saraswati
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Caressa D Lietman
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bin Li
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sijo Mathew
- Department of Pharmaceutical Sciences, School of Pharmacy, North Dakota State University, Fargo, ND, USA
| | - Roy Zent
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Pampee P Young
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.,American Red Cross, Biomedical Division, Washington, DC, USA
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14
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Panatta E, Lena AM, Mancini M, Smirnov A, Marini A, Delli Ponti R, Botta-Orfila T, Tartaglia GG, Mauriello A, Zhang X, Calin GA, Melino G, Candi E. Long non-coding RNA uc.291 controls epithelial differentiation by interfering with the ACTL6A/BAF complex. EMBO Rep 2020. [PMID: 32017402 DOI: 10.5252/embr.201846734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023] Open
Abstract
The mechanisms that regulate the switch between epidermal progenitor state and differentiation are not fully understood. Recent findings indicate that the chromatin remodelling BAF complex (Brg1-associated factor complex or SWI/SNF complex) and the transcription factor p63 mutually recruit one another to open chromatin during epidermal differentiation. Here, we identify a long non-coding transcript that includes an ultraconserved element, uc.291, which physically interacts with ACTL6A and modulates chromatin remodelling to allow differentiation. Loss of uc.291 expression, both in primary keratinocytes and in three-dimensional skin equivalents, inhibits differentiation as indicated by epidermal differentiation complex genes down-regulation. ChIP experiments reveal that upon uc.291 depletion, ACTL6A is bound to the differentiation gene promoters and inhibits BAF complex targeting to induce terminal differentiation genes. In the presence of uc.291, the ACTL6A inhibitory effect is released, allowing chromatin changes to promote the expression of differentiation genes. Thus, uc.291 interacts with ACTL6A to modulate chromatin remodelling activity, allowing the transcription of late differentiation genes.
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Affiliation(s)
- Emanuele Panatta
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Anna Maria Lena
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | | | - Artem Smirnov
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Alberto Marini
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Riccardo Delli Ponti
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Teresa Botta-Orfila
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Alessandro Mauriello
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Xinna Zhang
- The Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - George A Calin
- The Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gerry Melino
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Eleonora Candi
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
- IDI-IRCCS, Rome, Italy
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15
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Panatta E, Lena AM, Mancini M, Smirnov A, Marini A, Delli Ponti R, Botta-Orfila T, Tartaglia GG, Mauriello A, Zhang X, Calin GA, Melino G, Candi E. Long non-coding RNA uc.291 controls epithelial differentiation by interfering with the ACTL6A/BAF complex. EMBO Rep 2020; 21:e46734. [PMID: 32017402 PMCID: PMC7054673 DOI: 10.15252/embr.201846734] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 12/23/2019] [Accepted: 01/08/2020] [Indexed: 11/29/2022] Open
Abstract
The mechanisms that regulate the switch between epidermal progenitor state and differentiation are not fully understood. Recent findings indicate that the chromatin remodelling BAF complex (Brg1‐associated factor complex or SWI/SNF complex) and the transcription factor p63 mutually recruit one another to open chromatin during epidermal differentiation. Here, we identify a long non‐coding transcript that includes an ultraconserved element, uc.291, which physically interacts with ACTL6A and modulates chromatin remodelling to allow differentiation. Loss of uc.291 expression, both in primary keratinocytes and in three‐dimensional skin equivalents, inhibits differentiation as indicated by epidermal differentiation complex genes down‐regulation. ChIP experiments reveal that upon uc.291 depletion, ACTL6A is bound to the differentiation gene promoters and inhibits BAF complex targeting to induce terminal differentiation genes. In the presence of uc.291, the ACTL6A inhibitory effect is released, allowing chromatin changes to promote the expression of differentiation genes. Thus, uc.291 interacts with ACTL6A to modulate chromatin remodelling activity, allowing the transcription of late differentiation genes.
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Affiliation(s)
- Emanuele Panatta
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.,MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Anna Maria Lena
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | | | - Artem Smirnov
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Alberto Marini
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.,MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Riccardo Delli Ponti
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Teresa Botta-Orfila
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Alessandro Mauriello
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Xinna Zhang
- The Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - George A Calin
- The Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gerry Melino
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.,MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Eleonora Candi
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.,IDI-IRCCS, Rome, Italy
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16
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Leick KM, Obeid JM, Bekiranov S, Slingluff CL. Systems analysis of barrier molecule and ARNT-related gene expression regulation in melanoma. Oncoimmunology 2019; 8:e1665978. [PMID: 31741768 PMCID: PMC6844300 DOI: 10.1080/2162402x.2019.1665978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/03/2019] [Accepted: 09/06/2019] [Indexed: 12/22/2022] Open
Abstract
Background: We have identified, in melanomas, a set of genes encoding proteins that mediate mechanical barrier function in normal skin (barrier molecule genes, BMGs) and whose overexpression is associated with decreased immune signatures and shorter patient survival. The most overexpressed of these, filaggrin (FLG), is expressed on chromosome 1q21.3, which also encodes genes of the epidermal differentiation complex (EDC). EDC genes may be regulated by the transcription factors (TFs) AHR and ARNT. We hypothesized that ARNT-related genes would be expressed concordantly with BMG and EDC genes, inversely associated with immune signatures, and enhanced by 1q21.3 copy gain. Methods: Gene expression data from human melanomas in the Cancer Genome Atlas (TCGA), and a validation GEO dataset were evaluated, with copy number profiles from TCGA. Expression of Th1 immune genes and BMG/EDCs at 1q21.3 was visualized using clustered copy number and mRNA profiles. Associations of clusters and 1q21.3 copy number with patient survival and mRNA expression were assessed using Kaplan Meier curves, log-rank tests, and Wilcoxon rank sum tests. Results: BMGs are concordantly expressed with EDC genes. Clustering divided tumors into 4 categories: (1) ImmuneHI, (2) BMG/EDCHI, (3) ARNTHI, (4) Mixed. Both ARNTHI and BMG/EDCHI tumors had low immune signatures and significantly shortened survival. KLF4 and FOXF2 are putative TFs that may regulate these genes. Conclusions: ARNTHI tumors may represent another subset of tumors, in addition to BMG/EDCHI tumors, with barriers to immune infiltrates, likely with different mechanisms. These genes have prognostic significance and may be relevant targets for future therapy.
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Affiliation(s)
- Katie M Leick
- Division of Surgical Oncology, Department of Surgery, University of Virginia, Charlottesville, VA, USA.,Department of Surgery, University of Iowa, Iowa City, IA, USA.,Carter Immunology Center, University of Virginia, Charlottesville, VA, USA
| | - Joseph M Obeid
- Division of Surgical Oncology, Department of Surgery, University of Virginia, Charlottesville, VA, USA.,Carter Immunology Center, University of Virginia, Charlottesville, VA, USA
| | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Craig L Slingluff
- Division of Surgical Oncology, Department of Surgery, University of Virginia, Charlottesville, VA, USA.,Carter Immunology Center, University of Virginia, Charlottesville, VA, USA
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17
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Ghosh D, Bernstein JA, Khurana Hershey GK, Rothenberg ME, Mersha TB. Leveraging Multilayered "Omics" Data for Atopic Dermatitis: A Road Map to Precision Medicine. Front Immunol 2018; 9:2727. [PMID: 30631320 PMCID: PMC6315155 DOI: 10.3389/fimmu.2018.02727] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/05/2018] [Indexed: 12/14/2022] Open
Abstract
Atopic dermatitis (AD) is a complex multifactorial inflammatory skin disease that affects ~280 million people worldwide. About 85% of AD cases begin in childhood, a significant portion of which can persist into adulthood. Moreover, a typical progression of children with AD to food allergy, asthma or allergic rhinitis has been reported (“allergic march” or “atopic march”). AD comprises highly heterogeneous sub-phenotypes/endotypes resulting from complex interplay between intrinsic and extrinsic factors, such as environmental stimuli, and genetic factors regulating cutaneous functions (impaired barrier function, epidermal lipid, and protease abnormalities), immune functions and the microbiome. Though the roles of high-throughput “omics” integrations in defining endotypes are recognized, current analyses are primarily based on individual omics data and using binary clinical outcomes. Although individual omics analysis, such as genome-wide association studies (GWAS), can effectively map variants correlated with AD, the majority of the heritability and the functional relevance of discovered variants are not explained or known by the identified variants. The limited success of singular approaches underscores the need for holistic and integrated approaches to investigate complex phenotypes using trans-omics data integration strategies. Integrating omics layers (e.g., genome, epigenome, transcriptome, proteome, metabolome, lipidome, exposome, microbiome), which often have complementary and synergistic effects, might provide the opportunity to capture the flow of information underlying AD disease manifestation. Overlapping genes/candidates derived from multiple omics types include FLG, SPINK5, S100A8, and SERPINB3 in AD pathogenesis. Overlapping pathways include macrophage, endothelial cell and fibroblast activation pathways, in addition to well-known Th1/Th2 and NFkB activation pathways. Interestingly, there was more multi-omics overlap at the pathway level than gene level. Further analysis of multi-omics overlap at the tissue level showed that among 30 tissue types from the GTEx database, skin and esophagus were significantly enriched, indicating the biological interconnection between AD and food allergy. The present work explores multi-omics integration and provides new biological insights to better define the biological basis of AD etiology and confirm previously reported AD genes/pathways. In this context, we also discuss opportunities and challenges introduced by “big omics data” and their integration.
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Affiliation(s)
- Debajyoti Ghosh
- Division of Immunology, Allergy & Rheumatology, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, United States
| | - Jonathan A Bernstein
- Division of Immunology, Allergy & Rheumatology, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, United States
| | - Gurjit K Khurana Hershey
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, United States
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, United States
| | - Tesfaye B Mersha
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, United States
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18
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Abstract
Atopic dermatitis is a common skin disorder with a complex, evolving pathogenesis. Research on the pathogenesis has shifted from focusing primarily on generalized immune system abnormalities in T helper 1/T helper 2 (Th1/Th2) activity to more targeted immune and skin barrier abnormalities contributing to the overall phenotype. Specific signaling pathways recently implicated in atopic dermatitis include production of interleukin (IL) 4 and IL-13, which promote immunoglobulin E production, Th17 and Th22 cells, and production of cytokines. Barrier defect abnormalities, such as a shared filaggrin mutation noted in ichthyosis vulgaris and atopic dermatitis, as well as reduced structural proteins and lipids (eg, ceramides), have been discovered as well. These alterations contribute to increased transepidermal water loss in addition to increased allergen exposure, resulting in debate over the "inside out" versus "outside in" theories-that is, the concept that immunity triggers barrier breakdown versus barrier abnormalities triggering immunologic alteration toward atopy. In fact, it is likely that all of these contribute to pathogenesis, with some individuals initially experiencing immunologic abnormalities more strongly than barrier defects and vice versa. Genetic analyses have continued to advance, leading to the discovery of potential candidate genes relating both to the impaired skin barrier and the altered immune system pathways. This review outlines the evolution of the field of current pathogenesis of atopic dermatitis, highlighting the most pertinent recent findings.
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19
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Kuberappa PH, Bagalad BS, Ananthaneni A, Kiresur MA, Srinivas GV. Certainty of S100 from Physiology to Pathology. J Clin Diagn Res 2016; 10:ZE10-5. [PMID: 27504432 DOI: 10.7860/jcdr/2016/17949.8022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 03/16/2016] [Indexed: 12/29/2022]
Abstract
S100 exists in wide variety of tissues and cell types, originally isolated from brain tissue and they are of low molecular weight proteins. S100 is evenly distributed in cytoplasm and also in nucleoplasm and is involved in both intercellular and extracellular functions. S100 protein is generally expressed in normal and also in pathological conditions. In current review, we discuss: a) update nomenclature of the various S100 proteins, b) expression of S100 in oral diseases (different soft tissue tumors, odontogenic cyst and tumor) for diagnostic value and also to know their histogenesis, c) role of S100 and RAGE receptor in oral squamous cell carcinoma.
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Affiliation(s)
- Puneeth Horatti Kuberappa
- Senior Lecturer, Department of Oral Pathology and Microbiology, St Joseph Dental College , Eluru, Andhra Pradesh, India
| | - Bhavana Shivanand Bagalad
- Senior Lecturer, Department of Oral Pathology and Microbiology, St Joseph Dental College , Eluru, Andhra Pradesh, India
| | - Anuradha Ananthaneni
- Professor, Department of Oral Pathology and Microbiology, St Joseph Dental College , Eluru, Andhra Pradesh, India
| | - Md Asif Kiresur
- Senior Lecturer, Department of Oral Pathology and Microbiology, St Joseph Dental College , Eluru, Andhra Pradesh, India
| | - Guduru Vijay Srinivas
- Professor and Head, Department of Oral Pathology and Microbiology, St Joseph Dental College , Eluru, Andhra Pradesh, India
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20
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Increased Risk of Psoriasis due to combined effect of HLA-Cw6 and LCE3 risk alleles in Indian population. Sci Rep 2016; 6:24059. [PMID: 27048876 PMCID: PMC4822143 DOI: 10.1038/srep24059] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 03/16/2016] [Indexed: 11/29/2022] Open
Abstract
HLA-Cw6 is one of the most associated alleles in psoriasis. Recently, Late Cornified Envelop 3 (LCE3) genes were identified as a susceptibility factor for psoriasis. Some population showed epistatic interaction of LCE3 risk variants with HLA-Cw6, while some population failed to show any association. We determined the associations of a 32.2 kb deletion comprising LCE3C-3B genes and three SNPs (rs1886734, rs4112788; rs7516108) at the LCE3 gene cluster among the psoriasis patients in India. All three SNPs at the LCE3 gene cluster failed to show any association. In contrary, for patients with HLA-Cw6 allele, all three SNPs and the LCE3C-3B deletion showed significant associations. While, all five LCE3 genes were upregulated in psoriatic skin, only LCE3A showed significant overexpression with homozygous risk genotype compared to the non-risk genotype. LCE3B also showed significant overexpression in patients with HLA-Cw6 allele. Moreover, LCE3A showed significantly higher expression in patients bearing homozygous risk genotype in presence of HLA-Cw6 allele but not in those having non-risk genotype, demonstrating the combined effect of HLA-Cw6 allele and risk associated genotype near LCE3A gene. Integration of genetic and gene expression data thus allowed us to identify the actual disease variants at the LCE3 cluster among the psoriasis patients in India.
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21
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Sobiak B, Graczyk‐Jarzynka A, Leśniak W. Comparison of DNA Methylation and Expression Pattern of S100 and Other Epidermal Differentiation Complex Genes in Differentiating Keratinocytes. J Cell Biochem 2015; 117:1092-8. [DOI: 10.1002/jcb.25392] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 10/05/2015] [Indexed: 02/05/2023]
Affiliation(s)
- Barbara Sobiak
- Department of Molecular and Cellular NeurobiologyNencki Institute of Experimental Biology, 3 Pasteur StreetWarsaw02‐093Poland
| | - Agnieszka Graczyk‐Jarzynka
- Department of Molecular and Cellular NeurobiologyNencki Institute of Experimental Biology, 3 Pasteur StreetWarsaw02‐093Poland
| | - Wiesława Leśniak
- Department of Molecular and Cellular NeurobiologyNencki Institute of Experimental Biology, 3 Pasteur StreetWarsaw02‐093Poland
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22
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Salahshourifar I, Vincent-Chong VK, Chang HY, Ser HL, Ramanathan A, Kallarakkal TG, Rahman ZAA, Ismail SM, Prepageran N, Mustafa WMW, Abraham MT, Tay KK, Zain RB. Downregulation of CRNN gene and genomic instability at 1q21.3 in oral squamous cell carcinoma. Clin Oral Investig 2015; 19:2273-83. [PMID: 25846277 DOI: 10.1007/s00784-015-1467-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 03/23/2015] [Indexed: 12/14/2022]
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23
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Stephens DN, Klein RH, Salmans ML, Gordon W, Ho H, Andersen B. The Ets transcription factor EHF as a regulator of cornea epithelial cell identity. J Biol Chem 2013; 288:34304-24. [PMID: 24142692 DOI: 10.1074/jbc.m113.504399] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The cornea is the clear, outermost portion of the eye composed of three layers: an epithelium that provides a protective barrier while allowing transmission of light into the eye, a collagen-rich stroma, and an endothelium monolayer. How cornea development and aging is controlled is poorly understood. Here we characterize the mouse cornea transcriptome from early embryogenesis through aging and compare it with transcriptomes of other epithelial tissues, identifying cornea-enriched genes, pathways, and transcriptional regulators. Additionally, we profiled cornea epithelium and stroma, defining genes enriched in these layers. Over 10,000 genes are differentially regulated in the mouse cornea across the time course, showing dynamic expression during development and modest expression changes in fewer genes during aging. A striking transition time point for gene expression between postnatal days 14 and 28 corresponds with completion of cornea development at the transcriptional level. Clustering classifies co-expressed, and potentially co-regulated, genes into biologically informative categories, including groups that exhibit epithelial or stromal enriched expression. Based on these findings, and through loss of function studies and ChIP-seq, we show that the Ets transcription factor EHF promotes cornea epithelial fate through complementary gene activating and repressing activities. Furthermore, we identify potential interactions between EHF, KLF4, and KLF5 in promoting cornea epithelial differentiation. These data provide insights into the mechanisms underlying epithelial development and aging, identifying EHF as a regulator of cornea epithelial identity and pointing to interactions between Ets and KLF factors in promoting epithelial fate. Furthermore, this comprehensive gene expression data set for the cornea is a powerful tool for discovery of novel cornea regulators and pathways.
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24
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Wei YJ, Hu QQ, Gu CY, Wang YP, Han ZG, Cai B. Up-regulation of NICE-3 as a novel EDC gene could contribute to human hepatocellular carcinoma. Asian Pac J Cancer Prev 2013; 13:4363-8. [PMID: 23167344 DOI: 10.7314/apjcp.2012.13.9.4363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The epidermal differentiation complex (EDC) contains a large number of gene products which are crucial for the maturation of the human epidermis and can contribute to skin diseases, even carcinogenesis. It is generally acepted that activation of oncogenes and/or inactivation of tumor suppressor genes play pivotal roles in the process of carcinogenesis. Here, NICE-3, a novel EDC gene, was found to be up-regulated in human hepatocellular carcinoma (HCC) by quantitative real-time RT-PCR. Furthermore, overexpression of exogenous NICE-3 by recombinant plasmids could significantly promote cell proliferation, colony formation and soft agar colony formation in Focus and WRL-68 HCC cell lines. Reversely, NICE-3 silencing by RNA interference could markedly inhibit these malignant phenotypes in YY-8103 and MHCC-97H cells. Moreover, cell cycle analysis of MHCC-97H transfected with siRNA by flow cytometry showed that NICE-3 knockdown may inhibit cell growth via arrest in G0/G1 phase and hindering entry of cells into S phase. All data of our findings indicate that NICE-3 may contribute to human hepatocellular carcinoma by promoting cell proliferation.
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Affiliation(s)
- Yuan-Jiang Wei
- Department of Hepatobiliary Surgery, Wuxi Municipal People's Hospital of Nanjing Medical University, Nanjing, China
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25
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Cytokines and the skin barrier. Int J Mol Sci 2013; 14:6720-45. [PMID: 23531535 PMCID: PMC3645662 DOI: 10.3390/ijms14046720] [Citation(s) in RCA: 210] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 03/05/2013] [Accepted: 03/18/2013] [Indexed: 12/11/2022] Open
Abstract
The skin is the largest organ of the human body and builds a barrier to protect us from the harmful environment and also from unregulated loss of water. Keratinocytes form the skin barrier by undergoing a highly complex differentiation process that involves changing their morphology and structural integrity, a process referred to as cornification. Alterations in the epidermal cornification process affect the formation of the skin barrier. Typically, this results in a disturbed barrier, which allows the entry of substances into the skin that are immunologically reactive. This contributes to and promotes inflammatory processes in the skin but also affects other organs. In many common skin diseases, including atopic dermatitis and psoriasis, a defect in the formation of the skin barrier is observed. In these diseases the cytokine composition within the skin is different compared to normal human skin. This is the result of resident skin cells that produce cytokines, but also because additional immune cells are recruited. Many of the cytokines found in defective skin are able to influence various processes of differentiation and cornification. Here we summarize the current knowledge on cytokines and their functions in healthy skin and their contributions to inflammatory skin diseases.
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26
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Grzmil P, Altmann ME, Adham IM, Engel U, Jarry H, Schweyer S, Wolf S, Mänz J, Engel W. Embryo implantation failure and other reproductive defects in Ube2q1-deficient female mice. Reproduction 2013; 145:45-56. [PMID: 23108111 DOI: 10.1530/rep-12-0054] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The ubiquitination process is indispensable for proteome regulation. Three classes of ubiquitin (Ub)-related proteins can be distinguished: E1, E2 and E3. Proteins from the E2 class are responsible for the transfer of Ubls from E1 to the target protein. For this activity, interaction with class E3 ligases is usually required. Ub-conjugating enzyme E2Q 1 (UBE2Q1) belongs to the E2 class of Ub-related enzymes and is demonstrated to be involved in the regulation of membrane B4GALT1 protein. Here, we demonstrate that human UBE2Q1 and mouse Ube2q1 are widely expressed and highly conserved genes. To elucidate the function of UBE2Q1 protein, we generated knockout mouse model. No overt phenotype was detected in UBE2Q1-deficient males, but in mutant females, pleiotropic reproductive defects were observed including altered oestrus cycle, abnormal sexual behaviour and reduced offspring care. Moreover, in the uterus of mutant females, significantly increased embryonic lethality and decreased implantation capacity of homozygous mutant embryos were noticed. We found that Ube2q1 is not expressed in the uterus of non-pregnant females but its expression is up-regulated during pregnancy. Taken together, Ube2q1 is involved in different aspects of female fertility.
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Affiliation(s)
- Pawel Grzmil
- Institute of Human Genetics, University of Göttingen, Heinrich Düker Weg 12, 37073 Göttingen, Germany.
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Kennedy Crispin M, Fuentes-Duculan J, Gulati N, Johnson-Huang LM, Lentini T, Sullivan-Whalen M, Gilleaudeau P, Cueto I, Suárez-Fariñas M, Lowes MA, Krueger JG. Gene profiling of narrowband UVB-induced skin injury defines cellular and molecular innate immune responses. J Invest Dermatol 2012; 133:692-701. [PMID: 23151847 DOI: 10.1038/jid.2012.359] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The acute response of human skin to UVB radiation has not been fully characterized. We sought to define the cutaneous response at 24 hours following narrowband UVB (NB-UVB, 312-nm peak), a therapeutically relevant source of UVB, using transcriptional profiling, immunohistochemistry, and immunofluorescence. There were 1,522 unique differentially regulated genes, including upregulated genes encoding antimicrobial peptides (AMPs) (S100A7, S100A12, human beta-defensin 2, and elafin), as well as neutrophil and monocyte/dendritic cell (DC) chemoattractants (IL-8, CXCL1, CCL20, CCL2). Ingenuity pathway analysis demonstrated activation of innate defense and early adaptive immune pathways. Immunohistochemistry confirmed increased epidermal staining for AMPs (S100A7, S100A12, human beta-defensin 2, and elafin). Inflammatory myeloid CD11c(+)BDCA1(-) DCs were increased in irradiated skin, which were immature as shown by minimal colocalization with DC-LAMP, and coexpressed inflammatory markers tumor necrosis factor (TNF) and TNF-related apoptosis-inducing ligand in irradiated skin. There were increased BDCA3(+) DCs, a cross-presenting DC subtype with immunosuppressive functions, and these cells have not been previously characterized as part of the response to UVB. These results show that the acute response of human skin to erythemogenic doses of NB-UVB includes activation of innate defense mechanisms, as well as early infiltration of multiple subtypes of inflammatory DCs, which could serve as a link between innate and adaptive immunity.
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Affiliation(s)
- Milène Kennedy Crispin
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, New York, USA
| | - Judilyn Fuentes-Duculan
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, New York, USA
| | - Nicholas Gulati
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, New York, USA
| | - Leanne M Johnson-Huang
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, New York, USA
| | - Tim Lentini
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, New York, USA
| | - Mary Sullivan-Whalen
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, New York, USA
| | - Patricia Gilleaudeau
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, New York, USA
| | - Inna Cueto
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, New York, USA
| | - Mayte Suárez-Fariñas
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, New York, USA; The Center for Clinical and Translational Science, Rockefeller University, New York, New York, USA
| | - Michelle A Lowes
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, New York, USA
| | - James G Krueger
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, New York, USA.
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Pavón MA, Parreño M, Téllez-Gabriel M, Sancho FJ, López M, Céspedes MV, Casanova I, Lopez-Pousa A, Mangues MA, Quer M, Barnadas A, León X, Mangues R. Gene expression signatures and molecular markers associated with clinical outcome in locally advanced head and neck carcinoma. Carcinogenesis 2012; 33:1707-16. [PMID: 22696598 DOI: 10.1093/carcin/bgs207] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The purpose of this study was to identify molecular markers associated with tumor recurrence and survival in patients with locally advanced head and neck squamous cell carcinoma (HNSCC). We studied the expression profile of 63 pre-treatment tumor biopsies obtained from locally advanced HNSCCs treated with standard treatments. Cluster analysis identified three tumor subtypes associated with significant differences in local recurrence-free survival (LRFS) (P<0.001), progression free-survival (PFS) (P<0.009) and overall survival (OS) (P<0.004). Tumor subtype 1, associated with short LRFS, PFS and OS, showed features of epithelial-mesenchymal transition and undifferentiation. It also overexpressed genes involved in cell adhesion, NF-κB and integrin signalling. Tumor subtype 3, associated with longer LRFS, PFS and OS, showed a high degree of differentiation and overexpressed genes located in chromosomal regions 19q13 and 1q21. Tumor subtype 2, which had an intermediate clinical outcome between subtype 1 and subtype 3, overexpressed genes involved in branching morphogenesis. Finally, we validated the association between gene cluster classification and patient survival using Gene Set Enrichment Analysis and two HNSCC data sets obtained from two independent patient cohorts. In conclusion, we generated a gene prognostic signature associated with survival in locally advanced patients using the expression profile of the pre-treatment tumor biopsy. Independent prospective studies would be necessary to assess if the proposed survival signature could help to guide clinical management of HNSCC.
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Affiliation(s)
- M A Pavón
- Grup d'Oncogènesi i Antitumorals, Institut d'Investigacions Biomèdiques Sant Pau, Barcelona, Spain
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29
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Walker MB, King BL, Paigen K. Clusters of ancestrally related genes that show paralogy in whole or in part are a major feature of the genomes of humans and other species. PLoS One 2012; 7:e35274. [PMID: 22563380 PMCID: PMC3338513 DOI: 10.1371/journal.pone.0035274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 03/14/2012] [Indexed: 11/22/2022] Open
Abstract
Arrangements of genes along chromosomes are a product of evolutionary processes, and we can expect that preferable arrangements will prevail over the span of evolutionary time, often being reflected in the non-random clustering of structurally and/or functionally related genes. Such non-random arrangements can arise by two distinct evolutionary processes: duplications of DNA sequences that give rise to clusters of genes sharing both sequence similarity and common sequence features and the migration together of genes related by function, but not by common descent [1], [2], [3]. To provide a background for distinguishing between the two, which is important for future efforts to unravel the evolutionary processes involved, we here provide a description of the extent to which ancestrally related genes are found in proximity. Towards this purpose, we combined information from five genomic datasets, InterPro, SCOP, PANTHER, Ensembl protein families, and Ensembl gene paralogs. The results are provided in publicly available datasets (http://cgd.jax.org/datasets/clustering/paraclustering.shtml) describing the extent to which ancestrally related genes are in proximity beyond what is expected by chance (i.e. form paraclusters) in the human and nine other vertebrate genomes, as well as the D. melanogaster, C. elegans, A. thaliana, and S. cerevisiae genomes. With the exception of Saccharomyces, paraclusters are a common feature of the genomes we examined. In the human genome they are estimated to include at least 22% of all protein coding genes. Paraclusters are far more prevalent among some gene families than others, are highly species or clade specific and can evolve rapidly, sometimes in response to environmental cues. Altogether, they account for a large portion of the functional clustering previously reported in several genomes.
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Affiliation(s)
| | - Benjamin L. King
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
- Mount Desert Island Biological Laboratory, Salisbury Cove, Maine, United States of America
| | - Kenneth Paigen
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
- * E-mail:
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Supp DM. Genomic Reprogramming and Skin-Like Maturation of Engineered Human Skin Substitutes. Adv Wound Care (New Rochelle) 2012; 1:63-68. [PMID: 24527282 DOI: 10.1089/wound.2011.0336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Cultured skin substitutes (CSS) have been evaluated in clinical trials as an adjunctive treatment for large full-thickness burn wounds. Prepared with autologous fibroblasts, keratinocytes, and biopolymers, CSS can provide permanent wound closure upon engraftment to excised burns. THE PROBLEM CSS containing only two cell types are limited in anatomy and physiology compared with normal uninjured skin. Identifying deficiencies in CSS can instruct further tissue engineering advances. BASIC/CLINICAL SCIENCE ADVANCES Expression profiling of CSS during in vitro maturation and after transplantation in vivo with Affymetrix GeneChip® Arrays was used to characterize pathways that are abnormal or deficient in CSS compared with normal human skin. Examination of the large data set generated from microarray expression analysis revealed similarities between healed CSS and normal skin, particularly in expression of genes involved in epidermal differentiation and barrier function. However, deficiencies in several pathways were also noted, such as the genetic pathways regulating development of adnexal structures, including hair follicles. CLINICAL CARE RELEVANCE A deeper understanding of the cellular and molecular events guiding morphogenesis of engineered skin can lead to improvements that will increase clinical efficacy. CONCLUSION The results of GeneChip analysis highlighted the processes that act to regulate tissue development in vitro and adaptation to the wound environment and healing in vivo. This knowledge can be used to inform modifications to the model that will facilitate incorporation of additional cell types for increased homology with native human skin and improved functional outcome for burn patients treated with engineered skin grafts.
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Affiliation(s)
- Dorothy M. Supp
- Research Department, Shriners Hospitals for Children–Cincinnati, Cincinnati, Ohio
- Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, Ohio
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Lindenbergh A, de Pagter M, Ramdayal G, Visser M, Zubakov D, Kayser M, Sijen T. A multiplex (m)RNA-profiling system for the forensic identification of body fluids and contact traces. Forensic Sci Int Genet 2012; 6:565-77. [PMID: 22361234 DOI: 10.1016/j.fsigen.2012.01.009] [Citation(s) in RCA: 162] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2011] [Revised: 01/12/2012] [Accepted: 01/29/2012] [Indexed: 01/08/2023]
Abstract
In current forensic practice, information about the possible biological origin of forensic traces is mostly determined using protein-based presumptive testing. Recently, messenger RNA-profiling has emerged as an alternative strategy to examine the biological origin. Here we describe the development of a single multiplex mRNA-based system for the discrimination of the most common forensic body fluids as well as skin cells. A DNA/RNA co-isolation protocol was established that results in DNA yields equivalent to our standard in-house validated DNA extraction procedure which uses silica-based columns. An endpoint RT-PCR assay was developed that simultaneously amplifies 19 (m)RNA markers. This multiplex assay analyses three housekeeping, three blood, two saliva, two semen, two menstrual secretion, two vaginal mucosa, three general mucosa and two skin markers. The assay has good sensitivity as full RNA profiles for blood, semen and saliva were obtained when using ≥0.05 μL body fluid starting material whereas full DNA profiles were obtained with ≥0.1 μL. We investigated the specificity of the markers by analysing 15 different sets of each type of body fluid and skin with each set consisting of 8 individuals. Since skin markers have not been incorporated in multiplex endpoint PCR assays previously, we analysed these markers in more detail. Interestingly, both skin markers gave a positive result in samplings of the hands, feet, back and lips but negative in tongue samplings. Positive identification (regarding both DNA- and RNA-profiling) was obtained for specimens stored for many years, e.g. blood (28 years-old), semen (28 years-old), saliva (6 years-old), skin (10 years-old) and menstrual secretion (4 years-old). The described approach of combined DNA- and RNA-profiling of body fluids and contact traces assists in the interpretation of forensic stains by providing information about not only the donor(s) that contributed to the stain but also by indicating which cell types are present.
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Affiliation(s)
- Alexander Lindenbergh
- Department of Human Biological Traces, Netherlands Forensic Institute, P.O. Box 24044, 2490 AA The Hague, The Netherlands.
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Gyurján I, Sonderegger B, Naef F, Duboule D. Analysis of the dynamics of limb transcriptomes during mouse development. BMC DEVELOPMENTAL BIOLOGY 2011; 11:47. [PMID: 21801425 PMCID: PMC3160909 DOI: 10.1186/1471-213x-11-47] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 07/29/2011] [Indexed: 11/10/2022]
Abstract
BACKGROUND The development of vertebrate limbs has been a traditional system to study fundamental processes at work during ontogenesis, such as the establishment of spatial cellular coordinates, the effect of diffusible morphogenetic molecules or the translation between gene activity and morphogenesis. In addition, limbs are amongst the first targets of malformations in human and they display a huge realm of evolutionary variations within tetrapods, which make them a paradigm to study the regulatory genome. RESULTS As a reference resource for future biochemical and genetic analyses, we used genome-wide tiling arrays to establish the transcriptomes of mouse limb buds at three different stages, during which major developmental events take place. We compare the three time-points and discuss some aspects of these datasets, for instance related to transcriptome dynamics or to the potential association between active genes and the distribution of intergenic transcriptional activity. CONCLUSIONS These datasets provide a valuable resource, either for research projects involving gene expression and regulation in developing mouse limbs, or as examples of tissue-specific, genome-wide transcriptional activities.
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Affiliation(s)
- Istvan Gyurján
- School of Life Sciences, Ecole Polytechnique Fédérale, Station 19, Lausanne, 1215 Switzerland
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Association screening in the Epidermal Differentiation Complex (EDC) identifies an SPRR3 repeat number variant as a risk factor for eczema. J Invest Dermatol 2011; 131:1644-9. [PMID: 21490620 DOI: 10.1038/jid.2011.90] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The genetically determined impairment of the skin barrier is a primary cause of eczema. As numerous genes essential for an intact epidermis reside within the epidermal differentiation complex (EDC), we screened the National Center for Biotechnology Information (NCBI) database for putatively functional polymorphisms in the EDC genes and tested them for association with eczema. We identified 20 polymorphisms with predicted major impact on protein function. Of these, 4 were validated in 94 eczema patients: a nonsense mutation in FLG2 (rs12568784), a stop codon mutation in LCE1D (rs41268500), a 24-bp deletion in SPRR3 (rs28989168), and a frameshift mutation in S100A3 (rs11390146). The minor allele frequencies were 15.1, 6.1, 47.2, and 0.4%, respectively. Association testing of the validated polymorphisms in 555 eczema patients and 375 controls identified a significant effect of rs28989168 (SPRR3) on eczema. The association was replicated in another 1,314 cases and 1,322 controls, yielding an overall odds ratio of 1.30 (95% confidence interval 1.12-1.51; P=0.00067) for a dominant mode of inheritance. Small proline-rich proteins (SPRRs) are crossbridging proteins in the cornified cell envelope (CE), which provides the main barrier function of stratified squamous epithelia. The SPRR3 variant associated with eczema carried an extra 24-bp repeat in the central domain, which may alter the physical properties of the CE.
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Marionnet C, Grether-Beck S, Seité S, Marini A, Jaenicke T, Lejeune F, Bastien P, Rougier A, Bernerd F, Krutmann J. A broad-spectrum sunscreen prevents UVA radiation-induced gene expression in reconstructed skin in vitro and in human skin in vivo. Exp Dermatol 2011; 20:477-82. [DOI: 10.1111/j.1600-0625.2011.01265.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Chen XY, Jin LW, Chen YW, Tian H, Yuan WT, Niu ZM, Zhang J, Huang W, Zheng J. The association between the IL-20-1723C→G allele on the 1q chromosome and psoriasis triggered or exacerbated by an upper respiratory tract infection in the Chinese Han population. Dermatology 2010; 222:24-30. [PMID: 21109726 DOI: 10.1159/000320772] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Accepted: 08/30/2010] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Psoriasis is a cutaneous disorder of multifactorial etiology influenced by both genetic and environmental factors such as infection. METHODS We conducted a genome analysis with 20 microsatellite markers spanning the long arm of chromosome 1 in 36 Chinese families with psoriasis and detected evidence for linkage at 1q21 with a nonparametric linkage score of 1.74, p=0.03, and 1q32 with one of 1.84, p=0.03. According to the positional and functional candidate principle, we further investigated the single-nucleotide polymorphisms of the HAX-1 gene (located in 1q21) and IL-20 gene (located in 1q32) in a case-control study including 340 sporadic patients and 199 controls. RESULTS We determined that the frequency of the G allele of IL-20-1723C→G (rs1713239) was significantly higher among psoriatic patients (38.5% in cases vs. 31.2% in controls, p=0.015, odds ratio, OR=1.39, 95% confidence interval, CI=1.07-1.80). When we stratified our analysis by psoriasis triggered or exacerbated by infection of the upper respiratory tract, a significant difference was detected (42.4% in stratified cases vs. 31.2% in controls, p=0.005, OR=1.63, 95% CI=1.15-2.30). CONCLUSION We assume that triggered or exacerbated by respiratory tract infection, the population with the G allele of IL-20-1723C→G are predisposed to psoriasis.
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Affiliation(s)
- Xiao-Ying Chen
- Department of Dermatology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
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Manconi B, Cabras T, Pisano E, Nemolato S, Inzitari R, Iavarone F, Fanali C, Sanna MT, Tirone C, Vento G, Romagnoli C, Faa G, Castagnola M, Messana I. Characterization of two isoforms of human SPRR3 from saliva of preterm human newborn and autoptic fetal oral mucosa, parotid and submandibular gland samples. Biochem Biophys Res Commun 2010; 398:477-81. [DOI: 10.1016/j.bbrc.2010.06.103] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2010] [Accepted: 06/26/2010] [Indexed: 11/26/2022]
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Lee JS, Kim MR, Kim NS, Kim YS, Yang JM, Cho AY, Lee Y, Kim CD, Lee JH. Expression profiling of calcium induced genes in cultured human keratinocytes. J Korean Med Sci 2010; 25:619-25. [PMID: 20358008 PMCID: PMC2844606 DOI: 10.3346/jkms.2010.25.4.619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2009] [Accepted: 07/27/2009] [Indexed: 11/20/2022] Open
Abstract
Terminal differentiation of skin keratinocytes is a vertically directed multi-step process that is tightly controlled by the sequential expression of a variety of genes. To examine the gene expression profile in calcium-induced keratinocyte differentiation, we constructed a normalized cDNA library using mRNA isolated from these calcium-treated keratinocytes. After sequencing about 10,000 clones, we were able to obtain 4,104 independent genes. They consisted of 3,699 annotated genes and 405 expressed sequence tags (ESTs). Some were the genes involved in constituting epidermal structures and others were unknown genes that are probably associated with keratinocytes. In particular, we were able to identify genes located at the chromosome 1q21, the locus for the epidermal differentiation complex, and 19q13.1, another probable locus for epidermal differentiation-related gene clusters. One EST located at the chromosome 19q13.1 showed increased expression by calcium treatment, suggesting a novel candidate gene relevant to keratinocyte differentiation. These results demonstrate the complexity of the transcriptional profile of keratinocytes, providing important clues on which to base further investigations of the molecular events underlying keratinocyte differentiation.
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Affiliation(s)
- Jung-Suk Lee
- Department of Dermatology and Research Institute for Medical Sciences, School of Medicine, Chungnam National University, Daejeon, Korea
| | - Mi-Rang Kim
- Human Genomics Laboratory, Genome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Nam-Soon Kim
- Human Genomics Laboratory, Genome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Yong Sung Kim
- Human Genomics Laboratory, Genome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Jun-Mo Yang
- Department of Dermatology, Sungkyunkwan University School of Medicine, Samsung Medical Center, Seoul, Korea
| | - Ah Young Cho
- Department of Dermatology and Research Institute for Medical Sciences, School of Medicine, Chungnam National University, Daejeon, Korea
| | - Young Lee
- Department of Dermatology and Research Institute for Medical Sciences, School of Medicine, Chungnam National University, Daejeon, Korea
| | - Chang Deok Kim
- Department of Dermatology and Research Institute for Medical Sciences, School of Medicine, Chungnam National University, Daejeon, Korea
| | - Jeung-Hoon Lee
- Department of Dermatology and Research Institute for Medical Sciences, School of Medicine, Chungnam National University, Daejeon, Korea
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Silvers AL, Lin L, Bass AJ, Chen G, Wang Z, Thomas DG, Lin J, Giordano TJ, Orringer MB, Beer DG, Chang AC. Decreased selenium-binding protein 1 in esophageal adenocarcinoma results from posttranscriptional and epigenetic regulation and affects chemosensitivity. Clin Cancer Res 2010; 16:2009-21. [PMID: 20332323 DOI: 10.1158/1078-0432.ccr-09-2801] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
PURPOSE The chemopreventive effects of selenium have been extensively examined, but its role in cancer development or as a chemotherapeutic agent has only recently been explored. Because selenium-binding protein 1 (SELENBP1, SBP1, hSP56) has been shown to bind selenium covalently and selenium deficiency has been associated with esophageal adenocarcinoma (EAC), we examined its role in EAC development and its potential effect on chemosensitivity in the presence of selenium. EXPERIMENTAL DESIGN SELENBP1 expression level and copy number variation were determined by oligonucleotide microarrays, real-time reverse transcription-PCR, tissue microarrays, immunoblotting, and single-nucleotide polymorphism arrays. Bisulfite sequencing and sequence analysis of reverse transcription-PCR-amplified products explored epigenetic and posttranscriptional regulation of SELENBP1 expression, respectively. WST-1 cell proliferation assays, senescence-associated beta-galactosidase staining, immunoblotting, and flow cytometry were done to evaluate the biological significance of SELENBP1 overexpression in selenium-supplemented EAC cells. RESULTS SELENBP1 expression decreased significantly in Barrett's esophagus to adenocarcinoma progression. Both epigenetic and posttranscriptional mechanisms seemed to modulate SELENBP1 expression. Stable overexpression of SELENBP1 in methylseleninic acid-supplemented Flo-1 cells resulted in enhanced apoptosis, increased cellular senescence, and enhanced cisplatin cytotoxicity. Although inorganic sodium selenite similarly enhanced cisplatin cytotoxicity, these two forms of selenium elicited different cellular responses. CONCLUSIONS SELENBP1 expression may be an important predictor of response to chemoprevention or chemosensitization with certain forms of selenium in esophageal tissues. AACR.
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Affiliation(s)
- Amy L Silvers
- Section of Thoracic Surgery, Department of Surgery and Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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Blanchard C, Stucke EM, Burwinkel K, Caldwell JM, Collins MH, Ahrens A, Buckmeier BK, Jameson SC, Greenberg A, Kaul A, Franciosi JP, Kushner JP, Martin LJ, Putnam PE, Abonia JP, Wells SI, Rothenberg ME. Coordinate interaction between IL-13 and epithelial differentiation cluster genes in eosinophilic esophagitis. THE JOURNAL OF IMMUNOLOGY 2010; 184:4033-41. [PMID: 20208004 DOI: 10.4049/jimmunol.0903069] [Citation(s) in RCA: 218] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have previously proposed that the pathogenesis of eosinophilic esophagitis (EE) is mediated by an IL-13-driven epithelial cell response associated with marked gene dysregulation including eotaxin-3 overproduction. In this study, we compared epithelial responses between healthy patients and those with EE, aiming to uncover molecular explanations for EE pathogenesis. Esophageal epithelial cells could be maintained for up to five passages, with 67% and 62% of cell lines reaching confluence in healthy controls and EE cases, respectively. Both sets of epithelial cells avidly responded to IL-13 at similar levels as assessed by eotaxin-3 production. Acidic pH increased cellular release of eotaxin-3 (4.6 +/- 1.98 ng/ml versus 12.46 +/- 2.90 ng/ml at pH 7.4 and 4, respectively; p < 0.05). Numerous epidermal differentiation complex (EDC) genes, such as filaggrin and SPRR3, were downregulated both in IL-13-stimulated esophageal epithelial cells and in EE biopsies specimens compared with healthy controls. Whereas the filaggrin loss of function mutation 2282del4 was overrepresented in EE compared with control individuals (6.1% versus 1.3% respectively; p = 0.0172), the decreased filaggrin expression was uniformly seen in all EE cases in vivo. Indeed, expression of the EDC genes filaggrin and involucrin was strongly decreased directly by IL-13. These results establish that the epithelial response in EE involves a cooperative interaction between IL-13 and expression of EDC genes.
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Affiliation(s)
- Carine Blanchard
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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Lonergan KM, Chari R, Coe BP, Wilson IM, Tsao MS, Ng RT, MacAulay C, Lam S, Lam WL. Transcriptome profiles of carcinoma-in-situ and invasive non-small cell lung cancer as revealed by SAGE. PLoS One 2010; 5:e9162. [PMID: 20161782 PMCID: PMC2820080 DOI: 10.1371/journal.pone.0009162] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2009] [Accepted: 01/07/2010] [Indexed: 12/29/2022] Open
Abstract
Background Non-small cell lung cancer (NSCLC) presents as a progressive disease spanning precancerous, preinvasive, locally invasive, and metastatic lesions. Identification of biological pathways reflective of these progressive stages, and aberrantly expressed genes associated with these pathways, would conceivably enhance therapeutic approaches to this devastating disease. Methodology/Principal Findings Through the construction and analysis of SAGE libraries, we have determined transcriptome profiles for preinvasive carcinoma-in-situ (CIS) and invasive squamous cell carcinoma (SCC) of the lung, and compared these with expression profiles generated from both bronchial epithelium, and precancerous metaplastic and dysplastic lesions using Ingenuity Pathway Analysis. Expression of genes associated with epidermal development, and loss of expression of genes associated with mucociliary biology, are predominant features of CIS, largely shared with precancerous lesions. Additionally, expression of genes associated with xenobiotic metabolism/detoxification is a notable feature of CIS, and is largely maintained in invasive cancer. Genes related to tissue fibrosis and acute phase immune response are characteristic of the invasive SCC phenotype. Moreover, the data presented here suggests that tissue remodeling/fibrosis is initiated at the early stages of CIS. Additionally, this study indicates that alteration in copy-number status represents a plausible mechanism for differential gene expression in CIS and invasive SCC. Conclusions/Significance This study is the first report of large-scale expression profiling of CIS of the lung. Unbiased expression profiling of these preinvasive and invasive lesions provides a platform for further investigations into the molecular genetic events relevant to early stages of squamous NSCLC development. Additionally, up-regulated genes detected at extreme differences between CIS and invasive cancer may have potential to serve as biomarkers for early detection.
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Affiliation(s)
- Kim M. Lonergan
- Genetics Unit, Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
- * E-mail:
| | - Raj Chari
- Genetics Unit, Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Bradley P. Coe
- Genetics Unit, Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Ian M. Wilson
- Genetics Unit, Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Ming-Sound Tsao
- Ontario Cancer Institute, Princess Margaret Hospital, Toronto, Ontario, Canada
| | - Raymond T. Ng
- Genetics Unit, Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
- Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Calum MacAulay
- Imaging Unit, Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Stephen Lam
- Imaging Unit, Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Wan L. Lam
- Genetics Unit, Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
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Zhang Z, Mo D, Ling F, Wang C, Li A, Zhao X, Li Y, Chen Y. Characterization and promoter activity analysis of a new porcine gene: NICE-3. DNA Cell Biol 2009; 29:141-7. [PMID: 19895337 DOI: 10.1089/dna.2009.0946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Through comparative gene mapping, NICE-3, which is closely linked to tropomyosin 3 in human chromosome 1, was selected to be investigated as a new candidate gene associated with the muscle development in pigs. This gene was sequenced, chromosome mapped, expression analyzed, subcellularly localized, and promoter activity analyzed. After screening and sequencing, porcine NICE-3 was found in a bacterial artificial chromosome clone containing tropomyosin 3. Quantitative reverse transcription-polymerase chain reaction revealed that NICE-3 mRNA was widely expressed, with highest expression levels in longissimus dorsi muscles, followed by heart, biceps femoris, liver, kidney, back fat, and lowest expression levels in spleen, brain, lymph, lung, stomach, and small and large intestines. Fluorescence and confocal microscopy assay demonstrated that the fusion protein, GFP-NICE-3, was distributed throughout the cytoplasm, including the plasma membrane. NICE-3 was mapped to Sus scrofa chromosome 4, in a region of conserved synteny with human chromosome 1, where the homologous human gene is localized. Results of dual reporter gene assays and mutation experiments combined with electrophoresis mobility shift assays showed that the retinoid X receptor might be an important transcription factor affecting the promoter activity of this gene.
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Affiliation(s)
- Zongwu Zhang
- Sun Yat-Sen University, Guangzhou, Guangdong, China
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Wassler MJ, Shur BD, Zhou W, Geng YJ. Characterization of a novel ubiquitin-conjugating enzyme that regulates beta1,4-galactosyltransferase-1 in embryonic stem cells. Stem Cells 2008; 26:2006-18. [PMID: 18511602 DOI: 10.1634/stemcells.2007-1080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In this study we identified a novel galactosyltransferase 1-associating protein (GTAP) by cDNA cloning from a murine embryonic cDNA library using the two-hybrid yeast system. GTAP is expressed in early embryonic tissues, as well as in adult tissues with active cell turnover, and belongs to the class III ubiquitin-conjugating (E2) enzyme family. Its COOH-terminal domain contains a consensus sequence for ubiquitin binding shared by all the ubiquitin-conjugating enzymes, whereas its NH(2)-terminal domain appears critical for the binding and internalization of cell surface galactosyltransferase 1 (GalT1) in embryonic stem cells through a monensin- and MG132-dependent pathway. We have found that GTAP regulates GalT1-associated, laminin-dependent embryonic cell adhesion and the formation of embryoid bodies. Thus, GTAP functions as an evolutionarily conserved E2 enzyme, which may participate in intercellular adhesion and embryonic development. Disclosure of potential conflicts of interest is found at the end of this article.
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Affiliation(s)
- Michael J Wassler
- Center for Cardiovascular Biology and Atherosclerosis Research, Division of Cardiology, Department of Internal Medicine, The University of Texas Health Science Center at Houston, School of Medicine, Houston 77030, USA.
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Suda N. Comprehensive gene expression analysis in human periodontal ligaments of the mandibular third molars performing vertical movement and the maxillary second premolars with occlusal contact. Orthod Craniofac Res 2008; 11:1-7. [PMID: 18199074 DOI: 10.1111/j.1601-6343.2008.00397.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
OBJECTIVES The periodontal ligament (PDL) is thought to be an important tissue in vertical movement during tooth eruption, but the precise molecular mechanism is not known. Thereto, comprehensive gene expression was analyzed in human PDL of mandibular third molars performing vertical movement and maxillary second premolars with occlusal contact. DESIGN The expression profile of 9,243 genes in the PDL of one subject was compared between vertically moving third molars and second premolars with occlusal contact by DNA microarray. RESULTS The expression of 27 genes showed more than a 10-fold difference between third molars and second premolars. The expression of CALB1 (encoding calbindin 1), CYP26A1 (encoding cytochrome P450, family 26, subfamily A, polypeptide 1), SPOCK3 (encoding testican-3), CCK (encoding cholecystokinin) and SCRG1 (encoding scrapie responsive protein 1) was more than 30-fold higher in PDLs of the third molars than the second premolars. CALB1 is reported to increase at the pressure side of PDL during experimental orthodontic tooth movement in rats. Interestingly, in this study, CALB1 expression showed the largest difference. In contrast, CRCT1 (encoding cysteine-rich C-terminal 1), SPRP3 (encoding small proline-rich protein 3), IL8 (encoding interleukin 8) and MMP12 (encoding matrix metalloproteinase 12) showed more than 100-fold higher expression in PDLs of the second premolars than the third molars. CONCLUSION The present comprehensive gene expression in PDLs provides new insights into the molecular mechanism during the vertical tooth movement.
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Affiliation(s)
- N Suda
- Department of Maxillofacial Reconstruction and Function, Division of Maxillofacial/Neck Reconstruction, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan.
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Araya J, Cambier S, Markovics JA, Wolters P, Jablons D, Hill A, Finkbeiner W, Jones K, Broaddus VC, Sheppard D, Barzcak A, Xiao Y, Erle DJ, Nishimura SL. Squamous metaplasia amplifies pathologic epithelial-mesenchymal interactions in COPD patients. J Clin Invest 2008; 117:3551-62. [PMID: 17965775 DOI: 10.1172/jci32526] [Citation(s) in RCA: 196] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2007] [Accepted: 08/29/2007] [Indexed: 11/17/2022] Open
Abstract
Squamous metaplasia (SM) is common in smokers and is associated with airway obstruction in chronic obstructive pulmonary disease (COPD). A major mechanism of airway obstruction in COPD is thickening of the small airway walls. We asked whether SM actively contributes to airway wall thickening through alteration of epithelial-mesenchymal interactions in COPD. Using immunohistochemical staining, airway morphometry, and fibroblast culture of lung samples from COPD patients; genome-wide analysis of an in vitro model of SM; and in vitro modeling of human airway epithelial-mesenchymal interactions, we provide evidence that SM, through the increased secretion of IL-1beta, induces a fibrotic response in adjacent airway fibroblasts. We identify a pivotal role for integrin-mediated TGF-beta activation in amplifying SM and driving IL-1beta-dependent profibrotic mesenchymal responses. Finally, we show that SM correlates with increased severity of COPD and that fibroblast expression of the integrin alpha(v)beta(8), which is the major mediator of airway fibroblast TGF-beta activation, correlated with disease severity and small airway wall thickening in COPD. Our findings have identified TGF-beta as a potential therapeutic target for COPD.
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Affiliation(s)
- Jun Araya
- Department of Pathology, Lung Biology Center, UCSF, San Francisco, California 94110, USA
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Org T, Chignola F, Hetényi C, Gaetani M, Rebane A, Liiv I, Maran U, Mollica L, Bottomley MJ, Musco G, Peterson P. The autoimmune regulator PHD finger binds to non-methylated histone H3K4 to activate gene expression. EMBO Rep 2008; 9:370-6. [PMID: 18292755 PMCID: PMC2261226 DOI: 10.1038/sj.embor.2008.11] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2007] [Revised: 12/07/2007] [Accepted: 01/09/2008] [Indexed: 12/28/2022] Open
Abstract
Mutations in the gene autoimmune regulator (AIRE) cause autoimmune polyendocrinopathy candidiasis ectodermal dystrophy. AIRE is expressed in thymic medullary epithelial cells, where it promotes the expression of tissue-restricted antigens. By the combined use of biochemical and biophysical methods, we show that AIRE selectively interacts with histone H3 through its first plant homeodomain (PHD) finger (AIRE-PHD1) and preferentially binds to non-methylated H3K4 (H3K4me0). Accordingly, in vivo AIRE binds to and activates promoters containing low levels of H3K4me3 in human embryonic kidney 293 cells. We conclude that AIRE-PHD1 is an important member of a newly identified class of PHD fingers that specifically recognize H3K4me0, thus providing a new link between the status of histone modifications and the regulation of tissue-restricted antigen expression in thymus.
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Affiliation(s)
- Tõnis Org
- Molecular Pathology, University of Tartu, Tartu 50411, Estonia
| | - Francesca Chignola
- Biomolecular NMR Laboratory, Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Milan 20132, Italy
| | - Csaba Hetényi
- Institute of Chemical Physics, University of Tartu, Tartu 51010, Estonia
| | - Massimiliano Gaetani
- Biomolecular NMR Laboratory, Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Milan 20132, Italy
| | - Ana Rebane
- Molecular Pathology, University of Tartu, Tartu 50411, Estonia
| | - Ingrid Liiv
- Molecular Pathology, University of Tartu, Tartu 50411, Estonia
| | - Uko Maran
- Institute of Chemical Physics, University of Tartu, Tartu 51010, Estonia
| | - Luca Mollica
- Biomolecular NMR Laboratory, Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Milan 20132, Italy
| | - Matthew J Bottomley
- Istituto di Ricerche di Biologia Molecolare, via Pontina km 30.600, Pomezia (Rome), 00040, Italy
| | - Giovanna Musco
- Biomolecular NMR Laboratory, Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Milan 20132, Italy
| | - Pärt Peterson
- Molecular Pathology, University of Tartu, Tartu 50411, Estonia
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Org T, Chignola F, Hetényi C, Gaetani M, Rebane A, Liiv I, Maran U, Mollica L, Bottomley MJ, Musco G, Peterson P. The autoimmune regulator PHD finger binds to non-methylated histone H3K4 to activate gene expression. EMBO Rep 2008. [PMID: 18292755 PMCID: PMC2261226 DOI: 10.1038/embor.2008.11] [Citation(s) in RCA: 163] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mutations in the gene autoimmune regulator (AIRE) cause autoimmune polyendocrinopathy candidiasis ectodermal dystrophy. AIRE is expressed in thymic medullary epithelial cells, where it promotes the expression of tissue-restricted antigens. By the combined use of biochemical and biophysical methods, we show that AIRE selectively interacts with histone H3 through its first plant homeodomain (PHD) finger (AIRE–PHD1) and preferentially binds to non-methylated H3K4 (H3K4me0). Accordingly, in vivo AIRE binds to and activates promoters containing low levels of H3K4me3 in human embryonic kidney 293 cells. We conclude that AIRE–PHD1 is an important member of a newly identified class of PHD fingers that specifically recognize H3K4me0, thus providing a new link between the status of histone modifications and the regulation of tissue-restricted antigen expression in thymus.
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Affiliation(s)
- Tõnis Org
- Molecular Pathology, University of Tartu, Tartu 50411, Estonia
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Takeda K, Takahashi NH, Shibahara S. Neuroendocrine functions of melanocytes: beyond the skin-deep melanin maker. TOHOKU J EXP MED 2007; 211:201-21. [PMID: 17347546 DOI: 10.1620/tjem.211.201] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The skin is armored with "dead cells", the stratum corneum, and is continuously exposed to external stressful environments, such as atmospheric oxygen, solar radiations, and thermal and chemical insults. Melanocytes of neural crest origin are located in the skin, eye, inner ear, and leptomeninges. Melanin pigment in the skin is produced by melanocytes under the influence of various endogenous factors, derived from neighboring keratinocytes and underlying fibroblasts. The differentiation and functions of melanocytes are regulated at multiple processes, including transcription, RNA editing, melanin synthesis, and the transport of melanosomes to keratinocytes. Impairment at each step causes the pigmentary disorders in humans, with the historical example of oculocutaneous albinism. Moreover, heterozygous mutations in the gene coding for microphthalmia-associated transcription factor, a key regulator for melanocyte development, are associated with Waardenburg syndrome type 2, an auditory-pigmentary disorder. Sun tanning, melasma, aging spots (lentigo senilis), hair graying, and melanoma are well-known melanocyte-related pathologies. Melanocytes therefore have attracted much attention of many ladies, makeup artists and molecular biologists. More recently, we have shown that lipocalin-type prostaglandin D synthase (L-PGDS) is expressed in melanocytes but not in other skin cell types. L-PGDS generates prostaglandin D2 and also functions as an inter-cellular carrier protein for lipophilic ligands, such as bilirubin and thyroid hormones. Thus, melanocytes may exert hitherto unknown functions through L-PGDS and prostaglandin D2. Here we update the neuroendocrine functions of melanocytes and discuss the possible involvement of melanocytes in the control of the central chemosensor that generates respiratory rhythm.
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Affiliation(s)
- Kazuhisa Takeda
- Department of Molecular Biology and Applied Physiology, Tohoku University School of Medicine, Sendai, Japan
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48
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Brown SJ, Tilli CMLJ, Jackson B, Avilion AA, MacLeod MC, Maltais LJ, Lovering RC, Byrne C. Rodent Lce gene clusters; new nomenclature, gene organization, and divergence of human and rodent genes. J Invest Dermatol 2007; 127:1782-6. [PMID: 17410201 DOI: 10.1038/sj.jid.5700792] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
The S100 proteins are exclusively expressed in vertebrates and are the largest subgroup within the superfamily of EF-hand Ca2(+)-binding proteins Generally, S100 proteins are organized as tight homodimers (some as heterodimers). Each subunit is composed of a C-terminal, 'canonical' EF-hand, common to all EF-hand proteins, and a N-terminal, 'pseudo' EF-hand, characteristic of S100 proteins. Upon Ca2(+)-binding, the C-terminal EF-hand undergoes a large conformational change resulting in the exposure of a hydrophobic surface responsible for target binding A unique feature of this protein family is that some members are secreted from cells upon stimulation, exerting cytokine- and chemokine-like extracellular activities via the Receptor for Advanced Glycation Endproducts, RAGE. Recently, larger assemblies of some S100 proteins (hexamers, tetramers, octamers) have been also observed and are suggested to be the active extracellular species required for receptor binding and activation through receptor multimerization Most S100 genes are located in a gene cluster on human chromosome 1q21, a region frequently rearranged in human cancer The functional diversification of S100 proteins is achieved by their specific cell- and tissue-expression patterns, structural variations, different metal ion binding properties (Ca2+, Zn2+ and Cu2+) as well as their ability to form homo-, hetero- and oligomeric assemblies Here, we review the most recent developments focussing on the biological functions of the S100 proteins and we discuss the presently available S100-specific mouse models and their possible use as human disease models In addition, the S100-RAGE interaction and the activation of various cellular pathways will be discussed. Finally, the close association of S100 proteins with cardiomyopathy, cancer, inflammation and brain diseases is summarized as well as their use in diagnosis and their potential as drug targets to improve therapies in the future.
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Affiliation(s)
- C W Heizmann
- Division of Clinical Chemistry and Biochemistry, Department of Pediatrics, University of Zurich, Switzerland.
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50
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Daly-Burns B, Alam TN, Mackay A, Clark J, Shepherd CJ, Rizzo S, Tatoud R, O'Hare MJ, Masters JR, Hudson DL. A conditionally immortalized cell line model for the study of human prostatic epithelial cell differentiation. Differentiation 2007; 75:35-48. [PMID: 17244020 DOI: 10.1111/j.1432-0436.2006.00113.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
In the normal human prostate, undifferentiated proliferative cells reside in the basal layer and give rise to luminal secretory cells. There are, however, few epithelial cell lines that have a basal cell phenotype and are able to differentiate. We set out to develop a cell line with these characteristics that would be suitable for the study of the early stages of prostate epithelial cell differentiation. We produced a matched pair of conditionally immortalized prostate epithelial and stromal cell lines derived from the same patient. The growth of these cells is temperature dependent and differentiation can be induced following a rise in culture temperature. Three-dimensional co-cultures of these cell lines elicited gland-like structures reminiscent of prostatic acini. cDNA microarray analysis of the epithelial line demonstrated changes in gene expression consistent with epithelial differentiation. These genes may prove useful as markers for different prostate cell types. The cell lines provide a model system with which to study the process of prostatic epithelial differentiation and stromal-epithelial interactions. This may prove to be useful in the development of differentiation-targeted prostate cancer therapies.
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Affiliation(s)
- Bernadette Daly-Burns
- Prostate Cancer Research Centre, Institute of Urology, University College London, 67 Riding House Street, London W1W 7EJ, UK
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