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Yadav R, Kumar Y, Dahiya D, Bhatia A. Claudins: The Newly Emerging Targets in Breast Cancer. Clin Breast Cancer 2022; 22:737-752. [PMID: 36175290 DOI: 10.1016/j.clbc.2022.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 09/04/2022] [Indexed: 01/25/2023]
Abstract
Claudin-low breast cancers are recently described entities showing low expression of certain claudins and cell adhesion molecules. Claudins constitute the backbone of tight junctions (TJs) formed between 2 cells. Their dysregulation plays a vital role in tumorigenesis. First part of the article focuses on the role of claudins in the TJ organization, their structural-functional characteristics, and post-transcriptional and translational modifications. The latter part of the review attempts to summarize existing knowledge regarding the status of claudins in breast cancer. The article also provides an overview of the effect of claudins on tumor progression, metastasis, stemness, chemotherapy resistance, and their crosstalk with relevant signaling pathways in breast cancer. Claudins can act as 2-edged swords in tumors. Some claudins have either tumor-suppressive/ promoting action, while others work as both in a context-dependent manner. Claudins regulate many important events in breast cancer. However, the intricacies involved in their activity are poorly understood. Post-translational modifications in claudins and their impact on TJ integrity, function, and tumor behavior are still unclear. Although their role in adverse events in breast cancer is recognized, their potential to serve as relevant targets for future therapeutics, especially for difficult-to-treat subtypes of the above malignancy, remains to be explored.
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Affiliation(s)
- Reena Yadav
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Yashwant Kumar
- Department of Immunopathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Divya Dahiya
- Department of General Surgery, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Alka Bhatia
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
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2
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Expression of tight junction transmembrane protein Claudin-1 in gastric carcinoma and effects on tumor cell proliferation, invasion and migration. REV ROMANA MED LAB 2022. [DOI: 10.2478/rrlm-2022-0007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
Background: Claudin-1 is involved in various cancers, but its expression and role in gastric carcinoma remain unclear.
Materials and Methods: Gastric carcinoma and adjacent normal tissues were harvested from 60 patients. Claudin-1 expression was detected by RT-qPCR. The expressions in human gastric carcinoma MKN45, SGC7901 and MKN28 cells and immortalized human gastric epithelium GES-1 cells were determined by RT-qPCR and Western blotting. Claudin-1 was overexpressed in SGC7901 cells by lentiviral transfection, and they were divided into Control (untransfected), normal control (NC) (transfected with lentiviral vector) and Claudin-1 (transfected with Claudin-1 overexpression lentivirus) groups. The proliferation, invasion and migration of gastric carcinoma cells were detected through cell counting kit-8, Transwell and wound healing assays, respectively. The effects of Claudin-1 on the expressions of epithelial-mesenchymal transition (EMT) marker proteins E-cadherin and N-cadherin were detected by Western blotting. Ten 4-week-old male BALB/c nude mice were subcutaneously injected with lentivirus-treated SGC7901 cells to establish the transplanted tumor model, and the effect of overexpression of Claudin-1 was explored.
Results: The expression of Claudin-1 in gastric carcinoma tissues was significantly lower than that in adjacent tissues (P<0.05). Overexpression of Claudin-1 significantly inhibited the proliferation, invasion and migration of SGC7901 cells, increased the expression of E-cadherin, and decreased that of N-cadherin (P<0.05). Overexpression of Claudin-1 in the mouse model significantly inhibited the growth of subcutaneous transplanted tumors (P<0.05).
Conclusion: Claudin-1 has low expression in gastric carcinoma tissues. Overexpression of Claudin-1 inhibits the proliferation, invasion, migration, and EMT of gastric carcinoma cells, and subcutaneous tumorigenesis in nude mice.
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3
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Edechi CA, Amini M, Hamedani MK, Terceiro LE, Nickel BE, Leygue E, Myal Y. Comparison of Fixation Methods for the Detection of Claudin 1 and E-Cadherin in Breast Cancer Cell Lines by Immunofluorescence. J Histochem Cytochem 2022; 70:181-187. [PMID: 34715746 PMCID: PMC8777374 DOI: 10.1369/00221554211055240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The tight junction membrane protein claudin 1 and the adherens junction protein E-cadherin play critical roles in cell-cell communication and in cell signaling. As a result, their protein levels and distribution in cancer have been a focus of cancer researchers in recent years. The loss of sensitivity to contact inhibition and the establishment of invasive properties in cancer are thought to be a result of the mislocalization of these membrane proteins to the cytoplasm. However, reports on their distribution and levels have been inconsistent. It is therefore critical that the techniques used to determine the cellular localization of these proteins be both consistent and reliable. This study was undertaken to determine the optimal fixation method, methanol or formalin, for the detection of claudin 1 and E-cadherin by immunofluorescence in five different human breast cancer cell lines. Both methods exhibited staining of the cell membrane and cytoplasm, but the strongest and most distinct signals were obtained using methanol fixation. Interestingly, cell-specific differences were also observed that appeared to be associated with levels of claudin 1 and E-cadherin as seen by Western blotting. Therefore, when evaluating cellular localization of the junction proteins claudin 1 and E-cadherin, expression level and cell type differences must be considered.
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Affiliation(s)
| | | | | | | | - Barbara E. Nickel
- Institute of Cardiovascular Sciences, St.
Boniface Hospital Albrechtsen Research Centre, Winnipeg, MB, Canada
| | - Etienne Leygue
- Department of Biochemistry,Max Rady College of Medicine, University of
Manitoba, Winnipeg, MB, Canada, CancerCare Manitoba Research Institute,
Winnipeg, MB, Canada
| | - Yvonne Myal
- Yvonne Myal, Department of Pathology, Max
Rady College of Medicine, University of Manitoba, 401 Brodie Centre, 727
McDermot Avenue, Winnipeg, MB R3E 3P5, Canada. E-mail:
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4
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Ouban A. Expression of Claudin-1 in laryngeal squamous cell carcinomas (LSCCs) and its significance. Histol Histopathol 2021; 36:437-446. [PMID: 33629735 DOI: 10.14670/hh-18-320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND A large body of scientific evidence points to the important roles of tight junction proteins in tumor development, progression and dissemination. The larynx has only a few studies, analyzing the role of this group of junctional proteins in its oncogenesis. In this study, the author sheds some light on the expression and possible role of claudin-1 in laryngeal squamous cell carcinomas. MATERIALS AND METHODS This study analyzed the expression of claudin-1, using immunohistochemistry, in a tissue microarray of 80 cases of laryngeal squamous cell cancers. Clinicopathological parameters were analyzed according to claudin-1 expression in the tissue microarray. Furthermore, the expression of slug/snail1, an Epithelial-Mesenchymal Transition (EMT) linked protein, was analyzed by immunohistochemistry in the same microarray, and the expressions of the two proteins were assessed for correlation. RESULTS A significant majority of laryngeal squamous cell cancers exhibited positive expression of claudin-1 proteins. The majority of those tumors expressed claudin-1 in their cytoplasm. The overall majority of those same tumors also exhibited a cytoplasmic shift of the slug-snail-1 protein from the nuclei to the cytoplasm. There was also evidence of correlation of the two proteins' expressions in the cytoplasm of laryngeal tumors. CONCLUSION The above may suggest a role for claudin-1 in the development and progression of laryngeal squamous cell carcinoma. Overall, claudin-1's aberrant expression in laryngeal cancer is in line with evidence seen in other head and neck cancers. Its co-expression with slug/snail-1 in LSCC patients should be investigated further to understand the nature of the relationship of the two proteins in LSCC and their possible contribution to its development and progression.
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Affiliation(s)
- Abderrahman Ouban
- Department of Pathology, College of Medicine , Alfaisal University, Riyadh, Saudi Arabia.
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5
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Glucose-limiting conditions induce an invasive population of MDA-MB-231 breast cancer cells with increased connexin 43 expression and membrane localization. J Cell Commun Signal 2021; 15:223-236. [PMID: 33591483 PMCID: PMC7991056 DOI: 10.1007/s12079-020-00601-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 12/09/2020] [Indexed: 01/10/2023] Open
Abstract
Gap junctional intercellular communication (GJIC) is a homeostatic process mediated by membrane channels composed of a protein family known as connexins. Alterations to channel activity can modulate suppression or facilitation of cancer progression. These varying roles are influenced by the cancer cell genetic profile and the context-dependent mechanisms of a dynamic extracellular environment that encompasses fluctuations to nutrient availability. To better explore the effects of altered cellular metabolism on GJIC in breast cancer, we generated a derivative of the triple-negative breast cancer cell line MDA-MB-231 optimized for growth in low-glucose. Reduced availability of glucose is commonly encountered during tumor development and leads to metabolic reprogramming in cancer cells. MDA-MB-231 low-glucose adapted cells exhibited a larger size with improved cell–cell contact and upregulation of cadherin-11. Additionally, increased protein levels of connexin 43 and greater plasma membrane localization were observed with a corresponding improvement in GJIC activity compared to the parental cell line. Since GJIC has been shown to affect cellular invasion in multiple cancer cell types, we evaluated the invasive qualities of these cells using multiple three-dimensional Matrigel growth models. Results of these experiments demonstrated a significantly more invasive phenotype. Moreover, a decrease in invasion was noted when GJIC was inhibited. Our results indicate a potential response of triple-negative breast cancer cells to reduced glucose availability that results in changes to GJIC and invasiveness. Delineation of this relationship may help elucidate mechanisms by which altered cancer cell metabolism affects GJIC and how cancer cells respond to nutrient availability in this regard.
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Claudin 1 inhibits cell migration and increases intercellular adhesion in triple-negative breast cancer cell line. Mol Biol Rep 2020; 47:7643-7653. [PMID: 32979166 DOI: 10.1007/s11033-020-05835-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/09/2020] [Indexed: 12/12/2022]
Abstract
Triple-negative "claudin 1 low" subtype represents around 15% of breast cancer and displays poor prognosis. The loss of claudin 1 is correlated with increased invasiveness and higher recurrence of the disease. Claudin 1 constitutes the backbone of the tight junction and is involved in cell-cell adhesion and migration processes. However, studies showed a controversial role of claudin 1 in cell migration. In this study, we aimed to clarify the effect of claudin 1 on migration of mesenchymal triple-negative breast cancer cells (TNBC). We reported that transient over expression of claudin 1 in MDA-MB-231 and Hs578T "claudin 1 low" TNBC cells inhibited cell migration using wound healing and transwell migration assays. In order to investigate more specifically the involvement of claudin 1, we generated stable MDA-MB-231 clones overexpressing claudin 1. Interestingly, the level of claudin 1 was correlated to the inhibition of cell migration and to the increase of cell-cell aggregation associated with enhanced formation of β-catenin adherens junction and occludin tight junction. Finally, we reported for the first time the key role of claudin 1 in the inhibition of cell migration process associated with the disappearance of stress fibers. These data suggest that re-expression of claudin 1 could be a promising strategy for regulating the migration of TNBC which no longer express claudin 1.
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Bhat AA, Uppada S, Achkar IW, Hashem S, Yadav SK, Shanmugakonar M, Al-Naemi HA, Haris M, Uddin S. Tight Junction Proteins and Signaling Pathways in Cancer and Inflammation: A Functional Crosstalk. Front Physiol 2019; 9:1942. [PMID: 30728783 PMCID: PMC6351700 DOI: 10.3389/fphys.2018.01942] [Citation(s) in RCA: 232] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 12/22/2018] [Indexed: 12/14/2022] Open
Abstract
The ability of epithelial cells to organize through cell–cell adhesion into a functioning epithelium serves the purpose of a tight epithelial protective barrier. Contacts between adjacent cells are made up of tight junctions (TJ), adherens junctions (AJ), and desmosomes with unique cellular functions and a complex molecular composition. These proteins mediate firm mechanical stability, serves as a gatekeeper for the paracellular pathway, and helps in preserving tissue homeostasis. TJ proteins are involved in maintaining cell polarity, in establishing organ-specific apical domains and also in recruiting signaling proteins involved in the regulation of various important cellular functions including proliferation, differentiation, and migration. As a vital component of the epithelial barrier, TJs are under a constant threat from proinflammatory mediators, pathogenic viruses and bacteria, aiding inflammation and the development of disease. Inflammatory bowel disease (IBD) patients reveal loss of TJ barrier function, increased levels of proinflammatory cytokines, and immune dysregulation; yet, the relationship between these events is partly understood. Although TJ barrier defects are inadequate to cause experimental IBD, mucosal immune activation is changed in response to augmented epithelial permeability. Thus, the current studies suggest that altered barrier function may predispose or increase disease progression and therapies targeted to specifically restore the barrier function may provide a substitute or supplement to immunologic-based therapies. This review provides a brief introduction about the TJs, AJs, structure and function of TJ proteins. The link between TJ proteins and key signaling pathways in cell proliferation, transformation, and metastasis is discussed thoroughly. We also discuss the compromised intestinal TJ integrity under inflammatory conditions, and the signaling mechanisms involved that bridge inflammation and cancer.
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Affiliation(s)
- Ajaz A Bhat
- Division of Translational Medicine, Research Branch, Sidra Medicine, Doha, Qatar
| | - Srijayaprakash Uppada
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, United States
| | - Iman W Achkar
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Sheema Hashem
- Division of Translational Medicine, Research Branch, Sidra Medicine, Doha, Qatar
| | - Santosh K Yadav
- Division of Translational Medicine, Research Branch, Sidra Medicine, Doha, Qatar
| | | | - Hamda A Al-Naemi
- Laboratory Animal Research Center, Qatar University, Doha, Qatar.,Department of Biological and Environmental Sciences, Qatar University, Doha, Qatar
| | - Mohammad Haris
- Division of Translational Medicine, Research Branch, Sidra Medicine, Doha, Qatar.,Laboratory Animal Research Center, Qatar University, Doha, Qatar
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
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Gao W, Hua J, Jia Z, Ding J, Han Z, Dong Y, Lin Q, Yao Y. Expression of miR-146a-5p in breast cancer and its role in proliferation of breast cancer cells. Oncol Lett 2018; 15:9884-9888. [PMID: 29928360 PMCID: PMC6004703 DOI: 10.3892/ol.2018.8589] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 03/07/2018] [Indexed: 12/16/2022] Open
Abstract
In the present study, the expression level of microRNA-146a-5p (miR-146a-5p) in breast cancer tissue and cell lines was investigated and its effects on proliferation of breast cancer cells. miR-146a-5p expression was detected by reverse transcription-quantitative polymerase chain reaction in breast cancer tissues, paraneoplastic tissue (collected by The Department of Oncology of Changhai Hospital from January 2014 to June 2015), breast cancer cell line MCF-7 and normal breast epithelial cell line MCF 10A. Bioinformatics analysis was conducted to forecast target genes of miR-146a-5p, which was further verified by fluorescent reporter gene detection. The results demonstrated the expression level of miR-146a-5p in breast cancer tissue was significantly higher, compared with paraneoplastic tissue (P<0.01), and the expression level of miR-146a-5p in MCF-7 cells was significantly higher, compared with MCF 10A cells (P<0.01). Overexpression of miR-146a-5p in MCF-7 cells can promote the proliferation, and low expression miR-146a-5p in MCF-7 can inhibit the proliferation. BRCA1 was further identified as a target gene of miR-146a-5p by bioinformatics analysis and fluorescent reporter gene detection. It was concluded that miR-146a-5p is expressed in breast cancer tissue and breast cancer cell line and may regulate the proliferation of MCF-7 via BRCA1.
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Affiliation(s)
- Wei Gao
- Department of Radiation Oncology, 9th People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 201999, P.R. China
| | - Jing Hua
- Department of Emergency, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, P.R. China
| | - Zhaoyang Jia
- Department of Radiation Oncology, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P.R. China
| | - Jiping Ding
- Department of Radiation Oncology, 9th People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 201999, P.R. China
| | - Zengwei Han
- Department of Radiation Oncology, 9th People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 201999, P.R. China
| | - Yun Dong
- Department of Radiation Oncology, 9th People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 201999, P.R. China
| | - Qing Lin
- Department of Radiation Oncology, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P.R. China
| | - Yuan Yao
- Department of Radiation Oncology, 9th People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 201999, P.R. China
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9
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Paquet-Fifield S, Koh SL, Cheng L, Beyit LM, Shembrey C, Mølck C, Behrenbruch C, Papin M, Gironella M, Guelfi S, Nasr R, Grillet F, Prudhomme M, Bourgaux JF, Castells A, Pascussi JM, Heriot AG, Puisieux A, Davis MJ, Pannequin J, Hill AF, Sloan EK, Hollande F. Tight Junction Protein Claudin-2 Promotes Self-Renewal of Human Colorectal Cancer Stem-like Cells. Cancer Res 2018; 78:2925-2938. [PMID: 29510994 DOI: 10.1158/0008-5472.can-17-1869] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 01/22/2018] [Accepted: 03/01/2018] [Indexed: 12/31/2022]
Abstract
Posttreatment recurrence of colorectal cancer, the third most lethal cancer worldwide, is often driven by a subpopulation of cancer stem cells (CSC). The tight junction (TJ) protein claudin-2 is overexpressed in human colorectal cancer, where it enhances cell proliferation, colony formation, and chemoresistance in vitro While several of these biological processes are features of the CSC phenotype, a role for claudin-2 in the regulation of these has not been identified. Here, we report that elevated claudin-2 expression in stage II/III colorectal tumors is associated with poor recurrence-free survival following 5-fluorouracil-based chemotherapy, an outcome in which CSCs play an instrumental role. In patient-derived organoids, primary cells, and cell lines, claudin-2 promoted colorectal cancer self-renewal in vitro and in multiple mouse xenograft models. Claudin-2 enhanced self-renewal of ALDHHigh CSCs and increased their proportion in colorectal cancer cell populations, limiting their differentiation and promoting the phenotypic transition of non-CSCs toward the ALDHHigh phenotype. Next-generation sequencing in ALDHHigh cells revealed that claudin-2 regulated expression of nine miRNAs known to control stem cell signaling. Among these, miR-222-3p was instrumental for the regulation of self-renewal by claudin-2, and enhancement of this self-renewal required activation of YAP, most likely upstream from miR-222-3p. Taken together, our results indicate that overexpression of claudin-2 promotes self-renewal within colorectal cancer stem-like cells, suggesting a potential role for this protein as a therapeutic target in colorectal cancer.Significance: Claudin-2-mediated regulation of YAP activity and miR-222-3p expression drives CSC renewal in colorectal cancer, making it a potential target for therapy. Cancer Res; 78(11); 2925-38. ©2018 AACR.
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Affiliation(s)
- Sophie Paquet-Fifield
- Department of Clinical Pathology, The University of Melbourne, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Shir Lin Koh
- Department of Clinical Pathology, The University of Melbourne, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Lesley Cheng
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Australia
| | - Laura M Beyit
- Department of Clinical Pathology, The University of Melbourne, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Carolyn Shembrey
- Department of Clinical Pathology, The University of Melbourne, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Christina Mølck
- Department of Clinical Pathology, The University of Melbourne, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Corina Behrenbruch
- Department of Clinical Pathology, The University of Melbourne, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia.,Peter MacCallum Cancer Centre, Division of Cancer Surgery, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Marina Papin
- Centre National de la Recherche Scientifique (CNRS), UMR5203, Institut de Génomique Fonctionnelle, Montpellier, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier, France.,Université Montpellier 1 et 2, Montpellier, France
| | - Meritxell Gironella
- Gastrointestinal and Pancreatic Oncology Group, Hospital Clínic of Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Sophie Guelfi
- Centre National de la Recherche Scientifique (CNRS), UMR5203, Institut de Génomique Fonctionnelle, Montpellier, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier, France.,Université Montpellier 1 et 2, Montpellier, France
| | - Ramona Nasr
- Centre National de la Recherche Scientifique (CNRS), UMR5203, Institut de Génomique Fonctionnelle, Montpellier, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier, France.,Université Montpellier 1 et 2, Montpellier, France
| | - Fanny Grillet
- Centre National de la Recherche Scientifique (CNRS), UMR5203, Institut de Génomique Fonctionnelle, Montpellier, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier, France.,Université Montpellier 1 et 2, Montpellier, France
| | | | | | - Antoni Castells
- Gastrointestinal and Pancreatic Oncology Group, Hospital Clínic of Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Jean-Marc Pascussi
- Centre National de la Recherche Scientifique (CNRS), UMR5203, Institut de Génomique Fonctionnelle, Montpellier, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier, France.,Université Montpellier 1 et 2, Montpellier, France
| | - Alexander G Heriot
- Peter MacCallum Cancer Centre, Division of Cancer Surgery, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | | | - Melissa J Davis
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Julie Pannequin
- Centre National de la Recherche Scientifique (CNRS), UMR5203, Institut de Génomique Fonctionnelle, Montpellier, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier, France.,Université Montpellier 1 et 2, Montpellier, France
| | - Andrew F Hill
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Australia
| | - Erica K Sloan
- Peter MacCallum Cancer Centre, Division of Cancer Surgery, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia.,Monash Institute of Pharmaceutical Sciences, Drug Discovery Biology Theme, Monash University, Parkville Victoria, Australia.,Cousins Center for PNI, UCLA Semel Institute, Jonsson Comprehensive Cancer Center, and UCLA AIDS Institute, University of California Los Angeles, Los Angeles, California
| | - Frédéric Hollande
- Department of Clinical Pathology, The University of Melbourne, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia.
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10
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Restrepo P, Movassagh M, Alomran N, Miller C, Li M, Trenkov C, Manchev Y, Bahl S, Warnken S, Spurr L, Apanasovich T, Crandall K, Edwards N, Horvath A. Overexpressed somatic alleles are enriched in functional elements in Breast Cancer. Sci Rep 2017; 7:8287. [PMID: 28811643 PMCID: PMC5557904 DOI: 10.1038/s41598-017-08416-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 07/10/2017] [Indexed: 12/31/2022] Open
Abstract
Asymmetric allele content in the transcriptome can be indicative of functional and selective features of the underlying genetic variants. Yet, imbalanced alleles, especially from diploid genome regions, are poorly explored in cancer. Here we systematically quantify and integrate the variant allele fraction from corresponding RNA and DNA sequence data from patients with breast cancer acquired through The Cancer Genome Atlas (TCGA). We test for correlation between allele prevalence and functionality in known cancer-implicated genes from the Cancer Gene Census (CGC). We document significant allele-preferential expression of functional variants in CGC genes and across the entire dataset. Notably, we find frequent allele-specific overexpression of variants in tumor-suppressor genes. We also report a list of over-expressed variants from non-CGC genes. Overall, our analysis presents an integrated set of features of somatic allele expression and points to the vast information content of the asymmetric alleles in the cancer transcriptome.
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Affiliation(s)
- Paula Restrepo
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA.,McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA
| | - Mercedeh Movassagh
- University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, 01605, USA
| | - Nawaf Alomran
- McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA.,Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, School of Medicine, Washington, DC, 20057, USA
| | - Christian Miller
- McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA
| | - Muzi Li
- McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA.,Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, School of Medicine, Washington, DC, 20057, USA
| | - Chris Trenkov
- McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA
| | - Yulian Manchev
- McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA
| | - Sonali Bahl
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA
| | - Stephanie Warnken
- Computational Biology Institute, The George Washington University, Washington, DC, 20037, USA
| | - Liam Spurr
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA.,McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA
| | - Tatiyana Apanasovich
- Department of Statistics, The George Washington University, Washington, DC, 20037, USA
| | - Keith Crandall
- Computational Biology Institute, The George Washington University, Washington, DC, 20037, USA
| | - Nathan Edwards
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, School of Medicine, Washington, DC, 20057, USA
| | - Anelia Horvath
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA. .,McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA. .,Department of Statistics, The George Washington University, Washington, DC, 20037, USA. .,Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA.
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