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Zhu QM, Hsu YHH, Lassen FH, MacDonald BT, Stead S, Malolepsza E, Kim A, Li T, Mizoguchi T, Schenone M, Guzman G, Tanenbaum B, Fornelos N, Carr SA, Gupta RM, Ellinor PT, Lage K. Protein interaction networks in the vasculature prioritize genes and pathways underlying coronary artery disease. Commun Biol 2024; 7:87. [PMID: 38216744 PMCID: PMC10786878 DOI: 10.1038/s42003-023-05705-1] [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: 09/18/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024] Open
Abstract
Population-based association studies have identified many genetic risk loci for coronary artery disease (CAD), but it is often unclear how genes within these loci are linked to CAD. Here, we perform interaction proteomics for 11 CAD-risk genes to map their protein-protein interactions (PPIs) in human vascular cells and elucidate their roles in CAD. The resulting PPI networks contain interactions that are outside of known biology in the vasculature and are enriched for genes involved in immunity-related and arterial-wall-specific mechanisms. Several PPI networks derived from smooth muscle cells are significantly enriched for genetic variants associated with CAD and related vascular phenotypes. Furthermore, the networks identify 61 genes that are found in genetic loci associated with risk of CAD, prioritizing them as the causal candidates within these loci. These findings indicate that the PPI networks we have generated are a rich resource for guiding future research into the molecular pathogenesis of CAD.
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Affiliation(s)
- Qiuyu Martin Zhu
- Cardiovascular Disease Initiative & Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Yu-Han H Hsu
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Frederik H Lassen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Bryan T MacDonald
- Cardiovascular Disease Initiative & Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephanie Stead
- Cardiovascular Disease Initiative & Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Edyta Malolepsza
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - April Kim
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Taibo Li
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Taiji Mizoguchi
- Cardiovascular Disease Initiative & Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Monica Schenone
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gaelen Guzman
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin Tanenbaum
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nadine Fornelos
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Steven A Carr
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rajat M Gupta
- Divisions of Cardiovascular Medicine and Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative & Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.
| | - Kasper Lage
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA.
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.
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2
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Challa D, Pandi C, Kannan B, Priyadharsini VJ, Arumugam P. Exploring the Expression of BCAS3 in Head and Neck Squamous Cell Carcinoma and Its Association With Prognosis. Cureus 2023; 15:e50995. [PMID: 38259392 PMCID: PMC10801345 DOI: 10.7759/cureus.50995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/23/2023] [Indexed: 01/24/2024] Open
Abstract
Background Head and neck squamous cell carcinoma (HNSCC) is a prominent global cancer that manifests across diverse sites such as the oral cavity, oropharynx, and larynx. Human papillomavirus (HPV) infection and genetic alterations contribute to HNSCC development. Objective To investigate the complex role of breast carcinoma amplified sequence (BCAS3) in HNSCC pathogenesis. Methods We used multiple databases to analyze BCAS3 expression in HNSCC using The Cancer Genome Atlas-Head-Neck Squamous Cell Carcinoma (TCGA-HNSC) dataset and validated it in oral squamous cell carcinoma (OSCC) using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The BCAS3 gene and protein networks were analyzed to identify their functional pathways. Results The results revealed significant overexpression of BCAS3 was observed in HNSCC and OSCC tumors. Our study explores BCAS3's correlation with clinicopathological features and patient prognosis, suggesting its involvement in tumor aggressiveness. Notably, BCAS3 expression in HPV-positive and HPV-negative HNSCC samples emphasizes the intricate viral interactions. Kaplan-Meier plots demonstrate BCAS3's impact on patient survival. Furthermore, BCAS3's association between tumor immune infiltration and autophagy was uncovered. Conclusion Our study contributes to the understanding of BCAS3's role in HNSCC and suggests its potential as a therapeutic target and diagnostic marker for these malignancies.
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Affiliation(s)
- Devanand Challa
- Oral Medicine, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Chandra Pandi
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Balachander Kannan
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Vijayashree J Priyadharsini
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Paramasivam Arumugam
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
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3
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BCAS3 accelerates glioblastoma tumorigenesis by restraining the P53/GADD45α signaling pathway. Exp Cell Res 2022; 417:113231. [PMID: 35659972 DOI: 10.1016/j.yexcr.2022.113231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 05/17/2022] [Accepted: 05/28/2022] [Indexed: 11/20/2022]
Abstract
As in many other cancers, highly malignant proliferation and disordered cell division play irreplaceable roles in the exceedingly easy recurrence and complex progression of glioblastoma multiforme (GBM); however, mechanistic studies of the numerous regulators involved in this process are still insufficiently thorough. The role of BCAS3 has been studied in other cancers, but its role in GBM is unclear. Here, our goal was to investigate the expression pattern of BCAS3 in GBM and its potential mechanism of action. Using TCGA database and human GBM samples, we found that BCAS3 expression was up-regulated in GBM, and its high expression predicted poor prognosis. To further investigate the relationship between BCAS3 and GBM characteristics, we up-regulated and down-regulated BCAS3 expression in GBM to detect its effect on cell proliferation and cell cycle. At the same time, we established U87 cells stably overexpressing BCAS3 and generated an intracranial xenograft model to investigate the Potential role of BCAS3 in vivo. Finally, based on in vitro cell experiments and in vivo GBM xenograft models, we observed that BCAS3 significantly regulates GBM cell proliferation and cell cycle and that this regulation is associated with p53/GADD45α Signaling pathway. Taken together, our findings suggest that BCAS3 is inextricably linked to the progression of GBM and that targeting BCAS3 may have therapeutic effects in GBM patients.
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Wong WK, Troedson C, Damme M, Goetti R, Temple SEL, Schöls L, Balousha G, Prelog K, Buckley M, Roscioli T, Hengel H, Mohammad SS. BCAS3-Related Neurodevelopmental Disorder Shows Magnetic Resonance Imaging Features Resembling Brain Iron Accumulation. Mov Disord 2022; 37:870-872. [PMID: 34981858 DOI: 10.1002/mds.28915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/12/2021] [Accepted: 12/17/2021] [Indexed: 11/05/2022] Open
Affiliation(s)
- Wui-Kwan Wong
- TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Children's Hospital at Westmead Clinical School, Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales, Australia
| | - Christopher Troedson
- TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Markus Damme
- Institut für Biochemie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Robert Goetti
- Children's Hospital at Westmead Clinical School, Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales, Australia.,Department of Medical Imaging, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Suzanna E L Temple
- Department of Clinical Genetics, Liverpool Hospital, Sydney, New South Wales, Australia.,School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Ludger Schöls
- Department of Neurology and Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center of Neurodegenerative Diseases, Tübingen, Germany
| | - Ghassan Balousha
- Department of Pathology and Histology, Al-Quds University, Eastern Jerusalem, Palestine
| | - Kristina Prelog
- Department of Medical Imaging, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Michael Buckley
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, Australia
| | - Tony Roscioli
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia.,Neuroscience Research Australia and Prince of Wales Clinical School, University of New South Wales, Sydney, Australia
| | - Holger Hengel
- Department of Neurology and Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center of Neurodegenerative Diseases, Tübingen, Germany
| | - Shekeeb S Mohammad
- TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Children's Hospital at Westmead Clinical School, Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales, Australia
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5
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Zhou Z, Qiu R, Liu W, Yang T, Li G, Huang W, Teng X, Yang Y, Yu H, Yang Y, Wang Y. BCAS3 exhibits oncogenic properties by promoting CRL4A-mediated ubiquitination of p53 in breast cancer. Cell Prolif 2021; 54:e13088. [PMID: 34240781 PMCID: PMC8349660 DOI: 10.1111/cpr.13088] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/10/2021] [Accepted: 06/13/2021] [Indexed: 12/12/2022] Open
Abstract
Objectives Breast cancer‐amplified sequence 3 (BCAS3) was initially found to be amplified in human breast cancer (BRCA); however, there has been little consensus on the functions of BCAS3 in breast tumours. Materials and methods We analysed BCAS3 expression in BRCA using bio‐information tools. Affinity purification and mass spectrometry were employed to identify BCAS3‐associated proteins. GST pull‐down and ubiquitination assays were performed to analyse the interaction mechanism between BCAS3/p53 and CUL4A‐RING E3 ubiquitin ligase (CRL4A) complex. BCAS3 was knocked down individually or in combination with p53 in MCF‐7 cells to further explore the biological functions of the BCAS3/p53 axis. The clinical values of BCAS3 for BRCA progression were evaluated via semiquantitative immunohistochemistry (IHC) analysis and Cox regression. Results We reported that the expression level of BCAS3 in BRCA was higher than that in adjacent normal tissues. High BCAS3 expression promoted growth, inhibited apoptosis and conferred chemoresistance in breast cancer cells. Mechanistically, BCAS3 overexpression fostered BRCA cell growth by interacting with the CRL4A complex and promoting ubiquitination and proteasomal degradation of p53. Furthermore, BCAS3 could regulate cell growth, apoptosis and chemoresistance through a p53‐mediated mechanism. Clinically, BCAS3 overexpression was significantly correlated with a malignant phenotype. Moreover, higher expression of BCAS3 correlates with shorter overall survival (OS) in BRCA. Conclusions The functional characterization of BCAS3 offers new insights into the oncogenic properties and chemotherapy resistance in breast cancer.
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Affiliation(s)
- Zhe Zhou
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Rongfang Qiu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Zhejiang Provincial Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Hospital of Zhejiang University, Lishui, China
| | - Wei Liu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Tianshu Yang
- Beijing Key Laboratory for Tumor Invasion and Metastasis, Advanced Innovation Center for Human Brain Protection, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Gen Li
- Beijing Key Laboratory for Tumor Invasion and Metastasis, Advanced Innovation Center for Human Brain Protection, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Wei Huang
- Beijing Key Laboratory for Tumor Invasion and Metastasis, Advanced Innovation Center for Human Brain Protection, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Xu Teng
- Beijing Key Laboratory for Tumor Invasion and Metastasis, Advanced Innovation Center for Human Brain Protection, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Yunkai Yang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hefen Yu
- Beijing Key Laboratory for Tumor Invasion and Metastasis, Advanced Innovation Center for Human Brain Protection, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Yang Yang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Zhejiang Provincial Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Hospital of Zhejiang University, Lishui, China
| | - Yan Wang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Beijing Key Laboratory for Tumor Invasion and Metastasis, Advanced Innovation Center for Human Brain Protection, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Hengel H, Hannan SB, Dyack S, MacKay SB, Schatz U, Fleger M, Kurringer A, Balousha G, Ghanim Z, Alkuraya FS, Alzaidan H, Alsaif HS, Mitani T, Bozdogan S, Pehlivan D, Lupski JR, Gleeson JJ, Dehghani M, Mehrjardi MY, Sherr EH, Parks KC, Argilli E, Begtrup A, Galehdari H, Balousha O, Shariati G, Mazaheri N, Malamiri RA, Pagnamenta AT, Kingston H, Banka S, Jackson A, Osmond M, Rieß A, Haack TB, Nägele T, Schuster S, Hauser S, Admard J, Casadei N, Velic A, Macek B, Ossowski S, Houlden H, Maroofian R, Schöls L, Maroofian R, Schöls L. Bi-allelic loss-of-function variants in BCAS3 cause a syndromic neurodevelopmental disorder. Am J Hum Genet 2021; 108:1069-1082. [PMID: 34022130 PMCID: PMC8206390 DOI: 10.1016/j.ajhg.2021.04.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/29/2021] [Indexed: 12/27/2022] Open
Abstract
BCAS3 microtubule-associated cell migration factor (BCAS3) is a large, highly conserved cytoskeletal protein previously proposed to be critical in angiogenesis and implicated in human embryogenesis and tumorigenesis. Here, we established BCAS3 loss-of-function variants as causative for a neurodevelopmental disorder. We report 15 individuals from eight unrelated families with germline bi-allelic loss-of-function variants in BCAS3. All probands share a global developmental delay accompanied by pyramidal tract involvement, microcephaly, short stature, strabismus, dysmorphic facial features, and seizures. The human phenotype is less severe compared with the Bcas3 knockout mouse model and cannot be explained by angiogenic defects alone. Consistent with being loss-of-function alleles, we observed absence of BCAS3 in probands' primary fibroblasts. By comparing the transcriptomic and proteomic data based on probands' fibroblasts with those of the knockout mouse model, we identified similar dysregulated pathways resulting from over-representation analysis, while the dysregulation of some proposed key interactors could not be confirmed. Together with the results from a tissue-specific Drosophila loss-of-function model, we demonstrate a vital role for BCAS3 in neural tissue development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Reza Maroofian
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK.
| | - Ludger Schöls
- Department of Neurology and Hertie-Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany; German Center of Neurodegenerative Diseases, 72076 Tübingen, Germany.
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7
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Hennig EE, Kluska A, Piątkowska M, Kulecka M, Bałabas A, Zeber-Lubecka N, Goryca K, Ambrożkiewicz F, Karczmarski J, Olesiński T, Zyskowski Ł, Ostrowski J. GWAS Links New Variant in Long Non-Coding RNA LINC02006 with Colorectal Cancer Susceptibility. BIOLOGY 2021; 10:biology10060465. [PMID: 34070617 PMCID: PMC8229782 DOI: 10.3390/biology10060465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 01/10/2023]
Abstract
Simple Summary Identifying risk factors for cancer development can allow for appropriate stratification and surveillance of individuals at risk, increasing their chances of benefiting from early disease detection; however, most of the genetic factors contributing to the risk of colorectal cancer (CRC) remain undetermined. Here, we adopted a new approach for selecting index polymorphism for further validation in combination with a genome-wide association study of pooled DNA samples for CRC susceptibility variants in the Polish population. This study, including 2013 patients and controls, uncovered five susceptibility loci not previously reported for CRC. Four of identified variants were located within genes likely involved in tumor invasiveness and metastasis, suggesting that they could be markers of poor prognosis in CRC patients. Our results provide evidence that conducting association studies on small but homogenous populations can help us discover new common risk variants specific to the studied population. Abstract Despite great efforts, most of the genetic factors contributing to the risk of colorectal cancer (CRC) remain undetermined. Including small but homogenous populations in genome-wide association studies (GWAS) can help us discover new common risk variants specific to the studied population. In this study, including 465 CRC patients and 1548 controls, a pooled DNA samples-based GWAS was conducted in search of genetic variants associated with CRC in a Polish population. Combined with a new method of selecting single-nucleotide polymorphisms (SNPs) for verification in individual DNA samples, this approach allowed the detection of five new susceptibility loci not previously reported for CRC. The discovered loci were found to explain 10% of the overall risk of developing CRC. The strongest association was observed for rs10935945 in long non-coding RNA LINC02006 (3q25.2). Three other SNPs were also located within genes (rs17575184 in NEGR1, rs11060839 in PIWIL1, rs12935896 in BCAS3), while one was intergenic (rs9927668 at 16p13.2). An expression quantitative trait locus (eQTL) bioinformatic analysis suggested that these polymorphisms may affect transcription factor binding sites. In conclusion, four of the identified variants were located within genes likely involved in tumor invasiveness and metastasis. Therefore, they could possibly be markers of poor prognosis in CRC patients.
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Affiliation(s)
- Ewa E. Hennig
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781 Warsaw, Poland; (M.K.); (N.Z.-L.); (J.O.)
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.K.); (M.P.); (A.B.); (K.G.); (F.A.); (J.K.)
- Correspondence:
| | - Anna Kluska
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.K.); (M.P.); (A.B.); (K.G.); (F.A.); (J.K.)
| | - Magdalena Piątkowska
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.K.); (M.P.); (A.B.); (K.G.); (F.A.); (J.K.)
| | - Maria Kulecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781 Warsaw, Poland; (M.K.); (N.Z.-L.); (J.O.)
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.K.); (M.P.); (A.B.); (K.G.); (F.A.); (J.K.)
| | - Aneta Bałabas
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.K.); (M.P.); (A.B.); (K.G.); (F.A.); (J.K.)
| | - Natalia Zeber-Lubecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781 Warsaw, Poland; (M.K.); (N.Z.-L.); (J.O.)
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.K.); (M.P.); (A.B.); (K.G.); (F.A.); (J.K.)
| | - Krzysztof Goryca
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.K.); (M.P.); (A.B.); (K.G.); (F.A.); (J.K.)
| | - Filip Ambrożkiewicz
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.K.); (M.P.); (A.B.); (K.G.); (F.A.); (J.K.)
| | - Jakub Karczmarski
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.K.); (M.P.); (A.B.); (K.G.); (F.A.); (J.K.)
| | - Tomasz Olesiński
- Department of Gastroenterological Oncology, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (T.O.); (Ł.Z.)
| | - Łukasz Zyskowski
- Department of Gastroenterological Oncology, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (T.O.); (Ł.Z.)
| | - Jerzy Ostrowski
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781 Warsaw, Poland; (M.K.); (N.Z.-L.); (J.O.)
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.K.); (M.P.); (A.B.); (K.G.); (F.A.); (J.K.)
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8
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Luo C, Huang J, Guo Z, Guo J, Zeng X, Li Y, Liu M. Methylated biomarkers for breast cancer identified through public database analysis and plasma target capture sequencing. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:683. [PMID: 33987381 PMCID: PMC8106113 DOI: 10.21037/atm-21-1128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Background Aberrant methylation is common during the early stage of cancer development. This study was designed to investigate DNA methylation as biomarker for breast cancer. Methods Public database analysis and methylation-specific whole-gene sequencing were conducted to identify methylated biomarkers that would enable early non-invasive diagnosis of breast cancer. Firstly, the data was obtained from the TCGA Database and the Blueprint Epigenome Database. Secondly, methylation-specific whole-gene sequencing was conducted in 10 female patients with early-stage breast cancer and 10 healthy female volunteers from Nanfang Hospital of Southern Medical University between March 2018 and July 2018. Thirdly, the R language was used for data analysis, and KEGG and DAVID online tool was used for annotations. Results We found that methylation levels at 13 cytosine-phosphate-guanine (CpG) sites (cg04066177, cg04281344, cg05995576, cg06221609, cg08642731, cg11388802, cg12665414, cg14557216, cg19404723, cg19457909, cg24570211, cg25818763, and cg26215982) in the malignant tissue DNA were highly comparable to those of circulating cell-free DNA (cfDNA) of breast cancer patients, but were significantly different from those of normal tissue DNA, cfDNA of healthy women, and leukocyte DNA. In addition, three CpG sites (cg04281344, cg24570211, and cg26215982) were confirmed in clinical research, which showed that the sensitivity and specificity of these CpGs as biomarkers for breast cancer were 69.4–83.7% and 85.7–88.6%, respectively. Conclusions New biomarkers were identified and confirmed for breast cancer by comparing the methylation of tumour tissues, leukocytes, and non-plasma DNA.
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Affiliation(s)
- Can Luo
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jiaheng Huang
- Department of Surgery, First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhaoze Guo
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jingyun Guo
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaoqi Zeng
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yimin Li
- General Surgery, Yangjiang Hospital, Qiongzhong, China
| | - Minfeng Liu
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
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9
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Kojima W, Yamano K, Kosako H, Imai K, Kikuchi R, Tanaka K, Matsuda N. Mammalian BCAS3 and C16orf70 associate with the phagophore assembly site in response to selective and non-selective autophagy. Autophagy 2021; 17:2011-2036. [PMID: 33499712 PMCID: PMC8386740 DOI: 10.1080/15548627.2021.1874133] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Macroautophagy/autophagy is an intracellular degradation process that delivers cytosolic materials and/or damaged organelles to lysosomes. De novo synthesis of the autophagosome membrane occurs within a phosphatidylinositol-3-phosphate-rich region of the endoplasmic reticulum, and subsequent expansion is critical for cargo encapsulation. This process is complex, especially in mammals, with many regulatory factors. In this study, by utilizing PRKN (parkin RBR E3 ubiquitin protein ligase)-mediated mitochondria autophagy (mitophagy)-inducing conditions in conjunction with chemical crosslinking and mass spectrometry, we identified human BCAS3 (BCAS3 microtubule associated cell migration factor) and C16orf70 (chromosome 16 open reading frame 70) as novel proteins that associate with the autophagosome formation site during both non-selective and selective autophagy. We demonstrate that BCAS3 and C16orf70 form a complex and that their association with the phagophore assembly site requires both proteins. In silico structural modeling, mutational analyses in cells and in vitro phosphoinositide-binding assays indicate that the WD40 repeat domain in human BCAS3 directly binds phosphatidylinositol-3-phosphate. Furthermore, overexpression of the BCAS3-C16orf70 complex affects the recruitment of several core autophagy proteins to the phagophore assembly site. This study demonstrates regulatory roles for human BCAS3 and C16orf70 in autophagic activity. Abbreviations: AO: antimycin A and oligomycin; Ash: assembly helper; ATG: autophagy-related; BCAS3: BCAS3 microtubule associated cell migration factor; C16orf70: chromosome 16 open reading frame 70; DAPI: 4‘,6-diamidino-2-phenylindole; DKO: double knockout; DMSO: dimethyl sulfoxide; ER: endoplasmic reticulum; fluoppi: fluorescent-based technology detecting protein-protein interactions; FIS1: fission, mitochondrial 1; FKBP: FKBP prolyl isomerase family member 1C; FRB: FKBP-rapamycin binding; hAG: humanized azami-green; IP: immunoprecipitation; IRES: internal ribosome entry site; KO: knockout; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MFN2: mitofusin 2; MS: mass spectrometry; MT-CO2: mitochondrially encoded cytochrome c oxidase II; mtDNA: mitochondrial DNA; OPTN: optineurin; PFA: paraformaldehyde; PE: phosphatidylethanolamine; PtdIns3K: phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate; PtdIns(3,5)P2: phosphatidylinositol-3,5-bisphosphate; PINK1: PTEN induced kinase 1; PRKN/Parkin: parkin RBR E3 ubiquitin protein ligase; PROPPIN: β-propellers that bind polyphosphoinositides; RB1CC1/FIP200: RB1 inducible coiled-coil 1; TOMM20: translocase of outer mitochondrial membrane 20; ULK1: unc-51 like autophagy activating kinase 1; WDR45B/WIPI3: WD repeat domain 45B; WDR45/WIPI4: WD repeat domain 45; WIPI: WD repeat domain, phosphoinositide interacting; WT: wild type; ZFYVE1/DFCP1: zinc finger FYVE-type containing 1
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Affiliation(s)
- Waka Kojima
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.,Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Japan
| | - Koji Yamano
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima, Japan
| | - Kenichiro Imai
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.,Molecular Profiling Research Center for Drug Discovery (Molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Reika Kikuchi
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Noriyuki Matsuda
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
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10
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Joshi D, Inamdar MS. Rudhira/BCAS3 couples microtubules and intermediate filaments to promote cell migration for angiogenic remodeling. Mol Biol Cell 2019; 30:1437-1450. [PMID: 30995157 PMCID: PMC6724693 DOI: 10.1091/mbc.e18-08-0484] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Blood vessel formation requires endothelial cell (EC) migration that depends on dynamic remodeling of the cytoskeleton. Rudhira/Breast Carcinoma Amplified Sequence 3 (BCAS3) is a cytoskeletal protein essential for EC migration and sprouting angiogenesis during mouse development and is implicated in metastatic disease. Here, we report that Rudhira mediates cytoskeleton organization and dynamics during EC migration. Rudhira binds to both microtubules (MTs) and vimentin intermediate filaments (IFs) and stabilizes MTs. Rudhira depletion impairs cytoskeletal cross-talk, MT stability, and hence focal adhesion disassembly. The BCAS3 domain of Rudhira is necessary and sufficient for MT-IF cross-linking and cell migration. Pharmacologically restoring MT stability rescues gross cytoskeleton organization and angiogenic sprouting in Rudhira-depleted cells. Our study identifies the novel and essential role of Rudhira in cytoskeletal cross-talk and assigns function to the conserved BCAS3 domain. Targeting Rudhira could allow tissue-restricted cytoskeleton modulation to control cell migration and angiogenesis in development and disease.
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Affiliation(s)
- Divyesh Joshi
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Maneesha S Inamdar
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India.,Institute for Stem Cell Biology and Regenerative Medicine, Bangalore 560065, India
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11
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Zhu W, Deng Y, Zhou X. Multiple Membrane Transporters and Some Immune Regulatory Genes are Major Genetic Factors to Gout. Open Rheumatol J 2018; 12:94-113. [PMID: 30123371 PMCID: PMC6062909 DOI: 10.2174/1874312901812010094] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 05/30/2018] [Accepted: 06/20/2018] [Indexed: 01/10/2023] Open
Abstract
Gout is a common form of inflammatory arthritis caused by hyperuricemia and the deposition of Monosodium Urate (MSU) crystals. It is also considered as a complex disorder in which multiple genetic factors have been identified in association with its susceptibility and/or clinical outcomes. Major genes that were associated with gout include URAT1, GLUT9, OAT4, NPT1 (SLC17A1), NPT4 (SLC17A3), NPT5 (SLC17A4), MCT9, ABCG2, ABCC4, KCNQ1, PDZK1, NIPAL1, IL1β, IL-8, IL-12B, IL-23R, TNFA, MCP-1/CCL2, NLRP3, PPARGC1B, TLR4, CD14, CARD8, P2X7R, EGF, A1CF, HNF4G and TRIM46, LRP2, GKRP, ADRB3, ADH1B, ALDH2, COMT, MAOA, PRKG2, WDR1, ALPK1, CARMIL (LRRC16A), RFX3, BCAS3, CNIH-2, FAM35A and MYL2-CUX2. The proteins encoded by these genes mainly function in urate transport, inflammation, innate immunity and metabolism. Understanding the functions of gout-associated genes will provide important insights into future studies to explore the pathogenesis of gout, as well as to develop targeted therapies for gout.
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Affiliation(s)
- Weifeng Zhu
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Nanchang University, Nanchang, China.,Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Yan Deng
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA.,Department of Ophthalmology of Children, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaodong Zhou
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
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12
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Hishida A, Nakatochi M, Akiyama M, Kamatani Y, Nishiyama T, Ito H, Oze I, Nishida Y, Hara M, Takashima N, Turin TC, Watanabe M, Suzuki S, Ibusuki R, Shimoshikiryo I, Nakamura Y, Mikami H, Ikezaki H, Furusyo N, Kuriki K, Endoh K, Koyama T, Matsui D, Uemura H, Arisawa K, Sasakabe T, Okada R, Kawai S, Naito M, Momozawa Y, Kubo M, Wakai K. Genome-Wide Association Study of Renal Function Traits: Results from the Japan Multi-Institutional Collaborative Cohort Study. Am J Nephrol 2018; 47:304-316. [PMID: 29779033 DOI: 10.1159/000488946] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/29/2018] [Indexed: 11/19/2022]
Abstract
BACKGROUND Chronic kidney disease (CKD) is a rapidly growing, worldwide public health problem. Recent advances in genome-wide-association studies (GWAS) revealed several genetic loci associated with renal function traits worldwide. METHODS We investigated the association of genetic factors with the levels of serum creatinine (SCr) and the estimated glomerular filtration rate (eGFR) in Japanese population-based cohorts analyzing the GWAS imputed data with 11,221 subjects and 12,617,569 variants, and replicated the findings with the 148,829 hospital-based Japanese subjects. RESULTS In the discovery phase, 28 variants within 4 loci (chromosome [chr] 2 with 8 variants including rs3770636 in the LDL receptor related protein 2 gene locus, on chr 5 with 2 variants including rs270184, chr 17 with 15 variants including rs3785837 in the BCAS3 gene locus, and chr 18 with 3 variants including rs74183647 in the nuclear factor of -activated T-cells 1 gene locus) reached the suggestive level of p < 1 × 10-6 in association with eGFR and SCr, and 2 variants on chr 4 (including rs78351985 in the microsomal triglyceride transfer protein gene locus) fulfilled the suggestive level in association with the risk of CKD. In the replication phase, 25 variants within 3 loci (chr 2 with 7 variants, chr 17 with 15 variants and chr 18 with 3 variants) in association with eGFR and SCr, and 2 variants on chr 4 associated with the risk of CKD became nominally statistically significant after Bonferroni correction, among which 15 variants on chr 17 and 3 variants on chr 18 reached genome-wide significance of p < 5 × 10-8 in the combined study meta-analysis. The associations of the loci on chr 2 and 18 with eGFR and SCr as well as that on chr 4 with CKD risk have not been previously reported in the Japanese and East Asian populations. CONCLUSION Although the present GWAS of renal function traits included the largest sample of Japanese participants to date, we did not identify novel loci for renal traits. However, we identified the novel associations of the genetic loci on chr 2, 4, and 18 with renal function traits in the Japanese population, suggesting these are transethnic loci. Further investigations of these associations are expected to further validate our findings for the potential establishment of personalized prevention of renal disease in the Japanese and East Asian populations.
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MESH Headings
- Adult
- Aged
- Asian People/genetics
- Chromosomes, Human, Pair 18/genetics
- Chromosomes, Human, Pair 2/genetics
- Chromosomes, Human, Pair 4/genetics
- Cohort Studies
- Creatinine/blood
- Female
- Genetic Loci
- Genetic Predisposition to Disease
- Genome-Wide Association Study
- Glomerular Filtration Rate
- Humans
- Japan/epidemiology
- Kidney/physiopathology
- Male
- Middle Aged
- Polymorphism, Single Nucleotide
- Prevalence
- Renal Insufficiency, Chronic/blood
- Renal Insufficiency, Chronic/epidemiology
- Renal Insufficiency, Chronic/genetics
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Affiliation(s)
- Asahi Hishida
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masahiro Nakatochi
- Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - Masato Akiyama
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoichiro Kamatani
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takeshi Nishiyama
- Department of Public Health, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Hidemi Ito
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Isao Oze
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Yuichiro Nishida
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Megumi Hara
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Naoyuki Takashima
- Department of Health Science, Shiga University of Medical Science, Otsu, Japan
| | - Tanvir Chowdhury Turin
- Department of Family Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Miki Watanabe
- Department of Public Health, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Sadao Suzuki
- Department of Public Health, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Rie Ibusuki
- Department of International Island and Community Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Ippei Shimoshikiryo
- Department of International Island and Community Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Yohko Nakamura
- Cancer Prevention Center, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Haruo Mikami
- Cancer Prevention Center, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Hiroaki Ikezaki
- Department of Geriatric Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Norihiro Furusyo
- Department of Geriatric Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kiyonori Kuriki
- Laboratory of Public Health, School of Food and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
| | - Kaori Endoh
- Laboratory of Public Health, School of Food and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
| | - Teruhide Koyama
- Department of Epidemiology for Community Health and Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Daisuke Matsui
- Department of Epidemiology for Community Health and Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hirokazu Uemura
- Department of Preventive Medicine, Institute of Health Biosciences, University of Tokushima Graduate School, Tokushima, Japan
| | - Kokichi Arisawa
- Department of Preventive Medicine, Institute of Health Biosciences, University of Tokushima Graduate School, Tokushima, Japan
| | - Tae Sasakabe
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Rieko Okada
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Sayo Kawai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mariko Naito
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
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13
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Rudhira/BCAS3 is essential for mouse development and cardiovascular patterning. Sci Rep 2018; 8:5632. [PMID: 29618843 PMCID: PMC5884795 DOI: 10.1038/s41598-018-24014-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/22/2018] [Indexed: 01/23/2023] Open
Abstract
Rudhira/Breast Carcinoma Amplified Sequence 3 (BCAS3) is a cytoskeletal protein that promotes directional cell migration and angiogenesis in vitro and is implicated in human carcinomas and coronary artery disease. To study the role of Rudhira during development in vivo, we generated the first knockout mouse for rudhira and show that Rudhira is essential for mouse development. Rudhira null embryos die at embryonic day (E) 9.5 accompanied by severe vascular patterning defects in embryonic and extra-embryonic tissues. To identify the molecular processes downstream of rudhira, we analyzed the transcriptome of intact knockout yolk sacs. Genome-wide transcriptome analysis showed that Rudhira functions in angiogenesis and its related processes such as cell adhesion, extracellular matrix organization, peptidase activity and TGFβ signaling. Since Rudhira is also expressed in endothelial cells (ECs), we further generated Tie2Cre-mediated endothelial knockout (CKO) of rudhira. CKO embryos survive to E11.5 and similar to the global knockout, display gross vascular patterning defects, showing that endothelial Rudhira is vital for development. Further, Rudhira knockdown ECs in culture fail to sprout in a spheroid-sprouting assay, strongly supporting its role in vascular patterning. Our study identifies an essential role for Rudhira in blood vessel remodeling and provides a mouse model for cardiovascular development.
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14
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Byars SG, Huang QQ, Gray LA, Bakshi A, Ripatti S, Abraham G, Stearns SC, Inouye M. Genetic loci associated with coronary artery disease harbor evidence of selection and antagonistic pleiotropy. PLoS Genet 2017; 13:e1006328. [PMID: 28640878 PMCID: PMC5480811 DOI: 10.1371/journal.pgen.1006328] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 05/02/2017] [Indexed: 12/18/2022] Open
Abstract
Traditional genome-wide scans for positive selection have mainly uncovered selective sweeps associated with monogenic traits. While selection on quantitative traits is much more common, very few signals have been detected because of their polygenic nature. We searched for positive selection signals underlying coronary artery disease (CAD) in worldwide populations, using novel approaches to quantify relationships between polygenic selection signals and CAD genetic risk. We identified new candidate adaptive loci that appear to have been directly modified by disease pressures given their significant associations with CAD genetic risk. These candidates were all uniquely and consistently associated with many different male and female reproductive traits suggesting selection may have also targeted these because of their direct effects on fitness. We found that CAD loci are significantly enriched for lifetime reproductive success relative to the rest of the human genome, with evidence that the relationship between CAD and lifetime reproductive success is antagonistic. This supports the presence of antagonistic-pleiotropic tradeoffs on CAD loci and provides a novel explanation for the maintenance and high prevalence of CAD in modern humans. Lastly, we found that positive selection more often targeted CAD gene regulatory variants using HapMap3 lymphoblastoid cell lines, which further highlights the unique biological significance of candidate adaptive loci underlying CAD. Our study provides a novel approach for detecting selection on polygenic traits and evidence that modern human genomes have evolved in response to CAD-induced selection pressures and other early-life traits sharing pleiotropic links with CAD.
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Affiliation(s)
- Sean G. Byars
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Qin Qin Huang
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Lesley-Ann Gray
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Andrew Bakshi
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Samuli Ripatti
- Institute of Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Gad Abraham
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Stephen C. Stearns
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States of America
| | - Michael Inouye
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
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15
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Janssen SF, Gorgels TG, Ramdas WD, Klaver CC, van Duijn CM, Jansonius NM, Bergen AA. The vast complexity of primary open angle glaucoma: Disease genes, risks, molecular mechanisms and pathobiology. Prog Retin Eye Res 2013; 37:31-67. [DOI: 10.1016/j.preteyeres.2013.09.001] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 07/26/2013] [Accepted: 09/03/2013] [Indexed: 12/21/2022]
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16
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Ziebarth JD, Bhattacharya A, Cui Y. Integrative analysis of somatic mutations altering microRNA targeting in cancer genomes. PLoS One 2012; 7:e47137. [PMID: 23091610 PMCID: PMC3473044 DOI: 10.1371/journal.pone.0047137] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 09/11/2012] [Indexed: 12/13/2022] Open
Abstract
Determining the functional impact of somatic mutations is crucial to understanding tumorigenesis and metastasis. Recent sequences of several cancers have provided comprehensive lists of somatic mutations across entire genomes, enabling investigation of the functional impact of somatic mutations in non-coding regions. Here, we study somatic mutations in 3'UTRs of genes that have been identified in four cancers and computationally predict how they may alter miRNA targeting, potentially resulting in dysregulation of the expression of the genes harboring these mutations. We find that somatic mutations create or disrupt putative miRNA target sites in the 3'UTRs of many genes, including several genes, such as MITF, EPHA3, TAL1, SCG3, and GSDMA, which have been previously associated with cancer. We also integrate the somatic mutations with germline mutations and results of association studies. Specifically, we identify putative miRNA target sites in the 3'UTRs of BMPR1B, KLK3, and SPRY4 that are disrupted by both somatic and germline mutations and, also, are in linkage disequilibrium blocks with high scoring markers from cancer association studies. The somatic mutation in BMPR1B is located in a target site of miR-125b; germline mutations in this target site have previously been both shown to disrupt regulation of BMPR1B by miR-125b and linked with cancer.
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Affiliation(s)
- Jesse D. Ziebarth
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Anindya Bhattacharya
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Yan Cui
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
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17
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Jain M, Bhat GP, Vijayraghavan K, Inamdar MS. Rudhira/BCAS3 is a cytoskeletal protein that controls Cdc42 activation and directional cell migration during angiogenesis. Exp Cell Res 2012; 318:753-67. [PMID: 22300583 DOI: 10.1016/j.yexcr.2012.01.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2011] [Revised: 01/11/2012] [Accepted: 01/15/2012] [Indexed: 12/19/2022]
Abstract
Cell migration is a common cellular process in angiogenesis and tumor metastasis. Rudhira/BCAS3 (Breast Cancer Amplified Sequence 3) is a conserved protein expressed in the embryonic vasculature and malignant tumors. Here, we show for the first time that Rudhira plays an active role in directional cell migration. Rudhira depletion in endothelial cells inhibits Matrigel-induced tube formation and retards healing of wounded cell monolayers. We demonstrate that during wound healing, Rudhira rapidly re-localizes and promotes Cdc42 activation and recruitment to the leading edge of migrating cells. Rudhira deficient cells show impaired downstream signaling of Cdc42 leading to dramatic changes in actin organization and classic cell polarity defects such as loss of microtubule organizing center (MTOC) and Golgi re-orientation. Biochemical assays and co-localization studies show that Rudhira interacts with microtubules as well as intermediate filaments. Thus, Rudhira could control directional cell migration and angiogenesis by facilitating crosstalk between cytoskeletal elements.
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Affiliation(s)
- Mamta Jain
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
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18
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Josse R, Dumont J, Fautrel A, Robin MA, Guillouzo A. Identification of early target genes of aflatoxin B1 in human hepatocytes, inter-individual variability and comparison with other genotoxic compounds. Toxicol Appl Pharmacol 2012; 258:176-87. [DOI: 10.1016/j.taap.2011.10.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 10/17/2011] [Accepted: 10/26/2011] [Indexed: 12/26/2022]
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19
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Pozzesi N, Pierangeli S, Vacca C, Falchi L, Pettorossi V, Martelli MP, Thuy TT, Ninh PT, Liberati AM, Riccardi C, Sung TV, Delfino DV. Maesopsin 4-O-beta-D-glucoside, a natural compound isolated from the leaves of Artocarpus tonkinensis, inhibits proliferation and up-regulates HMOX1, SRXN1 and BCAS3 in acute myeloid leukemia. J Chemother 2011; 23:150-7. [PMID: 21742584 DOI: 10.1179/joc.2011.23.3.150] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
The leaves of Artocarpus tonkinensis are used in Vietnamese traditional medicine for treatment of arthritis, and the compound maesopsin 4-O-β-D-glucoside (TAT-2), isolated from them, inhibits the proliferation of activated T cells. Our goal was to test the anti-proliferative activity of TAT-2 on the T-cell leukemia, Jurkat, and on the acute myeloid leukemia, OCI-AML. TAT-2 inhibited the growth of OCI-AML (and additional acute myeloid leukemia cells) but not Jurkat cells. Growth inhibition was shown to be due to inhibition of proliferation rather than increase in cell death. Analysis of cytokine release showed that TAT-2 stimulated the release of TGF-β, yet TGF-β neutralization did not reverse the maesopsin-dependent effect. Gene expression profiling determined that maesopsin modulated 19 identifiable genes. Transcription factor CP2 was the gene most significantly modulated. Real-time PCR validated that up-regulation of sulphiredoxin 1 homolog (SRXN1), hemeoxygenase 1 (HMOX1), and breast carcinoma amplified sequence 3 (BCAS3) were consistently modulated.
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Affiliation(s)
- N Pozzesi
- Section of Pharmacology, Toxicology and Chemotherapy, Department of Clinical and Experimental Medicine, University of Perugia, Via del Giochetto, Perugia, Italy
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20
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Ota K, Dohi Y, Brydun A, Nakanome A, Ito S, Igarashi K. Identification of senescence-associated genes and their networks under oxidative stress by the analysis of Bach1. Antioxid Redox Signal 2011; 14:2441-51. [PMID: 21110788 DOI: 10.1089/ars.2010.3574] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Cellular senescence is induced in response to DNA damage, caused by genotoxic stresses, including oxidative stress, and serves as a barrier against malignant transformation. Tumor-suppressor protein p53 induces genes critical for implementing cellular senescence. However, the identities of p53 target genes and other regulators that achieve senescence under oxidative stress remain to be elucidated. Effector genes for oxidative stress-induced cellular senescence were sought, based on the fact that transcription factor Bach1 inhibits this response by impeding the transcriptional activity of p53. pRb became hypophosphorylated more rapidly in Bach1-deficient MEFs than in wild-type cells, suggesting that pRb activation was involved in their senescence. Bach1-deficient MEFs bypassed the senescence state when the expression of a subset of p53 target genes, including p21, Pai1, Noxa, and Perp, was simultaneously reduced by using RNAi. Combined knockdown of p21 and pRb resulted in vigorous re-proliferation. These results suggest that oxidative stress-induced cellular senescence is registered by multiple p53 target genes, which arrest proliferation redundantly, in part by activating pRb. Our elucidations contrast with previous reports describing monopolistic regulations of senescence by single p53 target genes.
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Affiliation(s)
- Kazushige Ota
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai, Japan
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Gonzalez Bosquet J, Peedicayil A, Maguire J, Chien J, Rodriguez GC, Whitaker R, Petitte JN, Anderson KE, Barnes HJ, Shridhar V, Cliby WA. Comparison of gene expression patterns between avian and human ovarian cancers. Gynecol Oncol 2010; 120:256-64. [PMID: 21093898 DOI: 10.1016/j.ygyno.2010.10.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2010] [Revised: 09/01/2010] [Accepted: 10/22/2010] [Indexed: 12/27/2022]
Abstract
OBJECTIVES A putative model of spontaneous cancer has been described in the laying hen that bears significant similarities to human ovarian cancer. Our objective was to characterize and compare the patterns of gene expression in chicken and human forms of this disease. METHODS RNA from 20 localized and metastatic ovarian and oviductal chicken tumor samples was isolated, amplified using in vitro transcription, and hybridized against normal ovarian epithelium to a customized cDNA microarray constructed for these studies. Differentially expressed genes were identified for localized ovarian, metastatic ovarian, and oviductal (or tubal) cancer by class comparison using BRB-ArrayTools. Results were validated with semi-quantitative PCR. A gene list (prediction model) constructed with the class prediction tool was used in a human ovarian cancer microarray obtained from the GEO datasets (GSE6008) in order to compare these results across species. RESULTS Class comparison analysis between localized ovarian, metastatic ovarian and oviductal cancer yielded 41 different informative probes that coded for 27 unique genes. Localized ovarian samples clustered between metastatic ovarian and oviductal cancer samples. Using our chicken data as a training set and leaving oviductal samples out of the analysis, we created a prediction model that classified early stage and advanced stage human ovarian cancer gene expression arrays with 78% overall accuracy. CONCLUSIONS Gene expression of spontaneous ovarian cancer in the chicken is comparable to gene expression patterns of human ovarian cancer.
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Affiliation(s)
- Jesus Gonzalez Bosquet
- Gynecologic Oncology, Department of Women's Oncology, Moffitt Cancer and Research Center, Tampa, FL 33612, USA.
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Venu P, Chakraborty S, Inamdar MS. Analysis of long-term culture properties and pluripotent character of two sibling human embryonic stem cell lines derived from discarded embryos. In Vitro Cell Dev Biol Anim 2010; 46:200-5. [PMID: 20178003 PMCID: PMC2855808 DOI: 10.1007/s11626-010-9277-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Accepted: 01/14/2010] [Indexed: 11/24/2022]
Abstract
We had earlier reported the derivation and characterization of two new sibling human embryonic stem cell lines BJNhem19 and BJNhem20, from discarded grade III embryos of Indian origin. We report here the characteristics of the two sibling cell lines after long-term continuous culture for over 2 yr during which they have been passaged over 200 times. We show that both cell lines adapt well to culture on various mouse and human feeders as well as in feeder-free conditions. The cells show normal diploid karyotype and continue to express all pluripotency markers. Both cell lines differentiate to derivatives of all three germ layers in vitro. However as reported earlier, BJNhem19 is unable to generate teratomas in nude or SCID mice or differentiate to beating cardiomyocytes when tested over several passages during long-term stable culture. On the other hand, the cardiac differentiation capacity of BJNhem20 is greatly increased, and it can generate beating cardiomyocytes that proliferate when isolated and cultured further. In conclusion, the two cell lines have maintained a stable phenotype for over 2 yr and are indeed immortal. Their derivation from grade III embryos does not seem to have any adverse effect on their long-term phenotype. The cells can be obtained for research purposes from the UK Stem Cell Bank and from the authors.
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Affiliation(s)
- Parvathy Venu
- Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore 560064, India
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Inamdar MS, Venu P, Srinivas M, Rao K, VijayRaghavan K. Derivation and Characterization of Two Sibling Human Embryonic Stem Cell Lines From Discarded Grade III Embryos. Stem Cells Dev 2009; 18:423-33. [DOI: 10.1089/scd.2008.0131] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
| | - Parvathy Venu
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - M.S. Srinivas
- Bangalore Assisted Conception Centre, Bangalore, India
| | - Kamini Rao
- Bangalore Assisted Conception Centre, Bangalore, India
| | - K. VijayRaghavan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
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Abstract
Human embryonic stem cells (HESCs) are the in vitro descendants of the pluripotent inner cell mass (ICM) of human blastocyst stage embryos. HESCs can be kept undifferentiated in culture or be differentiated to tissues representing all three germ layers, both in vivo and in vitro. These properties make HESC-based therapy remarkably appealing for the treatment of various disorders. Upon transplantation in vivo, undifferentiated HESCs rapidly generate the formation of large tumors called teratomas. These are benign masses of haphazardly differentiated tissues. Teratomas also appear spontaneously in humans and in mice. When they also encompass a core of malignant undifferentiated cells, these tumors are defined as teratocarcinomas. These malignant undifferentiated cells are termed embryonic carcinoma (EC), and are the malignant counterparts of embryonic stem cells. Here we review the history of experimental teratomas and teratocarcinomas, from spontaneous teratocarcinomas in mice to induced teratomas by HESC transplantation. We then discuss cellular and molecular aspects of the tumorigenicity of HESCs. We also describe the utilization of HESC-induced teratomas for the modeling of early human embryogenesis and for modeling developmental diseases. The problem of HESC-induced teratomas may also impede or prevent future HESC-based therapies. We thus conclude with a survey of approaches to evade HESC-induced tumor formation.
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Affiliation(s)
- Barak Blum
- Stem Cells Unit, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
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