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Hu J, Wang SG, Hou Y, Chen Z, Liu L, Li R, Li N, Zhou L, Yang Y, Wang L, Wang L, Yang X, Lei Y, Deng C, Li Y, Deng Z, Ding Y, Kuang Y, Yao Z, Xun Y, Li F, Li H, Hu J, Liu Z, Wang T, Hao Y, Jiao X, Guan W, Tao Z, Ren S, Chen K. Multi-omic profiling of clear cell renal cell carcinoma identifies metabolic reprogramming associated with disease progression. Nat Genet 2024; 56:442-457. [PMID: 38361033 PMCID: PMC10937392 DOI: 10.1038/s41588-024-01662-5] [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: 02/20/2023] [Accepted: 01/10/2024] [Indexed: 02/17/2024]
Abstract
Clear cell renal cell carcinoma (ccRCC) is a complex disease with remarkable immune and metabolic heterogeneity. Here we perform genomic, transcriptomic, proteomic, metabolomic and spatial transcriptomic and metabolomic analyses on 100 patients with ccRCC from the Tongji Hospital RCC (TJ-RCC) cohort. Our analysis identifies four ccRCC subtypes including De-clear cell differentiated (DCCD)-ccRCC, a subtype with distinctive metabolic features. DCCD cancer cells are characterized by fewer lipid droplets, reduced metabolic activity, enhanced nutrient uptake capability and a high proliferation rate, leading to poor prognosis. Using single-cell and spatial trajectory analysis, we demonstrate that DCCD is a common mode of ccRCC progression. Even among stage I patients, DCCD is associated with worse outcomes and higher recurrence rate, suggesting that it cannot be cured by nephrectomy alone. Our study also suggests a treatment strategy based on subtype-specific immune cell infiltration that could guide the clinical management of ccRCC.
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Affiliation(s)
- Junyi Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shao-Gang Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yaxin Hou
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhaohui Chen
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lilong Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ruizhi Li
- Shanghai Luming Biotech, Shanghai, China
| | - Nisha Li
- Shanghai Luming Biotech, Shanghai, China
- Shanghai OE Biotech, Shanghai, China
| | - Lijie Zhou
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yu Yang
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Liping Wang
- Department of Pathology, Baylor Scott & White Medical Center, Temple, TX, USA
| | - Liang Wang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiong Yang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yichen Lei
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Changqi Deng
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhiyao Deng
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuhong Ding
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yingchun Kuang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhipeng Yao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Xun
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fan Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Heng Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jia Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zheng Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Hao
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuanmao Jiao
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Philadelphia, PA, USA
| | - Wei Guan
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Zhen Tao
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Tianjin's Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Shancheng Ren
- Department of Urology, Second Affiliated Hospital of Naval Medical University, Shanghai, China.
| | - Ke Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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2
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Urinary tract endometriosis masquerading as a renal mass in hepatocyte nuclear factor-1 beta gene mutation. Int Urol Nephrol 2022; 55:1383-1384. [PMID: 36370216 DOI: 10.1007/s11255-022-03411-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
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3
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Yang J, Bai X, Liu G, Li X. A transcriptional regulatory network of HNF4α and HNF1α involved in human diseases and drug metabolism. Drug Metab Rev 2022; 54:361-385. [PMID: 35892182 DOI: 10.1080/03602532.2022.2103146] [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: 01/07/2023]
Abstract
HNF4α and HNF1α are core transcription factors involved in the development and progression of a variety of human diseases and drug metabolism. They play critical roles in maintaining the normal growth and function of multiple organs, mainly the liver, and in the metabolism of endogenous and exogenous substances. The twelve isoforms of HNF4α may exhibit different physiological functions, and HNF4α and HNF1α show varying or even opposing effects in different types of diseases, particularly cancer. Additionally, the regulation of CYP450, phase II drug-metabolizing enzymes, and drug transporters is affected by several factors. This article aims to review the role of HNF4α and HNF1α in human diseases and drug metabolism, including their structures and physiological functions, affected diseases, regulated drug metabolism genes, influencing factors, and related mechanisms. We also propose a transcriptional regulatory network of HNF4α and HNF1α that regulates the expression of target genes related to disease and drug metabolism.
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Affiliation(s)
- Jianxin Yang
- Research Center for High Altitude Medicine, Qinghai University Medical College, Xining, China
| | - Xue Bai
- Research Center for High Altitude Medicine, Qinghai University Medical College, Xining, China
| | - Guiqin Liu
- Research Center for High Altitude Medicine, Qinghai University Medical College, Xining, China
| | - Xiangyang Li
- Research Center for High Altitude Medicine, Qinghai University Medical College, Xining, China.,State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
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4
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Li LM, Jiang BG, Sun LL. HNF1A:From Monogenic Diabetes to Type 2 Diabetes and Gestational Diabetes Mellitus. Front Endocrinol (Lausanne) 2022; 13:829565. [PMID: 35299962 PMCID: PMC8921476 DOI: 10.3389/fendo.2022.829565] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/03/2022] [Indexed: 12/12/2022] Open
Abstract
Diabetes, a disease characterized by hyperglycemia, has a serious impact on the lives and families of patients as well as on society. Diabetes is a group of highly heterogeneous metabolic diseases that can be classified as type 1 diabetes (T1D), type 2 diabetes (T2D), gestational diabetes mellitus (GDM), or other according to the etiology. The clinical manifestations are more or less similar among the different types of diabetes, and each type is highly heterogeneous due to different pathogenic factors. Therefore, distinguishing between various types of diabetes and defining their subtypes are major challenges hindering the precise treatment of the disease. T2D is the main type of diabetes in humans as well as the most heterogeneous. Fortunately, some studies have shown that variants of certain genes involved in monogenic diabetes also increase the risk of T2D. We hope this finding will enable breakthroughs regarding the pathogenesis of T2D and facilitate personalized treatment of the disease by exploring the function of the signal genes involved. Hepatocyte nuclear factor 1 homeobox A (HNF1α) is widely expressed in pancreatic β cells, the liver, the intestines, and other organs. HNF1α is highly polymorphic, but lacks a mutation hot spot. Mutations can be found at any site of the gene. Some single nucleotide polymorphisms (SNPs) cause maturity-onset diabetes of the young type 3 (MODY3) while some others do not cause MODY3 but increase the susceptibility to T2D or GDM. The phenotypes of MODY3 caused by different SNPs also differ. MODY3 is among the most common types of MODY, which is a form of monogenic diabetes mellitus caused by a single gene mutation. Both T2D and GDM are multifactorial diseases caused by both genetic and environmental factors. Different types of diabetes mellitus have different clinical phenotypes and treatments. This review focuses on HNF1α gene polymorphisms, HNF1A-MODY3, HNF1A-associated T2D and GDM, and the related pathogenesis and treatment methods. We hope this review will provide a valuable reference for the precise and individualized treatment of diabetes caused by abnormal HNF1α by summarizing the clinical heterogeneity of blood glucose abnormalities caused by HNF1α mutation.
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Affiliation(s)
- Li-Mei Li
- Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Bei-Ge Jiang
- Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
- *Correspondence: Bei-Ge Jiang, ; Liang-Liang Sun,
| | - Liang-Liang Sun
- Department of Endocrinology and Metabolism, Changzheng Hospital, Naval Medical University, Shanghai, China
- *Correspondence: Bei-Ge Jiang, ; Liang-Liang Sun,
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5
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Teeli AS, Łuczyńska K, Haque E, Gayas MA, Winiarczyk D, Taniguchi H. Disruption of Tumor Suppressors HNF4α/HNF1α Causes Tumorigenesis in Liver. Cancers (Basel) 2021; 13:cancers13215357. [PMID: 34771521 PMCID: PMC8582545 DOI: 10.3390/cancers13215357] [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: 09/13/2021] [Revised: 10/14/2021] [Accepted: 10/18/2021] [Indexed: 12/18/2022] Open
Abstract
The hepatocyte nuclear factor-4α (HNF4α) and hepatocyte nuclear factor-1α (HNF1α) are transcription factors that influence the development and maintenance of homeostasis in a variety of tissues, including the liver. As such, disruptions in their transcriptional networks can herald a number of pathologies, such as tumorigenesis. Largely considered tumor suppressants in liver cancer, these transcription factors regulate key events of inflammation, epithelial-mesenchymal transition, metabolic reprogramming, and the differentiation status of the cell. High-throughput analysis of cancer cell genomes has identified a number of hotspot mutations in HNF1α and HNF4α in liver cancer. Such results also showcase HNF1α and HNF4α as important therapeutic targets helping us step into the era of personalized medicine. In this review, we update current findings on the roles of HNF1α and HNF4α in liver cancer development and progression. It covers the molecular mechanisms of HNF1α and HNF4α dysregulation and also highlights the potential of HNF4α as a therapeutic target in liver cancer.
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Affiliation(s)
- Aamir Salam Teeli
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, 05-552 Jastrzebiec, Poland; (A.S.T.); (K.Ł.); (E.H.); (D.W.)
| | - Kamila Łuczyńska
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, 05-552 Jastrzebiec, Poland; (A.S.T.); (K.Ł.); (E.H.); (D.W.)
| | - Effi Haque
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, 05-552 Jastrzebiec, Poland; (A.S.T.); (K.Ł.); (E.H.); (D.W.)
| | - Mohmmad Abrar Gayas
- Department of Surgery and Radiology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Jammu 19000, India;
| | - Dawid Winiarczyk
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, 05-552 Jastrzebiec, Poland; (A.S.T.); (K.Ł.); (E.H.); (D.W.)
| | - Hiroaki Taniguchi
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, 05-552 Jastrzebiec, Poland; (A.S.T.); (K.Ł.); (E.H.); (D.W.)
- Correspondence:
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6
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Chandra S, Srinivasan S, Batra J. Hepatocyte nuclear factor 1 beta: A perspective in cancer. Cancer Med 2021; 10:1791-1804. [PMID: 33580750 PMCID: PMC7940219 DOI: 10.1002/cam4.3676] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 12/17/2022] Open
Abstract
Hepatocyte nuclear factor 1 beta (HNF1 β/B) exists as a homeobox transcription factor having a vital role in the embryonic development of organs mainly liver, kidney and pancreas. Initially described as a gene causing maturity‐onset diabetes of the young (MODY), HNF1β expression deregulation and single nucleotide polymorphisms in HNF1β have now been associated with several tumours including endometrial, prostate, ovarian, hepatocellular, renal and colorectal cancers. Its function has been studied either as homodimer or heterodimer with HNF1α. In this review, the role of HNF1B in different cancers will be discussed along with the role of its splice variants, and its emerging role as a potential biomarker in cancer.
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Affiliation(s)
- Shubhra Chandra
- Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology, Brisbane, QLD, Australia.,Translational Research Institute, Woolloongabba, QLD, Australia
| | - Srilakshmi Srinivasan
- Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology, Brisbane, QLD, Australia.,Translational Research Institute, Woolloongabba, QLD, Australia
| | - Jyotsna Batra
- Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology, Brisbane, QLD, Australia.,Translational Research Institute, Woolloongabba, QLD, Australia
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7
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HNF1β is a sensitive and specific novel marker for yolk sac tumor: a tissue microarray analysis of 601 testicular germ cell tumors. Mod Pathol 2020; 33:2354-2360. [PMID: 32561848 DOI: 10.1038/s41379-020-0597-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/04/2020] [Accepted: 06/05/2020] [Indexed: 12/15/2022]
Abstract
Hepatocyte Nuclear Factor 1 beta (HNF1β) is a transcription factor which plays an important role during early organogenesis, especially of the pancreato-biliary and urogenital tract. Furthermore, HNF1β is an established marker in the differential diagnosis of ovarian cancer and shows a distinct nuclear expression in the clear cell carcinoma subtype. Recently, it has been described in yolk sac tumor, which represents a common component in many non-seminomatous germ cell tumors. Due to its broad histologic diversity, the diagnosis may be challenging and additional tools are very helpful in the workup of germ cell tumors. Immunohistochemistry was used to study HNF1β expression in a tissue microarray (TMA) of 601 testicular germ cell tumors including seminoma, embryonal carcinoma, yolk sac tumor, choriocarcinoma, teratoma, germ cell neoplasia in situ (GCNIS), and normal tissue. The expression pattern was compared to glypican 3 (GPC3) and α-fetoprotein (AFP), two markers currently in use for the detection of yolk sac tumor. HNF1β showed a distinct nuclear staining in comparison to the cytoplasmic pattern of GPC3 and AFP. The sensitivity and specificity of HNF1β were 85.4% and 96.5%, of GPC3 83.3% and 90.7%, of AFP 62.5% and 97.7%. We conclude that HNF1β allows a reliable distinction of yolk sac tumor from other germ cell tumor components. Therefore, we propose HNF1β as a novel and robust marker in the immunohistochemical workup of testicular germ cell tumors.
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8
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Analysis of expression, epigenetic, and genetic changes of HNF1B in 130 kidney tumours. Sci Rep 2020; 10:17151. [PMID: 33051485 PMCID: PMC7555858 DOI: 10.1038/s41598-020-74059-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 09/23/2020] [Indexed: 12/18/2022] Open
Abstract
Hepatocyte nuclear factor 1 beta (HNF1B) is a transcription factor which plays a crucial role in nephronogenesis, and its germline mutations have been associated with kidney developmental disorders. However, the effects of HNF1B somatic exonic mutations and its role in the pathogenesis of kidney tumours has not yet been elucidated. Depending on the type of the tumour HNF1B may act as a tumour suppressor or oncogene, although the exact mechanism by which HNF1B participates in the process of cancerogenesis is unknown. Using an immunohistochemical approach, and methylation and mutation analysis, we have investigated the expression, epigenetic, and genetic changes of HNF1B in 130 cases of renal tumours (121 renal cell carcinomas, 9 oncocytomas). In the subset of clear cell renal cell carcinoma (ccRCC), decreased HNF1B expression was associated with a higher tumour grade and higher T stage. The mutation analysis revealed no mutations in the analysed samples. Promoter methylation was detected in two ccRCCs and one oncocytoma. The results of our work on a limited sample set suggest that while in papillary renal cell carcinoma HNF1B functions as an oncogene, in ccRCC and chRCC it may act in a tumour suppressive fashion.
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Mullen DJ, Yan C, Kang DS, Zhou B, Borok Z, Marconett CN, Farnham PJ, Offringa IA, Rhie SK. TENET 2.0: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma. PLoS Genet 2020; 16:e1009023. [PMID: 32925947 PMCID: PMC7515200 DOI: 10.1371/journal.pgen.1009023] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 09/24/2020] [Accepted: 08/02/2020] [Indexed: 01/09/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related death and lung adenocarcinoma is its most common subtype. Although genetic alterations have been identified as drivers in subsets of lung adenocarcinoma, they do not fully explain tumor development. Epigenetic alterations have been implicated in the pathogenesis of tumors. To identify epigenetic alterations driving lung adenocarcinoma, we used an improved version of the Tracing Enhancer Networks using Epigenetic Traits method (TENET 2.0) in primary normal lung and lung adenocarcinoma cells. We found over 32,000 enhancers that appear differentially activated between normal lung and lung adenocarcinoma. Among the identified transcriptional regulators inactivated in lung adenocarcinoma vs. normal lung, NKX2-1 was linked to a large number of silenced enhancers. Among the activated transcriptional regulators identified, CENPA, FOXM1, and MYBL2 were linked to numerous cancer-specific enhancers. High expression of CENPA, FOXM1, and MYBL2 is particularly observed in a subgroup of lung adenocarcinomas and is associated with poor patient survival. Notably, CENPA, FOXM1, and MYBL2 are also key regulators of cancer-specific enhancers in breast adenocarcinoma of the basal subtype, but they are associated with distinct sets of activated enhancers. We identified individual lung adenocarcinoma enhancers linked to CENPA, FOXM1, or MYBL2 that were associated with poor patient survival. Knockdown experiments of FOXM1 and MYBL2 suggest that these factors regulate genes involved in controlling cell cycle progression and cell division. For example, we found that expression of TK1, a potential target gene of a MYBL2-linked enhancer, is associated with poor patient survival. Identification and characterization of key transcriptional regulators and associated enhancers in lung adenocarcinoma provides important insights into the deregulation of lung adenocarcinoma epigenomes, highlighting novel potential targets for clinical intervention.
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Affiliation(s)
- Daniel J. Mullen
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States of America
- Department of Surgery, Keck School of Medicine, University of Southern California, CA, United States of America
| | - Chunli Yan
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States of America
- Department of Surgery, Keck School of Medicine, University of Southern California, CA, United States of America
| | - Diane S. Kang
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States of America
- Department of Surgery, Keck School of Medicine, University of Southern California, CA, United States of America
| | - Beiyun Zhou
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, CA, United States of America
| | - Zea Borok
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States of America
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, CA, United States of America
| | - Crystal N. Marconett
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States of America
- Department of Surgery, Keck School of Medicine, University of Southern California, CA, United States of America
| | - Peggy J. Farnham
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States of America
| | - Ite A. Offringa
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States of America
- Department of Surgery, Keck School of Medicine, University of Southern California, CA, United States of America
| | - Suhn Kyong Rhie
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States of America
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Bártů M, Hojný J, Hájková N, Michálková R, Krkavcová E, Simon K, Frýba V, Stružinská I, Němejcová K, Dundr P. Expression, Epigenetic, and Genetic Changes of HNF1B in Colorectal Lesions: an Analysis of 145 Cases. Pathol Oncol Res 2020; 26:2337-2350. [PMID: 32488808 DOI: 10.1007/s12253-020-00830-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 05/21/2020] [Indexed: 12/20/2022]
Abstract
Hepatocyte nuclear factor 1 beta (HNF1B) is transcription factor which plays a crucial role in the regulation of the development of several organs, but also seems to be implicated in the development of certain tumours, especially the subset of clear cell carcinomas of the ovary and kidney. Depending on the type of the tumour, HNF1B may act as either a tumour suppressor or an oncogene, although the exact mechanism by which HNF1B participates in the process of cancerogenesis is unknown. Using immunohistochemical approach and methylation and mutation analysis, we have investigated the expression, epigenetic, and genetic changes of HNF1B on 40 cases of colorectal adenomas and 105 cases of colorectal carcinomas. The expression of HNF1B was correlated with the benign or malignant behaviour of the lesion, given that carcinomas showed significantly lower levels of expression compared to adenomas. In carcinomas, lower levels of HNF1B expression were associated with recurrence and shortened disease-free survival. The mutation analysis revealed three somatic mutations (two frameshift and one nonsense) in the carcinoma sample set. Promoter methylation was detected in three carcinomas. These results suggest that in colorectal cancer, HNF1B may play a part in the pathogenesis and act in a tumour suppressive fashion.
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Affiliation(s)
- Michaela Bártů
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studnickova 2, 12800, Prague 2, Czech Republic
| | - Jan Hojný
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studnickova 2, 12800, Prague 2, Czech Republic
| | - Nikola Hájková
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studnickova 2, 12800, Prague 2, Czech Republic
| | - Romana Michálková
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studnickova 2, 12800, Prague 2, Czech Republic
| | - Eva Krkavcová
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studnickova 2, 12800, Prague 2, Czech Republic
| | - Karol Simon
- First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800, Prague, Czech Republic
| | - Vladimír Frýba
- 1st Department of Surgery - Department of Abdominal, Thoracic Surgery and Traumatology, First Faculty of Medicine, Charles University and General University Hospital, 12808, Prague, Czech Republic
| | - Ivana Stružinská
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studnickova 2, 12800, Prague 2, Czech Republic
| | - Kristýna Němejcová
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studnickova 2, 12800, Prague 2, Czech Republic
| | - Pavel Dundr
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studnickova 2, 12800, Prague 2, Czech Republic.
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11
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Verkarre V, Morini A, Denize T, Ferlicot S, Richard S. [Hereditary kidney cancers: The pathologist's view in 2020]. Ann Pathol 2020; 40:148-167. [PMID: 32197858 DOI: 10.1016/j.annpat.2020.02.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 02/10/2020] [Accepted: 02/18/2020] [Indexed: 12/23/2022]
Abstract
Hereditary predispositions to adult kidney tumors involve around 5% of tumors and include a dozen of autosomal dominant syndromes. The most frequent tumors encountered in these setting are clear cell renal cell carcinomas, papillary renal cell carcinomas, chromophobe renal cell carcinomas and angiomyolipomas. Their detection is essential in order to adapt individual care and perform genetic screening of at-risk relatives, especially in the national french network PREDIR, labeled by the National Cancer Institute and dedicated to hereditary predispositions to kidney tumors. Targeted genetic analysis, which was guided in particular by the renal tumor subtype, has recently evolved into genetic analysis using panels of genes. Pathologist contribution's remains however central in the diagnosis of hereditary forms since we currently have immunohistochemical biomarkers that allow us to diagnose two specifically hereditary entities: hereditary leiomyomatosis and renal cell carcinoma associated-renal cell carcinoma, associated with a loss of fumarate hydratase and succinate dehydrogenase-deficient renal cell carcinoma associated with a loss of succinate deshydrogenase B expression. These diagnoses must however be confirmed by the identification of pathogenic germline variation in the corresponding genes. Improvement of kidney tumors characterization has also lead to identify new subtypes, expanding the algorithm of renal tumors associated with hereditary setting. Here we aim to review all subtypes of adult renal tumors encountered in predisposition syndromes.
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Affiliation(s)
- Virginie Verkarre
- Service d'anatomie pathologique, université de Paris, hôpital européen Georges-Pompidou, Assistance publique-Hôpitaux de Paris-Centre, 20, rue Leblanc, 75015 Paris, France; Inserm U970, équipe labellisée par la Ligue contre le cancer, PARCC, université de Paris, Paris, France; Réseau national de référence pour cancers rares de l'adulte PREDIR (« Maladie de von Hippel-Lindau et prédispositions héréditaires au cancer rénal ») labellisée par l'Institut national du cancer, université Paris Saclay, Assistance publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France.
| | - Aurélien Morini
- Service d'anatomie pathologique, université de Paris, hôpital européen Georges-Pompidou, Assistance publique-Hôpitaux de Paris-Centre, 20, rue Leblanc, 75015 Paris, France
| | - Thomas Denize
- Service d'anatomie pathologique, université de Paris, hôpital européen Georges-Pompidou, Assistance publique-Hôpitaux de Paris-Centre, 20, rue Leblanc, 75015 Paris, France
| | - Sophie Ferlicot
- Réseau national de référence pour cancers rares de l'adulte PREDIR (« Maladie de von Hippel-Lindau et prédispositions héréditaires au cancer rénal ») labellisée par l'Institut national du cancer, université Paris Saclay, Assistance publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France; Service d'anatomie pathologique des hôpitaux universitaires Paris Sud, université Paris Saclay, hôpital de Bicêtre, Assistance publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France; Génétique oncologique EPHE, PSL Université, UMR 9019 CNRS, université Paris-Saclay, institut Gustave-Roussy, Villejuif, France
| | - Stéphane Richard
- Réseau national de référence pour cancers rares de l'adulte PREDIR (« Maladie de von Hippel-Lindau et prédispositions héréditaires au cancer rénal ») labellisée par l'Institut national du cancer, université Paris Saclay, Assistance publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France; Génétique oncologique EPHE, PSL Université, UMR 9019 CNRS, université Paris-Saclay, institut Gustave-Roussy, Villejuif, France
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12
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Abstract
MODY (Maturity Onset Diabetes of the Young) is a type of diabetes resulting from a pathogenic effect of gene mutations. Up to date, 13 MODY genes are known. Gene HNF1A is one of the most common causes of MODY diabetes (HNF1A-MODY; MODY3). This gene is polymorphic and more than 1200 pathogenic and non-pathogenic HNF1A variants were described in its UTRs, exons and introns. For HNF1A-MODY, not just gene but also phenotype heterogeneity is typical. Although there are some clinical instructions, HNF1A-MODY patients often do not meet every diagnostic criteria or they are still misdiagnosed as type 1 and type 2 diabetics. There is a constant effort to find suitable biomarkers to help with in distinguishing of MODY3 from Type 1 Diabetes (T1D) and Type 2 Diabetes (T2D). DNA sequencing is still necessary for unambiguous confirmation of clinical suspicion of MODY. NGS (Next Generation Sequencing) methods brought discoveries of multiple new gene variants and new instructions for their pathogenicity classification were required. The most actual problem is classification of variants with uncertain significance (VUS) which is a stumbling-block for clinical interpretation. Since MODY is a hereditary disease, DNA analysis of family members is helpful or even crucial. This review is updated summary about HNF1A-MODY genetics, pathophysiology, clinics functional studies and variant classification.
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13
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Wang L, Zhu M, Wang Y, Fan J, Sun Q, Ji M, Fan X, Xie J, Dai J, Jin G, Hu Z, Ma H, Shen H. Cross-Cancer Pleiotropic Analysis Reveals Novel Susceptibility Loci for Lung Cancer. Front Oncol 2020; 9:1492. [PMID: 32010612 PMCID: PMC6974684 DOI: 10.3389/fonc.2019.01492] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/11/2019] [Indexed: 12/27/2022] Open
Abstract
Genome-wide association studies (GWASs) have identified hundreds of single nucleotide polymorphisms (SNPs) associated with cancer risk, several of which have shown pleiotropic effects across cancers. Therefore, we performed a systematic cross-cancer pleiotropic analysis to detect the effects of GWAS-identified variants from non-lung cancers on lung cancer risk in 12,843 cases and 12,639 controls from four lung cancer GWASs. The overall association between variants in each cancer and risk of lung cancer was explored using sequential kernel association test (SKAT) analysis. For single variant analysis, we combined the result of specific study using fixed-effect meta-analysis. We performed functional exploration of significant associations based on features from public databases. To further detect the biological mechanism underlying identified observations, pathway enrichment analysis were conducted with R package “clusterProfiler.” SNP-set analysis revealed the overall associations between variants of 8 cancer types and lung cancer risk. Single variant analysis identified 6 novel SNPs related to lung cancer risk after multiple correction (Pfdr < 0.10), including rs1707302 (1p34.1, OR = 0.93, 95% CI: 0.90–0.97, P = 7.60 × 10−4), rs2516448 (6p21.33, OR = 1.07, 95% CI: 1.03–1.11, P = 1.00 × 10−3), rs3869062 (6p22.1, OR = 0.91, 95% CI: 0.86–0.96, P = 7.10 × 10−4), rs174549 (11q12.2, OR = 0.90, 95% CI: 0.87–0.94, P = 1.00 × 10−7), rs7193541 (16q23.1, OR = 0.93, 95% CI: 0.90–0.96, P = 1.20 × 10−4), and rs8064454 (17q12, OR = 1.07, 95% CI: 1.03–1.11, P = 4.30 × 10−4). The eQTL analysis and functional annotation suggested that these variants might modify lung cancer susceptibility through regulating the expression of related genes. Pathway enrichment analysis showed that genes modulated by these variants play important roles in cancer carcinogenesis. Our findings demonstrate the pleiotropic associations between non-lung cancer susceptibility loci and lung cancer risk, providing important insights into the shared mechanisms of carcinogenesis across cancers.
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Affiliation(s)
- Lijuan Wang
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Meng Zhu
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yuzhuo Wang
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jingyi Fan
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qi Sun
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Mengmeng Ji
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xikang Fan
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Junxing Xie
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Guangfu Jin
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Hongxia Ma
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
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14
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Carazo F, Campuzano L, Cendoya X, Planes FJ, Rubio A. TranscriptAchilles: a genome-wide platform to predict isoform biomarkers of gene essentiality in cancer. Gigascience 2019; 8:giz021. [PMID: 30942869 PMCID: PMC6446222 DOI: 10.1093/gigascience/giz021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 12/18/2018] [Accepted: 02/07/2019] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Aberrant alternative splicing plays a key role in cancer development. In recent years, alternative splicing has been used as a prognosis biomarker, a therapy response biomarker, and even as a therapeutic target. Next-generation RNA sequencing has an unprecedented potential to measure the transcriptome. However, due to the complexity of dealing with isoforms, the scientific community has not sufficiently exploited this valuable resource in precision medicine. FINDINGS We present TranscriptAchilles, the first large-scale tool to predict transcript biomarkers associated with gene essentiality in cancer. This application integrates 412 loss-of-function RNA interference screens of >17,000 genes, together with their corresponding whole-transcriptome expression profiling. Using this tool, we have studied which are the cancer subtypes for which alternative splicing plays a significant role to state gene essentiality. In addition, we include a case study of renal cell carcinoma that shows the biological soundness of the results. The databases, the source code, and a guide to build the platform within a Docker container are available at GitLab. The application is also available online. CONCLUSIONS TranscriptAchilles provides a user-friendly web interface to identify transcript or gene biomarkers of gene essentiality, which could be used as a starting point for a drug development project. This approach opens a wide range of translational applications in cancer.
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Affiliation(s)
- Fernando Carazo
- Tecnun (University of Navarra), Paseo Manuel Lardizábal 15, 20018 San Sebastián, Spain. Department of Biomedical Engineering and Sciences
| | - Lucía Campuzano
- University of Luxembourg, 2, avenue de l'Université, 4365 Esch-sur-Alzette, Luxembourg
| | - Xabier Cendoya
- Tecnun (University of Navarra), Paseo Manuel Lardizábal 15, 20018 San Sebastián, Spain. Department of Biomedical Engineering and Sciences
| | - Francisco J Planes
- Tecnun (University of Navarra), Paseo Manuel Lardizábal 15, 20018 San Sebastián, Spain. Department of Biomedical Engineering and Sciences
| | - Angel Rubio
- Tecnun (University of Navarra), Paseo Manuel Lardizábal 15, 20018 San Sebastián, Spain. Department of Biomedical Engineering and Sciences
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15
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Siebenthall KT, Miller CP, Vierstra JD, Mathieu J, Tretiakova M, Reynolds A, Sandstrom R, Rynes E, Haugen E, Johnson A, Nelson J, Bates D, Diegel M, Dunn D, Frerker M, Buckley M, Kaul R, Zheng Y, Himmelfarb J, Ruohola-Baker H, Akilesh S. Integrated epigenomic profiling reveals endogenous retrovirus reactivation in renal cell carcinoma. EBioMedicine 2019; 41:427-442. [PMID: 30827930 PMCID: PMC6441874 DOI: 10.1016/j.ebiom.2019.01.063] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Transcriptional dysregulation drives cancer formation but the underlying mechanisms are still poorly understood. Renal cell carcinoma (RCC) is the most common malignant kidney tumor which canonically activates the hypoxia-inducible transcription factor (HIF) pathway. Despite intensive study, novel therapeutic strategies to target RCC have been difficult to develop. Since the RCC epigenome is relatively understudied, we sought to elucidate key mechanisms underpinning the tumor phenotype and its clinical behavior. METHODS We performed genome-wide chromatin accessibility (DNase-seq) and transcriptome profiling (RNA-seq) on paired tumor/normal samples from 3 patients undergoing nephrectomy for removal of RCC. We incorporated publicly available data on HIF binding (ChIP-seq) in a RCC cell line. We performed integrated analyses of these high-resolution, genome-scale datasets together with larger transcriptomic data available through The Cancer Genome Atlas (TCGA). FINDINGS Though HIF transcription factors play a cardinal role in RCC oncogenesis, we found that numerous transcription factors with a RCC-selective expression pattern also demonstrated evidence of HIF binding near their gene body. Examination of chromatin accessibility profiles revealed that some of these transcription factors influenced the tumor's regulatory landscape, notably the stem cell transcription factor POU5F1 (OCT4). Elevated POU5F1 transcript levels were correlated with advanced tumor stage and poorer overall survival in RCC patients. Unexpectedly, we discovered a HIF-pathway-responsive promoter embedded within a endogenous retroviral long terminal repeat (LTR) element at the transcriptional start site of the PSOR1C3 long non-coding RNA gene upstream of POU5F1. RNA transcripts are induced from this promoter and read through PSOR1C3 into POU5F1 producing a novel POU5F1 transcript isoform. Rather than being unique to the POU5F1 locus, we found that HIF binds to several other transcriptionally active LTR elements genome-wide correlating with broad gene expression changes in RCC. INTERPRETATION Integrated transcriptomic and epigenomic analysis of matched tumor and normal tissues from even a small number of primary patient samples revealed remarkably convergent shared regulatory landscapes. Several transcription factors appear to act downstream of HIF including the potent stem cell transcription factor POU5F1. Dysregulated expression of POU5F1 is part of a larger pattern of gene expression changes in RCC that may be induced by HIF-dependent reactivation of dormant promoters embedded within endogenous retroviral LTRs.
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Affiliation(s)
- Kyle T Siebenthall
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Chris P Miller
- Department of Pathology, University of Washington, Seattle, WA 98195, United States
| | - Jeff D Vierstra
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Julie Mathieu
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA 98109, United States; Department of Comparative Medicine, University of Washington, Seattle, WA 98195, United States
| | - Maria Tretiakova
- Department of Pathology, University of Washington, Seattle, WA 98195, United States
| | - Alex Reynolds
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Richard Sandstrom
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Eric Rynes
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Eric Haugen
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Audra Johnson
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Jemma Nelson
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Daniel Bates
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Morgan Diegel
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Douglass Dunn
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Mark Frerker
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Michael Buckley
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Rajinder Kaul
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, United States
| | - Ying Zheng
- Department of Bioengineering, University of Washington, Seattle, WA 98195, United States; Kidney Research Institute, Seattle, WA 98104, United States
| | - Jonathan Himmelfarb
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA 98195, United States; Kidney Research Institute, Seattle, WA 98104, United States
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, United States; Institute for Stem Cell and Regenerative Medicine, Seattle, WA 98109, United States
| | - Shreeram Akilesh
- Department of Pathology, University of Washington, Seattle, WA 98195, United States; Kidney Research Institute, Seattle, WA 98104, United States.
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16
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Wu J, Wang H, Ricketts CJ, Yang Y, Merino MJ, Zhang H, Shi G, Gan H, Linehan WM, Zhu Y, Ye D. Germline mutations of renal cancer predisposition genes and clinical relevance in Chinese patients with sporadic, early-onset disease. Cancer 2018; 125:1060-1069. [PMID: 30548481 DOI: 10.1002/cncr.31908] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/04/2018] [Accepted: 11/12/2018] [Indexed: 12/24/2022]
Abstract
BACKGROUND An inherited susceptibility to renal cancers is associated with multiple predisposing genes, but most screening tests are limited to patients with a family history. Next-generation sequencing (NGS)-based multigene panels provide an efficient and adaptable tool for investigating pathogenic germline mutations on a larger scale. This study investigated the frequency of pathogenic germline mutations in renal cancer predisposition genes in patients with sporadic, early-onset disease. METHODS An NGS-based panel of 23 known and potential renal cancer predisposition genes was used to analyze germline mutations in 190 unrelated Chinese patients under the age of 45 years who presented with renal tumors. The detected variants were filtered for pathogenicity, and then their frequencies were calculated and correlated with clinical features. Germline variants of the fumarate hydratase (FH) and BRCA1-associated protein 1 (BAP1) genes were comprehensively analyzed because of their aggressive potential. RESULTS In total, 18 patients (9.5%) had germline mutations in 10 genes. Twelve of these 18 patients had alterations in renal cancer predisposition genes (6.3%), and 6 patients had mutations in potential predisposition genes such as BRCA1/2. Notably, pathogenic mutation carriers had a significant family history in second-degree relatives in comparison with those without pathogenic mutations (P < .001). Variants of unknown clinical significance in FH and BAP1 demonstrated evidence of additional somatic loss in tumors. CONCLUSIONS In patients with early-onset disease, a multigene panel identified a high pathogenic germline mutation rate in renal cancer predisposition genes. This study emphasizes the importance of screening patients with early-onset disease for mutations in cancer predisposition genes. Germline screening should be encouraged in early-onset patients to provide personalized medicine and improve patient outcomes.
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Affiliation(s)
- Junlong Wu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Hongkai Wang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Youfeng Yang
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Maria J Merino
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Hailiang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Guohai Shi
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Hualei Gan
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China.,Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Yao Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
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17
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Gjorgjieva M, Monteillet L, Calderaro J, Mithieux G, Rajas F. Polycystic kidney features of the renal pathology in glycogen storage disease type I: possible evolution to renal neoplasia. J Inherit Metab Dis 2018; 41:955-963. [PMID: 29869165 DOI: 10.1007/s10545-018-0207-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/07/2018] [Accepted: 05/22/2018] [Indexed: 12/12/2022]
Abstract
Glycogen storage disease type I (GSDI) is a rare genetic pathology characterized by glucose-6 phosphatase (G6Pase) deficiency, translating in hypoglycemia during short fasts. Besides metabolic perturbations, GSDI patients develop long-term complications, especially chronic kidney disease (CKD). In GSDI patients, CKD is characterized by an accumulation of glycogen and lipids in kidneys, leading to a gradual decline in renal function. At a molecular level, the activation of the renin-angiotensin system is responsible for the development of renal fibrosis, eventually leading to renal failure. The same CKD phenotype was observed in a mouse model with a kidney-specific G6Pase deficiency (K.G6pc-/- mice). Furthermore, GSDI patients and mice develop frequently renal cysts at late stages of the nephropathy, classifying GSDI as a potential polycystic kidney disease (PKD). PKDs are genetic disorders characterized by multiple renal cyst formation, frequently caused by the loss of expression of polycystic kidney genes, such as PKD1/2 and PKHD1. Interestingly, these genes are deregulated in K.G6pc-/- kidneys, suggesting their possible role in GSDI cystogenesis. Finally, renal cysts are known to predispose to renal malignancy development. In addition, HNF1B loss is a malignancy prediction factor. Interestingly, Hnf1b expression was decreased in K.G6pc-/- kidneys. While a single case of renal cancer has been reported in a GSDI patient, a clear cell renal carcinoma was recently observed in one K.G6pc-/- mouse (out of 36 studied mice) at a later stage of the disease. This finding highlights the need to further analyze renal cyst development in GSDI patients in order to evaluate the possible associated risk of carcinogenesis, even if the risk might be limited.
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Affiliation(s)
- Monika Gjorgjieva
- Institut National de la Santé et de la Recherche by Inserm, U1213, 69008, Lyon, France
- Université de Lyon, 69008, Lyon, France
- Université Lyon1, 69622, Villeurbanne, France
| | - Laure Monteillet
- Institut National de la Santé et de la Recherche by Inserm, U1213, 69008, Lyon, France
- Université de Lyon, 69008, Lyon, France
- Université Lyon1, 69622, Villeurbanne, France
| | - Julien Calderaro
- Inserm UMR-1162, Université Paris Descartes, Labex Immuno-Oncology, Université Paris Diderot, Université Paris 13, Paris, France
- APHP, Assistance-Publique Hôpitaux-de-Paris, Département de Pathologie, Hôpital Henri Mondor, 94010, Créteil, France
| | - Gilles Mithieux
- Institut National de la Santé et de la Recherche by Inserm, U1213, 69008, Lyon, France
- Université de Lyon, 69008, Lyon, France
- Université Lyon1, 69622, Villeurbanne, France
| | - Fabienne Rajas
- Institut National de la Santé et de la Recherche by Inserm, U1213, 69008, Lyon, France.
- Université de Lyon, 69008, Lyon, France.
- Université Lyon1, 69622, Villeurbanne, France.
- Inserm U1213, Université Lyon 1 Laennec, 7 rue Guillaume Paradin, 69372, Lyon Cedex 08, France.
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18
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Zhang W, Flemington EK, Deng HW, Zhang K. Epigenetically Silenced Candidate Tumor Suppressor Genes in Prostate Cancer: Identified by Modeling Methylation Stratification and Applied to Progression Prediction. Cancer Epidemiol Biomarkers Prev 2018; 28:198-207. [DOI: 10.1158/1055-9965.epi-18-0491] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/23/2018] [Accepted: 09/19/2018] [Indexed: 11/16/2022] Open
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19
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Li YF, Altman RB. Systematic target function annotation of human transcription factors. BMC Biol 2018; 16:4. [PMID: 29325558 PMCID: PMC5795274 DOI: 10.1186/s12915-017-0469-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 12/06/2017] [Indexed: 01/03/2023] Open
Abstract
Background Transcription factors (TFs), the key players in transcriptional regulation, have attracted great experimental attention, yet the functions of most human TFs remain poorly understood. Recent capabilities in genome-wide protein binding profiling have stimulated systematic studies of the hierarchical organization of human gene regulatory network and DNA-binding specificity of TFs, shedding light on combinatorial gene regulation. We show here that these data also enable a systematic annotation of the biological functions and functional diversity of TFs. Result We compiled a human gene regulatory network for 384 TFs covering the 146,096 TF–target gene (TF–TG) relationships, extracted from over 850 ChIP-seq experiments as well as the literature. By integrating this network of TF–TF and TF–TG relationships with 3715 functional concepts from six sources of gene function annotations, we obtained over 9000 confident functional annotations for 279 TFs. We observe extensive connectivity between TFs and Mendelian diseases, GWAS phenotypes, and pharmacogenetic pathways. Further, we show that TFs link apparently unrelated functions, even when the two functions do not share common genes. Finally, we analyze the pleiotropic functions of TFs and suggest that the increased number of upstream regulators contributes to the functional pleiotropy of TFs. Conclusion Our computational approach is complementary to focused experimental studies on TF functions, and the resulting knowledge can guide experimental design for the discovery of unknown roles of TFs in human disease and drug response. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0469-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yong Fuga Li
- Stanford Genome Technology Center, Stanford, CA, USA. .,Department of Bioengineering, Stanford University, Stanford, CA, USA. .,Present address: Department of Bioinformatics, Illumina Inc., San Diego, CA, USA.
| | - Russ B Altman
- Department of Bioengineering, Stanford University, Stanford, CA, USA. .,Department of Genetics, Stanford University, Stanford, CA, USA.
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20
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Sun M, Tong P, Kong W, Dong B, Huang Y, Park IY, Zhou L, Liu XD, Ding Z, Zhang X, Bai S, German P, Powell R, Wang Q, Tong X, Tannir NM, Matin SF, Rathmell WK, Fuller GN, McCutcheon IE, Walker CL, Wang J, Jonasch E. HNF1B Loss Exacerbates the Development of Chromophobe Renal Cell Carcinomas. Cancer Res 2017; 77:5313-5326. [PMID: 28807937 DOI: 10.1158/0008-5472.can-17-0986] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 06/16/2017] [Accepted: 07/25/2017] [Indexed: 12/25/2022]
Abstract
Chromophobe renal cell carcinoma (ChRCC) is characterized by major changes in chromosomal copy number (CN). No model is available to precisely elucidate the molecular drivers of this tumor type. HNF1B is a master regulator of gene expression. Here, we report that the transcription factor HNF1B is downregulated in the majority of ChRCC and that the magnitude of HNF1B loss is unique to ChRCC. We also observed a strong correlation between reduced HNF1B expression and aneuploidy in ChRCC patients. In murine embryonic fibroblasts or ACHN cells, HNF1B deficiency reduced expression of the spindle checkpoint proteins MAD2L1 and BUB1B, and the cell-cycle checkpoint proteins RB1 and p27. Furthermore, it altered the chromatin accessibility of Mad2l1, Bub1b, and Rb1 genes and triggered aneuploidy development. Analysis of The Cancer Genome Atlas database revealed TP53 mutations in 33% of ChRCC where HNF1B expression was repressed. In clinical specimens, combining HNF1B loss with TP53 mutation produced an association with poor patient prognosis. In cells, combining HNF1B loss and TP53 mutation increased cell proliferation and aneuploidy. Our results show how HNF1B loss leads to abnormal mitotic protein regulation and induction of aneuploidy. We propose that coordinate loss of HNF1B and TP53 may enhance cellular survival and confer an aggressive phenotype in ChRCC. Cancer Res; 77(19); 5313-26. ©2017 AACR.
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Affiliation(s)
- Mianen Sun
- Department of Genitourinary Medical Oncology, University of Texas at MD Anderson Cancer Center, Houston, Texas
| | - Pan Tong
- Department of Bioinformatics and Computational Biology, University of Texas at MD Anderson Cancer Center, Houston, Texas
| | - Wen Kong
- Department of Urology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Baijun Dong
- Department of Urology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yiran Huang
- Department of Urology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - In Young Park
- Institute of Biosciences and Technology, Texas A&M University Health Science Center, Bryan, Texas
| | - Lijun Zhou
- Department of Genitourinary Medical Oncology, University of Texas at MD Anderson Cancer Center, Houston, Texas
| | - Xian-De Liu
- Department of Genitourinary Medical Oncology, University of Texas at MD Anderson Cancer Center, Houston, Texas
| | - Zhiyong Ding
- Department of System Biology, University of Texas at MD Anderson Cancer Center, Houston, Texas
| | - Xuesong Zhang
- Department of Genitourinary Medical Oncology, University of Texas at MD Anderson Cancer Center, Houston, Texas
| | - Shanshan Bai
- Department of Genitourinary Medical Oncology, University of Texas at MD Anderson Cancer Center, Houston, Texas
| | - Peter German
- Department of Genitourinary Medical Oncology, University of Texas at MD Anderson Cancer Center, Houston, Texas
| | - Reid Powell
- Institute of Biosciences and Technology, Texas A&M University Health Science Center, Bryan, Texas
| | - Quan Wang
- Institute of Biosciences and Technology, Texas A&M University Health Science Center, Bryan, Texas
| | - Xuefei Tong
- Institute of Biosciences and Technology, Texas A&M University Health Science Center, Bryan, Texas
| | - Nizar M Tannir
- Institute of Biosciences and Technology, Texas A&M University Health Science Center, Bryan, Texas
| | - Surena F Matin
- Department of Urology, University of Texas at MD Anderson Cancer Center, Houston, Texas
| | - W Kimryn Rathmell
- Department of Urology, University of North Carolina, Chapel Hill, North Carolina
| | - Gregory N Fuller
- Department of Pathology, University of Texas at MD Anderson Cancer Center, Houston, Texas
| | - Ian E McCutcheon
- Department of Neurosurgery, University of Texas at MD Anderson Cancer Center, Houston, Texas
| | - Cheryl L Walker
- Institute of Biosciences and Technology, Texas A&M University Health Science Center, Bryan, Texas
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, University of Texas at MD Anderson Cancer Center, Houston, Texas
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21
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Melloni GEM, Mazzarella L, Bernard L, Bodini M, Russo A, Luzi L, Pelicci PG, Riva L. A knowledge-based framework for the discovery of cancer-predisposing variants using large-scale sequencing breast cancer data. Breast Cancer Res 2017; 19:63. [PMID: 28569218 PMCID: PMC5452392 DOI: 10.1186/s13058-017-0854-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/08/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The landscape of cancer-predisposing genes has been extensively investigated in the last 30 years with various methodologies ranging from candidate gene to genome-wide association studies. However, sequencing data are still poorly exploited in cancer predisposition studies due to the lack of statistical power when comparing millions of variants at once. METHOD To overcome these power limitations, we propose a knowledge-based framework founded on the characteristics of known cancer-predisposing variants and genes. Under our framework, we took advantage of a combination of previously generated datasets of sequencing experiments to identify novel breast cancer-predisposing variants, comparing the normal genomes of 673 breast cancer patients of European origin against 27,173 controls matched by ethnicity. RESULTS We detected several expected variants on known breast cancer-predisposing genes, like BRCA1 and BRCA2, and 11 variants on genes associated with other cancer types, like RET and AKT1. Furthermore, we detected 183 variants that overlap with somatic mutations in cancer and 41 variants associated with 38 possible loss-of-function genes, including PIK3CB and KMT2C. Finally, we found a set of 19 variants that are potentially pathogenic, negatively correlate with age at onset, and have never been associated with breast cancer. CONCLUSIONS In this study, we demonstrate the usefulness of a genomic-driven approach nested in a classic case-control study to prioritize cancer-predisposing variants. In addition, we provide a resource containing variants that may affect susceptibility to breast cancer.
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Affiliation(s)
- Giorgio E M Melloni
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Via Adamello 16, Milan, Italy
| | - Luca Mazzarella
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan, Italy.,Division of New Drug Development, European Institute of Oncology, Via Ripamonti 435, Milan, Italy
| | - Loris Bernard
- Clinical Genomics Lab, European Institute of Oncology, via Ripamonti 435, Milano, Italy
| | - Margherita Bodini
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Via Adamello 16, Milan, Italy
| | - Anna Russo
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan, Italy
| | - Lucilla Luzi
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan, Italy.,Department of Oncology and Hemato-oncology, University of Milan, via Festa del Perdono 7, Milan, Italy
| | - Laura Riva
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Via Adamello 16, Milan, Italy.
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22
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Germline mutations predisposing to diffuse large B-cell lymphoma. Blood Cancer J 2017; 7:e532. [PMID: 28211887 PMCID: PMC5386333 DOI: 10.1038/bcj.2017.15] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 01/04/2017] [Accepted: 01/10/2017] [Indexed: 12/21/2022] Open
Abstract
Genetic studies of diffuse large B-cell lymphomas (DLBCLs) in humans have revealed numerous targets of somatic mutations and an increasing number of potentially relevant germline alterations. The latter often affect genes involved in DNA repair and/or immune function. In general, defects in these genes also predispose to other conditions. Knowledge of these mutations can lead to disease-preventing measures in the patient and relatives thereof. Conceivably, these germline mutations will be taken into account in future therapy of the lymphoma. In other hematological malignancies, mutations originally found as somatic aberrations have also been shown to confer predisposition to these diseases, when occurring in the germline. Further interrogations of the genome in DLBCL patients are therefore expected to reveal additional hereditary predisposition genes. Our review shows that germline mutations have already been described in over one-third of the genes that are somatically mutated in DLBCL. Whether such germline mutations predispose carriers to DLBCL is an open question. Symptoms of the inherited syndromes associated with these genes range from anatomical malformations to intellectual disability, immunodeficiencies and malignancies other than DLBCL. Inherited or de novo alterations in protein-coding and non-coding genes are envisioned to underlie this lymphoma.
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23
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Najmi LA, Aukrust I, Flannick J, Molnes J, Burtt N, Molven A, Groop L, Altshuler D, Johansson S, Bjørkhaug L, Njølstad PR. Functional Investigations of HNF1A Identify Rare Variants as Risk Factors for Type 2 Diabetes in the General Population. Diabetes 2017; 66:335-346. [PMID: 27899486 PMCID: PMC5860263 DOI: 10.2337/db16-0460] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 11/18/2016] [Indexed: 12/18/2022]
Abstract
Variants in HNF1A encoding hepatocyte nuclear factor 1α (HNF-1A) are associated with maturity-onset diabetes of the young form 3 (MODY 3) and type 2 diabetes. We investigated whether functional classification of HNF1A rare coding variants can inform models of diabetes risk prediction in the general population by analyzing the effect of 27 HNF1A variants identified in well-phenotyped populations (n = 4,115). Bioinformatics tools classified 11 variants as likely pathogenic and showed no association with diabetes risk (combined minor allele frequency [MAF] 0.22%; odds ratio [OR] 2.02; 95% CI 0.73-5.60; P = 0.18). However, a different set of 11 variants that reduced HNF-1A transcriptional activity to <60% of normal (wild-type) activity was strongly associated with diabetes in the general population (combined MAF 0.22%; OR 5.04; 95% CI 1.99-12.80; P = 0.0007). Our functional investigations indicate that 0.44% of the population carry HNF1A variants that result in a substantially increased risk for developing diabetes. These results suggest that functional characterization of variants within MODY genes may overcome the limitations of bioinformatics tools for the purposes of presymptomatic diabetes risk prediction in the general population.
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Affiliation(s)
- Laeya Abdoli Najmi
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Ingvild Aukrust
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Jason Flannick
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
| | - Janne Molnes
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
| | - Noel Burtt
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
| | - Anders Molven
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Clinical Research Center, Lund University, Malmö, Sweden
| | - David Altshuler
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
- Departments of Genetics and Medicine, Harvard Medical School, Boston, MA
- Departments of Molecular Biology and Diabetes Unit, Massachusetts General Hospital, Boston, MA
| | - Stefan Johansson
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Lise Bjørkhaug
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Biomedical Laboratory Sciences, Bergen University College, Bergen, Norway
| | - Pål Rasmus Njølstad
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
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24
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Timsit J, Saint-Martin C, Dubois-Laforgue D, Bellanné-Chantelot C. Searching for Maturity-Onset Diabetes of the Young (MODY): When and What for? Can J Diabetes 2016; 40:455-461. [DOI: 10.1016/j.jcjd.2015.12.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/02/2015] [Accepted: 12/21/2015] [Indexed: 12/17/2022]
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25
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Calcineurin Inhibitors Downregulate HNF-1β and May Affect the Outcome of HNF1B Patients After Renal Transplantation. Transplantation 2016; 100:1970-8. [DOI: 10.1097/tp.0000000000000993] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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Voevoda MI, Ivanova AA, Shakhtshneider EV, Ovsyannikova AK, Mikhailova SV, Astrakova KS, Voevoda SM, Rymar OD. Molecular genetics of maturity-onset diabetes of the young. TERAPEVT ARKH 2016. [DOI: 10.17116/terarkh2016884117-124] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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27
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Expression, Epigenetic and Genetic Changes of HNF1B in Endometrial Lesions. Pathol Oncol Res 2015; 22:523-30. [PMID: 26685938 DOI: 10.1007/s12253-015-0037-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/15/2015] [Indexed: 12/19/2022]
Abstract
Hepatocyte nuclear factor 1-beta (HNF-1-beta) is a transcription factor involved in cancerogenesis of various tumors, including endometrioid carcinoma. We performed comprehensive analysis of HNF-1-beta in lesions of the endometrium, including protein expression and genetic and epigenetic changes. Expression of HNF-1-beta was analyzed immunohistochemically in 320 cases including both tumor and non-tumor endometrial lesions. Promoter methylation and genetic variants were evaluated, using bisulphite and direct sequencing, in 30 (18 fresh frozen, 12 FFPE tumors) endometrioid carcinomas (ECs) and 15 ovarian clear cell carcinomas (OCCCs) as a control group. We detected expression of HNF-1-beta in 28 % of ECs (51/180 cases), 26 % of serous carcinoma (7/27 cases), 83 % of endometrial clear cell carcinoma (15/18 cases), 93 % of hyperplastic polyps with atypias (13/14 cases), 100 % of hyperplastic polyps without atypias (16/16 cases), 88 % of hyperplasias with atypias (14/16 cases), 91 % of hyperplasias without atypias (10/11 cases), and in ≥80 % of different normal endometrium samples. The control group of OCCCs showed HNF-1-beta expression in 95 % (18/19 cases). Methylation in promoter region was detected in 13.3 % (4/30) of ECs, but not in corresponding normal tissue where available, nor in OCCCs (0/15 cases). Mutation analysis revealed truncating variant c.454C > T (p.Gln152X) in one EC and missense variant c.848C > T (p.Ala283Val) was detected in one OCCC. In conclusion, expression of HNF-1-beta was detected in various extents in all types of lesions analyzed, nevertheless its strong expression was mostly limited to clear cell carcinomas. Biological significance of genetic and epigenetic changes needs further investigation.
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28
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Yu DD, Guo SW, Jing YY, Dong YL, Wei LX. A review on hepatocyte nuclear factor-1beta and tumor. Cell Biosci 2015; 5:58. [PMID: 26464794 PMCID: PMC4603907 DOI: 10.1186/s13578-015-0049-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 10/01/2015] [Indexed: 01/06/2023] Open
Abstract
Hepatocyte nuclear factor-1beta (HNF1β) was initially identified as a liver-specific transcription factor. It is a homeobox transcription factor that functions as a homodimer or heterodimer with HNF1α. HNF1β plays an important role in organogenesis during embryonic stage, especially of the liver, kidney, and pancreas. Mutations in the HNF1β gene cause maturity-onset diabetes of the young type 5 (MODY5), renal cysts, genital malformations, and pancreas atrophy. Recently, it has been shown that the expression of HNF1β is associated with cancer risk in several tumors, including hepatocellular carcinoma, pancreatic carcinoma, renal cancer, ovarian cancer, endometrial cancer, and prostate cancer. HNF1β also regulates the expression of genes associated with stem/progenitor cells, which indicates that HNF1β may play an important role in stem cell regulation. In this review, we discuss some of the current developments about HNF1β and tumor, the relationship between HNF1β and stem/progenitor cells, and the potential pathogenesis of HNF1β in various tumors.
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Affiliation(s)
- Dan-Dan Yu
- Tumor Immunology and Gene Therapy Center, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, 225 Changhai Road, 200438 Shanghai, China
| | - Shi-Wei Guo
- Tumor Immunology and Gene Therapy Center, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, 225 Changhai Road, 200438 Shanghai, China
| | - Ying-Ying Jing
- Tumor Immunology and Gene Therapy Center, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, 225 Changhai Road, 200438 Shanghai, China
| | - Yu-Long Dong
- Tumor Immunology and Gene Therapy Center, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, 225 Changhai Road, 200438 Shanghai, China
| | - Li-Xin Wei
- Tumor Immunology and Gene Therapy Center, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, 225 Changhai Road, 200438 Shanghai, China
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29
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Nault JC, Datta S, Imbeaud S, Franconi A, Mallet M, Couchy G, Letouzé E, Pilati C, Verret B, Blanc JF, Balabaud C, Calderaro J, Laurent A, Letexier M, Bioulac-Sage P, Calvo F, Zucman-Rossi J. Recurrent AAV2-related insertional mutagenesis in human hepatocellular carcinomas. Nat Genet 2015; 47:1187-93. [PMID: 26301494 DOI: 10.1038/ng.3389] [Citation(s) in RCA: 357] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 07/31/2015] [Indexed: 11/09/2022]
Abstract
Hepatocellular carcinomas (HCCs) are liver tumors related to various etiologies, including alcohol intake and infection with hepatitis B (HBV) or C (HCV) virus. Additional risk factors remain to be identified, particularly in patients who develop HCC without cirrhosis. We found clonal integration of adeno-associated virus type 2 (AAV2) in 11 of 193 HCCs. These AAV2 integrations occurred in known cancer driver genes, namely CCNA2 (cyclin A2; four cases), TERT (telomerase reverse transcriptase; one case), CCNE1 (cyclin E1; three cases), TNFSF10 (tumor necrosis factor superfamily member 10; two cases) and KMT2B (lysine-specific methyltransferase 2B; one case), leading to overexpression of the target genes. Tumors with viral integration mainly developed in non-cirrhotic liver (9 of 11 cases) and without known risk factors (6 of 11 cases), suggesting a pathogenic role for AAV2 in these patients. In conclusion, AAV2 is a DNA virus associated with oncogenic insertional mutagenesis in human HCC.
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Affiliation(s)
- Jean-Charles Nault
- INSERM, Unité Mixte de Recherche (UMR) 1162, Génomique Fonctionnelle des Tumeurs Solides, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Université Paris Descartes, Labex Immuno-Oncology, Sorbonne Paris Cité, Paris, France.,Université Paris 13, Sorbonne Paris Cité, Unité de Formation et de Recherche (UFR) Santé, Médecine, Biologie Humaine (SMBH), Bobigny, France.,Université Paris Diderot, Institut Universitaire d'Hématologie, Paris, France.,Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Paris-Seine Saint-Denis, Site Jean Verdier, Pôle d'Activité Cancérologique Spécialisée, Service d'Hépatologie, Bondy, France
| | - Shalini Datta
- INSERM, Unité Mixte de Recherche (UMR) 1162, Génomique Fonctionnelle des Tumeurs Solides, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Université Paris Descartes, Labex Immuno-Oncology, Sorbonne Paris Cité, Paris, France.,Université Paris 13, Sorbonne Paris Cité, Unité de Formation et de Recherche (UFR) Santé, Médecine, Biologie Humaine (SMBH), Bobigny, France.,Université Paris Diderot, Institut Universitaire d'Hématologie, Paris, France
| | - Sandrine Imbeaud
- INSERM, Unité Mixte de Recherche (UMR) 1162, Génomique Fonctionnelle des Tumeurs Solides, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Université Paris Descartes, Labex Immuno-Oncology, Sorbonne Paris Cité, Paris, France.,Université Paris 13, Sorbonne Paris Cité, Unité de Formation et de Recherche (UFR) Santé, Médecine, Biologie Humaine (SMBH), Bobigny, France.,Université Paris Diderot, Institut Universitaire d'Hématologie, Paris, France
| | - Andrea Franconi
- INSERM, Unité Mixte de Recherche (UMR) 1162, Génomique Fonctionnelle des Tumeurs Solides, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Université Paris Descartes, Labex Immuno-Oncology, Sorbonne Paris Cité, Paris, France.,Université Paris 13, Sorbonne Paris Cité, Unité de Formation et de Recherche (UFR) Santé, Médecine, Biologie Humaine (SMBH), Bobigny, France.,Université Paris Diderot, Institut Universitaire d'Hématologie, Paris, France
| | - Maxime Mallet
- INSERM, Unité Mixte de Recherche (UMR) 1162, Génomique Fonctionnelle des Tumeurs Solides, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Université Paris Descartes, Labex Immuno-Oncology, Sorbonne Paris Cité, Paris, France.,Université Paris 13, Sorbonne Paris Cité, Unité de Formation et de Recherche (UFR) Santé, Médecine, Biologie Humaine (SMBH), Bobigny, France.,Université Paris Diderot, Institut Universitaire d'Hématologie, Paris, France
| | - Gabrielle Couchy
- INSERM, Unité Mixte de Recherche (UMR) 1162, Génomique Fonctionnelle des Tumeurs Solides, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Université Paris Descartes, Labex Immuno-Oncology, Sorbonne Paris Cité, Paris, France.,Université Paris 13, Sorbonne Paris Cité, Unité de Formation et de Recherche (UFR) Santé, Médecine, Biologie Humaine (SMBH), Bobigny, France.,Université Paris Diderot, Institut Universitaire d'Hématologie, Paris, France
| | - Eric Letouzé
- INSERM, Unité Mixte de Recherche (UMR) 1162, Génomique Fonctionnelle des Tumeurs Solides, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Université Paris Descartes, Labex Immuno-Oncology, Sorbonne Paris Cité, Paris, France.,Université Paris 13, Sorbonne Paris Cité, Unité de Formation et de Recherche (UFR) Santé, Médecine, Biologie Humaine (SMBH), Bobigny, France.,Université Paris Diderot, Institut Universitaire d'Hématologie, Paris, France
| | - Camilla Pilati
- INSERM, Unité Mixte de Recherche (UMR) 1162, Génomique Fonctionnelle des Tumeurs Solides, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Université Paris Descartes, Labex Immuno-Oncology, Sorbonne Paris Cité, Paris, France.,Université Paris 13, Sorbonne Paris Cité, Unité de Formation et de Recherche (UFR) Santé, Médecine, Biologie Humaine (SMBH), Bobigny, France.,Université Paris Diderot, Institut Universitaire d'Hématologie, Paris, France
| | - Benjamin Verret
- INSERM, Unité Mixte de Recherche (UMR) 1162, Génomique Fonctionnelle des Tumeurs Solides, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Université Paris Diderot, Institut Universitaire d'Hématologie, Paris, France
| | - Jean-Frédéric Blanc
- Centre Hospitalier Universitaire (CHU) de Bordeaux, Department of Hepatology, Hôpital Saint-André, Bordeaux, France.,INSERM, UMR 1053, Bordeaux, France.,Université de Bordeaux, Bordeaux, France
| | - Charles Balabaud
- INSERM, UMR 1053, Bordeaux, France.,Université de Bordeaux, Bordeaux, France
| | - Julien Calderaro
- INSERM, Unité Mixte de Recherche (UMR) 1162, Génomique Fonctionnelle des Tumeurs Solides, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Université Paris Descartes, Labex Immuno-Oncology, Sorbonne Paris Cité, Paris, France.,Université Paris 13, Sorbonne Paris Cité, Unité de Formation et de Recherche (UFR) Santé, Médecine, Biologie Humaine (SMBH), Bobigny, France.,Université Paris Diderot, Institut Universitaire d'Hématologie, Paris, France.,AP-HP, Department of Pathology, CHU Henri Mondor, Créteil, France
| | - Alexis Laurent
- AP-HP, Department of Digestive and Hepatobiliary Surgery, CHU Henri Mondor, Créteil, France.,INSERM, U955, Créteil, France
| | | | - Paulette Bioulac-Sage
- INSERM, UMR 1053, Bordeaux, France.,Université de Bordeaux, Bordeaux, France.,CHU de Bordeaux, Pellegrin Hospital, Department of Pathology, Bordeaux, France
| | - Fabien Calvo
- INSERM, Unité Mixte de Recherche (UMR) 1162, Génomique Fonctionnelle des Tumeurs Solides, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Université Paris Descartes, Labex Immuno-Oncology, Sorbonne Paris Cité, Paris, France.,Université Paris 13, Sorbonne Paris Cité, Unité de Formation et de Recherche (UFR) Santé, Médecine, Biologie Humaine (SMBH), Bobigny, France.,Université Paris Diderot, Institut Universitaire d'Hématologie, Paris, France.,Institut Gustave Roussy, Core Europe, Villejuif, France
| | - Jessica Zucman-Rossi
- INSERM, Unité Mixte de Recherche (UMR) 1162, Génomique Fonctionnelle des Tumeurs Solides, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Université Paris Descartes, Labex Immuno-Oncology, Sorbonne Paris Cité, Paris, France.,Université Paris 13, Sorbonne Paris Cité, Unité de Formation et de Recherche (UFR) Santé, Médecine, Biologie Humaine (SMBH), Bobigny, France.,Université Paris Diderot, Institut Universitaire d'Hématologie, Paris, France.,AP-HP, Hôpital Européen Georges Pompidou, Paris, France
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Hajarnis SS, Patel V, Aboudehen K, Attanasio M, Cobo-Stark P, Pontoglio M, Igarashi P. Transcription Factor Hepatocyte Nuclear Factor-1β (HNF-1β) Regulates MicroRNA-200 Expression through a Long Noncoding RNA. J Biol Chem 2015; 290:24793-805. [PMID: 26292219 DOI: 10.1074/jbc.m115.670646] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Indexed: 12/31/2022] Open
Abstract
The transcription factor hepatocyte nuclear factor-1β (HNF-1β) regulates tissue-specific gene expression in the kidney and other epithelial organs. Mutations of HNF-1β produce kidney cysts, and previous studies have shown that HNF-1β regulates the transcription of cystic disease genes, including Pkd2 and Pkhd1. Here, we combined chromatin immunoprecipitation and next-generation sequencing (ChIP-Seq) with microarray analysis to identify microRNAs (miRNAs) that are directly regulated by HNF-1β in renal epithelial cells. These studies identified members of the epithelial-specific miR-200 family (miR-200b/200a/429) as novel transcriptional targets of HNF-1β. HNF-1β binds to two evolutionarily conserved sites located 28 kb upstream to miR-200b. Luciferase reporter assays showed that the HNF-1β binding sites were located within a promoter that was active in renal epithelial cells. Mutations of the HNF-1β binding sites abolished promoter activity. RT-PCR analysis revealed that a long noncoding RNA (lncRNA) is transcribed from the promoter and encodes the miR-200 cluster. Inhibition of the lncRNA with siRNAs decreased the levels of miR-200 but did not affect expression of the Ttll10 host gene. The expression of the lncRNA and miR-200 was decreased in kidneys from HNF-1β knock-out mice and renal epithelial cells expressing dominant-negative mutant HNF-1β. The expression of miR-200 targets, Zeb2 and Pkd1, was increased in HNF-1β knock-out kidneys and in cells expressing mutant HNF-1β. Overexpression of miR-200 decreased the expression of Zeb2 and Pkd1 in HNF-1β mutant cells. These studies reveal a novel pathway whereby HNF-1β directly contributes to the control of miRNAs that are involved in epithelial-mesenchymal transition and cystic kidney disease.
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Affiliation(s)
| | | | | | | | | | - Marco Pontoglio
- Départment de Génétique et Développement, INSERM U1016, CNRS UMR 8104, Université Paris-Descartes. Institut Cochin, 75014 Paris, France
| | - Peter Igarashi
- From the Departments of Internal Medicine and Pediatrics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390 and
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Suzuki E, Kajita S, Takahashi H, Matsumoto T, Tsuruta T, Saegusa M. Transcriptional upregulation of HNF-1β by NF-κB in ovarian clear cell carcinoma modulates susceptibility to apoptosis through alteration in bcl-2 expression. J Transl Med 2015; 95:962-72. [PMID: 26030369 DOI: 10.1038/labinvest.2015.73] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 04/08/2015] [Accepted: 04/21/2015] [Indexed: 11/09/2022] Open
Abstract
Hepatocyte nuclear factor-1β (HNF-1β) is a transcriptional factor that has an important role in endometriosis-ovarian clear cell carcinoma (OCCC) sequence by modulating cell kinetics and glucose metabolism. However, little is known about the detailed molecular mechanisms that govern its regulation and function. Herein, we focus on upstream and downstream regulatory factors of HNF-1β in OCCCs. In clinical samples, HNF-1β expression was positively correlated with the active form of NF-κB/p65 in OCCCs, and closely linked with a low nuclear grade and non-solid architecture. In cell lines, transfection of p65 resulted in increased HNF-1β mRNA and protein expression in TOV-21G cells (OCCC cell line with endogenous HNF-1β expression), in line with activation of the promoter, probably through interacting with the basic transcriptional machinery. Suppression of endogenous HNF-1β expression by siRNA increased apoptosis in TOV-21G cells, while treatment of Hec251 cells (endometrial carcinoma cell line with extremely low endogenous HNF-1β expression) stably overexpressing exogenous HNF-1β with doxorubicin abrogated apoptosis of the cells, along with increased ratio of bcl-2 relative to bax. Moreover, overexpression of HNF-1β led to upregulation of bcl-2 expression at the transcriptional level in TOV-21G cells, which provided evidence for a positive correlation between HNF-1β and bcl-2 expression in OCCCs. These data, therefore, suggest that association between HNF-1β and NF-κB signaling may participate in cell survival by alteration of apoptotic events, particularly in mitochondria-mediated pathways, through upregulation of bcl-2 expression in OCCCs.
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Affiliation(s)
- Erina Suzuki
- Department of Pathology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Japan
| | - Sabine Kajita
- Department of Pathology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Japan
| | - Hiroyuki Takahashi
- Department of Pathology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Japan
| | - Toshihide Matsumoto
- Department of Pathology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Japan
| | - Tomoko Tsuruta
- Department of Pathology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Japan
| | - Makoto Saegusa
- Department of Pathology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Japan
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ARPKD and early manifestations of ADPKD: the original polycystic kidney disease and phenocopies. Pediatr Nephrol 2015; 30:15-30. [PMID: 24584572 PMCID: PMC4240914 DOI: 10.1007/s00467-013-2706-2] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 11/11/2013] [Accepted: 11/12/2013] [Indexed: 12/11/2022]
Abstract
Renal cysts are clinically and genetically heterogeneous conditions. Polycystic kidney disease (PKD) is common and its characterization has paved the way for the identification of a growing number of cilia-related disorders (ciliopathies) of which most show cystic kidneys. While the recessive form of PKD (ARPKD) virtually always presents in childhood, early onset can, in some instances, also occur in the dominant form (ADPKD). Both ADPKD genes (PKD1 and PKD2) can also be inherited in a recessive way, making the story more complex with evidence for a dosage-sensitive network. Several phenocopies are known, and mutations in HNF1ß or genes that typically cause other ciliopathies, such as nephronophthisis, Bardet-Biedl, Joubert syndrome and related disorders, can mimic PKD. An accurate genetic diagnosis is crucial for genetic counseling, prenatal diagnostics, and the clinical management of patients and their families. The increasing number of genes that have to be considered in patients with cystic kidney disease is challenging to address by conventional techniques and largely benefits from next-generation sequencing-based approaches. The parallel analysis of targeted genes considerably increases the detection rate, allows for better interpretation of identified variants, and avoids genetic misdiagnoses.
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Clissold RL, Hamilton AJ, Hattersley AT, Ellard S, Bingham C. HNF1B-associated renal and extra-renal disease—an expanding clinical spectrum. Nat Rev Nephrol 2014; 11:102-12. [DOI: 10.1038/nrneph.2014.232] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Kanthimathi S, Balamurugan K, Mohan V, Shanthirani CS, Gayathri V, Radha V. Identification and molecular characterization of HNF1B gene mutations in Indian diabetic patients with renal abnormalities. Ann Hum Genet 2014; 79:10-9. [PMID: 25441779 DOI: 10.1111/ahg.12093] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 10/05/2014] [Indexed: 01/10/2023]
Abstract
Heterozygous mutations of the HNF1B gene (HNF1B-MODY or MODY5) are associated with a wide clinical spectrum of renal and extrarenal disease without clear genotype-phenotype correlation. In this study, we investigated the prevalence of HNF1B gene mutations in young Indian diabetic patients with various renal abnormalities. Fifty unrelated young diabetic patients, who also had renal abnormalities, were selected from the electronic records of a large diabetes centre in Chennai, in southern India. All patients were sequenced for HNF1B gene mutations. The whole or partial gene deletion was analyzed by MLPA. Functional characterization of the novel variant (Asn321Asp) was also performed using transcriptional activation and subcellular localization assays. We identified six different HNF1B gene mutations which included four previously reported (-67C>T, Arg165His, IVS2nt+2insT, Met1_Trp557del) and two novel variations (Asn321Asp, IVS3nt-4C>G). The functional study revealed that the novel variation Asn321Asp in both the heterozygous and homozygous state showed similar transcriptional activity, expression levels and normal transportation of protein to the nucleus similar to wild type, suggesting that it is not likely to be pathogenic. This is the first major study of HNF1B-MODY from India and shows that about 10% of young diabetic subjects with renal abnormalities seen at a tertiary diabetes centre harbor HNF1B gene mutations.
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Affiliation(s)
- Sekar Kanthimathi
- Department of Molecular Genetics, Madras Diabetes Research Foundation, Chennai, India
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Chen CP, Chang SD, Wang TH, Wang LK, Tsai JD, Liu YP, Chern SR, Wu PS, Su JW, Chen YT, Wang W. Detection of recurrent transmission of 17q12 microdeletion by array comparative genomic hybridization in a fetus with prenatally diagnosed hydronephrosis, hydroureter, and multicystic kidney, and variable clinical spectrum in the family. Taiwan J Obstet Gynecol 2014; 52:551-7. [PMID: 24411042 DOI: 10.1016/j.tjog.2013.10.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 08/14/2013] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVE This study was aimed at detection of recurrent transmission of the 17q12 microdeletion in a fetus with congenital anomalies of the kidney and urinary tract. MATERIALS AND METHODS A 35-year-old woman was referred to the hospital at 20 weeks' gestation because of hydronephrosis in the fetus. The mother was normal and healthy. Her second child was a girl who had bilateral dysplastic kidneys that required hemodialysis, and died at the age of 5 years. During this pregnancy, the woman underwent amniocentesis at 18 weeks' gestation because of advanced maternal age. Cytogenetic analysis revealed a karyotype of 46,XY. Prenatal ultrasound showed left hydronephrosis with a tortuous ureter, right hydronephrosis, and increased echogenicity of the kidneys. Fetal magnetic resonance imaging showed right dilated renal calyces, left hydronephrosis, hydroureter, and multicystic kidney. The pregnancy was subsequently terminated. Array comparative genomic hybridization (aCGH) and fluorescence in situ hybridization were applied for genetic analysis using umbilical cord, maternal blood, and cultured amniocytes. RESULTS aCGH analysis on umbilical cord detected a 1.75-Mb deletion at 17q12 including haploinsufficiency of LHX1 and HNF1B. aCGH analysis on maternal blood detected a 1.54-Mb deletion at 17q12 including haploinsufficiency of LHX1 and HNF1B. Metaphase fluorescence in situ hybridization analysis on cultured amniocytes and maternal blood lymphocytes using 17q12-specific bacterial artificial chromosome probe showed 17q12 microdeletion in the fetus and the mother. CONCLUSION Prenatal diagnosis of recurrent renal and urinary tract abnormalities in the fetus should include a differential diagnosis of familial 17q12 microdeletion.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan; Department of Biotechnology, Asia University, Taichung, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
| | - Shuenn-Dyh Chang
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, Lin-Kou Medical Center, Tao-Yuan, Taiwan; Department of Obstetrics and Gynecology, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
| | - Tzu-Hao Wang
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, Lin-Kou Medical Center, Tao-Yuan, Taiwan; Department of Obstetrics and Gynecology, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan; Genomic Medicine Research Core Laboratory (GMRCL), Chang Gung Memorial Hospital, Lin-Kou Medical Center, Tao-Yuan, Taiwan
| | - Liang-Kai Wang
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Jeng-Daw Tsai
- Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan
| | - Yu-Peng Liu
- Mackay Junior College of Medicine, Nursing and Management, Taipei, Taiwan; Department of Radiology, Mackay Memorial Hospital Hsinchu Branch, Hsinchu, Taiwan
| | - Schu-Rern Chern
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan
| | | | - Jun-Wei Su
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan; Department of Obstetrics and Gynecology, China Medical University Hospital, Taichung, Taiwan
| | - Yu-Ting Chen
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan
| | - Wayseen Wang
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan; Department of Bioengineering, Tatung University, Taipei, Taiwan
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Affiliation(s)
- James P Calvet
- Department of Biochemistry and Molecular Biology and Department of Cancer Biology and the Kidney Institute, University of Kansas Medical Center, Kansas City, Kansas
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Li J, Zhang Y, Gao Y, Cui Y, Liu H, Li M, Tian Y. Downregulation of HNF1 homeobox B is associated with drug resistance in ovarian cancer. Oncol Rep 2014; 32:979-88. [PMID: 24968817 DOI: 10.3892/or.2014.3297] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 05/29/2014] [Indexed: 11/05/2022] Open
Abstract
The expression of HNF1 homeobox B (HNF1B) is associated with cancer risk in several tumors, including ovarian cancer, and its decreased expression play roles in cancer development. However, the study of HNF1B and cancer is limited, and its association with drug resistance in cancer has never been reported. On the basis of array data retrieved from Oncomine and Gene Expression Omnibus (GEO) online database, we found that the mRNA expression of HNF1B in 586 ovarian serous cystadenocarcinomas and in platinum-resistant A2780 epithelial ovarian cancer cells was significantly decreased, indicating a potential role of HNF1B in drug resistance in ovarian cancer. Based on this finding, comprehensive bioinformatics analyses, including protein/gene interaction, protein-small molecule/chemical interaction, biological process annotation, gene co-occurrence and pathway enrichment analysis and microRNA-mRNA interaction, were performed to illustrate the association of HNF1B with drug resistance in ovarian cancer. We found that among the proteins/genes, small molecules/chemicals and microRNAs which directly interacted with HNF1B, the majority was associated with drug resistance in cancer, particularly in ovarian cancer. Biological process annotation revealed that HNF1B closely related to 24 biological processes which were all notably associated with ovarian cancer and drug resistance. These results indicated that the downregulation of HNF1B may contribute to drug resistance in ovarian cancer, via its direct interactions with these drug resistance-related proteins/genes, small molecules/chemicals and microRNAs, and via its regulations on the drug resistance-related biological processes. Pathway enrichment analysis of 36 genes which co-occurred with HNF1B, ovarian cancer and drug resistance indicated that the HNF1B may perform its drug resistance-related functions through 4 pathways including ErbB signaling, focal adhesion, apoptosis and p53 signaling. Collectively, in this study, we illustrated for the first time that HNF1B may contribute to drug resistance in ovarian cancer, potentially through the 4 pathways. The present study may pave the way for further investigation of the drug resistance-related functions of HNF1B in ovarian cancer.
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Affiliation(s)
- Jianchao Li
- Department of Obstetrics and Gynecology, Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, P.R. China
| | - Yonghong Zhang
- Department of Obstetrics and Gynecology, Muping Traditional Chinese Medicine Hospital, Yantai, Shandong, P.R. China
| | - Yutao Gao
- Department of Obstetrics and Gynecology, Beijing Chao-Yang Hospital, Affiliated to Capital Medical University, Beijing, P.R. China
| | - Yuqian Cui
- Center for Reproductive Medicine, Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, P.R. China
| | - Hua Liu
- Department of Obstetrics and Gynecology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, P.R. China
| | - Mi Li
- Department of Nursing, Shandong College of Traditional Chinese Medicine, Yantai, Shandong, P.R. China
| | - Yongjie Tian
- Department of Obstetrics and Gynecology, Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, P.R. China
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Faguer S, Chassaing N, Bandin F, Prouheze C, Garnier A, Casemayou A, Huart A, Schanstra JP, Calvas P, Decramer S, Chauveau D. The HNF1B score is a simple tool to select patients for HNF1B gene analysis. Kidney Int 2014; 86:1007-15. [PMID: 24897035 DOI: 10.1038/ki.2014.202] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 03/19/2014] [Accepted: 04/10/2014] [Indexed: 12/29/2022]
Abstract
HNF1B-related disease is an emerging condition characterized by an autosomal-dominant inheritance, a 50% rate of de novo mutations, and a highly variable phenotype (renal involvement, maturity-onset diabetes of the young type 5, pancreatic hypoplasia, and urogenital tract and liver test abnormalities). Given the current lack of pathognomonic characteristics and the wide overlap with other conditions, a genetic test is the diagnostic gold standard. However, pre-genetic screening is mandatory because genetic testing has substantial costs. Our aim was to develop a HNF1B score, based on clinical, imaging, and biological variables, as a pivotal tool for rational genetic testing. A score was created using a weighted combination of the most discriminative characteristics based on the frequency and specificity in published series. The HNF1B score is calculated upon 17 items including antenatal discovery, family history, and organ involvement (kidney, pancreas, liver, and genital tract). The performance of the score was assessed by a ROC curve analysis in a 433-individual cohort containing 56 HNF1B cases. The HNF1B score efficiently and significantly discriminated between mutated and nonmutated cases (AUC 0.78). The optimal cutoff threshold for the negative predictive value to rule out HNF1B mutations in a suspected individual was 8 (sensitivity 98.2%, specificity 41.1%, and negative predictive value over 99%). Thus, the HNF1B score is a simple and accurate tool to provide a more rational approach to select patients for HNF1B screening.
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Affiliation(s)
- Stanislas Faguer
- 1] Département de Néphrologie et Transplantation d'organes, Hôpital Rangueil, CHU Toulouse, France [2] Centre de référence des maladies rénales rares, Toulouse, France [3] Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institute of Cardiovascular and Metabolic Disease, Toulouse, France [4] Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Nicolas Chassaing
- 1] Université Toulouse III Paul-Sabatier, Toulouse, France [2] Service de Génétique médicale et UPS III EA4555, Hôpital Purpan, CHU de Toulouse, France
| | - Flavio Bandin
- Centre de référence des maladies rénales rares, Toulouse, France
| | - Cathie Prouheze
- Centre de référence des maladies rénales rares, Toulouse, France
| | - Arnaud Garnier
- Service de Néphrologie Pédiatrique, HTA et Médecine Interne, Hôpital des Enfants, CHU Toulouse, France
| | - Audrey Casemayou
- 1] Centre de référence des maladies rénales rares, Toulouse, France [2] Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institute of Cardiovascular and Metabolic Disease, Toulouse, France
| | - Antoine Huart
- Département de Néphrologie et Transplantation d'organes, Hôpital Rangueil, CHU Toulouse, France
| | - Joost P Schanstra
- 1] Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institute of Cardiovascular and Metabolic Disease, Toulouse, France [2] Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Patrick Calvas
- 1] Université Toulouse III Paul-Sabatier, Toulouse, France [2] Service de Génétique médicale et UPS III EA4555, Hôpital Purpan, CHU de Toulouse, France
| | - Stéphane Decramer
- 1] Centre de référence des maladies rénales rares, Toulouse, France [2] Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institute of Cardiovascular and Metabolic Disease, Toulouse, France [3] Université Toulouse III Paul-Sabatier, Toulouse, France [4] Service de Néphrologie Pédiatrique, HTA et Médecine Interne, Hôpital des Enfants, CHU Toulouse, France
| | - Dominique Chauveau
- 1] Département de Néphrologie et Transplantation d'organes, Hôpital Rangueil, CHU Toulouse, France [2] Centre de référence des maladies rénales rares, Toulouse, France [3] Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institute of Cardiovascular and Metabolic Disease, Toulouse, France [4] Université Toulouse III Paul-Sabatier, Toulouse, France
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Chauveau D, Faguer S, Bandin F, Guigonis V, Chassaing N, Decramer S. HNF1B : paradigme d’un gène du développement et émergence inattendue d’une nouvelle maladie génétique rénale. Nephrol Ther 2013; 9:393-7. [DOI: 10.1016/j.nephro.2013.05.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2011] [Revised: 05/13/2013] [Accepted: 05/13/2013] [Indexed: 11/30/2022]
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Primary hepatocellular neoplasms in a MODY3 family with a novel HNF1A germline mutation. J Hepatol 2013; 59:904-7. [PMID: 23707370 DOI: 10.1016/j.jhep.2013.05.024] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Revised: 05/03/2013] [Accepted: 05/10/2013] [Indexed: 12/11/2022]
Abstract
Maturity onset diabetes of the young type 3 (MODY3) and hepatocellular adenomas (HCAs) are associated with mutations in the HNF1A gene. HNF1A codes for the transcription factor HNF1α, which interacts with DNA as a homodimer or a heterodimer with HNF1β, to regulate multiple cellular functions including glucidic metabolism, lipidic transport, and detoxication. We report three members of one family with a novel germline in-frame deletion of HNF1A exons 2-3 identified initially using array CGH and direct sequence analysis. All three family members have MODY3 in association with primary liver cell tumours (HCA, liver adenomatosis (LA), and hepatocellular carcinoma (HCC)). Additionally, a high rate of infant mortality was observed in the family. The described family demonstrates a novel HNF1A mutation associated with both benign and malignant primary liver cell tumours and MODY3.
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Integrative bioinformatics links HNF1B with clear cell carcinoma and tumor-associated thrombosis. PLoS One 2013; 8:e74562. [PMID: 24040285 PMCID: PMC3767734 DOI: 10.1371/journal.pone.0074562] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 07/14/2013] [Indexed: 01/21/2023] Open
Abstract
Clear cell carcinoma (CCC) is a histologically distinct carcinoma subtype that arises in several organ systems and is marked by cytoplasmic clearing, attributed to abundant intracellular glycogen. Previously, transcription factor hepatocyte nuclear factor 1-beta (HNF1B) was identified as a biomarker of ovarian CCC. Here, we set out to explore more broadly the relation between HNF1B and carcinomas with clear cell histology. HNF1B expression, evaluated by immunohistochemistry, was significantly associated with clear cell histology across diverse gynecologic and renal carcinomas (P<0.001), as was hypomethylation of the HNF1B promoter (P<0.001). From microarray analysis, an empirically-derived HNF1B signature was significantly enriched for computationally-predicted targets (with HNF1 binding sites) (P<0.03), as well as genes associated with glycogen metabolism, including glucose-6-phophatase, and strikingly the blood clotting cascade, including fibrinogen, prothrombin and factor XIII. Enrichment of the clotting cascade was also evident in microarray data from ovarian CCC versus other histotypes (P<0.01), and HNF1B-associated prothrombin expression was verified by immunohistochemistry (P = 0.015). Finally, among gynecologic carcinomas with cytoplasmic clearing, HNF1B immunostaining was linked to a 3.0-fold increased risk of clinically-significant venous thrombosis (P = 0.043), and with a 2.3-fold increased risk (P = 0.011) in a combined gynecologic and renal carcinoma cohort. Our results define HNF1B as a broad marker of clear cell phenotype, and support a mechanistic link to glycogen accumulation and thrombosis, possibly reflecting (for gynecologic CCC) derivation from secretory endometrium. Our findings also implicate a novel mechanism of tumor-associated thrombosis (a major cause of cancer mortality), based on the direct production of clotting factors by cancer cells.
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Bonner C, Nyhan KC, Bacon S, Kyithar MP, Schmid J, Concannon CG, Bray IM, Stallings RL, Prehn JHM, Byrne MM. Identification of circulating microRNAs in HNF1A-MODY carriers. Diabetologia 2013; 56:1743-51. [PMID: 23674172 DOI: 10.1007/s00125-013-2939-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 04/25/2013] [Indexed: 01/17/2023]
Abstract
AIMS/HYPOTHESIS HNF1A-MODY is a monogenic form of diabetes caused by mutations in the HNF1A gene. Here we identify, for the first time, HNF1A-MODY-associated microRNAs (miRNAs) that can be detected in the serum of HNF1A-MODY carriers. METHODS An miRNA array was carried out in rat INS-1 insulinoma cells inducibly expressing the common human Pro291fsinsC-HNF1A frame shift mutation. Differentially expressed miRNAs were validated by quantitative real-time PCR. Expression of miRNAs in the serum of HNF1A-MODY carriers (n = 31), MODY-negative family members (n = 10) and individuals with type 2 diabetes mellitus (n = 17) was quantified by absolute real-time PCR analysis. RESULTS Inducible expression of Pro291fsinsC-HNF1A in INS-1 cells caused a significant upregulation of three miRNAs (miR-103, miR-224, miR-292-3p). The differential expression of two miRNAs (miR-103 and miR-224) was validated in vitro. Strongly elevated levels of miR-103 and miR-224 could be detected in the serum of HNF1A-MODY carriers compared with MODY-negative family controls. Serum levels of miR-103 distinguished HNF1A-MODY carriers from HbA1c-matched individuals with type 2 diabetes mellitus. CONCLUSIONS/INTERPRETATION Our study demonstrates that the pathophysiology of HNF1A-MODY is associated with the overexpression of miR-103 and miR-224. Furthermore, our study demonstrates that these miRNAs can be readily detected in the serum of HNF1A-MODY carriers.
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Affiliation(s)
- C Bonner
- Department of Physiology and Medical Physics, Royal College of Surgeons, Dublin, Ireland
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Sun JZ, Yang XX, Hu NY, Li X, Li FX, Li M. Genetic Variants in MMP9 and TCF2 Contribute to Susceptibility to Lung Cancer. Chin J Cancer Res 2013; 23:183-7. [PMID: 23467666 DOI: 10.1007/s11670-011-0183-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2011] [Accepted: 05/17/2011] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVE The Wnt signaling pathway is crucial for pulmonary development and differentiation; dysregulation of the Wnt signaling pathway may impair lung function. Indeed, single nucleotide polymorphisms (SNPs) of Wnt pathway-related genes have been suggested as risk factors for certain types of cancers. In this study, we aimed to evaluate the influence of SNPs in Wnt-related genes (TCF2, MMP9) on susceptibility to lung cancer. METHODS Polymorphisms of TCF2 rs4430796, MMP9 rs2250889, and MMP9 rs17576 were studied in Han Chinese subjects, including 135 patients with lung cancer and 176 controls, using the Sequenom MassARRAY platform. The association of genotypes with susceptibility to lung cancer was analyzed using odds ratio (OR), with 95% confidence interval (95% CI) and χ(2). RESULTS The three SNPs (rs4430796, rs2250889, and rs17576) were found to be significantly associated with an increased risk of lung cancer. The AA genotype and AG+AA genotype of rs4430796 showed a significantly increased susceptibility to lung cancer compared with the GG genotype (adjusted OR=6.03, 95% CI: 1.30-28.09, P=0.022; 5.55, 95% CI: 1.20-25.58, P=0.028). Compared with the rs17576 GG genotype, the AG and AG+AA genotypes were also associated with a significant risk (adjusted OR=2.65, 95% CI: 1.60-4.37, P≤0.001; 2.57, 95% CI: 1.59-4.19, P≤0.001) whereas the rs2250889 CG and CG+GG genotypes had 2.97-fold (95% CI: 1.81-4.85; P≤0.001) and 2.80-fold increased associations with lung cancer (95% CI: 1.73-4.54; P≤0.001), respectively, compared with the rs2250889 CC genotype. Furthermore, the association of rs4430796 with lung cancer became insignificant (P>0.05) after adjusting for gender and rs2250889. CONCLUSION The three SNPs may play a role in the predisposition of members of the Han Chinese population to lung cancer.
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Affiliation(s)
- Jing-Zhe Sun
- School of Biotechnology, Southern Medical University, Guangzhou 510515, China
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Wang CC, Mao TL, Yang WC, Jeng YM. Underexpression of hepatocyte nuclear factor-1β in chromophobe renal cell carcinoma. Histopathology 2012; 62:589-94. [PMID: 23237209 DOI: 10.1111/his.12026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Accepted: 09/07/2012] [Indexed: 12/27/2022]
Abstract
AIMS Chromophobe renal cell carcinoma (ChRCC) is an uncommon malignant renal neoplasm with a generally indolent clinical behaviour. Previous studies revealed biallelic inactivation of the hepatocyte nuclear factor-1β (HNF1β) gene in several patients with ChRCC. The aims of this study were to determine HNF1β expression in renal neoplasms and the potential of HNF1β as a diagnostic marker for ChRCC. METHODS AND RESULTS We performed immunohistochemical staining of 79 samples taken from patients with primary renal neoplasm [19 renal oncocytomas, 18 ChRCCs, 24 clear cell renal cell carcinomas (CCRCCs), and 18 papillary renal cell carcinomas]. HNF1β was underexpressed in 16 of 18 cases of ChRCC (88.9%). By contrast, HNF1β expression was preserved in the majority of renal oncocytoma (94.7%, 18/19) and CCRCC (95.8%, 23/24) cases. The combined use of HNF1β and cytokeratin 7 (CK7) further increased the diagnostic sensitivity and specificity; the profile of HNF1β positivity and CK7 negativity was not visible in any ChRCC sample, but was common in both renal oncocytoma (94.7%, 18/19) and CCRCC (91.7%, 22/24) samples. CONCLUSIONS The results suggest that a lack of HNF1β expression might play an important role in the pathogenesis of ChRCC, and may serve as a good diagnostic marker for this neoplasm.
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Affiliation(s)
- Chung-Chieh Wang
- Department of Pathology, National Taiwan University Hospital, National Taiwan University, Taipei, Taiwan
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Genetic and functional analyses implicate the NUDT11, HNF1B, and SLC22A3 genes in prostate cancer pathogenesis. Proc Natl Acad Sci U S A 2012; 109:11252-7. [PMID: 22730461 DOI: 10.1073/pnas.1200853109] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
One of the central goals of human genetics is to discover the genes and pathways driving human traits. To date, most of the common risk alleles discovered through genome-wide association studies (GWAS) map to nonprotein-coding regions. Because of our relatively poorer understanding of this part of the genome, the functional consequences of trait-associated variants pose a considerable challenge. To identify the genes through which risk loci act, we hypothesized that the risk variants are regulatory elements. For each of 12 known risk polymorphisms, we evaluated the correlation between risk allele status and transcript abundance for all annotated protein-coding transcripts within a 1-Mb interval. A total of 103 transcripts were evaluated in 662 prostate tissue samples [normal (n = 407) and tumor (n = 255)] from 483 individuals [European Americans (n = 233), Japanese (n = 127), and African Americans (n = 123)]. In a pooled analysis, 4 of the 12 risk variants were strongly associated with five transcripts (NUDT11, MSMB, NCOA4, SLC22A3, and HNF1B) in histologically normal tissue (P ≤ 0.001). Although associations were also observed in tumor tissue, they tended to be more attenuated. Previously, we showed that MSMB and NCOA4 participate in prostate cancer pathogenesis. Suppressing the expression of NUDT11, SLC22A3, and HNF1B influences cellular phenotypes associated with tumor-related properties in prostate cancer cells. Taken together, the data suggest that these transcripts contribute to prostate cancer pathogenesis.
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Azeem K, Kollarova H, Horakova D, Magnuskova S, Janout V. Genetic syndromes associated with renal cell carcinoma: a review. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2012; 155:231-8. [PMID: 22286808 DOI: 10.5507/bp.2011.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
AIMS A review of recent knowledge on heredital syndromes related to renal cell carcinoma. METHODS Aim of this review was to summarize the recent knowledge of genetic syndromes associated with renal cell carcinoma. RESULTS Summary of incidence and factors modulating risk of hereditary renal cell carcinoma development. CONCLUSIONS Hereditary forms of RCC are relatively rare. Their study is beneficial in many ways. In individuals at a higher risk of a hereditary syndrome, the knowledge of hereditary forms may help to significantly decrease the impact of the hereditary disease. In the general population, knowledge acquired by the study of hereditary forms of RCC may in the future contribute to both diagnosis and treatment of sporadic tumours.
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Affiliation(s)
- Katerina Azeem
- Department of Preventive Medicine, Palacky University Olomouc, Czech Republic.
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Sakellariou S, Al-Hussaini H, Scalori A, Samyn M, Heaton N, Portmann B, Tobal K, Quaglia A. Hepatocellular adenoma in glycogen storage disorder type I: a clinicopathological and molecular study. Histopathology 2012; 60:E58-65. [PMID: 22372484 DOI: 10.1111/j.1365-2559.2011.04153.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
AIMS Glycogen storage disease type I is a metabolic disorder resulting from deficiency of the glucose-6-phosphate complex. Long-term complications include the development of hepatocellular adenoma (HCA). In this retrospective study, our aim was to reclassify according to geno-phenotypic characteristics nodular lesions identified in hepatectomy specimens of such patients transplanted between 1998 and 2008 at our institution. METHODS AND RESULTS Clinicopathological data of seven consecutive transplanted patients with glycogen storage disease type I were reviewed. Liver nodules were re-examined histologically and by immunohistochemistry. Molecular analysis was performed additionally in a case with specific features. Four patients had multiple tumours. We concluded that 26 of 38 nodules available for study had features of inflammatory hepatocellular adenomas, seven comprised adenomas not otherwise specified and five were found to be focal nodular hyperplasia. CONCLUSIONS Further studies are needed to clarify the pathogenesis of hepatocellular adenomas in glycogen storage disease; in particular to determine whether they share abnormal metabolic pathways with inflammatory adenomas in the general population. Testing for acute phase proteins may be a helpful tool in the early detection of HCA in such patients. Finally, there is a need to further define their risk of malignant transformation, in relation to age and possible cofactors.
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Expression and clinicopathological significance of notch signaling and cell-fate genes in biliary tract cancer. Am J Gastroenterol 2012; 107:126-35. [PMID: 21931375 DOI: 10.1038/ajg.2011.305] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Biliary tract cancer (BTC) is a fatal cancer originating from epithelial cells of the intra- and extra-hepatic biliary duct system and the gallbladder. Genes and pathways regulating stem and progenitor cells as well as cell-fate decisions are increasingly recognized in tumorigenesis. We evaluated the expression of Notch1, Notch2, and HES1 (hairy and enhancer of split 1), as well as the biliary cell-fate regulators SOX9 (SRY (sex determining region Y)-box 9) and HNF1β (hepatocyte nuclear factor 1β), in BTC for correlation with clinicopathological parameters. METHODS Tissue microarrays including normal bile ducts and 111 BTCs consisting of 17 intrahepatic cholangiocarcinomas, 58 extrahepatic cholangiocarcinomas, and 36 gallbladder carcinomas were analyzed using immunohistochemistry. RESULTS Lack of cytoplasmic SOX9 expression was associated with a higher tumor grade (P=0.010) and a significantly reduced overall survival (P=0.002; median 6 months vs. 24 months) in univariate survival analysis, whereas lack of nuclear SOX9 expression was associated with a higher tumor stage (P=0.003). Notch pathway members showed high expression in BTC. However, no correlation was found between cytoplasmic or nuclear Notch1, Notch2, and HES1, as well as HNF1β expression, and any of the clinicopathological parameters. In multivariate analysis, cytoplasmic SOX9 expression was an independent prognostic factor for overall survival (P=0.031, relative risk=0.571). CONCLUSIONS We show strong Notch pathway activation and identify SOX9 as a prognostic marker in BTC. These results substantiate diagnostic and therapeutic approaches targeting developmentally active genes and pathways.
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GNAS-activating mutations define a rare subgroup of inflammatory liver tumors characterized by STAT3 activation. J Hepatol 2012; 56:184-91. [PMID: 21835143 DOI: 10.1016/j.jhep.2011.07.018] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 07/07/2011] [Accepted: 07/12/2011] [Indexed: 12/28/2022]
Abstract
BACKGROUND & AIMS Mosaic G-protein alpha-subunit (GNAS)-activating mutations are responsible for the McCune-Albright (MCA) syndrome. This oncogene that activates the adenylate cyclase is also mutated in various tumor types leading to the accumulation of cyclic-AMP. Identification of a hepatocellular adenoma (HCA) in two MCA patients led us to search for GNAS activation in benign and malignant hepatocellular carcinogenesis. METHODS GNAS mutations were screened by sequencing 164 HCA, 245 hepatocellular carcinoma (HCC), and 17 fibrolamellar carcinomas. Tumors were characterized by quantitative RT-PCR, gene mutation screening and pathological reviewing. The consequences of wild type and mutant GNAS expression were analyzed in hepatocellular cell lines. RESULTS A somatic GNAS-activating mutation was identified in 5 benign tumors and in 2 HCC. In benign tumors, GNAS mutations were exclusive from HNF1A, CTNNB1, and IL6ST mutations whereas one HCC demonstrated both CTNNB1 and GNAS mutations. Quantitative RT-PCR showed an activation of the IL-6 and interferon pathways in GNAS-mutated tumor tissues. Accordingly, pathological reviewing identified in GNAS-mutated tumors an inflammatory phenotype characterized by fibrosis and STAT3 activation. We further demonstrated in HCC cell lines that GNAS mutant expression induced inflammatory response and STAT3 activation. CONCLUSIONS We identified for the first time the association between two rare diseases, MCA syndrome and HCA occurrence, but also that somatic GNAS-activating mutations in sporadic benign and malignant liver tumors are characterized by an inflammatory phenotype. These results showed a cross-talk between cyclic-AMP and JAK/STAT pathways in liver tumors and they reinforce the role of STAT3 activation in liver tumorigenesis.
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Faguer S, Decramer S, Devuyst O, Lengelé JP, Fournié GJ, Chauveau D. Expression of Renal Cystic Genes in Patients with HNF1B Mutations. ACTA ACUST UNITED AC 2012; 120:c71-8. [DOI: 10.1159/000334954] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 10/27/2011] [Indexed: 12/20/2022]
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