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Tian Y, Xin S, Wan Z, Dong H, Liu L, Fan Z, Li T, Peng F, Xiong Y, Han Y. TCF19 promotes cell proliferation and tumor formation in lung cancer by activating the Raf/MEK/ERK signaling pathway. Transl Oncol 2024; 45:101978. [PMID: 38701650 PMCID: PMC11088346 DOI: 10.1016/j.tranon.2024.101978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/09/2024] [Accepted: 04/27/2024] [Indexed: 05/05/2024] Open
Abstract
OBJECTIVE This study aimed to investigate TCF19's role in lung cancer development, specifically its involvement in the RAF/MEK/ERK signaling pathway. METHODS Lung cancer tissue analysis revealed significant TCF19 overexpression. In vitro experiments using A549 and Hop62 cells with TCF19 overexpression demonstrated enhanced cell growth. Transgenic mouse models confirmed TCF19's role in primary tumor development. Transcriptome sequencing identified altered gene expression profiles, linking TCF19 to RAF/MEK/ERK pathway activation. Functional assays elucidated underlying mechanisms, revealing increased phosphorylation of Raf1, MEK1/2, and ERK1/2. Inhibiting RAF1 or ERK through shRaf1 or ERK inhibitor reduced cell cycle-related proteins and inhibited TCF19-overexpressing cell growth. RESULTS TCF19 was identified as an oncogene in lung carcinoma, specifically impacting the RAF/MEK/ERK pathway. Elevated TCF19 levels in lung cancer suggest targeting TCF19 or its associated pathways as a promising strategy for disease management. CONCLUSION This study unveils TCF19's oncogenic role in lung cancer, emphasizing its modulation of the RAF/MEK/ERK pathway and presenting a potential therapeutic target for TCF19-overexpressing lung cancers.
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Affiliation(s)
- Yahui Tian
- Department of Thoracic Surgery, Air Force Medical Center, Air Force Medical University, 30 Fucheng Rd, Beijing 100142, China; School of Basic Medical Sciences, Shandong Second Medical University, Weifang, China
| | - Shaowei Xin
- Department of Thoracic Surgery, Air Force Medical Center, Air Force Medical University, 30 Fucheng Rd, Beijing 100142, China
| | - Zitong Wan
- College of life Science, Northwestern University, Xi'an, China
| | - Honghong Dong
- Department of Thoracic Surgery, Air Force Medical Center, Air Force Medical University, 30 Fucheng Rd, Beijing 100142, China
| | - Lu Liu
- College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Zhenzhen Fan
- CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, China
| | - Tian Li
- School of Basic Medicine, Fourth Military Medical University, Xi'an 710032, China
| | - Fujun Peng
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang, China.
| | - Yanlu Xiong
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China.
| | - Yong Han
- Department of Thoracic Surgery, Air Force Medical Center, Air Force Medical University, 30 Fucheng Rd, Beijing 100142, China.
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2
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Ruan X, Liu Y, Wu S, Fu G, Tao M, Huang Y, Li D, Wei S, Gao M, Guo S, Ning J, Zheng X. Multidimensional data analysis revealed thyroiditis-associated TCF19 SNP rs2073724 as a highly ranked protective variant in thyroid cancer. Aging (Albany NY) 2024; 16:6488-6509. [PMID: 38579171 PMCID: PMC11042956 DOI: 10.18632/aging.205718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 03/14/2024] [Indexed: 04/07/2024]
Abstract
BACKGROUND Thyroid cancer represents the most prevalent malignant endocrine tumour, with rising incidence worldwide and high mortality rates among patients exhibiting dedifferentiation and metastasis. Effective biomarkers and therapeutic interventions are warranted in aggressive thyroid malignancies. The transcription factor 19 (TCF19) gene has been implicated in conferring a malignant phenotype in cancers. However, its contribution to thyroid neoplasms remains unclear. RESULTS In this study, we performed genome-wide and phenome-wide association studies to identify a potential causal relationship between TCF19 and thyroid cancer. Our analyses revealed significant associations between TCF19 and various autoimmune diseases and human cancers, including cervical cancer and autoimmune thyroiditis, with a particularly robust signal for the deleterious missense variation rs2073724 that is associated with thyroid function, hypothyroidism, and autoimmunity. Furthermore, functional assays and transcriptional profiling in thyroid cancer cells demonstrated that TCF19 regulates important biological processes, especially inflammatory and immune responses. We demonstrated that TCF19 could promote the progression of thyroid cancer in vitro and in vivo and the C>T variant of rs2073724 disrupted TCF19 protein binding to target gene promoters and their expression, thus reversing the effect of TCF19 protein. CONCLUSIONS Taken together, these findings implicate TCF19 as a promising therapeutic target in aggressive thyroid malignancies and designate rs2073724 as a causal biomarker warranting further investigation in thyroid cancer.
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Affiliation(s)
- Xianhui Ruan
- Department of Thyroid and Neck Tumor, 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 300060, China
| | - Yu Liu
- Department of Thyroid and Neck Tumor, 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 300060, China
| | - Shuping Wu
- Department of Thyroid and Neck Tumor, 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 300060, China
- Department of Head and Neck Surgery, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou 350014, Fujian, China
| | - Guiming Fu
- Department of Thyroid and Neck Tumor, 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 300060, China
- Thyroid-Otolaryngology Department, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu 610000, Sichuan, China
| | - Mei Tao
- Department of Thyroid and Neck Tumor, 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 300060, China
| | - Yue Huang
- Department of Thyroid and Neck Tumor, 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 300060, China
| | - Dapeng Li
- Department of Thyroid and Neck Tumor, 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 300060, China
| | - Songfeng Wei
- Department of Thyroid and Neck Tumor, 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 300060, China
| | - Ming Gao
- Department of Thyroid and Neck Tumor, 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 300060, China
- Department of Thyroid and Breast Surgery, Tianjin Union Medical Center, Tianjin 300121, China
- Tianjin Key Laboratory of General Surgery in Construction, Tianjin Union Medical Center, Tianjin 300121, China
| | - Shicheng Guo
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Junya Ning
- Department of Thyroid and Neck Tumor, 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 300060, China
- Department of Thyroid and Breast Surgery, Tianjin Union Medical Center, Tianjin 300121, China
| | - Xiangqian Zheng
- Department of Thyroid and Neck Tumor, 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 300060, China
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3
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Robert VJ, Caron M, Gely L, Adrait A, Pakulska V, Couté Y, Chevalier M, Riedel CG, Bedet C, Palladino F. SIN-3 acts in distinct complexes to regulate the germline transcriptional program in Caenorhabditis elegans. Development 2023; 150:dev201755. [PMID: 38771303 PMCID: PMC10617626 DOI: 10.1242/dev.201755] [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: 03/08/2023] [Accepted: 09/18/2023] [Indexed: 10/12/2023]
Abstract
The transcriptional co-regulator SIN3 influences gene expression through multiple interactions that include histone deacetylases. Haploinsufficiency and mutations in SIN3 are the underlying cause of Witteveen-Kolk syndrome and related intellectual disability and autism syndromes, emphasizing its key role in development. However, little is known about the diversity of its interactions and functions in developmental processes. Here, we show that loss of SIN-3, the single SIN3 homolog in Caenorhabditis elegans, results in maternal-effect sterility associated with de-regulation of the germline transcriptome, including de-silencing of X-linked genes. We identify at least two distinct SIN3 complexes containing specific histone deacetylases and show that they differentially contribute to fertility. Single-cell, single-molecule fluorescence in situ hybridization reveals that in sin-3 mutants the X chromosome becomes re-expressed prematurely and in a stochastic manner in individual germ cells, suggesting a role for SIN-3 in its silencing. Furthermore, we identify histone residues whose acetylation increases in the absence of SIN-3. Together, this work provides a powerful framework for the in vivo study of SIN3 and associated proteins.
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Affiliation(s)
- Valerie J. Robert
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, 69007 Lyon, France
| | - Matthieu Caron
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, 69007 Lyon, France
| | - Loic Gely
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, 69007 Lyon, France
| | - Annie Adrait
- Grenoble Alpes, CEA, Inserm, UA13 BGE, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Victoria Pakulska
- Grenoble Alpes, CEA, Inserm, UA13 BGE, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Yohann Couté
- Grenoble Alpes, CEA, Inserm, UA13 BGE, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Manon Chevalier
- Department of Biosciences and Nutrition, Karolinska Institutet, Blickagången 16, 14157 Huddinge, Sweden
| | - Christian G. Riedel
- Department of Biosciences and Nutrition, Karolinska Institutet, Blickagången 16, 14157 Huddinge, Sweden
| | - Cecile Bedet
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, 69007 Lyon, France
| | - Francesca Palladino
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, 69007 Lyon, France
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4
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Nishi K, Yoshii A, Abell L, Zhou B, Frausto R, Ritterhoff J, McMillen TS, Sweet I, Wang Y, Gao C, Tian R. Branched-chain keto acids inhibit mitochondrial pyruvate carrier and suppress gluconeogenesis in hepatocytes. Cell Rep 2023; 42:112641. [PMID: 37310861 PMCID: PMC10592489 DOI: 10.1016/j.celrep.2023.112641] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/06/2023] [Accepted: 05/29/2023] [Indexed: 06/15/2023] Open
Abstract
Branched-chain amino acid (BCAA) metabolism is linked to glucose homeostasis, but the underlying signaling mechanisms are unclear. We find that gluconeogenesis is reduced in mice deficient of Ppm1k, a positive regulator of BCAA catabolism, which protects against obesity-induced glucose intolerance. Accumulation of branched-chain keto acids (BCKAs) inhibits glucose production in hepatocytes. BCKAs suppress liver mitochondrial pyruvate carrier (MPC) activity and pyruvate-supported respiration. Pyruvate-supported gluconeogenesis is selectively suppressed in Ppm1k-deficient mice and can be restored with pharmacological activation of BCKA catabolism by BT2. Finally, hepatocytes lack branched-chain aminotransferase that alleviates BCKA accumulation via reversible conversion between BCAAs and BCKAs. This renders liver MPC most susceptible to circulating BCKA levels hence a sensor of BCAA catabolism.
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Affiliation(s)
- Kiyoto Nishi
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA; Department of Pharmacology, Shiga University of Medical Science, Otsu, Shiga 520-2182, Japan
| | - Akira Yoshii
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA
| | - Lauren Abell
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA
| | - Bo Zhou
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA
| | - Ricardo Frausto
- Department of Anesthesiology, Cardiovascular Research Laboratories, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Julia Ritterhoff
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA
| | - Timothy S McMillen
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA
| | - Ian Sweet
- University of Washington Medicine Diabetes Institute, University of Washington, 750 Republican Street, Seattle, WA 98109, USA
| | - Yibin Wang
- Department of Anesthesiology, Cardiovascular Research Laboratories, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; Signature Program in Cardiovascular and Metabolic Diseases, Duke-NUS School of Medicine, Singapore, Singapore
| | - Chen Gao
- Department of Anesthesiology, Cardiovascular Research Laboratories, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Pharmacology and Systems Physiology, University of Cincinnati, College of Medicine, Cincinnati, OH 45267-0575, USA.
| | - Rong Tian
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA.
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5
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Wu YL, Lin ZJ, Li CC, Lin X, Shan SK, Guo B, Zheng MH, Li F, Yuan LQ, Li ZH. Epigenetic regulation in metabolic diseases: mechanisms and advances in clinical study. Signal Transduct Target Ther 2023; 8:98. [PMID: 36864020 PMCID: PMC9981733 DOI: 10.1038/s41392-023-01333-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/02/2023] [Accepted: 01/18/2023] [Indexed: 03/04/2023] Open
Abstract
Epigenetics regulates gene expression and has been confirmed to play a critical role in a variety of metabolic diseases, such as diabetes, obesity, non-alcoholic fatty liver disease (NAFLD), osteoporosis, gout, hyperthyroidism, hypothyroidism and others. The term 'epigenetics' was firstly proposed in 1942 and with the development of technologies, the exploration of epigenetics has made great progresses. There are four main epigenetic mechanisms, including DNA methylation, histone modification, chromatin remodelling, and noncoding RNA (ncRNA), which exert different effects on metabolic diseases. Genetic and non-genetic factors, including ageing, diet, and exercise, interact with epigenetics and jointly affect the formation of a phenotype. Understanding epigenetics could be applied to diagnosing and treating metabolic diseases in the clinic, including epigenetic biomarkers, epigenetic drugs, and epigenetic editing. In this review, we introduce the brief history of epigenetics as well as the milestone events since the proposal of the term 'epigenetics'. Moreover, we summarise the research methods of epigenetics and introduce four main general mechanisms of epigenetic modulation. Furthermore, we summarise epigenetic mechanisms in metabolic diseases and introduce the interaction between epigenetics and genetic or non-genetic factors. Finally, we introduce the clinical trials and applications of epigenetics in metabolic diseases.
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Affiliation(s)
- Yan-Lin Wu
- National Clinical Research Center for Metabolic Disease, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Zheng-Jun Lin
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Chang-Chun Li
- National Clinical Research Center for Metabolic Disease, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Xiao Lin
- Department of Radiology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Su-Kang Shan
- National Clinical Research Center for Metabolic Disease, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Bei Guo
- National Clinical Research Center for Metabolic Disease, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Ming-Hui Zheng
- National Clinical Research Center for Metabolic Disease, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Fuxingzi Li
- National Clinical Research Center for Metabolic Disease, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Ling-Qing Yuan
- National Clinical Research Center for Metabolic Disease, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China.
| | - Zhi-Hong Li
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China. .,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China.
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6
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Deng Y, Huang H, Shi J, Jin H. Identification of Candidate Genes in Breast Cancer Induced by Estrogen Plus Progestogens Using Bioinformatic Analysis. Int J Mol Sci 2022; 23:ijms231911892. [PMID: 36233194 PMCID: PMC9569986 DOI: 10.3390/ijms231911892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/28/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022] Open
Abstract
Menopausal hormone therapy (MHT) was widely used to treat menopause-related symptoms in menopausal women. However, MHT therapies were controversial with the increased risk of breast cancer because of different estrogen and progestogen combinations, and the molecular basis behind this phenomenon is currently not understood. To address this issue, we identified differentially expressed genes (DEGs) between the estrogen plus progestogens treatment (EPT) and estrogen treatment (ET) using the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) data. As a result, a total of 96 upregulated DEGs were first identified. Seven DEGs related to the cell cycle (CCNE2, CDCA5, RAD51, TCF19, KNTC1, MCM10, and NEIL3) were validated by RT-qPCR. Specifically, these seven DEGs were increased in EPT compared to ET (p < 0.05) and had higher expression levels in breast cancer than adjacent normal tissues (p < 0.05). Next, we found that estrogen receptor (ER)-positive breast cancer patients with a higher CNNE2 expression have a shorter overall survival time (p < 0.05), while this effect was not observed in the other six DEGs (p > 0.05). Interestingly, the molecular docking results showed that CCNE2 might bind to 17β-estradiol (−6.791 kcal/mol), progesterone (−6.847 kcal/mol), and medroxyprogesterone acetate (−6.314 kcal/mol) with a relatively strong binding affinity, respectively. Importantly, CNNE2 protein level could be upregulated with EPT and attenuated by estrogen receptor antagonist, acolbifene and had interactions with cancer driver genes (AKT1 and KRAS) and high mutation frequency gene (TP53 and PTEN) in breast cancer patients. In conclusion, the current study showed that CCNE2, CDCA5, RAD51, TCF19, KNTC1, MCM10, and NEIL3 might contribute to EPT-related tumorigenesis in breast cancer, with CCNE2 might be a sensitive risk indicator of breast cancer risk in women using MHT.
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Affiliation(s)
- Yu Deng
- Department of Obstetrics and Gynecology, Peking University First Hospital, No. 8 Xishiku Street, Beijing 100034, China
| | - He Huang
- Department of Obstetrics and Gynecology, Peking University First Hospital, No. 8 Xishiku Street, Beijing 100034, China
| | - Jiangcheng Shi
- School of Life Sciences, Tiangong University, Tianjin 300387, China
| | - Hongyan Jin
- Department of Obstetrics and Gynecology, Peking University First Hospital, No. 8 Xishiku Street, Beijing 100034, China
- Correspondence:
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7
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Immunotherapeutic Value of Transcription Factor 19 (TCF19) Associated with Renal Clear Cell Carcinoma: A Comprehensive Analysis of 33 Human Cancer Cases. JOURNAL OF ONCOLOGY 2022; 2022:1488165. [PMID: 36111242 PMCID: PMC9470357 DOI: 10.1155/2022/1488165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 06/30/2022] [Accepted: 07/06/2022] [Indexed: 12/04/2022]
Abstract
Background We aimed to study the relationship between transcription factor 19 (TCF19) and cancer immunotherapy in the 33 types of human cancers. Methods The Cancer Genome Atlas database was analyzed to obtain the gene expression data and clinical characteristics for the cases of 33 types of cancers. GSE67501, GSE78220, and IMvigor 210 were included in the immunotherapy cohorts. Relevant data were obtained by analyzing the gene expression database. The prognostic value of TCF19 was determined by analyzing various clinical parameters, such as survival duration, age, the stage of the tumor, and sex of the patients. The single-sample gene set enrichment analysis method was used to determine the activity of TCF19 and the method was also used to assess the differences between the TCF19 transcriptome and protein levels. The correlation between TCF19 and various immune processes and elements such as immunosuppressants, stimulants, and major histocompatibility complexes were analyzed to gain insights into the role of TCF19. The coherent paths associated with the process of TCF19 signal transduction and the influence of TCF19 on immunotherapy biomarkers have also been discussed herein. Finally, three independent immunotherapy methods were used to understand the relationship between TCF19 and immunotherapy response. Results It was observed that TCF19 was not significantly influenced by the age (5/33), sex (3/33), or tumor stage (3/21) of cancer patients. But the results revealed that TCF19 exhibited a potential prognostic value and could predict the survival rate of the patients. In some cases of this study, the activity and expression of TCF19 were taken at the same level (7/33). Conclusion TCF19 is strongly related to immune cell infiltration, immunomodulators, and immunotherapy markers. Our study demonstrated that high expression levels of TCF19 are strongly linked with the immune-related pathways. Nevertheless, it is noteworthy that TCF19 is not significantly associated with immunotherapy response.
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8
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Sengupta I, Mondal P, Sengupta A, Mondal A, Singh V, Adhikari S, Dhang S, Roy S, Das C. Epigenetic regulation of Fructose‐1,6‐bisphosphatase 1 by host transcription factor Speckled 110
kDa
during hepatitis B virus infection. FEBS J 2022; 289:6694-6713. [DOI: 10.1111/febs.16544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 05/09/2022] [Accepted: 06/01/2022] [Indexed: 12/17/2022]
Affiliation(s)
- Isha Sengupta
- Biophysics and Structural Genomics Division Saha Institute of Nuclear Physics Kolkata India
| | - Payel Mondal
- Biophysics and Structural Genomics Division Saha Institute of Nuclear Physics Kolkata India
- Homi Bhaba National Institute Mumbai India
| | - Amrita Sengupta
- Biophysics and Structural Genomics Division Saha Institute of Nuclear Physics Kolkata India
| | - Atanu Mondal
- Biophysics and Structural Genomics Division Saha Institute of Nuclear Physics Kolkata India
- Homi Bhaba National Institute Mumbai India
| | - Vipin Singh
- Biophysics and Structural Genomics Division Saha Institute of Nuclear Physics Kolkata India
- Homi Bhaba National Institute Mumbai India
| | - Swagata Adhikari
- Biophysics and Structural Genomics Division Saha Institute of Nuclear Physics Kolkata India
- Homi Bhaba National Institute Mumbai India
| | - Sinjini Dhang
- Structural Biology & Bio‐Informatics Division CSIR‐Indian Institute of Chemical Biology Kolkata India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad India
| | - Siddhartha Roy
- Structural Biology & Bio‐Informatics Division CSIR‐Indian Institute of Chemical Biology Kolkata India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad India
| | - Chandrima Das
- Biophysics and Structural Genomics Division Saha Institute of Nuclear Physics Kolkata India
- Homi Bhaba National Institute Mumbai India
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9
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Yang Y, Luan Y, Feng Q, Chen X, Qin B, Ren KD, Luan Y. Epigenetics and Beyond: Targeting Histone Methylation to Treat Type 2 Diabetes Mellitus. Front Pharmacol 2022; 12:807413. [PMID: 35087408 PMCID: PMC8788853 DOI: 10.3389/fphar.2021.807413] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/24/2021] [Indexed: 12/30/2022] Open
Abstract
Diabetes mellitus is a global public health challenge with high morbidity. Type 2 diabetes mellitus (T2DM) accounts for 90% of the global prevalence of diabetes. T2DM is featured by a combination of defective insulin secretion by pancreatic β-cells and the inability of insulin-sensitive tissues to respond appropriately to insulin. However, the pathogenesis of this disease is complicated by genetic and environmental factors, which needs further study. Numerous studies have demonstrated an epigenetic influence on the course of this disease via altering the expression of downstream diabetes-related proteins. Further studies in the field of epigenetics can help to elucidate the mechanisms and identify appropriate treatments. Histone methylation is defined as a common histone mark by adding a methyl group (-CH3) onto a lysine or arginine residue, which can alter the expression of downstream proteins and affect cellular processes. Thus, in tthis study will discuss types and functions of histone methylation and its role in T2DM wilsed. We will review the involvement of histone methyltransferases and histone demethylases in the progression of T2DM and analyze epigenetic-based therapies. We will also discuss the potential application of histone methylation modification as targets for the treatment of T2DM.
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Affiliation(s)
- Yang Yang
- Department of Translational Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Luan
- Department of Physiology and Neurobiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Qi Feng
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou, China
| | - Xing Chen
- Department of Translational Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Bo Qin
- Department of Translational Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Kai-Di Ren
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, China
| | - Yi Luan
- Department of Translational Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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10
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Mondal A, Bhattacharya A, Singh V, Pandita S, Bacolla A, Pandita RK, Tainer JA, Ramos KS, Pandita TK, Das C. Stress Responses as Master Keys to Epigenomic Changes in Transcriptome and Metabolome for Cancer Etiology and Therapeutics. Mol Cell Biol 2022; 42:e0048321. [PMID: 34748401 PMCID: PMC8773053 DOI: 10.1128/mcb.00483-21] [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] [Indexed: 11/20/2022] Open
Abstract
From initiation through progression, cancer cells are subjected to a magnitude of endogenous and exogenous stresses, which aid in their neoplastic transformation. Exposure to these classes of stress induces imbalance in cellular homeostasis and, in response, cancer cells employ informative adaptive mechanisms to rebalance biochemical processes that facilitate survival and maintain their existence. Different kinds of stress stimuli trigger epigenetic alterations in cancer cells, which leads to changes in their transcriptome and metabolome, ultimately resulting in suppression of growth inhibition or induction of apoptosis. Whether cancer cells show a protective response to stress or succumb to cell death depends on the type of stress and duration of exposure. A thorough understanding of epigenetic and molecular architecture of cancer cell stress response pathways can unveil a plethora of information required to develop novel anticancer therapeutics. The present view highlights current knowledge about alterations in epigenome and transcriptome of cancer cells as a consequence of exposure to different physicochemical stressful stimuli such as reactive oxygen species (ROS), hypoxia, radiation, hyperthermia, genotoxic agents, and nutrient deprivation. Currently, an anticancer treatment scenario involving the imposition of stress to target cancer cells is gaining traction to augment or even replace conventional therapeutic regimens. Therefore, a comprehensive understanding of stress response pathways is crucial for devising and implementing novel therapeutic strategies.
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Affiliation(s)
- Atanu Mondal
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
- Homi Bhaba National Institute, Mumbai, India
| | - Apoorva Bhattacharya
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Vipin Singh
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
- Homi Bhaba National Institute, Mumbai, India
| | - Shruti Pandita
- Division of Hematology and Medical Oncology, St. Louis University, St. Louis, Missouri, USA
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Raj K. Pandita
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - John A. Tainer
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Kenneth S. Ramos
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, Texas, USA
| | - Tej K. Pandita
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, Texas, USA
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
- Homi Bhaba National Institute, Mumbai, India
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11
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Adhikari S, Guha D, Mohan C, Mukherjee S, Tyler JK, Das C. Reprogramming Carbohydrate Metabolism in Cancer and Its Role in Regulating the Tumor Microenvironment. Subcell Biochem 2022; 100:3-65. [PMID: 36301490 PMCID: PMC10760510 DOI: 10.1007/978-3-031-07634-3_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Altered metabolism has become an emerging feature of cancer cells impacting their proliferation and metastatic potential in myriad ways. Proliferating heterogeneous tumor cells are surrounded by other resident or infiltrating cells, along with extracellular matrix proteins, and other secretory factors constituting the tumor microenvironment. The diverse cell types of the tumor microenvironment exhibit different molecular signatures that are regulated at their genetic and epigenetic levels. The cancer cells elicit intricate crosstalks with these supporting cells, exchanging essential metabolites which support their anabolic processes and can promote their survival, proliferation, EMT, angiogenesis, metastasis and even therapeutic resistance. In this context, carbohydrate metabolism ensures constant energy supply being a central axis from which other metabolic and biosynthetic pathways including amino acid and lipid metabolism and pentose phosphate pathway are diverged. In contrast to normal cells, increased glycolytic flux is a distinguishing feature of the highly proliferative cancer cells, which supports them to adapt to a hypoxic environment and also protects them from oxidative stress. Such rewired metabolic properties are often a result of epigenetic alterations in the cancer cells, which are mediated by several factors including, DNA, histone and non-histone protein modifications and non-coding RNAs. Conversely, epigenetic landscapes of the cancer cells are also dictated by their diverse metabolomes. Altogether, this metabolic and epigenetic interplay has immense potential for the development of efficient anti-cancer therapeutic strategies. In this book chapter we emphasize upon the significance of reprogrammed carbohydrate metabolism in regulating the tumor microenvironment and cancer progression, with an aim to explore the different metabolic and epigenetic targets for better cancer treatment.
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Affiliation(s)
- Swagata Adhikari
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
- Homi Bhaba National Institute, Mumbai, India
| | - Deblina Guha
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Chitra Mohan
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shravanti Mukherjee
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Jessica K Tyler
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India.
- Homi Bhaba National Institute, Mumbai, India.
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12
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Mondal P, Tiwary N, Sengupta A, Dhang S, Roy S, Das C. Epigenetic Reprogramming of the Glucose Metabolic Pathways by the Chromatin Effectors During Cancer. Subcell Biochem 2022; 100:269-336. [PMID: 36301498 DOI: 10.1007/978-3-031-07634-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Glucose metabolism plays a vital role in regulating cellular homeostasis as it acts as the central axis for energy metabolism, alteration in which may lead to serious consequences like metabolic disorders to life-threatening diseases like cancer. Malignant cells, on the other hand, help in tumor progression through abrupt cell proliferation by adapting to the changed metabolic milieu. Metabolic intermediates also vary from normal cells to cancerous ones to help the tumor manifestation. However, metabolic reprogramming is an important phenomenon of cells through which they try to maintain the balance between normal and carcinogenic outcomes. In this process, transcription factors and chromatin modifiers play an essential role to modify the chromatin landscape of important genes related directly or indirectly to metabolism. Our chapter surmises the importance of glucose metabolism and the role of metabolic intermediates in the cell. Also, we summarize the influence of histone effectors in reprogramming the cancer cell metabolism. An interesting aspect of this chapter includes the detailed methods to detect the aberrant metabolic flux, which can be instrumental for the therapeutic regimen of cancer.
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Affiliation(s)
- Payel Mondal
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
- Homi Bhaba National Institute, Mumbai, India
| | - Niharika Tiwary
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Amrita Sengupta
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Sinjini Dhang
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Siddhartha Roy
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India.
- Homi Bhaba National Institute, Mumbai, India.
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13
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In Silico Analysis to Explore Lineage-Independent and -Dependent Transcriptional Programs Associated with the Process of Endothelial and Neural Differentiation of Human Induced Pluripotent Stem Cells. J Clin Med 2021; 10:jcm10184161. [PMID: 34575270 PMCID: PMC8471316 DOI: 10.3390/jcm10184161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/11/2021] [Accepted: 09/13/2021] [Indexed: 11/17/2022] Open
Abstract
Despite a major interest in understanding how the endothelial cell phenotype is established, the underlying molecular basis of this process is not yet fully understood. We have previously reported the generation of induced pluripotent stem cells (iPS) from human umbilical vein endothelial cells and differentiation of the resulting HiPS back to endothelial cells (Ec-Diff), as well as neural (Nn-Diff) cell lineage that contained both neurons and astrocytes. Furthermore, the identities of these cell lineages were established by gene array analysis. Here, we explored the same arrays to gain insight into the gene alteration processes that accompany the establishment of endothelial vs. non-endothelial neural cell phenotypes. We compared the expression of genes that code for transcription factors and epigenetic regulators when HiPS is differentiated into these endothelial and non-endothelial lineages. Our in silico analyses have identified cohorts of genes that are similarly up- or downregulated in both lineages, as well as those that exhibit lineage-specific alterations. Based on these results, we propose that genes that are similarly altered in both lineages participate in priming the stem cell for differentiation in a lineage-independent manner, whereas those that are differentially altered in endothelial compared to neural cells participate in a lineage-specific differentiation process. Specific GATA family members and their cofactors and epigenetic regulators (DNMT3B, PRDM14, HELLS) with a major role in regulating DNA methylation were among participants in priming HiPS for lineage-independent differentiation. In addition, we identified distinct cohorts of transcription factors and epigenetic regulators whose alterations correlated specifically with the establishment of endothelial vs. non-endothelial neural lineages.
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14
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Axsom JE, Schmidt HD, Matura LA, Libonati JR. The Influence of Epigenetic Modifications on Metabolic Changes in White Adipose Tissue and Liver and Their Potential Impact in Exercise. Front Physiol 2021; 12:686270. [PMID: 34512374 PMCID: PMC8427663 DOI: 10.3389/fphys.2021.686270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/30/2021] [Indexed: 12/27/2022] Open
Abstract
Background: Epigenetic marks are responsive to a wide variety of environmental stimuli and serve as important mediators for gene transcription. A number of chromatin modifying enzymes orchestrate epigenetic responses to environmental stimuli, with a growing body of research examining how changes in metabolic substrates or co-factors alter epigenetic modifications. Scope of Review: Here, we provide a systematic review of existing evidence of metabolism-related epigenetic changes in white adipose tissue (WAT) and the liver and generate secondary hypotheses on how exercise may impact metabolism-related epigenetic marks in these tissues. Major Conclusions: Epigenetic changes contribute to the complex transcriptional responses associated with WAT lipolysis, hepatic de novo lipogenesis, and hepatic gluconeogenesis. While these metabolic responses may hypothetically be altered with acute and chronic exercise, direct testing is needed.
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Affiliation(s)
- Jessie E Axsom
- Department of Biobehavioral Health Sciences, School of Nursing, University of Pennsylvania, Philadelphia, PA, United States.,Penn Cardiovascular Institute, Smilow Translational Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Heath D Schmidt
- Department of Biobehavioral Health Sciences, School of Nursing, University of Pennsylvania, Philadelphia, PA, United States.,Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Lea Ann Matura
- Department of Biobehavioral Health Sciences, School of Nursing, University of Pennsylvania, Philadelphia, PA, United States
| | - Joseph R Libonati
- Department of Biobehavioral Health Sciences, School of Nursing, University of Pennsylvania, Philadelphia, PA, United States
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15
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Mondal P, Gadad SS, Adhikari S, Ramos EI, Sen S, Prasad P, Das C. TCF19 and p53 regulate transcription of TIGAR and SCO2 in HCC for mitochondrial energy metabolism and stress adaptation. FASEB J 2021; 35:e21814. [PMID: 34369624 DOI: 10.1096/fj.202002486rr] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 06/23/2021] [Accepted: 07/07/2021] [Indexed: 11/11/2022]
Abstract
Alteration in glucose homeostasis during cancer metabolism is an important phenomenon. Though several important transcription factors have been well studied in the context of the regulation of metabolic gene expression, the role of epigenetic readers in this regard remains still elusive. Epigenetic reader protein transcription factor 19 (TCF19) has been recently identified as a novel glucose and insulin-responsive factor that modulates histone posttranslational modifications to regulate glucose homeostasis in hepatocytes. Here we report that TCF19 interacts with a non-histone, well-known tumor suppressor protein 53 (p53) and co-regulates a wide array of metabolic genes. Among these, the p53-responsive carbohydrate metabolic genes Tp53-induced glycolysis and apoptosis regulator (TIGAR) and Cytochrome C Oxidase assembly protein 2 (SCO2), which are the key regulators of glycolysis and oxidative phosphorylation respectively, are under direct regulation of TCF19. Remarkably, TCF19 can form different transcription activation/repression complexes which show substantial overlap with that of p53, depending on glucose-mediated variant stress situations as obtained from IP/MS studies. Interestingly, we observed that TCF19/p53 complexes either have CBP or HDAC1 to epigenetically program the expression of TIGAR and SCO2 genes depending on short-term high glucose or prolonged high glucose conditions. TCF19 or p53 knockdown significantly altered the cellular lactate production and led to increased extracellular acidification rate. Similarly, OCR and cellular ATP production were reduced and mitochondrial membrane potential was compromised upon depletion of TCF19 or p53. Subsequently, through RNA-Seq analysis from patients with hepatocellular carcinoma, we observed that TCF19/p53-mediated metabolic regulation is fundamental for sustenance of cancer cells. Together the study proposes that TCF19/p53 complexes can regulate metabolic gene expression programs responsible for mitochondrial energy homeostasis and stress adaptation.
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Affiliation(s)
- Payel Mondal
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India.,Department of Life Sciences, Homi Bhaba National Institute, Mumbai, India
| | - Shrikanth S Gadad
- Department of Molecular and Translational Medicine, Center of Emphasis in Cancer, Texas Tech University Health Sciences Center El Paso, El Paso, TX, USA
| | - Swagata Adhikari
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India.,Department of Life Sciences, Homi Bhaba National Institute, Mumbai, India
| | - Enrique I Ramos
- Department of Molecular and Translational Medicine, Center of Emphasis in Cancer, Texas Tech University Health Sciences Center El Paso, El Paso, TX, USA
| | - Sabyasachi Sen
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Parash Prasad
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India.,Department of Life Sciences, Homi Bhaba National Institute, Mumbai, India
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16
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Yang GH, Fontaine DA, Lodh S, Blumer JT, Roopra A, Davis DB. TCF19 Impacts a Network of Inflammatory and DNA Damage Response Genes in the Pancreatic β-Cell. Metabolites 2021; 11:metabo11080513. [PMID: 34436454 PMCID: PMC8400192 DOI: 10.3390/metabo11080513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/31/2021] [Accepted: 08/02/2021] [Indexed: 12/13/2022] Open
Abstract
Transcription factor 19 (TCF19) is a gene associated with type 1 diabetes (T1DM) and type 2 diabetes (T2DM) in genome-wide association studies. Prior studies have demonstrated that Tcf19 knockdown impairs β-cell proliferation and increases apoptosis. However, little is known about its role in diabetes pathogenesis or the effects of TCF19 gain-of-function. The aim of this study was to examine the impact of TCF19 overexpression in INS-1 β-cells and human islets on proliferation and gene expression. With TCF19 overexpression, there was an increase in nucleotide incorporation without any change in cell cycle gene expression, alluding to an alternate process of nucleotide incorporation. Analysis of RNA-seq of TCF19 overexpressing cells revealed increased expression of several DNA damage response (DDR) genes, as well as a tightly linked set of genes involved in viral responses, immune system processes, and inflammation. This connectivity between DNA damage and inflammatory gene expression has not been well studied in the β-cell and suggests a novel role for TCF19 in regulating these pathways. Future studies determining how TCF19 may modulate these pathways can provide potential targets for improving β-cell survival.
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Affiliation(s)
- Grace H. Yang
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA; (G.H.Y.); (D.A.F.); (S.L.); (J.T.B.)
| | - Danielle A. Fontaine
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA; (G.H.Y.); (D.A.F.); (S.L.); (J.T.B.)
| | - Sukanya Lodh
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA; (G.H.Y.); (D.A.F.); (S.L.); (J.T.B.)
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Joseph T. Blumer
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA; (G.H.Y.); (D.A.F.); (S.L.); (J.T.B.)
| | - Avtar Roopra
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA;
| | - Dawn Belt Davis
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA; (G.H.Y.); (D.A.F.); (S.L.); (J.T.B.)
- William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA
- Correspondence:
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17
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Leithner K. Epigenetic Marks Repressing Gluconeogenesis in Liver and Kidney Cancer. Cancer Res 2020; 80:657-658. [PMID: 32060227 DOI: 10.1158/0008-5472.can-19-3953] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 12/19/2019] [Indexed: 11/16/2022]
Abstract
Gluconeogenesis is frequently suppressed in tumors arising in gluconeogenic organs and reexpression of a gluconeogenesis enzyme, fructose-1,6-bisphosphatase (FBP1), was found to inhibit tumor growth. In this issue of Cancer Research, Liao and colleagues show that histone H3 trimethylation on lysine 27, induced by polycomb repressive complex 2 (PRC2), is responsible for downregulating FBP1 in liver and kidney cancer cells. Moreover, they identified FBP1 repression as an important downstream mechanism of PRC2-mediated carcinogenesis. FBP1 inhibits glycolysis but also directly interferes with PRC2 function, thus FBP1 and PRC2 are part of a novel negative feedback loop that is deregulated in liver and kidney cancer.See related article by Liao et al., p. 675.
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Affiliation(s)
- Katharina Leithner
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, Graz, Austria.
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18
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Zsidó BZ, Hetényi C. Molecular Structure, Binding Affinity, and Biological Activity in the Epigenome. Int J Mol Sci 2020; 21:ijms21114134. [PMID: 32531926 PMCID: PMC7311975 DOI: 10.3390/ijms21114134] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/07/2020] [Accepted: 06/08/2020] [Indexed: 02/07/2023] Open
Abstract
Development of valid structure–activity relationships (SARs) is a key to the elucidation of pathomechanisms of epigenetic diseases and the development of efficient, new drugs. The present review is based on selected methodologies and applications supplying molecular structure, binding affinity and biological activity data for the development of new SARs. An emphasis is placed on emerging trends and permanent challenges of new discoveries of SARs in the context of proteins as epigenetic drug targets. The review gives a brief overview and classification of the molecular background of epigenetic changes, and surveys both experimental and theoretical approaches in the field. Besides the results of sophisticated, cutting edge techniques such as cryo-electron microscopy, protein crystallography, and isothermal titration calorimetry, examples of frequently used assays and fast screening techniques are also selected. The review features how different experimental methods and theoretical approaches complement each other and result in valid SARs of the epigenome.
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19
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You JJ, Ren P, He S, Liang XF, Xiao QQ, Zhang YP. Histone Methylation of H3K4 Involved in the Anorexia of Carnivorous Mandarin Fish ( Siniperca chuatsi) After Feeding on a Carbohydrate-Rich Diet. Front Endocrinol (Lausanne) 2020; 11:323. [PMID: 32636801 PMCID: PMC7316955 DOI: 10.3389/fendo.2020.00323] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/27/2020] [Indexed: 12/15/2022] Open
Abstract
Food intake of carnivorous fish decreases after feeding on a carbohydrate-rich diet. However, the molecular mechanism underlying the anorexia caused by high-carbohydrate diets has remained elusive. We domesticated the mandarin fish to feed on carbohydrate-rich (8%) diets. After 61 days of feeding, several fish (Group A) fed well on artificial diets during the whole feeding period; the other fish (Group B) fed well on artificial diets at the beginning of the feeding period, with their food intake then decreasing to half (anorexia) and then to zero for 5 days; and, finally, a negative control (Group C) fed on live prey fish throughout the experimental process. The plasma glucose was significantly higher in the mandarin fish of Group B than in those of Group A, whereas levels of hepatic glycogen and plasma triglyceride were significantly lower. Using transcriptome sequencing, we investigated the differentially expressed genes between Groups A and B and excluded the genes that were not differentially expressed between Groups A and C. The activation of mTOR and Jak/STAT pathways were found in the mandarin fish with anorexia, which was consistent with the higher expression levels of pepck and pomc genes. We found a higher expression of histone methyltransferase setd1b gene and an increased histone H3 tri-methylated at lysine 4 (H3K4me3) in the fish of Group B. Furthermore, using ChIP assay and inhibitor treatment, we found that the up-regulated H3K4me3 could activate pepck expression, which might have contributed to the hyperglycemia and anorexia in the mandarin fish that fed on carbohydrate-rich diets. Our study initially indicated a link between histone methylation and pepck expression, which might be a novel regulatory mechanism of fish who are fed a carbohydrate-rich diet.
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Affiliation(s)
- Jun-Jie You
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Ping Ren
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Shan He
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
- *Correspondence: Shan He
| | - Xu-Fang Liang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Qian-Qian Xiao
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
| | - Yan-Peng Zhang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, China
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20
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Zhou ZH, Chen G, Deng C, Tang JM, Xie L, Zhou HY, Ye X, Zhang DK, Shi RQ, Tian D, Qiao GB, Ben XS. TCF19 contributes to cell proliferation of non-small cell lung cancer by inhibiting FOXO1. Cell Biol Int 2019; 43:1416-1424. [PMID: 31141247 DOI: 10.1002/cbin.11189] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 05/25/2019] [Indexed: 01/24/2023]
Abstract
Transcription factor 19 (TCF19) harbors a forkhead association (FHA) domain, a proline-rich region, a PHD or RING finger region, suggesting that TCF19 possesses a powerful function. However, its expression and function remains unknown in non-small-cell lung cancer (NSCLC). The function cluster analysis was carried out using Metascape website. 3-(4,5-Dimethyl-2-thiazolyl)2,5-diphenyl-2H-tetrazolium bromide (MTT), colony formation, and anchorage-independent growth ability assay were carried out to detect the effect of TCF19 on cell proliferation. Bromodeoxyuridine (Brdu) labeling and flow cytometry assay were used to evaluate the effect of TCF19 on cell-cycle progression. Quantitative polymerase chain reaction and chromatin immunoprecipitation assay were performed to investigate the mechanism by which TCF19 is involved in cell-cycle transition. By analyzing the publicly available dataset, The Cancer Genome Atlas (TCGA), we found that TCF19 is significantly increased in the lung adenocarcinoma (LAC) and squamous cell carcinoma (SCC), two primary histological subtype of NSCLC. Besides, further function cluster analysis exhibited that TCF19 may mainly participate in cell cycle. MTT, colony formation, and anchorage-independent growth ability assay confirmed that overexpression of TCF19 enhances the proliferation of both LAC and SCC cells. Besides, further experiments revealed that TCF19 contributes to cell cycle G1/S transition. Not only that, upregulation of TCF19 can inhibit the expression of p21, p27, and p57, while promote the expression of cyclin D1 by inhibiting FOXO1. Our research offers important evidence that TCF19 can promote cell-cycle progression of NSCLC cells, and TCF19 may served as novel therapeutic targets.
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Affiliation(s)
- Zi-Hao Zhou
- Thoracic Surgery Department, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Science, Guangzhou, Guangdong, 510000, China
| | - Gang Chen
- Thoracic Surgery Department, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Science, Guangzhou, Guangdong, 510000, China
| | - Cheng Deng
- Thoracic Surgery Department, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Science, Guangzhou, Guangdong, 510000, China
| | - Ji-Ming Tang
- Thoracic Surgery Department, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Science, Guangzhou, Guangdong, 510000, China
| | - Liang Xie
- Thoracic Surgery Department, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Science, Guangzhou, Guangdong, 510000, China
| | - Hai-Yu Zhou
- Thoracic Surgery Department, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Science, Guangzhou, Guangdong, 510000, China
| | - Xiong Ye
- Thoracic Surgery Department, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Science, Guangzhou, Guangdong, 510000, China
| | - Dong-Kun Zhang
- Thoracic Surgery Department, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Science, Guangzhou, Guangdong, 510000, China
| | - Rui-Qing Shi
- Thoracic Surgery Department, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Science, Guangzhou, Guangdong, 510000, China
| | - Dan Tian
- Thoracic Surgery Department, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Science, Guangzhou, Guangdong, 510000, China
| | - Gui-Bin Qiao
- Thoracic Surgery Department, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Science, Guangzhou, Guangdong, 510000, China
| | - Xiao-Song Ben
- Thoracic Surgery Department, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Science, Guangzhou, Guangdong, 510000, China
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Mondal P, Sen S, Klein BJ, Tiwary N, Gadad SS, Kutateladze TG, Roy S, Das C. TCF19 Promotes Cell Proliferation through Binding to the Histone H3K4me3 Mark. Biochemistry 2019; 59:389-399. [DOI: 10.1021/acs.biochem.9b00771] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Payel Mondal
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhaba National Institute, Mumbai 400094, India
| | - Sabyasachi Sen
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| | - Brianna J. Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
| | - Niharika Tiwary
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| | - Shrikanth S. Gadad
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center, El Paso, Texas 79905, United States
| | - Tatiana G. Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
| | - Siddhartha Roy
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhaba National Institute, Mumbai 400094, India
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22
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Sen S, Das C. Managing the sugar factory: A new feather in the cap for nuclear factor Y. J Biol Chem 2019; 293:7905-7906. [PMID: 29777018 DOI: 10.1074/jbc.h118.002885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Gluconeogenesis in the liver converts lipids and several other noncarbohydrate precursors into glucose, ensuring that blood sugar levels are maintained at healthy levels, especially during fasting. Effective regulation of gluconeogenesis is therefore critical for maintaining systemic metabolic homeostasis. Zhang and colleagues have discovered that the ubiquitous transcriptional regulator nuclear factor Y (NF-Y) confers cAMP responsiveness to key gluconeogenic genes and up-regulates hepatic glucose production. The study expands our understanding of transcriptional regulation of hepatic gluconeogenesis and also presents critical insights into the function of NF-Y in the liver.
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Affiliation(s)
- Sabyasachi Sen
- From the Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| | - Chandrima Das
- From the Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
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23
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Went M, Kinnersley B, Sud A, Johnson DC, Weinhold N, Försti A, van Duin M, Orlando G, Mitchell JS, Kuiper R, Walker BA, Gregory WM, Hoffmann P, Jackson GH, Nöthen MM, da Silva Filho MI, Thomsen H, Broyl A, Davies FE, Thorsteinsdottir U, Hansson M, Kaiser M, Sonneveld P, Goldschmidt H, Stefansson K, Hemminki K, Nilsson B, Morgan GJ, Houlston RS. Transcriptome-wide association study of multiple myeloma identifies candidate susceptibility genes. Hum Genomics 2019; 13:37. [PMID: 31429796 PMCID: PMC6700979 DOI: 10.1186/s40246-019-0231-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 08/12/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND While genome-wide association studies (GWAS) of multiple myeloma (MM) have identified variants at 23 regions influencing risk, the genes underlying these associations are largely unknown. To identify candidate causal genes at these regions and search for novel risk regions, we performed a multi-tissue transcriptome-wide association study (TWAS). RESULTS GWAS data on 7319 MM cases and 234,385 controls was integrated with Genotype-Tissue Expression Project (GTEx) data assayed in 48 tissues (sample sizes, N = 80-491), including lymphocyte cell lines and whole blood, to predict gene expression. We identified 108 genes at 13 independent regions associated with MM risk, all of which were in 1 Mb of known MM GWAS risk variants. Of these, 94 genes, located in eight regions, had not previously been considered as a candidate gene for that locus. CONCLUSIONS Our findings highlight the value of leveraging expression data from multiple tissues to identify candidate genes responsible for GWAS associations which provide insight into MM tumorigenesis. Among the genes identified, a number have plausible roles in MM biology, notably APOBEC3C, APOBEC3H, APOBEC3D, APOBEC3F, APOBEC3G, or have been previously implicated in other malignancies. The genes identified in this TWAS can be explored for follow-up and validation to further understand their role in MM biology.
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Affiliation(s)
- Molly Went
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK.
- Division of Molecular Pathology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK.
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - David C Johnson
- Division of Molecular Pathology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Niels Weinhold
- Department of Internal Medicine V, University of Heidelberg, 69117, Heidelberg, Germany
| | - Asta Försti
- German Cancer Research Center, 69120, Heidelberg, Germany
| | - Mark van Duin
- Department of Hematology, Erasmus MC Cancer Institute, 3075, EA, Rotterdam, The Netherlands
| | - Giulia Orlando
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Jonathan S Mitchell
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Rowan Kuiper
- Department of Hematology, Erasmus MC Cancer Institute, 3075, EA, Rotterdam, The Netherlands
| | - Brian A Walker
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Walter M Gregory
- Clinical Trials Research Unit, University of Leeds, Leeds, LS2 9PH, UK
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, D-53127, Bonn, Germany
- Division of Medical Genetics, Department of Biomedicine, University of Basel, 4003, Basel, Switzerland
| | | | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, D-53127, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, D-53127, Bonn, Germany
| | | | - Hauke Thomsen
- German Cancer Research Center, 69120, Heidelberg, Germany
| | - Annemiek Broyl
- Department of Hematology, Erasmus MC Cancer Institute, 3075, EA, Rotterdam, The Netherlands
| | - Faith E Davies
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | | | - Markus Hansson
- Hematology Clinic, Skåne University Hospital, SE-221 85, Lund, Sweden
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, SE-221 84, Lund, Sweden
| | - Martin Kaiser
- Division of Molecular Pathology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Pieter Sonneveld
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, 69117, Heidelberg, Germany
- Institute of Human Genetics, University of Bonn, D-53127, Bonn, Germany
| | | | - Kari Hemminki
- German Cancer Research Center, 69120, Heidelberg, Germany
| | - Björn Nilsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, SE-221 84, Lund, Sweden
- Broad Institute, 7 Cambridge Center, Cambridge, MA, 02142, USA
| | - Gareth J Morgan
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
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