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Xing F, Han F, Wu Y, Lv B, Tian H, Wang W, Tian X, Xu C, Duan H, Zhang D, Wu Y. An epigenome-wide association study of waist circumference in Chinese monozygotic twins. Int J Obes (Lond) 2024; 48:1148-1156. [PMID: 38773251 DOI: 10.1038/s41366-024-01538-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 05/05/2024] [Accepted: 05/09/2024] [Indexed: 05/23/2024]
Abstract
OBJECTIVES Central obesity poses significant health risks because it increases susceptibility to multiple chronic diseases. Epigenetic features such as DNA methylation may be associated with specific obesity traits, which could help us understand how genetic and environmental factors interact to influence the development of obesity. This study aims to identify DNA methylation sites associated with the waist circumference (WC) in Northern Han Chinese population, and to elucidate potential causal relationships. METHODS A total of 59 pairs of WC discordant monozygotic twins (ΔWC >0) were selected from the Qingdao Twin Registry in China. Generalized estimated equation model was employed to estimate the methylation levels of CpG sites on WC. Causal relationships between methylation and WC were assessed through the examination of family confounding factors using FAmiliaL CONfounding (ICE FALCON). Additionally, the findings of the epigenome-wide analysis were corroborated in the validation stage. RESULTS We identified 26 CpG sites with differential methylation reached false discovery rate (FDR) < 0.05 and 22 differentially methylated regions (slk-corrected p < 0.05) strongly linked to WC. These findings provided annotations for 26 genes, with notable emphasis on MMP17, ITGA11, COL23A1, TFPI, A2ML1-AS1, MRGPRE, C2orf82, and NINJ2. ICE FALCON analysis indicated the DNA methylation of ITGA11 and TFPI had a causal effect on WC and vice versa (p < 0.05). Subsequent validation analysis successfully replicated 10 (p < 0.05) out of the 26 identified sites. CONCLUSIONS Our research has ascertained an association between specific epigenetic variations and WC in the Northern Han Chinese population. These DNA methylation features can offer fresh insights into the epigenetic regulation of obesity and WC as well as hints to plausible biological mechanisms.
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Affiliation(s)
- Fangjie Xing
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, China
| | - Fulei Han
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, China
| | - Yan Wu
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, China
| | - Bosen Lv
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, China
| | - Huimin Tian
- Zhonglou District Center for Disease Control and Prevention, Changzhou, Jiangsu, China
| | - Weijing Wang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, China
| | - Xiaocao Tian
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, Shandong, China
| | - Chunsheng Xu
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, Shandong, China
| | - Haiping Duan
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, Shandong, China
| | - Dongfeng Zhang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, China
| | - Yili Wu
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, China.
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2
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Dallali H, Boukhalfa W, Kheriji N, Fassatoui M, Jmel H, Hechmi M, Gouiza I, Gharbi M, Kammoun W, Mrad M, Taoueb M, Krir A, Trabelsi H, Bahlous A, Jamoussi H, Messaoud O, Abid A, Kefi R. The first exome wide association study in Tunisia: identification of candidate loci and pathways with biological relevance for type 2 diabetes. Front Endocrinol (Lausanne) 2023; 14:1293124. [PMID: 38192426 PMCID: PMC10773763 DOI: 10.3389/fendo.2023.1293124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/27/2023] [Indexed: 01/10/2024] Open
Abstract
Introduction Type 2 diabetes (T2D) is a multifactorial disease involving genetic and environmental components. Several genome-wide association studies (GWAS) have been conducted to decipher potential genetic aberrations promoting the onset of this metabolic disorder. These GWAS have identified over 400 associated variants, mostly in the intronic or intergenic regions. Recently, a growing number of exome genotyping or exome sequencing experiments have identified coding variants associated with T2D. Such studies were mainly conducted in European populations, and the few candidate-gene replication studies in North African populations revealed inconsistent results. In the present study, we aimed to discover the coding genetic etiology of T2D in the Tunisian population. Methods We carried out a pilot Exome Wide Association Study (EWAS) on 50 Tunisian individuals. Single variant analysis was performed as implemented in PLINK on potentially deleterious coding variants. Subsequently, we applied gene-based and gene-set analyses using MAGMA software to identify genes and pathways associated with T2D. Potential signals were further replicated in an existing large in-silico dataset, involving up to 177116 European individuals. Results Our analysis revealed, for the first time, promising associations between T2D and variations in MYORG gene, implicated in the skeletal muscle fiber development. Gene-set analysis identified two candidate pathways having nominal associations with T2D in our study samples, namely the positive regulation of neuron apoptotic process and the regulation of mucus secretion. These two pathways are implicated in the neurogenerative alterations and in the inflammatory mechanisms of metabolic diseases. In addition, replication analysis revealed nominal associations of the regulation of beta-cell development and the regulation of peptidase activity pathways with T2D, both in the Tunisian subjects and in the European in-silico dataset. Conclusions The present study is the first EWAS to investigate the impact of single genetic variants and their aggregate effects on T2D risk in Africa. The promising disease markers, revealed by our pilot EWAS, will promote the understanding of the T2D pathophysiology in North Africa as well as the discovery of potential treatments.
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Affiliation(s)
- Hamza Dallali
- Genetic typing service, Institut Pasteur of Tunis, Tunis, Tunisia
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur of Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Wided Boukhalfa
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur of Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Nadia Kheriji
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur of Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Meriem Fassatoui
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur of Tunis, Tunis, Tunisia
| | - Haifa Jmel
- Genetic typing service, Institut Pasteur of Tunis, Tunis, Tunisia
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur of Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Meriem Hechmi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur of Tunis, Tunis, Tunisia
| | - Ismail Gouiza
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur of Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- MitoLab Team, Unité MitoVasc, UMR CNRS 6015, INSERM U1083, SFR ICAT, University of Angers, Angers, France
| | - Mariem Gharbi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur of Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Wafa Kammoun
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur of Tunis, Tunis, Tunisia
| | - Mehdi Mrad
- Laboratory of Clinical Biochemistry and Hormonology, Institut Pasteur of Tunis, Tunis, Tunisia
| | - Marouen Taoueb
- Laboratory of Clinical Biochemistry and Hormonology, Institut Pasteur of Tunis, Tunis, Tunisia
| | - Asma Krir
- Laboratory of Clinical Biochemistry and Hormonology, Institut Pasteur of Tunis, Tunis, Tunisia
| | - Hajer Trabelsi
- Laboratory of Clinical Biochemistry and Hormonology, Institut Pasteur of Tunis, Tunis, Tunisia
| | - Afef Bahlous
- Laboratory of Clinical Biochemistry and Hormonology, Institut Pasteur of Tunis, Tunis, Tunisia
| | - Henda Jamoussi
- Research Unit on Obesity, Faculty of Medicine of Tunis, Tunis, Tunisia
| | - Olfa Messaoud
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur of Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Abdelmajid Abid
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur of Tunis, Tunis, Tunisia
| | - Rym Kefi
- Genetic typing service, Institut Pasteur of Tunis, Tunis, Tunisia
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur of Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
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3
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Glotov OS, Chernov AN, Glotov AS. Human Exome Sequencing and Prospects for Predictive Medicine: Analysis of International Data and Own Experience. J Pers Med 2023; 13:1236. [PMID: 37623486 PMCID: PMC10455459 DOI: 10.3390/jpm13081236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/26/2023] Open
Abstract
Today, whole-exome sequencing (WES) is used to conduct the massive screening of structural and regulatory genes in order to identify the allele frequencies of disease-associated polymorphisms in various populations and thus detect pathogenic genetic changes (mutations or polymorphisms) conducive to malfunctional protein sequences. With its extensive capabilities, exome sequencing today allows both the diagnosis of monogenic diseases (MDs) and the examination of seemingly healthy populations to reveal a wide range of potential risks prior to disease manifestation (in the future, exome sequencing may outpace costly and less informative genome sequencing to become the first-line examination technique). This review establishes the human genetic passport as a new WES-based clinical concept for the identification of new candidate genes, gene variants, and molecular mechanisms in the diagnosis, prediction, and treatment of monogenic, oligogenic, and multifactorial diseases. Various diseases are addressed to demonstrate the extensive potential of WES and consider its advantages as well as disadvantages. Thus, WES can become a general test with a broad spectrum pf applications, including opportunistic screening.
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Affiliation(s)
- Oleg S. Glotov
- Department of Genomic Medicine, D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, 199034 St. Petersburg, Russia;
- Department of Experimental Medical Virology, Molecular Genetics and Biobanking of Pediatric Research and Clinical Center for Infectious Diseases, 197022 St. Petersburg, Russia
| | - Alexander N. Chernov
- Department of Genomic Medicine, D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, 199034 St. Petersburg, Russia;
- Department of General Pathology and Pathological Physiology, Institute of Experimental Medicine, 197376 St. Petersburg, Russia
| | - Andrey S. Glotov
- Department of Genomic Medicine, D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, 199034 St. Petersburg, Russia;
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4
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Zhao X, Fang K, Liu X, Yao R, Wang M, Li F, Hao S, He J, Wang Y, Fan M, Huang W, Li Y, Gao C, Lin C, Luo Z. QSER1 preserves the suppressive status of the pro-apoptotic genes to prevent apoptosis. Cell Death Differ 2023; 30:779-793. [PMID: 36371602 PMCID: PMC9984391 DOI: 10.1038/s41418-022-01085-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 10/20/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022] Open
Abstract
Activation of the pro-apoptotic genes by the p53 family is a critical step in induction of apoptosis. However, the molecular signaling underlying their suppression remains largely unknown. Here, we report a general role of QSER1 in preventing apoptosis. QSER1 is widely up-regulated in multiple cancers, and its up-regulation correlates with poor clinic outcomes. QSER1 knockdown significantly promotes apoptosis in both p53 wild type and mutant cancer cells. Interestingly, we show that QSER1 and p53 occupy distinct cis-regulatory regions in a common subset of the pro-apoptotic genes, and function antagonistically to maintain their proper expression. Furthermore, we identify a key regulatory DNA element named QSER1 binding site in PUMA (QBP). Deletion of QBP de-represses PUMA and induces apoptosis. Mechanistically, QSER1 functions together with SIN3A to suppress PUMA in a p53-dependent and -independent manner, suggesting that QSER1 inhibition might be a potential therapeutic strategy to induce apoptosis in cancers.
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Affiliation(s)
- Xiru Zhao
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, 210096, China
| | - Ke Fang
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, 210096, China
| | - Xiaoxu Liu
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, 210096, China
| | - Ruihuan Yao
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, 210096, China
| | - Min Wang
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, 210096, China
| | - Fanfan Li
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, 210096, China
| | - Shaohua Hao
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, 210096, China
| | - Jingjing He
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, 210096, China
| | - Yan Wang
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, 210096, China
| | - Menghan Fan
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, 210096, China
| | - Wei Huang
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Yiping Li
- Department of Pathology, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Chun Gao
- Department of Gastroenterology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Chengqi Lin
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, 210096, China.
- Shenzhen Research Institute, Southeast University, 19 Gaoxin South 4th Road, Nanshan District, Shenzhen, 518063, China.
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, School of Life Science and Technology, Southeast University, Nanjing, 210096, China.
| | - Zhuojuan Luo
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, 210096, China.
- Shenzhen Research Institute, Southeast University, 19 Gaoxin South 4th Road, Nanshan District, Shenzhen, 518063, China.
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Life Science and Technology, Southeast University, Nanjing, 210096, China.
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5
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Impact of diet and host genetics on the murine intestinal mycobiome. Nat Commun 2023; 14:834. [PMID: 36788222 PMCID: PMC9929102 DOI: 10.1038/s41467-023-36479-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/01/2023] [Indexed: 02/16/2023] Open
Abstract
The mammalian gut is home to a diverse microbial ecosystem, whose composition affects various physiological traits of the host. Next-generation sequencing-based metagenomic approaches demonstrated how the interplay of host genetics, bacteria, and environmental factors shape complex traits and clinical outcomes. However, the role of fungi in these complex interactions remains understudied. Here, using 228 males and 363 females from an advanced-intercross mouse line, we provide evidence that fungi are regulated by host genetics. In addition, we map quantitative trait loci associated with various fungal species to single genes in mice using whole genome sequencing and genotyping. Moreover, we show that diet and its' interaction with host genetics alter the composition of fungi in outbred mice, and identify fungal indicator species associated with different dietary regimes. Collectively, in this work, we uncover an association of the intestinal fungal community with host genetics and a regulatory role of diet in this ecological niche.
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6
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Lazareva TE, Barbitoff YA, Changalidis AI, Tkachenko AA, Maksiutenko EM, Nasykhova YA, Glotov AS. Biobanking as a Tool for Genomic Research: From Allele Frequencies to Cross-Ancestry Association Studies. J Pers Med 2022; 12:jpm12122040. [PMID: 36556260 PMCID: PMC9783756 DOI: 10.3390/jpm12122040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/19/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
In recent years, great advances have been made in the field of collection, storage, and analysis of biological samples. Large collections of samples, biobanks, have been established in many countries. Biobanks typically collect large amounts of biological samples and associated clinical information; the largest collections include over a million samples. In this review, we summarize the main directions in which biobanks aid medical genetics and genomic research, from providing reference allele frequency information to allowing large-scale cross-ancestry meta-analyses. The largest biobanks greatly vary in the size of the collection, and the amount of available phenotype and genotype data. Nevertheless, all of them are extensively used in genomics, providing a rich resource for genome-wide association analysis, genetic epidemiology, and statistical research into the structure, function, and evolution of the human genome. Recently, multiple research efforts were based on trans-biobank data integration, which increases sample size and allows for the identification of robust genetic associations. We provide prominent examples of such data integration and discuss important caveats which have to be taken into account in trans-biobank research.
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Affiliation(s)
- Tatyana E. Lazareva
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Yury A. Barbitoff
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Correspondence: (Y.A.B.); (A.S.G.)
| | - Anton I. Changalidis
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Faculty of Software Engineering and Computer Systems, ITMO University, 197101 St. Petersburg, Russia
| | - Alexander A. Tkachenko
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
| | - Evgeniia M. Maksiutenko
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
| | - Yulia A. Nasykhova
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
| | - Andrey S. Glotov
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Correspondence: (Y.A.B.); (A.S.G.)
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7
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Warlo EMK, Bratseth V, Pettersen AÅR, Holme PA, Arnesen H, Seljeflot I, Opstad TB. Genetic Variation in ADAMTS13 is Related to VWF Levels, Atrial Fibrillation and Cerebral Ischemic Events. Clin Appl Thromb Hemost 2022; 28:10760296221141893. [PMID: 36474435 PMCID: PMC9732802 DOI: 10.1177/10760296221141893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION ADAMTS13 cleaves von Willebrand factor (VWF) multimers into less active fragments. Both markers have been related to cardiovascular disease (CVD). We aimed to investigate the influence of ADAMTS13 single nucleotide polymorphisms (SNPs) on levels of ADAMTS13 and VWF, and CVD. METHODS The c.1342C>G, g.41635A>G and c.2699C>T polymorphisms were determined in patients with chronic coronary syndrome (n = 1000). VWF and ADAMTS13 were analyzed. Clinical endpoints after 2 years (n = 106) were unstable angina pectoris, myocardial infarction, non-hemorrhagic stroke and death. RESULTS The SNPs did not affect ADAMTS13 levels. The 41635A-allele associated with higher VWF levels (P < .001). Patients with the 1342G-allele had significantly higher frequency of previous atrial fibrillation (n = 26, P = .016) and cerebral ischemic events (n = 47, P = .030). Heterozygous of the 1342CG variant experienced more clinical endpoints compared to homozygous (CC and GG) (P = .028). CONCLUSION The association between the 41635A-allele and VWF indicates a role for this polymorphism in VWF regulation. ADAMTS13 has previously been linked to atrial fibrillation and ischemic stroke, and our findings suggest that the 1342G-allele may be of significance. The association between the 1342CG genotype and endpoints needs further investigations.Clinicaltrials.gov, ASCET, NCT00222261. https://clinicaltrials.gov/ct2/show/NCT00222261?term=NCT00222261&draw=2&rank=1.
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Affiliation(s)
- Ellen M. K. Warlo
- Center for Clinical Heart Research, Department of Cardiology,
Oslo
University Hospital, Oslo, Norway,Institute of
Clinical Medicine,
University of
Oslo, Oslo, Norway,Ellen M. K. Warlo, Center for Clinical
Heart Research, Department of Cardiology, Oslo University Hospital, Ullevaal. Pb
4956 Nydalen, 0424 Oslo, Norway.
| | - Vibeke Bratseth
- Center for Clinical Heart Research, Department of Cardiology,
Oslo
University Hospital, Oslo, Norway
| | - Alf-Åge R. Pettersen
- Center for Clinical Heart Research, Department of Cardiology,
Oslo
University Hospital, Oslo, Norway,Department of Medicine, Vestre Viken HF,
Ringerike
Hospital, Hønefoss, Norway
| | - Pål Andre Holme
- Institute of
Clinical Medicine,
University of
Oslo, Oslo, Norway,Department of Haematology, Oslo University
Hospital, Oslo, Norway
| | - Harald Arnesen
- Center for Clinical Heart Research, Department of Cardiology,
Oslo
University Hospital, Oslo, Norway,Institute of
Clinical Medicine,
University of
Oslo, Oslo, Norway
| | - Ingebjørg Seljeflot
- Center for Clinical Heart Research, Department of Cardiology,
Oslo
University Hospital, Oslo, Norway,Institute of
Clinical Medicine,
University of
Oslo, Oslo, Norway
| | - Trine B. Opstad
- Center for Clinical Heart Research, Department of Cardiology,
Oslo
University Hospital, Oslo, Norway,Institute of
Clinical Medicine,
University of
Oslo, Oslo, Norway
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8
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Lv B, Yang X, An T, Wu Y, He Z, Li B, Wang Y, Tan F, Wang T, Zhu J, Hu Y, Liu X, Jiang G. Combined analysis of whole-exome sequencing and RNA sequencing in type 2 diabetes mellitus patients with thirst and fatigue. Diabetol Metab Syndr 2022; 14:111. [PMID: 35941691 PMCID: PMC9358875 DOI: 10.1186/s13098-022-00884-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 07/28/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The principal objective of this study was to gain a better understanding of the mechanisms of type 2 diabetes mellitus (T2DM) patients with fatigue (D-T2DM) through exome and transcriptome sequencing. METHODS After whole-exome sequencing on peripheral blood of 6 D-T2DM patients, the consensus mutations were screen out and analyzed by a series of bioinformatics analyses. Then, we combined whole-exome sequencing and transcriptome sequencing results to find the important genes that changed at both the DNA and RNA levels. RESULTS The results showed that a total of 265,393 mutation sites were found in D-T2DM patients compared with normal individuals, 235 of which were consensus mutations shared with D-T2DM patients. These genes significantly enriched in HIF-1 signaling pathway and sphingolipid signaling pathway. At the RNA level, a total of 375 genes were identified to be differentially expressed. After the DNA-RNA joint analysis, eight genes were screened that changed at both DNA and RNA levels. Among these genes, FUS and LMNA were related to carbohydrate metabolism, energy metabolism, and mitochondrial function. Subsequently, we predicted the herbs, including Qin Pi and Hei Zhi Ma, that might play a therapeutic role in D-T2DM through the SymMap database. CONCLUSION These findings have significant implications for understanding the mechanisms of D-T2DM and provide potential targets for D-T2DM diagnosis and treatment.
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Affiliation(s)
- Bohan Lv
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
| | - Xiuyan Yang
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
| | - Tian An
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
| | - Yanxiang Wu
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
| | - Zhongchen He
- Department of Endocrinology, Beijing He Ping li Hospital, Beijing, China
| | - Bowu Li
- Department of Endocrinology, Beijing He Ping li Hospital, Beijing, China
| | - Yijiao Wang
- Department of Endocrinology, Beijing He Ping li Hospital, Beijing, China
| | - Fang Tan
- Department of Endocrinology, Beijing He Ping li Hospital, Beijing, China
| | - Tingye Wang
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
| | - Jiajian Zhu
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
| | - Yuanyuan Hu
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
| | - Xiaokun Liu
- Department of Cardiology, Gongren Hospital of Tangshan City, Tangshan, China
| | - Guangjian Jiang
- Traditional Chinese Medicine School, Beijing University of Chinese Medicine, Beijing, China
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9
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Kopylova OV, Ershova AI, Pokrovskaya MS, Meshkov AN, Efimova IA, Serebryanskaya ZZ, Blokhina AV, Borisova AL, Kondratskaya VA, Limonova AS, Smetnev SА, Skirko OP, Shalnova SА, Metelskaya VA, Kontsevaya AV, Drapkina OM. Population-nosological research biobank of the National Medical Research Center for Therapy and Preventive Medicine: analysis of biosamples, principles of collecting and storing information. КАРДИОВАСКУЛЯРНАЯ ТЕРАПИЯ И ПРОФИЛАКТИКА 2022. [DOI: 10.15829/1728-8800-2021-3119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Aim. To analyze the structure of clinical data, as well as the principles of collecting and storing related data of the biobank of the National Medical Research Center for Therapy and Preventive Medicine (hereinafter Biobank).Material and methods. The analysis was carried out using the documentation available in the Biobank, as well as the databases used in its work. The paper presents clinical data on biosamples available in the Biobank as of August 18, 2021.Results. At the time of analysis, the Biobank had 373547 samples collected from 54192 patients within 37 research projects. The article presents the analysis of data representation and quantitative assessment of the presence/absence of common diagnoses in clinical projects. Approaches to documenting clinical information associated with biological samples stored in the Biobank were assessed. The methods and tools used for standardization and automation of processes used in the Biobank were substantiated.Conclusion. The Biobank of the National Medical Research Center for Therapy and Preventive Medicine is the largest research biobank in Russia, which meets all modern international requirements and is one of the key structures that improve the research quality and intensify their conduct both within the one center and in cooperation with other biobanks and scientific institutions. The collection and systematic storage of clinical abstracts of biological samples is an integral and most important part of the Biobank’s work.
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Affiliation(s)
- O. V. Kopylova
- National Medical Research Center for Therapy and Preventive Medicine
| | - A. I. Ershova
- National Medical Research Center for Therapy and Preventive Medicine
| | - M. S. Pokrovskaya
- National Medical Research Center for Therapy and Preventive Medicine
| | - A. N. Meshkov
- National Medical Research Center for Therapy and Preventive Medicine
| | - I. A. Efimova
- National Medical Research Center for Therapy and Preventive Medicine
| | | | - A. V. Blokhina
- National Medical Research Center for Therapy and Preventive Medicine
| | - A. L. Borisova
- National Medical Research Center for Therapy and Preventive Medicine
| | | | - A. S. Limonova
- National Medical Research Center for Therapy and Preventive Medicine
| | - S. А. Smetnev
- National Medical Research Center for Therapy and Preventive Medicine
| | - O. P. Skirko
- National Medical Research Center for Therapy and Preventive Medicine
| | - S. А. Shalnova
- National Medical Research Center for Therapy and Preventive Medicine
| | - V. A. Metelskaya
- National Medical Research Center for Therapy and Preventive Medicine
| | | | - O. M. Drapkina
- National Medical Research Center for Therapy and Preventive Medicine
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10
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Sluysmans S, Méan I, Xiao T, Boukhatemi A, Ferreira F, Jond L, Mutero A, Chang CJ, Citi S. PLEKHA5, PLEKHA6, and PLEKHA7 bind to PDZD11 to target the Menkes ATPase ATP7A to the cell periphery and regulate copper homeostasis. Mol Biol Cell 2021; 32:ar34. [PMID: 34613798 PMCID: PMC8693958 DOI: 10.1091/mbc.e21-07-0355] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/24/2021] [Accepted: 09/28/2021] [Indexed: 01/12/2023] Open
Abstract
Copper homeostasis is crucial for cellular physiology and development, and its dysregulation leads to disease. The Menkes ATPase ATP7A plays a key role in copper efflux, by trafficking from the Golgi to the plasma membrane upon cell exposure to elevated copper, but the mechanisms that target ATP7A to the cell periphery are poorly understood. PDZD11 interacts with the C-terminus of ATP7A, which contains sequences involved in ATP7A trafficking, but the role of PDZD11 in ATP7A localization is unknown. Here we identify PLEKHA5 and PLEKHA6 as new interactors of PDZD11 that bind to the PDZD11 N-terminus through their WW domains similarly to the junctional protein PLEKHA7. Using CRISPR-KO kidney epithelial cells, we show by immunofluorescence microscopy that WW-PLEKHAs (PLEKHA5, PLEKHA6, PLEKHA7) recruit PDZD11 to distinct plasma membrane localizations and that they are required for the efficient anterograde targeting of ATP7A to the cell periphery in elevated copper conditions. Pull-down experiments show that WW-PLEKHAs promote PDZD11 interaction with the C-terminus of ATP7A. However, WW-PLEKHAs and PDZD11 are not necessary for ATP7A Golgi localization in basal copper, ATP7A copper-induced exit from the Golgi, and ATP7A retrograde trafficking to the Golgi. Finally, measuring bioavailable and total cellular copper, metallothionein-1 expression, and cell viability shows that WW-PLEKHAs and PDZD11 are required for maintaining low intracellular copper levels when cells are exposed to elevated copper. These data indicate that WW-PLEKHAs-PDZD11 complexes regulate the localization and function of ATP7A to promote copper extrusion in elevated copper.
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Affiliation(s)
- Sophie Sluysmans
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1205 Geneva, Switzerland
| | - Isabelle Méan
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1205 Geneva, Switzerland
| | - Tong Xiao
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720
| | - Amina Boukhatemi
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1205 Geneva, Switzerland
| | - Flavio Ferreira
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1205 Geneva, Switzerland
| | - Lionel Jond
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1205 Geneva, Switzerland
| | - Annick Mutero
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1205 Geneva, Switzerland
| | - Christopher J. Chang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Sandra Citi
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1205 Geneva, Switzerland
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11
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Sluysmans S, Méan I, Jond L, Citi S. WW, PH and C-Terminal Domains Cooperate to Direct the Subcellular Localizations of PLEKHA5, PLEKHA6 and PLEKHA7. Front Cell Dev Biol 2021; 9:729444. [PMID: 34568338 PMCID: PMC8458771 DOI: 10.3389/fcell.2021.729444] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/20/2021] [Indexed: 01/11/2023] Open
Abstract
PLEKHA5, PLEKHA6, and PLEKHA7 (WW-PLEKHAs) are members of the PLEKHA family of proteins that interact with PDZD11 through their tandem WW domains. WW-PLEKHAs contribute to the trafficking and retention of transmembrane proteins, including nectins, Tspan33, and the copper pump ATP7A, at cell-cell junctions and lateral membranes. However, the structural basis for the distinct subcellular localizations of PLEKHA5, PLEKHA6, and PLEKHA7 is not clear. Here we expressed mutant and chimeric proteins of WW-PLEKHAs in cultured cells to clarify the role of their structural domains in their localization. We found that the WW-mediated interaction between PLEKHA5 and PDZD11 is required for their respective association with cytoplasmic microtubules. The PH domain of PLEKHA5 is required for its localization along the lateral plasma membrane and promotes the lateral localization of PLEKHA7 in a chimeric molecule. Although the PH domain of PLEKHA7 is not required for its localization at the adherens junctions (AJ), it promotes a AJ localization of chimeric proteins. The C-terminal region of PLEKHA6 and PLEKHA7 and the coiled-coil region of PLEKHA7 promote their localization at AJ of epithelial cells. These observations indicate that the localizations of WW-PLEKHAs at specific subcellular sites, where they recruit PDZD11, are the result of multiple cooperative protein-lipid and protein-protein interactions and provide a rational basis for the identification of additional proteins involved in trafficking and sorting of WW-PLEKHAs.
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Affiliation(s)
| | | | | | - Sandra Citi
- Department of Cell Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
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12
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Dixon G, Pan H, Yang D, Rosen BP, Jashari T, Verma N, Pulecio J, Caspi I, Lee K, Stransky S, Glezer A, Liu C, Rivas M, Kumar R, Lan Y, Torregroza I, He C, Sidoli S, Evans T, Elemento O, Huangfu D. QSER1 protects DNA methylation valleys from de novo methylation. Science 2021; 372:eabd0875. [PMID: 33833093 PMCID: PMC8185639 DOI: 10.1126/science.abd0875] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 02/23/2021] [Indexed: 12/12/2022]
Abstract
DNA methylation is essential to mammalian development, and dysregulation can cause serious pathological conditions. Key enzymes responsible for deposition and removal of DNA methylation are known, but how they cooperate to regulate the methylation landscape remains a central question. Using a knockin DNA methylation reporter, we performed a genome-wide CRISPR-Cas9 screen in human embryonic stem cells to discover DNA methylation regulators. The top screen hit was an uncharacterized gene, QSER1, which proved to be a key guardian of bivalent promoters and poised enhancers of developmental genes, especially those residing in DNA methylation valleys (or canyons). We further demonstrate genetic and biochemical interactions of QSER1 and TET1, supporting their cooperation to safeguard transcriptional and developmental programs from DNMT3-mediated de novo methylation.
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Affiliation(s)
- Gary Dixon
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | - Heng Pan
- Department of Physiology and Biophysics, Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Dapeng Yang
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | - Bess P Rosen
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | - Therande Jashari
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | - Nipun Verma
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
- Weill Graduate School of Medical Sciences at Cornell University-The Rockefeller University-Sloan Kettering Institute Tri-Institutional M.D.-Ph.D. Program, New York, NY 10065, USA
| | - Julian Pulecio
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | - Inbal Caspi
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | - Kihyun Lee
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Abigail Glezer
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | - Chang Liu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Marco Rivas
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Ritu Kumar
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | - Yahui Lan
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ingrid Torregroza
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Todd Evans
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA.
| | - Danwei Huangfu
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA.
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13
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Wang H, Ma L, Pan X, Du Z, Chen Y. Novel associations of SNPs MYLIP rs3757354 and ABCA1 2230806 gene with early-onset-preeclampsia: A case-control candidate genetic study. Pregnancy Hypertens 2021; 23:185-190. [PMID: 33450693 DOI: 10.1016/j.preghy.2020.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 12/17/2022]
Abstract
OBJECTIVE To investigate the association between MYLIP rs3757354 and ABCA1 2230806 single nucleotide polymorphisms in women with preeclampsia in China. STUDY DESIGN The case-control study involved 205 patients with preeclampsia and 145 controls. All women with preeclampsia were divided into two groups: 78 patients with early-onset preeclampsia and 127 with late-onset preeclampsia. MAIN OUTCOME MEASURE MYLIP rs3757354 and ABCA1 rs2230806 SNPs were analyzed through multiplex PCR for targeted next-generation sequencing technology. A secondary outcome was lipid profile changes and liver function in women with PE. RESULTS Maternal age (OR: 1.073, 95% CI = 1.006-1.145), BMI (OR: 1.118, 95% CI = 1.040-1.201), TG/HDL-C (OR: 1.536, 95% CI = 1.080-2.183), and TT genotype of SNP rs3757354 (OR: 3.238, 95% CI = 1.313-7.990) were associated with EOPE risk. Our study found that patients with TT genotype of ABCA1 rs2230806 had more severe hepatic dysfunction and higher HDL levels in the EOPE group compared with CC/CT genotype. There was no association between rs2230806 and the risk of PE. CONCLUSION The polymorphisms of rs3757354 are associated with the risk of EOPE in Chinese pregnant women. The TT genotype in ABCA1 rs2230806 is a strong predictive risk for elevated aminotransferase levels in pregnant women with EOPE.
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Affiliation(s)
- He Wang
- The First Hospital of Jilin University, Department of Obstetrics, Changchun, Jilin Province 130021, China
| | - Lingyu Ma
- The First Hospital of Jilin University, Department of Obstetrics, Changchun, Jilin Province 130021, China
| | - Xuefeng Pan
- The First Hospital of Jilin University, Department of Obstetrics, Changchun, Jilin Province 130021, China
| | - Zhaoli Du
- Institute of Genetic Technology, Yinfeng Bilogical Group, Yinfeng Gene Technology Company Limited, Jinan, Shandong Province 250014, China
| | - Ying Chen
- The First Hospital of Jilin University, Department of Obstetrics, Changchun, Jilin Province 130021, China.
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14
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Anisimov SV, Meshkov AN, Glotov AS, Borisova AL, Balanovsky OP, Belyaev VE, Granstrem OK, Grivtsova LY, Efimenko AY, Pokrovskaya MS, Semenenko TA, Sukhorukov VS, Kaprin AD, Drapkina OM. National Association of Biobanks and Biobanking Specialists: New Community for Promoting Biobanking Ideas and Projects in Russia. Biopreserv Biobank 2020; 19:73-82. [PMID: 33058731 DOI: 10.1089/bio.2020.0049] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The research biobanking field is developing rapidly in Russia. Over the course of the last decade, numerous biobanks were created or formed from existing collections of human and environmental biospecimens. The Russian National Association of Biobanks and Biobanking Specialists (NASBIO) was established in December 2018, aiming to: (1) unite professionals and research centers to create and develop a network of biobanks in Russia; (2) provide services and expertise in the field of biobanking; (3) execute various research projects utilizing biobanks' infrastructure; and (4) facilitate integration of Russian biomedical research centers into global research activities. The organizational structure, aims, and plans of this newly formed national association are reviewed in this article. The founders of NASBIO hope that the association will promote further development of biobanks and their networking in Russia, which is critically important for the success of national biomedical, pharmaceutical, and biotechnological research, and can facilitate international biobanking projects on a global scale.
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Affiliation(s)
| | - Alexey N Meshkov
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Andrey S Glotov
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint-Petersburg, Russia
| | - Anna L Borisova
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Oleg P Balanovsky
- N.I. Vavilov Institute of General Genetics, Research Centre for Medical Genetics, Biobank of North Eurasia, Moscow, Russia
| | - Vladimir E Belyaev
- Biobank, Institute for Regenerative Medicine, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | | | | | - Anastasiya Yu Efimenko
- Institute for Regenerative Medicine, Medical Research and Educational Center, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Maria S Pokrovskaya
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Tatyana A Semenenko
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Moscow, Russia
| | | | | | - Oxana M Drapkina
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
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15
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Nasykhova YA, Tonyan ZN, Mikhailova AA, Danilova MM, Glotov AS. Pharmacogenetics of Type 2 Diabetes-Progress and Prospects. Int J Mol Sci 2020; 21:ijms21186842. [PMID: 32961860 PMCID: PMC7555942 DOI: 10.3390/ijms21186842] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/11/2020] [Accepted: 09/16/2020] [Indexed: 12/11/2022] Open
Abstract
Type 2 diabetes mellitus (T2D) is a chronic metabolic disease resulting from insulin resistance and progressively reduced insulin secretion, which leads to impaired glucose utilization, dyslipidemia and hyperinsulinemia and progressive pancreatic beta cell dysfunction. The incidence of type 2 diabetes mellitus is increasing worldwide and nowadays T2D already became a global epidemic. The well-known interindividual variability of T2D drug actions such as biguanides, sulfonylureas/meglitinides, DPP-4 inhibitors/GLP1R agonists and SGLT-2 inhibitors may be caused, among other things, by genetic factors. Pharmacogenetic findings may aid in identifying new drug targets and obtaining in-depth knowledge of the causes of disease and its physiological processes, thereby, providing an opportunity to elaborate an algorithm for tailor or precision treatment. The aim of this article is to summarize recent progress and discoveries for T2D pharmacogenetics and to discuss the factors which limit the furthering accumulation of genetic variability knowledge in patient response to therapy that will allow improvement the personalized treatment of T2D.
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Affiliation(s)
- Yulia A. Nasykhova
- Department of Genomic Medicine, D.O. Ott’s Institute of Obstetrics, Gynecology and Reproductology, 199034 Saint-Petersburg, Russia; (Y.A.N.); (Z.N.T.); (A.A.M.); (M.M.D.)
- Laboratory of Biobanking and Genomic Medicine, Saint-Petersburg State University, 199034 Saint-Petersburg, Russia
| | - Ziravard N. Tonyan
- Department of Genomic Medicine, D.O. Ott’s Institute of Obstetrics, Gynecology and Reproductology, 199034 Saint-Petersburg, Russia; (Y.A.N.); (Z.N.T.); (A.A.M.); (M.M.D.)
| | - Anastasiia A. Mikhailova
- Department of Genomic Medicine, D.O. Ott’s Institute of Obstetrics, Gynecology and Reproductology, 199034 Saint-Petersburg, Russia; (Y.A.N.); (Z.N.T.); (A.A.M.); (M.M.D.)
- Laboratory of Biobanking and Genomic Medicine, Saint-Petersburg State University, 199034 Saint-Petersburg, Russia
| | - Maria M. Danilova
- Department of Genomic Medicine, D.O. Ott’s Institute of Obstetrics, Gynecology and Reproductology, 199034 Saint-Petersburg, Russia; (Y.A.N.); (Z.N.T.); (A.A.M.); (M.M.D.)
| | - Andrey S. Glotov
- Department of Genomic Medicine, D.O. Ott’s Institute of Obstetrics, Gynecology and Reproductology, 199034 Saint-Petersburg, Russia; (Y.A.N.); (Z.N.T.); (A.A.M.); (M.M.D.)
- Laboratory of Biobanking and Genomic Medicine, Saint-Petersburg State University, 199034 Saint-Petersburg, Russia
- Correspondence: ; Tel.: +7-9117832003
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16
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Deng YN, Xia Z, Zhang P, Ejaz S, Liang S. Transcription Factor RREB1: from Target Genes towards Biological Functions. Int J Biol Sci 2020; 16:1463-1473. [PMID: 32210733 PMCID: PMC7085234 DOI: 10.7150/ijbs.40834] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/06/2020] [Indexed: 02/05/2023] Open
Abstract
The Ras-responsive element binding protein 1(RREB1) is a member of zinc finger transcription factors, which is widely involved in biological processes including cell proliferation, transcriptional regulation and DNA damage repair. New findings reveal RREB1 functions as both transcriptional repressors and transcriptional activators for transcriptional regulation of target genes. The activation of RREB1 is regulated by MAPK pathway. We have summarized the target genes of RREB1 and discussed RREB1 roles in the cancer development. In addition, increasing evidences suggest that RREB1 is a potential risk gene for type 2 diabetes and obesity. We also review the current clinical application of RREB1 as a biomarker for melanoma detection. In conclusion, RREB1 is a promising diagnostic biomarker or new drug target for cancers and metabolic diseases.
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Affiliation(s)
- Ya-Nan Deng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, No.17, 3rd Section of People's South Road, Chengdu, 610041, P.R. China
| | - Zijing Xia
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, No.17, 3rd Section of People's South Road, Chengdu, 610041, P.R. China.,Department of Rheumatology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, P. R. China
| | - Peng Zhang
- Department of Urinary Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu, 610041, P. R. China
| | - Samina Ejaz
- Department of Biochemistry and Biotechnology, Baghdad Campus, The Islamia University of Bahawalpur, Pakistan
| | - Shufang Liang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, No.17, 3rd Section of People's South Road, Chengdu, 610041, P.R. China
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17
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Barbitoff YA, Skitchenko RK, Poleshchuk OI, Shikov AE, Serebryakova EA, Nasykhova YA, Polev DE, Shuvalova AR, Shcherbakova IV, Fedyakov MA, Glotov OS, Glotov AS, Predeus AV. Whole-exome sequencing provides insights into monogenic disease prevalence in Northwest Russia. Mol Genet Genomic Med 2019; 7:e964. [PMID: 31482689 PMCID: PMC6825859 DOI: 10.1002/mgg3.964] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/07/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Allele frequency data from large exome and genome aggregation projects such as the Genome Aggregation Database (gnomAD) are of ultimate importance to the interpretation of medical resequencing data. However, allele frequencies might significantly differ in poorly studied populations that are underrepresented in large-scale projects, such as the Russian population. METHODS In this work, we leveraged our access to a large dataset of 694 exome samples to analyze genetic variation in the Northwest Russia. We compared the spectrum of genetic variants to the dbSNP build 151, and made estimates of ClinVar-based autosomal recessive (AR) disease allele prevalence as compared to gnomAD r. 2.1. RESULTS An estimated 9.3% of discovered variants were not present in dbSNP. We report statistically significant overrepresentation of pathogenic variants for several Mendelian disorders, including phenylketonuria (PAH, rs5030858), Wilson's disease (ATP7B, rs76151636), factor VII deficiency (F7, rs36209567), kyphoscoliosis type of Ehlers-Danlos syndrome (FKBP14, rs542489955), and several other recessive pathologies. We also make primary estimates of monogenic disease incidence in the population, with retinal dystrophy, cystic fibrosis, and phenylketonuria being the most frequent AR pathologies. CONCLUSION Our observations demonstrate the utility of population-specific allele frequency data to the diagnosis of monogenic disorders using high-throughput technologies.
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Affiliation(s)
- Yury A. Barbitoff
- Bioinformatics InstituteSt. PetersburgRussia
- Department of Genetics and BiotechnologySt. Petersburg State UniversitySt. PetersburgRussia
| | | | | | - Anton E. Shikov
- Bioinformatics InstituteSt. PetersburgRussia
- City Hospital No. 40St. PetersburgRussia
| | - Elena A. Serebryakova
- Department of Genomic MedicineD.O. Ott Research Institute of Obstetrics, Gynaecology and ReproductionSt. PetersburgRussia
| | - Yulia A. Nasykhova
- Department of Genomic MedicineD.O. Ott Research Institute of Obstetrics, Gynaecology and ReproductionSt. PetersburgRussia
- Laboratory of Biobanking and Genomic Medicine of Institute of Translation BiomedicineSt. Petersburg State UniversitySt. PetersburgRussia
| | | | | | - Irina V. Shcherbakova
- Laboratory of Biobanking and Genomic Medicine of Institute of Translation BiomedicineSt. Petersburg State UniversitySt. PetersburgRussia
| | | | - Oleg S. Glotov
- City Hospital No. 40St. PetersburgRussia
- Department of Genomic MedicineD.O. Ott Research Institute of Obstetrics, Gynaecology and ReproductionSt. PetersburgRussia
| | - Andrey S. Glotov
- City Hospital No. 40St. PetersburgRussia
- Department of Genomic MedicineD.O. Ott Research Institute of Obstetrics, Gynaecology and ReproductionSt. PetersburgRussia
- Laboratory of Biobanking and Genomic Medicine of Institute of Translation BiomedicineSt. Petersburg State UniversitySt. PetersburgRussia
- Institute of Living SystemsImmanuel Kant Baltic Federal UniversityKaliningradRussia
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18
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Pokrovskaya MS, Sivakova OV, Efimova IA, Meshkov AN, Metelskaya VA, Shalnova SA, Drapkina OM. Biobanking as a necessary tool for research in the field of personalized medicine in the scientific medical center. Per Med 2019; 16:501-509. [DOI: 10.2217/pme-2019-0049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The National Medical Research Center for Preventive Medicine of Russia (NMRCPM) conducts epidemiological and clinical research for the development of personalized medicine. This is why NMRCPM has faced the problem of how to standardize preanalytical conditions for all biospecimens from various scientific projects and of how to provide long-term responsible standardized regulated safe storage of blood and its derivatives. This article describes various aspects of establishing a biobank in a large medical center dedicated to integrating the biomarkers research activities of different departments. To date, >205,000 serum/plasma/whole blood specimens have been stored. Collaboration with >25 scientific projects as well as the biobank’s own research project has been organized. The availability of this biobank became a platform for the establishment of the Personalized Medicine Center in NMRCPM.
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Affiliation(s)
- Maria Sergeevna Pokrovskaya
- Federal State Institution National Research Center for Preventive Medicine, Petroverigskii lane, 10/3, Moscow, Russia, 101990
| | - Oksana Victorovna Sivakova
- Federal State Institution National Research Center for Preventive Medicine, Petroverigskii lane, 10/3, Moscow, Russia, 101990
| | - Irina Aleksandrovna Efimova
- Federal State Institution National Research Center for Preventive Medicine, Petroverigskii lane, 10/3, Moscow, Russia, 101990
| | - Aleksey Nikolaevich Meshkov
- Federal State Institution National Research Center for Preventive Medicine, Petroverigskii lane, 10/3, Moscow, Russia, 101990
| | - Victoria Alekseevna Metelskaya
- Federal State Institution National Research Center for Preventive Medicine, Petroverigskii lane, 10/3, Moscow, Russia, 101990
| | - Svetlana Anatolievna Shalnova
- Federal State Institution National Research Center for Preventive Medicine, Petroverigskii lane, 10/3, Moscow, Russia, 101990
| | - Oxana Mikhailovna Drapkina
- Federal State Institution National Research Center for Preventive Medicine, Petroverigskii lane, 10/3, Moscow, Russia, 101990
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Nasykhova YA, Barbitoff YA, Serebryakova EA, Katserov DS, Glotov AS. Recent advances and perspectives in next generation sequencing application to the genetic research of type 2 diabetes. World J Diabetes 2019; 10:376-395. [PMID: 31363385 PMCID: PMC6656706 DOI: 10.4239/wjd.v10.i7.376] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/23/2019] [Accepted: 06/11/2019] [Indexed: 02/05/2023] Open
Abstract
Type 2 diabetes (T2D) mellitus is a common complex disease that currently affects more than 400 million people worldwide and has become a global health problem. High-throughput sequencing technologies such as whole-genome and whole-exome sequencing approaches have provided numerous new insights into the molecular bases of T2D. Recent advances in the application of sequencing technologies to T2D research include, but are not limited to: (1) Fine mapping of causal rare and common genetic variants; (2) Identification of confident gene-level associations; (3) Identification of novel candidate genes by specific scoring approaches; (4) Interrogation of disease-relevant genes and pathways by transcriptional profiling and epigenome mapping techniques; and (5) Investigation of microbial community alterations in patients with T2D. In this work we review these advances in application of next-generation sequencing methods for elucidation of T2D pathogenesis, as well as progress and challenges in implementation of this new knowledge about T2D genetics in diagnosis, prevention, and treatment of the disease.
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Affiliation(s)
- Yulia A Nasykhova
- Laboratory of Biobanking and Genomic Medicine of Institute of Translation Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology and Reproductology, St. Petersburg 199034, Russia
| | - Yury A Barbitoff
- Laboratory of Biobanking and Genomic Medicine of Institute of Translation Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
- Bioinformatics Institute, St. Petersburg 194021, Russia
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Elena A Serebryakova
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology and Reproductology, St. Petersburg 199034, Russia
- Department of Genetics, City Hospital No. 40, St. Petersburg 197706, Russia
| | - Dmitry S Katserov
- Institute of Living Systems, Immanuel Kant Baltic Federal University, Kaliningrad 236016, Russia
| | - Andrey S Glotov
- Laboratory of Biobanking and Genomic Medicine of Institute of Translation Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology and Reproductology, St. Petersburg 199034, Russia
- Department of Genetics, City Hospital No. 40, St. Petersburg 197706, Russia
- Institute of Living Systems, Immanuel Kant Baltic Federal University, Kaliningrad 236016, Russia
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