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Yin X, Guo Z, Song C. AMPK, a key molecule regulating aging-related myocardial ischemia-reperfusion injury. Mol Biol Rep 2024; 51:257. [PMID: 38302614 DOI: 10.1007/s11033-023-09050-8] [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: 05/17/2023] [Accepted: 10/10/2023] [Indexed: 02/03/2024]
Abstract
Aging leads to the threat of more diseases to the biological anatomical structure and the decline of disease resistance, increasing the incidence and mortality of myocardial ischemia-reperfusion injury (MI/RI). Moreover, MI/RI promotes damage to an aging heart. Notably, 5'-adenosine monophosphate-activated protein kinase (AMPK) regulates cellular energy metabolism, stress response, and protein metabolism, participates in aging-related signaling pathways, and plays an essential role in ischemia-reperfusion (I/R) injury diseases. This study aims to introduce the aging theory, summarize the interaction between aging and MI/RI, and describe the crosstalk of AMPK in aging and MI/RI. We show how AMPK can offer protective effects against age-related stressors, lifestyle factors such as alcohol consumption and smoking, and hypertension. We also review some of the clinical prospects for the development of interventions that harness the effect of AMPK to treat MI/RI and other age-related cardiovascular diseases.
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Affiliation(s)
- Xiaorui Yin
- Department of Cardiology, Second Hospital of Jilin University, No.218 Ziqiang Street, Changchun, 130041, China
| | - Ziyuan Guo
- Department of Cardiology, Second Hospital of Jilin University, No.218 Ziqiang Street, Changchun, 130041, China
| | - Chunli Song
- Department of Cardiology, Second Hospital of Jilin University, No.218 Ziqiang Street, Changchun, 130041, China.
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2
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Wu B, Yee SW, Xiao S, Xu F, Sridhar SB, Yang M, Hochstadt S, Cabral W, Lanfear DE, Hedderson MM, Giacomini KM, Williams LK. Genome-Wide Association Study Identifies Pharmacogenomic Variants Associated With Metformin Glycemic Response in African American Patients With Type 2 Diabetes. Diabetes Care 2024; 47:208-215. [PMID: 37639712 PMCID: PMC10834390 DOI: 10.2337/dc22-2494] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 08/03/2023] [Indexed: 08/31/2023]
Abstract
OBJECTIVE Metformin is the most common treatment for type 2 diabetes (T2D). However, there have been no pharmacogenomic studies for T2D in which a population of color was used in the discovery analysis. This study sought to identify genomic variants associated with metformin response in African American patients with diabetes. RESEARCH DESIGN AND METHODS Patients in the discovery set were adult, African American participants from the Diabetes Multi-omic Investigation of Drug Response (DIAMOND), a cohort study of patients with T2D from a health system serving southeast Michigan. DIAMOND participants had genome-wide genotype data and longitudinal electronic records of laboratory results and medication fills. The genome-wide discovery analysis identified polymorphisms correlated to changes in glycated hemoglobin (HbA1c) levels among individuals on metformin monotherapy. Lead associations were assessed for replication in an independent cohort of African American participants from Kaiser Permanente Northern California (KPNC) and in European American participants from DIAMOND. RESULTS The discovery set consisted of 447 African American participants, whereas the replication sets included 353 African American KPNC participants and 466 European American DIAMOND participants. The primary analysis identified a variant, rs143276236, in the gene ARFGEF3, which met the threshold for genome-wide significance, replicated in KPNC African Americans, and was still significant in the meta-analysis (P = 1.17 × 10-9). None of the significant discovery variants replicated in European Americans DIAMOND participants. CONCLUSIONS We identified a novel and biologically plausible genetic variant associated with a change in HbA1c levels among African American patients on metformin monotherapy. These results highlight the importance of diversity in pharmacogenomic studies.
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Affiliation(s)
- Baojun Wu
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI
| | - Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences and Institute for Human Genetics, School of Pharmacy, University of California San Francisco, San Francisco, CA
| | - Shujie Xiao
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI
| | - Fei Xu
- Division of Research, Kaiser Permanente Northern California, Oakland, CA
| | - Sneha B. Sridhar
- Division of Research, Kaiser Permanente Northern California, Oakland, CA
| | - Mao Yang
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI
| | - Samantha Hochstadt
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI
| | - Whitney Cabral
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI
| | - David E. Lanfear
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI
| | | | - Kathleen M. Giacomini
- Department of Bioengineering and Therapeutic Sciences and Institute for Human Genetics, School of Pharmacy, University of California San Francisco, San Francisco, CA
| | - L. Keoki Williams
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI
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3
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Goodwin PJ, Chen BE, Gelmon KA, Whelan TJ, Ennis M, Lemieux J, Ligibel JA, Hershman DL, Mayer IA, Hobday TJ, Bliss JM, Rastogi P, Rabaglio-Poretti M, Thompson AM, Rea DW, Stos PM, Shepherd LE, Stambolic V, Parulekar WR. Effect of Metformin Versus Placebo on New Primary Cancers in Canadian Cancer Trials Group MA.32: A Secondary Analysis of a Phase III Randomized Double-Blind Trial in Early Breast Cancer. J Clin Oncol 2023; 41:5356-5362. [PMID: 37695982 PMCID: PMC10713140 DOI: 10.1200/jco.23.00296] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/28/2023] [Accepted: 07/20/2023] [Indexed: 09/13/2023] Open
Abstract
Clinical trials frequently include multiple end points that mature at different times. The initial report, typically based on the primary end point, may be published when key planned coprimary or secondary analyses are not yet available. Clinical trial updates provide an opportunity to disseminate additional results from studies, published in JCO or elsewhere, for which the primary end point has already been reported.Metformin has been associated with lower cancer risk in epidemiologic and preclinical research. In the MA.32 randomized adjuvant breast cancer trial, metformin (v placebo) did not affect invasive disease-free or overall survival. Here, we report metformin effects on the risk of new cancer. Between 2010 and 2013, 3,649 patients with breast cancer younger than 75 years without diabetes with high-risk T1-3, N0-3 M0 breast cancer (any estrogen receptor, progesterone receptor, human epidermal growth factor receptor 2) were randomly assigned to metformin 850 mg orally twice a day or placebo twice a day for 5 years. New primary invasive cancers (outside the ipsilateral breast) developing as a first event were identified. Time to events was described by the competing risks method; two-sided likelihood ratio tests adjusting for age, BMI, smoking, and alcohol intake were used to compare metformin versus placebo arms. A total of 184 patients developed new invasive cancers: 102 metformin and 82 placebo, hazard ratio (HR), 1.25; 95% CI, 0.94 to 1.68; P = .13. These included 48 contralateral invasive breast cancers (27 metformin v 21 placebo), HR, 1.29; 95% CI, 0.72 to 2.27; P = .40 and 136 new nonbreast primary cancers (75 metformin v 61 placebo), HR, 1.24; 95% CI, 0.88 to 1.74; P = .21. Metformin did not reduce the risk of new cancer development in these nondiabetic patients with breast cancer.
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Affiliation(s)
- Pamela J. Goodwin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, and Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Bingshu E. Chen
- Canadian Cancer Trials Group, Queen's University, Kingston, ON, Canada
| | - Karen A. Gelmon
- University of British Columbia, BC Cancer Agency, Vancouver, BC, Canada
| | | | | | | | | | - Dawn L. Hershman
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY
| | | | | | - Judith M. Bliss
- ICR-CTSU, Institute of Cancer Research (UK), London, United Kingdom
| | - Priya Rastogi
- NRG Oncology and University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Manuela Rabaglio-Poretti
- IBCSG and Department of Oncology, Bern University Hospital, University of Bern, Berne, Switzerland
| | | | - Daniel W. Rea
- Cancer Research UK Clinical Trials Unit (CRCTU), Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Paul M. Stos
- Canadian Cancer Trials Group, Queen's University, Kingston, ON, Canada
| | - Lois E. Shepherd
- Canadian Cancer Trials Group, Queen's University, Kingston, ON, Canada
| | - Vuk Stambolic
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
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4
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Sims AA, Gurkar AU. DNA damage-induced stalling of transcription drives aging through gene expression imbalance. DNA Repair (Amst) 2023; 125:103483. [PMID: 36921370 DOI: 10.1016/j.dnarep.2023.103483] [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: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023]
Abstract
Age-related changes in gene expression have long been examined to understand the biology of aging. The hallmarks of aging are biological processes known to be associated with aging, but whether there is a unifying driver of these attributes, is not well understood. With the advent of technology over the last few years, it is quite clear that aging leads to global decline in transcription. In this Perspective, we highlight a new study in Nature Genetics that aimed to determine why global transcription rate reduces with age and how this phenomenon is the driver that interconnects multiple hallmarks of aging. This study recognizes that age-related accumulation of DNA damage, particularly transcription-blocking lesions, stalls RNA polymerase. This phenomenon affects longer genes leading to a gradual loss of transcription and skewing the transcriptome. In order to design a successful aging intervention, future work will be needed to test how some promising therapies in pre-clinical trials target affect transcriptional rate.
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Affiliation(s)
- Austin A Sims
- Aging Institute of UPMC and the University of Pittsburgh School of Medicine, 100 Technology Dr, Pittsburgh, PA 15219, USA
| | - Aditi U Gurkar
- Aging Institute of UPMC and the University of Pittsburgh School of Medicine, 100 Technology Dr, Pittsburgh, PA 15219, USA.
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5
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Stoeger T, Grant RA, McQuattie-Pimentel AC, Anekalla KR, Liu SS, Tejedor-Navarro H, Singer BD, Abdala-Valencia H, Schwake M, Tetreault MP, Perlman H, Balch WE, Chandel NS, Ridge KM, Sznajder JI, Morimoto RI, Misharin AV, Budinger GRS, Nunes Amaral LA. Aging is associated with a systemic length-associated transcriptome imbalance. NATURE AGING 2022; 2:1191-1206. [PMID: 37118543 PMCID: PMC10154227 DOI: 10.1038/s43587-022-00317-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 10/21/2022] [Indexed: 12/14/2022]
Abstract
Aging is among the most important risk factors for morbidity and mortality. To contribute toward a molecular understanding of aging, we analyzed age-resolved transcriptomic data from multiple studies. Here, we show that transcript length alone explains most transcriptional changes observed with aging in mice and humans. We present three lines of evidence supporting the biological importance of the uncovered transcriptome imbalance. First, in vertebrates the length association primarily displays a lower relative abundance of long transcripts in aging. Second, eight antiaging interventions of the Interventions Testing Program of the National Institute on Aging can counter this length association. Third, we find that in humans and mice the genes with the longest transcripts enrich for genes reported to extend lifespan, whereas those with the shortest transcripts enrich for genes reported to shorten lifespan. Our study opens fundamental questions on aging and the organization of transcriptomes.
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Affiliation(s)
- Thomas Stoeger
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL, USA.
- Center for Genetic Medicine, Northwestern University, Evanston, IL, USA.
| | - Rogan A Grant
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
| | | | - Kishore R Anekalla
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
| | - Sophia S Liu
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | | | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University, Evanston, IL, USA
| | - Hiam Abdala-Valencia
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
| | - Michael Schwake
- Department of Neurology, Northwestern University, Evanston, IL, USA
- Faculty of Chemistry, University of Bielefeld, Bielefeld, Germany
| | - Marie-Pier Tetreault
- Division of Gastroenterology and Hepatology, Northwestern University, Evanston, IL, USA
| | - Harris Perlman
- Division of Rheumatology, Northwestern University, Evanston, IL, USA
| | | | - Navdeep S Chandel
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA
| | - Karen M Ridge
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA
| | - Jacob I Sznajder
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA
| | - Richard I Morimoto
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
- Rice Institute for Biomedical Research, Northwestern University, Evanston, IL, USA.
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA.
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA.
| | - G R Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA.
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA.
| | - Luis A Nunes Amaral
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL, USA.
- Department of Physics and Astronomy, Northwestern University, Evanston, IL, USA.
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6
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Metformin Treatment Modulates Long Non-Coding RNA Isoforms Expression in Human Cells. Noncoding RNA 2022; 8:ncrna8050068. [PMID: 36287120 PMCID: PMC9607547 DOI: 10.3390/ncrna8050068] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) undergo splicing and have multiple transcribed isoforms. Nevertheless, for lncRNAs, as well as for mRNA, measurements of expression are routinely performed only at the gene level. Metformin is the first-line oral therapy for type 2 diabetes mellitus and other metabolic diseases. However, its mechanism of action remains not thoroughly explained. Transcriptomic analyses using metformin in different cell types reveal that only protein-coding genes are considered. We aimed to characterize lncRNA isoforms that were differentially affected by metformin treatment on multiple human cell types (three cancer, two non-cancer) and to provide insights into the lncRNA regulation by this drug. We selected six series to perform a differential expression (DE) isoform analysis. We also inferred the biological roles for lncRNA DE isoforms using in silico tools. We found the same isoform of an lncRNA (AC016831.6-205) highly expressed in all six metformin series, which has a second exon putatively coding for a peptide with relevance to the drug action. Moreover, the other two lncRNA isoforms (ZBED5-AS1-207 and AC125807.2-201) may also behave as cis-regulatory elements to the expression of transcripts in their vicinity. Our results strongly reinforce the importance of considering DE isoforms of lncRNA for understanding metformin mechanisms at the molecular level.
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7
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A resource for integrated genomic analysis of the human liver. Sci Rep 2022; 12:15151. [PMID: 36071064 PMCID: PMC9452507 DOI: 10.1038/s41598-022-18506-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 08/08/2022] [Indexed: 11/18/2022] Open
Abstract
In this study, we generated whole-transcriptome RNA-Seq from n = 192 genotyped liver samples and used these data with existing data from the GTEx Project (RNA-Seq) and previous liver eQTL (microarray) studies to create an enhanced transcriptomic sequence resource in the human liver. Analyses of genotype-expression associations show pronounced enrichment of associations with genes of drug response. The associations are primarily consistent across the two RNA-Seq datasets, with some modest variation, indicating the importance of obtaining multiple datasets to produce a robust resource. We further used an empirical Bayesian model to compare eQTL patterns in liver and an additional 20 GTEx tissues, finding that MHC genes, and especially class II genes, are enriched for liver-specific eQTL patterns. To illustrate the utility of the resource to augment GWAS analysis with small sample sizes, we developed a novel meta-analysis technique to combine several liver eQTL data sources. We also illustrate its application using a transcriptome-enhanced re-analysis of a study of neutropenia in pancreatic cancer patients. The associations of genotype with liver expression, including splice variation and its genetic associations, are made available in a searchable genome browser.
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8
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Metformin and breast cancer: an opportunity for pharmacogenetics. Aging (Albany NY) 2022; 14:5612-5613. [PMID: 35852878 PMCID: PMC9365564 DOI: 10.18632/aging.204180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/11/2022] [Indexed: 11/25/2022]
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9
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Integrated or Independent Actions of Metformin in Target Tissues Underlying Its Current Use and New Possible Applications in the Endocrine and Metabolic Disorder Area. Int J Mol Sci 2021; 22:ijms222313068. [PMID: 34884872 PMCID: PMC8658259 DOI: 10.3390/ijms222313068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/18/2021] [Accepted: 11/29/2021] [Indexed: 12/14/2022] Open
Abstract
Metformin is considered the first-choice drug for type 2 diabetes treatment. Actually, pleiotropic effects of metformin have been recognized, and there is evidence that this drug may have a favorable impact on health beyond its glucose-lowering activity. In summary, despite its long history, metformin is still an attractive research opportunity in the field of endocrine and metabolic diseases, age-related diseases, and cancer. To this end, its mode of action in distinct cell types is still in dispute. The aim of this work was to review the current knowledge and recent findings on the molecular mechanisms underlying the pharmacological effects of metformin in the field of metabolic and endocrine pathologies, including some endocrine tumors. Metformin is believed to act through multiple pathways that can be interconnected or work independently. Moreover, metformin effects on target tissues may be either direct or indirect, which means secondary to the actions on other tissues and consequent alterations at systemic level. Finally, as to the direct actions of metformin at cellular level, the intracellular milieu cooperates to cause differential responses to the drug between distinct cell types, despite the primary molecular targets may be the same within cells. Cellular bioenergetics can be regarded as the primary target of metformin action. Metformin can perturb the cytosolic and mitochondrial NAD/NADH ratio and the ATP/AMP ratio within cells, thus affecting enzymatic activities and metabolic and signaling pathways which depend on redox- and energy balance. In this context, the possible link between pyruvate metabolism and metformin actions is extensively discussed.
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10
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Quan X, Zhao C, Gao Z, Zhang Y, Zhao R, Wang J, Zhang Q. DDX10 and BYSL as the potential targets of chondrosarcoma and glioma. Medicine (Baltimore) 2021; 100:e27669. [PMID: 34797290 PMCID: PMC8601295 DOI: 10.1097/md.0000000000027669] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/10/2021] [Indexed: 01/05/2023] Open
Abstract
To provide reliable molecular markers and effective therapeutic targets for chondrosarcoma and glioma.Gene Set Enrichment (GSE) 29745 and GSE48420 were downloaded from the Gene Expression Omnibus (GEO) database. Differently expressed genes (DEGs) were identified by the GEO2R. We annotated the function of common DEGs through Digital Audio/Video Interactive Decoder (DAVID) and Metascape. Protein-protein interaction network construction was performed through STRING. Hub genes were identified by the two different algorithms (MCC, EPC). DDX10 and BYSL were key factors in embryo implantation and development, and plays a role in a variety of cancers. The role of the DDX10 and BYSL on the glioma derived from the chondrosarcoma would be explored by the clinical samples.A total of 1442 DEGs were identified. The variations in DEGs were mainly enriched in vasculature development, cell motion, blood vessel development, cell migration, regulation of cell proliferation, regulation of cell proliferation, wound healing, biological adhesion, growth factor binding, identical pathways in cancer, and p53 signaling pathway. Dead-box helicase 10 (DDX10), Bystin-like (BYSL), and WD repeat domain 12 (WDR12) were identified as the hub genes, and the three hub genes were up-regulated in the chondrosarcoma. Chondrosarcoma patients with high expression levels of DDX10 (Logrank P = .0052; HR (high) = 1.8; n (high) = 131, 50%), and BYSL (P = 6.5e-05; HR (high) = 2.3; n (high) = 131, 50%) had poorer overall survival times than those with low expression levels.DDX10 and BYSL genes may provide reliable molecular markers and effective therapeutic targets for chondrosarcoma and glioma.
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Metformin Actions on the Liver: Protection Mechanisms Emerging in Hepatocytes and Immune Cells against NASH-Related HCC. Int J Mol Sci 2021; 22:ijms22095016. [PMID: 34065108 PMCID: PMC8126028 DOI: 10.3390/ijms22095016] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/03/2021] [Accepted: 05/06/2021] [Indexed: 02/07/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is strongly linked to the global epidemic of obesity and type 2 diabetes mellitus (T2DM). Notably, NAFLD can progress from the mildest form of simple steatosis to nonalcoholic steatohepatitis (NASH) that increases the risk for hepatocellular carcinoma (HCC), which is a malignancy with a dismal prognosis and rising incidence in the United States and other developed counties, possibly due to the epidemic of NAFLD. Metformin, the first-line drug for T2DM, has been suggested to reduce risks for several types of cancers including HCC and protect against NASH-related HCC, as revealed by epidemical studies on humans and preclinical studies on animal models. This review focuses on the pathogenesis of NASH-related HCC and the mechanisms by which metformin inhibits the initiation and progression of NASH-related HCC. Since the functional role of immune cells in liver homeostasis and pathogenesis is increasingly appreciated in developing anti-cancer therapies on liver malignancies, we discuss both the traditional targets of metformin in hepatocytes and the recently defined effects of metformin on immune cells.
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12
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Inhibition of mitochondrial function by metformin increases glucose uptake, glycolysis and GDF-15 release from intestinal cells. Sci Rep 2021; 11:2529. [PMID: 33510216 PMCID: PMC7843649 DOI: 10.1038/s41598-021-81349-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/04/2021] [Indexed: 02/07/2023] Open
Abstract
Even though metformin is widely used to treat type2 diabetes, reducing glycaemia and body weight, the mechanisms of action are still elusive. Recent studies have identified the gastrointestinal tract as an important site of action. Here we used intestinal organoids to explore the effects of metformin on intestinal cell physiology. Bulk RNA-sequencing analysis identified changes in hexose metabolism pathways, particularly glycolytic genes. Metformin increased expression of Slc2a1 (GLUT1), decreased expression of Slc2a2 (GLUT2) and Slc5a1 (SGLT1) whilst increasing GLUT-dependent glucose uptake and glycolytic rate as observed by live cell imaging of genetically encoded metabolite sensors and measurement of oxygen consumption and extracellular acidification rates. Metformin caused mitochondrial dysfunction and metformin's effects on 2D-cultures were phenocopied by treatment with rotenone and antimycin-A, including upregulation of GDF15 expression, previously linked to metformin dependent weight loss. Gene expression changes elicited by metformin were replicated in 3D apical-out organoids and distal small intestines of metformin treated mice. We conclude that metformin affects glucose uptake, glycolysis and GDF-15 secretion, likely downstream of the observed mitochondrial dysfunction. This may explain the effects of metformin on intestinal glucose utilisation and food balance.
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13
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Le J, Fu Y, Han Q, Wei X, Ji H, Chen Y, Wang Q, Pi P, Li J, Lin X, Zhang X, Zhang Y, Ye J. Restoration of mRNA Expression of Solute Carrier Proteins in Liver of Diet-Induced Obese Mice by Metformin. Front Endocrinol (Lausanne) 2021; 12:720784. [PMID: 34659115 PMCID: PMC8515182 DOI: 10.3389/fendo.2021.720784] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 09/08/2021] [Indexed: 02/05/2023] Open
Abstract
Metformin (MET), the most common medicine for type 2 diabetes (T2DM), improves insulin sensitivity by targeting the liver, intestine and other organs. Its impact on expression of the solute carrier (Slc) transporter genes have not been reported in the mechanism of insulin sensitization. In this study, we examined Slc gene expression in the liver and colon of diet-induced obese (DIO) mice treated with MET by transcriptomic analysis. There were 939 differentially expressed genes (DEGs) in the liver of DIO mice vs lean mice, which included 34 Slc genes. MET altered 489 DEGs in the liver of DIO mice, in which 23 were Slc genes. Expression of 20 MET-responsive Slc DEGs was confirmed by qRT-PCR, in which 15 Slc genes were altered in DIO mice and their expressions were restored by MET, including Slc2a10, Slc2a13, Slc5a9, Slc6a14, Slc7a9, Slc9a2, Slc9a3, Slc13a2, Slc15a2, Slc26a3, Slc34a2, Slc37a1, Slc44a4, Slc51b and Slc52a3. While, there were only 97 DEGs in the colon of DIO mice with 5 Slc genes, whose expression was not restored by MET. The data suggest that more genes were altered in the liver over the colon by the high fat diet (HFD). There were 20 Slc genes with alteration confirmed in the liver of DIO mice and 15 of them were restored by MET, which was associated with improvement of insulin sensitivity and obesity. The restoration may improve the uptake of glucose, amino acids, mannose, fructose, 1,5-anhydro-D-glucitol and bumetanide in hepatocytes of the liver of DIO mice. The study provides new insight into the mechanism of metformin action in insulin sensitization and obesity.
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Affiliation(s)
- Jiamei Le
- Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
- Shanghai Key Laboratory of Molecular Imaging, Collaborative Innovation Center for Biomedicine, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Yi Fu
- Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
- Shanghai Key Laboratory of Molecular Imaging, Collaborative Innovation Center for Biomedicine, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Qiuqin Han
- Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
- Shanghai Key Laboratory of Molecular Imaging, Collaborative Innovation Center for Biomedicine, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Xindong Wei
- Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
- Department of Surgical Oncology, Nanjing University of Chinese Medicin Affiliated 81st Hospital, Nanjing, China
| | - Houlin Ji
- Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
- Graduate School, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yifan Chen
- Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
- Shanghai Key Laboratory of Molecular Imaging, Collaborative Innovation Center for Biomedicine, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Qiuying Wang
- Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
- Shanghai Key Laboratory of Molecular Imaging, Collaborative Innovation Center for Biomedicine, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Peixian Pi
- Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
- Shanghai Key Laboratory of Molecular Imaging, Collaborative Innovation Center for Biomedicine, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Jilei Li
- Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
- Shanghai Key Laboratory of Molecular Imaging, Collaborative Innovation Center for Biomedicine, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Xinjie Lin
- Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
- Shanghai Key Laboratory of Molecular Imaging, Collaborative Innovation Center for Biomedicine, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Xiaoying Zhang
- Metabolic Disease Research Center, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Yong Zhang
- Metabolic Disease Research Center, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Jianping Ye
- Metabolic Disease Research Center, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
- Center for Advanced Medicine, College of Medicine, Zhengzhou University, Zhengzhou, China
- Shanghai Diabetes Institute, Shanghai Jiaotong University Affiliated Sixth People’s Hospital, Shanghai, China
- *Correspondence: Jianping Ye, ;
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14
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Maude H, Sanchez-Cabanillas C, Cebola I. Epigenetics of Hepatic Insulin Resistance. Front Endocrinol (Lausanne) 2021; 12:681356. [PMID: 34046015 PMCID: PMC8147868 DOI: 10.3389/fendo.2021.681356] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/20/2021] [Indexed: 01/14/2023] Open
Abstract
Insulin resistance (IR) is largely recognized as a unifying feature that underlies metabolic dysfunction. Both lifestyle and genetic factors contribute to IR. Work from recent years has demonstrated that the epigenome may constitute an interface where different signals may converge to promote IR gene expression programs. Here, we review the current knowledge of the role of epigenetics in hepatic IR, focusing on the roles of DNA methylation and histone post-translational modifications. We discuss the broad epigenetic changes observed in the insulin resistant liver and its associated pathophysiological states and leverage on the wealth of 'omics' studies performed to discuss efforts in pinpointing specific loci that are disrupted by these changes. We envision that future studies, with increased genomic resolution and larger cohorts, will further the identification of biomarkers of early onset hepatic IR and assist the development of targeted interventions. Furthermore, there is growing evidence to suggest that persistent epigenetic marks may be acquired over prolonged exposure to disease or deleterious exposures, highlighting the need for preventative medicine and long-term lifestyle adjustments to avoid irreversible or long-term alterations in gene expression.
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Affiliation(s)
| | | | - Inês Cebola
- *Correspondence: Hannah Maude, ; Inês Cebola,
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15
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Makki N, Zhao J, Liu Z, Eckalbar WL, Ushiki A, Khanshour AM, Wu J, Rios J, Gray RS, Wise CA, Ahituv N. Genomic characterization of the adolescent idiopathic scoliosis-associated transcriptome and regulome. Hum Mol Genet 2020; 29:3606-3615. [PMID: 33179741 PMCID: PMC7823110 DOI: 10.1093/hmg/ddaa242] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 08/24/2020] [Accepted: 10/12/2020] [Indexed: 12/27/2022] Open
Abstract
Adolescent idiopathic scoliosis (AIS), a sideways curvature of the spine, is the most common pediatric musculoskeletal disorder, affecting ~3% of the population worldwide. However, its genetic bases and tissues of origin remain largely unknown. Several genome-wide association studies (GWAS) have implicated nucleotide variants in non-coding sequences that control genes with important roles in cartilage, muscle, bone, connective tissue and intervertebral disks (IVDs) as drivers of AIS susceptibility. Here, we set out to define the expression of AIS-associated genes and active regulatory elements by performing RNA-seq and chromatin immunoprecipitation-sequencing against H3 lysine 27 acetylation in these tissues in mouse and human. Our study highlights genetic pathways involving AIS-associated loci that regulate chondrogenesis, IVD development and connective tissue maintenance and homeostasis. In addition, we identify thousands of putative AIS-associated regulatory elements which may orchestrate tissue-specific expression in musculoskeletal tissues of the spine. Quantification of enhancer activity of several candidate regulatory elements from our study identifies three functional enhancers carrying AIS-associated GWAS SNPs at the ADGRG6 and BNC2 loci. Our findings provide a novel genome-wide catalog of AIS-relevant genes and regulatory elements and aid in the identification of novel targets for AIS causality and treatment.
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Affiliation(s)
- Nadja Makki
- Department of Anatomy and Cell Biology, University of Florida, College of Medicine, Gainesville, FL, USA
| | - Jingjing Zhao
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Zhaoyang Liu
- Department of Pediatrics and Nutritional Sciences, Dell Pediatric Research Institute, University of Texas at Austin, Austin, TX, USA
| | - Walter L Eckalbar
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Aki Ushiki
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Anas M Khanshour
- Center for Pediatric Bone Biology and Translational Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA
| | - Joe Wu
- Health Science Center Libraries, University of Florida, Gainesville, FL, USA
| | - Jonathan Rios
- Center for Pediatric Bone Biology and Translational Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA.,McDermott Center for Human Growth and Development and Departments of Orthopaedic Surgery and Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ryan S Gray
- Department of Pediatrics and Nutritional Sciences, Dell Pediatric Research Institute, University of Texas at Austin, Austin, TX, USA
| | - Carol A Wise
- Center for Pediatric Bone Biology and Translational Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA.,McDermott Center for Human Growth and Development and Departments of Orthopaedic Surgery and Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
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16
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García-Calzón S, Perfilyev A, Martinell M, Ustinova M, Kalamajski S, Franks PW, Bacos K, Elbere I, Pihlajamäki J, Volkov P, Vaag A, Groop L, Maziarz M, Klovins J, Ahlqvist E, Ling C. Epigenetic markers associated with metformin response and intolerance in drug-naïve patients with type 2 diabetes. Sci Transl Med 2020; 12:12/561/eaaz1803. [DOI: 10.1126/scitranslmed.aaz1803] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/27/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022]
Abstract
Metformin is the first-line pharmacotherapy for managing type 2 diabetes (T2D). However, many patients with T2D do not respond to or tolerate metformin well. Currently, there are no phenotypes that successfully predict glycemic response to, or tolerance of, metformin. We explored whether blood-based epigenetic markers could discriminate metformin response and tolerance by analyzing genome-wide DNA methylation in drug-naïve patients with T2D at the time of their diagnosis. DNA methylation of 11 and 4 sites differed between glycemic responders/nonresponders and metformin-tolerant/intolerant patients, respectively, in discovery and replication cohorts. Greater methylation at these sites associated with a higher risk of not responding to or not tolerating metformin with odds ratios between 1.43 and 3.09 per 1-SD methylation increase. Methylation risk scores (MRSs) of the 11 identified sites differed between glycemic responders and nonresponders with areas under the curve (AUCs) of 0.80 to 0.98. MRSs of the 4 sites associated with future metformin intolerance generated AUCs of 0.85 to 0.93. Some of these blood-based methylation markers mirrored the epigenetic pattern in adipose tissue, a key tissue in diabetes pathogenesis, and genes to which these markers were annotated to had biological functions in hepatocytes that altered metformin-related phenotypes. Overall, we could discriminate between glycemic responders/nonresponders and participants tolerant/intolerant to metformin at diagnosis by measuring blood-based epigenetic markers in drug-naïve patients with T2D. This epigenetics-based tool may be further developed to help patients with T2D receive optimal therapy.
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Affiliation(s)
- Sonia García-Calzón
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, 214 28 Malmö, Sweden
- Department of Nutrition, Food Science and Physiology, University of Navarra, 31008 Pamplona, Spain
| | - Alexander Perfilyev
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, 214 28 Malmö, Sweden
| | - Mats Martinell
- Department of Public Health and Caring Sciences, Uppsala University, 751 22 Uppsala, Sweden
| | - Monta Ustinova
- Latvian Biomedical Research and Study Centre, Rātsupītes Street 1, k-1, Riga LV-1067, Latvia
| | - Sebastian Kalamajski
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, 214 28 Malmö, Sweden
| | - Paul W. Franks
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, 214 28 Malmö, Sweden
| | - Karl Bacos
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, 214 28 Malmö, Sweden
| | - Ilze Elbere
- Latvian Biomedical Research and Study Centre, Rātsupītes Street 1, k-1, Riga LV-1067, Latvia
| | - Jussi Pihlajamäki
- Institute of Public Health and Clinical Nutrition, Internal Medicine, University of Eastern Finland, 70211 Kuopio, Finland
- Clinical Nutrition and Obesity Center, Kuopio University Hospital, 70210 Kuopio, Finland
| | - Petr Volkov
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, 214 28 Malmö, Sweden
| | - Allan Vaag
- Type 2 Diabetes Biology Research, Steno Diabetes Center, 2820 Gentofte, Denmark
| | - Leif Groop
- Genomics, Diabetes and Endocrinology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, 214 28 Malmö, Sweden
| | - Marlena Maziarz
- Bioinformatics Unit, Department of Clinical Sciences, Lund University Diabetes Centre, 214 28 Malmö, Sweden
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Rātsupītes Street 1, k-1, Riga LV-1067, Latvia
- Faculty of Biology, University of Latvia, Riga LV-1004, Latvia
| | - Emma Ahlqvist
- Genomics, Diabetes and Endocrinology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, 214 28 Malmö, Sweden
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, 214 28 Malmö, Sweden
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17
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Ustinova M, Ansone L, Silamikelis I, Rovite V, Elbere I, Silamikele L, Kalnina I, Fridmanis D, Sokolovska J, Konrade I, Pirags V, Klovins J. Whole-blood transcriptome profiling reveals signatures of metformin and its therapeutic response. PLoS One 2020; 15:e0237400. [PMID: 32780768 PMCID: PMC7418999 DOI: 10.1371/journal.pone.0237400] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/25/2020] [Indexed: 12/18/2022] Open
Abstract
Metformin, a biguanide agent, is the first-line treatment for type 2 diabetes mellitus due to its glucose-lowering effect. Despite its wide application in the treatment of multiple health conditions, the glycemic response to metformin is highly variable, emphasizing the need for reliable biomarkers. We chose the RNA-Seq-based comparative transcriptomics approach to evaluate the systemic effect of metformin and highlight potential predictive biomarkers of metformin response in drug-naïve volunteers with type 2 diabetes in vivo. The longitudinal blood-derived transcriptome analysis revealed metformin-induced differential expression of novel and previously described genes involved in cholesterol homeostasis (SLC46A1 and LRP1), cancer development (CYP1B1, STAB1, CCR2, TMEM176B), and immune responses (CD14, CD163) after administration of metformin for three months. We demonstrate for the first time a transcriptome-based molecular discrimination between metformin responders (delta HbA1c ≥ 1% or 12.6 mmol/mol) and non-responders (delta HbA1c < 1% or 12.6 mmol/mol), that is determined by expression levels of 56 genes, explaining 13.9% of the variance in the therapeutic efficacy of the drug. Moreover, we found a significant upregulation of IRS2 gene (log2FC 0.89) in responders compared to non-responders before the use of metformin. Finally, we provide evidence for the mitochondrial respiratory complex I as one of the factors related to the high variability of the therapeutic response to metformin in patients with type 2 diabetes mellitus.
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Affiliation(s)
- Monta Ustinova
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Laura Ansone
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | - Vita Rovite
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Ilze Elbere
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | - Ineta Kalnina
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | | | - Ilze Konrade
- Latvian Biomedical Research and Study Centre, Riga, Latvia
- Faculty of Medicine, Riga Stradins University, Riga, Latvia
| | - Valdis Pirags
- Latvian Biomedical Research and Study Centre, Riga, Latvia
- Faculty of Medicine, University of Latvia, Riga, Latvia
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Riga, Latvia
- * E-mail:
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18
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Linhares ND, Pereira DA, Conceição IM, Franco GR, Eckalbar WL, Ahituv N, Luizon MR. Noncoding SNPs associated with increased GDF15 levels located in a metformin-activated enhancer region upstream of GDF15. Pharmacogenomics 2020; 21:509-520. [PMID: 32427048 DOI: 10.2217/pgs-2020-0010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: GDF15 levels are a biomarker for metformin use. We performed the functional annotation of noncoding genome-wide association study (GWAS) SNPs for GDF15 levels and the Genotype-Tissue Expression (GTEx)-expression quantitative trait loci (eQTLs) for GDF15 expression within metformin-activated enhancers around GDF15. Materials & methods: These enhancers were identified using chromatin immunoprecipitation followed by sequencing data for active (H3K27ac) and silenced (H3K27me3) histone marks on human hepatocytes treated with metformin, Encyclopedia of DNA Elements data and cis-regulatory elements assignment tools. Results: The GWAS lead SNP rs888663, the SNP rs62122429 associated with GDF15 levels in the Outcome Reduction with Initial Glargine Intervention trial, and the GTEx-expression quantitative trait locus rs4808791 for GDF15 expression in whole blood are located in a metformin-activated enhancer upstream of GDF15 and tightly linked in Europeans and East Asians. Conclusion: Noncoding variation within a metformin-activated enhancer may increase GDF15 expression and help to predict GDF15 levels.
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Affiliation(s)
- Natália D Linhares
- Programa de Pós-Graduação em Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Daniela A Pereira
- Programa de Pós-Graduação em Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Izabela McA Conceição
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Glória R Franco
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Walter L Eckalbar
- Institute for Human Genetics, The University of California, San Francisco, CA 94143, USA.,Department of Bioengineering & Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Nadav Ahituv
- Institute for Human Genetics, The University of California, San Francisco, CA 94143, USA.,Department of Bioengineering & Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Marcelo R Luizon
- Programa de Pós-Graduação em Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.,Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
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19
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Metformin: Sentinel of the Epigenetic Landscapes That Underlie Cell Fate and Identity. Biomolecules 2020; 10:biom10050780. [PMID: 32443566 PMCID: PMC7277648 DOI: 10.3390/biom10050780] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/08/2020] [Accepted: 05/15/2020] [Indexed: 12/14/2022] Open
Abstract
The biguanide metformin is the first drug to be tested as a gerotherapeutic in the clinical trial TAME (Targeting Aging with Metformin). The current consensus is that metformin exerts indirect pleiotropy on core metabolic hallmarks of aging, such as the insulin/insulin-like growth factor 1 and AMP-activated protein kinase/mammalian Target Of Rapamycin signaling pathways, downstream of its primary inhibitory effect on mitochondrial respiratory complex I. Alternatively, but not mutually exclusive, metformin can exert regulatory effects on components of the biologic machinery of aging itself such as chromatin-modifying enzymes. An integrative metabolo-epigenetic outlook supports a new model whereby metformin operates as a guardian of cell identity, capable of retarding cellular aging by preventing the loss of the information-theoretic nature of the epigenome. The ultimate anti-aging mechanism of metformin might involve the global preservation of the epigenome architecture, thereby ensuring cell fate commitment and phenotypic outcomes despite the challenging effects of aging noise. Metformin might therefore inspire the development of new gerotherapeutics capable of preserving the epigenome architecture for cell identity. Such gerotherapeutics should replicate the ability of metformin to halt the erosion of the epigenetic landscape, mitigate the loss of cell fate commitment, delay stochastic/environmental DNA methylation drifts, and alleviate cellular senescence. Yet, it remains a challenge to confirm if regulatory changes in higher-order genomic organizers can connect the capacity of metformin to dynamically regulate the three-dimensional nature of epigenetic landscapes with the 4th dimension, the aging time.
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20
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Bouras H, Roig SR, Kurstjens S, Tack CJJ, Kebieche M, de Baaij JHF, Hoenderop JGJ. Metformin regulates TRPM6, a potential explanation for magnesium imbalance in type 2 diabetes patients. Can J Physiol Pharmacol 2020; 98:400-411. [PMID: 32017603 DOI: 10.1139/cjpp-2019-0570] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Metformin therapy is associated with lower serum magnesium (Mg2+) levels in type 2 diabetes patients. The TRPM6 channel determines the fine-tuning of Mg2+ (re)absorption in intestine and kidney. Therefore, we aimed to investigate the short- and long-term effects of metformin on TRPM6. Patch clamp recordings and biotinylation assays were performed upon 1 h of incubation with metformin in TRPM6-transfected HEK293 cells. Additionally, 24 h of treatment of mDCT15 kidney and hCaco-2 colon cells with metformin was applied to measure the effects on endogenous TRPM6 expression by quantitative real-time PCR. To assess Mg2+ absorption, 25Mg2+ uptake measurements were performed using inductively coupled plasma mass spectrometry. Short-term effects of metformin significantly increased TRPM6 activity and its cell surface trafficking. In contrast, long-term effects significantly decreased TRPM6 mRNA expression and 25Mg2+ uptake. Metformin lowered TRPM6 mRNA levels independently of insulin- and AMPK-mediated pathways. Moreover, in type 2 diabetes patients, metformin therapy was associated with lower plasma Mg2+ concentrations and fractional excretion of Mg2+. Thereby, short-term metformin treatment increases TRPM6 activity explained by enhanced cell surface expression. Conversely, long-term metformin treatment results in downregulation of TRPM6 gene expression in intestine and kidney cells. This long-term effect translated in an inverse correlation between metformin and plasma Mg2+ concentration in type 2 diabetes patients.
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Affiliation(s)
- Hacene Bouras
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.,Faculty of Nature and Life Sciences, University of Mohamed Seddik Ben Yahia, Jijel, Algeria
| | - Sara R Roig
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Steef Kurstjens
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Cees J J Tack
- Department of Internal Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Mohamed Kebieche
- Faculty of Nature and Life Sciences, University of Batna2, Algeria
| | - Jeroen H F de Baaij
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Joost G J Hoenderop
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
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21
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Park S, Yoo HJ, Jee SH, Lee JH, Kim M. Weighting approaches for a genetic risk score and an oxidative stress score for predicting the incidence of obesity. Diabetes Metab Res Rev 2020; 36:e3230. [PMID: 31654550 DOI: 10.1002/dmrr.3230] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/09/2019] [Accepted: 10/06/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND We aimed to predict the incidence of obesity in a Korean population using a genetic risk score (GRS) constructed with obesity-related single nucleotide polymorphisms (SNPs) along with an oxidative stress score (OSS). METHODS A total of 9460 Korean subjects and 356 974 SNPs were included. The GRS was constructed using three significant obesity-related SNP loci, and the OSS was calculated with three reliable oxidative stress biomarkers. RESULTS The GRS showed a more significant association with increased obesity (OR = 2.879) than did individual SNPs after adjusting for age and sex. Three oxidative stress biomarkers, including malondialdehyde, oxidized low-density lipoprotein, and 8-epi-prostaglandin F2α , showed significantly high levels in the obese group. The OSS, which was the sum of each oxidative stress biomarker score, showed a markedly high association with the incidence of obesity, with an OR of 3.213. Based on the results of the regression tests and a receiver-operating characteristic (ROC) curve analysis, we found that HOMA-IR, high-sensitivity C-reactive protein (hs-CRP), the GRS, and the OSS were the most relevant factors for the increased risk of obesity and were significantly associated with the incidence of obesity. The area under the ROC curve was improved when the GRS was added to the model (from 74.2% to 75.1%). CONCLUSIONS We first identified that subjects with an obesity GRS and a high OSS might have a higher risk of obesity. Our findings and weighting approaches were effective in predicting the incidence of obesity; furthermore, the GRS is a relevant factor that significantly predicts the risk of obesity.
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Affiliation(s)
- Seonmin Park
- Department of Science for Aging, Graduate School of Yonsei University, Seoul, Korea
| | - Hye Jin Yoo
- Research Center for Silver Science, Institute of Symbiotic Life-TECH, Yonsei University, Seoul, Korea
- National Leading Research Laboratory of Clinical Nutrigenetics/Nutrigenomics, Department of Food and Nutrition, College of Human Ecology, Yonsei University, Seoul, Korea
| | - Sun Ha Jee
- Department of Epidemiology and Health Promotion, Institute for Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, Korea
| | - Jong Ho Lee
- Research Center for Silver Science, Institute of Symbiotic Life-TECH, Yonsei University, Seoul, Korea
- National Leading Research Laboratory of Clinical Nutrigenetics/Nutrigenomics, Department of Food and Nutrition, College of Human Ecology, Yonsei University, Seoul, Korea
| | - Minjoo Kim
- Research Center for Silver Science, Institute of Symbiotic Life-TECH, Yonsei University, Seoul, Korea
- National Leading Research Laboratory of Clinical Nutrigenetics/Nutrigenomics, Department of Food and Nutrition, College of Human Ecology, Yonsei University, Seoul, Korea
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22
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Etheridge AS, Gallins PJ, Jima D, Broadaway KA, Ratain MJ, Schuetz E, Schadt E, Schroder A, Molony C, Zhou Y, Mohlke KL, Wright FA, Innocenti F. A New Liver Expression Quantitative Trait Locus Map From 1,183 Individuals Provides Evidence for Novel Expression Quantitative Trait Loci of Drug Response, Metabolic, and Sex-Biased Phenotypes. Clin Pharmacol Ther 2020; 107:1383-1393. [PMID: 31868224 DOI: 10.1002/cpt.1751] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 11/05/2019] [Indexed: 12/28/2022]
Abstract
Expression quantitative trait locus (eQTL) studies in human liver are crucial for elucidating how genetic variation influences variability in disease risk and therapeutic outcomes and may help guide strategies to obtain maximal efficacy and safety of clinical interventions. Associations between expression microarray and genome-wide genotype data from four human liver eQTL studies (n = 1,183) were analyzed. More than 2.3 million cis-eQTLs for 15,668 genes were identified. When eQTLs were filtered against a list of 1,496 drug response genes, 187,829 cis-eQTLs for 1,191 genes were identified. Additionally, 1,683 sex-biased cis-eQTLs were identified, as well as 49 and 73 cis-eQTLs that colocalized with genome-wide association study signals for blood metabolite or lipid levels, respectively. Translational relevance of these results is evidenced by linking DPYD eQTLs to differences in safety of chemotherapy, linking the sex-biased regulation of PCSK9 expression to anti-lipid therapy, and identifying the G-protein coupled receptor GPR180 as a novel drug target for hypertriglyceridemia.
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Affiliation(s)
- Amy S Etheridge
- Eshelman School of Pharmacy and Center for Pharmacogenomics and Individualized Therapy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Paul J Gallins
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | - Dereje Jima
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | - K Alaine Broadaway
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mark J Ratain
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Erin Schuetz
- Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Adrian Schroder
- Center for Bioinformatics Tübingen (ZBIT), University of Tübingen, Tübingen, Germany
| | - Cliona Molony
- Computation Biomedicine, Pfizer, Inc., Boston, Massachusetts, USA
| | - Yihui Zhou
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Fred A Wright
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | - Federico Innocenti
- Eshelman School of Pharmacy and Center for Pharmacogenomics and Individualized Therapy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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23
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Transcriptome profiling reveals the antihyperglycemic mechanism of pelargonidin-3-O-glucoside extracted from wild raspberry. J Funct Foods 2020. [DOI: 10.1016/j.jff.2019.103657] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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24
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Inoue F, Kreimer A, Ashuach T, Ahituv N, Yosef N. Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction. Cell Stem Cell 2019; 25:713-727.e10. [PMID: 31631012 PMCID: PMC6850896 DOI: 10.1016/j.stem.2019.09.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 07/15/2019] [Accepted: 09/26/2019] [Indexed: 12/16/2022]
Abstract
Epigenomic regulation and lineage-specific gene expression act in concert to drive cellular differentiation, but the temporal interplay between these processes is largely unknown. Using neural induction from human pluripotent stem cells (hPSCs) as a paradigm, we interrogated these dynamics by performing RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), and assay for transposase accessible chromatin using sequencing (ATAC-seq) at seven time points during early neural differentiation. We found that changes in DNA accessibility precede H3K27ac, which is followed by gene expression changes. Using massively parallel reporter assays (MPRAs) to test the activity of 2,464 candidate regulatory sequences at all seven time points, we show that many of these sequences have temporal activity patterns that correlate with their respective cell-endogenous gene expression and chromatin changes. A prioritization method incorporating all genomic and MPRA data further identified key transcription factors involved in driving neural fate. These results provide a comprehensive resource of genes and regulatory elements that orchestrate neural induction and illuminate temporal frameworks during differentiation.
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Affiliation(s)
- Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Anat Kreimer
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Tal Ashuach
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Nir Yosef
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA; Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA.
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25
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García G, Gutiérrez-Lara EJ, Centurión D, Granados-Soto V, Murbartián J. Fructose-Induced Insulin Resistance as a Model of Neuropathic Pain in Rats. Neuroscience 2019; 404:233-245. [DOI: 10.1016/j.neuroscience.2019.01.063] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 01/29/2019] [Accepted: 01/30/2019] [Indexed: 12/21/2022]
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26
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Cuyàs E, Buxó M, Ferri Iglesias MJ, Verdura S, Pernas S, Dorca J, Álvarez I, Martínez S, Pérez-Garcia JM, Batista-López N, Rodríguez-Sánchez CA, Amillano K, Domínguez S, Luque M, Morilla I, Stradella A, Viñas G, Cortés J, Joven J, Brunet J, López-Bonet E, Garcia M, Saidani S, Queralt Moles X, Martin-Castillo B, Menendez JA. The C Allele of ATM rs11212617 Associates With Higher Pathological Complete Remission Rate in Breast Cancer Patients Treated With Neoadjuvant Metformin. Front Oncol 2019; 9:193. [PMID: 30984619 PMCID: PMC6447648 DOI: 10.3389/fonc.2019.00193] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/06/2019] [Indexed: 12/21/2022] Open
Abstract
Background: The minor allele (C) of the single-nucleotide polymorphism (SNP) rs11212617, located near the ataxia telangiectasia mutated (ATM) gene, has been associated with an increased likelihood of treatment success with metformin in type 2 diabetes. We herein investigated whether the same SNP would predict clinical response to neoadjuvant metformin in women with early breast cancer (BC). Methods: DNA was collected from 79 patients included in the intention-to-treat population of the METTEN study, a phase 2 clinical trial of HER2-positive BC patients randomized to receive either metformin combined with anthracycline/taxane-based chemotherapy and trastuzumab or equivalent regimen without metformin, before surgery. SNP rs11212617 genotyping was assessed using allelic discrimination by quantitative polymerase chain reaction. Results: Logistic regression analyses revealed a significant relationship between the rs11212617 genotype and the ability of treatment arms to achieve a pathological complete response (pCR) in patients (odds ratio [OR]genotype×arm = 10.33, 95% confidence interval [CI]: 1.29-82.89, p = 0.028). In the metformin-containing arm, patients bearing the rs11212617 C allele had a significantly higher probability of pCR (OR A/C,C/C = 7.94, 95%CI: 1.60-39.42, p = 0.011). Conversely, no association was found between rs11212617 and clinical response in the reference arm (OR A/C,C/C = 0.77, 95%CI: 0.20-2.92, p = 0.700). After controlling for tumor size and hormone receptor status, the rs11212617 C allele remained a significant predictor of pCR solely in the metformin-containing arm. Conclusions: If reproducible, the rs11212617 C allele might warrant consideration as a predictive clinical biomarker to inform the personalized use of metformin in BC patients. Trial Registration: EU Clinical Trials Register, EudraCT number 2011-000490-30. Registered 28 February 2011, https://www.clinicaltrialsregister.eu/ctr-search/trial/2011-000490-30/ES.
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Affiliation(s)
- Elisabet Cuyàs
- Program Against Cancer Therapeutic Resistance (ProCURE), Metabolism and Cancer Group, Catalan Institute of Oncology, Girona, Spain.,Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Maria Buxó
- Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | | | - Sara Verdura
- Program Against Cancer Therapeutic Resistance (ProCURE), Metabolism and Cancer Group, Catalan Institute of Oncology, Girona, Spain.,Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Sonia Pernas
- Breast Unit, Department of Medical Oncology, Catalan Institute of Oncology-Hospital Universitari de Bellvitge-Bellvitge Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Joan Dorca
- Medical Oncology, Catalan Institute of Oncology, Girona, Spain
| | - Isabel Álvarez
- Medical Oncology Service, Hospital Universitario Donostia, Donostia-San Sebastián, Spain.,Biodonostia Health Research Institute, Donostia-San Sebastián, Spain
| | - Susana Martínez
- Medical Oncology Department, Hospital de Mataró, Mataró, Barcelona, Spain
| | | | - Norberto Batista-López
- Medical Oncology Service, Hospital Universitario de Canarias, San Cristóbal de La Laguna, Spain
| | - César A Rodríguez-Sánchez
- Medical Oncology Service, Hospital Universitario de Salamanca, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Kepa Amillano
- Medical Oncology, Hospital Universitari Sant Joan, Reus, Spain
| | - Severina Domínguez
- Medical Oncology Service, Hospital Universitario Araba, Vitoria-Gasteiz, Spain
| | - Maria Luque
- Department of Medical Oncology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Idoia Morilla
- Breast Unit, Department of Medical Oncology, Catalan Institute of Oncology-Hospital Universitari de Bellvitge-Bellvitge Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Agostina Stradella
- Breast Unit, Department of Medical Oncology, Catalan Institute of Oncology-Hospital Universitari de Bellvitge-Bellvitge Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Gemma Viñas
- Medical Oncology, Catalan Institute of Oncology, Girona, Spain
| | - Javier Cortés
- Department of Medical Oncology, Ramón y Cajal University Hospital, Madrid, Spain
| | - Jorge Joven
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, IISPV, Rovira i Virgili University, Reus, Spain
| | - Joan Brunet
- Medical Oncology, Catalan Institute of Oncology, Girona, Spain.,Hereditary Cancer Programme, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain.,Hereditary Cancer Programme, Catalan Institute of Oncology (ICO), Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Eugeni López-Bonet
- Department of Anatomical Pathology, Dr. Josep Trueta Hospital of Girona, Girona, Spain
| | - Margarita Garcia
- Clinical Research Unit, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Samiha Saidani
- Unit of Clinical Research, Catalan Institute of Oncology, Girona, Spain
| | | | | | - Javier A Menendez
- Program Against Cancer Therapeutic Resistance (ProCURE), Metabolism and Cancer Group, Catalan Institute of Oncology, Girona, Spain.,Girona Biomedical Research Institute (IDIBGI), Girona, Spain
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27
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Mannino GC, Andreozzi F, Sesti G. Pharmacogenetics of type 2 diabetes mellitus, the route toward tailored medicine. Diabetes Metab Res Rev 2019; 35:e3109. [PMID: 30515958 PMCID: PMC6590177 DOI: 10.1002/dmrr.3109] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/27/2018] [Accepted: 11/30/2018] [Indexed: 12/11/2022]
Abstract
Type 2 diabetes mellitus (T2DM) is a chronic disease that has reached the levels of a global epidemic. In order to achieve optimal glucose control, it is often necessary to rely on combination therapy of multiple drugs or insulin because uncontrolled glucose levels result in T2DM progression and enhanced risk of complications and mortality. Several antihyperglycemic agents have been developed over time, and T2DM pharmacotherapy should be prescribed based on suitability for the individual patient's characteristics. Pharmacogenetics is the branch of genetics that investigates how our genome influences individual responses to drugs, therapeutic outcomes, and incidence of adverse effects. In this review, we evaluated the pharmacogenetic evidences currently available in the literature, and we identified the top informative genetic variants associated with response to the most common anti-diabetic drugs: metformin, DPP-4 inhibitors/GLP1R agonists, thiazolidinediones, and sulfonylureas/meglitinides. Overall, we found 40 polymorphisms for each drug class in a total of 71 loci, and we examined the possibility of encouraging genetic screening of these variants/loci in order to critically implement decision-making about the therapeutic approach through precision medicine strategies. It is possible then to anticipate that when the clinical practice will take advantage of the genetic information of the diabetic patients, this will provide a useful resource for the prevention of T2DM progression, enabling the identification of the precise drug that is most likely to be effective and safe for each patient and the reduction of the economic impact on a global scale.
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Affiliation(s)
- Gaia Chiara Mannino
- Department of Medical and Surgical SciencesUniversity Magna Graecia of CatanzaroCatanzaroItaly
| | - Francesco Andreozzi
- Department of Medical and Surgical SciencesUniversity Magna Graecia of CatanzaroCatanzaroItaly
| | - Giorgio Sesti
- Department of Medical and Surgical SciencesUniversity Magna Graecia of CatanzaroCatanzaroItaly
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28
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Srinivasan S, Yee SW, Giacomini KM. Pharmacogenetics of Antidiabetic Drugs. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2018; 83:361-389. [PMID: 29801583 PMCID: PMC10999281 DOI: 10.1016/bs.apha.2018.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Pharmacogenetic studies of antidiabetic drugs have so far focused largely on response to metformin, which is the first-line therapy for treatment of type 2 diabetes (T2D). The first studies of metformin pharmacogenetics were focused on candidate genes that were implicated in metformin pharmacokinetics and transport. Since 2011, genome-wide association studies have been conducted in large cohorts of individuals with T2D identifying genes that are associated with glycemic response to metformin. There have been fewer pharmacogenetic studies of other antidiabetic drugs, and those have been largely limited to candidate gene studies with small sample sizes. Understanding the pharmacogenetics of antidiabetes medications is important for the integration of genetic screening into therapeutic decision making, and to achieve the goal of "precision medicine" for patients with T2D. In this chapter, we provide a review of the pharmacogenetics investigations of metformin and other antidiabetes medications. In addition, we highlight the importance of collaborative efforts with large sample size and representation from multiple ethnic groups in pharmacogenetics studies.
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Affiliation(s)
- Shylaja Srinivasan
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States; Division of Pediatric Endocrinology and Diabetes, University of California, San Francisco, San Francisco, CA, United States
| | - Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States.
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29
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Hu H, Li L, Guo Q, Zong H, Yan Y, Yin Y, Wang Y, Oh Y, Feng Y, Wu Q, Gu N. RNA sequencing analysis shows that titanium dioxide nanoparticles induce endoplasmic reticulum stress, which has a central role in mediating plasma glucose in mice. Nanotoxicology 2018; 12:341-356. [DOI: 10.1080/17435390.2018.1446560] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Hailong Hu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, PR China
| | - Li Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, PR China
| | - Qian Guo
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, PR China
| | - He Zong
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, PR China
| | - Yuheng Yan
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, PR China
| | - Yao Yin
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, PR China
| | - Yu Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, PR China
| | - Yuri Oh
- Faculty of Education, Wakayama University, Wakayama, Japan
| | - Yujie Feng
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, PR China
| | - Qiong Wu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, PR China
| | - Ning Gu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, PR China
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30
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Aravalli RN, Steer CJ. CRISPR/Cas9 therapeutics for liver diseases. J Cell Biochem 2018; 119:4265-4278. [PMID: 29266637 DOI: 10.1002/jcb.26627] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/18/2017] [Indexed: 12/20/2022]
Abstract
The development of innovative genome editing techniques in recent years has revolutionized the field of biomedicine. Among the novel approaches, the clustered regularly interspaced short palindromic repeat/CRISPR-associated protein (CRISPR/Cas9) technology has become the most popular, in part due to its matchless ability to carry out gene editing at the target site with great precision. With considerable successes in animal and preclinical studies, CRISPR/Cas9-mediated gene editing has paved the way for its use in human trials, including patients with a variety of liver diseases. Gene editing is a logical therapeutic approach for liver diseases because many metabolic and acquired disorders are caused by mutations within a single gene. In this review, we provide an overview on current and emerging therapeutic strategies for the treatment of liver diseases using the CRISPR/Cas9 technology.
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Affiliation(s)
- Rajagopal N Aravalli
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Clifford J Steer
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota.,Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
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31
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Merino J, Florez JC. Precision medicine in diabetes: an opportunity for clinical translation. Ann N Y Acad Sci 2018; 1411:140-152. [PMID: 29377200 PMCID: PMC6686889 DOI: 10.1111/nyas.13588] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/27/2017] [Accepted: 12/04/2017] [Indexed: 12/12/2022]
Abstract
Metabolic disorders present a public health challenge of staggering proportions. In diabetes, there is an urgent need to better understand disease heterogeneity, clinical trajectories, and related comorbidities. A pressing and timely question is whether we are ready for precision medicine in diabetes. Some biological insights that have emerged during the last decade have already been used to direct clinical decision making, especially in monogenic forms of diabetes. However, much work is necessary to integrate high-dimensional explorations into complex disease architectures, less penetrant biological alterations, and broader phenotypes, such as type 2 diabetes. In addition, for precision medicine to take hold in diabetes, reproducibility, interpretability, and actionability remain key guiding objectives. In this review, we examine how mounting data sets generated during the last decade to understand biological variability are now inspiring new venues to clarify diabetes nosology and ultimately translate findings into more effective prevention and treatment strategies.
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Affiliation(s)
- Jordi Merino
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Jose C. Florez
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
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32
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Aliper A, Jellen L, Cortese F, Artemov A, Karpinsky-Semper D, Moskalev A, Swick AG, Zhavoronkov A. Towards natural mimetics of metformin and rapamycin. Aging (Albany NY) 2017; 9:2245-2268. [PMID: 29165314 PMCID: PMC5723685 DOI: 10.18632/aging.101319] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/02/2017] [Indexed: 12/14/2022]
Abstract
Aging is now at the forefront of major challenges faced globally, creating an immediate need for safe, widescale interventions to reduce the burden of chronic disease and extend human healthspan. Metformin and rapamycin are two FDA-approved mTOR inhibitors proposed for this purpose, exhibiting significant anti-cancer and anti-aging properties beyond their current clinical applications. However, each faces issues with approval for off-label, prophylactic use due to adverse effects. Here, we initiate an effort to identify nutraceuticals-safer, naturally-occurring compounds-that mimic the anti-aging effects of metformin and rapamycin without adverse effects. We applied several bioinformatic approaches and deep learning methods to the Library of Integrated Network-based Cellular Signatures (LINCS) dataset to map the gene- and pathway-level signatures of metformin and rapamycin and screen for matches among over 800 natural compounds. We then predicted the safety of each compound with an ensemble of deep neural network classifiers. The analysis revealed many novel candidate metformin and rapamycin mimetics, including allantoin and ginsenoside (metformin), epigallocatechin gallate and isoliquiritigenin (rapamycin), and withaferin A (both). Four relatively unexplored compounds also scored well with rapamycin. This work revealed promising candidates for future experimental validation while demonstrating the applications of powerful screening methods for this and similar endeavors.
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Affiliation(s)
- Alexander Aliper
- Insilico Medicine, Inc, Research Department, Baltimore, MD 21218, USA
| | - Leslie Jellen
- Insilico Medicine, Inc, Research Department, Baltimore, MD 21218, USA
| | - Franco Cortese
- Biogerontology Research Foundation, Research Department, Oxford, United Kingdom
- Department of Biomedical and Molecular Science, Queen's University School of Medicine, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Artem Artemov
- Insilico Medicine, Inc, Research Department, Baltimore, MD 21218, USA
| | | | - Alexey Moskalev
- Laboratory of Molecular Radiobiology and Gerontology, Institute of Biology of Komi Science Center of Ural Branch of Russian Academy of Sciences, Syktyvkar, 167982, Russia
| | | | - Alex Zhavoronkov
- Insilico Medicine, Inc, Research Department, Baltimore, MD 21218, USA
- Biogerontology Research Foundation, Research Department, Oxford, United Kingdom
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33
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García-Calzón S, Perfilyev A, Männistö V, de Mello VD, Nilsson E, Pihlajamäki J, Ling C. Diabetes medication associates with DNA methylation of metformin transporter genes in the human liver. Clin Epigenetics 2017; 9:102. [PMID: 28947922 PMCID: PMC5609005 DOI: 10.1186/s13148-017-0400-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/04/2017] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Given that metformin is the most common pharmacological therapy for type 2 diabetes, understanding the function of this drug is of great importance. Hepatic metformin transporters are responsible for the pharmacologic action of metformin. However, epigenetics in genes encoding metformin transporters has not been fully elucidated. We examined the DNA methylation of these genes in the liver of subjects with type 2 diabetes and tested whether epigenetic alterations associate with diabetes medication, i.e., metformin or insulin plus metformin treatment. RESULTS DNA methylation in OCT1 encoded by SLC22A1, OCT3 encoded by SLC22A3, and MATE1 encoded by SLC47A1 was assessed in the human liver. Lower average and promoter DNA methylation of SLC22A1, SLC22A3, and SLC47A1 was found in diabetic subjects receiving just metformin, compared to those who took insulin plus metformin or no diabetes medication. Moreover, diabetic subjects receiving just metformin had a similar DNA methylation pattern in these genes compared to non-diabetic subjects. Notably, DNA methylation was also associated with gene expression, glucose levels, and body mass index, i.e., higher SLC22A3 methylation was related to lower SLC22A3 expression and to insulin plus metformin treatment, higher fasting glucose levels and higher body mass index. Importantly, metformin treatment did also directly decrease DNA methylation of SLC22A1 in hepatocytes cultured in vitro. CONCLUSIONS Our study supports that metformin decreases DNA methylation of metformin transporter genes in the human liver. Moreover, higher methylation levels in these genes associate with hyperglycaemia and obesity.
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Affiliation(s)
- Sonia García-Calzón
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, Jan Waldenströms gata 35, CRC 91:12, 205 02 Malmö, Sweden
| | - Alexander Perfilyev
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, Jan Waldenströms gata 35, CRC 91:12, 205 02 Malmö, Sweden
| | - Ville Männistö
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, 70210 Kuopio, Finland
| | - Vanessa D de Mello
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 80100 Joensuu, Finland
| | - Emma Nilsson
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, Jan Waldenströms gata 35, CRC 91:12, 205 02 Malmö, Sweden
| | - Jussi Pihlajamäki
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 80100 Joensuu, Finland.,Clinical Nutrition and Obesity Center, Kuopio University Hospital, 70210 Kuopio, Finland
| | - Charlotte Ling
- Department of Clinical Sciences, Epigenetics and Diabetes Unit, Lund University Diabetes Centre, Jan Waldenströms gata 35, CRC 91:12, 205 02 Malmö, Sweden
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34
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Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation. Sci Rep 2017; 7:7533. [PMID: 28790348 PMCID: PMC5548911 DOI: 10.1038/s41598-017-07757-w] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 06/29/2017] [Indexed: 01/29/2023] Open
Abstract
Standard cell culture guidelines often use media supplemented with antibiotics to prevent cell contamination. However, relatively little is known about the effect of antibiotic use in cell culture on gene expression and the extent to which this treatment could confound results. To comprehensively characterize the effect of antibiotic treatment on gene expression, we performed RNA-seq and ChIP-seq for H3K27ac on HepG2 cells, a human liver cell line commonly used for pharmacokinetic, metabolism and genomic studies, cultured in media supplemented with penicillin-streptomycin (PenStrep) or vehicle control. We identified 209 PenStrep-responsive genes, including transcription factors such as ATF3 that are likely to alter the regulation of other genes. Pathway analyses found a significant enrichment for "xenobiotic metabolism signaling" and "PXR/RXR activation" pathways. Our H3K27ac ChIP-seq identified 9,514 peaks that are PenStrep responsive. These peaks were enriched near genes that function in cell differentiation, tRNA modification, nuclease activity and protein dephosphorylation. Our results suggest that PenStrep treatment can significantly alter gene expression and regulation in a common liver cell type such as HepG2, advocating that antibiotic treatment should be taken into account when carrying out genetic, genomic or other biological assays in cultured cells.
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35
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Pankowicz FP, Jarrett KE, Lagor WR, Bissig KD. CRISPR/Cas9: at the cutting edge of hepatology. Gut 2017; 66:1329-1340. [PMID: 28487442 PMCID: PMC5878048 DOI: 10.1136/gutjnl-2016-313565] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 04/07/2017] [Indexed: 12/14/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 genome engineering has revolutionised biomedical science and we are standing on the cusp of medical transformation. The therapeutic potential of this technology is tremendous, however, its translation to the clinic will be challenging. In this article, we review recent progress using this genome editing technology and explore its potential uses in studying and treating diseases of the liver. We discuss the development of new research tools and animal models as well as potential clinical applications, strategies and challenges.
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Affiliation(s)
- Francis P Pankowicz
- Center for Cell and Gene Therapy, Center for Stem Cells and
Regenerative Medicine, Baylor College of Medicine, Houston, Texas, USA,Graduate Program Department of Molecular & Cellular Biology,
Baylor College of Medicine, Houston, Texas, USA
| | - Kelsey E Jarrett
- Department of Molecular Physiology and Biophysics, Baylor College of
Medicine, Houston, Texas, USA,Integrative Molecular and Biomedical Sciences Graduate Program,
Baylor College of Medicine, Houston, Texas, USA
| | - William R Lagor
- Center for Cell and Gene Therapy, Center for Stem Cells and
Regenerative Medicine, Baylor College of Medicine, Houston, Texas, USA,Department of Molecular Physiology and Biophysics, Baylor College of
Medicine, Houston, Texas, USA,Integrative Molecular and Biomedical Sciences Graduate Program,
Baylor College of Medicine, Houston, Texas, USA,Texas Medical Center Digestive Diseases Center, Baylor College of
Medicine, Houston, Texas, USA
| | - Karl-Dimiter Bissig
- Center for Cell and Gene Therapy, Center for Stem Cells and
Regenerative Medicine, Baylor College of Medicine, Houston, Texas, USA,Graduate Program Department of Molecular & Cellular Biology,
Baylor College of Medicine, Houston, Texas, USA,Texas Medical Center Digestive Diseases Center, Baylor College of
Medicine, Houston, Texas, USA,Graduate Program in Translational Biology and Molecular Medicine,
Baylor College of Medicine, Houston, Texas, USA,Department of Molecular and Cellular Biology, Baylor College of
Medicine, Houston, Texas, USA,Program in Developmental Biology, Baylor College of Medicine,
Houston, Texas, USA,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston,
Texas, USA
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36
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Luizon MR, Palei ACT, Cavalli RC, Sandrim VC. Pharmacogenetics in the treatment of pre-eclampsia: current findings, challenges and perspectives. Pharmacogenomics 2017; 18:571-583. [DOI: 10.2217/pgs-2016-0198] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Pre-eclampsia (PE) is defined as pregnancy-induced hypertension and proteinuria, and is a major cause of maternal and perinatal morbidity and mortality. A large subgroup of pregnant women with PE is nonresponsive to antihypertensive drugs, including methyldopa, nifedipine and hydralazine. Pharmacogenomics may help to guide the individualized therapy for this nonresponsive subgroup. However, just a few pharmacogenetic studies examined the effects of genetic polymorphisms on response to antihypertensive drugs in PE, and the criteria of responsiveness used to define responsive or nonresponsive subgroups to antihypertensive therapy should be replicated by others. We review these gene–drugs interactions, novel approaches to pharmacogenomics research and potential novel drugs for PE therapy. Finally, we discuss the challenges and perspectives of pharmacogenetics in the treatment of PE.
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Affiliation(s)
- Marcelo R Luizon
- Department of Pharmacology, Institute of Biosciences of Botucatu, Universidade Estadual Paulista (UNESP), Botucatu, Sao Paulo 18680-000, Brazil
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Ana CT Palei
- Department of Surgery, Division of Pediatric & Congenital Heart Surgery, University of Mississippi Medical Center, Jackson, MS 39216, USA
- Cardiovascular-Renal Research Center, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Ricardo C Cavalli
- Department of Gynecology & Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo 14049-900, Brazil
| | - Valeria C Sandrim
- Department of Pharmacology, Institute of Biosciences of Botucatu, Universidade Estadual Paulista (UNESP), Botucatu, Sao Paulo 18680-000, Brazil
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