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Merrill CB, Titos I, Pabon MA, Montgomery AB, Rodan AR, Rothenfluh A. Iterative assay for transposase-accessible chromatin by sequencing to isolate functionally relevant neuronal subtypes. SCIENCE ADVANCES 2024; 10:eadi4393. [PMID: 38536919 PMCID: PMC10971406 DOI: 10.1126/sciadv.adi4393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 02/21/2024] [Indexed: 04/18/2024]
Abstract
The Drosophila brain contains tens of thousands of distinct cell types. Thousands of different transgenic lines reproducibly target specific neuron subsets, yet most still express in several cell types. Furthermore, most lines were developed without a priori knowledge of where the transgenes would be expressed. To aid in the development of cell type-specific tools for neuronal identification and manipulation, we developed an iterative assay for transposase-accessible chromatin (ATAC) approach. Open chromatin regions (OCRs) enriched in neurons, compared to whole bodies, drove transgene expression preferentially in subsets of neurons. A second round of ATAC-seq from these specific neuron subsets revealed additional enriched OCR2s that further restricted transgene expression within the chosen neuron subset. This approach allows for continued refinement of transgene expression, and we used it to identify neurons relevant for sleep behavior. Furthermore, this approach is widely applicable to other cell types and to other organisms.
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Affiliation(s)
- Collin B. Merrill
- Department of Psychiatry, Huntsman Mental Health Institute, University of Utah, Salt Lake City, UT 84108, USA
| | - Iris Titos
- Department of Psychiatry, Huntsman Mental Health Institute, University of Utah, Salt Lake City, UT 84108, USA
| | - Miguel A. Pabon
- Molecular Medicine Program, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Aylin R. Rodan
- Molecular Medicine Program, University of Utah, Salt Lake City, UT 84112, USA
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah, Salt Lake City, UT 84132, USA
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
- Medical Service, Veterans Affairs Salt Lake City Health Care System, Salt Lake City, UT, USA
| | - Adrian Rothenfluh
- Department of Psychiatry, Huntsman Mental Health Institute, University of Utah, Salt Lake City, UT 84108, USA
- Molecular Medicine Program, University of Utah, Salt Lake City, UT 84112, USA
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
- Department of Neurobiology, University of Utah, Salt Lake City, UT 84112, USA
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2
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Rönn T, Ofori JK, Perfilyev A, Hamilton A, Pircs K, Eichelmann F, Garcia-Calzon S, Karagiannopoulos A, Stenlund H, Wendt A, Volkov P, Schulze MB, Mulder H, Eliasson L, Ruhrmann S, Bacos K, Ling C. Genes with epigenetic alterations in human pancreatic islets impact mitochondrial function, insulin secretion, and type 2 diabetes. Nat Commun 2023; 14:8040. [PMID: 38086799 PMCID: PMC10716521 DOI: 10.1038/s41467-023-43719-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
Epigenetic dysregulation may influence disease progression. Here we explore whether epigenetic alterations in human pancreatic islets impact insulin secretion and type 2 diabetes (T2D). In islets, 5,584 DNA methylation sites exhibit alterations in T2D cases versus controls and are associated with HbA1c in individuals not diagnosed with T2D. T2D-associated methylation changes are found in enhancers and regions bound by β-cell-specific transcription factors and associated with reduced expression of e.g. CABLES1, FOXP1, GABRA2, GLR1A, RHOT1, and TBC1D4. We find RHOT1 (MIRO1) to be a key regulator of insulin secretion in human islets. Rhot1-deficiency in β-cells leads to reduced insulin secretion, ATP/ADP ratio, mitochondrial mass, Ca2+, and respiration. Regulators of mitochondrial dynamics and metabolites, including L-proline, glycine, GABA, and carnitines, are altered in Rhot1-deficient β-cells. Islets from diabetic GK rats present Rhot1-deficiency. Finally, RHOT1methylation in blood is associated with future T2D. Together, individuals with T2D exhibit epigenetic alterations linked to mitochondrial dysfunction in pancreatic islets.
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Affiliation(s)
- Tina Rönn
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Jones K Ofori
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Alexander Perfilyev
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Alexander Hamilton
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
- Department of Biology, University of Copenhagen, København, Denmark
| | - Karolina Pircs
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
- HCEMM-Su, Neurobiology and Neurodegenerative Diseases Research Group, Budapest, Hungary
- Institute of Translational Medicine, Semmelweis University, Budapest, Hungary
| | - Fabian Eichelmann
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Sonia Garcia-Calzon
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
- Department of Food Science and Physiology, Centre for Nutrition Research, University of Navarra, Pamplona, Spain
| | - Alexandros Karagiannopoulos
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Hans Stenlund
- Swedish Metabolomics Centre, Umeå University, Umeå, Sweden
| | - Anna Wendt
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Petr Volkov
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Matthias B Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
- Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
| | - Hindrik Mulder
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Lena Eliasson
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Sabrina Ruhrmann
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Karl Bacos
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
| | - Charlotte Ling
- Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden.
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3
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Zammit NW, Wong YY, Walters SN, Warren J, Barry SC, Grey ST. RELA governs a network of islet-specific metabolic genes necessary for beta cell function. Diabetologia 2023; 66:1516-1531. [PMID: 37311878 PMCID: PMC10317895 DOI: 10.1007/s00125-023-05931-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/14/2023] [Indexed: 06/15/2023]
Abstract
AIMS/HYPOTHESIS NF-κB activation unites metabolic and inflammatory responses in many diseases yet less is known about the role that NF-κB plays in normal metabolism. In this study we investigated how RELA impacts the beta cell transcriptional landscape and provides network control over glucoregulation. METHODS We generated novel mouse lines harbouring beta cell-specific deletion of either the Rela gene, encoding the canonical NF-κB transcription factor p65 (βp65KO mice), or the Ikbkg gene, encoding the NF-κB essential modulator NEMO (βNEMOKO mice), as well as βA20Tg mice that carry beta cell-specific and forced transgenic expression of the NF-κB-negative regulator gene Tnfaip3, which encodes the A20 protein. Mouse studies were complemented by bioinformatics analysis of human islet chromatin accessibility (assay for transposase-accessible chromatin with sequencing [ATAC-seq]), promoter capture Hi-C (pcHi-C) and p65 binding (chromatin immunoprecipitation-sequencing [ChIP-seq]) data to investigate genome-wide control of the human beta cell metabolic programme. RESULTS Rela deficiency resulted in complete loss of stimulus-dependent inflammatory gene upregulation, consistent with its known role in governing inflammation. However, Rela deletion also rendered mice glucose intolerant because of functional loss of insulin secretion. Glucose intolerance was intrinsic to beta cells as βp65KO islets failed to secrete insulin ex vivo in response to a glucose challenge and were unable to restore metabolic control when transplanted into secondary chemical-induced hyperglycaemic recipients. Maintenance of glucose tolerance required Rela but was independent of classical NF-κB inflammatory cascades, as blocking NF-κB signalling in vivo by beta cell knockout of Ikbkg (NEMO), or beta cell overexpression of Tnfaip3 (A20), did not cause severe glucose intolerance. Thus, basal p65 activity has an essential and islet-intrinsic role in maintaining normal glucose homeostasis. Genome-wide bioinformatic mapping revealed the presence of p65 binding sites in the promoter regions of specific metabolic genes and in the majority of islet enhancer hubs (~70% of ~1300 hubs), which are responsible for shaping beta cell type-specific gene expression programmes. Indeed, the islet-specific metabolic genes Slc2a2, Capn9 and Pfkm identified within the large network of islet enhancer hub genes showed dysregulated expression in βp65KO islets. CONCLUSIONS/INTERPRETATION These data demonstrate an unappreciated role for RELA as a regulator of islet-specific transcriptional programmes necessary for the maintenance of healthy glucose metabolism. These findings have clinical implications for the use of anti-inflammatories, which influence NF-κB activation and are associated with diabetes.
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Affiliation(s)
- Nathan W Zammit
- Transplantation Immunology Laboratory, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Translation Science Pillar, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Ying Ying Wong
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Stacey N Walters
- Transplantation Immunology Laboratory, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Translation Science Pillar, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Joanna Warren
- Transplantation Immunology Laboratory, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Translation Science Pillar, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Simon C Barry
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Shane T Grey
- Transplantation Immunology Laboratory, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.
- Translation Science Pillar, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia.
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Bai J, Lin Y, Zhang J, Chen Z, Wang Y, Li M, Li J. Profiling of Chromatin Accessibility in Pigs across Multiple Tissues and Developmental Stages. Int J Mol Sci 2023; 24:11076. [PMID: 37446255 DOI: 10.3390/ijms241311076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/27/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
The study of chromatin accessibility across tissues and developmental stages is essential for elucidating the transcriptional regulation of various phenotypes and biological processes. However, the chromatin accessibility profiles of multiple tissues in newborn pigs and across porcine liver development remain poorly investigated. Here, we used ATAC-seq and rRNA-depleted RNA-seq to profile open chromatin maps and transcriptional features of heart, kidney, liver, lung, skeletal muscle, and spleen in newborn pigs and porcine liver tissue in the suckling and adult stages, respectively. Specifically, by analyzing a union set of protein-coding genes (PCGs) and two types of transcripts (lncRNAs and TUCPs), we obtained a comprehensive annotation of consensus ATAC-seq peaks for each tissue and developmental stage. As expected, the PCGs with tissue-specific accessible promoters had active transcription and were relevant to tissue-specific functions. In addition, other non-coding tissue-specific peaks were involved in both physical activity and the morphogenesis of neonatal tissues. We also characterized stage-specific peaks and observed a close association between dynamic chromatin accessibility and hepatic function transition during liver postnatal development. Overall, this study expands our current understanding of epigenetic regulation in mammalian tissues and organ development, which can benefit both economic trait improvement and improve the biomedical usage of pigs.
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Affiliation(s)
- Jingyi Bai
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu Lin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiaman Zhang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Ziyu Chen
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yujie Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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Lu Y, Qie D, Yang F, Wu J. LncRNA MEG3 aggravates adipocyte inflammation and insulin resistance by targeting IGF2BP2 to activate TLR4/NF-κB signaling pathway. Int Immunopharmacol 2023; 121:110467. [PMID: 37348228 DOI: 10.1016/j.intimp.2023.110467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/24/2023]
Abstract
Recently, emerging evidence has shown that LncRNA MEG3 is involved in adipocyte inflammation and insulin resistance progression, however, the specific mechanism of action remains unclear. In this study, we found that LncRNA MEG3 expression was increased in TNF-α stimulated 3T3-L1 mature adipocytes, and inflammatory factors IL-6 and MCP-1 secretion levels were increased, cell apoptosis and caspase3 activity was enhanced, ROS content was increased, and iNOS protein expression was increased. Moreover, TNF-α treatment attenuated glucose uptake, promoted triglyceride accumulation, inhibited GLUT4 protein expression at the plasma membrane, and reduced the phosphorylation levels of AMPK and ACC in the cells. Interestingly, we found that transfection of si-MEG3 reversed TNF-α caused inflammatory injury and insulin resistance of 3T3-L1 mature adipocytes. Next, we found that IGF2BP2 is an RNA binding protein of LncRNA MGE3 and transfection of si-IGF2BP2 reversed TNF-α caused inflammatory injury and insulin resistance in 3T3-L1 mature adipocytes, the same effects as transfection of si-MEG3. Mechanistically, LncRNA MGE3 was able to aggravate adipocyte inflammatory injury and dysregulation of insulin sensitivity by activating TLR4 pathway through upregulating the protein expression of IGF2BP2. In vivo findings showed that HFD mice with knockdown of MEG3 had reduced body weight, lower glucose concentrations and insulin levels in plasma, decreased inflammatory factors secretion, and reduced MEG3 and IGF2BP2 expression in epididymal adipose tissues and reduced fat accumulation in mice compared with HFD mice. Our results indicate that LncRNA MEG3 can aggravate chronic inflammation and insulin resistance in adipocytes by activating TLR4/NF-κB signaling pathway via targeting IGF2BP2.
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Affiliation(s)
- You Lu
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China.; Key Laboratory of Birth Defects and Related Diseases of Women and children (Sichuan University), Ministry of Education, Chengdu 610041, Sichuan, China
| | - Di Qie
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China.; Key Laboratory of Birth Defects and Related Diseases of Women and children (Sichuan University), Ministry of Education, Chengdu 610041, Sichuan, China
| | - Fan Yang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China.; Key Laboratory of Birth Defects and Related Diseases of Women and children (Sichuan University), Ministry of Education, Chengdu 610041, Sichuan, China..
| | - Jinhui Wu
- Key Laboratory of Birth Defects and Related Diseases of Women and children (Sichuan University), Ministry of Education, Chengdu 610041, Sichuan, China.; Department of Child Healthcare nursing, West China Second University Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu 610041, Sichuan, China..
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6
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Jackson JT, Nutt SL, McCormack MP. The Haematopoietically-expressed homeobox transcription factor: roles in development, physiology and disease. Front Immunol 2023; 14:1197490. [PMID: 37398663 PMCID: PMC10313424 DOI: 10.3389/fimmu.2023.1197490] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/01/2023] [Indexed: 07/04/2023] Open
Abstract
The Haematopoietically expressed homeobox transcription factor (Hhex) is a transcriptional repressor that is of fundamental importance across species, as evident by its evolutionary conservation spanning fish, amphibians, birds, mice and humans. Indeed, Hhex maintains its vital functions throughout the lifespan of the organism, beginning in the oocyte, through fundamental stages of embryogenesis in the foregut endoderm. The endodermal development driven by Hhex gives rise to endocrine organs such as the pancreas in a process which is likely linked to its role as a risk factor in diabetes and pancreatic disorders. Hhex is also required for the normal development of the bile duct and liver, the latter also importantly being the initial site of haematopoiesis. These haematopoietic origins are governed by Hhex, leading to its crucial later roles in definitive haematopoietic stem cell (HSC) self-renewal, lymphopoiesis and haematological malignancy. Hhex is also necessary for the developing forebrain and thyroid gland, with this reliance on Hhex evident in its role in endocrine disorders later in life including a potential role in Alzheimer's disease. Thus, the roles of Hhex in embryological development throughout evolution appear to be linked to its later roles in a variety of disease processes.
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Affiliation(s)
- Jacob T. Jackson
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Stephen L. Nutt
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Matthew P. McCormack
- The Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
- iCamuno Biotherapeutics, Melbourne, VIC, Australia
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7
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Cao R, Tian H, Zhang Y, Liu G, Xu H, Rao G, Tian Y, Fu X. Signaling pathways and intervention for therapy of type 2 diabetes mellitus. MedComm (Beijing) 2023; 4:e283. [PMID: 37303813 PMCID: PMC10248034 DOI: 10.1002/mco2.283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/18/2023] [Accepted: 04/27/2023] [Indexed: 06/13/2023] Open
Abstract
Type 2 diabetes mellitus (T2DM) represents one of the fastest growing epidemic metabolic disorders worldwide and is a strong contributor for a broad range of comorbidities, including vascular, visual, neurological, kidney, and liver diseases. Moreover, recent data suggest a mutual interplay between T2DM and Corona Virus Disease 2019 (COVID-19). T2DM is characterized by insulin resistance (IR) and pancreatic β cell dysfunction. Pioneering discoveries throughout the past few decades have established notable links between signaling pathways and T2DM pathogenesis and therapy. Importantly, a number of signaling pathways substantially control the advancement of core pathological changes in T2DM, including IR and β cell dysfunction, as well as additional pathogenic disturbances. Accordingly, an improved understanding of these signaling pathways sheds light on tractable targets and strategies for developing and repurposing critical therapies to treat T2DM and its complications. In this review, we provide a brief overview of the history of T2DM and signaling pathways, and offer a systematic update on the role and mechanism of key signaling pathways underlying the onset, development, and progression of T2DM. In this content, we also summarize current therapeutic drugs/agents associated with signaling pathways for the treatment of T2DM and its complications, and discuss some implications and directions to the future of this field.
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Affiliation(s)
- Rong Cao
- Department of Endocrinology and MetabolismState Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center of BiotherapyChengduSichuanChina
| | - Huimin Tian
- Department of Endocrinology and MetabolismState Key Laboratory of Biotherapy and Cancer CenterWest China Medical School, West China HospitalSichuan UniversityChengduSichuanChina
| | - Yu Zhang
- Department of Endocrinology and MetabolismState Key Laboratory of Biotherapy and Cancer CenterWest China Medical School, West China HospitalSichuan UniversityChengduSichuanChina
| | - Geng Liu
- Department of Endocrinology and MetabolismState Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center of BiotherapyChengduSichuanChina
| | - Haixia Xu
- Department of Endocrinology and MetabolismState Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center of BiotherapyChengduSichuanChina
| | - Guocheng Rao
- Department of Endocrinology and MetabolismState Key Laboratory of Biotherapy and Cancer CenterWest China Medical School, West China HospitalSichuan UniversityChengduSichuanChina
| | - Yan Tian
- Department of Endocrinology and MetabolismState Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center of BiotherapyChengduSichuanChina
| | - Xianghui Fu
- Department of Endocrinology and MetabolismState Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center of BiotherapyChengduSichuanChina
- Department of Endocrinology and MetabolismState Key Laboratory of Biotherapy and Cancer CenterWest China Medical School, West China HospitalSichuan UniversityChengduSichuanChina
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Pierantozzi E, Raucci L, Buonocore S, Rubino EM, Ding Q, Laurino A, Fiore F, Soldaini M, Chen J, Rossi D, Vangheluwe P, Chen H, Sorrentino V. Skeletal muscle overexpression of sAnk1.5 in transgenic mice does not predispose to type 2 diabetes. Sci Rep 2023; 13:8195. [PMID: 37210436 PMCID: PMC10199891 DOI: 10.1038/s41598-023-35393-0] [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: 01/09/2023] [Accepted: 05/17/2023] [Indexed: 05/22/2023] Open
Abstract
Genome-wide association studies (GWAS) and cis-expression quantitative trait locus (cis-eQTL) analyses indicated an association of the rs508419 single nucleotide polymorphism (SNP) with type 2 diabetes (T2D). rs508419 is localized in the muscle-specific internal promoter (P2) of the ANK1 gene, which drives the expression of the sAnk1.5 isoform. Functional studies showed that the rs508419 C/C variant results in increased transcriptional activity of the P2 promoter, leading to higher levels of sAnk1.5 mRNA and protein in skeletal muscle biopsies of individuals carrying the C/C genotype. To investigate whether sAnk1.5 overexpression in skeletal muscle might predispose to T2D development, we generated transgenic mice (TgsAnk1.5/+) in which the sAnk1.5 coding sequence was selectively overexpressed in skeletal muscle tissue. TgsAnk1.5/+ mice expressed up to 50% as much sAnk1.5 protein as wild-type (WT) muscles, mirroring the difference reported between individuals with the C/C or T/T genotype at rs508419. However, fasting glucose levels, glucose tolerance, insulin levels and insulin response in TgsAnk1.5/+ mice did not differ from those of age-matched WT mice monitored over a 12-month period. Even when fed a high-fat diet, TgsAnk1.5/+ mice only presented increased caloric intake, but glucose disposal, insulin tolerance and weight gain were comparable to those of WT mice fed a similar diet. Altogether, these data indicate that sAnk1.5 overexpression in skeletal muscle does not predispose mice to T2D susceptibility.
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Affiliation(s)
- E Pierantozzi
- Department of Molecular and Developmental Medicine, University of Siena, 53100, Siena, Italy
| | - L Raucci
- Department of Molecular and Developmental Medicine, University of Siena, 53100, Siena, Italy
| | - S Buonocore
- Department of Molecular and Developmental Medicine, University of Siena, 53100, Siena, Italy
| | - E M Rubino
- Department of Molecular and Developmental Medicine, University of Siena, 53100, Siena, Italy
| | - Q Ding
- Department of Cardio-Thoracic Surgery, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008, Jiangsu, China
| | - A Laurino
- Department of Molecular and Developmental Medicine, University of Siena, 53100, Siena, Italy
| | - F Fiore
- Department of Molecular and Developmental Medicine, University of Siena, 53100, Siena, Italy
| | - M Soldaini
- Department of Molecular and Developmental Medicine, University of Siena, 53100, Siena, Italy
| | - J Chen
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, Katholieke Universiteit Leuven (KU Leuven), 3000, Leuven, Belgium
| | - D Rossi
- Department of Molecular and Developmental Medicine, University of Siena, 53100, Siena, Italy
- Interdepartmental Program of Molecular Diagnosis and Pathogenetic Mechanisms of Rare Genetic Diseases, Azienda Ospedaliera Universitaria Senese, 53100, Siena, Italy
| | - P Vangheluwe
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, Katholieke Universiteit Leuven (KU Leuven), 3000, Leuven, Belgium
| | - H Chen
- Department of Cardio-Thoracic Surgery, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008, Jiangsu, China
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - V Sorrentino
- Department of Molecular and Developmental Medicine, University of Siena, 53100, Siena, Italy.
- Interdepartmental Program of Molecular Diagnosis and Pathogenetic Mechanisms of Rare Genetic Diseases, Azienda Ospedaliera Universitaria Senese, 53100, Siena, Italy.
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9
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Huynh K, Smith BR, Macdonald SJ, Long AD. Genetic variation in chromatin state across multiple tissues in Drosophila melanogaster. PLoS Genet 2023; 19:e1010439. [PMID: 37146087 PMCID: PMC10191298 DOI: 10.1371/journal.pgen.1010439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 05/17/2023] [Accepted: 04/20/2023] [Indexed: 05/07/2023] Open
Abstract
We use ATAC-seq to examine chromatin accessibility for four different tissues in Drosophila melanogaster: adult female brain, ovaries, and both wing and eye-antennal imaginal discs from males. Each tissue is assayed in eight different inbred strain genetic backgrounds, seven associated with a reference quality genome assembly. We develop a method for the quantile normalization of ATAC-seq fragments and test for differences in coverage among genotypes, tissues, and their interaction at 44099 peaks throughout the euchromatic genome. For the strains with reference quality genome assemblies, we correct ATAC-seq profiles for read mis-mapping due to nearby polymorphic structural variants (SVs). Comparing coverage among genotypes without accounting for SVs results in a highly elevated rate (55%) of identifying false positive differences in chromatin state between genotypes. After SV correction, we identify 1050, 30383, and 4508 regions whose peak heights are polymorphic among genotypes, among tissues, or exhibit genotype-by-tissue interactions, respectively. Finally, we identify 3988 candidate causative variants that explain at least 80% of the variance in chromatin state at nearby ATAC-seq peaks.
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Affiliation(s)
- Khoi Huynh
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, United States of America
| | - Brittny R. Smith
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Stuart J. Macdonald
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
- Center for Computational Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Anthony D. Long
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, United States of America
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10
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Mawla AM, van der Meulen T, Huising MO. Chromatin accessibility differences between alpha, beta, and delta cells identifies common and cell type-specific enhancers. BMC Genomics 2023; 24:202. [PMID: 37069576 PMCID: PMC10108528 DOI: 10.1186/s12864-023-09293-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 04/03/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND High throughput sequencing has enabled the interrogation of the transcriptomic landscape of glucagon-secreting alpha cells, insulin-secreting beta cells, and somatostatin-secreting delta cells. These approaches have furthered our understanding of expression patterns that define healthy or diseased islet cell types and helped explicate some of the intricacies between major islet cell crosstalk and glucose regulation. All three endocrine cell types derive from a common pancreatic progenitor, yet alpha and beta cells have partially opposing functions, and delta cells modulate and control insulin and glucagon release. While gene expression signatures that define and maintain cellular identity have been widely explored, the underlying epigenetic components are incompletely characterized and understood. However, chromatin accessibility and remodeling is a dynamic attribute that plays a critical role to determine and maintain cellular identity. RESULTS Here, we compare and contrast the chromatin landscape between mouse alpha, beta, and delta cells using ATAC-Seq to evaluate the significant differences in chromatin accessibility. The similarities and differences in chromatin accessibility between these related islet endocrine cells help define their fate in support of their distinct functional roles. We identify patterns that suggest that both alpha and delta cells are poised, but repressed, from becoming beta-like. We also identify patterns in differentially enriched chromatin that have transcription factor motifs preferentially associated with different regions of the genome. Finally, we not only confirm and visualize previously discovered common endocrine- and cell specific- enhancer regions across differentially enriched chromatin, but identify novel regions as well. We compiled our chromatin accessibility data in a freely accessible database of common endocrine- and cell specific-enhancer regions that can be navigated with minimal bioinformatics expertise. CONCLUSIONS Both alpha and delta cells appear poised, but repressed, from becoming beta cells in murine pancreatic islets. These data broadly support earlier findings on the plasticity in identity of non-beta cells under certain circumstances. Furthermore, differential chromatin accessibility shows preferentially enriched distal-intergenic regions in beta cells, when compared to either alpha or delta cells.
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Affiliation(s)
- Alex M Mawla
- Department of Neurobiology, Physiology & Behavior, College of Biological Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Talitha van der Meulen
- Department of Neurobiology, Physiology & Behavior, College of Biological Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Mark O Huising
- Department of Neurobiology, Physiology & Behavior, College of Biological Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA.
- Department of Physiology and Membrane Biology, School of Medicine, University of California, One Shields Avenue, Davis, CA, 95616, USA.
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11
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Chin HG, Vishnu US, Sun Z, Ponnaluri VKC, Zhang G, Xu SY, Benoukraf T, Cejas P, Spracklin G, Estève PO, Long HW, Pradhan S. Universal NicE-Seq: A Simple and Quick Method for Accessible Chromatin Detection in Fixed Cells. Methods Mol Biol 2023; 2611:39-52. [PMID: 36807062 DOI: 10.1007/978-1-0716-2899-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Genome-wide accessible chromatin sequencing and identification has enabled deciphering the epigenetic information encoded in chromatin, revealing accessible promoters, enhancers, nucleosome positioning, transcription factor occupancy, and other chromosomal protein binding. The starting biological materials are often fixed using formaldehyde crosslinking. Here, we describe accessible chromatin library preparation from low numbers of formaldehyde-crosslinked cells using a modified nick translation method, where a nicking enzyme nicks one strand of DNA and DNA polymerase incorporates biotin-conjugated dATP, dCTP, and methyl-dCTP. Once the DNA is labeled, it can be isolated for NGS library preparation. We termed this method as universal NicE-seq (nicking enzyme-assisted sequencing). We also demonstrate a single tube method that enables direct NGS library preparation from low cell numbers without DNA purification. Furthermore, we demonstrated universal NicE-seq on FFPE tissue section sample.
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Affiliation(s)
| | | | - Zhiyi Sun
- New England Biolabs Inc., Ipswich, MA, USA
| | | | | | | | - Touati Benoukraf
- Faculty of Medicine, Craig L. Dobbin Genetics Research Centre, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - George Spracklin
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | | | - Henry W Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
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12
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Bacos K, Perfilyev A, Karagiannopoulos A, Cowan E, Ofori JK, Bertonnier-Brouty L, Rönn T, Lindqvist A, Luan C, Ruhrmann S, Ngara M, Nilsson Å, Gheibi S, Lyons CL, Lagerstedt JO, Barghouth M, Esguerra JL, Volkov P, Fex M, Mulder H, Wierup N, Krus U, Artner I, Eliasson L, Prasad RB, Cataldo LR, Ling C. Type 2 diabetes candidate genes, including PAX5, cause impaired insulin secretion in human pancreatic islets. J Clin Invest 2023; 133:163612. [PMID: 36656641 PMCID: PMC9927941 DOI: 10.1172/jci163612] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/05/2023] [Indexed: 01/20/2023] Open
Abstract
Type 2 diabetes (T2D) is caused by insufficient insulin secretion from pancreatic β cells. To identify candidate genes contributing to T2D pathophysiology, we studied human pancreatic islets from approximately 300 individuals. We found 395 differentially expressed genes (DEGs) in islets from individuals with T2D, including, to our knowledge, novel (OPRD1, PAX5, TET1) and previously identified (CHL1, GLRA1, IAPP) candidates. A third of the identified expression changes in islets may predispose to diabetes, as expression of these genes associated with HbA1c in individuals not previously diagnosed with T2D. Most DEGs were expressed in human β cells, based on single-cell RNA-Seq data. Additionally, DEGs displayed alterations in open chromatin and associated with T2D SNPs. Mouse KO strains demonstrated that the identified T2D-associated candidate genes regulate glucose homeostasis and body composition in vivo. Functional validation showed that mimicking T2D-associated changes for OPRD1, PAX5, and SLC2A2 impaired insulin secretion. Impairments in Pax5-overexpressing β cells were due to severe mitochondrial dysfunction. Finally, we discovered PAX5 as a potential transcriptional regulator of many T2D-associated DEGs in human islets. Overall, we have identified molecular alterations in human pancreatic islets that contribute to β cell dysfunction in T2D pathophysiology.
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Affiliation(s)
- Karl Bacos
- Epigenetics and Diabetes Unit, Department of Clinical Sciences and
| | | | - Alexandros Karagiannopoulos
- Unit of Islet Cell Exocytosis, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Scania, Sweden
| | - Elaine Cowan
- Unit of Islet Cell Exocytosis, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Scania, Sweden
| | - Jones K. Ofori
- Epigenetics and Diabetes Unit, Department of Clinical Sciences and
| | - Ludivine Bertonnier-Brouty
- Endocrine Cell Differentiation, Department of Laboratory Medicine, Lund Stem Cell Center, Malmö, Scania, Sweden
| | - Tina Rönn
- Epigenetics and Diabetes Unit, Department of Clinical Sciences and
| | - Andreas Lindqvist
- Neuroendocrine Cell Biology, Department of Experimental Medical Science
| | - Cheng Luan
- Unit of Islet Pathophysiology, Department of Clinical Sciences
| | - Sabrina Ruhrmann
- Epigenetics and Diabetes Unit, Department of Clinical Sciences and
| | - Mtakai Ngara
- Neuroendocrine Cell Biology, Department of Experimental Medical Science
| | - Åsa Nilsson
- Human Tissue Lab, Department of Clinical Sciences
| | - Sevda Gheibi
- Molecular Metabolism Unit, Department of Clinical Sciences, and
| | - Claire L. Lyons
- Molecular Metabolism Unit, Department of Clinical Sciences, and
| | - Jens O. Lagerstedt
- Unit of Islet Cell Exocytosis, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Scania, Sweden
| | | | - Jonathan L.S. Esguerra
- Unit of Islet Cell Exocytosis, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Scania, Sweden
| | - Petr Volkov
- Epigenetics and Diabetes Unit, Department of Clinical Sciences and
| | - Malin Fex
- Molecular Metabolism Unit, Department of Clinical Sciences, and
| | - Hindrik Mulder
- Molecular Metabolism Unit, Department of Clinical Sciences, and
| | - Nils Wierup
- Neuroendocrine Cell Biology, Department of Experimental Medical Science
| | - Ulrika Krus
- Human Tissue Lab, Department of Clinical Sciences
| | - Isabella Artner
- Endocrine Cell Differentiation, Department of Laboratory Medicine, Lund Stem Cell Center, Malmö, Scania, Sweden
| | - Lena Eliasson
- Unit of Islet Cell Exocytosis, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Scania, Sweden
| | - Rashmi B. Prasad
- Genomics, Diabetes and Endocrinology, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, Malmö, Scania, Sweden.,Institute of Molecular Medicine (FIMM), Helsinki University, Helsinki, Finland
| | - Luis Rodrigo Cataldo
- Molecular Metabolism Unit, Department of Clinical Sciences, and,The Novo Nordisk Foundation Centre for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences and
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13
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Immunotherapeutic Approaches in Ovarian Cancer. Curr Issues Mol Biol 2023; 45:1233-1249. [PMID: 36826026 PMCID: PMC9955550 DOI: 10.3390/cimb45020081] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Ovarian cancer (OC) is gynecological cancer, and diagnosis and treatment are continuously advancing. Next-generation sequencing (NGS)-based diagnoses have emerged as novel methods for identifying molecules and pathways in cancer research. The NGS-based applications have expanded in OC research for early detection and identification of aberrant genes and dysregulation pathways, demonstrating comprehensive views of the entire transcriptome, such as fusion genes, genetic mutations, and gene expression profiling. Coinciding with advances in NGS-based diagnosis, treatment strategies for OC, such as molecular targeted therapy and immunotherapy, have also advanced. Immunotherapy is effective against many other cancers, and its efficacy against OC has also been demonstrated at the clinical phase. In this review, we describe several NGS-based applications for therapeutic targets of OC, and introduce current immunotherapeutic strategies, including vaccines, checkpoint inhibitors, and chimeric antigen receptor (CAR)-T cell transplantation, for effective diagnosis and treatment of OC.
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14
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Regué L, Wang W, Ji F, Avruch J, Wang H, Dai N. Human T2D-Associated Gene IMP2/IGF2BP2 Promotes the Commitment of Mesenchymal Stem Cells Into Adipogenic Lineage. Diabetes 2023; 72:33-44. [PMID: 36219823 PMCID: PMC9797317 DOI: 10.2337/db21-1087] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 10/06/2022] [Indexed: 01/19/2023]
Abstract
Excessive adiposity is the main cause of obesity and type two diabetes (T2D). Variants in human IMP2/IGF2BP2 gene are associated with increased risk of T2D. However, little is known about its role in adipogenesis and in insulin resistance. Here, we investigate the function of IMP2 during adipocyte development. Mice with Imp2 deletion in mesenchymal stem cells (MSC) are resistant to diet-induced obesity without glucose and insulin tolerance affected. Imp2 is essential for the early commitment of adipocyte-derived stem cells (ADSC) into preadipocytes, but the deletion of Imp2 in MSC is not required for the proliferation and terminal differentiation of committed preadipocytes. Mechanistically, Imp2 binds Wnt receptor Fzd8 mRNA and promotes its degradation by recruiting CCR4-NOT deadenylase complex in an mTOR-dependent manner. Our data demonstrate that Imp2 is required for maintaining white adipose tissue homeostasis through controlling mRNA stability in ADSC. However, the contribution of IMP2 to insulin resistance, a main risk of T2D, is not evident.
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Affiliation(s)
- Laura Regué
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA
- Diabetes Unit of the Medical Services, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - William Wang
- The Lundquist Institute, Torrance, CA
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Joseph Avruch
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA
- Diabetes Unit of the Medical Services, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Hua Wang
- The Lundquist Institute, Torrance, CA
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Ning Dai
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA
- Diabetes Unit of the Medical Services, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
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15
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Ling C, Bacos K, Rönn T. Epigenetics of type 2 diabetes mellitus and weight change - a tool for precision medicine? Nat Rev Endocrinol 2022; 18:433-448. [PMID: 35513492 DOI: 10.1038/s41574-022-00671-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/29/2022] [Indexed: 12/12/2022]
Abstract
Pioneering studies performed over the past few decades demonstrate links between epigenetics and type 2 diabetes mellitus (T2DM), the metabolic disorder with the most rapidly increasing prevalence in the world. Importantly, these studies identified epigenetic modifications, including altered DNA methylation, in pancreatic islets, adipose tissue, skeletal muscle and the liver from individuals with T2DM. As non-genetic factors that affect the risk of T2DM, such as obesity, unhealthy diet, physical inactivity, ageing and the intrauterine environment, have been associated with epigenetic modifications in healthy individuals, epigenetics probably also contributes to T2DM development. In addition, genetic factors associated with T2DM and obesity affect the epigenome in human tissues. Notably, causal mediation analyses found DNA methylation to be a potential mediator of genetic associations with metabolic traits and disease. In the past few years, translational studies have identified blood-based epigenetic markers that might be further developed and used for precision medicine to help patients with T2DM receive optimal therapy and to identify patients at risk of complications. This Review focuses on epigenetic mechanisms in the development of T2DM and the regulation of body weight in humans, with a special focus on precision medicine.
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Affiliation(s)
- Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden.
| | - Karl Bacos
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Tina Rönn
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
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16
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Autophagy enhanced by curcumin ameliorates inflammation in atherogenesis via the TFEB-P300-BRD4 axis. Acta Pharm Sin B 2022; 12:2280-2299. [PMID: 35646539 PMCID: PMC9136579 DOI: 10.1016/j.apsb.2021.12.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 11/13/2021] [Accepted: 11/17/2021] [Indexed: 12/26/2022] Open
Abstract
Disturbance of macrophage-associated lipid metabolism plays a key role in atherosclerosis. Crosstalk between autophagy deficiency and inflammation response in foam cells (FCs) through epigenetic regulation is still poorly understood. Here, we demonstrate that in macrophages, oxidized low-density lipoprotein (ox-LDL) leads to abnormal crosstalk between autophagy and inflammation, thereby causing aberrant lipid metabolism mediated through a dysfunctional transcription factor EB (TFEB)–P300–bromodomain-containing protein 4 (BRD4) axis. ox-LDL led to macrophage autophagy deficiency along with TFEB cytoplasmic accumulation and increased reactive oxygen species generation. This activated P300 promoted BRD4 binding on the promoter regions of inflammatory genes, consequently contributing to inflammation with atherogenesis. Particularly, ox-LDL activated BRD4-dependent super-enhancer associated with liquid–liquid phase separation (LLPS) on the regulatory regions of inflammatory genes. Curcumin (Cur) prominently restored FCs autophagy by promoting TFEB nuclear translocation, optimizing lipid catabolism, and reducing inflammation. The consequences of P300 and BRD4 on super-enhancer formation and inflammatory response in FCs could be prevented by Cur. Furthermore, the anti-atherogenesis effect of Cur was inhibited by macrophage-specific Brd4 overexpression or Tfeb knock-out in Apoe knock-out mice via bone marrow transplantation. The findings identify a novel TFEB-P300-BRD4 axis and establish a new epigenetic paradigm by which Cur regulates autophagy, inhibits inflammation, and decreases lipid content.
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Key Words
- ATG5, autophagy-related 5
- Acetyl-H3, acetyl-histone 3
- Atherosclerosis
- Autophagy
- BET, bromodomain and extra-terminal
- BRD4
- BRD4, bromodomain protein 4
- CQ, chloroquine
- CVDs, cardiovascular diseases
- ChIP, chromatin immunoprecipitation
- Cur, curcumin
- Curcumin
- Dil-ox-LDL, 1,1′-dioctadecyl-3,3,3′,3′-tetramethy-lindocarbocyanine perchlorate labeled oxidized low-density lipoprotein
- FCs, foam cells
- HFD, high-fat diet
- IL-1β, interleukin 1β
- Inflammation
- LIR, LC3-interacting region
- MCP-1, monocyte chemotactic protein 1
- Macrophage
- NAC, N-acetyl-l-cysteine
- ORO, Oil red O
- P300
- ROS, reactive oxygen species
- Re-ChIP, re-chromatin immunoprecipitation
- SE, super-enhancer
- TFEB
- TFEB, transcription factor EB
- TNF-α, tumor necrosis factor α
- mTORC1, mammalian target of rapamycin complex 1
- ox-LDL, oxidized low-density lipoprotein
- qRT-PCR, quantitative real-time polymerase chain reaction
- siRNAs, small interference RNAs
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17
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Role of the Transcription Factor MAFA in the Maintenance of Pancreatic β-Cells. Int J Mol Sci 2022; 23:ijms23094478. [PMID: 35562869 PMCID: PMC9101179 DOI: 10.3390/ijms23094478] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/16/2022] [Accepted: 04/17/2022] [Indexed: 02/04/2023] Open
Abstract
Pancreatic β-cells are specialized to properly regulate blood glucose. Maintenance of the mature β-cell phenotype is critical for glucose metabolism, and β-cell failure results in diabetes mellitus. Recent studies provide strong evidence that the mature phenotype of β-cells is maintained by several transcription factors. These factors are also required for β-cell differentiation from endocrine precursors or maturation from immature β-cells during pancreatic development. Because the reduction or loss of these factors leads to β-cell failure and diabetes, inducing the upregulation or inhibiting downregulation of these transcription factors would be beneficial for studies in both diabetes and stem cell biology. Here, we discuss one such factor, i.e., the transcription factor MAFA. MAFA is a basic leucine zipper family transcription factor that can activate the expression of insulin in β-cells with PDX1 and NEUROD1. MAFA is indeed indispensable for the maintenance of not only insulin expression but also function of adult β-cells. With loss of MAFA in type 2 diabetes, β-cells cannot maintain their mature phenotype and are dedifferentiated. In this review, we first briefly summarize the functional roles of MAFA in β-cells and then mainly focus on the molecular mechanism of cell fate conversion regulated by MAFA.
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18
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Merrill CB, Pabon MA, Montgomery AB, Rodan AR, Rothenfluh A. Optimized assay for transposase-accessible chromatin by sequencing (ATAC-seq) library preparation from adult Drosophila melanogaster neurons. Sci Rep 2022; 12:6043. [PMID: 35411004 PMCID: PMC9001676 DOI: 10.1038/s41598-022-09869-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/14/2022] [Indexed: 01/07/2023] Open
Abstract
Assay for transposase-accessible chromatin by sequencing (ATAC-seq) is rapidly becoming the assay of choice to investigate chromatin-mediated gene regulation, largely because of low input requirements, a fast workflow, and the ability to interrogate the entire genome in an untargeted manner. Many studies using ATAC-seq use mammalian or human-derived tissues, and established protocols work well in these systems. However, ATAC-seq is not yet widely used in Drosophila. Vinegar flies present several advantages over mammalian systems that make them an excellent model for ATAC-seq studies, including abundant genetic tools that allow straightforward targeting, transgene expression, and genetic manipulation that are not available in mammalian models. Because current ATAC-seq protocols are not optimized to use flies, we developed an optimized workflow that accounts for several complicating factors present in Drosophila. We examined parameters affecting nuclei isolation, including input size, freezing time, washing, and possible confounds from retinal pigments. Then, we optimized the enzymatic steps of library construction to account for the smaller Drosophila genome size. Finally, we used our optimized protocol to generate ATAC-seq libraries that meet ENCODE quality metrics. Our optimized protocol enables extensive ATAC-seq experiments in Drosophila, thereby leveraging the advantages of this powerful model system to understand chromatin-mediated gene regulation.
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Affiliation(s)
- Collin B. Merrill
- grid.223827.e0000 0001 2193 0096Department of Psychiatry, Huntsman Mental Health Institute, University of Utah, Salt Lake City, UT 84108 USA
| | - Miguel A. Pabon
- grid.223827.e0000 0001 2193 0096Molecular Medicine Program, University of Utah, Salt Lake City, UT 84112 USA
| | - Austin B. Montgomery
- grid.223827.e0000 0001 2193 0096Molecular Medicine Program, University of Utah, Salt Lake City, UT 84112 USA
| | - Aylin R. Rodan
- grid.223827.e0000 0001 2193 0096Molecular Medicine Program, University of Utah, Salt Lake City, UT 84112 USA ,grid.223827.e0000 0001 2193 0096Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah, Salt Lake City, UT 84112 USA ,grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah, Salt Lake City, UT 84112 USA ,grid.280807.50000 0000 9555 3716Medical Service, Veterans Affairs Salt Lake City Health Care System, Salt Lake City, UT 84148 USA
| | - Adrian Rothenfluh
- grid.223827.e0000 0001 2193 0096Department of Psychiatry, Huntsman Mental Health Institute, University of Utah, Salt Lake City, UT 84108 USA ,grid.223827.e0000 0001 2193 0096Molecular Medicine Program, University of Utah, Salt Lake City, UT 84112 USA ,grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah, Salt Lake City, UT 84112 USA ,grid.223827.e0000 0001 2193 0096Department of Neurobiology, University of Utah, Salt Lake City, UT 84112 USA
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19
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Fanter C, Madelaire C, Genereux DP, van Breukelen F, Levesque D, Hindle A. Epigenomics as a paradigm to understand the nuances of phenotypes. J Exp Biol 2022; 225:274619. [PMID: 35258621 DOI: 10.1242/jeb.243411] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Quantifying the relative importance of genomic and epigenomic modulators of phenotype is a focal challenge in comparative physiology, but progress is constrained by availability of data and analytic methods. Previous studies have linked physiological features to coding DNA sequence, regulatory DNA sequence, and epigenetic state, but few have disentangled their relative contributions or unambiguously distinguished causative effects ('drivers') from correlations. Progress has been limited by several factors, including the classical approach of treating continuous and fluid phenotypes as discrete and static across time and environment, and difficulty in considering the full diversity of mechanisms that can modulate phenotype, such as gene accessibility, transcription, mRNA processing and translation. We argue that attention to phenotype nuance, progressing to association with epigenetic marks and then causal analyses of the epigenetic mechanism, will enable clearer evaluation of the evolutionary path. This would underlie an essential paradigm shift, and power the search for links between genomic and epigenomic features and physiology. Here, we review the growing knowledge base of gene-regulatory mechanisms and describe their links to phenotype, proposing strategies to address widely recognized challenges.
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Affiliation(s)
- Cornelia Fanter
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Carla Madelaire
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Diane P Genereux
- Vertebrate Genome Biology, Broad Institute, Cambridge, MA 02142, USA
| | - Frank van Breukelen
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Danielle Levesque
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
| | - Allyson Hindle
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
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20
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Son J, Ding H, Farb TB, Efanov AM, Sun J, Gore JL, Syed SK, Lei Z, Wang Q, Accili D, Califano A. BACH2 inhibition reverses β cell failure in type 2 diabetes models. J Clin Invest 2021; 131:153876. [PMID: 34907913 DOI: 10.1172/jci153876] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/28/2021] [Indexed: 12/31/2022] Open
Abstract
Type 2 diabetes (T2D) is associated with defective insulin secretion and reduced β cell mass. Available treatments provide a temporary reprieve, but secondary failure rates are high, making insulin supplementation necessary. Reversibility of β cell failure is a key translational question. Here, we reverse engineered and interrogated pancreatic islet-specific regulatory networks to discover T2D-specific subpopulations characterized by metabolic inflexibility and endocrine progenitor/stem cell features. Single-cell gain- and loss-of-function and glucose-induced Ca2+ flux analyses of top candidate master regulatory (MR) proteins in islet cells validated transcription factor BACH2 and associated epigenetic effectors as key drivers of T2D cell states. BACH2 knockout in T2D islets reversed cellular features of the disease, restoring a nondiabetic phenotype. BACH2-immunoreactive islet cells increased approximately 4-fold in diabetic patients, confirming the algorithmic prediction of clinically relevant subpopulations. Treatment with a BACH inhibitor lowered glycemia and increased plasma insulin levels in diabetic mice, and restored insulin secretion in diabetic mice and human islets. The findings suggest that T2D-specific populations of failing β cells can be reversed and indicate pathways for pharmacological intervention, including via BACH2 inhibition.
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Affiliation(s)
- Jinsook Son
- Department of Medicine and.,Naomi Berrie Diabetes Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Hongxu Ding
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Thomas B Farb
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, USA
| | - Alexander M Efanov
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, USA
| | - Jiajun Sun
- Shanghai National Clinical Research Center for Endocrine and Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Institute of Endocrine and Metabolic Disease, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Julie L Gore
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, USA
| | - Samreen K Syed
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, USA
| | - Zhigang Lei
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, USA
| | - Qidi Wang
- Shanghai National Clinical Research Center for Endocrine and Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Institute of Endocrine and Metabolic Disease, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Domenico Accili
- Department of Medicine and.,Naomi Berrie Diabetes Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, USA
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21
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Imai Y. Deciphering regulatory protein activity in human pancreatic islets via reverse engineering of single-cell sequencing data. J Clin Invest 2021; 131:e154482. [PMID: 34907912 PMCID: PMC8670832 DOI: 10.1172/jci154482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The loss of functional β cell mass contributes to development and progression of type 2 diabetes (T2D). However, the molecular mechanisms differentiating islet dysfunction in T2D from nondiabetic states remain elusive. In this issue of the JCI, Son et al. applied reverse engineering to obtain the activity of gene expression regulatory proteins from single-cell RNA sequencing data of nondiabetic and T2D human islets. The authors identify unique patterns of regulatory protein activities associated with T2D. Furthermore, BACH2 emerged as a potential transcription factor that drives activation of T2D-associated regulatory proteins in human islets.
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Affiliation(s)
- Yumi Imai
- Division of Endocrinology and Metabolism, Department of Internal Medicine, and
- Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, Iowa, USA
- Iowa City Veterans Affairs Medical Center, Iowa City, Iowa, USA
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22
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Guerin LN, Barnett KR, Hodges E. Dual detection of chromatin accessibility and DNA methylation using ATAC-Me. Nat Protoc 2021; 16:5377-5397. [PMID: 34663963 PMCID: PMC11057009 DOI: 10.1038/s41596-021-00608-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 08/02/2021] [Indexed: 01/05/2023]
Abstract
The epigenome is multidimensional, with individual molecular components operating on different levels to control transcriptional output. Techniques that combine measurements of these features can reveal their precise correspondence in genomic space, or temporal connectivity, to better understand how they jointly regulate genes. ATAC-Me is an integrated method to probe DNA methylation and chromatin accessibility from a single DNA fragment library. Intact nuclei undergo Tn5 transposition to isolate DNA fragments within nucleosome-free regions. Isolated fragments are exposed to sodium bisulfite before library amplification and sequencing. A typical ATAC-Me experiment detects ~60,000-75,000 peak regions (P < 0.05), covering ~3-4 million CpG sites with at least 5× coverage. These sites display a range of methylation values depending on the cellular and genomic context. The approach is well suited for time course studies that aim to capture chromatin and DNA methylation dynamics in tandem during cellular differentiation. The protocol is completed in 2 d with standard molecular biology equipment and expertise. Analysis of resulting data uses publicly available software requiring basic bioinformatics skills to interpret results.
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Affiliation(s)
- Lindsey N. Guerin
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kelly R. Barnett
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Emily Hodges
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
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23
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Nair VD, Vasoya M, Nair V, Smith GR, Pincas H, Ge Y, Douglas CM, Esser KA, Sealfon SC. Differential analysis of chromatin accessibility and gene expression profiles identifies cis-regulatory elements in rat adipose and muscle. Genomics 2021; 113:3827-3841. [PMID: 34547403 DOI: 10.1016/j.ygeno.2021.09.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/08/2021] [Accepted: 09/15/2021] [Indexed: 01/04/2023]
Abstract
Chromatin accessibility is a key factor influencing gene expression. We optimized the Omni-ATAC-seq protocol and used it together with RNA-seq to investigate cis-regulatory elements in rat white adipose and skeletal muscle, two tissues with contrasting metabolic functions. While promoter accessibility correlated with RNA expression, integration of the two datasets identified tissue-specific differentially accessible regions (DARs) that predominantly localized in intergenic and intron regions. DARs were mapped to differentially expressed (DE) genes enriched in distinct biological processes in each tissue. Randomly selected DE genes were validated by qPCR. Top enriched motifs in DARs predicted binding sites for transcription factors (TFs) showing tissue-specific up-regulation. The correlation between differential chromatin accessibility at a given TF binding motif and differential expression of target genes further supported the functional relevance of that motif. Our study identified cis-regulatory regions that likely play a major role in the regulation of tissue-specific gene expression in adipose and muscle.
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Affiliation(s)
- Venugopalan D Nair
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Mital Vasoya
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Vishnu Nair
- Department of Computer Sciences, Columbia University, New York, NY 10027, USA
| | - Gregory R Smith
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hanna Pincas
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yongchao Ge
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Collin M Douglas
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, FL 32610, USA
| | - Karyn A Esser
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, FL 32610, USA
| | - Stuart C Sealfon
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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24
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Cao J, Yan W, Ma X, Huang H, Yan H. Insulin-like Growth Factor 2 mRNA-Binding Protein 2-a Potential Link Between Type 2 Diabetes Mellitus and Cancer. J Clin Endocrinol Metab 2021; 106:2807-2818. [PMID: 34061963 PMCID: PMC8475209 DOI: 10.1210/clinem/dgab391] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Indexed: 12/12/2022]
Abstract
CONTEXT Type 2 diabetes mellitus (T2DM) and cancer share a variety of risk factors and pathophysiological features. It is becoming increasingly accepted that the 2 diseases are related, and that T2DM increases the risk of certain malignancies. OBJECTIVE This review summarizes recent advancements in the elucidation of functions of insulin-like growth factor 2 (IGF-2) messenger RNA (mRNA)-binding protein 2 (IGF2BP2) in T2DM and cancer. METHODS A PubMed review of the literature was conducted, and search terms included IGF2BP2, IMP2, or p62 in combination with cancer or T2DM. Additional sources were identified through manual searches of reference lists. The increased risk of multiple malignancies and cancer-associated mortality in patients with T2DM is believed to be driven by insulin resistance, hyperinsulinemia, hyperglycemia, chronic inflammation, and dysregulation of adipokines and sex hormones. Furthermore, IGF-2 is oncogenic, and its loss-of-function splice variant is protective against T2DM, which highlights the pivotal role of this growth factor in the pathogenesis of these 2 diseases. IGF-2 mRNA-binding proteins, particularly IGF2BP2, are also involved in T2DM and cancer, and single-nucleotide variations (formerly single-nucleotide polymorphisms) of IGF2BP2 are associated with both diseases. Deletion of the IGF2BP2 gene in mice improves their glucose tolerance and insulin sensitivity, and mice with transgenic p62, a splice variant of IGF2BP2, are prone to diet-induced fatty liver disease and hepatocellular carcinoma, suggesting the biological significance of IGF2BP2 in T2DM and cancer. CONCLUSION Accumulating evidence has revealed that IGF2BP2 mediates the pathogenesis of T2DM and cancer by regulating glucose metabolism, insulin sensitivity, and tumorigenesis. This review provides insight into the potential involvement of this RNA binding protein in the link between T2DM and cancer.
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Affiliation(s)
- Junguo Cao
- Shaanxi Eye Hospital (Xi’an People’s Hospital), Affiliated Guangren Hospital, School of Medicine, Xi’an Jiaotong University, Xi’an 71004, Shaanxi Province, China
- Division of Experimental Neurosurgery, Department of Neurosurgery, University of Heidelberg, Heidelberg 69120, Germany
| | - Weijia Yan
- Shaanxi Eye Hospital (Xi’an People’s Hospital), Affiliated Guangren Hospital, School of Medicine, Xi’an Jiaotong University, Xi’an 71004, Shaanxi Province, China
- Department of Ophthalmology, University of Heidelberg, Heidelberg 69120, Germany
| | - Xiujian Ma
- Division of Molecular Neurogenetics, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Haiyan Huang
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun 130000, China
- Haiyan Huang, Department of Neurosurgery, The First Hospital of Jilin University, Xinmin St No.71, Changchun, China.
| | - Hong Yan
- Shaanxi Eye Hospital (Xi’an People’s Hospital), Affiliated Guangren Hospital, School of Medicine, Xi’an Jiaotong University, Xi’an 71004, Shaanxi Province, China
- Correspondence: Hong Yan, Shaanxi Eye Hospital (Xi’an People’s Hospital), Affiliated Guangren Hospital, School of Medicine, Xi’an Jiaotong University, Xi’an 71004, Shaanxi Province, China.
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25
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Long J, Long T, Li Y, Yuan P, Liu K, Li J, Cheng L. A Functional Polymorphism in Accessible Chromatin Region Confers Risk of Non-Small Cell Lung Cancer in Chinese Population. Front Oncol 2021; 11:698993. [PMID: 34552866 PMCID: PMC8450516 DOI: 10.3389/fonc.2021.698993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/17/2021] [Indexed: 11/21/2022] Open
Abstract
Background The disease-associated non-coding variants identified by genome-wide association studies (GWASs) were enriched in open chromatin regions (OCRs) and implicated in gene regulation. Genetic variants in OCRs thus may exert regulatory functions and contribute to non-small cell lung cancer (NSCLC) susceptibility. Objective To fine map potential functional variants in GWAS loci that contribute to NSCLC predisposition using chromatin accessibility and histone modification data and explore their functions by population study and biochemical experimental analyses. Methods We mapped the chromatin accessible regions of lung tissues using data of assay for transposase-accessible chromatin using sequencing (ATAC-seq) in The Cancer Genome Atlas (TCGA) and prioritized potential regulatory variants within lung cancer GWAS loci by aligning with histone signatures using data of chromatin immunoprecipitation assays followed by sequencing (ChIP-seq) in the Encyclopedia of DNA Elements (ENCODE). A two-stage case–control study with 1,830 cases and 2,001 controls was conducted to explore the associations between candidate variants and NSCLC risk in Chinese population. Bioinformatic annotations and biochemical experiments were performed to further reveal the potential functions of significant variants. Results Sixteen potential functional single-nucleotide polymorphisms (SNPs) were selected as candidates from bioinformatics analyses. Three variants out of the 16 candidate SNPs survived after genotyping in stage 1 case–control study, and only the results of SNP rs13064999 were successfully validated in the analyses of stage 2 case–control study. In combined analyses, rs13064999 was significantly associated with NSCLC risk [additive model; odds ratio (OR) = 1.17; 95%CI, 1.07–1.29; p = 0.001]. Functional annotations indicated its potential enhancer bioactivity, and dual-luciferase reporter assays revealed a significant increase in luciferase activity for the reconstructed plasmid with rs13064999 A allele, when compared to the one with wild-type G allele (pA549 < 0.001, pSK-MES-1 = 0.004). Further electrophoretic mobility shift assays (EMSA) and super-shift assays confirmed a stronger affinity of HP1γ for the binding motif containing SNP rs13064999 A allele. Conclusion These findings suggested that the functional variant rs13064999, identified by the integration of ATAC-seq and ChIP-seq data, contributes to the susceptibility of NSCLC by affecting HP1γ binding, while the exact biological mechanism awaits further exploration.
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Affiliation(s)
- Jieyi Long
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tingting Long
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Li
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peihong Yuan
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ke Liu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiaoyuan Li
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liming Cheng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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26
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Golson ML. Islet Epigenetic Impacts on β-Cell Identity and Function. Compr Physiol 2021; 11:1961-1978. [PMID: 34061978 DOI: 10.1002/cphy.c200004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The development and maintenance of differentiation is vital to the function of mature cells. Terminal differentiation is achieved by locking in the expression of genes essential for the function of those cells. Gene expression and its memory through generations of cell division is controlled by transcription factors and a host of epigenetic marks. In type 2 diabetes, β cells have altered gene expression compared to controls, accompanied by altered chromatin marks. Mutations, diet, and environment can all disrupt the implementation and preservation of the distinctive β-cell transcriptional signature. Understanding of the full complement of genomic control in β cells is still nascent. This article describes the known effects of histone marks and variants, DNA methylation, how they are regulated in the β cell, and how they affect cell-fate specification, maintenance, and lineage propagation. © 2021 American Physiological Society. Compr Physiol 11:1-18, 2021.
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Affiliation(s)
- Maria L Golson
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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27
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Evidence from oyster suggests an ancient role for Pdx in regulating insulin gene expression in animals. Nat Commun 2021; 12:3117. [PMID: 34035261 PMCID: PMC8149454 DOI: 10.1038/s41467-021-23216-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 04/19/2021] [Indexed: 11/17/2022] Open
Abstract
Hox and ParaHox genes encode transcription factors with similar expression patterns in divergent animals. The Pdx (Xlox) homeobox gene, for example, is expressed in a sharp spatial domain in the endodermal cell layer of the gut in chordates, echinoderms, annelids and molluscs. The significance of comparable gene expression patterns is unclear because it is not known if downstream transcriptional targets are also conserved. Here, we report evidence indicating that a classic transcriptional target of Pdx1 in vertebrates, the insulin gene, is a likely direct target of Pdx in Pacific oyster adults. We show that one insulin-related gene, cgILP, is co-expressed with cgPdx in oyster digestive tissue. Transcriptomic comparison suggests that this tissue plays a similar role to the vertebrate pancreas. Using ATAC-seq and ChIP, we identify an upstream regulatory element of the cgILP gene which shows binding interaction with cgPdx protein in oyster hepatopancreas and demonstrate, using a cell culture assay, that the oyster Pdx can act as a transcriptional activator through this site, possibly in synergy with NeuroD. These data argue that a classic homeodomain-target gene interaction dates back to the origin of Bilateria. In vertebrates insulin is a direct transcriptional target of Pdx: the same is true in Pacific oysters and the authors show insulin-related gene, cgILP, is co-expressed with cgPdx in oyster digestive tissue, showing this gene interaction dates back to the origin of Bilateria.
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28
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Scrt1, a transcriptional regulator of β-cell proliferation identified by differential chromatin accessibility during islet maturation. Sci Rep 2021; 11:8800. [PMID: 33888791 PMCID: PMC8062533 DOI: 10.1038/s41598-021-88003-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 03/25/2021] [Indexed: 12/12/2022] Open
Abstract
Glucose-induced insulin secretion, a hallmark of mature β-cells, is achieved after birth and is preceded by a phase of intense proliferation. These events occurring in the neonatal period are decisive for establishing an appropriate functional β-cell mass that provides the required insulin throughout life. However, key regulators of gene expression involved in functional maturation of β-cells remain to be elucidated. Here, we addressed this issue by mapping open chromatin regions in newborn versus adult rat islets using the ATAC-seq assay. We obtained a genome-wide picture of chromatin accessible sites (~ 100,000) among which 20% were differentially accessible during maturation. An enrichment analysis of transcription factor binding sites identified a group of transcription factors that could explain these changes. Among them, Scrt1 was found to act as a transcriptional repressor and to control β-cell proliferation. Interestingly, Scrt1 expression was controlled by the transcriptional repressor RE-1 silencing transcription factor (REST) and was increased in an in vitro reprogramming system of pancreatic exocrine cells to β-like cells. Overall, this study led to the identification of several known and unforeseen key transcriptional events occurring during β-cell maturation. These findings will help defining new strategies to induce the functional maturation of surrogate insulin-producing cells.
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29
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Han B, Jiang W, Cui P, Zheng K, Dang C, Wang J, Li H, Chen L, Zhang R, Wang QM, Ju Z, Hao J. Microglial PGC-1α protects against ischemic brain injury by suppressing neuroinflammation. Genome Med 2021; 13:47. [PMID: 33771213 PMCID: PMC8004413 DOI: 10.1186/s13073-021-00863-5] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 03/04/2021] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Neuroinflammation and immune responses occurring minutes to hours after stroke are associated with brain injury after acute ischemic stroke (AIS). PPARγ coactivator-1α (PGC-1α), as a master coregulator of gene expression in mitochondrial biogenesis, was found to be transiently upregulated in microglia after AIS. However, the role of microglial PGC-1α in poststroke immune modulation remains unknown. METHODS PGC-1α expression in microglia from human and mouse brain samples following ischemic stroke was first determined. Subsequently, we employed transgenic mice with microglia-specific overexpression of PGC-1α for middle cerebral artery occlusion (MCAO). The morphology and gene expression profile of microglia with PGC-1α overexpression were evaluated. Downstream inflammatory cytokine production and NLRP3 activation were also determined. ChIP-Seq analysis was performed to detect PGC-1α-binding sites in microglia. Autophagic and mitophagic activity was further monitored by immunofluorescence staining. Unc-51-like autophagy activating kinase 1 (ULK1) expression was evaluated under the PGC-1α interaction with ERRα. Finally, pharmacological inhibition and genomic knockdown of ULK1 were performed to estimate the role of ULK1 in mediating mitophagic activity after ischemic stroke. RESULTS PGC-1α expression was shortly increased after ischemic stroke, not only in human brain samples but also in mouse brain samples. Microglia-specific PGC-1α overexpressing mice exhibited significantly decreased neurologic deficits after ischemic injury, with reduced NLRP3 activation and proinflammatory cytokine production. ChIP-Seq analysis and KEGG pathway analysis revealed that mitophagy was significantly enhanced. PGC-1α significantly promoted autophagic flux and induced autolysosome formation. More specifically, the autophagic clearance of mitochondria was enhanced by PGC-1α regulation, indicating the important role of mitophagy. Pharmacological inhibition or knockdown of ULK1 expression impaired autophagic/mitophagic activity, thus abolishing the neuroprotective effects of PGC-1α. CONCLUSIONS Mechanistically, in AIS, PGC-1α promotes autophagy and mitophagy through ULK1 and reduces NLRP3 activation. Our findings indicate that microglial PGC-1α may be a promising therapeutic target for AIS.
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Affiliation(s)
- Bin Han
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Wei Jiang
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Pan Cui
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Kai Zheng
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Chun Dang
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Junjie Wang
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - He Li
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Lin Chen
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Rongxin Zhang
- Laboratory of Immunology and Inflammation, Department of Immunology and Research Center of Basic Medical Sciences, Key Laboratory of Immune Microenvironments and Diseases of Educational Ministry, Tianjin Medical University, Tianjin, 300070, China
| | - Qing Mei Wang
- Stroke Biological Recovery Laboratory, Department of Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital, the teaching affiliate of Harvard Medical School Charlestown, Boston, MA, 02129, USA
| | - Zhenyu Ju
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou, 510632, China
| | - Junwei Hao
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China.
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, 300052, China.
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Regué L, Zhao L, Ji F, Wang H, Avruch J, Dai N. RNA m6A reader IMP2/IGF2BP2 promotes pancreatic β-cell proliferation and insulin secretion by enhancing PDX1 expression. Mol Metab 2021; 48:101209. [PMID: 33705986 PMCID: PMC8076713 DOI: 10.1016/j.molmet.2021.101209] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/23/2021] [Accepted: 03/05/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Type 2 diabetes (T2D) is a common metabolic disease. Variants in human IGF2 mRNA binding protein 2 (IMP2/IGF2BP2) are associated with increased risk of T2D. IMP2 contributes to T2D susceptibility primarily through effects on insulin secretion. However, the underlying mechanism is not known. METHODS To understand the role of IMP2 in insulin secretion and T2D pathophysiology, we generated Imp2 pancreatic β-cell specific knockout mice (βIMP2KO) by recombining the Imp2flox allele with Cre recombinase driven by the rat insulin 2 promoter. We further characterized metabolic phenotypes of βIMP2KO mice and assessed their β-cell functions. RESULTS The deletion of IMP2 in pancreatic β-cells leads to reduced compensatory β-cell proliferation and function. Mechanically, IMP2 directly binds to Pdx1 mRNA and stimulates its translation in an m6A dependent manner. Moreover, IMP2 orchestrates IGF2-AKT-GSK3β-PDX1 signaling to stable PDX1 polypeptides. In human EndoC-βH1 cells, the over-expression of IMP2 is capable to enhance cell proliferation, PDX1 protein level and insulin secretion. CONCLUSION Our work therefore reveals IMP2 as a critical regulator of pancreatic β-cell proliferation and function; highlights the importance of posttranscriptional gene expression in T2D pathology.
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MESH Headings
- Adenosine/analogs & derivatives
- Adenosine/metabolism
- Animals
- Cell Line
- Cell Proliferation/genetics
- Diabetes Mellitus, Type 2/genetics
- Diabetes Mellitus, Type 2/metabolism
- Diet, High-Fat/adverse effects
- Disease Models, Animal
- Gene Knockout Techniques
- Homeodomain Proteins/metabolism
- Humans
- Insulin Secretion/genetics
- Insulin, Regular, Human/administration & dosage
- Insulin, Regular, Human/genetics
- Insulin, Regular, Human/metabolism
- Insulin-Secreting Cells/metabolism
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Middle Aged
- Promoter Regions, Genetic
- RNA, Messenger/metabolism
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Rats
- Signal Transduction/genetics
- Trans-Activators/metabolism
- Transfection
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Affiliation(s)
- Laura Regué
- Department of Molecular Biology and Diabetes Unit of the Medical Services, Massachusetts General Hospital, Boston, 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Liping Zhao
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Fei Ji
- Department of Molecular Biology and Diabetes Unit of the Medical Services, Massachusetts General Hospital, Boston, 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Hua Wang
- The Lundquist Institute, Harbor-UCLA, Torrance, CA, 90502, USA
| | - Joseph Avruch
- Department of Molecular Biology and Diabetes Unit of the Medical Services, Massachusetts General Hospital, Boston, 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Ning Dai
- Department of Molecular Biology and Diabetes Unit of the Medical Services, Massachusetts General Hospital, Boston, 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
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31
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Minnoye L, Marinov GK, Krausgruber T, Pan L, Marand AP, Secchia S, Greenleaf WJ, Furlong EEM, Zhao K, Schmitz RJ, Bock C, Aerts S. Chromatin accessibility profiling methods. NATURE REVIEWS. METHODS PRIMERS 2021; 1:10. [PMID: 38410680 PMCID: PMC10895463 DOI: 10.1038/s43586-020-00008-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/01/2020] [Indexed: 02/06/2023]
Abstract
Chromatin accessibility, or the physical access to chromatinized DNA, is a widely studied characteristic of the eukaryotic genome. As active regulatory DNA elements are generally 'accessible', the genome-wide profiling of chromatin accessibility can be used to identify candidate regulatory genomic regions in a tissue or cell type. Multiple biochemical methods have been developed to profile chromatin accessibility, both in bulk and at the single-cell level. Depending on the method, enzymatic cleavage, transposition or DNA methyltransferases are used, followed by high-throughput sequencing, providing a view of genome-wide chromatin accessibility. In this Primer, we discuss these biochemical methods, as well as bioinformatics tools for analysing and interpreting the generated data, and insights into the key regulators underlying developmental, evolutionary and disease processes. We outline standards for data quality, reproducibility and deposition used by the genomics community. Although chromatin accessibility profiling is invaluable to study gene regulation, alone it provides only a partial view of this complex process. Orthogonal assays facilitate the interpretation of accessible regions with respect to enhancer-promoter proximity, functional transcription factor binding and regulatory function. We envision that technological improvements including single-molecule, multi-omics and spatial methods will bring further insight into the secrets of genome regulation.
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Affiliation(s)
- Liesbeth Minnoye
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Thomas Krausgruber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Lixia Pan
- Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
| | | | - Stefano Secchia
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | | | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
| | | | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Institute of Artificial Intelligence and Decision Support, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Stein Aerts
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
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Griffith BGC, Upstill-Goddard R, Brunton H, Grimes GR, Biankin AV, Serrels B, Byron A, Frame MC. FAK regulates IL-33 expression by controlling chromatin accessibility at c-Jun motifs. Sci Rep 2021; 11:229. [PMID: 33420223 PMCID: PMC7794255 DOI: 10.1038/s41598-020-80111-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/10/2020] [Indexed: 01/29/2023] Open
Abstract
Focal adhesion kinase (FAK) localizes to focal adhesions and is overexpressed in many cancers. FAK can also translocate to the nucleus, where it binds to, and regulates, several transcription factors, including MBD2, p53 and IL-33, to control gene expression by unknown mechanisms. We have used ATAC-seq to reveal that FAK controls chromatin accessibility at a subset of regulated genes. Integration of ATAC-seq and RNA-seq data showed that FAK-dependent chromatin accessibility is linked to differential gene expression, including of the FAK-regulated cytokine and transcriptional regulator interleukin-33 (Il33), which controls anti-tumor immunity. Analysis of the accessibility peaks on the Il33 gene promoter/enhancer regions revealed sequences for several transcription factors, including ETS and AP-1 motifs, and we show that c-Jun, a component of AP-1, regulates Il33 gene expression by binding to its enhancer in a FAK kinase-dependent manner. This work provides the first demonstration that FAK controls transcription via chromatin accessibility, identifying a novel mechanism by which nuclear FAK regulates biologically important gene expression.
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Affiliation(s)
- Billie G C Griffith
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Rosanna Upstill-Goddard
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Holly Brunton
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Graeme R Grimes
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Bryan Serrels
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK.
- NanoString Technologies, Inc, Seattle, WA, 98109, USA.
| | - Adam Byron
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XR, UK.
| | - Margaret C Frame
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XR, UK.
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Hu M, Cherkaoui I, Misra S, Rutter GA. Functional Genomics in Pancreatic β Cells: Recent Advances in Gene Deletion and Genome Editing Technologies for Diabetes Research. Front Endocrinol (Lausanne) 2020; 11:576632. [PMID: 33162936 PMCID: PMC7580382 DOI: 10.3389/fendo.2020.576632] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022] Open
Abstract
The inheritance of variants that lead to coding changes in, or the mis-expression of, genes critical to pancreatic beta cell function can lead to alterations in insulin secretion and increase the risk of both type 1 and type 2 diabetes. Recently developed clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) gene editing tools provide a powerful means of understanding the impact of identified variants on cell function, growth, and survival and might ultimately provide a means, most likely after the transplantation of genetically "corrected" cells, of treating the disease. Here, we review some of the disease-associated genes and variants whose roles have been probed up to now. Next, we survey recent exciting developments in CRISPR/Cas9 technology and their possible exploitation for β cell functional genomics. Finally, we will provide a perspective as to how CRISPR/Cas9 technology may find clinical application in patients with diabetes.
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Affiliation(s)
- Ming Hu
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Ines Cherkaoui
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Shivani Misra
- Metabolic Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Guy A. Rutter
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, United Kingdom
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Dai N. The Diverse Functions of IMP2/IGF2BP2 in Metabolism. Trends Endocrinol Metab 2020; 31:670-679. [PMID: 32586768 DOI: 10.1016/j.tem.2020.05.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/28/2020] [Accepted: 05/26/2020] [Indexed: 12/13/2022]
Abstract
The human insulin-like growth factor 2 (IGF2) mRNA binding protein family (IMPs/IGF2BPs) is involved in a spectrum of biological processes, including development, tumorigenesis, and stemness. IMPs play a major role in post-transcriptional regulation of RNAs through the ribonucleoprotein complex (RNP). They have emerged as direct mammalian target of rapamycin (mTOR) substrates that coordinate nutrient stimulation and RNA life cycle control. IMP2 is a human type 2 diabetes (T2D) gene associated with impaired insulin secretion. Recently, using murine models, the substantial progress in understanding disease mechanisms has highlighted the significance of IMP2 in metabolism. This new knowledge may have the potential for therapeutic benefit.
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Affiliation(s)
- Ning Dai
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA.
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35
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Ling C. Epigenetic regulation of insulin action and secretion - role in the pathogenesis of type 2 diabetes. J Intern Med 2020; 288:158-167. [PMID: 32363639 DOI: 10.1111/joim.13049] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/17/2020] [Accepted: 01/30/2020] [Indexed: 12/21/2022]
Abstract
The prevalence of type 2 diabetes (T2D) is rapidly increasing worldwide. Obesity, physical inactivity and ageing increase the risk of T2D. Epigenetic modifications can change due to environmental exposures and may thereby predispose to disease. This review aims at summarizing recent advances in epigenetics related to T2D, with a special focus on impaired insulin action and secretion in humans. There will be an emphasis on analyses in human tissues; both from T2D case-control cohorts and intervention studies. Current data support an important role for epigenetics in the pathogenesis of T2D. Numerous studies have found differential DNA methylation and gene expression in skeletal muscle, adipose tissue, the liver and pancreatic islets from subjects with T2D compared with nondiabetic controls. For example, PDX1 has increased DNA methylation and decreased expression in pancreatic islets from patients with T2D compared with nondiabetic controls. Nongenetic risk factors for T2D such as ageing, unhealthy diets and physical activity do also impact the epigenome in human tissues. Interestingly, physical activity altered DNA methylation of candidate genes for T2D such as THADA in muscle and FTO, KCNQ1 and TCF7L2 in adipose tissue. There is also a strong interaction between genetic and epigenetic factors that together seem to affect T2D. mQTL studies in human adipose tissue and pancreatic islets showed that SNPs associated with DNA methylation levels in numerous sites. Several of these SNPs are also associated with T2D. Recent data also support that DNA methylation of some sites in blood may be developed into biomarkers that predict T2D since methylation of, for example TXNIP, ABCG1 and SREBF1 associated with future T2D. Future studies should use this information for development of new therapies and biomarkers and thereby improve prediction, prevention and treatment of T2D and its complications.
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Affiliation(s)
- C Ling
- From the, Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
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36
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Kamies R, Martinez-Jimenez CP. Advances of single-cell genomics and epigenomics in human disease: where are we now? Mamm Genome 2020; 31:170-180. [PMID: 32270277 PMCID: PMC7368869 DOI: 10.1007/s00335-020-09834-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/28/2020] [Indexed: 02/07/2023]
Abstract
Cellular heterogeneity is revolutionizing the way to study, monitor and dissect complex diseases. This has been possible with the technological and computational advances associated to single-cell genomics and epigenomics. Deeper understanding of cell-to-cell variation and its impact on tissue function will open new avenues for early disease detection, accurate diagnosis and personalized treatments, all together leading to the next generation of health care. This review focuses on the recent discoveries that single-cell genomics and epigenomics have facilitated in the context of human health. It highlights the potential of single-cell omics to further advance the development of personalized treatments and precision medicine in cancer, diabetes and chronic age-related diseases. The promise of single-cell technologies to generate new insights about the differences in function between individual cells is just emerging, and it is paving the way for identifying biomarkers and novel therapeutic targets to tackle age, complex diseases and understand the effect of life style interventions and environmental factors.
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Affiliation(s)
- Rizqah Kamies
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, 85764 Neuherberg, Germany
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37
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de Toledo M, Lopez-Mejia IC, Cavelier P, Pratlong M, Barrachina C, Gromada X, Annicotte JS, Tazi J, Chavey C. Lamin C Counteracts Glucose Intolerance in Aging, Obesity, and Diabetes Through β-Cell Adaptation. Diabetes 2020; 69:647-660. [PMID: 32005707 DOI: 10.2337/db19-0377] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 01/27/2020] [Indexed: 11/13/2022]
Abstract
Aging-dependent changes in tissue function are associated with the development of metabolic diseases. However, the molecular connections linking aging, obesity, and diabetes remain unclear. Lamin A, lamin C, and progerin, products of the Lmna gene, have antagonistic functions on energy metabolism and life span. Lamin C, albeit promoting obesity, increases life span, suggesting that this isoform is crucial for maintaining healthy conditions under metabolic stresses. Because β-cell loss during obesity or aging leads to diabetes, we investigated the contribution of lamin C to β-cell function in physiopathological conditions. We demonstrate that aged lamin C only-expressing mice (Lmna LCS/LCS ) become obese but remain glucose tolerant due to adaptive mechanisms including increased β-cell mass and insulin secretion. Triggering diabetes in young mice revealed that Lmna LCS/LCS animals normalize their fasting glycemia by both increasing insulin secretion and regenerating β-cells. Genome-wide analyses combined to functional analyses revealed an increase of mitochondrial biogenesis and global translational rate in Lmna LCS/LCS islets, two major processes involved in insulin secretion. Altogether, our results demonstrate for the first time that the sole expression of lamin C protects from glucose intolerance through a β-cell-adaptive transcriptional program during metabolic stresses, highlighting Lmna gene processing as a new therapeutic target for diabetes treatment.
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Affiliation(s)
- Marion de Toledo
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | | | - Patricia Cavelier
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Marine Pratlong
- Montpellier GenomiX, Biocampus Montpellier, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Célia Barrachina
- Montpellier GenomiX, Biocampus Montpellier, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Xavier Gromada
- Université Lille, CNRS, CHU Lille, Institut Pasteur de Lille, UMR 8199, European Genomic Institute for Diabetes, Lille, France
| | - Jean-Sébastien Annicotte
- Université Lille, CNRS, CHU Lille, Institut Pasteur de Lille, UMR 8199, European Genomic Institute for Diabetes, Lille, France
| | - Jamal Tazi
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Carine Chavey
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
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Abstract
PURPOSE OF REVIEW Common genetic variants that associate with type 2 diabetes risk are markedly enriched in pancreatic islet transcriptional enhancers. This review discusses current advances in the annotation of islet enhancer variants and their target genes. RECENT FINDINGS Recent methodological advances now allow genetic and functional mapping of diabetes causal variants at unprecedented resolution. Mapping of enhancer-promoter interactions in human islets has provided a unique appreciation of the complexity of islet gene regulatory processes and enabled direct association of noncoding diabetes risk variants to their target genes. The recently improved human islet enhancer annotations constitute a framework for the interpretation of diabetes genetic signals in the context of pancreatic islet gene regulation. In the future, integration of existing and yet to come regulatory maps with genetic fine-mapping efforts and in-depth functional characterization will foster the discovery of novel diabetes molecular risk mechanisms.
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Affiliation(s)
- Inês Cebola
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, ICTEM 5th floor, Du Cane Road, London, W12 0NN, UK.
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39
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Jacobson DA, Shyng SL. Ion Channels of the Islets in Type 2 Diabetes. J Mol Biol 2019; 432:1326-1346. [PMID: 31473158 DOI: 10.1016/j.jmb.2019.08.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 02/06/2023]
Abstract
Ca2+ is an essential signal for pancreatic β-cell function. Ca2+ plays critical roles in numerous β-cell pathways such as insulin secretion, transcription, metabolism, endoplasmic reticulum function, and the stress response. Therefore, β-cell Ca2+ handling is tightly controlled. At the plasma membrane, Ca2+ entry primarily occurs through voltage-dependent Ca2+ channels. Voltage-dependent Ca2+ channel activity is dependent on orchestrated fluctuations in the plasma membrane potential or voltage, which are mediated via the activity of many ion channels. During the pathogenesis of type 2 diabetes the β-cell is exposed to stressful conditions, which result in alterations of Ca2+ handling. Some of the changes in β-cell Ca2+ handling that occur under stress result from perturbations in ion channel activity, expression or localization. Defective Ca2+ signaling in the diabetic β-cell alters function, limits insulin secretion and exacerbates hyperglycemia. In this review, we focus on the β-cell ion channels that control Ca2+ handling and how they impact β-cell dysfunction in type 2 diabetes.
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Affiliation(s)
- David A Jacobson
- Department of Molecular Physiology and Biophysics, Vanderbilt University, 7415 MRB4 (Langford), 2213 Garland Avenue, Nashville, TN 37232, USA.
| | - Show-Ling Shyng
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, L224, MRB 624, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.
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