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Malhi NK, Luo Y, Tang X, Chadha RS, Tapia A, Liu X, Chen M, Yuan D, Qi M, Wei L, Cooke JP, Natarajan R, Southerland KW, Chen ZB. Mapping Endothelial-Macrophage Interactions in Diabetic Vasculature: Role of TREM2 in Vascular Inflammation and Ischemic Response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594235. [PMID: 38798611 PMCID: PMC11118321 DOI: 10.1101/2024.05.14.594235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Vasculopathies occur 15 years earlier in individuals with diabetes mellitus (DM) as compared to those without, but the underlying mechanisms driving diabetic vasculopathy remain incompletely understood. Endothelial cells (ECs) and macrophages (MΦ) are critical players in vascular wall and their crosstalk is crucial in diabetic vasculopathy. In diabetes, EC activation enables monocyte recruitment, which transmigrate into the intima and differentiate into macrophages (MΦ). Beyond this established model of diapedesis, EC-MΦ interplay is highly intricate and heterogenous. To capture these highly context dependent EC-MΦ interactions, we leveraged single-cell (sc)RNA-seq in conjunction with spatial transcriptome (ST)-seq profiling to analyze human mesenteric arteries from non-diabetic (ND) and type 2 diabetic (T2D) donors. We provide in this study a transcriptomic map encompassing major arterial vascular cells, e.g., EC, mononuclear phagocyte (MP), and T cells, and their interactions associated with human T2D. Furthermore, we identified Triggering Receptor Expressed on Myeloid Cells 2 ( TREM2) as a top T2D-induced gene in MP, with concomitant increase of TREM2 ligands in ECs. TREM2 induction was confirmed in mouse models of T2D and monocyte/MΦ subjected to DM-mimicking stimuli. Perturbing TREM2 with either an antibody or silencing RNA in MPs led to decreased pro-inflammatory responses in MPs and ECs and increased EC migration in vitro . In a mouse model of diabetes, TREM2 expression and its interaction with ECs are increased in the ischemic, as compared to non-ischemic muscles. Importantly, neutralization of TREM2 using a neutralizing antibody enhanced ischemic recovery and flow reperfusion in the diabetic mice, suggesting a role of TREM2 in promoting diabetic PAD. Finally, we verified that both TREM2 expression and the TREM2-EC-interaction are increased in human patients with DM-PAD. Collectively, our study presents the first atlas of human diabetic vessels with a focus on EC-MP interactions. Exemplified by TREM2, our study provides valuable insights into EC-MΦ interactions, key processes contributing to diabetic vasculopathies and the potential of targeting these interactions for therapeutic development.
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Laver TW, Wakeling MN, Caswell RC, Bunce B, Yau D, Männistö JME, Houghton JAL, Hopkins JJ, Weedon MN, Saraff V, Kershaw M, Honey EM, Murphy N, Giri D, Nath S, Tangari Saredo A, Banerjee I, Hussain K, Owens NDL, Flanagan SE. Chromosome 20p11.2 deletions cause congenital hyperinsulinism via the loss of FOXA2 or its regulatory elements. Eur J Hum Genet 2024:10.1038/s41431-024-01593-z. [PMID: 38605124 DOI: 10.1038/s41431-024-01593-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 02/20/2024] [Accepted: 03/11/2024] [Indexed: 04/13/2024] Open
Abstract
Persistent congenital hyperinsulinism (HI) is a rare genetically heterogeneous condition characterised by dysregulated insulin secretion leading to life-threatening hypoglycaemia. For up to 50% of affected individuals screening of the known HI genes does not identify a disease-causing variant. Large deletions have previously been used to identify novel regulatory regions causing HI. Here, we used genome sequencing to search for novel large (>1 Mb) deletions in 180 probands with HI of unknown cause and replicated our findings in a large cohort of 883 genetically unsolved individuals with HI using off-target copy number variant calling from targeted gene panels. We identified overlapping heterozygous deletions in five individuals (range 3-8 Mb) spanning chromosome 20p11.2. The pancreatic beta-cell transcription factor gene, FOXA2, a known cause of HI was deleted in two of the five individuals. In the remaining three, we found a minimal deleted region of 2.4 Mb adjacent to FOXA2 that encompasses multiple non-coding regulatory elements that are in conformational contact with FOXA2. Our data suggests that the deletions in these three children may cause disease through the dysregulation of FOXA2 expression. These findings provide new insights into the regulation of FOXA2 in the beta-cell and confirm an aetiological role for chromosome 20p11.2 deletions in syndromic HI.
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Affiliation(s)
- Thomas W Laver
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK
| | - Matthew N Wakeling
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK
| | - Richard C Caswell
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK
| | - Benjamin Bunce
- The Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Daphne Yau
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK
- Department of Paediatric Endocrinology, Royal Manchester Children's Hospital, Manchester, UK
| | - Jonna M E Männistö
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK
- Department of Health Sciences, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Jayne A L Houghton
- The Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Jasmin J Hopkins
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK
| | - Michael N Weedon
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK
| | - Vrinda Saraff
- Department of Paediatric Endocrinology and Diabetes, Birmingham Women's and Children's Hospital, Birmingham, UK
| | - Melanie Kershaw
- Department of Paediatric Endocrinology and Diabetes, Birmingham Women's and Children's Hospital, Birmingham, UK
| | - Engela M Honey
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Nuala Murphy
- Department of Paediatric Endocrinology, Children's University Hospital, Dublin, Ireland
| | - Dinesh Giri
- Department of Paediatric Endocrinology, Bristol Royal Hospital for Children, Bristol, UK
| | | | | | - Indraneel Banerjee
- Department of Paediatric Endocrinology, Royal Manchester Children's Hospital, Manchester, UK
| | - Khalid Hussain
- Department of Paediatrics, Division of Endocrinology, Sidra Medicine, Doha, Qatar
| | - Nick D L Owens
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK
| | - Sarah E Flanagan
- Department of Clinical and Biomedical Science, University of Exeter Medical School, Exeter, UK.
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Hill TG, Hill DJ. The Importance of Intra-Islet Communication in the Function and Plasticity of the Islets of Langerhans during Health and Diabetes. Int J Mol Sci 2024; 25:4070. [PMID: 38612880 PMCID: PMC11012451 DOI: 10.3390/ijms25074070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Islets of Langerhans are anatomically dispersed within the pancreas and exhibit regulatory coordination between islets in response to nutritional and inflammatory stimuli. However, within individual islets, there is also multi-faceted coordination of function between individual beta-cells, and between beta-cells and other endocrine and vascular cell types. This is mediated partly through circulatory feedback of the major secreted hormones, insulin and glucagon, but also by autocrine and paracrine actions within the islet by a range of other secreted products, including somatostatin, urocortin 3, serotonin, glucagon-like peptide-1, acetylcholine, and ghrelin. Their availability can be modulated within the islet by pericyte-mediated regulation of microvascular blood flow. Within the islet, both endocrine progenitor cells and the ability of endocrine cells to trans-differentiate between phenotypes can alter endocrine cell mass to adapt to changed metabolic circumstances, regulated by the within-islet trophic environment. Optimal islet function is precariously balanced due to the high metabolic rate required by beta-cells to synthesize and secrete insulin, and they are susceptible to oxidative and endoplasmic reticular stress in the face of high metabolic demand. Resulting changes in paracrine dynamics within the islets can contribute to the emergence of Types 1, 2 and gestational diabetes.
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Affiliation(s)
- Thomas G. Hill
- Oxford Centre for Diabetes, Endocrinology, and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - David J. Hill
- Lawson Health Research Institute, St. Joseph’s Health Care, London, ON N6A 4V2, Canada;
- Departments of Medicine, Physiology and Pharmacology, Western University, London, ON N6A 3K7, Canada
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Fang X, Zhang Y, Miao R, Zhang Y, Yin R, Guan H, Huang X, Tian J. Single-cell sequencing: A promising approach for uncovering the characteristic of pancreatic islet cells in type 2 diabetes. Biomed Pharmacother 2024; 173:116292. [PMID: 38394848 DOI: 10.1016/j.biopha.2024.116292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/03/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024] Open
Abstract
Single-cell sequencing is a novel and rapidly advancing high-throughput technique that can be used to investigating genomics, transcriptomics, and epigenetics at a single-cell level. Currently, single-cell sequencing can not only be used to draw the pancreatic islet cells map and uncover the characteristics of cellular heterogeneity in type 2 diabetes, but can also be used to label and purify functional beta cells in pancreatic stem cells, improving stem cells and islet organoids therapies. In addition, this technology helps to analyze islet cell dedifferentiation and can be applied to the treatment of type 2 diabetes. In this review, we summarize the development and process of single-cell sequencing, describe the potential applications of single-cell sequencing in the field of type 2 diabetes, and discuss the prospects and limitations of single-cell sequencing to provide a new direction for exploring the pathogenesis of type 2 diabetes and finding therapeutic targets.
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Affiliation(s)
- Xinyi Fang
- Institute of Metabolic Diseases, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, China; Graduate College, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Yanjiao Zhang
- Institute of Metabolic Diseases, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, China
| | - Runyu Miao
- Institute of Metabolic Diseases, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, China; Graduate College, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Yuxin Zhang
- Institute of Metabolic Diseases, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, China
| | - Ruiyang Yin
- Institute of Metabolic Diseases, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, China
| | - Huifang Guan
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Jilin 130117, China
| | - Xinyue Huang
- First Clinical Medical College, Changzhi Medical College, Shanxi 046013, China
| | - Jiaxing Tian
- Institute of Metabolic Diseases, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, China.
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Lu J, Zhao RX, Xiong FR, Zhu JJ, Shi TT, Zhang YC, Peng GX, Yang JK. All-potassium channel CRISPR screening reveals a lysine-specific pathway of insulin secretion. Mol Metab 2024; 80:101885. [PMID: 38246588 PMCID: PMC10847698 DOI: 10.1016/j.molmet.2024.101885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/04/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
OBJECTIVE Genome-scale CRISPR-Cas9 knockout coupled with single-cell RNA sequencing (scRNA-seq) has been used to identify function-related genes. However, this method may knock out too many genes, leading to low efficiency in finding genes of interest. Insulin secretion is controlled by several electrophysiological events, including fluxes of KATP depolarization and K+ repolarization. It is well known that glucose stimulates insulin secretion from pancreatic β-cells, mainly via the KATP depolarization channel, but whether other nutrients directly regulate the repolarization K+ channel to promote insulin secretion is unknown. METHODS We used a system involving CRISPR-Cas9-mediated knockout of all 83 K+ channels and scRNA-seq in a pancreatic β cell line to identify genes associated with insulin secretion. RESULTS The expression levels of insulin genes were significantly increased after all-K+ channel knockout. Furthermore, Kcnb1 and Kcnh6 were the two most important repolarization K+ channels for the increase in high-glucose-dependent insulin secretion that occurred upon application of specific inhibitors of the channels. Kcnh6 currents, but not Kcnb1 currents, were reduced by one of the amino acids, lysine, in both transfected cells, primary cells and mice with β-cell-specific deletion of Kcnh6. CONCLUSIONS Our function-related CRISPR screen with scRNA-seq identifies Kcnh6 as a lysine-specific channel.
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Affiliation(s)
- Jing Lu
- Department of Endocrinology, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China; Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Diabetes Research and Care, Beijing 100730, China
| | - Ru-Xuan Zhao
- Department of Endocrinology, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China; Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Diabetes Research and Care, Beijing 100730, China
| | - Feng-Ran Xiong
- Department of Endocrinology, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China; Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Diabetes Research and Care, Beijing 100730, China
| | - Juan-Juan Zhu
- Department of Endocrinology, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China; Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Diabetes Research and Care, Beijing 100730, China
| | - Ting-Ting Shi
- Department of Endocrinology, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China; Beijing Key Laboratory of Diabetes Research and Care, Beijing 100730, China
| | - Ying-Chao Zhang
- Department of Endocrinology, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China; Beijing Key Laboratory of Diabetes Research and Care, Beijing 100730, China
| | - Gong-Xin Peng
- Center for Bioinformatics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100740, China
| | - Jin-Kui Yang
- Department of Endocrinology, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China; Laboratory for Clinical Medicine, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Diabetes Research and Care, Beijing 100730, China.
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Schmidt MD, Ishahak M, Augsornworawat P, Millman JR. Comparative and integrative single cell analysis reveals new insights into the transcriptional immaturity of stem cell-derived β cells. BMC Genomics 2024; 25:105. [PMID: 38267908 PMCID: PMC10807170 DOI: 10.1186/s12864-024-10013-x] [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: 11/30/2023] [Accepted: 01/14/2024] [Indexed: 01/26/2024] Open
Abstract
Diabetes cell replacement therapy has the potential to be transformed by human pluripotent stem cell-derived β cells (SC-β cells). However, the precise identity of SC-β cells in relationship to primary fetal and adult β-cells remains unclear. Here, we used single-cell sequencing datasets to characterize the transcriptional identity of islets from in vitro differentiation, fetal islets, and adult islets. Our analysis revealed that SC-β cells share a core β-cell transcriptional identity with human adult and fetal β-cells, however SC-β cells possess a unique transcriptional profile characterized by the persistent expression and activation of progenitor and neural-biased gene networks. These networks are present in SC-β cells, irrespective of the derivation protocol used. Notably, fetal β-cells also exhibit this neural signature at the transcriptional level. Our findings offer insights into the transcriptional identity of SC-β cells and underscore the need for further investigation of the role of neural transcriptional networks in their development.
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Affiliation(s)
- Mason D Schmidt
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
| | - Matthew Ishahak
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
| | - Punn Augsornworawat
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO, 63130, USA
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Jeffrey R Millman
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, 660 South Euclid Avenue, St. Louis, MO, 63110, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO, 63130, USA.
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Roy G, Syed R, Lazaro O, Robertson S, McCabe SD, Rodriguez D, Mawla AM, Johnson TS, Kalwat MA. Identification of type 2 diabetes- and obesity-associated human β-cells using deep transfer learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576260. [PMID: 38328172 PMCID: PMC10849510 DOI: 10.1101/2024.01.18.576260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Diabetes affects >10% of adults worldwide and is caused by impaired production or response to insulin, resulting in chronic hyperglycemia. Pancreatic islet β-cells are the sole source of endogenous insulin and our understanding of β-cell dysfunction and death in type 2 diabetes (T2D) is incomplete. Single-cell RNA-seq data supports heterogeneity as an important factor in β-cell function and survival. However, it is difficult to identify which β-cell phenotypes are critical for T2D etiology and progression. Our goal was to prioritize specific disease-related β-cell subpopulations to better understand T2D pathogenesis and identify relevant genes for targeted therapeutics. To address this, we applied a deep transfer learning tool, DEGAS, which maps disease associations onto single-cell RNA-seq data from bulk expression data. Independent runs of DEGAS using T2D or obesity status identified distinct β-cell subpopulations. A singular cluster of T2D-associated β-cells was identified; however, β-cells with high obese-DEGAS scores contained two subpopulations derived largely from either non-diabetic or T2D donors. The obesity-associated non-diabetic cells were enriched for translation and unfolded protein response genes compared to T2D cells. We selected DLK1 for validation by immunostaining in human pancreas sections from healthy and T2D donors. DLK1 was heterogeneously expressed among β-cells and appeared depleted from T2D islets. In conclusion, DEGAS has the potential to advance our holistic understanding of the β-cell transcriptomic phenotypes, including features that distinguish β-cells in obese non-diabetic or lean T2D states. Future work will expand this approach to additional human islet omics datasets to reveal the complex multicellular interactions driving T2D.
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8
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Sturgill D, Wang L, Arda HE. PancrESS - a meta-analysis resource for understanding cell-type specific expression in the human pancreas. BMC Genomics 2024; 25:76. [PMID: 38238687 PMCID: PMC10797729 DOI: 10.1186/s12864-024-09964-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 01/03/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND The human pancreas is composed of specialized cell types producing hormones and enzymes critical to human health. These specialized functions are the result of cell type-specific transcriptional programs which manifest in cell-specific gene expression. Understanding these programs is essential to developing therapies for pancreatic disorders. Transcription in the human pancreas has been widely studied by single-cell RNA technologies, however the diversity of protocols and analysis methods hinders their interpretability in the aggregate. RESULTS In this work, we perform a meta-analysis of pancreatic single-cell RNA sequencing data. We present a database for reference transcriptome abundances and cell-type specificity metrics. This database facilitates the identification and definition of marker genes within the pancreas. Additionally, we introduce a versatile tool which is freely available as an R package, and should permit integration into existing workflows. Our tool accepts count data files generated by widely-used single-cell gene expression platforms in their original format, eliminating an additional pre-formatting step. Although we designed it to calculate expression specificity of pancreas cell types, our tool is agnostic to the biological source of count data, extending its applicability to other biological systems. CONCLUSIONS Our findings enhance the current understanding of expression specificity within the pancreas, surpassing previous work in terms of scope and detail. Furthermore, our database and tool enable researchers to perform similar calculations in diverse biological systems, expanding the applicability of marker gene identification and facilitating comparative analyses.
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Affiliation(s)
- David Sturgill
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Li Wang
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - H Efsun Arda
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
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Jeuken GS, Käll L. Pathway analysis through mutual information. Bioinformatics 2024; 40:btad776. [PMID: 38195928 PMCID: PMC10783954 DOI: 10.1093/bioinformatics/btad776] [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: 03/14/2023] [Revised: 12/09/2023] [Accepted: 01/08/2024] [Indexed: 01/11/2024] Open
Abstract
MOTIVATION In pathway analysis, we aim to establish a connection between the activity of a particular biological pathway and a difference in phenotype. There are many available methods to perform pathway analysis, many of them rely on an upstream differential expression analysis, and many model the relations between the abundances of the analytes in a pathway as linear relationships. RESULTS Here, we propose a new method for pathway analysis, MIPath, that relies on information theoretical principles and, therefore, does not model the association between pathway activity and phenotype, resulting in relatively few assumptions. For this, we construct a graph of the data points for each pathway using a nearest-neighbor approach and score the association between the structure of this graph and the phenotype of these same samples using Mutual Information while adjusting for the effects of random chance in each score. The initial nearest neighbor approach evades individual gene-level comparisons, hence making the method scalable and less vulnerable to missing values. These properties make our method particularly useful for single-cell data. We benchmarked our method on several single-cell datasets, comparing it to established and new methods, and found that it produces robust, reproducible, and meaningful scores. AVAILABILITY AND IMPLEMENTATION Source code is available at https://github.com/statisticalbiotechnology/mipath, or through Python Package Index as "mipathway."
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Affiliation(s)
- Gustavo S Jeuken
- Science for Life Laboratory, KTH – Royal Institute of Technology, Stockholm 171 65, Sweden
- Computer Science Department, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, The Netherlands
| | - Lukas Käll
- Science for Life Laboratory, KTH – Royal Institute of Technology, Stockholm 171 65, Sweden
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Sue N, Thai LM, Saito A, Boyer CK, Fordham AM, Yan C, Davenport A, Tao J, Bensellam M, Cantley J, Shi YC, Stephens SB, Imaizumi K, Biden TJ. Independent activation of CREB3L2 by glucose fills a regulatory gap in mouse β-cells by co-ordinating insulin biosynthesis with secretory granule formation. Mol Metab 2024; 79:101845. [PMID: 38013154 PMCID: PMC10755490 DOI: 10.1016/j.molmet.2023.101845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 11/29/2023] Open
Abstract
OBJECTIVE Although individual steps have been characterized, there is little understanding of the overall process whereby glucose co-ordinates the biosynthesis of insulin with its export out of the endoplasmic reticulum (ER) and incorporation into insulin secretory granules (ISGs). Here we investigate a role for the transcription factor CREB3L2 in this context. METHODS MIN6 cells and mouse islets were analysed by immunoblotting after treatment with glucose, fatty acids, thapsigargin and various inhibitors. Knockdown of CREB3L2 was achieved using si or sh constructs by transfection, or viral delivery. In vivo metabolic phenotyping was conducted after deletion of CREB3L2 in β-cells of adult mice using Ins1-CreER+. Islets were isolated for RNAseq and assays of glucose-stimulated insulin secretion (GSIS). Trafficking was monitored in islet monolayers using a GFP-tagged proinsulin construct that allows for synchronised release from the ER. RESULTS With a Km ≈3.5 mM, glucose rapidly (T1/2 0.9 h) increased full length (FL) CREB3L2 followed by a slower rise (T1/2 2.5 h) in its transcriptionally-active cleavage product, P60 CREB3L2. Glucose stimulation repressed the ER stress marker, CHOP, and this was partially reverted by knockdown of CREB3L2. Activation of CREB3L2 by glucose was not due to ER stress, however, but a combination of O-GlcNAcylation, which impaired proteasomal degradation of FL-CREB3L2, and mTORC1 stimulation, which enhanced its conversion to P60. cAMP generation also activated CREB3L2, but independently of glucose. Deletion of CREB3L2 inhibited GSIS ex vivo and, following a high-fat diet (HFD), impaired glucose tolerance and insulin secretion in vivo. RNAseq revealed that CREB3L2 regulated genes controlling trafficking to-and-from the Golgi, as well as a broader cohort associated with β-cell compensation during a HFD. Although post-Golgi trafficking appeared intact, knockdown of CREB3L2 impaired the generation of both nascent ISGs and proinsulin condensates in the Golgi, implying a defect in ER export of proinsulin and/or its processing in the Golgi. CONCLUSION The stimulation of CREB3L2 by glucose defines a novel, rapid and direct mechanism for co-ordinating the synthesis, packaging and storage of insulin, thereby minimizing ER overload and optimizing β-cell function under conditions of high secretory demand. Upregulation of CREB3L2 also potentially contributes to the benefits of GLP1 agonism and might in itself constitute a novel means of treating β-cell failure.
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Affiliation(s)
- Nancy Sue
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia
| | - Le May Thai
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia
| | - Atsushi Saito
- Department of Biochemistry, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Cierra K Boyer
- Fraternal Order of Eagles Diabetes Research Center, Department of Internal Medicine, University of Iowa, Iowa City, IA 52246, USA
| | - Ashleigh M Fordham
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia
| | - Chenxu Yan
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia
| | - Aimee Davenport
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia
| | - Jiang Tao
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia
| | - Mohammed Bensellam
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia
| | - James Cantley
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia
| | - Yan-Chuan Shi
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, The University of New South Wales, Sydney, Australia
| | - Samuel B Stephens
- Fraternal Order of Eagles Diabetes Research Center, Department of Internal Medicine, University of Iowa, Iowa City, IA 52246, USA
| | - Kazunori Imaizumi
- Department of Biochemistry, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Trevor J Biden
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, The University of New South Wales, Sydney, Australia.
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11
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Fan Z, Sun J, Thorpe H, Lee S, Kim S, Park HJ. Deep neural network learning biological condition information refines gene-expression-based cell subtypes. Brief Bioinform 2023; 25:bbad512. [PMID: 38233089 PMCID: PMC10794113 DOI: 10.1093/bib/bbad512] [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: 07/24/2023] [Revised: 11/18/2023] [Accepted: 12/05/2023] [Indexed: 01/19/2024] Open
Abstract
With the recent advent of single-cell level biological understanding, a growing interest is in identifying cell states or subtypes that are homogeneous in terms of gene expression and are also enriched in certain biological conditions, including disease samples versus normal samples (condition-specific cell subtype). Despite the importance of identifying condition-specific cell subtypes, existing methods have the following limitations: since they train models separately between gene expression and the biological condition information, (1) they do not consider potential interactions between them, and (2) the weights from both types of information are not properly controlled. Also, (3) they do not consider non-linear relationships in the gene expression and the biological condition. To address the limitations and accurately identify such condition-specific cell subtypes, we develop scDeepJointClust, the first method that jointly trains both types of information via a deep neural network. scDeepJointClust incorporates results from the power of state-of-the-art gene-expression-based clustering methods as an input, incorporating their sophistication and accuracy. We evaluated scDeepJointClust on both simulation data in diverse scenarios and biological data of different diseases (melanoma and non-small-cell lung cancer) and showed that scDeepJointClust outperforms existing methods in terms of sensitivity and specificity. scDeepJointClust exhibits significant promise in advancing our understanding of cellular states and their implications in complex biological systems.
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Affiliation(s)
- Zhenjiang Fan
- Department of Computer Science, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| | - Jie Sun
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| | - Henry Thorpe
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| | - Stephen Lee
- Department of Computer Science, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| | - Soyeon Kim
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hyun Jung Park
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
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12
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Doke M, Álvarez-Cubela S, Klein D, Altilio I, Schulz J, Mateus Gonçalves L, Almaça J, Fraker CA, Pugliese A, Ricordi C, Qadir MMF, Pastori RL, Domínguez-Bendala J. Dynamic scRNA-seq of live human pancreatic slices reveals functional endocrine cell neogenesis through an intermediate ducto-acinar stage. Cell Metab 2023; 35:1944-1960.e7. [PMID: 37898119 DOI: 10.1016/j.cmet.2023.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 08/23/2023] [Accepted: 10/03/2023] [Indexed: 10/30/2023]
Abstract
Human pancreatic plasticity is implied from multiple single-cell RNA sequencing (scRNA-seq) studies. However, these have been invariably based on static datasets from which fate trajectories can only be inferred using pseudotemporal estimations. Furthermore, the analysis of isolated islets has resulted in a drastic underrepresentation of other cell types, hindering our ability to interrogate exocrine-endocrine interactions. The long-term culture of human pancreatic slices (HPSs) has presented the field with an opportunity to dynamically track tissue plasticity at the single-cell level. Combining datasets from same-donor HPSs at different time points, with or without a known regenerative stimulus (BMP signaling), led to integrated single-cell datasets storing true temporal or treatment-dependent information. This integration revealed population shifts consistent with ductal progenitor activation, blurring of ductal/acinar boundaries, formation of ducto-acinar-endocrine differentiation axes, and detection of transitional insulin-producing cells. This study provides the first longitudinal scRNA-seq analysis of whole human pancreatic tissue, confirming its plasticity in a dynamic fashion.
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Affiliation(s)
- Mayur Doke
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Silvia Álvarez-Cubela
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Dagmar Klein
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Isabella Altilio
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Joseph Schulz
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Luciana Mateus Gonçalves
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Joana Almaça
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Christopher A Fraker
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Alberto Pugliese
- Arthur Riggs Diabetes & Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Camillo Ricordi
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Mirza M F Qadir
- Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Ricardo L Pastori
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
| | - Juan Domínguez-Bendala
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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13
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Weng C, Gu A, Zhang S, Lu L, Ke L, Gao P, Liu X, Wang Y, Hu P, Plummer D, MacDonald E, Zhang S, Xi J, Lai S, Leskov K, Yuan K, Jin F, Li Y. Single cell multiomic analysis reveals diabetes-associated β-cell heterogeneity driven by HNF1A. Nat Commun 2023; 14:5400. [PMID: 37669939 PMCID: PMC10480445 DOI: 10.1038/s41467-023-41228-3] [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: 01/31/2023] [Accepted: 08/29/2023] [Indexed: 09/07/2023] Open
Abstract
Broad heterogeneity in pancreatic β-cell function and morphology has been widely reported. However, determining which components of this cellular heterogeneity serve a diabetes-relevant function remains challenging. Here, we integrate single-cell transcriptome, single-nuclei chromatin accessibility, and cell-type specific 3D genome profiles from human islets and identify Type II Diabetes (T2D)-associated β-cell heterogeneity at both transcriptomic and epigenomic levels. We develop a computational method to explicitly dissect the intra-donor and inter-donor heterogeneity between single β-cells, which reflect distinct mechanisms of T2D pathogenesis. Integrative transcriptomic and epigenomic analysis identifies HNF1A as a principal driver of intra-donor heterogeneity between β-cells from the same donors; HNF1A expression is also reduced in β-cells from T2D donors. Interestingly, HNF1A activity in single β-cells is significantly associated with lower Na+ currents and we nominate a HNF1A target, FXYD2, as the primary mitigator. Our study demonstrates the value of investigating disease-associated single-cell heterogeneity and provides new insights into the pathogenesis of T2D.
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Affiliation(s)
- Chen Weng
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- The Biomedical Sciences Training Program (BSTP), School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Anniya Gu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- Medical Scientist Training Program (MSTP), School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Shanshan Zhang
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- The Biomedical Sciences Training Program (BSTP), School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Leina Lu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Luxin Ke
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- The Biomedical Sciences Training Program (BSTP), School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Peidong Gao
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Xiaoxiao Liu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Yuntong Wang
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Peinan Hu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- The Biomedical Sciences Training Program (BSTP), School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Dylan Plummer
- Department of Computer and Data Sciences, School of Engineering, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Elise MacDonald
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Saixian Zhang
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Jiajia Xi
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Sisi Lai
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- The Biomedical Sciences Training Program (BSTP), School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Konstantin Leskov
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Kyle Yuan
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Fulai Jin
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
- Department of Computer and Data Sciences, School of Engineering, Case Western Reserve University, Cleveland, OH, 44106, USA.
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA.
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
| | - Yan Li
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
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14
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Hrovatin K, Bastidas-Ponce A, Bakhti M, Zappia L, Büttner M, Salinno C, Sterr M, Böttcher A, Migliorini A, Lickert H, Theis FJ. Delineating mouse β-cell identity during lifetime and in diabetes with a single cell atlas. Nat Metab 2023; 5:1615-1637. [PMID: 37697055 PMCID: PMC10513934 DOI: 10.1038/s42255-023-00876-x] [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: 12/21/2022] [Accepted: 07/26/2023] [Indexed: 09/13/2023]
Abstract
Although multiple pancreatic islet single-cell RNA-sequencing (scRNA-seq) datasets have been generated, a consensus on pancreatic cell states in development, homeostasis and diabetes as well as the value of preclinical animal models is missing. Here, we present an scRNA-seq cross-condition mouse islet atlas (MIA), a curated resource for interactive exploration and computational querying. We integrate over 300,000 cells from nine scRNA-seq datasets consisting of 56 samples, varying in age, sex and diabetes models, including an autoimmune type 1 diabetes model (NOD), a glucotoxicity/lipotoxicity type 2 diabetes model (db/db) and a chemical streptozotocin β-cell ablation model. The β-cell landscape of MIA reveals new cell states during disease progression and cross-publication differences between previously suggested marker genes. We show that β-cells in the streptozotocin model transcriptionally correlate with those in human type 2 diabetes and mouse db/db models, but are less similar to human type 1 diabetes and mouse NOD β-cells. We also report pathways that are shared between β-cells in immature, aged and diabetes models. MIA enables a comprehensive analysis of β-cell responses to different stressors, providing a roadmap for the understanding of β-cell plasticity, compensation and demise.
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Affiliation(s)
- Karin Hrovatin
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Aimée Bastidas-Ponce
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Medical Faculty, Technical University of Munich, Munich, Germany
| | - Mostafa Bakhti
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Luke Zappia
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Mathematics, Technical University of Munich, Garching, Germany
| | - Maren Büttner
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Ciro Salinno
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Medical Faculty, Technical University of Munich, Munich, Germany
| | - Michael Sterr
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Anika Böttcher
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Adriana Migliorini
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- McEwen Stem Cell Institute, University Health Network (UHN), Toronto, Ontario, Canada
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany.
- German Center for Diabetes Research (DZD), Neuherberg, Germany.
- Medical Faculty, Technical University of Munich, Munich, Germany.
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.
- Department of Mathematics, Technical University of Munich, Garching, Germany.
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15
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Spears E, Stanley JE, Shou M, Yin L, Li X, Dai C, Bradley A, Sellick K, Poffenberger G, Coate KC, Shrestha S, Jenkins R, Sloop KW, Wilson KT, Attie AD, Keller MP, Chen W, Powers AC, Dean ED. Pancreatic islet α cell function and proliferation requires the arginine transporter SLC7A2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552656. [PMID: 37645716 PMCID: PMC10461917 DOI: 10.1101/2023.08.10.552656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Interrupting glucagon signaling decreases gluconeogenesis and the fractional extraction of amino acids by liver from blood resulting in lower glycemia. The resulting hyperaminoacidemia stimulates α cell proliferation and glucagon secretion via a liver-α cell axis. We hypothesized that α cells detect and respond to circulating amino acids levels via a unique amino acid transporter repertoire. We found that Slc7a2ISLC7A2 is the most highly expressed cationic amino acid transporter in α cells with its expression being three-fold greater in α than β cells in both mouse and human. Employing cell culture, zebrafish, and knockout mouse models, we found that the cationic amino acid arginine and SLC7A2 are required for α cell proliferation in response to interrupted glucagon signaling. Ex vivo and in vivo assessment of islet function in Slc7a2-/- mice showed decreased arginine-stimulated glucagon and insulin secretion. We found that arginine activation of mTOR signaling and induction of the glutamine transporter SLC38A5 was dependent on SLC7A2, showing that both's role in α cell proliferation is dependent on arginine transport and SLC7A2. Finally, we identified single nucleotide polymorphisms in SLC7A2 associated with HbA1c. Together, these data indicate a central role for SLC7A2 in amino acid-stimulated α cell proliferation and islet hormone secretion.
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Affiliation(s)
- Erick Spears
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Department of Biology, Belmont University, Nashville, TN
| | - Jade E. Stanley
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN
| | - Matthew Shou
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Linlin Yin
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN
| | - Xuan Li
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN
| | - Chunhua Dai
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Amber Bradley
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Katelyn Sellick
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Greg Poffenberger
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Katie C. Coate
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Shristi Shrestha
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Regina Jenkins
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Kyle W. Sloop
- Diabetes and Complications, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN
| | - Keith T. Wilson
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN
| | - Alan D. Attie
- Department of Biochemistry, University of Wisconsin, Madison, WI
| | - Mark P. Keller
- Department of Biochemistry, University of Wisconsin, Madison, WI
| | - Wenbiao Chen
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN
| | - Alvin C. Powers
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN
| | - E. Danielle Dean
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN
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16
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Park SY, Ter-Saakyan S, Faraci G, Lee HY. Immune cell identifier and classifier (ImmunIC) for single cell transcriptomic readouts. Sci Rep 2023; 13:12093. [PMID: 37495649 PMCID: PMC10372073 DOI: 10.1038/s41598-023-39282-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 07/22/2023] [Indexed: 07/28/2023] Open
Abstract
Single cell RNA sequencing has a central role in immune profiling, identifying specific immune cells as disease markers and suggesting therapeutic target genes of immune cells. Immune cell-type annotation from single cell transcriptomics is in high demand for dissecting complex immune signatures from multicellular blood and organ samples. However, accurate cell type assignment from single-cell RNA sequencing data alone is complicated by a high level of gene expression heterogeneity. Many computational methods have been developed to respond to this challenge, but immune cell annotation accuracy is not highly desirable. We present ImmunIC, a simple and robust tool for immune cell identification and classification by combining marker genes with a machine learning method. With over two million immune cells and half-million non-immune cells from 66 single cell RNA sequencing studies, ImmunIC shows 98% accuracy in the identification of immune cells. ImmunIC outperforms existing immune cell classifiers, categorizing into ten immune cell types with 92% accuracy. We determine peripheral blood mononuclear cell compositions of severe COVID-19 cases and healthy controls using previously published single cell transcriptomic data, permitting the identification of immune cell-type specific differential pathways. Our publicly available tool can maximize the utility of single cell RNA profiling by functioning as a stand-alone bioinformatic cell sorter, advancing cell-type specific immune profiling for the discovery of disease-specific immune signatures and therapeutic targets.
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Affiliation(s)
- Sung Yong Park
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Sonia Ter-Saakyan
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Gina Faraci
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Ha Youn Lee
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, USA.
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17
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Pettway YD, Saunders DC, Brissova M. The human α cell in health and disease. J Endocrinol 2023; 258:e220298. [PMID: 37114672 PMCID: PMC10428003 DOI: 10.1530/joe-22-0298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/27/2023] [Indexed: 04/29/2023]
Abstract
In commemoration of 100 years since the discovery of glucagon, we review current knowledge about the human α cell. Alpha cells make up 30-40% of human islet endocrine cells and play a major role in regulating whole-body glucose homeostasis, largely through the direct actions of their main secretory product - glucagon - on peripheral organs. Additionally, glucagon and other secretory products of α cells, namely acetylcholine, glutamate, and glucagon-like peptide-1, have been shown to play an indirect role in the modulation of glucose homeostasis through autocrine and paracrine interactions within the islet. Studies of glucagon's role as a counterregulatory hormone have revealed additional important functions of the α cell, including the regulation of multiple aspects of energy metabolism outside that of glucose. At the molecular level, human α cells are defined by the expression of conserved islet-enriched transcription factors and various enriched signature genes, many of which have currently unknown cellular functions. Despite these common threads, notable heterogeneity exists amongst human α cell gene expression and function. Even greater differences are noted at the inter-species level, underscoring the importance of further study of α cell physiology in the human context. Finally, studies on α cell morphology and function in type 1 and type 2 diabetes, as well as other forms of metabolic stress, reveal a key contribution of α cell dysfunction to dysregulated glucose homeostasis in disease pathogenesis, making targeting the α cell an important focus for improving treatment.
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Affiliation(s)
- Yasminye D. Pettway
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232, USA
| | - Diane C. Saunders
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, 37232, USA
| | - Marcela Brissova
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, 37232, USA
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18
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Aoyama S, Nishida Y, Uzawa H, Himuro M, Kanai A, Ueki K, Ito M, Iida H, Tanida I, Miyatsuka T, Fujitani Y, Matsumoto M, Watada H. Monitoring autophagic flux in vivo revealed its physiological response and significance of heterogeneity in pancreatic beta cells. Cell Chem Biol 2023; 30:658-671.e4. [PMID: 36944338 DOI: 10.1016/j.chembiol.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 01/12/2023] [Accepted: 02/28/2023] [Indexed: 03/23/2023]
Abstract
Autophagy plays an essential role in preserving cellular homeostasis in pancreatic beta cells. However, the extent of autophagic flux in pancreatic islets induced in various physiological settings remains unclear. In this study, we generate transgenic mice expressing pHluorin-LC3-mCherry reporter for monitoring systemic autophagic flux by measuring the pHluorin/mCherry ratio, validating them in the starvation and insulin-deficient model. Our findings reveal that autophagic flux in pancreatic islets enhances after starvation, and suppression of the flux after short-term refeeding needs more prolonged re-starvation in islets than in the other insulin-targeted organs. Furthermore, heterogeneity of autophagic flux in pancreatic beta cells manifests under insulin resistance, and intracellular calcium influx by glucose stimulation increases more in high- than low-autophagic flux beta cells, with differential gene expression, including lipoprotein lipase. Our pHluorin-LC3-mCherry mice enable us to reveal biological insight into heterogeneity in autophagic flux in pancreatic beta cells.
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Affiliation(s)
- Shuhei Aoyama
- Department of Metabolism and Endocrinology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Yuya Nishida
- Department of Metabolism and Endocrinology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.
| | - Hirotsugu Uzawa
- Department of Metabolism and Endocrinology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Miwa Himuro
- Department of Metabolism and Endocrinology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Akiko Kanai
- Department of Metabolism and Endocrinology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Kyosei Ueki
- Department of Metabolism and Endocrinology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Minami Ito
- Department of Metabolism and Endocrinology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Hitoshi Iida
- Department of Metabolism and Endocrinology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Isei Tanida
- Department of Cellular and Molecular Neuropathology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Takeshi Miyatsuka
- Department of Endocrinology, Diabetes and Metabolism, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0374, Japan
| | - Yoshio Fujitani
- Laboratory of Developmental Biology and Metabolism, Institute for Molecular and Cellular Regulation, Gunma University, 3-39-15 Showa-machi, Maebashi 371-8512, Japan
| | - Masaki Matsumoto
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, 757 Ichibancho, Asahimachi-dori, Chuo-ku, Niigata City, Niigata 951-8510, Japan
| | - Hirotaka Watada
- Department of Metabolism and Endocrinology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
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19
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Theodoris CV, Xiao L, Chopra A, Chaffin MD, Al Sayed ZR, Hill MC, Mantineo H, Brydon EM, Zeng Z, Liu XS, Ellinor PT. Transfer learning enables predictions in network biology. Nature 2023; 618:616-624. [PMID: 37258680 PMCID: PMC10949956 DOI: 10.1038/s41586-023-06139-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/27/2023] [Indexed: 06/02/2023]
Abstract
Mapping gene networks requires large amounts of transcriptomic data to learn the connections between genes, which impedes discoveries in settings with limited data, including rare diseases and diseases affecting clinically inaccessible tissues. Recently, transfer learning has revolutionized fields such as natural language understanding1,2 and computer vision3 by leveraging deep learning models pretrained on large-scale general datasets that can then be fine-tuned towards a vast array of downstream tasks with limited task-specific data. Here, we developed a context-aware, attention-based deep learning model, Geneformer, pretrained on a large-scale corpus of about 30 million single-cell transcriptomes to enable context-specific predictions in settings with limited data in network biology. During pretraining, Geneformer gained a fundamental understanding of network dynamics, encoding network hierarchy in the attention weights of the model in a completely self-supervised manner. Fine-tuning towards a diverse panel of downstream tasks relevant to chromatin and network dynamics using limited task-specific data demonstrated that Geneformer consistently boosted predictive accuracy. Applied to disease modelling with limited patient data, Geneformer identified candidate therapeutic targets for cardiomyopathy. Overall, Geneformer represents a pretrained deep learning model from which fine-tuning towards a broad range of downstream applications can be pursued to accelerate discovery of key network regulators and candidate therapeutic targets.
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Affiliation(s)
- Christina V Theodoris
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School Genetics Training Program, Boston, USA.
| | - Ling Xiao
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Anant Chopra
- Precision Cardiology Laboratory, Bayer US LLC, Cambridge, MA, USA
| | - Mark D Chaffin
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zeina R Al Sayed
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew C Hill
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Helene Mantineo
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | | | - Zexian Zeng
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.
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20
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Wang G, Chiou J, Zeng C, Miller M, Matta I, Han JY, Kadakia N, Okino ML, Beebe E, Mallick M, Camunas-Soler J, Dos Santos T, Dai XQ, Ellis C, Hang Y, Kim SK, MacDonald PE, Kandeel FR, Preissl S, Gaulton KJ, Sander M. Integrating genetics with single-cell multiomic measurements across disease states identifies mechanisms of beta cell dysfunction in type 2 diabetes. Nat Genet 2023; 55:984-994. [PMID: 37231096 PMCID: PMC10550816 DOI: 10.1038/s41588-023-01397-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 04/12/2023] [Indexed: 05/27/2023]
Abstract
Dysfunctional pancreatic islet beta cells are a hallmark of type 2 diabetes (T2D), but a comprehensive understanding of the underlying mechanisms, including gene dysregulation, is lacking. Here we integrate information from measurements of chromatin accessibility, gene expression and function in single beta cells with genetic association data to nominate disease-causal gene regulatory changes in T2D. Using machine learning on chromatin accessibility data from 34 nondiabetic, pre-T2D and T2D donors, we identify two transcriptionally and functionally distinct beta cell subtypes that undergo an abundance shift during T2D progression. Subtype-defining accessible chromatin is enriched for T2D risk variants, suggesting a causal contribution of subtype identity to T2D. Both beta cell subtypes exhibit activation of a stress-response transcriptional program and functional impairment in T2D, which is probably induced by the T2D-associated metabolic environment. Our findings demonstrate the power of multimodal single-cell measurements combined with machine learning for characterizing mechanisms of complex diseases.
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Affiliation(s)
- Gaowei Wang
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Joshua Chiou
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
- Biomedical Graduate Studies Program, University of California San Diego, La Jolla, CA, USA
| | - Chun Zeng
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Michael Miller
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Ileana Matta
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Jee Yun Han
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Nikita Kadakia
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Mei-Lin Okino
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Elisha Beebe
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Medhavi Mallick
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | | | - Theodore Dos Santos
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Xiao-Qing Dai
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Cara Ellis
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Yan Hang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Departments of Medicine and of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Seung K Kim
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Departments of Medicine and of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Patrick E MacDonald
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Fouad R Kandeel
- Department of Clinical Diabetes, Endocrinology & Metabolism, City of Hope, Duarte, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA.
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Kyle J Gaulton
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Maike Sander
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
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21
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Gong L, Cretella A, Lin Y. Microfluidic systems for particle capture and release: A review. Biosens Bioelectron 2023; 236:115426. [PMID: 37276636 DOI: 10.1016/j.bios.2023.115426] [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: 01/10/2023] [Revised: 05/17/2023] [Accepted: 05/24/2023] [Indexed: 06/07/2023]
Abstract
Microfluidic technology has emerged as a promising tool in various applications, including biosensing, disease diagnosis, and environmental monitoring. One of the notable features of microfluidic devices is their ability to selectively capture and release specific cells, biomolecules, bacteria, and particles. Compared to traditional bulk analysis instruments, microfluidic capture-and-release platforms offer several advantages, such as contactless operation, label-free detection, high accuracy, good sensitivity, and minimal reagent requirements. However, despite significant efforts dedicated to developing innovative capture mechanisms in the past, the release and recovery efficiency of trapped particles have often been overlooked. Many previous studies have focused primarily on particle capture techniques and their efficiency, disregarding the crucial role of successful particle release for subsequent analysis. In reality, the ability to effectively release trapped particles is particularly essential to ensure ongoing, high-throughput analysis. To address this gap, this review aims to highlight the importance of both capture and release mechanisms in microfluidic systems and assess their effectiveness. The methods are classified into two categories: those based on physical principles and those using biochemical approaches. Furthermore, the review offers a comprehensive summary of recent applications of microfluidic platforms specifically designed for particle capture and release. It outlines the designs and performance of these devices, highlighting their advantages and limitations in various target applications and purposes. Finally, the review concludes with discussions on the current challenges faced in the field and presents potential future directions.
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Affiliation(s)
- Liyuan Gong
- Department of Mechanical, Industrial and Systems Engineering, University of Rhode Island, Kingston, RI, 02881, USA
| | - Andrew Cretella
- Department of Mechanical, Industrial and Systems Engineering, University of Rhode Island, Kingston, RI, 02881, USA
| | - Yang Lin
- Department of Mechanical, Industrial and Systems Engineering, University of Rhode Island, Kingston, RI, 02881, USA.
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22
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Wieder N, Fried JC, Kim C, Sidhom EH, Brown MR, Marshall JL, Arevalo C, Dvela-Levitt M, Kost-Alimova M, Sieber J, Gabriel KR, Pacheco J, Clish C, Abbasi HS, Singh S, Rutter JC, Therrien M, Yoon H, Lai ZW, Baublis A, Subramanian R, Devkota R, Small J, Sreekanth V, Han M, Lim D, Carpenter AE, Flannick J, Finucane H, Haigis MC, Claussnitzer M, Sheu E, Stevens B, Wagner BK, Choudhary A, Shaw JL, Pablo JL, Greka A. FALCON systematically interrogates free fatty acid biology and identifies a novel mediator of lipotoxicity. Cell Metab 2023; 35:887-905.e11. [PMID: 37075753 PMCID: PMC10257950 DOI: 10.1016/j.cmet.2023.03.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 02/21/2023] [Accepted: 03/27/2023] [Indexed: 04/21/2023]
Abstract
Cellular exposure to free fatty acids (FFAs) is implicated in the pathogenesis of obesity-associated diseases. However, there are no scalable approaches to comprehensively assess the diverse FFAs circulating in human plasma. Furthermore, assessing how FFA-mediated processes interact with genetic risk for disease remains elusive. Here, we report the design and implementation of fatty acid library for comprehensive ontologies (FALCON), an unbiased, scalable, and multimodal interrogation of 61 structurally diverse FFAs. We identified a subset of lipotoxic monounsaturated fatty acids associated with decreased membrane fluidity. Furthermore, we prioritized genes that reflect the combined effects of harmful FFA exposure and genetic risk for type 2 diabetes (T2D). We found that c-MAF-inducing protein (CMIP) protects cells from FFA exposure by modulating Akt signaling. In sum, FALCON empowers the study of fundamental FFA biology and offers an integrative approach to identify much needed targets for diverse diseases associated with disordered FFA metabolism.
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Affiliation(s)
- Nicolas Wieder
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Department of Neurology with Experimental Neurology and Berlin Institute of Health, Charité, 10117 Berlin, Germany
| | - Juliana Coraor Fried
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Choah Kim
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Eriene-Heidi Sidhom
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Matthew R Brown
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Carlos Arevalo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Moran Dvela-Levitt
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | | | - Jonas Sieber
- Department of Endocrinology, Metabolism and Cardiovascular Systems, University of Fribourg, Fribourg, Switzerland
| | | | - Julian Pacheco
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Shantanu Singh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Justine C Rutter
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA
| | | | - Haejin Yoon
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center for Cancer Research at Harvard, Boston, MA 02115, USA
| | - Zon Weng Lai
- Harvard Chan Advanced Multiomics Platform, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Aaron Baublis
- Harvard Chan Advanced Multiomics Platform, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Renuka Subramanian
- Laboratory for Surgical and Metabolic Research, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ranjan Devkota
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jonnell Small
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vedagopuram Sreekanth
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Myeonghoon Han
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Donghyun Lim
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Jason Flannick
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Hilary Finucane
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Mass General Hospital, Boston, MA 02114, USA
| | - Marcia C Haigis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center for Cancer Research at Harvard, Boston, MA 02115, USA
| | - Melina Claussnitzer
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eric Sheu
- Laboratory for Surgical and Metabolic Research, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Beth Stevens
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Boston Children's Hospital, F.M. Kirby Neurobiology Center, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Bridget K Wagner
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amit Choudhary
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jillian L Shaw
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Anna Greka
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
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23
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Patil AR, Schug J, Naji A, Kaestner KH, Faryabi RB, Vahedi G. Single-cell expression profiling of islets generated by the Human Pancreas Analysis Program. Nat Metab 2023; 5:713-715. [PMID: 37188822 PMCID: PMC10731597 DOI: 10.1038/s42255-023-00806-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Affiliation(s)
- Abhijeet R Patil
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jonathan Schug
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ali Naji
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Klaus H Kaestner
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Robert B Faryabi
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Golnaz Vahedi
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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24
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Chung JY, Ma Y, Zhang D, Bickerton HH, Stokes E, Patel SB, Tse HM, Feduska J, Welner RS, Banerjee RR. Pancreatic islet cell type-specific transcriptomic changes during pregnancy and postpartum. iScience 2023; 26:106439. [PMID: 37020962 PMCID: PMC10068570 DOI: 10.1016/j.isci.2023.106439] [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: 11/29/2022] [Revised: 01/11/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
Pancreatic β-cell mass expands during pregnancy and regresses in the postpartum period in conjunction with dynamic metabolic demands on maternal glucose homeostasis. To understand transcriptional changes driving these adaptations in β-cells and other islet cell types, we performed single-cell RNA sequencing on islets from virgin, late gestation, and early postpartum mice. We identified transcriptional signatures unique to gestation and the postpartum in β-cells, including induction of the AP-1 transcription factor subunits and other genes involved in the immediate-early response (IEGs). In addition, we found pregnancy and postpartum-induced changes differed within each endocrine cell type, and in endothelial cells and antigen-presenting cells within islets. Together, our data reveal insights into cell type-specific transcriptional changes responsible for adaptations by islet cells to pregnancy and their resolution postpartum.
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Affiliation(s)
- Jin-Yong Chung
- Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - Yongjie Ma
- Department of Pharmacology, the University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Dingguo Zhang
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, The University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Hayden H. Bickerton
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, The University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Eric Stokes
- Department of Pharmacology, University of Colorado Denver/Anschutz, Aurora, CO 80045, USA
| | - Sweta B. Patel
- Division of Hematology and Oncology, Department of Medicine, The University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Hubert M. Tse
- Department of Microbiology, the University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Joseph Feduska
- Department of Microbiology, the University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Rob S. Welner
- Division of Hematology and Oncology, Department of Medicine, The University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Ronadip R. Banerjee
- Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
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25
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Rubio-Navarro A, Gómez-Banoy N, Stoll L, Dündar F, Mawla AM, Ma L, Cortada E, Zumbo P, Li A, Reiterer M, Montoya-Oviedo N, Homan EA, Imai N, Gilani A, Liu C, Naji A, Yang B, Chong ACN, Cohen DE, Chen S, Cao J, Pitt GS, Huising MO, Betel D, Lo JC. A beta cell subset with enhanced insulin secretion and glucose metabolism is reduced in type 2 diabetes. Nat Cell Biol 2023; 25:565-578. [PMID: 36928765 PMCID: PMC10449536 DOI: 10.1038/s41556-023-01103-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 02/02/2023] [Indexed: 03/18/2023]
Abstract
The pancreatic islets are composed of discrete hormone-producing cells that orchestrate systemic glucose homeostasis. Here we identify subsets of beta cells using a single-cell transcriptomic approach. One subset of beta cells marked by high CD63 expression is enriched for the expression of mitochondrial metabolism genes and exhibits higher mitochondrial respiration compared with CD63lo beta cells. Human and murine pseudo-islets derived from CD63hi beta cells demonstrate enhanced glucose-stimulated insulin secretion compared with pseudo-islets from CD63lo beta cells. We show that CD63hi beta cells are diminished in mouse models of and in humans with type 2 diabetes. Finally, transplantation of pseudo-islets generated from CD63hi but not CD63lo beta cells into diabetic mice restores glucose homeostasis. These findings suggest that loss of a specific subset of beta cells may lead to diabetes. Strategies to reconstitute or maintain CD63hi beta cells may represent a potential anti-diabetic therapy.
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Affiliation(s)
- Alfonso Rubio-Navarro
- Weill Center for Metabolic Health, Cardiovascular Research Institute, Division of Cardiology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Excellence Research Unit "Modeling Nature" (MNat), CTS-963-Center of Biomedical Research (CIBM), University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), University Hospitals of Granada-University of Granada, Granada, Spain
| | - Nicolás Gómez-Banoy
- Weill Center for Metabolic Health, Cardiovascular Research Institute, Division of Cardiology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lisa Stoll
- Weill Center for Metabolic Health, Cardiovascular Research Institute, Division of Cardiology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Friederike Dündar
- Department of Physiology and Biophysics, Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
| | - Alex M Mawla
- Department of Neurobiology, Physiology and Behavior, College of Biological Sciences, University of California, Davis, CA, USA
| | - Lunkun Ma
- Weill Center for Metabolic Health, Cardiovascular Research Institute, Division of Cardiology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Eric Cortada
- Weill Center for Metabolic Health, Cardiovascular Research Institute, Division of Cardiology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Paul Zumbo
- Department of Physiology and Biophysics, Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
| | - Ang Li
- Weill Center for Metabolic Health, Cardiovascular Research Institute, Division of Cardiology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Moritz Reiterer
- Weill Center for Metabolic Health, Cardiovascular Research Institute, Division of Cardiology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Nathalia Montoya-Oviedo
- Weill Center for Metabolic Health, Cardiovascular Research Institute, Division of Cardiology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Lipids and Diabetes Laboratory, Department of Physiological Sciences, Faculty of Medicine, National University of Colombia, Bogotá, Colombia
| | - Edwin A Homan
- Weill Center for Metabolic Health, Cardiovascular Research Institute, Division of Cardiology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Norihiro Imai
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Ankit Gilani
- Weill Center for Metabolic Health, Cardiovascular Research Institute, Division of Cardiology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Chengyang Liu
- Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Ali Naji
- Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Boris Yang
- Weill Center for Metabolic Health, Cardiovascular Research Institute, Division of Cardiology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - David E Cohen
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
| | - Jingli Cao
- Cardiovascular Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Geoffrey S Pitt
- Cardiovascular Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Mark O Huising
- Department of Neurobiology, Physiology and Behavior, College of Biological Sciences, University of California, Davis, CA, USA
- Department of Physiology and Membrane Biology, School of Medicine, University of California Davis, Davis, CA, USA
| | - Doron Betel
- Department of Physiology and Biophysics, Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Division of Hematology and Medical Oncology, Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
| | - James C Lo
- Weill Center for Metabolic Health, Cardiovascular Research Institute, Division of Cardiology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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26
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Szlachcic WJ, Letai KC, Scavuzzo MA, Borowiak M. Deep into the niche: Deciphering local endoderm-microenvironment interactions in development, homeostasis, and disease of pancreas and intestine. Bioessays 2023; 45:e2200186. [PMID: 36871153 DOI: 10.1002/bies.202200186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 01/11/2023] [Accepted: 01/23/2023] [Indexed: 03/06/2023]
Abstract
Unraveling molecular and functional heterogeneity of niche cells within the developing endoderm could resolve mechanisms of tissue formation and maturation. Here, we discuss current unknowns in molecular mechanisms underlying key developmental events in pancreatic islet and intestinal epithelial formation. Recent breakthroughs in single-cell and spatial transcriptomics, paralleled with functional studies in vitro, reveal that specialized mesenchymal subtypes drive the formation and maturation of pancreatic endocrine cells and islets via local interactions with epithelium, neurons, and microvessels. Analogous to this, distinct intestinal niche cells regulate both epithelial development and homeostasis throughout life. We propose how this knowledge can be used to progress research in the human context using pluripotent stem cell-derived multilineage organoids. Overall, understanding the interactions between the multitude of microenvironmental cells and how they drive tissue development and function could help us make more therapeutically relevant in vitro models.
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Affiliation(s)
- Wojciech J Szlachcic
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Katherine C Letai
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Marissa A Scavuzzo
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Malgorzata Borowiak
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
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27
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Miranda MA, Macias-Velasco JF, Schmidt H, Lawson HA. Integrated transcriptomics contrasts fatty acid metabolism with hypoxia response in β-cell subpopulations associated with glycemic control. BMC Genomics 2023; 24:156. [PMID: 36978008 PMCID: PMC10052828 DOI: 10.1186/s12864-023-09232-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 03/07/2023] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND Understanding how heterogeneous β-cell function impacts diabetes is imperative for therapy development. Standard single-cell RNA sequencing analysis illuminates some factors driving heterogeneity, but new strategies are required to enhance information capture. RESULTS We integrate pancreatic islet single-cell and bulk RNA sequencing data to identify β-cell subpopulations based on gene expression and characterize genetic networks associated with β-cell function in obese SM/J mice. We identify β-cell subpopulations associated with basal insulin secretion, hypoxia response, cell polarity, and stress response. Network analysis associates fatty acid metabolism and basal insulin secretion with hyperglycemic-obesity, while expression of Pdyn and hypoxia response is associated with normoglycemic-obesity. CONCLUSIONS By integrating single-cell and bulk islet transcriptomes, our study explores β-cell heterogeneity and identifies novel subpopulations and genetic pathways associated with β-cell function in obesity.
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Affiliation(s)
- Mario A Miranda
- Department of Genetics, Washington University School of Medicine, 660 South Euclid Ave, Campus Box 8232, Saint Louis, MO, 63110, USA
| | - Juan F Macias-Velasco
- Department of Genetics, Washington University School of Medicine, 660 South Euclid Ave, Campus Box 8232, Saint Louis, MO, 63110, USA
| | - Heather Schmidt
- Department of Genetics, Washington University School of Medicine, 660 South Euclid Ave, Campus Box 8232, Saint Louis, MO, 63110, USA
| | - Heather A Lawson
- Department of Genetics, Washington University School of Medicine, 660 South Euclid Ave, Campus Box 8232, Saint Louis, MO, 63110, USA.
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28
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Wieder N, Fried JC, Kim C, Sidhom EH, Brown MR, Marshall JL, Arevalo C, Dvela-Levitt M, Kost-Alimova M, Sieber J, Gabriel KR, Pacheco J, Clish C, Abbasi HS, Singh S, Rutter J, Therrien M, Yoon H, Lai ZW, Baublis A, Subramanian R, Devkota R, Small J, Sreekanth V, Han M, Lim D, Carpenter AE, Flannick J, Finucane H, Haigis MC, Claussnitzer M, Sheu E, Stevens B, Wagner BK, Choudhary A, Shaw JL, Pablo JL, Greka A. FALCON systematically interrogates free fatty acid biology and identifies a novel mediator of lipotoxicity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.19.529127. [PMID: 36865221 PMCID: PMC9979987 DOI: 10.1101/2023.02.19.529127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Cellular exposure to free fatty acids (FFA) is implicated in the pathogenesis of obesity-associated diseases. However, studies to date have assumed that a few select FFAs are representative of broad structural categories, and there are no scalable approaches to comprehensively assess the biological processes induced by exposure to diverse FFAs circulating in human plasma. Furthermore, assessing how these FFA- mediated processes interact with genetic risk for disease remains elusive. Here we report the design and implementation of FALCON (Fatty Acid Library for Comprehensive ONtologies) as an unbiased, scalable and multimodal interrogation of 61 structurally diverse FFAs. We identified a subset of lipotoxic monounsaturated fatty acids (MUFAs) with a distinct lipidomic profile associated with decreased membrane fluidity. Furthermore, we developed a new approach to prioritize genes that reflect the combined effects of exposure to harmful FFAs and genetic risk for type 2 diabetes (T2D). Importantly, we found that c-MAF inducing protein (CMIP) protects cells from exposure to FFAs by modulating Akt signaling and we validated the role of CMIP in human pancreatic beta cells. In sum, FALCON empowers the study of fundamental FFA biology and offers an integrative approach to identify much needed targets for diverse diseases associated with disordered FFA metabolism. Highlights FALCON (Fatty Acid Library for Comprehensive ONtologies) enables multimodal profiling of 61 free fatty acids (FFAs) to reveal 5 FFA clusters with distinct biological effectsFALCON is applicable to many and diverse cell typesA subset of monounsaturated FAs (MUFAs) equally or more toxic than canonical lipotoxic saturated FAs (SFAs) leads to decreased membrane fluidityNew approach prioritizes genes that represent the combined effects of environmental (FFA) exposure and genetic risk for diseaseC-Maf inducing protein (CMIP) is identified as a suppressor of FFA-induced lipotoxicity via Akt-mediated signaling.
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Affiliation(s)
- Nicolas Wieder
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston USA
- Harvard Medical School, Boston, USA
- Department of Neurology with Experimental Neurology, Charité, Berlin, Germany
| | - Juliana Coraor Fried
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston USA
- Harvard Medical School, Boston, USA
| | - Choah Kim
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston USA
- Harvard Medical School, Boston, USA
| | - Eriene-Heidi Sidhom
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston USA
- Harvard Medical School, Boston, USA
| | | | | | | | - Moran Dvela-Levitt
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston USA
- Harvard Medical School, Boston, USA
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | | | - Jonas Sieber
- Department of Endocrinology, Metabolism and Cardiovascular Systems, University of Fribourg, Fribourg, Switzerland
| | | | | | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, USA
| | | | | | - Justine Rutter
- Broad Institute of MIT and Harvard, Cambridge, USA
- Harvard Medical School, Boston, USA
| | | | - Haejin Yoon
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Ludwig Center for Cancer Research at Harvard, Boston, MA 02115, USA
| | - Zon Weng Lai
- Harvard Chan Advanced Multiomics Platform, Harvard T.H. Chan School of Public Health, Boston MA 02115 USA
| | - Aaron Baublis
- Harvard Chan Advanced Multiomics Platform, Harvard T.H. Chan School of Public Health, Boston MA 02115 USA
| | - Renuka Subramanian
- Laboratory for Surgical and Metabolic Research, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Ranjan Devkota
- Broad Institute of MIT and Harvard, Cambridge, USA
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonnell Small
- Broad Institute of MIT and Harvard, Cambridge, USA
- Harvard Medical School, Boston, USA
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vedagopuram Sreekanth
- Broad Institute of MIT and Harvard, Cambridge, USA
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, MA, USA
| | | | - Donghyun Lim
- Broad Institute of MIT and Harvard, Cambridge, USA
| | | | - Jason Flannick
- Broad Institute of MIT and Harvard, Cambridge, USA
- Harvard Medical School, Boston, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
| | - Hilary Finucane
- Broad Institute of MIT and Harvard, Cambridge, USA
- Analytic and Translational Genetics Unit, Mass General Hospital, Boston, MA, USA
| | - Marcia C. Haigis
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Ludwig Center for Cancer Research at Harvard, Boston, MA 02115, USA
| | - Melina Claussnitzer
- Broad Institute of MIT and Harvard, Cambridge, USA
- Harvard Medical School, Boston, USA
- Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric Sheu
- Laboratory for Surgical and Metabolic Research, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Beth Stevens
- Broad Institute of MIT and Harvard, Cambridge, USA
- Harvard Medical School, Boston, USA
- Boston Children’s Hospital, F.M. Kirby Neurobiology Center, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Bridget K. Wagner
- Broad Institute of MIT and Harvard, Cambridge, USA
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amit Choudhary
- Broad Institute of MIT and Harvard, Cambridge, USA
- Harvard Medical School, Boston, USA
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, MA, USA
| | | | | | - Anna Greka
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston USA
- Harvard Medical School, Boston, USA
- Lead Contact
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29
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Juan-Mateu J, Bajew S, Miret-Cuesta M, Íñiguez LP, Lopez-Pascual A, Bonnal S, Atla G, Bonàs-Guarch S, Ferrer J, Valcárcel J, Irimia M. Pancreatic microexons regulate islet function and glucose homeostasis. Nat Metab 2023; 5:219-236. [PMID: 36759540 DOI: 10.1038/s42255-022-00734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 12/21/2022] [Indexed: 02/11/2023]
Abstract
Pancreatic islets control glucose homeostasis by the balanced secretion of insulin and other hormones, and their abnormal function causes diabetes or hypoglycaemia. Here we uncover a conserved programme of alternative microexons included in mRNAs of islet cells, particularly in genes involved in vesicle transport and exocytosis. Islet microexons (IsletMICs) are regulated by the RNA binding protein SRRM3 and represent a subset of the larger neural programme that are particularly sensitive to SRRM3 levels. Both SRRM3 and IsletMICs are induced by elevated glucose levels, and depletion of SRRM3 in human and rat beta cell lines and mouse islets, or repression of particular IsletMICs using antisense oligonucleotides, leads to inappropriate insulin secretion. Consistently, mice harbouring mutations in Srrm3 display defects in islet cell identity and function, leading to hyperinsulinaemic hypoglycaemia. Importantly, human genetic variants that influence SRRM3 expression and IsletMIC inclusion in islets are associated with fasting glucose variation and type 2 diabetes risk. Taken together, our data identify a conserved microexon programme that regulates glucose homeostasis.
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Affiliation(s)
- Jonàs Juan-Mateu
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Simon Bajew
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marta Miret-Cuesta
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luis P Íñiguez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Amaya Lopez-Pascual
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sophie Bonnal
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Goutham Atla
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Sílvia Bonàs-Guarch
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Jorge Ferrer
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Juan Valcárcel
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
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30
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Wang G, Chiou J, Zeng C, Miller M, Matta I, Han JY, Kadakia N, Okino ML, Beebe E, Mallick M, Camunas-Soler J, dos Santos T, Dai XQ, Ellis C, Hang Y, Kim SK, MacDonald PE, Kandeel FR, Preissl S, Gaulton KJ, Sander M. Integration of single-cell multiomic measurements across disease states with genetics identifies mechanisms of beta cell dysfunction in type 2 diabetes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2022.12.31.522386. [PMID: 36711922 PMCID: PMC9881862 DOI: 10.1101/2022.12.31.522386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Altered function and gene regulation of pancreatic islet beta cells is a hallmark of type 2 diabetes (T2D), but a comprehensive understanding of mechanisms driving T2D is still missing. Here we integrate information from measurements of chromatin activity, gene expression and function in single beta cells with genetic association data to identify disease-causal gene regulatory changes in T2D. Using machine learning on chromatin accessibility data from 34 non-diabetic, pre-T2D and T2D donors, we robustly identify two transcriptionally and functionally distinct beta cell subtypes that undergo an abundance shift in T2D. Subtype-defining active chromatin is enriched for T2D risk variants, suggesting a causal contribution of subtype identity to T2D. Both subtypes exhibit activation of a stress-response transcriptional program and functional impairment in T2D, which is likely induced by the T2D-associated metabolic environment. Our findings demonstrate the power of multimodal single-cell measurements combined with machine learning for identifying mechanisms of complex diseases.
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Affiliation(s)
- Gaowei Wang
- Department of Pediatrics, University of California San Diego, La Jolla CA, USA
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla CA, USA
| | - Joshua Chiou
- Department of Pediatrics, University of California San Diego, La Jolla CA, USA
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla CA, USA
- Biomedical Graduate Studies Program, University of California San Diego, La Jolla CA, USA
| | - Chun Zeng
- Department of Pediatrics, University of California San Diego, La Jolla CA, USA
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla CA, USA
| | - Michael Miller
- Center for Epigenomics, University of California San Diego, La Jolla CA, USA
| | - Ileana Matta
- Department of Pediatrics, University of California San Diego, La Jolla CA, USA
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla CA, USA
| | - Jee Yun Han
- Center for Epigenomics, University of California San Diego, La Jolla CA, USA
| | - Nikita Kadakia
- Department of Pediatrics, University of California San Diego, La Jolla CA, USA
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla CA, USA
| | - Mei-Lin Okino
- Department of Pediatrics, University of California San Diego, La Jolla CA, USA
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla CA, USA
| | - Elisha Beebe
- Department of Pediatrics, University of California San Diego, La Jolla CA, USA
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla CA, USA
| | - Medhavi Mallick
- Department of Pediatrics, University of California San Diego, La Jolla CA, USA
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla CA, USA
| | | | - Theodore dos Santos
- Department of Pharmacology, University of Alberta, Edmonton, AB, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Xiao-Qing Dai
- Department of Pharmacology, University of Alberta, Edmonton, AB, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Cara Ellis
- Department of Pharmacology, University of Alberta, Edmonton, AB, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Yan Hang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Departments of Medicine and of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Seung K. Kim
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Departments of Medicine and of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Patrick E. MacDonald
- Department of Pharmacology, University of Alberta, Edmonton, AB, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Fouad R. Kandeel
- Department of Clinical Diabetes, Endocrinology & Metabolism, City of Hope, Duarte, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego, La Jolla CA, USA
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kyle J Gaulton
- Department of Pediatrics, University of California San Diego, La Jolla CA, USA
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla CA, USA
| | - Maike Sander
- Department of Pediatrics, University of California San Diego, La Jolla CA, USA
- Pediatric Diabetes Research Center, University of California San Diego, La Jolla CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla CA, USA
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
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31
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Mameri A, Côté J. JAZF1: A metabolic actor subunit of the NuA4/TIP60 chromatin modifying complex. Front Cell Dev Biol 2023; 11:1134268. [PMID: 37091973 PMCID: PMC10119425 DOI: 10.3389/fcell.2023.1134268] [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: 12/30/2022] [Accepted: 03/29/2023] [Indexed: 04/25/2023] Open
Abstract
The multisubunit NuA4/TIP60 complex is a lysine acetyltransferase, chromatin modifying factor and gene co-activator involved in diverse biological processes. The past decade has seen a growing appreciation for its role as a metabolic effector and modulator. However, molecular insights are scarce and often contradictory, underscoring the need for further mechanistic investigation. A particularly exciting route emerged with the recent identification of a novel subunit, JAZF1, which has been extensively linked to metabolic homeostasis. This review summarizes the major findings implicating NuA4/TIP60 in metabolism, especially in light of JAZF1 as part of the complex.
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32
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He X, Liu X, Zuo F, Shi H, Jing J. Artificial intelligence-based multi-omics analysis fuels cancer precision medicine. Semin Cancer Biol 2023; 88:187-200. [PMID: 36596352 DOI: 10.1016/j.semcancer.2022.12.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/16/2022] [Accepted: 12/29/2022] [Indexed: 01/02/2023]
Abstract
With biotechnological advancements, innovative omics technologies are constantly emerging that have enabled researchers to access multi-layer information from the genome, epigenome, transcriptome, proteome, metabolome, and more. A wealth of omics technologies, including bulk and single-cell omics approaches, have empowered to characterize different molecular layers at unprecedented scale and resolution, providing a holistic view of tumor behavior. Multi-omics analysis allows systematic interrogation of various molecular information at each biological layer while posing tricky challenges regarding how to extract valuable insights from the exponentially increasing amount of multi-omics data. Therefore, efficient algorithms are needed to reduce the dimensionality of the data while simultaneously dissecting the mysteries behind the complex biological processes of cancer. Artificial intelligence has demonstrated the ability to analyze complementary multi-modal data streams within the oncology realm. The coincident development of multi-omics technologies and artificial intelligence algorithms has fuelled the development of cancer precision medicine. Here, we present state-of-the-art omics technologies and outline a roadmap of multi-omics integration analysis using an artificial intelligence strategy. The advances made using artificial intelligence-based multi-omics approaches are described, especially concerning early cancer screening, diagnosis, response assessment, and prognosis prediction. Finally, we discuss the challenges faced in multi-omics analysis, along with tentative future trends in this field. With the increasing application of artificial intelligence in multi-omics analysis, we anticipate a shifting paradigm in precision medicine becoming driven by artificial intelligence-based multi-omics technologies.
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Affiliation(s)
- Xiujing He
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, PR China
| | - Xiaowei Liu
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, PR China
| | - Fengli Zuo
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, PR China
| | - Hubing Shi
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, PR China
| | - Jing Jing
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, PR China.
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33
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Identifying type 2 diabetes risk genes by β-cell CRISPR screening. Nat Genet 2023; 55:4-5. [PMID: 36639508 DOI: 10.1038/s41588-022-01269-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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34
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Non-coding variants disrupting a tissue-specific regulatory element in HK1 cause congenital hyperinsulinism. Nat Genet 2022; 54:1615-1620. [PMID: 36333503 PMCID: PMC7614032 DOI: 10.1038/s41588-022-01204-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 09/16/2022] [Indexed: 11/06/2022]
Abstract
Gene expression is tightly regulated, with many genes exhibiting cell-specific silencing when their protein product would disrupt normal cellular function1. This silencing is largely controlled by non-coding elements, and their disruption might cause human disease2. We performed gene-agnostic screening of the non-coding regions to discover new molecular causes of congenital hyperinsulinism. This identified 14 non-coding de novo variants affecting a 42-bp conserved region encompassed by a regulatory element in intron 2 of the hexokinase 1 gene (HK1). HK1 is widely expressed across all tissues except in the liver and pancreatic beta cells and is thus termed a 'disallowed gene' in these specific tissues. We demonstrated that the variants result in a loss of repression of HK1 in pancreatic beta cells, thereby causing insulin secretion and congenital hyperinsulinism. Using epigenomic data accessed from public repositories, we demonstrated that these variants reside within a regulatory region that we determine to be critical for cell-specific silencing. Importantly, this has revealed a disease mechanism for non-coding variants that cause inappropriate expression of a disallowed gene.
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35
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Liu X, Xie X, Li D, Liu Z, Niu Y, Shen B, Zhang B, Song Y, Ma J, Zhang M, Shi Z, Shen C. Transcriptome reveals the dysfunction of pancreatic islets after wound healing in severely burned mice. J Trauma Acute Care Surg 2022; 93:712-718. [PMID: 36301128 DOI: 10.1097/ta.0000000000003697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Severely burned patients have a higher risk of diabetes mellitus after healing, but its mechanism remains unclear. Therefore, the purpose of the study was to explore the influence of burns on pancreatic islets of mice after wound healing. METHODS Forty-two male C57BL/6 mice were randomized into a sham group and a burn group and subjected to sham treatment or a third-degree burn model of 30% total body surface area. Fasting blood glucose was detected weekly for 8 weeks after severe burns. Glucose-stimulated insulin secretion was measured 8 weeks post severe burns. Islets of the two groups were isolated and mRNA libraries were sequenced by the Illumina sequencing platform. The expressions of differentially expressed genes (DEGs) related to the cell cycle and the amounts of mitochondrial DNA were detected by quantitative real-time polymerase chain reaction after gene ontology, gene set enrichment analysis, and protein-protein network analysis. Hematoxylin-eosin staining of pancreatic tail tissue and adenosine triphosphate (ATP) assay of islets were performed. RESULTS The levels of fasting blood glucose were significantly higher within 8 weeks post severe burns. Glucose-stimulated insulin secretion was impaired at the eighth week post severe burns. Totally 128 DEGs were selected. Gene ontology and gene set enrichment analysis indicated that the pathways related to the cell cycle, protein processing, and oxidative phosphorylation were downregulated. The expressions of DEGs related to the cell cycle showed a consistent trend with mRNA sequencing data, and most of them were downregulated post severe burns. The cell mass of the burn group was less than that of the sham group. Also, the concentration of ATP and the amount of mitochondrial DNA were lower in the burn group. CONCLUSION In the model of severe-burned mice, disorders in glucose metabolism persist for 8 weeks after burns, which may be related to low islet cell proliferation, downregulation of protein processing, and less ATP production.
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Affiliation(s)
- Xinzhu Liu
- From the Department of Burns and Plastic Surgery (X.L., J.M., D.L., Z.L., Y.N., B.S., B.Z., Y.S., M.Z., Z.S., C.S.), the Fourth Medical Center, Chinese PLA General Hospital; and Medical School of Chinese PLA (X.X., X.L., J.M.), Beijing, China
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Tritschler S, Thomas M, Böttcher A, Ludwig B, Schmid J, Schubert U, Kemter E, Wolf E, Lickert H, Theis FJ. A transcriptional cross species map of pancreatic islet cells. Mol Metab 2022; 66:101595. [PMID: 36113773 PMCID: PMC9526148 DOI: 10.1016/j.molmet.2022.101595] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 08/20/2022] [Accepted: 09/03/2022] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVE Pancreatic islets of Langerhans secrete hormones to regulate systemic glucose levels. Emerging evidence suggests that islet cells are functionally heterogeneous to allow a fine-tuned and efficient endocrine response to physiological changes. A precise description of the molecular basis of this heterogeneity, in particular linking animal models to human islets, is an important step towards identifying the factors critical for endocrine cell function in physiological and pathophysiological conditions. METHODS In this study, we used single-cell RNA sequencing to profile more than 50'000 endocrine cells isolated from healthy human, pig and mouse pancreatic islets and characterize transcriptional heterogeneity and evolutionary conservation of those cells across the three species. We systematically delineated endocrine cell types and α- and β-cell heterogeneity through prior knowledge- and data-driven gene sets shared across species, which altogether capture common and differential cellular properties, transcriptional dynamics and putative driving factors of state transitions. RESULTS We showed that global endocrine expression profiles correlate, and that critical identity and functional markers are shared between species, while only approximately 20% of cell type enriched expression is conserved. We resolved distinct human α- and β-cell states that form continuous transcriptional landscapes. These states differentially activate maturation and hormone secretion programs, which are related to regulatory hormone receptor expression, signaling pathways and different types of cellular stress responses. Finally, we mapped mouse and pig cells to the human reference and observed that the spectrum of human α- and β-cell heterogeneity and aspects of such functional gene expression are better recapitulated in the pig than mouse data. CONCLUSIONS Here, we provide a high-resolution transcriptional map of healthy human islet cells and their murine and porcine counterparts, which is easily queryable via an online interface. This comprehensive resource informs future efforts that focus on pancreatic endocrine function, failure and regeneration, and enables to assess molecular conservation in islet biology across species for translational purposes.
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Affiliation(s)
- Sophie Tritschler
- Institute of Computational Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technical University of Munich, School of Life Sciences Weihenstephan, 85354 Freising, Germany
| | - Moritz Thomas
- Technical University of Munich, School of Life Sciences Weihenstephan, 85354 Freising, Germany; Institute of AI for Health, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Anika Böttcher
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Barbara Ludwig
- Department of Medicine III, University Hospital Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden of Helmholtz Zentrum München, University Hospital Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Janine Schmid
- Department of Medicine III, University Hospital Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Undine Schubert
- Department of Medicine III, University Hospital Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Elisabeth Kemter
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Chair for Molecular Animal Breeding and Biotechnology, Gene Center, LMU Munich, 81377 Munich, Germany; Center for Innovative Medical Models (CiMM), Department of Veterinary Sciences, LMU Munich, 85764 Oberschleißheim, Germany
| | - Eckhard Wolf
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Chair for Molecular Animal Breeding and Biotechnology, Gene Center, LMU Munich, 81377 Munich, Germany; Center for Innovative Medical Models (CiMM), Department of Veterinary Sciences, LMU Munich, 85764 Oberschleißheim, Germany
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Technical University of Munich, Medical Faculty, 81675 Munich, Germany.
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Technical University of Munich, Department of Mathematics, 85748 Garching b. Munich, Germany.
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Cuesta-Gomez N, Verhoeff K, Jasra IT, Pawlick R, Dadheech N, Shapiro AMJ. Characterization of stem-cell-derived islets during differentiation and after implantation. Cell Rep 2022; 40:111238. [PMID: 36001981 DOI: 10.1016/j.celrep.2022.111238] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 05/26/2022] [Accepted: 07/27/2022] [Indexed: 12/11/2022] Open
Abstract
Recapitulation of embryonic pancreatic development has enabled development of methods for in vitro islet cell differentiation using human pluripotent stem cells (hPSCs), which have the potential to cure diabetes. Advanced methods for optimal generation of stem-cell-derived islets (SC-islets) has enabled successful diabetes reversal in rodents and shown promising early clinical trial outcomes. The main impediment for use of SC-islets is concern about safety because of off-target growth resulting from contaminated residual cells. In this review, we summarize the different endocrine and non-endocrine cell populations that have been described to emerge throughout β cell differentiation and after transplantation. We discuss the most recent approaches to enrich endocrine populations and remove off-target cells. Finally, we discuss the critical quality control and release criteria testing that we anticipate will be required prior to transplantation to ensure product safety.
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Affiliation(s)
- Nerea Cuesta-Gomez
- Alberta Diabetes Institute, Department of Surgery, 1-002 Li Ka Shing Centre for Health Research Innovation, University of Alberta, 112 St. NW & 87 Ave. NW, Edmonton, AB T6G 2E1, Canada
| | - Kevin Verhoeff
- Alberta Diabetes Institute, Department of Surgery, 1-002 Li Ka Shing Centre for Health Research Innovation, University of Alberta, 112 St. NW & 87 Ave. NW, Edmonton, AB T6G 2E1, Canada
| | - Ila Tewari Jasra
- Alberta Diabetes Institute, Department of Surgery, 1-002 Li Ka Shing Centre for Health Research Innovation, University of Alberta, 112 St. NW & 87 Ave. NW, Edmonton, AB T6G 2E1, Canada
| | - Rena Pawlick
- Alberta Diabetes Institute, Department of Surgery, 1-002 Li Ka Shing Centre for Health Research Innovation, University of Alberta, 112 St. NW & 87 Ave. NW, Edmonton, AB T6G 2E1, Canada
| | - Nidheesh Dadheech
- Alberta Diabetes Institute, Department of Surgery, 1-002 Li Ka Shing Centre for Health Research Innovation, University of Alberta, 112 St. NW & 87 Ave. NW, Edmonton, AB T6G 2E1, Canada.
| | - A M James Shapiro
- Alberta Diabetes Institute, Department of Surgery, 1-002 Li Ka Shing Centre for Health Research Innovation, University of Alberta, 112 St. NW & 87 Ave. NW, Edmonton, AB T6G 2E1, Canada.
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Abstract
Islet dysfunction is central in type 2 diabetes and full-blown type 2 diabetes develops first when the beta cells lose their ability to secrete adequate amounts of insulin in response to raised plasma glucose. Several mechanisms behind beta cell dysfunction have been put forward but many important questions still remain. Furthermore, our understanding of the contribution of each islet cell type in type 2 diabetes pathophysiology has been limited by technical boundaries. Closing this knowledge gap will lead to a leap forward in our understanding of the islet as an organ and potentially lead to improved treatments. The development of single-cell RNA sequencing (scRNAseq) has led to a breakthrough for characterising the transcriptome of each islet cell type and several important observations on the regulation of cell-type-specific gene expression have been made. When it comes to identifying type 2 diabetes disease mechanisms, the outcome is still limited. Several studies have identified differentially expressed genes, although there is very limited consensus between the studies. As with all new techniques, scRNAseq has limitations; in addition to being extremely expensive, genes expressed at low levels may not be detected, noise may not be appropriately filtered and selection biases for certain cell types are at hand. Furthermore, recent advances suggest that commonly used computational tools may be suboptimal for analysis of scRNAseq data in small-scale studies. Fortunately, development of new computational tools holds promise for harnessing the full potential of scRNAseq data. Here we summarise how scRNAseq has contributed to increasing the understanding of various aspects of islet biology as well as type 2 diabetes disease mechanisms. We also focus on challenges that remain and propose steps to promote the utilisation of the full potential of scRNAseq in this area.
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Affiliation(s)
| | - Nils Wierup
- Lund University Diabetes Centre, Malmö, Sweden.
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van Gurp L, Fodoulian L, Oropeza D, Furuyama K, Bru-Tari E, Vu AN, Kaddis JS, Rodríguez I, Thorel F, Herrera PL. Generation of human islet cell type-specific identity genesets. Nat Commun 2022; 13:2020. [PMID: 35440614 PMCID: PMC9019032 DOI: 10.1038/s41467-022-29588-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/23/2022] [Indexed: 12/23/2022] Open
Abstract
Generation of surrogate cells with stable functional identities is crucial for developing cell-based therapies. Efforts to produce insulin-secreting replacement cells to treat diabetes require reliable tools to assess islet cellular identity. Here, we conduct a thorough single-cell transcriptomics meta-analysis to identify robustly expressed markers used to build genesets describing the identity of human α-, β-, γ- and δ-cells. These genesets define islet cellular identities better than previously published genesets. We show their efficacy to outline cell identity changes and unravel some of their underlying genetic mechanisms, whether during embryonic pancreas development or in experimental setups aiming at developing glucose-responsive insulin-secreting cells, such as pluripotent stem-cell differentiation or in adult islet cell reprogramming protocols. These islet cell type-specific genesets represent valuable tools that accurately benchmark gain and loss in islet cell identity traits.
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Affiliation(s)
- Léon van Gurp
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Leon Fodoulian
- Department of Genetics and Evolution, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211, Geneva, Switzerland
| | - Daniel Oropeza
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Kenichiro Furuyama
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, rue Michel-Servet 1, 1211, Geneva, Switzerland
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin-Kawahara, Sakyo, 606-8507, Kyoto, Japan
| | - Eva Bru-Tari
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Anh Nguyet Vu
- Department of Diabetes & Cancer Discovery Science, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, 1500 E Duarte Rd, Duarte, CA, 91010, USA
| | - John S Kaddis
- Department of Diabetes & Cancer Discovery Science, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, 1500 E Duarte Rd, Duarte, CA, 91010, USA
| | - Iván Rodríguez
- Department of Genetics and Evolution, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211, Geneva, Switzerland
| | - Fabrizio Thorel
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Pedro L Herrera
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, rue Michel-Servet 1, 1211, Geneva, Switzerland.
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Fu H, Sun H, Kong H, Lou B, Chen H, Zhou Y, Huang C, Qin L, Shan Y, Dai S. Discoveries in Pancreatic Physiology and Disease Biology Using Single-Cell RNA Sequencing. Front Cell Dev Biol 2022; 9:732776. [PMID: 35141228 PMCID: PMC8819087 DOI: 10.3389/fcell.2021.732776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
Transcriptome analysis is used to study gene expression in human tissues. It can promote the discovery of new therapeutic targets for related diseases by characterizing the endocrine function of pancreatic physiology and pathology, as well as the gene expression of pancreatic tumors. Compared to whole-tissue RNA sequencing, single-cell RNA sequencing (scRNA-seq) can detect transcriptional activity within a single cell. The scRNA-seq had an invaluable contribution to discovering previously unknown cell subtypes in normal and diseased pancreases, studying the functional role of rare islet cells, and studying various types of cells in diabetes as well as cancer. Here, we review the recent in vitro and in vivo advances in understanding the pancreatic physiology and pathology associated with single-cell sequencing technology, which may provide new insights into treatment strategy optimization for diabetes and pancreatic cancer.
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Affiliation(s)
- Haotian Fu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Hongwei Sun
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, Wenzhou, China
| | - Hongru Kong
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Bin Lou
- Department of Surgery, The Third People’s Hospital of Yuhang District, Hangzhou, China
| | - Hao Chen
- Department of Thyroid Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yilin Zhou
- Department of Biology, Boston University, Boston, MA, United States
| | - Chaohao Huang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lei Qin
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- *Correspondence: Lei Qin, ; Yunfeng Shan, ; Shengjie Dai,
| | - Yunfeng Shan
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, Wenzhou, China
- *Correspondence: Lei Qin, ; Yunfeng Shan, ; Shengjie Dai,
| | - Shengjie Dai
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- *Correspondence: Lei Qin, ; Yunfeng Shan, ; Shengjie Dai,
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41
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Bartolomé A. Stem Cell-Derived β Cells: A Versatile Research Platform to Interrogate the Genetic Basis of β Cell Dysfunction. Int J Mol Sci 2022; 23:501. [PMID: 35008927 PMCID: PMC8745644 DOI: 10.3390/ijms23010501] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 02/07/2023] Open
Abstract
Pancreatic β cell dysfunction is a central component of diabetes progression. During the last decades, the genetic basis of several monogenic forms of diabetes has been recognized. Genome-wide association studies (GWAS) have also facilitated the identification of common genetic variants associated with an increased risk of diabetes. These studies highlight the importance of impaired β cell function in all forms of diabetes. However, how most of these risk variants confer disease risk, remains unanswered. Understanding the specific contribution of genetic variants and the precise role of their molecular effectors is the next step toward developing treatments that target β cell dysfunction in the era of personalized medicine. Protocols that allow derivation of β cells from pluripotent stem cells, represent a powerful research tool that allows modeling of human development and versatile experimental designs that can be used to shed some light on diabetes pathophysiology. This article reviews different models to study the genetic basis of β cell dysfunction, focusing on the recent advances made possible by stem cell applications in the field of diabetes research.
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Affiliation(s)
- Alberto Bartolomé
- Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
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42
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Yang F, Zhao S, Zhang X, Ding S, Xu Y. RNF6 Targeted by miR-26a-5p Protects Pancreatic β-Cell Function Against Type 2 Diabetes. Diabetes Metab Syndr Obes 2022; 15:93-102. [PMID: 35046680 PMCID: PMC8761081 DOI: 10.2147/dmso.s335088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/17/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Type 2 diabetes (T2D) is characterized by progressive β-cell dysfunction. Regulatory microRNAs (miRNAs) may be associated with this. METHODS Serum miR-26a-5p and RNF6 levels were detected in T2D patients and healthy volunteers via qRT-PCR. Subsequently, the role of specific dysregulated miR-26a-5p or RNF6 in regulating insulin content, cell proliferation, and apoptosis was studied in INS-1 cells. The targeting correlation between miR-26a-5p and RNF6 was detected using a luciferase assay. RESULTS RNF6 expression was significantly decreased in T2D individuals and INS-1 cells treated with high glucose, while miR-26a-5p expression was increased. In INS-1 cells, RNF6 overexpression or miR-26a-5p downregulation significantly increased insulin content and secretion, induced proliferation, and inhibited apoptosis. RNF6 has been identified as an miR-26a-5p target, which negatively regulates RNF6 to worsen INS-1 cell function. CONCLUSION RNF6 promoted insulin secretion and induced cell proliferation in INS-1 cells. This may be related to miR-26a-5p targeting and negatively regulating T2D pathogenesis.
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Affiliation(s)
- Fan Yang
- Department of Endocrinology, Wuhan University Zhongnan Hospital, Wuhan, 430000, Hubei, People’s Republic of China
| | - Shengxun Zhao
- Department of Geriatrics, The First Hospital of Wuhan, Wuhan, 430000, Hubei, People’s Republic of China
| | - Xuyan Zhang
- Department of Endocrinology, The Central Hospital of Wuhan, Wuhan, 430014, Hubei, People’s Republic of China
| | - Sheng Ding
- Department of Endocrinology, The Central Hospital of Wuhan, Wuhan, 430014, Hubei, People’s Republic of China
| | - Yancheng Xu
- Department of Endocrinology, Wuhan University Zhongnan Hospital, Wuhan, 430000, Hubei, People’s Republic of China
- Correspondence: Yancheng Xu Department of Endocrinology, Wuhan University Zhongnan Hospital, No. 169, Donghu Road, Wuchang District, Wuhan, 430000, Hubei, People’s Republic of ChinaTel +86 13907116967 Email
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Holter MM, Saikia M, Cummings BP. Alpha-cell paracrine signaling in the regulation of beta-cell insulin secretion. Front Endocrinol (Lausanne) 2022; 13:934775. [PMID: 35957816 PMCID: PMC9360487 DOI: 10.3389/fendo.2022.934775] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/28/2022] [Indexed: 01/14/2023] Open
Abstract
As an incretin hormone, glucagon-like peptide 1 (GLP-1) lowers blood glucose levels by enhancing glucose-stimulated insulin secretion from pancreatic beta-cells. Therapies targeting the GLP-1 receptor (GLP-1R) use the classical incretin model as a physiological framework in which GLP-1 secreted from enteroendocrine L-cells acts on the beta-cell GLP-1R. However, this model has come into question, as evidence demonstrating local, intra-islet GLP-1 production has advanced the competing hypothesis that the incretin activity of GLP-1 may reflect paracrine signaling of GLP-1 from alpha-cells on GLP-1Rs on beta-cells. Additionally, recent studies suggest that alpha-cell-derived glucagon can serve as an additional, albeit less potent, ligand for the beta-cell GLP-1R, thereby expanding the role of alpha-cells beyond that of a counterregulatory cell type. Efforts to understand the role of the alpha-cell in the regulation of islet function have revealed both transcriptional and functional heterogeneity within the alpha-cell population. Further analysis of this heterogeneity suggests that functionally distinct alpha-cell subpopulations display alterations in islet hormone profile. Thus, the role of the alpha-cell in glucose homeostasis has evolved in recent years, such that alpha-cell to beta-cell communication now presents a critical axis regulating the functional capacity of beta-cells. Herein, we describe and integrate recent advances in our understanding of the impact of alpha-cell paracrine signaling on insulin secretory dynamics and how this intra-islet crosstalk more broadly contributes to whole-body glucose regulation in health and under metabolic stress. Moreover, we explore how these conceptual changes in our understanding of intra-islet GLP-1 biology may impact our understanding of the mechanisms of incretin-based therapeutics.
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Affiliation(s)
- Marlena M. Holter
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
- *Correspondence: Marlena M. Holter,
| | - Mridusmita Saikia
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, United States
| | - Bethany P. Cummings
- School of Medicine, Department of Surgery, Center for Alimentary and Metabolic Sciences, University of California, Davis, Sacramento, CA, United States
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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: 26] [Impact Index Per Article: 8.7] [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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Oppenländer L, Palit S, Stemmer K, Greisle T, Sterr M, Salinno C, Bastidas-Ponce A, Feuchtinger A, Böttcher A, Ansarullah, Theis FJ, Lickert H. Vertical sleeve gastrectomy triggers fast β-cell recovery upon overt diabetes. Mol Metab 2021; 54:101330. [PMID: 34500108 PMCID: PMC8487975 DOI: 10.1016/j.molmet.2021.101330] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/17/2021] [Accepted: 08/24/2021] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE The effectiveness of bariatric surgery in restoring β-cell function has been described in type-2 diabetes (T2D) patients and animal models for years, whereas the mechanistic underpinnings are largely unknown. The possibility of vertical sleeve gastrectomy (VSG) to rescue far-progressed, clinically-relevant T2D and to promote β-cell recovery has not been investigated on a single-cell level. Nevertheless, characterization of the heterogeneity and functional states of β-cells after VSG is a fundamental step to understand mechanisms of glycaemic recovery and to ultimately develop alternative, less-invasive therapies. METHODS We performed VSG in late-stage diabetic db/db mice and analyzed the islet transcriptome using single-cell RNA sequencing (scRNA-seq). Immunohistochemical analyses and quantification of β-cell area and proliferation complement our findings from scRNA-seq. RESULTS We report that VSG was superior to calorie restriction in late-stage T2D and rapidly restored normoglycaemia in morbidly obese and overt diabetic db/db mice. Single-cell profiling of islets of Langerhans showed that VSG induced distinct, intrinsic changes in the β-cell transcriptome, but not in that of α-, δ-, and PP-cells. VSG triggered fast β-cell redifferentiation and functional improvement within only two weeks of intervention, which is not seen upon calorie restriction. Furthermore, VSG expanded β-cell area by means of redifferentiation and by creating a proliferation competent β-cell state. CONCLUSION Collectively, our study reveals the superiority of VSG in the remission of far-progressed T2D and presents paths of β-cell regeneration and molecular pathways underlying the glycaemic benefits of VSG.
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Affiliation(s)
- Lena Oppenländer
- Institute of Diabetes and Regeneration Research, Helmholtz Center Munich, 85764, Neuherberg, Germany; Technical University of Munich, School of Medicine, 81675, Munich, Germany; German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
| | - Subarna Palit
- Institute of Computational Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany; Technical University of Munich, TUM School of Life Sciences Weihenstephan, 85354, Freising, Germany
| | - Kerstin Stemmer
- Institute of Diabetes and Obesity, Helmholtz Center Munich, 85764, Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany; Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392, Giessen, Germany
| | - Tobias Greisle
- Institute of Diabetes and Regeneration Research, Helmholtz Center Munich, 85764, Neuherberg, Germany; Technical University of Munich, School of Medicine, 81675, Munich, Germany; German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
| | - Michael Sterr
- Institute of Diabetes and Regeneration Research, Helmholtz Center Munich, 85764, Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
| | - Ciro Salinno
- Institute of Diabetes and Regeneration Research, Helmholtz Center Munich, 85764, Neuherberg, Germany; Technical University of Munich, School of Medicine, 81675, Munich, Germany; German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
| | - Aimée Bastidas-Ponce
- Institute of Diabetes and Regeneration Research, Helmholtz Center Munich, 85764, Neuherberg, Germany; Technical University of Munich, School of Medicine, 81675, Munich, Germany; German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
| | - Annette Feuchtinger
- Core Facility Pathology and Tissue Analytics, Helmholtz Center Munich, 85764, Neuherberg, Germany
| | - Anika Böttcher
- Institute of Diabetes and Regeneration Research, Helmholtz Center Munich, 85764, Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
| | - Ansarullah
- Institute of Diabetes and Regeneration Research, Helmholtz Center Munich, 85764, Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany.
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany; Department of Mathematics, Technical University of Munich, 85748, Garching, Germany; Technical University of Munich, TUM School of Life Sciences Weihenstephan, 85354, Freising, Germany.
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Center Munich, 85764, Neuherberg, Germany; Technical University of Munich, School of Medicine, 81675, Munich, Germany; German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany; Department of Medicine, Technical University of Munich, 81675, Munich, Germany.
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Kalwat MA, Scheuner D, Rodrigues-dos-Santos K, Eizirik DL, Cobb MH. The Pancreatic ß-cell Response to Secretory Demands and Adaption to Stress. Endocrinology 2021; 162:bqab173. [PMID: 34407177 PMCID: PMC8459449 DOI: 10.1210/endocr/bqab173] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Indexed: 02/06/2023]
Abstract
Pancreatic β cells dedicate much of their protein translation capacity to producing insulin to maintain glucose homeostasis. In response to increased secretory demand, β cells can compensate by increasing insulin production capability even in the face of protracted peripheral insulin resistance. The ability to amplify insulin secretion in response to hyperglycemia is a critical facet of β-cell function, and the exact mechanisms by which this occurs have been studied for decades. To adapt to the constant and fast-changing demands for insulin production, β cells use the unfolded protein response of the endoplasmic reticulum. Failure of these compensatory mechanisms contributes to both type 1 and 2 diabetes. Additionally, studies in which β cells are "rested" by reducing endogenous insulin demand have shown promise as a therapeutic strategy that could be applied more broadly. Here, we review recent findings in β cells pertaining to the metabolic amplifying pathway, the unfolded protein response, and potential advances in therapeutics based on β-cell rest.
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Affiliation(s)
- Michael A Kalwat
- Indiana Biosciences Research Institute, Indianapolis, IN 46202, USA
| | - Donalyn Scheuner
- Indiana Biosciences Research Institute, Indianapolis, IN 46202, USA
| | | | - Decio L Eizirik
- Indiana Biosciences Research Institute, Indianapolis, IN 46202, USA
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Melanie H Cobb
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
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Rowton M, Guzzetta A, Rydeen AB, Moskowitz IP. Control of cardiomyocyte differentiation timing by intercellular signaling pathways. Semin Cell Dev Biol 2021; 118:94-106. [PMID: 34144893 PMCID: PMC8968240 DOI: 10.1016/j.semcdb.2021.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/19/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023]
Abstract
Congenital Heart Disease (CHD), malformations of the heart present at birth, is the most common class of life-threatening birth defect (Hoffman (1995) [1], Gelb (2004) [2], Gelb (2014) [3]). A major research challenge is to elucidate the genetic determinants of CHD and mechanistically link CHD ontogeny to a molecular understanding of heart development. Although the embryonic origins of CHD are unclear in most cases, dysregulation of cardiovascular lineage specification, patterning, proliferation, migration or differentiation have been described (Olson (2004) [4], Olson (2006) [5], Srivastava (2006) [6], Dunwoodie (2007) [7], Bruneau (2008) [8]). Cardiac differentiation is the process whereby cells become progressively more dedicated in a trajectory through the cardiac lineage towards mature cardiomyocytes. Defects in cardiac differentiation have been linked to CHD, although how the complex control of cardiac differentiation prevents CHD is just beginning to be understood. The stages of cardiac differentiation are highly stereotyped and have been well-characterized (Kattman et al. (2011) [9], Wamstad et al. (2012) [10], Luna-Zurita et al. (2016) [11], Loh et al. (2016) [12], DeLaughter et al. (2016) [13]); however, the developmental and molecular mechanisms that promote or delay the transition of a cell through these stages have not been as deeply investigated. Tight temporal control of progenitor differentiation is critically important for normal organ size, spatial organization, and cellular physiology and homeostasis of all organ systems (Raff et al. (1985) [14], Amthor et al. (1998) [15], Kopan et al. (2014) [16]). This review will focus on the action of signaling pathways in the control of cardiomyocyte differentiation timing. Numerous signaling pathways, including the Wnt, Fibroblast Growth Factor, Hedgehog, Bone Morphogenetic Protein, Insulin-like Growth Factor, Thyroid Hormone and Hippo pathways, have all been implicated in promoting or inhibiting transitions along the cardiac differentiation trajectory. Gaining a deeper understanding of the mechanisms controlling cardiac differentiation timing promises to yield insights into the etiology of CHD and to inform approaches to restore function to damaged hearts.
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Bao K, Cui Z, Wang H, Xiao H, Li T, Kong X, Liu T. Pseudotime Ordering Single-Cell Transcriptomic of β Cells Pancreatic Islets in Health and Type 2 Diabetes. PHENOMICS (CHAM, SWITZERLAND) 2021; 1:199-210. [PMID: 36939754 PMCID: PMC9590480 DOI: 10.1007/s43657-021-00024-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/21/2021] [Accepted: 08/27/2021] [Indexed: 12/17/2022]
Abstract
β cells are defined by the ability to produce and secret insulin. Recent studies have evaluated that human pancreatic β cells are heterogeneous and demonstrated the transcript alterations of β cell subpopulation in diabetes. Single-cell RNA sequence (scRNA-seq) analysis helps us to refine the cell types signatures and understand the role of the β cells during metabolic challenges and diseases. Here, we construct the pseudotime trajectory of β cells from publicly available scRNA-seq data in health and type 2 diabetes (T2D) based on highly dispersed and highly expressed genes using Monocle2. We identified three major states including 1) Normal branch, 2) Obesity-like branch and 3) T2D-like branch based on biomarker genes and genes that give rise to bifurcation in the trajectory. β cell function-maintain-related genes, insulin expression-related genes, and T2D-related genes enriched in three branches, respectively. Continuous pseudotime spectrum might suggest that β cells transition among different states. The application of pseudotime analysis is conducted to clarify the different cell states, providing novel insights into the pathology of β cells in T2D. Supplementary Information The online version contains supplementary material is available at 10.1007/s43657-021-00024-z.
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Affiliation(s)
- Kaixuan Bao
- Human Phenome Institute, Fudan University, 825 Zhangheng Road, Shanghai, 201203 China
| | - Zhicheng Cui
- State Key Laboratory of Genetic Engineering, School of Life Sciences, and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, 200438 China
| | - Hui Wang
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, 200433 China
| | - Hui Xiao
- Human Phenome Institute, Fudan University, 825 Zhangheng Road, Shanghai, 201203 China
| | - Ting Li
- Human Phenome Institute, Fudan University, 825 Zhangheng Road, Shanghai, 201203 China
| | - Xingxing Kong
- State Key Laboratory of Genetic Engineering, School of Life Sciences, and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, 200438 China
| | - Tiemin Liu
- Human Phenome Institute, Fudan University, 825 Zhangheng Road, Shanghai, 201203 China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, 200438 China
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, 200433 China
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai, 200032 China
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Shrestha S, Saunders DC, Walker JT, Camunas-Soler J, Dai XQ, Haliyur R, Aramandla R, Poffenberger G, Prasad N, Bottino R, Stein R, Cartailler JP, Parker SC, MacDonald PE, Levy SE, Powers AC, Brissova M. Combinatorial transcription factor profiles predict mature and functional human islet α and β cells. JCI Insight 2021; 6:e151621. [PMID: 34428183 PMCID: PMC8492318 DOI: 10.1172/jci.insight.151621] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Islet-enriched transcription factors (TFs) exert broad control over cellular processes in pancreatic α and β cells, and changes in their expression are associated with developmental state and diabetes. However, the implications of heterogeneity in TF expression across islet cell populations are not well understood. To define this TF heterogeneity and its consequences for cellular function, we profiled more than 40,000 cells from normal human islets by single-cell RNA-Seq and stratified α and β cells based on combinatorial TF expression. Subpopulations of islet cells coexpressing ARX/MAFB (α cells) and MAFA/MAFB (β cells) exhibited greater expression of key genes related to glucose sensing and hormone secretion relative to subpopulations expressing only one or neither TF. Moreover, all subpopulations were identified in native pancreatic tissue from multiple donors. By Patch-Seq, MAFA/MAFB-coexpressing β cells showed enhanced electrophysiological activity. Thus, these results indicate that combinatorial TF expression in islet α and β cells predicts highly functional, mature subpopulations.
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Affiliation(s)
- Shristi Shrestha
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Creative Data Solutions, Vanderbilt Center for Stem Cell Biology, Nashville, Tennessee, USA
| | - Diane C Saunders
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - John T Walker
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Joan Camunas-Soler
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Xiao-Qing Dai
- Alberta Diabetes Institute and Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
| | - Rachana Haliyur
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Radhika Aramandla
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Greg Poffenberger
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Nripesh Prasad
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Rita Bottino
- Imagine Pharma, Devon, Pennsylvania, USA.,Institute of Cellular Therapeutics, Allegheny-Singer Research Institute, Allegheny Health Network, Pittsburgh, Pennsylvania, USA
| | - Roland Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | | | - Stephen Cj Parker
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Patrick E MacDonald
- Alberta Diabetes Institute and Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
| | - Shawn E Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Alvin C Powers
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.,VA Tennessee Valley Healthcare System, Nashville, Tennessee, USA
| | - Marcela Brissova
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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