Integrating genetics with single-cell multiomic measurements across disease states identifies mechanisms of beta cell dysfunction in type 2 diabetes

[1]  K. Kaestner,et al.  Understanding islet dysfunction in type 2 diabetes through multidimensional pancreatic phenotyping: The Human Pancreas Analysis Program. , 2022, Cell metabolism.

[2]  Robert C. Jones,et al.  Heterogenous impairment of α cell function in type 2 diabetes is linked to cell maturation state. , 2022, Cell metabolism.

[3]  Kyle J. Gaulton,et al.  Multi-ancestry genetic study of type 2 diabetes highlights the power of diverse populations for discovery and translation , 2020, Nature Genetics.

[4]  R. Benninger,et al.  The physiological role of β-cell heterogeneity in pancreatic islet function , 2021, Nature Reviews Endocrinology.

[5]  Jason M. Torres,et al.  TIGER: The gene expression regulatory variation landscape of human pancreatic islets , 2021, bioRxiv.

[6]  Xianjun Zhu,et al.  The phosphatidylserine flippase β-subunit Tmem30a is essential for normal insulin maturation and secretion , 2021, Molecular Therapy.

[7]  Kyle J. Gaulton,et al.  Single cell chromatin accessibility identifies pancreatic islet cell type- and state-specific regulatory programs of diabetes risk , 2021, Nature Genetics.

[8]  E. Bonifacio,et al.  Multi-omics profiling of living human pancreatic islet donors reveals heterogeneous beta cell trajectories toward type 2 diabetes , 2020, bioRxiv.

[9]  Brian E. Cade,et al.  Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program , 2019, Nature.

[10]  Ken Munene Nkonge,et al.  The epidemiology, molecular pathogenesis, diagnosis, and treatment of maturity-onset diabetes of the young (MODY) , 2020, Clinical Diabetes and Endocrinology.

[11]  D. Eizirik,et al.  Pancreatic β-cells in type 1 and type 2 diabetes mellitus: different pathways to failure , 2020, Nature Reviews Endocrinology.

[12]  S. Quake,et al.  Patch-Seq Links Single-Cell Transcriptomes to Human Islet Dysfunction in Diabetes. , 2020, Cell metabolism.

[13]  J. Weitz,et al.  Dysfunction of Persisting β Cells Is a Key Feature of Early Type 2 Diabetes Pathogenesis. , 2020, Cell reports.

[14]  Phillip A. Richmond,et al.  JASPAR 2020: update of the open-access database of transcription factor binding profiles , 2019, Nucleic Acids Res..

[15]  M. Cnop,et al.  Recent insights into mechanisms of β-cell lipo- and glucolipotoxicity in type 2 diabetes. , 2020, Journal of molecular biology.

[16]  V. Fellman,et al.  A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase , 2019, bioRxiv.

[17]  Xiang-Dong Fu,et al.  A tumorigenic index for quantitative analysis of liver cancer initiation and progression , 2019, Proceedings of the National Academy of Sciences.

[18]  M. Huising,et al.  Integrating the inputs that shape pancreatic islet hormone release , 2019, Nature Metabolism.

[19]  Jason D. Buenrostro,et al.  Inference and effects of barcode multiplets in droplet-based single-cell assays , 2019, Nature Communications.

[20]  Yurong Xin,et al.  Heterogeneity of human pancreatic β-cells , 2019, Molecular metabolism.

[21]  A. Kundaje,et al.  The ENCODE Blacklist: Identification of Problematic Regions of the Genome , 2019, Scientific Reports.

[22]  Howard Y. Chang,et al.  Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion , 2019, Nature Biotechnology.

[23]  E. Pratt,et al.  Regulation of cAMP accumulation and activity by distinct phosphodiesterase subtypes in INS-1 cells and human pancreatic β-cells , 2019, bioRxiv.

[24]  Yan Li,et al.  Single-Cell Heterogeneity Analysis and CRISPR Screen Identify Key β-Cell-Specific Disease Genes. , 2019, Cell reports.

[25]  K. Kaestner,et al.  Single-Cell RNA-Seq of the Pancreatic Islets--a Promise Not yet Fulfilled? , 2019, Cell metabolism.

[26]  Vincent A. Traag,et al.  From Louvain to Leiden: guaranteeing well-connected communities , 2018, Scientific Reports.

[27]  Fan Zhang,et al.  Fast, sensitive, and accurate integration of single cell data with Harmony , 2018, bioRxiv.

[28]  Andrew C. Adey,et al.  Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data. , 2018, Molecular cell.

[29]  C. Y. Chow,et al.  Baldspot/ELOVL6 is a conserved modifier of disease and the ER stress response , 2018, bioRxiv.

[30]  Jinrang Kim,et al.  Pseudotime Ordering of Single Human β-Cells Reveals States of Insulin Production and Unfolded Protein Response , 2018, Diabetes.

[31]  Fabian J Theis,et al.  SCANPY: large-scale single-cell gene expression data analysis , 2018, Genome Biology.

[32]  Kyle J. Gaulton.  Mechanisms of Type 2 Diabetes Risk Loci , 2017, Current Diabetes Reports.

[33]  William J. Greenleaf,et al.  chromVAR: Inferring transcription factor-associated accessibility from single-cell epigenomic data , 2017, Nature Methods.

[34]  C. Cohrs,et al.  Human beta cell mass and function in diabetes: Recent advances in knowledge and technologies to understand disease pathogenesis , 2017, Molecular metabolism.

[35]  Matthew T. Dickerson,et al.  Chronic β-Cell Depolarization Impairs β-Cell Identity by Disrupting a Network of Ca2+-Regulated Genes , 2017, Diabetes.

[36]  M. Akiyama,et al.  Clock Gene Dysregulation Induced by Chronic ER Stress Disrupts β-cell Function , 2017, EBioMedicine.

[37]  J. George,et al.  Single-cell transcriptomes identify human islet cell signatures and reveal cell-type–specific expression changes in type 2 diabetes , 2017, Genome research.

[38]  D. M. Smith,et al.  Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes , 2016, Cell metabolism.

[39]  A. Murphy,et al.  RNA Sequencing of Single Human Islet Cells Reveals Type 2 Diabetes Genes. , 2016, Cell metabolism.

[40]  Alan M. Kwong,et al.  Next-generation genotype imputation service and methods , 2016, Nature Genetics.

[41]  Jonathan Schug,et al.  Human islets contain four distinct subtypes of β cells , 2016, Nature Communications.

[42]  Andrew D. Rouillard,et al.  Enrichr: a comprehensive gene set enrichment analysis web server 2016 update , 2016, Nucleic Acids Res..

[43]  Tianqi Chen,et al.  XGBoost: A Scalable Tree Boosting System , 2016, KDD.

[44]  O. Brady,et al.  TFEB and TFE3 are novel components of the integrated stress response , 2016, The EMBO journal.

[45]  James D. Johnson,et al.  Reduced Insulin Production Relieves Endoplasmic Reticulum Stress and Induces β Cell Proliferation. , 2016, Cell metabolism.

[46]  Jonathan K. Pritchard,et al.  WASP: allele-specific software for robust molecular quantitative trait locus discovery , 2015, Nature Methods.

[47]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[48]  L. Groop,et al.  Global genomic and transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism , 2014, Proceedings of the National Academy of Sciences.

[49]  Samantha A. Morris,et al.  CellNet: Network Biology Applied to Stem Cell Engineering , 2014, Cell.

[50]  H. Sone,et al.  Ablation of Elovl6 protects pancreatic islets from high-fat diet-induced impairment of insulin secretion. , 2014, Biochemical and biophysical research communications.

[51]  S. Kahn,et al.  Pathophysiology and treatment of type 2 diabetes: perspectives on the past, present, and future , 2014, The Lancet.

[52]  Data production leads,et al.  An integrated encyclopedia of DNA elements in the human genome , 2012 .

[53]  ENCODEConsortium,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[54]  S. Ellard,et al.  SLC2A2 mutations can cause neonatal diabetes, suggesting GLUT2 may have a role in human insulin secretion , 2012, Diabetologia.

[55]  R. Chow,et al.  Inositol 1,4,5-trisphosphate receptor 1 mutation perturbs glucose homeostasis and enhances susceptibility to diet-induced diabetes. , 2011, The Journal of endocrinology.

[56]  M. Nawijn,et al.  Pim3 negatively regulates glucose-stimulated insulin secretion , 2010, Islets.

[57]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[58]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[59]  T. Berney,et al.  Insulin secretion from human beta cells is heterogeneous and dependent on cell-to-cell contacts , 2008, Diabetologia.

[60]  J. Bryan,et al.  ABCC8 and ABCC9: ABC transporters that regulate K+ channels , 2007, Pflügers Archiv - European Journal of Physiology.

[61]  R. Tibshirani,et al.  On testing the significance of sets of genes , 2006, math/0610667.

[62]  Jun Song,et al.  CEAS: cis-regulatory element annotation system , 2006, Nucleic Acids Res..

[63]  Terrence S. Furey,et al.  The UCSC Genome Browser Database: update 2006 , 2005, Nucleic Acids Res..

[64]  M. German,et al.  Genetic analysis reveals that PAX6 is required for normal transcription of pancreatic hormone genes and islet development. , 1997, Genes & development.