Single-cell chromatin accessibility identifies pancreatic islet cell type– and state-specific regulatory programs of diabetes risk (original) (raw)

• Maurano, M. T. et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 337, 1190–1195 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Cusanovich, D. A. et al. Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing. Science 348, 910–914 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Buenrostro, J. D. et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523, 486–490 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Preissl, S. et al. Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. Nat. Neurosci. 21, 432–439 (2018).
  Article CAS PubMed PubMed Central Google Scholar
• Litzenburger, U. M. et al. Single-cell epigenomic variability reveals functional cancer heterogeneity. Genome Biol. 18, 15 (2017).
  Article PubMed PubMed Central Google Scholar
• Buenrostro, J. D. et al. Integrated single-cell analysis maps the continuous regulatory landscape of human hematopoietic differentiation. Cell 173, 1535–1548.e16 (2018).
  Article CAS PubMed PubMed Central Google Scholar
• Ulirsch, J. C. et al. Interrogation of human hematopoiesis at single-cell and single-variant resolution. Nat. Genet. 51, 683–693 (2019).
  Article CAS PubMed PubMed Central Google Scholar
• Pliner, H. A. et al. Cicero predicts _cis_-regulatory DNA interactions from single-cell chromatin accessibility data. Mol. Cell 71, 858–871.e8 (2018).
  Article CAS PubMed PubMed Central Google Scholar
• Mahajan, A. et al. Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps. Nat. Genet. 50, 1505–1513 (2018).
  Article CAS PubMed PubMed Central Google Scholar
• Wood, A. R. et al. A genome-wide association study of IVGTT-based measures of first-phase insulin secretion refines the underlying physiology of type 2 diabetes variants. Diabetes 66, 2296–2309 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Dupuis, J. et al. New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk. Nat. Genet. 42, 105–116 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Manning, A. K. et al. A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance. Nat. Genet. 44, 659–669 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Scott, R. A. et al. Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways. Nat. Genet. 44, 991–1005 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Thurner, M. et al. Integration of human pancreatic islet genomic data refines regulatory mechanisms at type 2 diabetes susceptibility loci. eLife 7, e31977 (2018).
  Article PubMed PubMed Central Google Scholar
• Fuchsberger, C. et al. The genetic architecture of type 2 diabetes. Nature 536, 41–47 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Gaulton, K. J. et al. A map of open chromatin in human pancreatic islets. Nat. Genet. 42, 255–259 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Gaulton, K. J. et al. Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci. Nat. Genet. 47, 1415–1425 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Pasquali, L. et al. Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants. Nat. Genet. 46, 136–143 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• van der Meulen, T. et al. Urocortin3 mediates somatostatin-dependent negative feedback control of insulin secretion. Nat. Med. 21, 769–776 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Caicedo, A. Paracrine and autocrine interactions in the human islet: more than meets the eye. Semin. Cell Dev. Biol. 24, 11–21 (2013).
  Article CAS PubMed Google Scholar
• DiGruccio, M. R. et al. Comprehensive alpha, beta and delta cell transcriptomes reveal that ghrelin selectively activates delta cells and promotes somatostatin release from pancreatic islets. Mol. Metab. 5, 449–458 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Dorrell, C. et al. Human islets contain four distinct subtypes of β cells. Nat. Commun. 7, 11756 (2016).
  Article PubMed PubMed Central Google Scholar
• Xin, Y. et al. Pseudotime ordering of single human β-cells reveals states of insulin production and unfolded protein response. Diabetes 67, 1783–1794 (2018).
  Article CAS PubMed Google Scholar
• Korsunsky, I. et al. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat. Methods 16, 1289–1296 (2019).
  Article CAS PubMed PubMed Central Google Scholar
• Bader, E. et al. Identification of proliferative and mature β-cells in the islets of Langerhans. Nature 535, 430–434 (2016).
  Article CAS PubMed Google Scholar
• Liu, J. S. E. & Hebrok, M. All mixed up: defining roles for β-cell subtypes in mature islets. Genes Dev. 31, 228–240 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Greenwald, W. W. et al. Pancreatic islet chromatin accessibility and conformation reveals distal enhancer networks of type 2 diabetes risk. Nat. Commun. 10, 2078 (2019).
  Article PubMed PubMed Central Google Scholar
• Khetan, S. et al. Type 2 diabetes-associated genetic variants regulate chromatin accessibility in human islets. Diabetes 67, 2466–2477 (2018).
  Article CAS PubMed PubMed Central Google Scholar
• Varshney, A. et al. Genetic regulatory signatures underlying islet gene expression and type 2 diabetes. Proc. Natl Acad. Sci. USA 114, 2301–2306 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Baron, M. et al. A single-cell transcriptomic map of the human and mouse pancreas reveals inter- and intra-cell population structure. Cell Syst. 3, 346–360.e4 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Galvagni, F. et al. CD93 and dystroglycan cooperation in human endothelial cell adhesion and migration adhesion and migration. Oncotarget 7, 10090–10103 (2016).
  Article PubMed PubMed Central Google Scholar
• Zhang, Y. et al. Model-based analysis of ChIP-seq (MACS). Genome Biol. 9, R137 (2008).
  Article PubMed PubMed Central Google Scholar
• Schep, A. N., Wu, B., Buenrostro, J. D. & Greenleaf, W. J. chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data. Nat. Methods 14, 975–978 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Khan, A. et al. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res. 46, D1284 (2018).
  Article PubMed Google Scholar
• Wilson, M. E., Scheel, D. & German, M. S. Gene expression cascades in pancreatic development. Mech. Dev. 120, 65–80 (2003).
  Article CAS PubMed Google Scholar
• Conrad, E. et al. The MAFB transcription factor impacts islet α-cell function in rodents and represents a unique signature of primate islet β-cells. Am. J. Physiol. Endocrinol. Metab. 310, E91–E102 (2016).
  Article PubMed Google Scholar
• Katoh, M. C. MafB is critical for glucagon production and secretion in mouse pancreatic α cells in vivo. Mol. Cell. Biol. 38, e00504-17 (2018).
  Article PubMed PubMed Central Google Scholar
• Nishimura, W., Takahashi, S. & Yasuda, K. MafA is critical for maintenance of the mature beta cell phenotype in mice. Diabetologia 58, 566–574 (2015).
  Article CAS PubMed Google Scholar
• Ozato, K., Tailor, P. & Kubota, T. The interferon regulatory factor family in host defense: mechanism of action. J. Biol. Chem. 282, 20065–20069 (2007).
  Article CAS PubMed Google Scholar
• De Val, S. & Black, B. L. Transcriptional control of endothelial cell development. Dev. Cell 16, 180–195 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Segerstolpe, Å. et al. Single-cell transcriptome profiling of human pancreatic islets in health and type 2 diabetes. Cell Metab. 24, 593–607 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Lawlor, N. et al. Single-cell transcriptomes identify human islet cell signatures and reveal cell-type-specific expression changes in type 2 diabetes. Genome Res. 27, 208–222 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Mawla, A. M. & Huising, M. O. Navigating the depths and avoiding the shallows of pancreatic islet cell transcriptomes. Diabetes 68, 1380–1393 (2019).
  Article CAS PubMed PubMed Central Google Scholar
• Camunas-Soler, J. et al. Patch-seq links single-cell transcriptomes to human islet dysfunction in diabetes. Cell Metab. 31, 1017–1031.e4 (2020).
  Article CAS PubMed PubMed Central Google Scholar
• Trapnell, C. et al. Pseudo-temporal ordering of individual cells reveals dynamics and regulators of cell fate decisions. Nat. Biotechnol. 32, 381–386 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Parker, S. C. J. et al. Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants. Proc. Natl Acad. Sci. USA 110, 17921–17926 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Aylward, A., Chiou, J., Okino, M.-L., Kadakia, N. & Gaulton, K. J. Shared genetic risk contributes to type 1 and type 2 diabetes etiology. Hum. Mol. Genet. https://doi.org/10.1093/hmg/ddy314 (2018).
• Strawbridge, R. J. et al. Genome-wide association identifies nine common variants associated with fasting proinsulin levels and provides new insights into the pathophysiology of type 2 diabetes. Diabetes 60, 2624–2634 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Locke, A. E. et al. Genetic studies of body mass index yield new insights for obesity biology. Nature 518, 197–206 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Saxena, R. et al. Genetic variation in GIPR influences the glucose and insulin responses to an oral glucose challenge. Nat. Genet. 42, 142–148 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Wheeler, E. et al. Impact of common genetic determinants of hemoglobin A1c on type 2 diabetes risk and diagnosis in ancestrally diverse populations: a transethnic genome-wide meta-analysis. PLoS Med. 14, e1002383 (2017).
  Article PubMed PubMed Central Google Scholar
• Ripke, S. et al. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014).
  Article CAS PubMed Central Google Scholar
• de Lange, K. M. et al. Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease. Nat. Genet. 49, 256–261 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Bentham, J. et al. Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus. Nat. Genet. 47, 1457–1464 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Lambert, J. C. et al. Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer’s disease. Nat. Genet. 45, 1452–1458 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Wray, N. R. et al. Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression. Nat. Genet. 50, 668–681 (2018).
  Article CAS PubMed PubMed Central Google Scholar
• Nelson, C. P. et al. Association analyses based on false discovery rate implicate new loci for coronary artery disease. Nat. Genet. 49, 1385–1391 (2017).
  Article CAS PubMed Google Scholar
• Nielsen, J. B. et al. Biobank-driven genomic discovery yields new insight into atrial fibrillation biology. Nat. Genet. 50, 1234–1239 (2018).
  Article CAS PubMed PubMed Central Google Scholar
• Cordell, H. J. et al. International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways. Nat. Commun. 6, 8019 (2015).
  Article CAS PubMed Google Scholar
• Bulik-Sullivan, B. et al. An atlas of genetic correlations across human diseases and traits. Nat. Genet. 47, 1236–1241 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Bulik-Sullivan, B. K. et al. LD Score regression distinguishes confounding from polygenicity in genome-wide association studies. Nat. Genet. 47, 291–295 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Finucane, H. K. et al. Partitioning heritability by functional annotation using genome-wide association summary statistics. Nat. Genet. 47, 1228–1235 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Scott, R. A. et al. An expanded genome-wide association study of type 2 diabetes in Europeans. Diabetes 66, 2888–2902 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Pickrell, J. K. Joint analysis of functional genomic data and genome-wide association studies of 18 human traits. Am. J. Hum. Genet. 94, 559–573 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Lee, D. et al. A method to predict the impact of regulatory variants from DNA sequence. Nat. Genet. 47, 955–961 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• McCarthy, S. et al. A reference panel of 64,976 haplotypes for genotype imputation. Nat. Genet. 48, 1279–1283 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Wingender, E., Schoeps, T., Haubrock, M. & Dönitz, J. TFClass: a classification of human transcription factors and their rodent orthologs. Nucleic Acids Res. 43, D97–D102 (2015).
  Article CAS PubMed Google Scholar
• Shlyueva, D., Stampfel, G. & Stark, A. Transcriptional enhancers: from properties to genome-wide predictions. Nat. Rev. Genet. 15, 272–286 (2014).
  Article CAS PubMed Google Scholar
• Schmitt, A. D., Hu, M. & Ren, B. Genome-wide mapping and analysis of chromosome architecture. Nat. Rev. Mol. Cell Biol. 17, 743–755 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Thurman, R. E. et al. The accessible chromatin landscape of the human genome. Nature 489, 75–82 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Miguel-Escalada, I. et al. Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes. Nat. Genet. 51, 1137–1148 (2019).
  Article CAS PubMed PubMed Central Google Scholar
• Jian, X. & Felsenfeld, G. Insulin promoter in human pancreatic β cells contacts diabetes susceptibility loci and regulates genes affecting insulin metabolism. Proc. Natl Acad. Sci. USA 115, E4633–E4641 (2018).
  Article CAS PubMed PubMed Central Google Scholar
• Lawlor, N. et al. Multiomic profiling identifies _cis_-regulatory networks underlying human pancreatic β cell identity and function. Cell Rep. 26, 788–801.e6 (2019).
  Article CAS PubMed PubMed Central Google Scholar
• Rezania, A. et al. Reversal of diabetes with insulin-producing cells derived in vitro from human pluripotent stem cells. Nat. Biotechnol. 32, 1121–1133 (2014).
  Article CAS PubMed Google Scholar
• Claussnitzer, M. et al. FTO obesity variant circuitry and adipocyte browning in humans. N. Engl. J. Med. 373, 895–907 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Fogarty, M. P., Cannon, M. E., Vadlamudi, S., Gaulton, K. J. & Mohlke, K. L. Identification of a regulatory variant that binds FOXA1 and FOXA2 at the CDC123/CAMK1D type 2 diabetes GWAS locus. PLoS Genet. 10, e1004633 (2014).
  Article PubMed PubMed Central Google Scholar
• Rusu, V. et al. Type 2 diabetes variants disrupt function of SLC16A11 through two distinct mechanisms. Cell 170, 199–212.e20 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Carrat, G. R. et al. Decreased STARD10 expression is associated with defective insulin secretion in humans and mice. Am. J. Hum. Genet. 100, 238–256 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Claussnitzer, M. et al. Leveraging cross-species transcription factor binding site patterns: from diabetes risk loci to disease mechanisms. Cell 156, 343–358 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Roman, T. S. et al. A type 2 diabetes-associated functional regulatory variant in a pancreatic islet enhancer at the ADCY5 locus. Diabetes 66, 2521–2530 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Kycia, I. et al. A common type 2 diabetes risk variant potentiates activity of an evolutionarily conserved islet stretch enhancer and increases C2CD4A and C2CD4B expression. Am. J. Hum. Genet. 102, 620–635 (2018).
  Article CAS PubMed PubMed Central Google Scholar
• Avrahami, D., Klochendler, A., Dor, Y. & Glaser, B. Beta cell heterogeneity: an evolving concept. Diabetologia 60, 1363–1369 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Modi, H. et al. Ins2 gene bursting activity defines a mature β-cell state. Preprint at bioRxiv https://doi.org/10.1101/702589 (2019).
• Farack, L. et al. Transcriptional heterogeneity of beta cells in the intact pancreas. Dev. Cell 48, 115–125.e4 (2019).
  Article CAS PubMed Google Scholar
• Rai, V. et al. Single-cell ATAC-seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures. Mol. Metab. 32, 109–121 (2020).
  Article CAS PubMed Google Scholar
• Dunham, I. et al. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
  Article CAS Google Scholar
• Amemiya, H. M., Kundaje, A. & Boyle, A. P. The ENCODE blacklist: identification of problematic regions of the genome. Sci. Rep. 9, 9354 (2019).
• Wolf, F. A., Angerer, P. & Theis, F. J. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 19, 15 (2018).
  Article PubMed PubMed Central Google Scholar
• Traag, V. A., Waltman, L. & van Eck, N. J. From Louvain to Leiden: guaranteeing well-connected communities. Sci. Rep. 9, 5233 (2019).
  Article CAS PubMed PubMed Central Google Scholar
• Arda, H. E. et al. A chromatin basis for cell lineage and disease risk in the human pancreas. Cell Syst. 7, 310–322.e4 (2018).
  Article CAS PubMed Google Scholar
• Ackermann, A. M., Wang, Z., Schug, J., Naji, A. & Kaestner, K. H. Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes. Mol. Metab. 5, 233–244 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Kuleshov, M. V. et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 44, W90–W97 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545–15550 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Li, Y. I. et al. RNA splicing is a primary link between genetic variation and disease. Science 352, 600–604 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Bailey, T. L. et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37, W202–W208 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• van de Geijn, B., McVicker, G., Gilad, Y. & Pritchard, J. K. WASP: allele-specific software for robust molecular quantitative trait locus discovery. Nat. Methods 12, 1061–1063 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Durand, N. C. et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst. 3, 95–98 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Kerpedjiev, P. et al. HiGlass: web-based visual exploration and analysis of genome interaction maps. Genome Biol. 19, 125 (2018).
  Article PubMed PubMed Central Google Scholar
• Raviram, R. et al. 4C-ker: a method to reproducibly identify genome-wide interactions captured by 4C-seq experiments. PLoS Comput. Biol. 12, e1004780 (2016).
  Article PubMed PubMed Central Google Scholar
• Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Velazco-Cruz, L. et al. Acquisition of dynamic function in human stem cell-derived β cells. Stem Cell Rep. 12, 351–365 (2019).
  Article CAS Google Scholar