The Polycomb-Dependent Epigenome Controls β Cell Dysfunction Dedifferentiation and Diabetes

摘要

class="head no_bottom_margin" id="sec1title">IntroductionComplex diseases such as cancer, autoimmunity, obesity, and diabetes represent some of the greatest socio-economic challenges of our day. They result from genetic predisposition but contain equally strong non-genetic components, often termed “environmental influences,” that alter susceptibility, reversibility, and triggering of disease. Non-genetic regulation is believed to converge upon chromatin-dependent processes, etiological contributions that remain poorly understood.Diabetes affects more than 400 million individuals worldwide (). It presents predominantly in either an early-onset autoimmune type 1 or a heterogeneous type 2 diabetes (T2D) associated with obesity, inflammation, and insulin resistance. Ultimately, diabetes results from insufficient insulin-secreting β cell mass, resulting from impaired function, increased cell death, or loss of cell identity. The last decades have seen major advances in our understanding of β cell identity, development, and plasticity. β Cells are believed to be highly plastic (, ), and pioneering studies over the last decades have revealed networks of transcriptional and chromatin regulators that drive β cell lineage development (, , , , , ) and that provide barriers against transdifferentiation or loss of β cell identity (, , , , , , href="#bib45" rid="bib45" class=" bibr popnode">Swisa et al., 2017, href="#bib17" rid="bib17" class=" bibr popnode">Ediger et al., 2017, href="#bib14" rid="bib14" class=" bibr popnode">Collombat et al., 2009, href="#bib24" rid="bib24" class=" bibr popnode">Gutiérrez et al., 2017).To date, it remains poorly understood how transcriptional programs are stabilized over the long cellular lifespans that can be found in vivo. Since adult β cells are both long-lived and highly plastic, mechanisms are thought to be in place to continuously reinforce and stabilize the terminally differentiated state (href="#bib13" rid="bib13" class=" bibr popnode">Cnop et al., 2011, href="#bib46" rid="bib46" class=" bibr popnode">Szabat et al., 2012). Seminal studies in both wild-type (href="#bib23" rid="bib23" class=" bibr popnode">Guo et al., 2013, href="#bib30" rid="bib30" class=" bibr popnode">Laybutt et al., 2003) and in genetic (href="#bib47" rid="bib47" class=" bibr popnode">Talchai et al., 2012, href="#bib10" rid="bib10" class=" bibr popnode">Brereton et al., 2014, href="#bib52" rid="bib52" class=" bibr popnode">Wang et al., 2014) models have highlighted relative losses of β cell identity, or “dedifferentiation,” with mounting metabolic stress. Dedifferentiation was coined to describe either a reversal of the differentiation trajectory back toward progenitor states or a loss of terminal differentiation markers and phenotypes (href="#bib27" rid="bib27" class=" bibr popnode">Holmberg and Perlmann, 2012, href="#bib53" rid="bib53" class=" bibr popnode">Weir et al., 2013). Studies have documented the phenomenon in culture (href="#bib39" rid="bib39" class=" bibr popnode">Russ et al., 2008) and in T2D, in rodents and in humans tissues, and have focused on re-appearance of progenitor markers (ALDH1A; href="#bib12" rid="bib12" class=" bibr popnode">Cinti et al., 2016), as well as loss of lineage-defining gene expression as cardinal features (PDX1, MAFA, NKX6-1, INS, and GLUT2; href="#bib23" rid="bib23" class=" bibr popnode">Guo et al., 2013). To date, aside from identification of a limited number of inducers (hyperglycemia, β cell inexcitability, and NPAS4 or FoxO1 deficiency), we understand little of the molecular mechanisms that define how and when dedifferentiation occurs (href="#bib40" rid="bib40" class=" bibr popnode">Sabatini et al., 2018, href="#bib6" rid="bib6" class=" bibr popnode">Bensellam et al., 2017).One chromatin-regulatory system important to defining cell fate trajectories is Polycomb. Polycomb comprises two sets of repressive complexes, PRC1 and PRC2, that mediate stable gene silencing through time and cell division (href="#bib33" rid="bib33" class=" bibr popnode">Margueron and Reinberg, 2011, href="#bib41" rid="bib41" class=" bibr popnode">Schuettengruber and Cavalli, 2009). PRC1 and PRC2 are non-redundant, with distinct loss-of-function phenotypes. PRC2 methylates the histone lysine residue H3K27 and is sufficient to silence gene expression (href="#bib33" rid="bib33" class=" bibr popnode">Margueron and Reinberg, 2011). PRC1 ubiquitinates H2AK119 at PRC2 marked domains, promoting chromatin compaction and further silencing (href="#bib42" rid="bib42" class=" bibr popnode">Simon and Kingston, 2013). Numerous PRC1 and PRC2 sub-complexes have emerged in recent literature, revealing additional unexplored complexities. Redundancies also exist, a prime example being the core PRC2 methyltransferases themselves, Ezh1 and Ezh2 (href="#bib56" rid="bib56" class=" bibr popnode">Xie et al., 2014, href="#bib18" rid="bib18" class=" bibr popnode">Ezhkova et al., 2011).Here, we used unbiased epigenome mapping and single-cell RNA sequencing (scRNA-seq) to explore the chromatin dependence of transcriptional regulation in β cells. We observed two signatures of chromatin-state-associated transcriptional dysregulation consistent between human T2D- and high-fat diet (HFD)-driven β cell dysfunction: first, a loss-of-silencing at poised/bivalent Polycomb domains, and, second, collapse of gene expression at a unique subset of highly accessible active domains including cardinal lineage determinants. β cell-specific loss of Eed/PRC2 not only recapitulated these key chromatin-state-associated changes, but also triggered highly penetrant, largely hyperglycemia-independent, β cell dedifferentiation, implicating impaired PRC2 function as exacerbatory in diabetes. These findings identify Eed/PRC2 as necessary for maintenance of global gene silencing and terminal differentiation in β cells, and suggest a “two-hit” (chromatin and hyperglycemia) model of β cell dedifferentiation.