Tet2 Controls the Responses of ß cells to Inflammation in Autoimmune Diabetes.

ß cells may participate and contribute to their own demise during Type 1 diabetes (T1D). Here we report a role of their expression of Tet2 in regulating immune killing. Tet2 is induced in murine and human ß cells with inflammation but its expression is reduced in surviving ß cells. Tet2-KO mice that receive WT bone marrow transplants develop insulitis but not diabetes and islet infiltrates do not eliminate ß cells even though immune cells from the mice can transfer diabetes to NOD/scid recipients. Tet2-KO recipients are protected from transfer of disease by diabetogenic immune cells.Tet2-KO ß cells show reduced expression of IFNγ-induced inflammatory genes that are needed to activate diabetogenic T cells. Here we show that Tet2 regulates pathologic interactions between ß cells and immune cells and controls damaging inflammatory pathways. Our data suggests that eliminating TET2 in ß cells may reduce activating pathologic immune cells and killing of ß cells.

Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR-FlowFISH.

Effective interpretation of genome function and genetic variation requires a shift from epigenetic mapping of cis-regulatory elements (CREs) to characterization of endogenous function. We developed hybridization chain reaction fluorescence in situ hybridization coupled with flow cytometry (HCR-FlowFISH), a broadly applicable approach to characterize CRISPR-perturbed CREs via accurate quantification of native transcripts, alongside CRISPR activity screen analysis (CASA), a hierarchical Bayesian model to quantify CRE activity. Across >325,000 perturbations, we provide evidence that CREs can regulate multiple genes, skip over the nearest gene and display activating and/or silencing effects. At the cholesterol-level-associated FADS locus, we combine endogenous screens with reporter assays to exhaustively characterize multiple genome-wide association signals, functionally nominate causal variants and, importantly, identify their target genes.

Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D.

Most signals detected by genome-wide association studies map to non-coding sequence and their tissue-specific effects influence transcriptional regulation. However, key tissues and cell-types required for functional inference are absent from large-scale resources. Here we explore the relationship between genetic variants influencing predisposition to type 2 diabetes (T2D) and related glycemic traits, and human pancreatic islet transcription using data from 420 donors. We find: (a) 7741 cis-eQTLs in islets with a replication rate across 44 GTEx tissues between 40% and 73%; (b) marked overlap between islet cis-eQTL signals and active regulatory sequences in islets, with reduced eQTL effect size observed in the stretch enhancers most strongly implicated in GWAS signal location; (c) enrichment of islet cis-eQTL signals with T2D risk variants identified in genome-wide association studies; and (d) colocalization between 47 islet cis-eQTLs and variants influencing T2D or glycemic traits, including DGKB and TCF7L2. Our findings illustrate the advantages of performing functional and regulatory studies in disease relevant tissues.

Cell Specificity of Human Regulatory Annotations and Their Genetic Effects on Gene Expression.

Epigenomic signatures from histone marks and transcription factor (TF)-binding sites have been used to annotate putative gene regulatory regions. However, a direct comparison of these diverse annotations is missing, and it is unclear how genetic variation within these annotations affects gene expression. Here, we compare five widely used annotations of active regulatory elements that represent high densities of one or more relevant epigenomic marks-"super" and "typical" (nonsuper) enhancers, stretch enhancers, high-occupancy target (HOT) regions, and broad domains-across the four matched human cell types for which they are available. We observe that stretch and super enhancers cover cell type-specific enhancer "chromatin states," whereas HOT regions and broad domains comprise more ubiquitous promoter states. Expression quantitative trait loci (eQTL) in stretch enhancers have significantly smaller effect sizes compared to those in HOT regions. Strikingly, chromatin accessibility QTL in stretch enhancers have significantly larger effect sizes compared to those in HOT regions. These observations suggest that stretch enhancers could harbor genetically primed chromatin to enable changes in TF binding, possibly to drive cell type-specific responses to environmental stimuli. Our results suggest that current eQTL studies are relatively underpowered or could lack the appropriate environmental context to detect genetic effects in the most cell type-specific "regulatory annotations," which likely contributes to infrequent colocalization of eQTL with genome-wide association study signals.

Single-cell transcriptomes identify human islet cell signatures and reveal cell-type-specific expression changes in type 2 diabetes.

Blood glucose levels are tightly controlled by the coordinated action of at least four cell types constituting pancreatic islets. Changes in the proportion and/or function of these cells are associated with genetic and molecular pathophysiology of monogenic, type 1, and type 2 (T2D) diabetes. Cellular heterogeneity impedes precise understanding of the molecular components of each islet cell type that govern islet (dys)function, particularly the less abundant delta and gamma/pancreatic polypeptide (PP) cells. Here, we report single-cell transcriptomes for 638 cells from nondiabetic (ND) and T2D human islet samples. Analyses of ND single-cell transcriptomes identified distinct alpha, beta, delta, and PP/gamma cell-type signatures. Genes linked to rare and common forms of islet dysfunction and diabetes were expressed in the delta and PP/gamma cell types. Moreover, this study revealed that delta cells specifically express receptors that receive and coordinate systemic cues from the leptin, ghrelin, and dopamine signaling pathways implicating them as integrators of central and peripheral metabolic signals into the pancreatic islet. Finally, single-cell transcriptome profiling revealed genes differentially regulated between T2D and ND alpha, beta, and delta cells that were undetectable in paired whole islet analyses. This study thus identifies fundamental cell-type-specific features of pancreatic islet (dys)function and provides a critical resource for comprehensive understanding of islet biology and diabetes pathogenesis.

Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma.

Synonymous mutations, which do not alter the protein sequence, have been shown to affect protein function [Sauna ZE, Kimchi-Sarfaty C (2011) Nat Rev Genet 12(10):683-691]. However, synonymous mutations are rarely investigated in the cancer genomics field. We used whole-genome and -exome sequencing to identify somatic mutations in 29 melanoma samples. Validation of one synonymous somatic mutation in BCL2L12 in 285 samples identified 12 cases that harbored the recurrent F17F mutation. This mutation led to increased BCL2L12 mRNA and protein levels because of differential targeting of WT and mutant BCL2L12 by hsa-miR-671-5p. Protein made from mutant BCL2L12 transcript bound p53, inhibited UV-induced apoptosis more efficiently than WT BCL2L12, and reduced endogenous p53 target gene transcription. This report shows selection of a recurrent somatic synonymous mutation in cancer. Our data indicate that silent alterations have a role to play in human cancer, emphasizing the importance of their investigation in future cancer genome studies.

Regulation of MBK-2/Dyrk kinase by dynamic cortical anchoring during the oocyte-to-zygote transition.

BACKGROUND: Successful transition from oocyte to zygote depends on the timely degradation of oocyte proteins to prepare for embryonic development. In C. elegans, degradation of the oocyte protein MEI-1 depends on MBK-2, a kinase that phosphorylates MEI-1 shortly after fertilization during the second meiotic division. RESULTS: Here we report that precise timing of MEI-1 phosphorylation depends on the cell cycle-regulated release of MBK-2 from the cortex. Prior to the meiotic divisions, MBK-2 is tethered at the cortex by EGG-3, an oocyte protein required for egg activation (see [1], accompanying paper in this issue). During the meiotic divisions, EGG-3 is internalized and degraded in an APC/C (anaphase-promoting complex/cyclosome)-dependent manner. EGG-3 internalization and degradation correlate with MBK-2 release from the cortex and MEI-1 phosphorylation in the cytoplasm. In an egg-3 mutant, MEI-1 is phosphorylated and degraded prematurely. CONCLUSION: We suggest that successful transition from an oocyte to a zygote depends on the cell cycle-regulated relocalization of key regulators from the cortex to the cytoplasm of the egg.

The C. elegans DYRK Kinase MBK-2 Marks Oocyte Proteins for Degradation in Response to Meiotic Maturation.

The oocyte-to-embryo transition transforms a differentiated germ cell into a totipotent zygote capable of somatic development. In C. elegans, several oocyte proteins, including the meiotic katanin subunit MEI-1 and the oocyte maturation protein OMA-1, must be degraded during this transition . Degradation of MEI-1 and OMA-1 requires the dual-specificity YAK-1-related (DYRK) kinase MBK-2 . Here, we demonstrate that MBK-2 directly phosphorylates MEI-1 and OMA-1 in vitro and that this activity is essential for degradation in vivo. Phosphorylation of MEI-1 by MBK-2 reaches maximal levels after the meiotic divisions, immediately preceding MEI-1 degradation. MEI-1 phosphorylation and degradation still occur in spe-9 eggs, which undergo meiotic maturation and exit in the absence of fertilization . In contrast, MEI-1 phosphorylation and degradation are blocked in cell-cycle mutants that arrest during the meiotic divisions, and are accelerated in wee-1.3(RNAi) oocytes, which prematurely enter meiotic M phase (A. Golden, personal communication). A GFP:MBK-2 fusion relocalizes from the cortex to the cytoplasm during the meiotic divisions, and this relocalization also depends on cell-cycle progression. Our findings suggest that regulators of meiotic M phase activate a remodeling program, independently of fertilization, to prepare eggs for embryogenesis.