To identify epigenetic patterns, which may predispose to type 2 diabetes (T2D) due to a family history (FH) of the disease, we analyzed DNA methylation genome-wide in skeletal muscle from individuals with (FH+) or without (FH−) an FH of T2D. We found differential DNA methylation of genes in biological pathways including mitogen-activated protein kinase (MAPK), insulin, and calcium signaling (P ≤ 0.007) and of individual genes with known function in muscle, including MAPK1, MYO18B, HOXC6, and the AMP-activated protein kinase subunit PRKAB1 in skeletal muscle of FH+ compared with FH− men. We further validated our findings from FH+ men in monozygotic twin pairs discordant for T2D, and 40% of 65 analyzed genes exhibited differential DNA methylation in muscle of both FH+ men and diabetic twins. We further examined if a 6-month exercise intervention modifies the genome-wide DNA methylation pattern in skeletal muscle of the FH+ and FH− individuals. DNA methylation of genes in retinol metabolism and calcium signaling pathways (P < 3 × 10−6) and with known functions in muscle and T2D including MEF2A, RUNX1, NDUFC2, and THADA decreased after exercise. Methylation of these human promoter regions suppressed reporter gene expression in vitro. In addition, both expression and methylation of several genes, i.e., ADIPOR1, BDKRB2, and TRIB1, changed after exercise. These findings provide new insights into how genetic background and environment can alter the human epigenome.

IntroductionThe murine hematopoietic system is a hierarchically organized process that arises from a small pool of self-renewing hematopoietic stem cells (HSCs). Upon induction of differentiation, HSCs lose self-renewal ability and develop through a series of specialized progenitor cell types that possess restricted differentiation potential. 1 Although several cell-intrinsic and microenvironmental factors that can control these processes have been identified, the precise molecular circuitry controlling HSC self-renewal and lineage restriction has yet to be fully elucidated.Recent observations suggest that epigenetic-based mechanisms play an important role in controlling HSC self-renewal or differentiation. 2,3 Epigenetic regulation of gene expression is largely controlled by the posttranslational modification of histones and DNA methylation, resulting in the alteration of chromatin structure and function at genes throughout cellular differentiation. 4 Core histones can be covalently modified, for example, by acetylation and methylation at multiple residues, offering combinatorial codes with diverse functional outcomes. 5 We and others have hypothesized previously that HSCs possess unique epigenetic signatures, whose inheritance by progenitor subsets allows for differentiation into mature blood cell types via highly coordinated gene activation and silencing. 4,6-9 These unique chromatin states may allow for the preassembling of critical transcription factors at lineage-specifying promoters in HSC and progenitor cells, before full gene expression in differentiated subsets. [10][11][12][13] This process, known as multilineage gene priming, is supported by the low-level transcription of several lineage-affiliated genes of lymphoid, myeloid, and erythroid genetic programs which occurs in HSCs and early progenitor cells. 8,[14][15][16] Most recently, genome-wide profiling of human hematopoietic stem/ progenitor cells and differentiated erythrocyte precursor cells has revealed epigenetic signatures that are proposed to be important for maintaining HSC multipotency. 17 Despite the insights gained from such studies, most have been based on either selected loci or global analysis of cell populations with heterogeneous lineage potentials. As a result, the true epigenetic status of functionally homogeneous stem and progenitor cell compartments may have been underestimated.We have undertaken a global analysis of highly purified and functionally validated murine HSCs, early hematopoietic progenitors, and mature CD4 ϩ T cells to reveal the epigenetic features associated with their unique functional properties. We show that promoters of genes affiliated with regulation of hematopoietic cell maturation are occupied by bivalent histone modifications in HSCs and their immediate progeny. In addition, many lineage-specifying promoters in these primitive cells possess a diverse range of histone modification patterns, together suggesting that specific combinations prepare these genes for selective expression or silencing during linea...

Despite the key role of primary and secondary lymphoid organ stroma in immunity, our understanding of the heterogeneity and ontogeny of these cells remains limited. Here, we identify a functionally distinct subset of BP3(-)PDPN(+)PDGFRβ(+)/α(+)CD34(+) stromal adventitial cells in both lymph nodes (LNs) and thymus that is located within the vascular niche surrounding PDPN(-)PDGFRβ(+)/α(-)Esam-1(+)ITGA7(+) pericytes. CD34(+) adventitial cells developed in late embryonic thymus and in postnatal LNs and in the thymus originated, along with pericytes, from a common anlage-seeding progenitor population. Using lymphoid organ re-aggregate grafts, we demonstrate that adult CD34(+) adventitial cells are capable of differentiating into multiple lymphoid stroma-like subsets including pericyte-, FRC-, MRC-, and FDC-like cells, the development of which was lymphoid environment-dependent. These findings extend the current understanding of lymphoid mesenchymal cell heterogeneity and highlight a role of the CD34(+) adventitia as a potential ubiquitous source of lymphoid stromal precursors in postnatal tissues.

Highlights d MYCN drives SHH medulloblastoma tumorigenesis in human iPSC-derived NES cells d NES cells from Gorlin syndrome (PTCH1 +/À) iPSCs generate SHH medulloblastoma d Mutation of DDX3X or GSE1 accelerates tumorigenesis in Gorlin NES cells