Global endometrial DNA methylation analysis reveals insights into mQTL regulation and associated endometriosis disease risk and endometrial function.

Endometriosis is a leading cause of pain and infertility affecting millions of women globally. Herein, we characterize variation in DNA methylation (DNAm) and its association with menstrual cycle phase, endometriosis, and genetic variants through analysis of genotype data and methylation in endometrial samples from 984 deeply-phenotyped participants. We estimate that 15.4% of the variation in endometriosis is captured by DNAm and identify significant differences in DNAm profiles associated with stage III/IV endometriosis, endometriosis sub-phenotypes and menstrual cycle phase, including opening of the window for embryo implantation. Menstrual cycle phase was a major source of DNAm variation suggesting cellular and hormonally-driven changes across the cycle can regulate genes and pathways responsible for endometrial physiology and function. DNAm quantitative trait locus (mQTL) analysis identified 118,185 independent cis-mQTLs including 51 associated with risk of endometriosis, highlighting candidate genes contributing to disease risk. Our work provides functional evidence for epigenetic targets contributing to endometriosis risk and pathogenesis. Data generated serve as a valuable resource for understanding tissue-specific effects of methylation on endometrial biology in health and disease.

CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis.

A hallmark of age-associated neurodegenerative diseases is the aggregation of proteins. Aggregation of the protein tau defines tauopathies, which include Alzheimer's disease and frontotemporal dementia. Specific neuronal subtypes are selectively vulnerable to the accumulation of tau aggregates, and subsequent dysfunction and death. The mechanisms underlying cell type-selective vulnerability are unknown. To systematically uncover the cellular factors controlling the accumulation of tau aggregates in human neurons, we conducted a genome-wide CRISPRi-based modifier screen in iPSC-derived neurons. The screen uncovered expected pathways, including autophagy, but also unexpected pathways including UFMylation and GPI anchor synthesis, that control tau oligomer levels. We identify the E3 ubiquitin ligase CUL5 as a tau interactor and potent modifier of tau levels. In addition, disruption of mitochondrial function increases tau oligomer levels and promotes proteasomal misprocessing of tau. These results reveal new principles of tau proteostasis in human neurons and pinpoint potential therapeutic targets for tauopathies.

Embryo-scale, single-cell spatial transcriptomics.

Spatial patterns of gene expression manifest at scales ranging from local (e.g., cell-cell interactions) to global (e.g., body axis patterning). However, current spatial transcriptomics methods either average local contexts or are restricted to limited fields of view. Here, we introduce sci-Space, which retains single-cell resolution while resolving spatial heterogeneity at larger scales. Applying sci-Space to developing mouse embryos, we captured approximate spatial coordinates and whole transcriptomes of about 120,000 nuclei. We identify thousands of genes exhibiting anatomically patterned expression, leverage spatial information to annotate cellular subtypes, show that cell types vary substantially in their extent of spatial patterning, and reveal correlations between pseudotime and the migratory patterns of differentiating neurons. Looking forward, we anticipate that sci-Space will facilitate the construction of spatially resolved single-cell atlases of mammalian development.

Guided vascularization in the rat heart leads to transient vessel patterning.

Recent progress in the production and maturation of iPSC-cardiomyocytes has facilitated major advances in building bioartificial heart tissue with functional cardiomyocytes. Despite this progress, vascularizing these constructs continues to be a barrier to clinical application. One emerging strategy for vascularization uses aligned "cords" of endothelial cells in tissue grafts to guide assembly of chimeric microvessels upon graft implantation. Here, we test whether this approach can guide vascularization of a bioartificial tissue implanted on the rat heart. We find that patterned cords of human endothelial cells anastomose and become perfused with host blood by 3 days post-implantation. Immunohistochemical staining confirmed that graft-derived micro-vessels persist in the patch for 7 days. Furthermore, we noted a shift in distribution of vessels in the patch from patterned cord-associated clustering at 3 days to a more diffuse distribution pattern at 7 days. This loss of patterning corresponded to an infiltration of CD68+ cells and an increase in collagen within the patch. Upon further engraftment of patches containing both cords and human cardiomyocytes, we identified human cardiomyocytes and graft derived vasculature at the time of explant. Our findings show that patterned endothelial cords guide transient vessel patterning on the rat heart. Our results also suggest that future work should be directed at further adapting vascularization strategies to the epicardial environment and add to an important emerging dialog in cardiac cell therapy that points to the need to characterize host response prior to or in parallel with efficacy studies.