Regulatory variants are often context specific, modulating gene expression in a subset of possible cellular states. Although these genetic effects can play important roles in disease, the molecular mechanisms underlying context specificity are poorly understood. Here, we identified shared quantitative trait loci (QTLs) for chromatin accessibility and gene expression in human macrophages exposed to IFNγ, Salmonella and IFNγ plus Salmonella. We observed that ~60% of stimulus-specific expression QTLs with a detectable effect on chromatin altered the chromatin accessibility in naive cells, thus suggesting that they perturb enhancer priming. Such variants probably influence binding of cell-type-specific transcription factors, such as PU.1, which can then indirectly alter the binding of stimulus-specific transcription factors, such as NF-κB or STAT2. Thus, although chromatin accessibility assays are powerful for fine-mapping causal regulatory variants, detecting their downstream effects on gene expression will be challenging, requiring profiling of large numbers of stimulated cellular states and time points.

Induced pluripotent stem cells (iPSCs), and cells derived from them, have become key tools to model biological processes, particularly in cell types that are difficult to access from living donors. We present the first map of regulatory variants in iPSC-derived neurons, based on 123 differentiations of iPSCs to a sensory neuronal fate. Gene expression was more variable across cultures than in primary dorsal root ganglion, particularly in genes related to nervous system development. Using single-cell RNA-sequencing, we found that the fraction of neuronal vs. contaminating cells was influenced by iPSC culture conditions prior to differentiation. Despite high differentiation-induced variability, using an allele-specific method we detected thousands of quantitative trait loci (QTLs) influencing gene expression, chromatin accessibility, and RNA splicing. Based on our QTLs, we estimate that recall-by-genotype studies using iPSC-derived cells will require at least 20-80 individuals to detect the effects of regulatory variants with moderately large effect sizes.

Growth plate cartilage contributes to the generation of a large variety in shapes and sizes of skeletal elements in the mammalian system. The removal of cartilage and how this process regulates bone shape are not well understood. Here we identify a non-bone-resorbing osteoclast subtype termed vessel associated osteoclast (VAO). Endothelial cells (ECs) at the bone-cartilage interface support VAOs through a RANKL-RANK signaling mechanism. Contrary to classical bone associated osteoclasts (BAOs), VAOs are dispensable for cartilage resorption and regulate anastomoses of type-H vessels. Remarkably, proteinases including Matrix metalloproteinase-9 (Mmp9) released from ECs, not osteoclasts, are essential for resorbing cartilage to lead directional bone growth. Importantly, disrupting the orientation of angiogenic blood vessels by misdirecting them results in contorted bone shape. This study identifies proteolytic functions of ECs in cartilage and provides a framework to explore tissue lytic features of blood vessels in fracture healing, arthritis and cancer.

Induced pluripotent stem cells (iPSCs), and cells derived from them, have become key tools to model biological processes and disease mechanisms, particularly in cell types such as neurons that are difficult to access from living donors. Here, we present the first map of regulatory variants in an iPSC-derived cell type. To investigate genetic contributions to human sensory function, we performed 123 differentiations of iPSCs from 103 unique donors to a sensory neuronal fate, and measured gene expression, chromatin accessibility, and neuronal excitability. Compared with primary dorsal root ganglion, where sensory nerves collect near the spinal cord, gene expression was more variable across iPSC-derived neuronal cultures, particularly in genes related to differentiation and nervous system development. Single cell RNA-sequencing revealed that although the majority of cells are neuronal and express the expected marker genes, a substantial fraction have a fibroblast-like expression profile. By applying an allele-specific method we identify 3,778 quantitative trait loci influencing gene expression, 6,318 for chromatin accessibility, and 2,097 for RNA splicing at FDR 10%. A number of these overlap with common disease associations, and suggest candidate causal variants and target genes. These include known causal variants at SNCA for Parkinson's disease and TNFRSF1A for multiple sclerosis, as well as new candidates for migraine, Parkinson's disease, and schizophrenia.