Project description:We performed multiomics analysis; single nucleus RNA-seq (snRNA-seq) combined with ATAC (snATAC-seq) with 10XGenomics Multiome platform to generate cell-type-specific gene expression and chromatin accessibility atlas of the mouse polycystic kidney disease on a time course.
Project description:Retinal neovascularization poses heightened risks of vision loss and blindness. Despite its clinical significance, the molecular mechanisms underlying the pathogenesis of retinal neovascularization remain elusive. This study utilized single-cell multiomics profiling in an oxygen-induced retinopathy (OIR) model to comprehensively investigate the intricate molecular landscape of retinal neovascularization.
Project description:We evaluated blood samples from 6 patients with metastatic melanoma treated with anti-LAG3+anti-PD1 (160+480 mg) in a phase I trial (NCT01968109) using single-cell RNA and T cell receptor (TCR) sequencing (scRNA+TCRαβ-seq, 10X 5') combined with other multiomics profiling (flow, cytokine, TCRb-seq) from a larger cohort of 40 patients. This data set include three time points, including baseline, 1 month, and 3 month. The sorting is CD45+.
Project description:Systematic interrogation of tumor-infiltrating lymphocytes is key to the development of immunotherapies and the prediction of their clinical responses in cancers. Here, we perform deep single-cell RNA sequencing on single T cells isolated from peripheral blood, tumor and adjacent normal tissues from hepatocellular carcinoma patients.
Project description:We combined lineage tracing of cycling (Ki67+) cells with single nuclear multiomics (single nucleus RNA-seq + single nucleus ATAC-seq) to characterize the long-term (4 weeks and 6 months) outcome of cells that initiate proliferation early after acute kidney injury (AKI). The data document a broad proliferative response to injury in epithelial and non-epithelial kidney cell types, identify novel transcription factors governing the adaptive and maladaptive proximal tubule cell state and highlight the importance of enhancer dynamics in determining cell states. Comparison of lineage traced with control proximal tubule cells reveals long-term effects of AKI on proximal tubule cells, even following adaptive repair.
Project description:Inborn errors of T cell development present a pediatric emergency in which timely curative therapy is informed by molecular diagnosis. In 9 affected patients across 3 consanguineous kindreds, we detected homozygosity for a single deleterious missense variant in the gene NudC domain containing 3 (NUDCD3). Two infants lacked T and B lymphocytes altogether (T-B- severe combined immunodeficiency, T-B- SCID) while 7 showed classical features of Omenn syndrome. Restricted antigen receptor gene usage by residual T lymphocytes implied impaired V(D)J recombination. Patient cells showed reduced expression of NUDCD3 protein and diminished ability to support RAG-mediated recombination in vitro, associated with pathologic sequestration of RAG1 in nucleoli. A mouse model bearing the homologous variant phenocopied these abnormalities, confirming a conserved, requisite role for NUDCD3 in V(D)J recombination.