Project description:The human kidneys are comprised of multiple different cell types in a complex anatomical arragemnt that is optimal for their key functions such as waste removal, regulation of fluid and electrolyte homeostasis and production of hormones. In chronic kidney disease (CKD) this arrangement is disrupted with de-differentiation and atrophy of epithelial cells, recruitment of immune cells and activation of myofibroblasts to produce excess scarring. A better understanding of cellular phenotypes, complex intercellular communication and intracellular signaling pathways that promote CKD could lead to development of novel therapies. We applied single-cell spatial transcriptomics (CosMx Spatial molecular imaging) to human kidney neprectomy speciemens with unilateral ureteral obstruction (UUO, n=5) and healthy kidneys (n=2).
Project description:The human kidneys are comprised of multiple different cell types in a complex anatomical arragemnt that is optimal for their key functions such as waste removal, regulation of fluid and electrolyte homeostasis and production of hormones. In chronic kidney disease (CKD) this arrangement is disrupted with de-differentiation and atrophy of epithelial cells, recruitment of immune cells and activation of myofibroblasts to produce excess scarring. A better understanding of cellular phenotypes, complex intercellular communication and intracellular signaling pathways that promote CKD could lead to development of novel therapies. We applied single-cell spatial transcriptomics (CosMx Spatial molecular imaging) to human kidney biopy and nephrectomy samples from patients with IgA nephropathy (n=6), minimal change disease (n=3) and advanced pyelonephritis (n=4).
Project description:Diffuse large B-cell lymphomas (DLBCLs) are a common and heterogeneous group of mature B-cell malignancies that typically arise in lymph nodes; sites in which stromal and endothelial cells, antigen-presenting cells and other myeloid cells facilitate adaptive immune responses by T-cells and B-cells against pathogens. In this study, we have leveraged the spatial transcriptomic platform of CosMx together with CODEX imaging technology to investigate the spatial immunology and pathobiology of DLBCL.
Project description:Inflammatory bowel diseases (IBDs) including ulcerative colitis (UC) and Crohn’s disease (CD) are chronic inflammatory diseases with increasing worldwide prevalence that show a perplexing heterogeneity in manifestations and response to treatment. We applied spatial transcriptomics at single-cell resolution (CosMx Spatial Molecular Imaging) to human inflamed and uninflamed intestine.
Project description:Patients with treatment-refractory pancreatic cancer often succumb to widespread systemic metastases; however, the transcriptomic heterogeneity that underlies recalcitrance to therapy remains understudied, particularly in the spatial context. We constructed high-resolution spatial maps of transcriptional heterogeneity, clonal architecture and lineage plasticity using spatially resolved transcriptomics (SRT) from 13 primary cancers and 36 corresponding liver, lung, and peritoneal metastases, collected via a rapid (“warm”) autopsy program. To validate findings from our SRT dataset at single-cell resolution, we performed CosMX SMI profiling (Nanostring) on 7 samples from 3 patients, including primary and/or liver metastasis.
Project description:Buffy coat PBMC RNA expression was tested using a custom Nanostring probe panel, to identify general immune and glucocorticoid receptor-associated immune genes. ClinicalTrials.gov Identifier: NCT00824941