Project description:RDD is a poorly understood disease with low incidence. Here, we performed whole genome sequencing, single cell RNA-seq and spatial transcriptome sequencing of a nodal RDD, describing its cell composition, spatial arrangement and molecular characteristics from a multi-omics perspective. By integrating single cell RNA-seq data, we found that compared with lymph node and LCH, RDD harbors completely different cell composition and molecular feature. Compared with lymph node, a subset of ion-responded macrophage appeared in RDD. Compared with LCH, macrophages in RDD are enriched for RHO GTPase pathway. And RHO GTPase high macrophages have unique cell-cell interactions and are the most actively proliferating cells in RDD. Our results provide a valuable insight for understanding the molecular basis of nodal RDD.
Project description:RDD is a poorly understood disease with low incidence. Here, we performed whole genome sequencing, single cell RNA-seq and spatial transcriptome sequencing of a nodal RDD, describing its cell composition, spatial arrangement and molecular characteristics from a multi-omics perspective. By integrating single cell RNA-seq data, we found that compared with lymph node and LCH, RDD harbors completely different cell composition and molecular feature. Compared with lymph node, a subset of ion-responded macrophage appeared in RDD. Compared with LCH, macrophages in RDD are enriched for RHO GTPase pathway. And RHO GTPase high macrophages have unique cell-cell interactions and are the most actively proliferating cells in RDD. Our results provide a valuable insight for understanding the molecular basis of nodal RDD.
Project description:Oncogenic PIK3CA mutations activate phosphoinositide 3-kinase (PI3K) and are among the commonest somatic mutations in cancer and mosaic, developmental overgrowth disorders. We recently demonstrated that the ‘hotspot’ variant PIK3CAH1047R exerts striking allele dose-dependent effects on stemness in human induced pluripotent stem cells (iPSCs), and moreover demonstrated multiple oncogenic PIK3CA copies in a substantial subset of human cancers. To identify the molecular mechanism underpinning PIK3CAH1047R allele dose-dependent stemness, we profiled isogenic wild-type, PIK3CAWT/H1047R and PIK3CAH1047R/H1047R iPSCs by high-depth transcriptomics, proteomics and reverse-phase protein arrays (RPPA). PIK3CAH1047R/H1047R iPSCs exhibited altered expression of 5644 genes and 248 proteins, whereas heterozygous hPSCs showed 492 and 54 differentially-expressed genes and proteins, respectively, confirming a nearly deterministic phenotypic effect of homozygosity for PIK3CAH1047R. Pathway and network-based analyses predicted a strong association between self-sustained TGFb/NODAL signaling and the ‘locked’ stemness phenotype induced by homozygosity for PIK3CAH1047R. This stemness gene signature was maintained without exogenous NODAL in PIK3CAH1047R/H1047R iPSCs and was reversed by pharmacological inhibition of TGFb/NODAL signaling but not by PIK3CA-specific inhibition. Analysis of PIK3CA-associated human breast cancers revealed increased expression of the stemness markers NODAL and POU5F1 as a function of disease stage and PIK3CAH1047R allele dosage. Together with emerging realization of the link between NODAL re-expression and aggressive cancer behavior, our data suggest that TGFb/NODAL inhibitors warrant testing in advanced breast tumors with multiple oncogenic PIK3CA copies.
Project description:Joint profiling of chromatin accessibility and gene expression from the same single cell provides critical information about cell types in a tissue and cell states during a dynamic process. These emerging multi-omics techniques help the investigation of cell-type resolved gene regulatory mechanisms. Here, we developed in situ SHERRY after ATAC-seq (ISSAAC-seq), a highly sensitive and flexible single cell multi-omics method to interrogate chromatin accessibility and gene expression from the same single cell. We demonstrated that ISSAAC-seq is sensitive and provides high quality data with orders of magnitude more features than existing methods. Using the joint profiles from thousands of nuclei from the mouse cerebral cortex, we uncovered major and rare cell types together with their cell-type specific regulatory elements and expression profiles. Finally, we revealed distinct dynamics and relationships of transcription and chromatin accessibility during an oligodendrocyte maturation trajectory.
Project description:Multi-omics molecular profiling was performed on post-radical prostatectomy material from a cohort of 132 patients with localized prostate adenocarcinoma. Unsupervised classification techniques were used to build a comprehensive classification of prostate tumours based on three molecular levels: DNA copy number, DNA methylation, and mRNA expression.