Project description:This study used Illumina single-end RNA-sequencing to examine gene expression differences between 2 mouse-derived pancreatic stellate cell lines (PSC4, PSC5) grown either in 2D monolayers, as 3D quiescent cultures, or as 3D activated transwell cocultures with 2 mouse tumor-derived pancreatic ductal organoid lines (T4, T5). Mouse pancreatic stellate cell (PSC) lines were derived from the pancreata of wild-type C57Bl/6J mice. Mouse tumor organoid lines were derived from mouse pancreata containing pancreatic ductal adenocarcinoma (PDAC) from the KrasLSL-G12D; Trp53LSL-R162H; Pdx1-Cre mouse model. We measured genes differentially expressed among 2D, quiescent, and 3D activated PSCs that may reflect the expression changes of heterogeneous CAF population in pancreatic tumors.
Project description:To understand the cell-type specific regulatory architectures of diabetes risk, we generated transcriptomic and 3D epigenomic profiles from sorted human pancreatic acinar, alpha, and beta cells using Arima Hi-C.
Project description:We investigate the spectrum of SVs and three-dimensional (3D) chromatin architecture in human pancreatic ductal epithelial cell carcinogenesis by using the state of art long-read single molecular real time (SMRT) and high-throughput chromosome conformation capture (Hi-C) sequencing techniques. Systematic integration of matched SMRT, in situ Hi-C, and RNA-seq datasets revealed the complicated dynamic interplay of SVs and 3D chromosome organization and their impacts on gene expression. Our studies identify and focus remodeling of chromatin folding domains associated with cross boundary SVs enabling aberrant interactions between regulatory elements. Moreover, our data also demonstrate the existence of complex genomic rearrangements associated with two key driver genes CDKN2A and SMAD4, and characterize their influence on cancer related gene expression from linear view to 3D perspective.
Project description:Capan1 (well differentiated pancreatic cancer cell line) was co-cultured with pancreatic stellate cell line (PS1) embedded in a 3D organotypic model and gene expression was analysed in comparison to cancer cells cultured alone without stellate cells. Pancreatic stellate cells were embedded within a gel matrix composing collagen type I and Matrigel, and cancer cells were seeded on top. The gel was lifted on to metal grid after 24 hour and fed from below. Gels were harvested on day 10 and frozen sections obtained. The cancer cell layer on top of the gel was captured by laser microdissection for RNA extraction.
Project description:Structural variation (SV) is a class of genetic variants involving long stretches of DNA and provides substantial innovations for adaptation and evolution. Investigation of SV profiles and turnover in nonhuman primates can help answer fundamental questions, such as what makes us uniquely human. Here, we present the high-resolution comparative 3D genome organizations of prefrontal cortex (PFC) of adult human and rhesus macaque. Based on a comprehensive SV atlas in rhesus macaque populations, we found that inversions are selectively constrained from the perspective of 3D genome, those inducing dramatic changes in chromosomal conformation tends to be purged by the action of purifying selection, implying the inconspicuous adaptive roles of inversions associated with strong effects. Furthermore, by integrating comparative genomics and multi-omics data across human and rhesus macaque, such as gene structures, regulatory elements and 3D genomic organizations, we highlighted a category of human-specific inversions with strong effects and found that they had undergone rapid fixation and caused significant changes in gene expression in human brain development, which may represent a driving force in human brain evolution. Overall, our findings reveal the great value of comparative 3D Hi-C maps in elucidating the adaptive functions of structural variants.