Project description:In this project we explore the cellular heterogeneity of a mouse model of heart failure with preserved ejection fraction (HFpEF) involving a two-hit model of feeding a high fat diet (HFD) along with L-NAME administration. Healthy adult male mice (C57BL/6J inbred) were fed either a normal chow diet or HFD/L-NAME for 10 weeks or 15 weeks before performing sequencing experiments. Both cardiomyocytes (CMs) and total interstitial population (TIP) were captured using a protocol to jointly capture and sequence single-nuclei (for cardiomyocytes) and single-cells (for TIP) using the 10x Genomics Chromium system.
Project description:This study was undertaken to assess transcriptional and epigenetic heterogeneity a the level of individual cells within neuroblastoma cell lines, and to compare cell lines with MYCN amplificaion to cell lines without MYCN amplification. Methods: We used 10X Genomics multiome sequencing technology to perform joint gene expression and ATAC profiling on thousands of nuclei isolated from the following human neuoblastoma cell lines: SHSY5Y, SK-N-AS, SK-N-SH, SK-N-DZ, Be-2c, and CHP134. Results: We found considerable gene expression and epigeneic heterogeneity both within and between neuroblastoma cell lines. Conclusion: Joint single-nucleus RNA sequencing and single-nucleus ATAC sequencing has demonsrated that neuroblastoma cell lines are heterogeneous, which may have implications for therapeutic strategies.
Project description:MultiPerturb-seq is a high-throughput CRISPR screening platform with joint single nucleus chromatin accessibility, transcriptome, and guide RNA capture. It uses combinatorial indexing combined with droplet microfluidics to scale throughput and integrate all three modalities. We apply MultiPerturb-seq to identify key genes whose loss can trigger differentiation in a rare pediatric cancer, atypical teratoid/rhabdoid tumor (AT/RT), which is driven by loss of the SWI/SNF chromatin remodeling subunit SMARCB1.
Project description:Microvascular dysfunction is an important determinant in HFpEF but the role of mural cells herein is still poorly investigated. We aimed to examine the transcriptomic signature of endothelial cells and mural cells of the micro- and macrovascular niche in healthy vs. HFpEF cell RNAsequencing.
Project description:MultiPerturb-seq is a high-throughput CRISPR screening platform with joint single nucleus chromatin accessibility, transcriptome, and guide RNA capture. It uses combinatorial indexing combined with droplet microfluidics to scale throughput and integrate all three modalities. We apply MultiPerturb-seq to identify key genes whose loss can trigger differentiation in a rare pediatric cancer, atypical teratoid/rhabdoid tumor (AT/RT), which is driven by loss of the SWI/SNF chromatin remodeling subunit SMARCB1.
Project description:We have demonstrated previously that adult cardiomyocytes can dedifferentiate and proliferate when cultured in vitro. To determine if cardiomyocyte dedifferentiation and cell cycling/proliferation happens in vivo, we applied here a novel multi-reporter transgenic mouse model (aMH-CMerCreMer;mT/MG;aMHC-H2BBFP) carrying reporter genes for permanent cardiomyocyte lineage mapping and maturity (dedifferentiation) reporting. With this new model, we deciphered the cellular sources and processes of cardiomyocyte dedifferentiation and proliferation in adult hearts. In this study, we used single-nucleus RNA-sequencing to tackle the challenges in analyzing the highly heterogeneous heart cell populations, and obtained datasets for a large number of cardiac single nuclei (both myocytes and non-myocytes) for control and post-infarct hearts. We identified specific cell populations in the heart using distinct transcriptomic clusters, transgenic reporters for ACM lineage and dedifferentiation, as well as cell cycle markers. The results demonstrated that the dedifferentiation and cell cycle progression of pre-existing CMs was augmented in post-infarct hearts, with a number of signaling pathways and gene sets affected. This is the first study dissecting the transcriptomic profiles and signaling pathways associated with cardiomyocyte dedifferentiation and cycling/proliferation in vivo using unbiased high-throughput single-nucleus RNA-Seq analysis, in junction with novel cell lineage (e.g. cardiomyocyte) and phenotyping (e.g. dedifferentiation) transgenic model systems.