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Comparison of single cell and single nuclei RNA sequencing for human bladder tissue

ABSTRACT: Single cell sequencing technologies have revolutionized our understanding of biology by mapping cell diversity and gene expression in healthy and diseased tissues. While single-cell RNA sequencing (scRNA-seq) has been widely used, interest in single-nucleus RNA sequencing (snRNA-seq) is growing due to its benefits, including the ability to analyze archival tissues and capture rare cell types that are challenging to dissociate. However, comparative studies across tissues have yielded mixed results, with some reporting enhanced cell type retention using snRNA-seq while others finding cell type identification to be challenging in snRNA-seq data. The GUDMAP consortium aims to construct a molecular atlas of the lower urinary tract (LUT); thus, we set out to determine the strengths and limitations of each approach in characterizing LUT cell types. Using the human bladder, we determined that scRNA-seq offered more discriminative gene sets for identification while snRNA-seq could facilitate capture of previously underrepresented cell types.

ORGANISM(S): Homo sapiens

PROVIDER: GSE267964 | GEO | 2024/11/18

REPOSITORIES: GEO

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Project description:Endometriosis is a debilitating gynecological disorder affecting approximately 10% of the female population. Despite its prevalence, robust methods to classify and treat endometriosis remain elusive. Changes throughout the menstrual cycle in tissue size, architecture, cellular composition, and individual cell phenotypes make it extraordinarily challenging to identify markers or cell types associated with uterine pathologies since disease-state alterations in gene and protein expression are convoluted with cycle phase variations. Here, we developed an integrated workflow to generate both proteomic and single-cell RNA-sequencing (scRNA-seq) data sets using tissues and cells isolated from the uteri of control and endometriotic donors. Using a linear mixed effect model (LMM), we identified proteins associated with cycle stage and disease, revealing a set of genes that drive separation across these two biological variables. Further, we analyzed our scRNA-seq data to identify cell types expressing cycle and disease- associated genes identified in our proteomic data. A module scoring approach was used to identify cell types driving the enrichment of certain biological pathways, revealing several pathways of interest across different cell subpopulations. Finally, we identified ligand-receptor pairs including Axl/Tyro3 – Gas6, that may modulate interactions between endometrial macrophages and/or endometrial stromal/epithelial cells. Analysis of these signaling pathways in an independent cohort of endometrial biopsies revealed a significant decrease in Tyro3 expression in patients with endometriosis compared to controls, both transcriptionally and through histological staining. This measured decrease in Tryo3 in patients with disease could serve as a novel diagnostic biomarker or treatment avenue for patients with endometriosis. Taken together, this integrated approach provides a framework for integrating LMMs, proteomic and RNA-seq data to deconvolve the complexities of complex uterine diseases and identify novel genes and pathways underlying endometriosis.

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Comparison of single cell and single nuclei RNA sequencing for human bladder tissue

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