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Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry [10X single-cell multiome]

ABSTRACT: Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry [10X single-cell multiome]

PROVIDER: PRJNA1023624 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR26274130_1.fastq.gz	Fastqsanger.gz
	SRR26274130_2.fastq.gz	Fastqsanger.gz
	SRR26274131_1.fastq.gz	Fastqsanger.gz
	SRR26274131_2.fastq.gz	Fastqsanger.gz

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Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry [10X single-cell multiome]

Project description:Single nuclei analysis is allowing robust classification of cell types in an organ that helps to establish relationships between cell-type specific gene expression and chromatin accessibility status of gene regulatory regions. Using breast tissues of 92 healthy donors of various genetic ancestry, we have developed a comprehensive chromatin accessibility and gene expression atlas of human breast tissues. Integrated analysis revealed 10 distinct cell types in the healthy breast, which included three major epithelial cell subtypes (luminal-hormone sensing, luminal adaptive secretory precursor, and basal-myoepithelial cells), two endothelial subtypes, two adipocyte subtypes, fibroblasts, T-cells, and macrophages. By integrating gene expression signatures derived from epithelial cell subtypes with spatial transcriptomics, we identify specific gene expression differences between lobular and ductal epithelial cells and age-associated changes in epithelial cell gene expression patterns and signaling networks. Among various cell types, luminal adaptive secretory cells and fibroblasts showed genetic ancestry dependent variability as a subpopulation of luminal adaptive secretory cells with alveolar progenitor (AP) cell state were enriched in Indigenous American (IA) ancestry and fibroblast populations were distinct in African ancestry. ESR1 expression pattern was distinctly different in tissues from IA compared to the rest, with a high level of ESR1 expression extending to AP cells and crosstalk between growth factors and Estrogen Receptor signaling is evident in these AP cells. In general, cell subtype-specific gene expression did not correlate with chromatin accessibility differences, suggesting that transcriptional regulation independent of chromatin accessibility governs cell type-specific gene expression in the breast.

2024-04-19 | GSE244585 | GEO

Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry [GeoMx]

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Peptide Ancestry Informative Markers in Uterine Neoplasms from Women of European, African and Asian Ancestry

Project description:Characterization of ancestry-linked peptide variants in disease-relevant patient tissues represents a foundational step to connect patient ancestry with molecular disease pathogenesis. Nonsynonymous single nucleotide polymorphisms (SNPs) encoding missense substitutions within tryptic peptides exhibiting high allele frequencies in European, African, and East Asian populations, termed peptide ancestry informative markers (pAIMs), were prioritized from 1000 genomes. In silico analysis shows that as few as 20 pAIMs can determine ancestry proportions similarly to >260K SNPs (R2=0.9905). Multiplexed proteomic analysis of >100 human endometrial cancer cell lines and uterine leiomyoma (ULM) tissues combined resulted in the quantitation of 62 pAIMs that correlate with self-described race and genotype-confirmed patient ancestry. Candidates include a D451E substitution in GC vitamin D-binding protein previously associated with altered vitamin D levels in African and European populations. These efforts describe a generalized set of markers for proteoancestry assessment that will further support studies investigating the impact of ancestry on the human proteome and how this relates to the pathogenesis of uterine neoplasms.

2022-02-16 | PXD029323 | Pride

Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry

Project description:Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry

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Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry [GeoMx]

Project description:Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry [GeoMx]

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Nuclei isolation from frozen heart tissues through an easy-to-operating, prompt, and inexpensive method for single-nucleus Multiome-seq

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Project description:Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry [scRNA-seq]

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