PubMed Health⌕ Search
Home/Archive/PubMed

PubMed · 40669467

The extracellular vesicle transcriptome provides tissue-specific functional genomic annotation relevant to disease susceptibility in obesity.

Emeli Chatterjee·Michael J Betti·Quanhu Sheng·Phillip Lin·Margo P Emont·Guoping Li·Kaushik Amancherla·Marta Garcia-Contreras·Priyanka Gokulnath·Worawan B Limpitikul·Olivia Rosina Whittaker·Kathy Luong·Christopher Azzam·Denise Gee·Matthew Hutter·Karen Flanders·Parul Sahu·Charles R Flynn·Jonathan Brown·Danxia Yu·Evan D Rosen·Kendall Van-Keuren Jensen·Eric R Gamazon·Ravi Shah·Saumya Das
View original source ↗Export metadata ↓

Abstract

We characterized circulating extracellular vesicles (EVs) in obese and lean humans, identifying transcriptional cargo differentially expressed in obesity (277 unique genes; false discovery rate < 10%). Since circulating EVs may have broad origin, we compared this obesity EV transcriptome with expression from human visceral-adipose-tissue-derived EVs from freshly collected and cultured biopsies from the same obese individuals, observing high concordance. Using a comprehensive set of adipose-specific epigenomic and chromatin conformation assays, we found that the differentially expressed transcripts from the EVs were those regulated in adipose by body mass index-associated SNPs (p < 5 &#xd7; 10-8) from a large-scale genome-wide association study (GWAS). Using a phenome-wide association study of the regulatory SNPs for the EV-derived transcripts, we identified a substantial enrichment for inflammatory phenotypes, including type 2 diabetes. Collectively, these findings represent the convergence of the GWAS (genetics), epigenomics (transcript regulation), and EV (liquid biopsy) fields, enabling powerful future genomic studies of complex diseases.

Explore related subjects

HumansExtracellular VesiclesObesityGenome-Wide Association StudyTranscriptomePolymorphism, Single NucleotideGenetic Predisposition to DiseaseMaleFemaleMiddle AgedAdultDiabetes Mellitus, Type 2Body Mass IndexOrgan SpecificityGenomicsBMIGWASPheWASRNAextracellular vesiclesobesityplasmavisceral adipose tissueJournal ArticleResearch Support, N.I.H., ExtramuralResearch Support, Non-U.S. Gov't

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Emeli Chatterjee, Michael J Betti, Quanhu Sheng, Phillip Lin, Margo P Emont, Guoping Li, Kaushik Amancherla, Marta Garcia-Contreras, Priyanka Gokulnath, Worawan B Limpitikul, Olivia Rosina Whittaker, Kathy Luong, Christopher Azzam, Denise Gee, Matthew Hutter, Karen Flanders, Parul Sahu, Charles R Flynn, Jonathan Brown, Danxia Yu, Evan D Rosen, Kendall Van-Keuren Jensen, Eric R Gamazon, Ravi Shah, Saumya Das. 2025-07-15. The extracellular vesicle transcriptome provides tissue-specific functional genomic annotation relevant to disease susceptibility in obesity.. https://doi.org/10.1016/j.xgen.2025.100925

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2027

Global Genomic Surveillance.

Global genomic surveillance has emerged as a foundational pillar of public health in the twenty-first century, enabling real-time tracking of pathogen evolution and informing outbreak response. This chapter examines the strategic architecture of global genomic surveillance, focusing on its application to arboviruses such as chikungunya virus (CHIKV). It explores the integration of genomic data with epidemiological, clinical, and environmental information within a One Health framework, while addressing critical challenges in governance, equity, and interoperability. The discussion covers the entire genomic surveillance workflow, from sample collection and sequencing to bioinformatic analysis and phylogenetic inference, and highlights the transformative role of artificial intelligence (AI) in predictive surveillance. By analyzing global initiatives, operational barriers, and emerging technologies, this chapter underscores the necessity of sustainable, equitable, and interoperable genomic systems to proactively address current and future infectious disease threats.

Humans↗
PubMed2027

Systematic Dissection of Key Driver Perturbation Signatures in Single Cells via ECCITE-seq.

CRISPR screens, such as expanded CRISPR-compatible cellular indexing of transcriptomes and epitopes by sequencing (ECCITE-seq), enable the simultaneous measurement of transcriptomes, gRNA identity, and cell-surface protein expression at single-cell resolution to systematically interrogate gene function. This platform provides a powerful and scalable experimental approach for validating disease-associated regulators identified by large-scale association studies and other computational methods, including network-based analyses of multi-omics data. Here, as an example application, we describe an ECCITE-seq framework to characterize the transcriptomic consequences of perturbing multiple neuronal key driver genes associated with Alzheimer's disease (AD) in human-induced pluripotent stem cell (hiPSC)-derived neurons. More broadly, by integrating customized pooled gRNA libraries with different CRISPR effectors across multiple cell types, this approach allows for the assessment of the regulatory impact of candidate genes implicated in development and disease processes.

Humans↗
PubMed2027

Identification of Genome-Wide Chromatin Structural Aberration in Cancer by Hi-C Analysis.

Aberrant three-dimensional genome organization is a hallmark of cancer, often driving oncogene activation through mechanisms such as enhancer hijacking. High-throughput chromosome conformation capture (Hi-C) maps these interactions on a genome-wide scale. Unlike earlier dilution-based methods, in situ Hi-C performs proximity ligation within intact nuclei, minimizing random ligation noise and enabling fine-scale structure detection. This chapter describes an optimized in situ Hi-C protocol tailored for cancer cell lines using MboI digestion and biotin-mediated pull-down to generate high-complexity libraries. We further outline a computational workflow that extends beyond standard topological mapping of compartments and topologically associating domains to identify cancer-specific aberrations. Specifically, we focus on detecting chromosomal rearrangements (structural variants) and characterizing the distinct circular topology of extrachromosomal DNA. This integrated experimental and analytical framework provides the necessary tools to dissect the spatial dysregulation underlying tumor evolution.

Humans↗