Evidence
Sci Adv. 2024 May 24;10(21):eadh2588. doi: 10.1126/sciadv.adh2588. Epub 2024 May 23.
ABSTRACT
Sample-wise deconvolution methods estimate cell-type proportions and gene expressions in bulk tissue samples, yet their performance and biological applications remain unexplored, particularly in human brain transcriptomic data. Here, nine deconvolution methods were evaluated with sample-matched data from bulk tissue RNA sequencing (RNA-seq), single-cell/nuclei (sc/sn) RNA-seq, and immunohistochemistry. A total of 1,130,767 nuclei per cells from 149 adult postmortem brains and 72 organoid samples were used. The results showed the best performance of dtangle for estimating cell proportions and bMIND for estimating sample-wise cell-type gene expressions. For eight brain cell types, 25,273 cell-type eQTLs were identified with deconvoluted expressions (decon-eQTLs). The results showed that decon-eQTLs explained more schizophrenia GWAS heritability than bulk tissue or single-cell eQTLs did alone. Differential gene expressions associated with Alzheimer’s disease, schizophrenia, and brain development were also examined using the deconvoluted data. Our findings, which were replicated in bulk tissue and single-cell data, provided insights into the biological applications of deconvoluted data in multiple brain disorders.
PMID:38781336 | DOI:10.1126/sciadv.adh2588
Estimated reading time: 3 minute(s)
Latest: Psychiatryai.com #RAISR4D Evidence
Cool Evidence: Engaging Young People and Students in Real-World Evidence
Real-Time Evidence Search [Psychiatry]
AI Research
Evaluating performance and applications of sample-wise cell deconvolution methods on human brain transcriptomic data
🌐 90 Days
Evidence Blueprint
Evaluating performance and applications of sample-wise cell deconvolution methods on human brain transcriptomic data
☊ AI-Driven Related Evidence Nodes
(recent articles with at least 5 words in title)
More Evidence