Single-Cell Deconvolution of Head and Neck Squamous Cell Carcinoma.
deconvolution
head and neck squamous cell carcinoma
regulatory T-cells
single-cell RNA sequencing
Journal
Cancers
ISSN: 2072-6694
Titre abrégé: Cancers (Basel)
Pays: Switzerland
ID NLM: 101526829
Informations de publication
Date de publication:
11 Mar 2021
11 Mar 2021
Historique:
received:
19
02
2021
accepted:
26
02
2021
entrez:
3
4
2021
pubmed:
4
4
2021
medline:
4
4
2021
Statut:
epublish
Résumé
Complexities in cell-type composition have rightfully led to skepticism and caution in the interpretation of bulk transcriptomic analyses. Recent studies have shown that deconvolution algorithms can be utilized to computationally estimate cell-type proportions from the gene expression data of bulk blood samples, but their performance when applied to tumor tissues, including those from head and neck, remains poorly characterized. Here, we use single-cell data (~6000 single cells) collected from 21 head and neck squamous cell carcinoma (HNSCC) samples to generate cell-type-specific gene expression signatures. We leverage bulk RNA-seq data from >500 HNSCC samples profiled by The Cancer Genome Atlas (TCGA), and using single-cell data as a reference, apply two newly developed deconvolution algorithms (CIBERSORTx and MuSiC) to the bulk transcriptome data to quantitatively estimate cell-type proportions for each tumor in TCGA. We show that these two algorithms produce similar estimates of constituent/major cell-type proportions and that a high T-cell fraction correlates with improved survival. By further characterizing T-cell subpopulations, we identify that regulatory T-cells (T
Identifiants
pubmed: 33799782
pii: cancers13061230
doi: 10.3390/cancers13061230
pmc: PMC7999850
pii:
doi:
Types de publication
Journal Article
Langues
eng
Subventions
Organisme : NIH HHS
ID : NCI K08CA237732
Pays : United States
Organisme : NCATS NIH HHS
ID : TL1 TR002344
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM007200
Pays : United States
Organisme : NIDCD NIH HHS
ID : T32 DC000022
Pays : United States
Organisme : NCI NIH HHS
ID : K08 CA237732
Pays : United States
Organisme : NIH HHS
ID : TL1 TR002344
Pays : United States
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