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Transcriptome- and DNA methylation-based cell-type deconvolutions produce similar estimates of differential gene expression and differential methylation.
Hannon, Emily R; Marsit, Carmen J; Dent, Arlene E; Embury, Paula; Ogolla, Sidney; Midem, David; Williams, Scott M; Kazura, James W.
Afiliación
  • Hannon ER; Center for Global Health and Diseases, Case Western Reserve University, 10900 Euclid Avenue LC:4983, Cleveland, OH, 44106, USA. erh90@case.edu.
  • Marsit CJ; Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA. erh90@case.edu.
  • Dent AE; Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA.
  • Embury P; Center for Global Health and Diseases, Case Western Reserve University, 10900 Euclid Avenue LC:4983, Cleveland, OH, 44106, USA.
  • Ogolla S; Division of Pediatric Infectious Diseases, Rainbow Babies and Children's Hospital, Cleveland, OH, 44106, USA.
  • Midem D; Center for Global Health and Diseases, Case Western Reserve University, 10900 Euclid Avenue LC:4983, Cleveland, OH, 44106, USA.
  • Williams SM; Kenya Medical Research Institute, Kisumu, Kenya.
  • Kazura JW; Chulaimbo Sub-county Hospital, Kisumu County, Kenya.
BioData Min ; 17(1): 21, 2024 Jul 11.
Article en En | MEDLINE | ID: mdl-38992677
ABSTRACT

BACKGROUND:

Changing cell-type proportions can confound studies of differential gene expression or DNA methylation (DNAm) from peripheral blood mononuclear cells (PBMCs). We examined how cell-type proportions derived from the transcriptome versus the methylome (DNAm) influence estimates of differentially expressed genes (DEGs) and differentially methylated positions (DMPs).

METHODS:

Transcriptome and DNAm data were obtained from PBMC RNA and DNA of Kenyan children (n = 8) before, during, and 6 weeks following uncomplicated malaria. DEGs and DMPs between time points were detected using cell-type adjusted modeling with Cibersortx or IDOL, respectively.

RESULTS:

Most major cell types and principal components had moderate to high correlation between the two deconvolution methods (r = 0.60-0.96). Estimates of cell-type proportions and DEGs or DMPs were largely unaffected by the method, with the greatest discrepancy in the estimation of neutrophils.

CONCLUSION:

Variation in cell-type proportions is captured similarly by both transcriptomic and methylome deconvolution methods for most major cell types.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: BioData Min Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: BioData Min Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido