- No file added yet -

FIGURE 2 from Integrative Metatranscriptomic Analysis Reveals Disease-specific Microbiome–host Interactions in Oral Squamous Cell Carcinoma

figure

posted on 2023-05-08, 14:20 authored by Vinay Jain, Divyashri Baraniya, Doaa E. El-Hadedy, Tsute Chen, Michael Slifker, Fadhl Alakwaa, Kathy Q. Cai, Kumaraswamy N. Chitrala, Christopher Fundakowski, Nezar N. Al-Hebshi

Host transcriptome. Sequences were mapped to human reference GRCh38 and quantified at the gene level using STAR aligner and HTSeq, respectively. DESeq2 was used to identify DEGs which are depicted in volcano plots for tumor versus adjacent normal (paired comparison; A), tumor versus HC (B), and adjacent normal versus HC (C)—the color code in the volcano plots corresponds to the fold change and FDR cutoffs (2 and 0.05, respectively). D, A PCA plot based on the most variable 1,500 DEGs, generated using “plotPCA" function from DESeq2 R/Bioconductor package. Lists of DEGs preranked by Wald statistic were used as input for GSEA to identify upregulated and downregulated pathways in each contrast (E–G) based on Hallmark gene sets (MSigDB 7.1).

Funding

HHS | NIH | National Institute of Dental and Craniofacial Research (NIDCR)

Dr. Cary. R. Klimen Oral Health Sciences Research Program Fund

History

ARTICLE ABSTRACT

Studies have shown that a distinct microbiome is associated with OSCC, but how the microbiome functions within the tumor interacts with the host cells remains unclear. By simultaneously characterizing the microbial and host transcriptomes in OSCC and control tissues, the study provides novel insights into microbiome-host interactions in OSCC which can be validated in future mechanistic studies.