SexAnnoDB, a Knowledgebase of Sex-Specific Regulations From Multi-omics Data of Human Cancers

Authors

Mengyuan Yang
Yuzhou Feng
Jiajia Liu
Hong Wang
Sijia Wu
Weiling Zhao
Pora Kim
Xiaobo Zhou

Publication Date

8-22-2024

Journal

Biology of Sex Differences

Abstract

Background

Sexual differences across molecular levels profoundly impact cancer biology and outcomes. Patient gender significantly influences drug responses, with divergent reactions between men and women to the same drugs. Despite databases on sex differences in human tissues, understanding regulations of sex disparities in cancer is limited. These resources lack detailed mechanistic studies on sex-biased molecules.

Methods

In this study, we conducted a comprehensive examination of molecular distinctions and regulatory networks across 27 cancer types, delving into sex-biased effects. Our analyses encompassed sex-biased competitive endogenous RNA networks, regulatory networks involving sex-biased RNA binding protein-exon skipping events, sex-biased transcription factor-gene regulatory networks, as well as sex-biased expression quantitative trait loci, sex-biased expression quantitative trait methylation, sex-biased splicing quantitative trait loci, and the identification of sex-biased cancer therapeutic drug target genes. All findings from these analyses are accessible on SexAnnoDB (https://ccsm.uth.edu/SexAnnoDB/).

Results

From these analyses, we defined 126 cancer therapeutic target sex-associated genes. Among them, 9 genes showed sex-biased at both the mRNA and protein levels. Specifically, S100A9 was the target of five drugs, of which calcium has been approved by the FDA for the treatment of colon and rectal cancers. Transcription factor (TF)-gene regulatory network analysis suggested that four TFs in the SARC male group targeted S100A9 and upregulated the expression of S100A9 in these patients. Promoter region methylation status was only associated with S100A9 expression in KIRP female patients. Hypermethylation inhibited S100A9 expression and was responsible for the downregulation of S100A9 in these female patients.

Conclusions

Comprehensive network and association analyses indicated that the sex differences at the transcriptome level were partially the result of corresponding sex-biased epigenetic and genetic molecules. Overall, SexAnnoDB offers a discipline-specific search platform that could potentially assist basic experimental researchers or physicians in developing personalized treatment plans.

Keywords

Female, Humans, Male, DNA Methylation, Gene Expression Regulation, Neoplastic, Gene Regulatory Networks, Knowledge Bases, Multiomics, Neoplasms, Quantitative Trait Loci, Sex Factors, Sex difference, Cancer, Multi-omics, Sex-biased regulatory network

DOI

10.1186/s13293-024-00638-8

PMID

39175079

PMCID

PMC11342657

PubMedCentral® Posted Date

8-22-2024

PubMedCentral® Full Text Version

Post-print

Published Open-Access

yes