MECOM Locus classical transcript isoforms affect tumor immune microenvironment and different targets in ovarian cancer

• Published in: Journal of ovarian research 2024-10, Vol.17 (1), p.207-13, Article 207
• Main Authors: Lan, Ning, Bai, Shuheng, Chen, Min, Wang, Xuan, Feng, Zhaode, Gao, Ying, Hui, Beina, Ma, Wen, Zhang, Xiangxiang, Hu, Fengyuan, Liu, Wanyi, Li, Wenyang, Wu, Fang, Ren, Juan
• Format: Article
• Language: English
• Subjects: Algorithms; Analysis; Chromatin; Development and progression; DNA binding proteins; Female; Gene Expression Regulation, Neoplastic; Genes; Genomes; Genomics; High-grade serous ovarian carcinoma (HGSOC); Humans; Isoforms; MECOM; Medical research; Medicine, Experimental; Ovarian cancer; Ovarian Neoplasms - genetics; Ovarian Neoplasms - immunology; Ovarian Neoplasms - mortality; Ovarian Neoplasms - pathology; Prognosis; Protein binding; Protein Isoforms - genetics; Regulatory targets; RNA; RNA sequencing; T cells; Transcription factors; Tumor immune microenvironment (TIME); Tumor Microenvironment - genetics; Tumor Microenvironment - immunology
• ISSN: 1757-2215; 1757-2215
• DOI: 10.1186/s13048-024-01522-0

The MECOM locus is a gene frequently amplified in high-grade serous ovarian carcinoma (HGSOC). Nevertheless, the body of research examining the associations among MECOM transcripts, patient prognosis, and their role in modulating the tumor immune microenvironment (TIME) remains sparse, particularly in large cohorts. This study assessed the expression of MECOM transcripts in 352 HGSOC patients and 88 normal ovarian tissues from the combined GTEx/TCGA database. Using resources such as the UCSC Genome Browser, Ensembl, and NextProt, two transcripts corresponding to classical protein isoforms from MECOM were identified. Cox proportional hazards regression analysis, Kaplan-Meier survival curves, and a comprehensive TIME evaluation algorithm were employed to elucidate the connections between the expression levels of these transcripts and both patient prognosis and TIME status. Chromatin Immunoprecipitation sequencing (ChIP-seq) data for the two protein isoforms, as well as RNA sequencing data post-targeted silencing, were analyzed to identify potential regulatory targets of the different transcription factors. Elevated expression of the MECOM isoform transcripts was correlated with poorer survival in HGSOC patients, potentially through the modulation of cancer-associated fibroblasts (CAFs) and immunosuppressive cell populations. In contrast, higher levels of EVI1 isoform transcripts were linked to enhanced survival, possibly due to the regulation of CD8 T cells, macrophages, and a reduction in the expression of JUN protein, or its DNA-binding activity on downstream genes. Diverse protein isoforms derived from MECOM were found to differentially affect the survival and tumor development in ovarian cancer patients through specific mechanisms. Investigating the molecular mechanisms underlying disease pathogenesis and identifying potential drug target proteins at the level of splice variant isoforms were deemed crucial.