Abstract 2293: Outstanding chromosomal expression patterning in human cancers

Abstract

Abstract Cancer transcriptome is an effect of abnormal genetic and/or epigenetic regulation. In the past, transcriptome was studied at the level of individual transcripts for their differential expression. Spatial gene expression patterns along chromosomes were not yet characterized for cancer. We hypothesized that gene expression patterning is not randomly distributed along the chromosomes in cancer versus normal tissues. We analyzed cancer transcriptome from the National Cancer Institute Genomic Data Commons, and identified genomic regions with significant shifts in expression from normal tissues to tumors. We used a novel highly efficient method in the Ckmeans.1d.dp package for clustering genes by chromosomal location and expression level. We identified two chromosomal zones of note that exhibit similar expression patterns across several cancer types. In breast, lung, liver, and esophageal cancers, a zone near 6p22.2 contains genes that are similarly highly upregulated in tumor tissues compared to matched normal tissues. This zone contains a group of histone cluster 1 genes, among which are 14 known cancer genes. In colorectal, lung, liver, and esophageal cancers, a zone on 14q32.33 exhibits either heavy up- or downregulation, dependent on the specific cancer. This zone is rich in immunoglobulin heavy variable genes. Table 1 lists genomic zones of note specific to six cancer types. Our study provides an atlas of outstanding chromosomal expression patterning that can be used as markers for cancer in general and also for specific cancer types. Table 1. Outstanding genomic zones specific to six human cancer types.Cancer type Chr:start-end (Mb) Cytogenetic band # Matched tumor/normal pairsBreastchr2:88-92p11.2112Colorectalchr7:141-146q3541Esophagealchr11:7-12p15.48Kidneychr12:85-91q21.3323Liverchr8:15-22p2250Lungchr8:121-126q24.1357 Citation Format: Spencer Barnes, Mingzhou Song. Outstanding chromosomal expression patterning in human cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2293.