Variation in the repulsive guidance molecule family in human populations

Abstract

Repulsive guidance molecules, RGMA, RGMB, and RGMC, are related proteins discovered independently through different experimental paradigms. They are encoded by single copy genes in mammalian and other vertebrate genomes, and are ~50% identical in amino acid sequence. The importance of RGM actions in human physiology has not been realized, as most research has focused on non‐human models, although mutations in RGMC are the cause of the severe iron storage disorder, juvenile hemochromatosis. Here I show that repositories of human genomic and population genetic data can be used as starting points for discovery and for developing new testable hypotheses about each of these paralogs in human biology and disease susceptibility. Information was extracted, aggregated, and analyzed from the Ensembl and UCSC Genome Browsers, the Exome Aggregation Consortium, the Genotype‐Tissue Expression project portal, the cBio portal for Cancer Genomics, and the National Cancer Institute Genomic Data Commons data site. Results identify extensive variation in gene expression patterns, substantial alternative RNA splicing, and possible missense alterations and other modifications in the coding regions of each of the three genes, with many putative mutations being detected in individuals with different types of cancers. Moreover, selected amino acid substitutions are highly prevalent in the world population, with minor allele frequencies of up to 37% for RGMA and up to 8% for RGMB. These results indicate that protein sequence variation is common in the human RGM family, and raises the possibility that individual variants will have a significant population impact on human physiology and/or disease predisposition.

RGMb impacts partial epithelial‐mesenchymal transition and BMP2‐Induced ID mRNA expression independent of PD‐L2 in nonsmall cell lung cancer cells

“…To further study the function of RGMb in HCC827 cells, we used CRISPR/Cas9 to create RGMb‐depleted HCC827 cells (HCC827dRGMB cells). For this, HCC827Cas9 cells were transduced with lentiviral particles carrying a sgRNA, sgRNA‐3, targeting the RGMb open reading frame in the first coding exon of mRNA isoform 2 and the second coding exon of mRNA isoform 1 (Rotwein, 2019). HCC827Cas9 cells were transduced with lentiviral particles carrying a scrambled sgRNA to generate HCC827 sgRNA control cells.…”

“…Fold change (FC) > 2 or FC < 0.5 and p < .05 are marked with #. lentiviral particles carrying a sgRNA, sgRNA-3, targeting the RGMb open reading frame in the first coding exon of mRNA isoform 2 and the second coding exon of mRNA isoform 1(Rotwein, 2019).HCC827Cas9 cells were transduced with lentiviral particles carrying a scrambled sgRNA to generate HCC827 sgRNA control cells. Sanger sequencing revealed an indel percentage of 91% and a percentage of the open reading frame-disrupting indels, hereafter termed knockout (KO) percentage, of 85% (Figure2a).…”

ZMAT2 in Humans and Other Primates: A Highly Conserved and Understudied Gene

“…Moreover, ZMAT2 is remarkably nonpolymorphic in humans, as judged by the fact that of more than 280 000 alleles studied in the gnomAD project, only 31 different potential codon changes that predict amino acid substitutions were identified, and these occurred collectively in only 0.014% of the alleles in the study population (Figure 8, Table 4), a percentage substantially lower than that had been described previously for the prevalence of variant alleles in at least 19 38,39 ). Moreover, and unlike these other genes, [35][36][37] no frameshift alterations or splicing site changes were found in human ZMAT2, and in addition, very few modifications were identified in different human cancers (Figure 8, Tables 4 and 5). A potential reason for this lack of variation could be that ZMAT2 plays a critical structural and functional role in pre-mRNA splicing in the nucleus.…”