Common and mutation specific phenotypes of KRAS and BRAF mutations in colorectal cancer cells revealed by integrative -omics analysis

Abstract

Background Genes in the Ras pathway have somatic mutations in at least 60 % of colorectal cancers. Despite activating the same pathway, the BRAF V600E mutation and the prevalent mutations in codon 12 and 13 of KRAS have all been linked to different clinical outcomes, but the molecular mechanisms behind these differences largely remain to be clarified. Methods To characterize the similarities and differences between common activating KRAS mutations and between KRAS and BRAF mutations, we used genome editing to engineer KRAS G12C/D/V and G13D mutations in colorectal cancer cells that had their mutant BRAF V600E allele removed and subjected them to transcriptome sequencing, global proteomics and metabolomics analyses. Results By intersecting differentially expressed genes, proteins and metabolites, we uncovered (i) two-fold more regulated genes and proteins when comparing KRAS to BRAF mutant cells to those lacking Ras pathway mutation, (ii) five differentially expressed proteins in KRAS mutants compared to cells lacking Ras pathway mutation (IFI16, S100A10, CD44, GLRX and AHNAK2) and 6 (CRABP2, FLNA, NXN, LCP1, S100A10 and S100A2) compared to BRAF mutant cells, (iii) 19 proteins expressed differentially in a KRAS mutation specific manner versus BRAF V600E cells, (iv) regulation of the Integrin Linked Kinase pathway by KRAS but not BRAF mutation, (v) regulation of amino acid metabolism, particularly of the tyrosine, histidine, arginine and proline pathways, the urea cycle and purine metabolism by Ras pathway mutations, (vi) increased free carnitine in KRAS and BRAF mutant RKO cells. Conclusions This comprehensive integrative -omics analysis confirms known and adds novel genes, proteins and metabolic pathways regulated by mutant KRAS and BRAF signaling in colorectal cancer. The results from the new model systems presented here can inform future development of diagnostic and therapeutic approaches targeting tumors with KRAS and BRAF mutations.

The ANXA2/S100A10 Complex—Regulation of the Oncogenic Plasminogen Receptor

“…Analysis with the RAS effector-loop mutants revealed the importance of the RalGDS pathways in regulating S100A10 gene expression. To directly compare the effects of KRAS and BRAF mutations in a genetic background originally dependent on pathway mutation, Kundu et al [ 111 ] engineered KRAS G12C , G12D , G12V , and G13D mutations in colorectal cancer RKO cells. They observed five differentially expressed proteins in KRAS mutants compared to cells lacking Ras pathway mutation (IFI16, S100A10, CD44, GLRX, and AHNAK2) and 6 (CRABP2, FLNA, NXN, LCP1, S100A10, and S100A2) compared to BRAF mutant cells.…”

Monitoring Metabolic Changes in Response to Chemotherapies in Cancer with Raman Spectroscopy and Metabolomics

“…We then identified 32 statistically significant peaks in RS using a Student’s t -test with the false discovery rate correction and corresponding metabolites that differentiated OX-treated cells from untreated control (Figure e); 28 of these metabolites decreased in the treatment group and 4 metabolites increased. To associate RS spectral data with specific metabolites and metabolite classes, we referred to the cited literature in Table that reports well-established RS peaks for key metabolites. − Tentative peak assignments were narrowed down based on literature on metabolites that are impacted in human CRC and cellular metabolites that change in response to treatment; these literature evidence supported the assigned Raman peaks to the metabolites we have listed. ,− As each RS peak arises from vibrational modes within a functional group, a specific peak is not exclusive to a metabolite. Therefore, our tentative peak assignments represent the most plausible major metabolites that contribute to these peaks.…”

“…72 Pathways associated with amino acids including histidine, tryptophan, and tyrosine metabolism are also amplified in KRAS-mutant cancer. 42 Perturbation and downregulation of these metabolisms may serve as an indicator of a reduction of KRAS-granted anti-EGFR resistance. Similar to amino acid metabolism perturbation, the impact on fatty acid metabolisms is also indicative of treatment response.…”

Increased MAD2L2 expression predicts poor clinical outcome in Colon Adenocarcinoma

“…The current work established MAD2L2's diagnostic and prognostic relevance in COAD, the processes behind its development, and its relationship with immune infiltration and mutation accumulation in hypoxic conditions. In recent years, many genes important for colorectal cancer progression have been identified (Mo et al, 2015;Kundu et al, 2021;Smeby et al, 2020;Golla et al, 2020;Voutsadakis, 2021;Liu et al, 2019aLiu et al, , 2019b, including KRAS, TP53, APC, PIK3CA, PPARD, and MORC2. With the continuous development of high-throughput technology, microarray analysis has been used to identify unknown colorectal cancer-related oncogenes and biological network analysis (Bogaert and Prenen, 2014).…”