Integrated multi-omics approach reveals a role of ALDH1A1 in lipid metabolism in human colon cancer cells

Abstract

Colorectal cancer (CRC) is the third most common cancer worldwide and one of the most common diseases diagnosed in the USA among both men and women [1]. Interestingly, the incidence and mortality rates have been declining in the United States over the past decades for those aged over 50, with the pace accelerating to 3% annually from 2003 to 2012. However, there has been an alarming increase (51%) in colorectal cancer incidence in those under 50 since 1994 [2–4]. The reasons for this increase are not fully understood. Known risk factors, such as obesity, alcohol, smoking and a sedentary lifestyle, are likely to underlie early-onset cancers [3]. Genetic predisposition and epigenetic alterations are likely to contribute to this increase. Both play an important role in the disruption of several oncogenic signaling pathways which have been identified in colorectal cancer. Numerous reports have highlighted the importance of early mutations in the adenomatous polyposis coli (APC) tumor suppressor gene and in the CTNNB1 (β-catenin) gene; both of these genes influence the Wnt/β pathway signaling by preventing axin-dependent phosphorylation and degradation of β-catenin [5–8]. In addition to these mutations, a synergistic interaction between the genetic and epigenetic alterations is believed to contribute in the development of CRC [8]. Methylations, such as H3K9 and H3K27, have been found to contribute to the regulation of gene expression in both embryonic stem cells and adult stem cells by silencing genes. On the other hand, H3K4 methylation is critical for gene activation [9]. Another mechanism, which is the subject of intensive research, is the one activated by aldehyde dehydrogenase (ALDH) and that promotes tumor growth. ALDH catalytic activity has been identified as a biomarker of many cancers and cancer stem cells [10]. Our group has recently shown that high ALDH1B1 expression was observed throughout the cells of human colon adenocarcinomas, suggesting a close association between ALDH1B1 presence and activation of Wnt/β-catenin [11, 12]. However, other groups have suggested the ALDH1A1 isozyme to be present in CRC [13, 14]. However, the mechanism by which ALDH1A1 contributes to CRC has not been elucidated. Athough important signaling pathways and genes have been identified as playing a role in CRC, identification of new prognostic biomarkers continues to be a challenge, because it is a highly heterogeneous cancer, with various molecular alterations taking place throughout the natural course of the disease [15]. Evaluation of the transcriptome allows investigation of alterations in the molecular constituents of the cells and tissues induced by disease. RNA-Seq is one approach that uses deep-sequencing technologies to measure the levels of transcripts and their isoforms, thereby providing a detailed insight into the transcriptome [16]. By identify cellular proteins, proteomics provides additional insights into cellular changes that are downstream of the transcriptome. Metabolite profiling (or metabolomics) provides information about the biochemical consequences of changes in protein expression. This is a powerful approach that measures and identifies small molecules that change during a disease, providing valuable insights into how biochemistry is linked to cell metabolism [17]. Each one of these approaches contributes in a different way in advancing to our understanding of the molecular basis and cellular changes occurring in diseases, such as CRC. They also facilitate the discovery novel biomarkers. For example, transcriptomics can identify the differences in gene expression profiles in key oncogenes and tumor suppressors CRC cells. Proteomics can provide insight into changes in proteins involved in molecular pathways contributing to the development and progression of CRC. Metabolomics can elucidate the biochemical pathways that are altered in the tumor tissue. Each of these approaches enhance our understanding of CRC biology. Recent advances in biocomputational tools make it feasible to (i) analyze large data sets from transcriptomic, proteomic and metabolomic studies, (ii) efficiently integrate them, and (iii) generate a comprehensive systems biology analysis of the disease [18–20]. The use of a multilayer “omics” approach that integrates transcriptomics, proteomics and metabolomics has the potential to greatly increase our understanding of the mechanisms underlying disease. The changes in the metabolome can be linked to alterations in enzymes identified with proteomics, and when combined with transcriptomics data, can enhance the interpretation of the genetic background of thedisease, leading to a more comprehensive molecular view of CRC. The end result of the multi “omics’” approaches to a disease should improve prognosis, and ultimately lead to improved treatment and patient outcomes. Using a multi-omics approach, we have investigated the impact of genetic suppression (shRNA) of ALDH1A1 expression on transcriptomics, proteomics and untargeted metabolomics analyses in a human colon cancer cell line (COLO320) which has a high constitutive expression of ALDH1A1. The present study (i) generates an integrative omic profile of scramble shRNA vs. ALDH1A1 shRNA COLO320 cells, and (ii) identifies possible alterations in biological pathways caused by suppression of ALDH1A1 expression.