Our investigation revealed cytogenomic changes associated with both the pathogenesis and the progression of CRC. Additionally, it was possible to distinguish the complex and heterogeneous molecular characteristics of tumor tissues, clearly revealing the genomic instability profile characteristic of these samples. We also revealed the presence of pathogenic CNVs in surrounding nonneoplastic tissues, which were not detectable in histopathological investigations. This may indicate an initial tumorigenesis process for these patients.
Short-arm loss of chromosome 18 and long-arm duplications of chromosome 20 are commonly associated with CIN in preliminary genomic events in CRC [4, 6, 8, 10], and our results showed both types of genomic alterations: deletions in 18p11.3 involving the THOC1 gene, and duplications in 20q13 involving the UCKL1 gene. Previous studies have also associated deletions near the terminal regions located at 18p and 18q with the malignant progression of adenomas to adenocarcinomas [15–18], suggesting that subtelomeric genomic changes may be closely involved in the CRC process. Others have reported the association of structural alterations on chromosome 20 with instability in CRC [6, 8, 10].
Our results also showed concomitant genomic changes, such as THOC1 gene losses in 18p11.3 and UCKL1 gene duplications in 20q13.3 in both tumoral and nontumoral tissues. Silencing of the THOC1 gene inhibits the proliferation of some cell cancer strains, while the UCKL1 gene is related to maintaining a high cell proliferation rate in tumors [17, 19–21]. Furthermore, chromosome 20 is a genomic target of extreme importance in tumors . We identified several genomic alterations associated with chromosome 20, including ROH regions and duplication and deletion of whole arms in one patient. Duplications in the 20q subtelomeric region are a marker of unfavorable prognosis in patients with CRC .
Lake et al.  studied the relationship of tumorigenesis in primary and metastatic conjunctival melanomas in their analysis of metastatic samples, finding that the gene OPRL1 (20q13.33) was frequently excluded. In our study, we recognized a genomic gain in the long arm of chromosome 20, including at a probe located in the OPRL1 by using MLPA. Additionally, they found by use of MLPA and SNP arrays that the ADRM1 gene (20q13.3), located on chromosome 20, was duplicated in colorectal tumor tissue. This gene encodes a plasma membrane protein that participates in cell adhesion and dysregulation of this protein has been implicated in carcinogenesis by inducing interferon gamma in some cancer cells [17, 22]. Fejzo et al.  have shown that the ubiquitin proteasome ADRM1 receptor is amplified in cancers, including gastric, ovarian and colonic cancer. This ADRM1 gene directs the protein levels of specific oncogenes, resulting in an increase in metastatic potential .
Some genomic changes not previously described in CRC were identified in our study, such as duplication of ADAP1 (7p22.3), DMRT1 (9p24.3), and DOCK8 (9p24.3), which may be important in the study of sporadic CRC pathophysiology, considering that all these genes are involved in cell cycle control. The ADAP1 gene codes a protein related to Arf6 signaling events and the B cell receptor signaling pathway. The DOCK8 gene has been identified as a putative gene associated with the progression of brain tumors, especially gliomas .
In addition to the CNVs detected in THOC1 and UCKL1, we found other genomic abnormalities concomitant in neoplastic and nonneoplastic surrounding tissues, including duplications in TNFRSF18 and deletions of the MTA1 and DECR2 genes . The TNFRSF18 gene, a member of the tumor necrosis factor receptor superfamily, plays a key role in the self-regulation of cellular apoptosis and the immune system, coding and regulating T cells . The MTA1 protein plays important roles in cell signaling processes, chromosomal remodeling and transcription that in turn participate in the progression, invasion and growth of metastatic cells .
The FBXO25 gene encodes a member of the F-box protein family, a subunit of an ubiquitin protein ligase complex hat functions in phosphorylation-dependent ubiquitination. A connection exists between CNVs and tumor suppressor genes such as FBXO25 with negative regulation of gene expression , which may help in further understanding the behavior of tumorigenesis and cancer progression. In the present investigation, we detected a deletion in the FBXO25 gene (8p23.3) in the tumor tissue using both techniques.
In this investigation, other genomic alterations detected in tumor samples included duplications in the PSPC1 gene (13q12.1), which encodes protein tyrosine kinase 6 and is involved in determining oncogenic subcellular translocations. Its positive regulation of PSPC1 is related to a prometastatic activator associated with a poor prognosis, while its negative regulation suppresses activated metastases and is a potential marker of improved cancer therapy outcomes .
In particular, duplication in 1p36 located in the TNFRSF18 gene in both tumoral and nontumoral tissues, was a relevant finding of our study. The tumor necrosis factor receptor-associated factor-6 protein (TRAF-6), which is encoded by one of the TNFRSF18 family genes, was abnormally expressed in positive CRC tissues and was closely linked to patient’s prognosis [29–31]. Thus, TNFRSF18 amplification deserves special attention to clarify its clinical significance in this patient’s profile [29–31].
In the present investigation, SNP array results of the surrounding nonneoplastic tissue samples from patients with metastases revealed different structural variations at 1q42.3, comprising the LYST gene, which has been previously associated with cancer and autoimmune diseases. LYST has been associated with immunodeficiency syndromes and with impaired cytotoxic lymphocytic function, especially among NK cells, which are very important in the defense against tumor growth .
When the amount of DNA damage is greater than the DNA repair capability, a checkpoint-signaling pathway is activated [29, 33–37]. One of the first steps in the cellular response to DNA damage induced by exogenous agents is DNA repair protein activation [35–37]. The literature suggests that CNVs may be important genetic variants that explain tumor heterogeneity and genetic instability in CRC [38–40]. Therefore, we suggest that these CNVs are initialization markers of cellular abnormality. Accordingly, our results demonstrate tumor cells characterized by different CNVs in subtelomeric regions, clearly indicating the presence of CIN confirmed by SNP test array results.
In sporadic tumors, CIN is characterized by gains and losses of small genomic segments or whole arms, that are mainly caused by chromosomal breaks [4, 6, 8, 41]. CIN can result from defects in chromosomal segregation, instability or loss of telomeres, or errors during a response to DNA damage. Double-strand breaks are a common mechanism in tumor instability, and usually occur through nonhomologous end joining [5, 7, 8, 38]. Furthermore, subtelomeric regions are more susceptible to rearrangement and have recently been implicated in a genomic rearrangement event known as chromothripsis, which has been reported in some types of cancer [41–44]. The aberrant chromosomal architecture -i.e., the variation of small insertions or deletions leading to major chromosomal changes such as premitotic defects, stress in replication and telomeric fusions- has an important role in CIN and is usually found in cancer genomes [6, 41, 45–48]. Studies have reported aneuploidies of whole chromosomes in 70% of colorectal tumors [45, 46]. Importantly, CIN may disturb the cell environment and immune signaling. The inhibition of the immune vigilance system has revealed altered expression of several genes involved in adaptive immunity and/or associated with cytotoxic cells and NK cells, suggesting a decrease in the level of immune cells and functioning as an immunosuppressant [45–48] Notably, Bakhoum et al.  discussed the complex effects of CIN as a central driver of tumor evolution based on genomic copy number heterogeneity. In our investigation, most of the patients studied (such as patients 23 and 26) had metastases and several genomic alterations detected by MLPA and an array with several CNVs in subtelomeric regions, indicating the presence of CIN.
Approximately 85% of CRC cases demonstrated chromosomal and ROH imbalances, which led to changed expressions of tumors and oncogene suppressor genes [45–50]. We observed several insertions and deletions and ROH in the array results in surrounding nonneoplastic tissue. There results indicate there was an unstable microenvironment growing around the tumor.
Our findings suggest the need for a more detailed molecular investigation of the altered genomic regions, considering an expanded study of the genomic profile in a larger population, using this model to confirm the discovery of relevant prognostic markers for this disease.
In conclusion, our findings show the importance of characterizing the genomic CRC profile to understand tumor initiation and progression in sporadic CRC patients. Structural variants may lead to chromosomal instability and directly influence genic transcription through genetic dosing that occurs via exclusions or gene amplifications. The identification of the concomitant CNVs in the tumors and surrounding nonneoplastic tissues, which should hypothetically be free of changes, opens the possibility for the use of MLPA and/or SNP array assays for early diagnosis in CRC cases.