Molecular markers associated with colorectal cancer

Avishek Roy

Scientific Liaison Manager
4baseCare

Colorectal cancer (CRC) is the third most common cancer globally in terms of morbidity and death. In terms of molecular genetic features and pathogenic mechanisms, CRC is quite diverse. In fact, a wide range of biomarkers are used for molecular subtype classification, prognosis, and estimating drug sensitivity. These biomarkers can include germline and somatic mutations, chromosomal aberrations, genomic abnormalities, gene expression modifications at the mRNA or protein level, and changes in DNA methylation status. Numerous molecular genetic studies of CRC have revealed that many genes have a high frequency of mutations (KRAS, NRAS, BRAF, PIK3CA, APC, TP53, SMAD2, SMAD4, ARID1A, SOX9, FAM123B/WTX, and FBXW7), copy number alterations (ERBB2 and IGF2), methylation status changes (MLH1), impaired mRNA or protein expression, and translocations.  Many gene mutations have prognostic significance for determining prognosis and drug sensitivity.

Precision oncology holds the promise of individualized strategies to CRC prevention and treatment. Molecular markers can be used to classify colorectal cancers. Microsatellite instability (MSI) analysis, as well as BRAF, TP53, APC and KRAS mutation analyses, are being employed in the evaluation of CRC patients. In colorectal cancers, the presence of MSI and/or specific mutations or epimutations provides clinicians with the information they need to determine the best treatment. Due to the wide range of clinical responses to CRC therapy, new predictive and prognostic molecular classifiers are needed to determine the optimal treatment selections for patients, taking into consideration their prognosis as well as their projected chemotherapeutic response.

Microsatellite Instability (MSI):
Changes in highly repetitive DNA sequences (microsatellites) are caused by mutations and/or epimutations in genes involved in the DNA mismatch repair system (MMR), such as MLH1, MSH2, MSH6, and PMS2. MSI is a defining feature of Lynch Condition, an inherited CRC syndrome that is utilized as a diagnostic marker. MSI is identified in 10–15 percent of sporadic CRC cancers, despite somatic mutations in MMR genes being uncommon. The bulk of sporadic CRC with MSI is caused by methylation-induced MLH1 silencing. Most clinical laboratories now use a panel of five mononucleotide markers (Bat-25, Bat26, NR-21, NR-24, and MONO-27) to identify MSI. MSI is more prevalent in the right colon, as well as in pathological forms with less differentiation, such as mucinous adenocarcinoma and medullary carcinoma. MSI can be used to determine whether or not individuals with stage II colorectal cancer should be treated with adjuvant chemotherapy. MSI-H colorectal cancer is not susceptible to fluorouracil (FU)-based adjuvant chemotherapy, according to studies, and cannot benefit from FU adjuvant treatment.

EGFR gene:
EGFR is a transmembrane tyrosine kinase receptor, belonging to the epidermal growth factor receptor (ErbB) family of cell expression receptors. The epidermal growth factor receptor (ErbB) family of cell expression receptors includes EGFR, which is a transmembrane tyrosine kinase receptor. When a ligand binds to EGFR, it activates the receptor’s downstream signaling pathways, which are mostly MAPK and PI3K signaling pathways. These pathways will be activated, which will result in cell proliferation, differentiation, metastasis, and death. According to studies, EGFR is expressed positively in 25–35 % of colorectal malignancies. Patients with colorectal cancer who have positive EGFR expression are poorly differentiated, and their prognosis is dismal. Positive EGFR expression is not linked to the efficacy of anti-EGFR targeted treatment, according to clinical studies.

KRAS gene:
The MAPK signalling pathway includes the KRAS gene, which is a downstream gene of EGFR. KRAS gene mutations are seen in 30–40 % of colorectal cancer patients. When the KRAS gene is mutated, GTPase activity is inhibited, and the KRAS protein is constantly active, causing problems in downstream signaling pathways and, ultimately leads to poor anti-EGFR therapeutic efficacy. Studies have reported that first-line chemotherapy combined with antiEGFR treatment had a longer PFS in patients with advanced colorectal cancer with KRAS mutations than chemotherapy alone.

BRAF gene:
BRAF is a component of the RAS-RAF-MAP2K (MEK)-MAPK signal pathway, which is involved in the onset and progression of colorectal cancer. The most frequent BRAF mutation is V600E, which causes the RAS/RAF/MEK/ERK genes to remain activated indefinitely. BRAF V600E gene mutations are identified in 5–10% of colorectal cancers, with BRAF V600E mutations being more common in older female patients with proximal colon cancer. In colorectal cancers, KRAS and BRAF mutations are usually mutually exclusive.  Recent studies suggest BRAF mutations may potentially be employed as a predictive marker for EGFR-targeted treatment.

PIK3CA and PTEN gene:
Another EGFR signaling pathway that can be influenced by PIK3CA mutations and PTEN gene inactivation is the PI3K-AKT pathway. PIK3CA mutations are seen in 14–18 % of colon cancer patients. Exon 9 and 20 mutations account for the majority of PIK3CA mutations. Exon 9 mutations are frequently linked to KRAS mutations, and patients with both KRAS and PIK3CA 9 exon mutations have a poor prognosis. The PTEN protein, which is encoded by the PTEN gene, can inhibit PI3K from functioning. The PTEN gene mutation rate in colorectal cancer is 13–18%.
HER2 gene: According to a study, HER2 positive patients made up 5% of KRAS wild-type advanced colorectal cancer patients. Anti-EGFR therapy was ineffective in these patients, while cetuximab with apatinib treatment was clinically effective, with a 35 % objective response rate.

CpG Island Methylator Phenotype (CIMP):
Since the revelation that methylation-driven transcriptional regulation causes colorectal carcinogenesis and that the CpG island methylator phenotype (CIMP) status correlates to a specific CRC subtype, the epimutation status of tumors has become more important. Women are more likely to have CIMP high colorectal cancers, which are linked to BRAF mutations. They have proximal tumour site, poor differentiation, mucinous histology, MSI, and a low frequency of TP53 mutations, among other features.

MicroRNAs:
Multiple experiments aimed at establishing a miRNA biomarker panel have been conducted as a consequence of mounting evidence that noncoding microRNAs (miRNAs) have a role in oncogenesis. When comparing CRC tissue to noncancerous tissue, researchers discovered a total of 362 differently expressed miRNAs, with 242 being upregulated and 120 being downregulated. To fully understand the clinical value of miRNAs as diagnostic, prognostic, and/or therapeutic tools, more research is needed.

The diagnosis and treatment of malignant tumors is advancing toward molecular level research and individualized treatment, due to the advances of precision oncology. Colorectal cancer treatment effectiveness has increased due to personalized therapy for cancers with diverse molecular characteristics. The proper application of molecular markers can help patients with colorectal cancer make treatment decisions and determine their prognosis