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Genetic and Genomic Research on Colorectal Cancer
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Genetic and Genomic Research on Colorectal Cancer

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Human Genomics and Genetic Diseases".

Deadline for manuscript submissions: closed (25 December 2024) | Viewed by 6217

Special Issue Editor

Dr. Martha Patricia Gallegos-Arreola

E-Mail Website
Guest Editor
División de Genética, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara 44340, Jalisco, Mexico
Interests: cancer; variants; polymorphism
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Colorectal cancer (CRC) is one of the most common cancers worldwide and causes a high number of deaths. Although it is a multifactorial disease, the genetic and genomic study of CRC has revolutionized our understanding of this disease by allowing us to identify key genetic and genomic alterations in its development and progression. Advances in this research have shown that CRC is genetically complex, involving alterations in key genes such as APC, TTN, TP53, KRAS, PIK3CA, and MUC16, among others, associated with various clinicopathological features of the disease. This Special Issue aims to advance genetic and genomic research in CRC, highlighting studies that explore the underlying genetic and genomic mechanisms and their clinical implications. Our objective is to deepen insights into genetic predispositions, genetic markers, comparative genomics, genetic diversity, and the overall genetic and genomic mechanisms driving CRC.

Dr. Martha Patricia Gallegos-Arreola
Guest Editor

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Keywords

  • colorectal cancer
  • genetic research
  • genomics
  • somatic mutations
  • DNA sequencing
  • susceptibility genetics
  • genetic variants

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Published Papers (5 papers)

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Research

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10 pages, 1615 KiB  
Article
Clinical Implications of Cell-Free DNA in Managing BRAF V600E Mutation-Positive Colorectal Cancer
by Takuma Iwai, Takeshi Yamada, Kay Uehara, Seiichi Shinji, Akihisa Matsuda, Yasuyuki Yokoyama, Goro Takahashi, Toshimitsu Miyasaka and Hiroshi Yoshida
Genes 2025, 16(3), 275; https://doi.org/10.3390/genes16030275 - 25 Feb 2025
Viewed by 561
Abstract
Background/Objectives: BRAFV600E-mutant colorectal cancer (CRC) is associated with poor prognosis, and despite the introduction of BEACON therapy, significant treatment challenges remain. This study investigates the clinical utility of BRAFV600E in cell-free DNA (cfDNA BRAFV600E) as a biomarker [...] Read more.
Background/Objectives: BRAFV600E-mutant colorectal cancer (CRC) is associated with poor prognosis, and despite the introduction of BEACON therapy, significant treatment challenges remain. This study investigates the clinical utility of BRAFV600E in cell-free DNA (cfDNA BRAFV600E) as a biomarker for real-time treatment monitoring in metastatic cases and for evaluating minimal residual disease (MRD) after curative resection. Methods: This single-center, prospective observational study included 37 patients with BRAFV600E-mutant CRC treated at Nippon Medical School Hospital between April 2017 and June 2024. Patients were divided into two cohorts: Cohort 1 (Stage IV cases): Evaluated cfDNA BRAFV600E for treatment monitoring. Cohort 2 (Stage I–III curatively resected cases): Assessed cfDNA BRAFV600E for recurrence risk prediction. Blood samples were collected before and during treatment and analyzed using droplet digital PCR (ddPCR) to measure cfDNA BRAFV600E levels. Results: Cohort 1 (Stage IV, n = 14): Pre-treatment cfDNA BRAFV600E was detected in 93% of cases. Patients with a decrease in cfDNA BRAFV600E variant allele frequency (VAF) after chemotherapy had significantly longer overall survival (511 vs. 189 days, p = 0.03) than those without a decrease. Cohort 2 (curatively resected, n = 23): cfDNA BRAFV600E was detected in 4/23 patients (17.4%) at 1 month post-surgery. cfDNA BRAFV600E showed better recurrence prediction compared to CEA (100% vs. 18.8%, p = 0.004). Among the seven patients who experienced recurrence, those with postoperative cfDNA BRAFV600E positivity had significantly shorter disease-free survival compared to cfDNA BRAFV600E-negative patients (179 vs. 840 days, p = 0.04). Conclusions: These findings support cfDNA BRAFV600E as a promising biomarker for monitoring treatment response and MRD detection in BRAFV600E-mutant CRC, reinforcing its role in guiding personalized treatment strategies and postoperative surveillance. Full article
(This article belongs to the Special Issue Genetic and Genomic Research on Colorectal Cancer)
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10 pages, 923 KiB  
Article
MLH1 Methylation Status and Microsatellite Instability in Patients with Colorectal Cancer
by Manuel Alejandro Rico-Méndez, Miguel Angel Trujillo-Rojas, María de la Luz Ayala-Madrigal, Jesús Arturo Hernández-Sandoval, Anahí González-Mercado, Melva Gutiérrez-Angulo, José Geovanni Romero-Quintana, Jesús Alonso Valenzuela-Pérez, Ruth Ramírez-Ramírez, Beatriz Armida Flores-López and José Miguel Moreno-Ortiz
Genes 2025, 16(2), 182; https://doi.org/10.3390/genes16020182 - 2 Feb 2025
Cited by 1 | Viewed by 1289
Abstract
Background/Objectives: The purpose of the current study was to compare the methylation of five regions of the CpG island of MLH1 with the presence of microsatellite instability (MSI) in colorectal cancer (CRC) patients. Methods: The study analyzed 138 CRC tumor samples. DNA extraction [...] Read more.
Background/Objectives: The purpose of the current study was to compare the methylation of five regions of the CpG island of MLH1 with the presence of microsatellite instability (MSI) in colorectal cancer (CRC) patients. Methods: The study analyzed 138 CRC tumor samples. DNA extraction was performed, followed by bisulfite conversion. MLH1 gene methylation was assessed by methylation-specific PCR (MS-PCR), and the resulting fragments were analyzed using polyacrylamide gels. MSI was evaluated using multiplex PCR, and the fragments were run through capillary electrophoresis. R studio (v4.4.1) and SPSS (v29.0) software were used for the statistical analysis, and values of p < 0.05 were considered statistically significant. Results: The study showed 75.4% unmethylated, 21% partially methylated, and 3.6% fully methylated samples, with region A frequently methylated. MSI was observed in 7.2% of cases (MSI-H: 5.8%, MSI-L: 1.4%). BAT-26 was the most unstable marker. A significant difference between MLH1 methylation and MSI-H (p < 0.01) was identified, but there was no relationship with specific MLH1 regions. Conclusions: No differences were identified when analyzing specific methylation regions in relation to MSI. This study is the first to describe MSI frequency in Mexican patients regardless of age. Full article
(This article belongs to the Special Issue Genetic and Genomic Research on Colorectal Cancer)
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17 pages, 3072 KiB  
Article
Association of Variants in IL-1RN (rs2234663) and IL-1β (rs1143627, rs16944) and Interleukin-1β Levels with Colorectal Cancer: Experimental Study and In Silico Analysis
by Martha Patricia Gallegos-Arreola, Asbiel Felipe Garibaldi-Ríos, Itzae Adonaí Gutiérrez-Hurtado, Guillermo Moisés Zúñiga-González, Luis E. Figuera, Belinda Claudia Gómez-Meda, Ana María Puebla-Pérez, José Elías García-Ortiz, Jorge I. Delgado-Saucedo, Paola Beatriz Castro-García, María de Jesús Rentería-Ramírez and Blanca Miriam Torres-Mendoza
Genes 2024, 15(12), 1528; https://doi.org/10.3390/genes15121528 - 27 Nov 2024
Viewed by 811
Abstract
Background/Objectives. Colorectal cancer (CRC) is a multifactorial disease where the inflammatory state is crucial. This study analyzes the association of the IL-1RN (rs2234663) and IL-1β (rs1143627, rs16944) variants and IL-1β levels with CRC. Methods. This study included 230 CRC patients and 256 controls. [...] Read more.
Background/Objectives. Colorectal cancer (CRC) is a multifactorial disease where the inflammatory state is crucial. This study analyzes the association of the IL-1RN (rs2234663) and IL-1β (rs1143627, rs16944) variants and IL-1β levels with CRC. Methods. This study included 230 CRC patients and 256 controls. Genotypes were determined by PCR and plasma IL-1β levels by ELISA. RegulomeDB analyzed the variants’ functional impacts, while OncoDB assessed IL-1β and IL-1RN expression’s influence on CRC. Results. The A1A1 genotype and dominant pattern of the rs2234663 variant were risk factors for CRC, whereas the A1A2 genotype showed a protective effect. The TC genotype of the rs1143627 variant and the T allele of rs16944 were associated with increased risk, whereas the C allele had a protective effect. The A1A1 genotype was associated with stage I–II CRC diagnosis, while the A2A2 genotype was associated with stage III–IV and ethanol consumption. The CC genotype of rs1143627 was associated with people younger than 50 years and tobacco use, and the TCCC genotype was related to stage III–IV stages and metastasis and hemorrhoids (p < 0.05). IL-1β levels were not associated with CRC. In silico analysis revealed that the variants are in located in important regions regulatory of genes. Elevated IL-1B and IL-1RN mRNA levels were found in CRC, linked to clinicopathological features of the disease. Conclusions. The analyzed variants are associated with CRC and may influence gene regulation by being located at critical sites of key genetic regulators. Full article
(This article belongs to the Special Issue Genetic and Genomic Research on Colorectal Cancer)
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8 pages, 261 KiB  
Article
Intronic Variants in the MSH2 (rs2303426 and rs10179950) and PMS2 (rs2286681 and rs62456178) Genes Are Not Associated with Colorectal Cancer in Mexican Patients
by Manuel Alejandro Rico-Méndez, Anna Guadalupe López-Ceballos, José Miguel Moreno-Ortiz, María de la Luz Ayala-Madrigal, Melva Gutiérrez-Angulo, Ruth Ramírez-Ramírez, Mirna Gisel González-Mercado and Anahí González-Mercado
Genes 2024, 15(11), 1380; https://doi.org/10.3390/genes15111380 - 26 Oct 2024
Viewed by 1149
Abstract
Background/Objectives: In the origin and development of colorectal cancer (CRC), a global public health problem, a dysfunction mismatch repair system appears to be a key factor. The objective was to determine the association of intronic variants in the MSH2 and PMS2 genes with [...] Read more.
Background/Objectives: In the origin and development of colorectal cancer (CRC), a global public health problem, a dysfunction mismatch repair system appears to be a key factor. The objective was to determine the association of intronic variants in the MSH2 and PMS2 genes with CRC in Mexican patients. Methods: Blood samples of 143 CRC patients and 146 reference individuals were genotyped through TaqMan® Genotyping Assays. Genotypic and allelic frequencies were determined by direct counting. To compare genotypic and allelic distributions, the chi-square test was used. For the association analysis, the risks of alleles and genotypes were estimated by odds ratio with 95% confidence intervals. Haplogroups were inferred with a Bayesian algorithm. Linkage disequilibrium was measured using D’ and r2 with Arlequin v3.5.2. The in silico analysis was carried out using the SpliceAI, UCSC, JASPAR and TRRUST platforms. All statistical analyses were performed with SPSS v29.0.2.0. Results: In the CRC group, the mean age was 58.2 ± 14.7 years and 60.8% were men. No variant was associated with CRC or implicated in gene post-replicative processing. Linkage disequilibrium was observed for loci rs2303426 and rs10179950 in MSH2 and for loci rs2286681 and rs62456178 in PMS2. Conclusions: The genotypic and allelic frequencies of the four variants are reported for the first time in Mexican patients with CRC. No association was found between gene variants and risk for CRC but there was a strong linkage disequilibrium between the loci of both MSH2 and PMS2 genes. None of the variants showed a possible repercussion on splicing. Full article
(This article belongs to the Special Issue Genetic and Genomic Research on Colorectal Cancer)

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19 pages, 849 KiB  
Systematic Review
Molecular Mechanism of Radioresponsiveness in Colorectal Cancer: A Systematic Review
by Matthew Y. H. Lau, Md Zahirul Islam Khan and Helen K. W. Law
Genes 2024, 15(10), 1257; https://doi.org/10.3390/genes15101257 - 26 Sep 2024
Cited by 1 | Viewed by 1793
Abstract
Background/Objectives: Colorectal cancer (CRC) is the third most diagnosed cancer globally. Radiotherapy is a common treatment strategy for patients but factors such as gene expressions and molecular mechanism effects may affect tumor radioresponse. The aim of this review is to systematically identify [...] Read more.
Background/Objectives: Colorectal cancer (CRC) is the third most diagnosed cancer globally. Radiotherapy is a common treatment strategy for patients but factors such as gene expressions and molecular mechanism effects may affect tumor radioresponse. The aim of this review is to systematically identify genes suggested to have molecular mechanism effects on the radioresponsiveness of CRC patients. Methods: By following the PRISMA guidelines, a comprehensive literature search was conducted on Pubmed, EMBASE and Cochrane Library. After exclusion and inclusion criteria sorting and critical appraisal for study quality, data were extracted from seven studies. A gene set analysis was conducted on reported genes. Results: From the seven studies, 56 genes were found to have an effect on CRC radioresponsiveness. Gene set analysis show that out of these 56 genes, 24 genes have roles in pathways which could affect cancer radioresponse. These are AKT1, APC, ATM, BRAF, CDKN2A, CTNNB1, EGFR, ERBB2, FLT3, KRAS, MET, mTOR, MYC, NFKB1, KRAS, PDGFRA, PIK3CA, PTEN, PTGS1, PTGS2, RAF1, RET, SMAD4 and TP53. The current project was conducted between the period May 2024 to August 2024. Conclusions: The current review systematically presented 56 genes which have been reported to be related to RT or CRT treatment effectiveness in rectal cancer patients. Gene set analysis shows that nearly half of the genes were involved in apoptosis, DNA damage response and repair, inflammation and cancer metabolism molecular pathways that could affect cancer radioresponse. The gene cohort identified in this study may be used as a foundation for future works focusing on the molecular mechanism of specific pathways contributing to the radioresponse of CRC. Full article
(This article belongs to the Special Issue Genetic and Genomic Research on Colorectal Cancer)
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