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Biomedicines
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Genetic Research on Colorectal Cancer
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Genetic Research on Colorectal Cancer

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Molecular Genetics and Genetic Diseases".

Deadline for manuscript submissions: closed (30 June 2024) | Viewed by 10199

Special Issue Editor

Dr. Chih-Hsiung Hsu

E-Mail Website
Guest Editor
School of Public Health, National Defense Medical Center, Taipei City 114, Taiwan
Interests: cancer epigenetics; methylation; colorectal cancer; oncogenesis; biomarkers; epidemiology

Special Issue Information

Dear Colleagues,

The latest WHO statistics on colorectal cancer (CRC) indicate that it is the third most prevalent cancer worldwide, with almost 2 million new cases diagnosed annually. It is also the second leading cause of cancer-related death, responsible for approximately 1 million fatalities annually.

The pathogenesis of CRC is classically attributed to genomic and epigenetic alterations in the healthy colon epithelium, which facilitate the progression to adenomatous and invasive adenocarcinomatous lesions. The genetic landscape of CRC is crucial. Variations in genes related to cell cycle regulation, DNA repair, and apoptosis significantly contribute to the onset and progression of CRC.

Over the decades, the genetic aspects of CRC, including, but not limited to, gene mutations, chromosomal instability, and genetic polymorphisms, have become increasingly recognized as critical factors in CRC diagnosis, prognosis, and response to treatment. In particular, advances in genomics have identified key genetic markers that offer new avenues for targeted therapies.

For this Special Issue, we invite basic and clinical oncologists to submit contributions that specifically focus on the genetics of colorectal cancer. This includes reviews, new methods, and original research articles. We welcome submissions covering various dimensions of CRC genetics, such as basic mechanistic studies, the genomics of CRC cells, translational research, therapeutic applications, and clinical trials involving targeted gene therapies.

Dr. Chih-Hsiung Hsu
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomedicines is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • colorectal cancers
  • genomics
  • epigenomics
  • genetic landscape
  • DNA methylation
  • chromosomal instability
  • targeted gene therapies

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Published Papers (6 papers)

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Research

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16 pages, 1854 KiB  
Article
Association of the rs1966265 and rs351855 FGFR4 Variants with Colorectal Cancer in a Mexican Population and Their Analysis In Silico
by Irving Alejandro Carrillo-Dávila, Asbiel Felipe Garibaldi-Ríos, Luis E. Figuera, Belinda Claudia Gómez-Meda, Guillermo M. Zúñiga-González, Ana María Puebla-Pérez, Patricia Montserrat García-Verdín, Paola Beatriz Castro-García, Itzae Adonai Gutiérrez-Hurtado, Blanca Miriam Torres-Mendoza and Martha Patricia Gallegos-Arreola
Biomedicines 2024, 12(3), 602; https://doi.org/10.3390/biomedicines12030602 - 7 Mar 2024
Cited by 1 | Viewed by 1516
Abstract
The aim of this study was to associate FGFR4 rs1966265 and rs351855 variants with colorectal cancer (CRC) in a Mexican population and to perform in silico analysis. Genomic DNA from 412 healthy individuals and 475 CRC patients was analyzed. In silico analysis was [...] Read more.
The aim of this study was to associate FGFR4 rs1966265 and rs351855 variants with colorectal cancer (CRC) in a Mexican population and to perform in silico analysis. Genomic DNA from 412 healthy individuals and 475 CRC patients was analyzed. In silico analysis was performed using the PolyPhen-V2, GEPIA, GTEx, and Cytoscape platforms. The GA genotype dominant model (GAAA) of rs1966265 and the AA genotype dominant and recessive models of rs351855 were identified as CRC risk factors (p < 0.05). CRC patients aged ≥ 50 years at diagnosis who consumed alcohol had a higher incidence of the rs351855 GA genotype than the control group (p < 0.05). Associations were observed between the rs1966265 GA genotype and patients with rectal cancer and stage III–IV disease. The rs351855 AA genotype was a risk factor for partial chemotherapy response, and the GA + AA genotype for age ≥ 50 years at diagnosis and rectal cancer was associated with a partial response to chemotherapy (p < 0.05). The AA haplotype was associated with increased susceptibility to CRC. In silico analysis indicated that the rs351855 variant is likely pathogenic (score = 0.998). Genotypic expression analysis in blood samples showed statistically significant differences (p < 0.05). EFNA4, SLC3A2, and HNF1A share signaling pathways with FGFR4. Therefore, rs1966265 and rs351855 may be potential CRC risk factors. Full article
(This article belongs to the Special Issue Genetic Research on Colorectal Cancer)
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14 pages, 2585 KiB  
Article
Correlations between MSH2 and MSH6 Concentrations in Different Biological Fluids and Clinicopathological Features in Colorectal Adenocarcinoma Patients and Their Contribution to Fast and Early Diagnosis of Colorectal Adenocarcinoma
by Alexandru Adrian Bratei and Raluca-Ioana Stefan-van Staden
Biomedicines 2023, 11(12), 3213; https://doi.org/10.3390/biomedicines11123213 - 4 Dec 2023
Viewed by 1407
Abstract
(1) Background: The human MutS homolog, hMSH2, is known to be involved in DNA mismatch repair and is responsible for maintaining the stability of the genome. When DNA damage occurs, MSH2 promotes cell apoptosis via the regulation of ATR/Chk2/p53 signal transduction, and MSH2 [...] Read more.
(1) Background: The human MutS homolog, hMSH2, is known to be involved in DNA mismatch repair and is responsible for maintaining the stability of the genome. When DNA damage occurs, MSH2 promotes cell apoptosis via the regulation of ATR/Chk2/p53 signal transduction, and MSH2 deficiency is also related to accelerated telomere shortening in humans. MSH2 missense mutations are involved in a defective DNA reparation process, and it can be implied in carcinogenesis, as it is already involved in well-known cancer-related syndromes such as Lynch syndrome. Human MSH6, which stands for mutS homolog 6, is a member of the MMR family that is responsible for the repair of post-replicative mismatched DNA bases. It is also one of the proteins with gene mutations that are associated with a high risk of developing Lynch syndrome, leading to a large series of tumors. (2) Methods: Patients and their clinical and pathological features were selected from the database of the project GRAPHSENSGASTROINTES and used accordingly, with ethics committee approval no. 32647/2018 awarded by the County Emergency Hospital from Targu-Mures. Analyses were conducted on whole blood, saliva, urine, and tumoral tissue samples using a stochastic method with stochastic microsensors. (3) Results: The results obtained using stochastic sensors were correlated with a series of macroscopic and microscopic pathological features for each sample type. Criteria or relationships were established for tumor location, vascular and perineural invasions, lymph node metastases, the presence of tumor deposits, and the presence of a mucus compound in the tumor mass. (4) Conclusions: The correlation between the concentrations of MSH2 in the four types of samples and the pathological features allowed for the fast characterization of a tumor, which can help surgeons and oncologists choose personalized treatments. Also, the colorectal tumor location was correlated with the concentration of MSH2 in whole blood, urine, and saliva. MSH6, which stands for mutS homolog 6, is not only useful in immunohistochemistry but in pathology practice as well. In this paper, the relationships between MSH6 levels in four biological fluids—whole blood, saliva, urine, and tissues—and tumor locations among the colorectal area, gross features, presence of a mucinous compound, molecular subtype, stroma features, and vascular invasions are presented. Full article
(This article belongs to the Special Issue Genetic Research on Colorectal Cancer)
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12 pages, 819 KiB  
Article
Association of miR-149 T>C and miR-196a2 C>T Polymorphisms with Colorectal Cancer Susceptibility: A Case-Control Study
by Bayram Bayramov, Nuru Bayramov, Hazi Aslanov, Nigar Karimova, Karim Gasimov, Ilham Shahmuradov, Christoph Reißfelder and Vugar Yagublu
Biomedicines 2023, 11(9), 2341; https://doi.org/10.3390/biomedicines11092341 - 23 Aug 2023
Cited by 1 | Viewed by 1384
Abstract
The principal aim of the current study was to investigate the relationship between miR-149 T>C (rs2292832) and miR-196a2 C>T (rs11614913) small non-coding RNA polymorphisms and the risk of developing CRC in the Azerbaijani population. The study included 120 patients diagnosed with CRC and [...] Read more.
The principal aim of the current study was to investigate the relationship between miR-149 T>C (rs2292832) and miR-196a2 C>T (rs11614913) small non-coding RNA polymorphisms and the risk of developing CRC in the Azerbaijani population. The study included 120 patients diagnosed with CRC and 125 healthy individuals. Peripheral blood samples were collected from all the subjects in EDTA tubes and DNA extraction was performed by salting out. Polymorphisms were determined using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. While comparing without gender distinction no statistical correlation was found between the heterozygous TC (OR = 0.66; 95% CI = 0.37–1.15; p = 0.142), mutant CC (OR = 1.23; 95% CI = 0.62–2.45; p = 0.550), and mutant C (OR = 1.03; 95% CI = 0.72–1.49; p = 0.859) alleles of the miR-149 gene and the CT (OR = 1.23; 95% CI = 0.69–2.20; p = 0.485), mutant TT (OR = 1.29; 95% CI = 0.67–2.47; p = 0.452), and mutant T (OR = 1.17; 95% CI = 0.82–1.67; p = 0.388) alleles of the miR-196a2 gene and the risk of CRC. However, among women, miR-149 TC (OR = 0.43; 95% CI = 0.19–1.01; p = 0.048) correlated with a reduced risk of CRC, whereas miR-196a2 CT (OR = 2.77; 95% CI = 1.13–6.79; p = 0.025) correlated with an increased risk of CRC. Our findings indicated that miR-149 T>C (rs2292832) might play a protective role in the development of CRC in female patients, whereas the miR-196a2 (rs11614913) polymorphism is associated with an increased risk of CRC in women in the Azerbaijani population, highlighting the importance of gender dimorphism in cancer etiology. Full article
(This article belongs to the Special Issue Genetic Research on Colorectal Cancer)
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13 pages, 1860 KiB  
Article
CT-Based Radiomics to Predict KRAS Mutation in CRC Patients Using a Machine Learning Algorithm: A Retrospective Study
by Jacobo Porto-Álvarez, Eva Cernadas, Rebeca Aldaz Martínez, Manuel Fernández-Delgado, Emilio Huelga Zapico, Víctor González-Castro, Sandra Baleato-González, Roberto García-Figueiras, J Ramon Antúnez-López and Miguel Souto-Bayarri
Biomedicines 2023, 11(8), 2144; https://doi.org/10.3390/biomedicines11082144 - 29 Jul 2023
Cited by 3 | Viewed by 1558
Abstract
Colorectal cancer (CRC) is one of the most common types of cancer worldwide. The KRAS mutation is present in 30–50% of CRC patients. This mutation confers resistance to treatment with anti-EGFR therapy. This article aims at proving that computer tomography (CT)-based radiomics can [...] Read more.
Colorectal cancer (CRC) is one of the most common types of cancer worldwide. The KRAS mutation is present in 30–50% of CRC patients. This mutation confers resistance to treatment with anti-EGFR therapy. This article aims at proving that computer tomography (CT)-based radiomics can predict the KRAS mutation in CRC patients. The piece is a retrospective study with 56 CRC patients from the Hospital of Santiago de Compostela, Spain. All patients had a confirmatory pathological analysis of the KRAS status. Radiomics features were obtained using an abdominal contrast enhancement CT (CECT) before applying any treatments. We used several classifiers, including AdaBoost, neural network, decision tree, support vector machine, and random forest, to predict the presence or absence of KRAS mutation. The most reliable prediction was achieved using the AdaBoost ensemble on clinical patient data, with a kappa and accuracy of 53.7% and 76.8%, respectively. The sensitivity and specificity were 73.3% and 80.8%. Using texture descriptors, the best accuracy and kappa were 73.2% and 46%, respectively, with sensitivity and specificity of 76.7% and 69.2%, also showing a correlation between texture patterns on CT images and KRAS mutation. Radiomics could help manage CRC patients, and in the future, it could have a crucial role in diagnosing CRC patients ahead of invasive methods. Full article
(This article belongs to the Special Issue Genetic Research on Colorectal Cancer)
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Review

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26 pages, 703 KiB  
Review
The Importance of Genetic Screening on the Syndromes of Colorectal Cancer and Gastric Cancer: A 2024 Update
by Iulia Lupan, Ciprian Silaghi, Claudia Stroe, Adriana Muntean, Diana Deleanu, Vasile Bintintan and Gabriel Samasca
Biomedicines 2024, 12(12), 2655; https://doi.org/10.3390/biomedicines12122655 - 21 Nov 2024
Viewed by 276
Abstract
Gastrointestinal cancers (GIC), encompassing colonic, rectal, and gastric malignancies, rank among the most prevalent cancer types globally, contributing significantly to cancer-related mortality. In the scientific literature, various syndromes associated with colorectal and gastric cancers have been elucidated, highlighting the intricate interplay between genetic [...] Read more.
Gastrointestinal cancers (GIC), encompassing colonic, rectal, and gastric malignancies, rank among the most prevalent cancer types globally, contributing significantly to cancer-related mortality. In the scientific literature, various syndromes associated with colorectal and gastric cancers have been elucidated, highlighting the intricate interplay between genetic factors and disease manifestation. The primary objective of this study was to conduct a genetic exploration aimed at elucidating these associations and identifying shared genetic determinants across these cancer types. Notably, considerable research has focused on the KRAS gene mutations, polymorphisms in nucleic acids, the Wnt signaling pathway, and the role of chemokine ligands in tumorigenesis. While investigations into natural plant extracts as potential therapeutic agents are still in their nascent stages, they represent a promising avenue for future research. Ongoing studies are essential to uncover suitable biomarkers that could facilitate the identification and understanding of the genetic links between these GIC. This exploration not only seeks to enhance our comprehension of the underlying genetic architecture but also aims to inform the development of targeted therapies and preventive strategies. Full article
(This article belongs to the Special Issue Genetic Research on Colorectal Cancer)
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14 pages, 1448 KiB  
Review
Targeting FGFR Pathways in Gastrointestinal Cancers: New Frontiers of Treatment
by Margherita Ratti, Elena Orlandi, Jens Claus Hahne, Stefano Vecchia, Chiara Citterio, Elisa Anselmi, Ilaria Toscani and Michele Ghidini
Biomedicines 2023, 11(10), 2650; https://doi.org/10.3390/biomedicines11102650 - 27 Sep 2023
Cited by 4 | Viewed by 2789
Abstract
In carcinogenesis of the gastrointestinal (GI) tract, the deregulation of fibroblast growth factor receptor (FGFR) signaling plays a critical role. The aberrant activity of this pathway is described in approximately 10% of gastric cancers and its frequency increases in intrahepatic cholangiocarcinomas (iCCAs), with [...] Read more.
In carcinogenesis of the gastrointestinal (GI) tract, the deregulation of fibroblast growth factor receptor (FGFR) signaling plays a critical role. The aberrant activity of this pathway is described in approximately 10% of gastric cancers and its frequency increases in intrahepatic cholangiocarcinomas (iCCAs), with an estimated frequency of 10–16%. Several selective FGFR inhibitors have been developed in the last few years with promising results. For example, targeting the FGFR pathway is now a fundamental part of clinical practice when treating iCCA and many clinical trials are ongoing to test the safety and efficacy of anti-FGFR agents in gastric, colon and pancreatic cancer, with variable results. However, the response rates of anti-FGFR drugs are modest and resistances emerge rapidly, limiting their efficacy and causing disease progression. In this review, we aim to explore the landscape of anti-FGFR inhibitors in relation to GI cancer, with particular focus on selective FGFR inhibitors and drug combinations that may lead to overcoming resistance mechanisms and drug-induced toxicities. Full article
(This article belongs to the Special Issue Genetic Research on Colorectal Cancer)
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