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Genetics and Genomics of Colorectal Cancer and Related Diseases
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Genetics and Genomics of Colorectal Cancer and Related Diseases

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 May 2023) | Viewed by 7415

Special Issue Editor

Dr. Koldo Garcia-Etxebarria

E-Mail Website
Guest Editor
Biodonostia, Gastrointestinal Genetics Group, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas Y Digestivas (CIBERehd), 20014 San Sebastian, Spain
Interests: genetics; genomics; omics; microbiome; gastrointestinal diseases

Special Issue Information

Dear Colleagues,

One in ten diagnosed cancers is colorectal cancer (CRC), which is the second cause of death among cancers in developed countries. Survival is conditioned by early diagnosis; therefore, the development of effective biomarkers for diagnosis and prognosis of CRC is essential. In addition, inflammatory processes could increase the risk of developing CRC. Thus, the genetic study (in a broad sense, from the genome to microbiome) of such diseases could be helpful to better understand their biological mechanisms, to find new biomarkers for diagnosis and prognosis, and to study the effect of enviromental factors (such as diet or lifestyle) on the genetic risk.

For this Special Issue of Genes, we welcome authors to submit reviews, new methods, commentaries, and original articles covering the genetics of CRC and related diseases, the effects of different omic layers, or their interplay. Contributions are expected to cover a broad range of topics and methods within the scope of the journal, such as the study of the genetic architecture of CRC and related diseases; the reuse of publicly available data to find new biological mechanisms involved in these diseases; and the applicability of genetic knowledge in the clinical management of these diseases. We look forward to your contributions.

Dr. Koldo Garcia-Etxebarria
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. Genes 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

  • genetics
  • genome
  • transcriptome
  • proteome
  • metabolome
  • microbiome
  • gene–environment interactions
  • colorectal cancer
  • inflammatory bowel diseases

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Published Papers (4 papers)

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Research

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12 pages, 1364 KiB  
Article
ERCC1 and MGMT Methylation as a Predictive Marker of Relapse and FOLFOX Response in Colorectal Cancer Patients from South Tunisia
by Dhouha Jamai, Raja Gargouri, Boulbaba Selmi and Abdelmajid Khabir
Genes 2023, 14(7), 1467; https://doi.org/10.3390/genes14071467 - 19 Jul 2023
Cited by 1 | Viewed by 1377
Abstract
Genetic and epigenetic modifications present a major cause of relapse and treatment failure in colorectal cancer. This study aims to appreciate the prognostic and predictive value of ERRC1 and MGMT methylation. We also studied the prognostic impact of the ERCC1 rs11615 polymorphism as [...] Read more.
Genetic and epigenetic modifications present a major cause of relapse and treatment failure in colorectal cancer. This study aims to appreciate the prognostic and predictive value of ERRC1 and MGMT methylation. We also studied the prognostic impact of the ERCC1 rs11615 polymorphism as well as its expression. Methylation profiles of ERCC1 and MGMT were tested by methylation-specific PCR. A polymorphism of ERCC1 was studied using PCR-RFLP and its expression was examined by immunohistochemistry. ERCC1 was methylated in 44.6% of colorectal adenocarcinoma while MGMT was methylated in 69% of cases. MGMT methylation was strongly associated with lymph node metastasis, lymph invasion, venous invasion, perineural invasion, distant metastasis and relapse. Patients with methylation of both genes were more likely to have a poor prognosis and display chemoresistance. IHC analysis revealed that ERCC1 staining was noted in 52.8% of colorectal adenocarcinoma and inversely related to distant metastasis and cancer recurrence. Kaplan Meier analysis revealed that the worst overall survival was significantly associated with ERCC1 and MGMT methylation while decreased ERCC1 expression and T/T genotype exhibited the best overall survival. The methylation of MGMT, alone or combined with ERCC1, is predictive for poor prognosis, short overall survival and chemotherapy response in colorectal cancer. Full article
(This article belongs to the Special Issue Genetics and Genomics of Colorectal Cancer and Related Diseases)
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14 pages, 2801 KiB  
Article
Transcriptional Dysregulations of Seven Non-Differentially Expressed Genes as Biomarkers of Metastatic Colon Cancer
by Xiaoying Lv, Xue Li, Shihong Chen, Gongyou Zhang, Kewei Li, Yueying Wang, Meiyu Duan, Fengfeng Zhou and Hongmei Liu
Genes 2023, 14(6), 1138; https://doi.org/10.3390/genes14061138 - 24 May 2023
Cited by 3 | Viewed by 1479
Abstract
Background: Colon cancer (CC) is common, and the mortality rate greatly increases as the disease progresses to the metastatic stage. Early detection of metastatic colon cancer (mCC) is crucial for reducing the mortality rate. Most previous studies have focused on the top-ranked [...] Read more.
Background: Colon cancer (CC) is common, and the mortality rate greatly increases as the disease progresses to the metastatic stage. Early detection of metastatic colon cancer (mCC) is crucial for reducing the mortality rate. Most previous studies have focused on the top-ranked differentially expressed transcriptomic biomarkers between mCC and primary CC while ignoring non-differentially expressed genes. Results: This study proposed that the complicated inter-feature correlations could be quantitatively formulated as a complementary transcriptomic view. We used a regression model to formulate the correlation between the expression levels of a messenger RNA (mRNA) and its regulatory transcription factors (TFs). The change between the predicted and real expression levels of a query mRNA was defined as the mqTrans value in the given sample, reflecting transcription regulatory changes compared with the model-training samples. A dark biomarker in mCC is defined as an mRNA gene that is non-differentially expressed in mCC but demonstrates mqTrans values significantly associated with mCC. This study detected seven dark biomarkers using 805 samples from three independent datasets. Evidence from the literature supports the role of some of these dark biomarkers. Conclusions: This study presented a complementary high-dimensional analysis procedure for transcriptome-based biomarker investigations with a case study on mCC. Full article
(This article belongs to the Special Issue Genetics and Genomics of Colorectal Cancer and Related Diseases)
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11 pages, 1111 KiB  
Article
Genetic Variants of HOTAIR Associated with Colorectal Cancer: A Case-Control Study in the Saudi Population
by Haya Saad Alzeer, Jilani P. Shaik, Narasimha Reddy Parine, Mohammad Alanazi, Abdullah Al Alamri, Ramesa Shafi Bhat and Sooad Al Daihan
Genes 2023, 14(3), 592; https://doi.org/10.3390/genes14030592 - 26 Feb 2023
Cited by 5 | Viewed by 2007
Abstract
Genetic polymorphism in long noncoding RNA (lncRNA) HOTAIR is linked with the risk and susceptibility of various cancers in humans. The mechanism involved in the development of CRC is not fully understood but single nucleotide polymorphisms (SNPs) can be used to predict its [...] Read more.
Genetic polymorphism in long noncoding RNA (lncRNA) HOTAIR is linked with the risk and susceptibility of various cancers in humans. The mechanism involved in the development of CRC is not fully understood but single nucleotide polymorphisms (SNPs) can be used to predict its risk and prognosis. In the present case-control study, we investigated the relationship between HOTAIR (rs12826786, rs920778, and rs1899663) polymorphisms and CRC risk in the Saudi population by genotyping using a TaqMan genotyping assay in 144 CRC cases and 144 age- and sex-matched controls. We found a significant (p < 0.05) association between SNP rs920778 G > A and CRC risk, and a protective role of SNPs rs12826786 (C > T) and rs1899663 (C > A) was noticed. The homozygous mutant “AA” genotype at rs920778 (G > A) showed a significant correlation with the female sex and colon tumor site. The homozygous TT in SNP rs12816786 (C > T) showed a significant protective association in the male and homozygous AA of SNP rs1899663 (C > A) with colon tumor site. These results indicate that HOTAIR can be a powerful biomarker for predicting the risk of colorectal cancer in the Saudi population. The association between HOTAIR gene polymorphisms and the risk of CRC in the Saudi population was reported for the first time here. Full article
(This article belongs to the Special Issue Genetics and Genomics of Colorectal Cancer and Related Diseases)
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Review

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11 pages, 713 KiB  
Review
From Omic Layers to Personalized Medicine in Colorectal Cancer: The Road Ahead
by Irati Romero-Garmendia and Koldo Garcia-Etxebarria
Genes 2023, 14(7), 1430; https://doi.org/10.3390/genes14071430 - 11 Jul 2023
Cited by 3 | Viewed by 2045
Abstract
Colorectal cancer is a major health concern since it is a highly diagnosed cancer and the second cause of death among cancers. Thus, the most suitable biomarkers for its diagnosis, prognosis, and treatment have been studied to improve and personalize the prevention and [...] Read more.
Colorectal cancer is a major health concern since it is a highly diagnosed cancer and the second cause of death among cancers. Thus, the most suitable biomarkers for its diagnosis, prognosis, and treatment have been studied to improve and personalize the prevention and clinical management of colorectal cancer. The emergence of omic techniques has provided a great opportunity to better study CRC and make personalized medicine feasible. In this review, we will try to summarize how the analysis of the omic layers can be useful for personalized medicine and the existing difficulties. We will discuss how single and multiple omic layer analyses have been used to improve the prediction of the risk of CRC and its outcomes and how to overcome the challenges in the use of omic layers in personalized medicine. Full article
(This article belongs to the Special Issue Genetics and Genomics of Colorectal Cancer and Related Diseases)
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