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Genes
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Genetic and Genomics of Colorectal Cancer
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Genetic and Genomics of 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 (15 August 2023) | Viewed by 12668

Special Issue Editor

Dr. Dandan Zhang

E-Mail Website
Guest Editor
Department of Pathology, School of Medicine, Zhejiang University, Hangzhou 310058, China
Interests: genetics of CRC; multi-omics analysis; QTL mappings; functional genetics; single-cell explorations

Special Issue Information

Dear Colleagues,

It is well known that genetic factors contribute to the pathogenesis of colorectal cancer (CRC). Currently, genome-wide association studies (GWASs) have identified more than 160 genetic loci associated with the risk of CRC. However, the effects of these variants, particularly their mechanisms, remain unclear. More and more efforts are being made with a focus on deciphering the biological mechanisms behind these potential causal variants by using multi-omics data and functional experiments. CRC is a very heterogeneous disease; single-cell measurements offer a finer-grained picture of tumor cells and help to uncover the heterogeneity. The aim of this Special Issue is to collect research findings on novel risk loci of association studies, functional investigation of loci from GWASs, integrative analysis of multi-omics data, and single-cell explorations of CRC.

Dr. Dandan Zhang
Guest Editor

Manuscript Submission Information

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Keywords

  • post-GWAS
  • functional genomics
  • molecular genetics
  • driver mutations
  • epigenetics
  • multi-omics analysis
  • single cell

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Published Papers (4 papers)

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Research

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15 pages, 8377 KiB  
Article
Unlocking the Potential of the CA2, CA7, and ITM2C Gene Signatures for the Early Detection of Colorectal Cancer: A Comprehensive Analysis of RNA-Seq Data by Utilizing Machine Learning Algorithms
by Neha Shree Maurya, Sandeep Kushwaha, Ramesh Raju Vetukuri and Ashutosh Mani
Genes 2023, 14(10), 1836; https://doi.org/10.3390/genes14101836 - 22 Sep 2023
Cited by 5 | Viewed by 2420
Abstract
Colorectal cancer affects the colon or rectum and is a common global health issue, with 1.1 million new cases occurring yearly. The study aimed to identify gene signatures for the early detection of CRC using machine learning (ML) algorithms utilizing gene expression data. [...] Read more.
Colorectal cancer affects the colon or rectum and is a common global health issue, with 1.1 million new cases occurring yearly. The study aimed to identify gene signatures for the early detection of CRC using machine learning (ML) algorithms utilizing gene expression data. The TCGA-CRC and GSE50760 datasets were pre-processed and subjected to feature selection using the LASSO method in combination with five ML algorithms: Adaboost, Random Forest (RF), Logistic Regression (LR), Gaussian Naive Bayes (GNB), and Support Vector Machine (SVM). The important features were further analyzed for gene expression, correlation, and survival analyses. Validation of the external dataset GSE142279 was also performed. The RF model had the best classification accuracy for both datasets. A feature selection process resulted in the identification of 12 candidate genes, which were subsequently reduced to 3 (CA2, CA7, and ITM2C) through gene expression and correlation analyses. These three genes achieved 100% accuracy in an external dataset. The AUC values for these genes were 99.24%, 100%, and 99.5%, respectively. The survival analysis showed a significant logrank p-value of 0.044 for the final gene signatures. The analysis of tumor immunocyte infiltration showed a weak correlation with the expression of the gene signatures. CA2, CA7, and ITM2C can serve as gene signatures for the early detection of CRC and may provide valuable information for prognostic and therapeutic decision making. Further research is needed to fully understand the potential of these genes in the context of CRC. Full article
(This article belongs to the Special Issue Genetic and Genomics of Colorectal Cancer)
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16 pages, 2790 KiB  
Article
TCF7L1 Regulates LGR5 Expression in Colorectal Cancer Cells
by Carli M. King, Olivia M. Marx, Wei Ding, Walter A. Koltun and Gregory S. Yochum
Genes 2023, 14(2), 481; https://doi.org/10.3390/genes14020481 - 14 Feb 2023
Cited by 5 | Viewed by 2821
Abstract
Mutations in components of the Wnt/β-catenin signaling pathway drive colorectal cancer (CRC), in part, by deregulating expression of genes controlled by the T-cell factor (TCF) family of transcription factors. TCFs contain a conserved DNA binding domain that mediates association with TCF binding elements [...] Read more.
Mutations in components of the Wnt/β-catenin signaling pathway drive colorectal cancer (CRC), in part, by deregulating expression of genes controlled by the T-cell factor (TCF) family of transcription factors. TCFs contain a conserved DNA binding domain that mediates association with TCF binding elements (TBEs) within Wnt-responsive DNA elements (WREs). Intestinal stem cell marker, leucine-rich-repeat containing G-protein-coupled receptor 5 (LGR5), is a Wnt target gene that has been implicated in CRC stem cell plasticity. However, the WREs at the LGR5 gene locus and how TCF factors directly regulate LGR5 gene expression in CRC have not been fully defined. Here, we report that TCF family member, TCF7L1, plays a significant role in regulating LGR5 expression in CRC cells. We demonstrate that TCF7L1 binds to a novel promoter-proximal WRE through association with a consensus TBE at the LGR5 locus to repress LGR5 expression. Using CRISPR activation and interference (CRISPRa/i) technologies to direct epigenetic modulation, we demonstrate that this WRE is a critical regulator of LGR5 expression and spheroid formation capacity of CRC cells. Furthermore, we found that restoring LGR5 expression rescues the TCF7L1-mediated reduction in spheroid formation efficiency. These results demonstrate a role for TCF7L1 in repressing LGR5 gene expression to govern the spheroid formation potential of CRC cells. Full article
(This article belongs to the Special Issue Genetic and Genomics of Colorectal Cancer)
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8 pages, 626 KiB  
Case Report
POLE-Mutant Colon Cancer Treated with PD-1 Blockade Showing Clearance of Circulating Tumor DNA and Prolonged Disease-Free Interval
by Mihir Bikhchandani, Farin Amersi, Andrew Hendifar, Alexandra Gangi, Arsen Osipov, Karen Zaghiyan, Katelyn Atkins, May Cho, Francesca Aguirre, Dennis Hazelett, Rocio Alvarez, Lisa Zhou, Megan Hitchins and Jun Gong
Genes 2023, 14(5), 1054; https://doi.org/10.3390/genes14051054 - 8 May 2023
Cited by 6 | Viewed by 4261
Abstract
Colon cancer with high microsatellite instability is characterized by a high tumor mutational burden and responds well to immunotherapy. Mutations in polymerase ɛ, a DNA polymerase involved in DNA replication and repair, are also associated with an ultra-mutated phenotype. We describe a case [...] Read more.
Colon cancer with high microsatellite instability is characterized by a high tumor mutational burden and responds well to immunotherapy. Mutations in polymerase ɛ, a DNA polymerase involved in DNA replication and repair, are also associated with an ultra-mutated phenotype. We describe a case where a patient with POLE-mutated and hypermutated recurrent colon cancer was treated with pembrolizumab. Treatment with immunotherapy in this patient also led to the clearance of circulating tumor DNA (ctDNA). ctDNA is beginning to emerge as a marker for minimal residual disease in many solid malignancies, including colon cancer. Its clearance with treatment suggests that the selection of pembrolizumab on the basis of identifying a POLE mutation on next-generation sequencing may increase disease-free survival in this patient. Full article
(This article belongs to the Special Issue Genetic and Genomics of Colorectal Cancer)
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10 pages, 1387 KiB  
Case Report
Biallelic PMS2 Mutations in a Family with Uncommon Clinical and Molecular Features
by Monica Pedroni, Maurizio Ponz de Leon, Luca Reggiani Bonetti, Giuseppina Rossi, Alessandra Viel, Emanuele Damiano Luca Urso and Luca Roncucci
Genes 2022, 13(11), 1953; https://doi.org/10.3390/genes13111953 - 26 Oct 2022
Cited by 1 | Viewed by 2168
Abstract
We describe a patient with constitutional mismatch repair-deficiency (CMMR-D) in whom the syndrome started at age 10 with the development of multiple adenomas in the large bowel. In the successive 25 years, four malignancies developed in different organs (rectum, ileum, duodenum, and lymphoid [...] Read more.
We describe a patient with constitutional mismatch repair-deficiency (CMMR-D) in whom the syndrome started at age 10 with the development of multiple adenomas in the large bowel. In the successive 25 years, four malignancies developed in different organs (rectum, ileum, duodenum, and lymphoid tissue). The patient had biallelic constitutional pathogenic variants in the PMS2 gene. We speculate that besides the PMS2 genotype, alterations of other genes might have contributed to the development of the complex phenotype. In the nuclear family, both parents carried different PMS2 germline mutations. They appeared in good clinical condition and did not develop polyps or cancer. The index case had a brother who died at age three of lymphoblastic leukemia, and a sister who was affected by sarcoidosis. Tumor tissue showed diffuse DNA microsatellite instability. A complete absence of immunoreactivity was observed for the PMS2 protein both in the tumors and normal tissues. Next-generation sequencing and multiple ligation-dependent probe amplification analyses revealed biallelic PMS2 germline pathogenic variants in the proband (genotype c.[137G>T];[(2174+1_2175-1)_(*160_?)del]), and one of the two variants was present in both parents—c.137G>T in the father and c.(2174+1-2175-1)_(*160_?)del in the mother—as well as c.137G>T in the sister. Moreover, Class 3 variants of MSH2 (c.1787A>G), APC (c.1589T>C), and CHEK2 (c.331G>T) genes were also detected in the proband. In conclusion, the recognition of CMMR-D may sometimes be difficult; however, the possible role of constitutional alterations of other genes in the development of the full-blown phenotype should be investigated in more detail. Full article
(This article belongs to the Special Issue Genetic and Genomics of Colorectal Cancer)
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