Article
Biochemical Research Methods
Lingling Li, Yulu Hu, Yunshan Xu, Sanyi Tang
Summary: Cumulative mutations in driver genes are the essential cause of cancer, including colorectal cancer. This study explores the mutation orders of the driver genes KRAS, APC, and TP53 in colorectal cancer patients and identifies the pathways that best fit the incidence rate of colorectal cancer at different ages. The findings provide guidelines for the treatment strategy of colorectal cancer.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Medicine, Research & Experimental
Jian Shi, Li Wang, Xiangzhe Yin, Lixia Wang, Lin Bo, Kailai Liu, Ke Feng, Shihua Lin, Yanjun Xu, Shangwei Ning, Hongying Zhao
Summary: Genomic studies of colorectal cancer have found that driver gene clonality can act as prognostic markers and potential therapeutic targets in the disease. This study systematically characterized the clonal architecture of 97 driver genes in colorectal cancer patients and found that a high proportion of clonal mutations were observed in these genes. Specific gene mutations were associated with clinicopathological factors and had a significant impact on patient outcomes. Subclonal ANK1 mutations were associated with poor prognosis possibly due to upregulation of genes involved in tumor immune evasion.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Article
Oncology
Julia Matas, Brendan Kohrn, Jeanne Fredrickson, Kelly Carter, Ming Yu, Ting Wang, Xianyong Gui, Thierry Soussi, Victor Moreno, William M. Grady, Miguel A. Peinado, Rosa Ana Risques
Summary: This study reveals that mutations in common colorectal cancer genes can be detected in the normal colon, highlighting the prevalent somatic evolution in patients with colorectal cancer. Somatic evolution contributes to clonal expansions in the normal colon, especially in individuals with early-onset colorectal cancer.
Article
Oncology
B. Hernando, M. Dietzen, G. Parra, M. Gil-Barrachina, G. Pitarch, L. Mahiques, F. Valcuende-Cavero, N. McGranahan, C. Martinez-Cadenas
Summary: This study reveals that UV-related somatic mutations accumulate exponentially with age in normal skin, matching skin cancer incidence. The increase in mutation burden is influenced by an individual's skin type, and somatic mutations tend to accumulate and clonally expand in specific cancer genes as individuals age.
ANNALS OF ONCOLOGY
(2021)
Article
Biochemical Research Methods
Xianghua Peng, Fang Liu, Ping Liu, Xing Li, Xinguo Lu
Summary: This study introduced a metabolic pathway based driver gene identification method (pathDriver) to distinguish different cancer types/subtypes. By using a protein-protein interaction network combined with metabolic pathways to construct a pathway network, the collaborative impact factor of genes in the pathway network was evaluated using Interaction Frequency (IF) and Inverse Pathway Frequency (IPF) to identify cancer-specific driver genes. The application of this method to 16 types of TCGA cancers for pan-cancer analysis successfully identified biologically significant known cancer genes and potential new candidate genes.
CURRENT BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Zexian Zeng, Chengsheng Mao, Andy Vo, Xiaoyu Li, Janna Ore Nugent, Seema A. Khan, Susan E. Clare, Yuan Luo
Summary: DeepCues is a deep learning model that utilizes convolutional neural networks to derive features unbiasedly from raw cancer DNA sequencing data for disease classification and relevant gene discovery. By amalgamating germline variants and somatic mutations, including insertions and deletions, DeepCues showed significant improvement in cancer type prediction and successfully identified new cancer relevant genes.
BMC BIOINFORMATICS
(2021)
Article
Oncology
Jongmin Lee, Sangtae Choi, Donghae Jung, YunJae Jung, Jung Ho Kim, Sungwon Jung, Won-Suk Lee
Summary: This study investigated the mutational characteristics of colorectal cancer in Korean patients using targeted next generation sequencing, revealing differences in mutation frequencies of key genes based on tumor location and stage. The study highlights the potential of next generation sequencing to provide valuable molecular information for colorectal cancer patients, aiding in better understanding of the disease.
Article
Medicine, Research & Experimental
Xiang-Yu Wang, Wen-Wei Zhu, Zheng Wang, Jian-Bo Huang, Sheng-Hao Wang, Fu-Mao Bai, Tian-En Li, Ying Zhu, Jing Zhao, Xin Yang, Lu Lu, Ju-Bo Zhang, Hu-Liang Jia, Qiong-Zhu Dong, Jin-Hong Chen, Jesper B. Andersen, Dan Ye, Lun-Xiu Qin
Summary: By analyzing genomic data, we established a clinically applicable genomic clustering system for intrahepatic cholangiocarcinoma (ICC), which can be used for prognostic prediction, molecular classification, and therapeutic optimization.
Article
Biochemistry & Molecular Biology
Feiyu Shi, Gaixia Liu, Yufeng Lin, Cosmos Liutao Guo, Jing Han, Eagle S. H. Chu, Chengxin Shi, Yaguang Li, Haowei Zhang, Chenhao Hu, Ruihan Liu, Shuixiang He, Gang Guo, Yinnan Chen, Xiang Zhang, Olabisi Oluwabukola Coker, Sunny Hei Wong, Jun Yu, Junjun She
Summary: Appendectomy is associated with an increased risk of colorectal cancer (CRC) due to gut microbial dysbiosis. A longitudinal study (cohort 1, n = 129,155) showed a 73.0% increase in CRC risk among appendectomy cases during a 20-year follow-up period. Fecal samples from another cohort (n = 314) revealed dysbiosis in the gut microbiome of appendectomy subjects, with enrichment of CRC-promoting bacteria and depletion of beneficial commensals. Microbial network analysis indicated stronger correlations and enriched oncogenic pathways among bacteria in appendectomy subjects compared to controls. Appendectomy was also found to promote colorectal tumorigenesis in mice through microbial dysbiosis and impaired intestinal barrier function. This study highlights the importance of the gut microbiome in CRC development following appendectomy.
Article
Biochemistry & Molecular Biology
Jeffrey Yung-chuan Chao, Hsin-Chuan Chang, Jeng-Kai Jiang, Chih-Yung Yang, Fang-Hsin Chen, Yo-Liang Lai, Wen -Jen Lin, Chia-Yang Li, Shu-Chi Wang, Muh-Hwa Yang, Yu-Feng Lin, Wei-Chung Cheng
Summary: This study identified CRC driver genes and prognostic genes through bioinformatics analysis of sequencing profiles and verified their presence in Taiwanese CRC patients, showing potential for early cancer detection and prognosis assessment.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Oncology
J. M. van Berge Henegouwen, M. Jebbink, L. R. Hoes, H. van der Wijngaart, L. J. Zeverijn, D. L. van der Velden, P. Roepman, W. W. J. de Leng, A. M. L. Jansen, E. van Werkhoven, V van der Noort, A. J. van der Wekken, A. J. de Langen, E. E. Voest, H. M. W. Verheul, E. F. Smit, H. Gelderblom
Summary: This study found that trastuzumab/pertuzumab treatment showed marginal activity in a subset of heavily pre-treated patients with HER2-mutant non-small cell lung cancer (NSCLC).
EUROPEAN JOURNAL OF CANCER
(2022)
Article
Biology
Hafiza Faiza, Majida Khan, Muhammad Rafiq, Anoshiya Ali Khan, Nadir Ali Rind, Syed Habib Ahmed Naqvi
Summary: The study identified various missense mutations in exon 2 of the BMP15 gene in infertile Pakistani females, potentially affecting protein function due to changes in amino acid codons. These mutations may lead to early blockage of folliculogenesis, requiring further research to understand their implications.
SAUDI JOURNAL OF BIOLOGICAL SCIENCES
(2021)
Review
Medicine, Research & Experimental
John M. Macharia, Ruth W. Mwangi, Nora Rozmann, Kaposztas Zsolt, Timea Varjas, Paschal O. Uchechukwu, Isabel N. Wagara, Bence L. Raposa
Summary: The development and identification of molecular compounds that can kill or inhibit transformed cells promoting carcinogenesis without toxic effects on normal cells are extremely important. This study conducted a systematic review and evaluated pharmacotherapeutic biomolecules active against colon cancer carcinogenesis. The research found that natural antioxidants in certain plants have inhibitory effects on the occurrence and progression of colon cancer.
BIOMEDICINE & PHARMACOTHERAPY
(2022)
Article
Oncology
R. L. Eefsen, K. S. Simonsen, P. Grundtvig, L. Klarskov, I. M. Chen, D. Hogdall, B. Jensen, T. Lorentzen, T. S. Poulsen, S. Theile, D. Nielsen, E. Hogdall
Summary: In this retrospective analysis, 90% of patients with treatment-refractory mCRC had cancer driver mutations identified through genomic sequencing, but only 2.5% of patients received targeted therapy that matched their mutations. The study highlights the challenge of limited targeted treatment options for mCRC patients with cancer driver mutations.
Review
Biochemistry & Molecular Biology
Refaat A. Eid, Muhammad Alaa Edeen, Eslam M. Shedid, Al Shaimaa S. Kamal, Mona M. Warda, Farag Mamdouh, Sohila A. Khedr, Mohamed A. Soltan, Hee Won Jeon, Mohamed Samir A. Zaki, Bonglee Kim
Summary: The concept of cancer stem cells (CSCs) has replaced the previous model of tumor composition, indicating that CSCs play a key role in cancer initiation, progression, and diversity. CSCs possess self-renewal and differentiation abilities, resistance to therapy, and tumor initiation potential. Various factors, including transcription factors and signaling pathways, regulate the functional capabilities of CSCs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)