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Pathira Kankanamge L, Mora A, Ondrechen MJ, Beuning PJ. Biochemical Activity of 17 Cancer-Associated Variants of DNA Polymerase Kappa Predicted by Electrostatic Properties. Chem Res Toxicol 2023; 36:1789-1803. [PMID: 37883788 PMCID: PMC10664756 DOI: 10.1021/acs.chemrestox.3c00233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/28/2023]
Abstract
DNA damage and repair have been widely studied in relation to cancer and therapeutics. Y-family DNA polymerases can bypass DNA lesions, which may result from external or internal DNA damaging agents, including some chemotherapy agents. Overexpression of the Y-family polymerase human pol kappa can result in tumorigenesis and drug resistance in cancer. This report describes the use of computational tools to predict the effects of single nucleotide polymorphism variants on pol kappa activity. Partial Order Optimum Likelihood (POOL), a machine learning method that uses input features from Theoretical Microscopic Titration Curve Shapes (THEMATICS), was used to identify amino acid residues most likely involved in catalytic activity. The μ4 value, a metric obtained from POOL and THEMATICS that serves as a measure of the degree of coupling between one ionizable amino acid and its neighbors, was then used to identify which protein mutations are likely to impact the biochemical activity. Bioinformatic tools SIFT, PolyPhen-2, and FATHMM predicted most of these variants to be deleterious to function. Along with computational and bioinformatic predictions, we characterized the catalytic activity and stability of 17 cancer-associated DNA pol kappa variants. We identified pol kappa variants R48I, H105Y, G147D, G154E, V177L, R298C, E362V, and R470C as having lower activity relative to wild-type pol kappa; the pol kappa variants T102A, H142Y, R175Q, E210K, Y221C, N330D, N338S, K353T, and L383F were identified as being similar in catalytic efficiency to WT pol kappa. We observed that POOL predictions can be used to predict which variants have decreased activity. Predictions from bioinformatic tools like SIFT, PolyPhen-2, and FATHMM are based on sequence comparisons and therefore are complementary to POOL but are less capable of predicting biochemical activity. These bioinformatic and computational tools can be used to identify SNP variants with deleterious effects and altered biochemical activity from a large data set.
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Affiliation(s)
- Lakindu
S. Pathira Kankanamge
- Department
of Chemistry and Chemical Biology and Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Alexandra Mora
- Department
of Chemistry and Chemical Biology and Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Mary Jo Ondrechen
- Department
of Chemistry and Chemical Biology and Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Penny J. Beuning
- Department
of Chemistry and Chemical Biology and Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
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Todorova VK, Byrum SD, Mackintosh SG, Jamshidi-Parsian A, Gies AJ, Washam CL, Jenkins SV, Spiva T, Bowman E, Reyna NS, Griffin RJ, Makhoul I. Exosomal MicroRNA and Protein Profiles of Hepatitis B Virus-Related Hepatocellular Carcinoma Cells. Int J Mol Sci 2023; 24:13098. [PMID: 37685904 PMCID: PMC10487651 DOI: 10.3390/ijms241713098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/14/2023] [Accepted: 08/18/2023] [Indexed: 09/10/2023] Open
Abstract
Infection with hepatitis B virus (HBV) is a main risk factor for hepatocellular carcinoma (HCC). Extracellular vesicles, such as exosomes, play an important role in tumor development and metastasis, including regulation of HBV-related HCC. In this study, we have characterized exosome microRNA and proteins released in vitro from hepatitis B virus (HBV)-related HCC cell lines SNU-423 and SNU-182 and immortalized normal hepatocyte cell lines (THLE2 and THLE3) using microRNA sequencing and mass spectrometry. Bioinformatics, including functional enrichment and network analysis, combined with survival analysis using data related to HCC in The Cancer Genome Atlas (TCGA) database, were applied to examine the prognostic significance of the results. More than 40 microRNAs and 200 proteins were significantly dysregulated (p < 0.05) in the exosomes released from HCC cells in comparison with the normal liver cells. The functional analysis of the differentially expressed exosomal miRNAs (i.e., mir-483, mir-133a, mir-34a, mir-155, mir-183, mir-182), their predicted targets, and exosomal differentially expressed proteins (i.e., POSTN, STAM, EXOC8, SNX9, COL1A2, IDH1, FN1) showed correlation with pathways associated with HBV, virus activity and invasion, exosome formation and adhesion, and exogenous protein binding. The results from this study may help in our understanding of the role of HBV infection in the development of HCC and in the development of new targets for treatment or non-invasive predictive biomarkers of HCC.
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Affiliation(s)
- Valentina K. Todorova
- Department of Internal Medicine/Division of Hematology/Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - Stephanie D. Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (S.D.B.); (S.G.M.); (A.J.G.); (C.L.W.)
| | - Samuel G. Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (S.D.B.); (S.G.M.); (A.J.G.); (C.L.W.)
| | - Azemat Jamshidi-Parsian
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (A.J.-P.); (S.V.J.); (R.J.G.)
| | - Allen J. Gies
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (S.D.B.); (S.G.M.); (A.J.G.); (C.L.W.)
| | - Charity L. Washam
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (S.D.B.); (S.G.M.); (A.J.G.); (C.L.W.)
| | - Samir V. Jenkins
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (A.J.-P.); (S.V.J.); (R.J.G.)
| | - Timothy Spiva
- Biology Department, Ouachita Baptist University, Arkadelphia, AR 71998, USA; (T.S.); (E.B.); (N.S.R.)
| | - Emily Bowman
- Biology Department, Ouachita Baptist University, Arkadelphia, AR 71998, USA; (T.S.); (E.B.); (N.S.R.)
| | - Nathan S. Reyna
- Biology Department, Ouachita Baptist University, Arkadelphia, AR 71998, USA; (T.S.); (E.B.); (N.S.R.)
| | - Robert J. Griffin
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (A.J.-P.); (S.V.J.); (R.J.G.)
| | - Issam Makhoul
- Department of Internal Medicine/Division of Hematology/Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
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Wu X, Li Z, Wang ZQ, Xu X. The neurological and non-neurological roles of the primary microcephaly-associated protein ASPM. Front Neurosci 2023; 17:1242448. [PMID: 37599996 PMCID: PMC10436222 DOI: 10.3389/fnins.2023.1242448] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 07/24/2023] [Indexed: 08/22/2023] Open
Abstract
Primary microcephaly (MCPH), is a neurological disorder characterized by small brain size that results in numerous developmental problems, including intellectual disability, motor and speech delays, and seizures. Hitherto, over 30 MCPH causing genes (MCPHs) have been identified. Among these MCPHs, MCPH5, which encodes abnormal spindle-like microcephaly-associated protein (ASPM), is the most frequently mutated gene. ASPM regulates mitotic events, cell proliferation, replication stress response, DNA repair, and tumorigenesis. Moreover, using a data mining approach, we have confirmed that high levels of expression of ASPM correlate with poor prognosis in several types of tumors. Here, we summarize the neurological and non-neurological functions of ASPM and provide insight into its implications for the diagnosis and treatment of MCPH and cancer.
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Affiliation(s)
- Xingxuan Wu
- Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, China
- Shenzhen University-Friedrich Schiller Universität Jena Joint PhD Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
- Laboratory of Genome Stability, Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Zheng Li
- Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, China
| | - Zhao-Qi Wang
- Shenzhen University-Friedrich Schiller Universität Jena Joint PhD Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
- Laboratory of Genome Stability, Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, China
- Shenzhen University-Friedrich Schiller Universität Jena Joint PhD Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
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Ginsenoside Rh2 suppresses colon cancer growth by targeting the miR-150-3p/SRCIN1/Wnt axis. Acta Biochim Biophys Sin (Shanghai) 2023; 55:633-648. [PMID: 36916297 DOI: 10.3724/abbs.2023032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023] Open
Abstract
Ginsenoside Rh2, which is extracted from ginseng, exerts antitumor activity. Recent studies suggest that Rh2 may suppress the growth of colon cancer (CC) in vitro. However, the underlying mechanism remains unclear. In this study, we identified the relative levels of miR-150-3p in CC tissues and cells by a comprehensive strategy of data mining, computational biology, and real-time reverse transcription PCR (qRT-PCR) experiments. The regulatory effects of miR-150-3p/SRCIN1 on the proliferative and invasive abilities of CC cells are evaluated by CCK-8, EdU, wound healing, and transwell assays. Cell cycle- and apoptosis-related protein levels are assessed by western blot analysis. An in vivo tumor formation assay was conducted to explore the effects of miR-150-3p on tumor growth. Furthermore, bioinformatics and dual luciferase reporter assays are applied to determine the functional binding of miRNA to mRNA of the target gene. Finally, the relationship between Rh2 and miR-150-3p was further verified in SW620 and HCT-116 cells. miR-150-3p is downregulated in CC tissues and cell lines. Functional assays indicate that the upregulation of miR-150-3p inhibits tumor growth both in vivo and in vitro. In addition, SRCIN1 is upregulated in CC and predicts a poor prognosis, and it is the direct target for miR-150-3p. Moreover, the miR-150-3p mimic decreases Topflash/Fopflash-dependent luciferase activity, resulting in the inhibition of Wnt pathway activity. Rh2 can suppress the growth of CC by increasing miR-150-3p expression. Rh2 alleviates the accelerating effect on Wnt pathway activity, cell proliferation/migration, and colony formation caused by miR-150-3p inhibition. Rh2 inhibits the miR-150-3p/SRCIN1/Wnt axis to suppress colon cancer growth.
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Holowatyj AN, Wen W, Gibbs T, Seagle HM, Keller SR, Edwards DRV, Washington MK, Eng C, Perea J, Zheng W, Guo X. Racial/Ethnic and Sex Differences in Somatic Cancer Gene Mutations among Patients with Early-Onset Colorectal Cancer. Cancer Discov 2023; 13:570-579. [PMID: 36520636 PMCID: PMC10436779 DOI: 10.1158/2159-8290.cd-22-0764] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/07/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Molecular features underlying colorectal cancer disparities remain uncharacterized. Here, we investigated somatic mutation patterns by race/ethnicity and sex among 5,856 non-Hispanic white (NHW), 535 non-Hispanic Black (NHB), and 512 Asian/Pacific Islander (API) patients with colorectal cancer (2,016 early-onset colorectal cancer patients: sequencing age <50 years). NHB patients with early-onset nonhypermutated colorectal cancer, but not API patients, had higher adjusted tumor mutation rates than NHW patients. There were significant differences for LRP1B, FLT4, FBXW7, RNF43, ATRX, APC, and PIK3CA mutation frequencies in early-onset nonhypermutated colorectal cancers between racial/ethnic groups. Heterogeneities by race/ethnicity were observed for the effect of APC, FLT4, and FAT1 between early-onset and late-onset nonhypermutated colorectal cancer. By sex, heterogeneity was observed for the effect of EP300, BRAF, WRN, KRAS, AXIN2, and SMAD2. Males and females with nonhypermutated colorectal cancer had different trends in EP300 mutations by age group. These findings define genomic patterns of early-onset nonhypermutated colorectal cancer by race/ethnicity and sex, which yields novel biological clues into early-onset colorectal cancer disparities. SIGNIFICANCE NHBs, but not APIs, with early-onset nonhypermutated colorectal cancer had higher adjusted tumor mutation rates versus NHWs. Differences for FLT4, FBXW7, RNF43, LRP1B, APC, PIK3CA, and ATRX mutation rates between racial/ethnic groups and EP300, KRAS, AXIN2, WRN, BRAF, and LRP1B mutation rates by sex were observed in tumors of young patients. See related commentary by Shen et al., p. 530 . This article is highlighted in the In This Issue feature, p. 517.
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Affiliation(s)
- Andreana N. Holowatyj
- Department of Medicine, Microbiology and Immunology
- Vanderbilt-Ingram Cancer Center, Nashville, TN
- Vanderbilt University School of Medicine, Nashville, TN
| | - Wanqing Wen
- Department of Medicine, Microbiology and Immunology
| | | | - Hannah M. Seagle
- Department of Medicine, Microbiology and Immunology
- Vanderbilt University School of Medicine, Nashville, TN
| | - Samantha R. Keller
- Department of Medicine, Microbiology and Immunology
- Vanderbilt University School of Medicine, Nashville, TN
| | - Digna R. Velez Edwards
- Department of Obstetrics and Gynecology; Vanderbilt University Medical Center, Nashville, TN
| | - Mary K. Washington
- Department of Pathology, Microbiology and Immunology
- Vanderbilt-Ingram Cancer Center, Nashville, TN
| | - Cathy Eng
- Department of Medicine, Microbiology and Immunology
- Vanderbilt-Ingram Cancer Center, Nashville, TN
| | - Jose Perea
- Molecular Medicine Unit, Department of Medicine, Biomedical Research Institute of Salamanca (IBSAL), Salamanca, Spain
- Department of Surgery, “Vithas Arturo Soria” University Hospital and School of Medicine, European University of Madrid, Madrid, Spain
| | - Wei Zheng
- Department of Medicine, Microbiology and Immunology
- Vanderbilt-Ingram Cancer Center, Nashville, TN
| | - Xingyi Guo
- Department of Medicine, Microbiology and Immunology
- Vanderbilt-Ingram Cancer Center, Nashville, TN
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6
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Shi S, Wang Q, Shang Y, Bu C, Lu M, Jiang M, Zhang H, Yu S, Zeng J, Zhang Z, Du Z, Xiao J. TSomVar: a tumor-only somatic and germline variant identification method with random forest. Brief Bioinform 2022; 23:6695269. [DOI: 10.1093/bib/bbac381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Somatic variants act as critical players during cancer occurrence and development. Thus, an accurate and robust method to identify them is the foundation of cutting-edge cancer genome research. However, due to low accessibility and high individual-/sample-specificity of the somatic variants in tumor samples, the detection is, to date, still crammed with challenges, particularly when lacking paired normal samples as control. To solve this burning issue, we developed a tumor-only somatic and germline variant identification method (TSomVar) using the random forest algorithm established on sample-specific variant datasets derived from genotype imputation, reads-mapping level annotation and functional annotation. We trained TSomVar by using genomic variant datasets of three major cancer types: colorectal cancer, hepatocellular carcinoma and skin cutaneous melanoma. Compared with existing tumor-only somatic variant identification tools, TSomVar shows excellent performances in somatic variant detection with higher accuracy and better capability of recalling for test datasets from colorectal cancer and skin cutaneous melanoma. In addition, TSomVar is equipped with the competence of accurately identifying germline variants in tumor samples. Taken together, TSomVar will undoubtedly facilitate and revolutionize somatic variant explorations in cancer research.
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Affiliation(s)
- Shuo Shi
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100049, China
- Burning Rock Biotech Ltd , Shanghai 201114, China
| | - Qi Wang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100049, China
- Qujiang Culture Finance Holding (Group) Co., Ltd , Xian 710061, China
| | - Yunfei Shang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Congfan Bu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
| | - Mingming Lu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Meiye Jiang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Hao Zhang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Shuhuan Yu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Jingyao Zeng
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
| | - Zaichao Zhang
- Department of Biology, The University of Western Ontario , London, Ontario N6A 5B7, Canada
| | - Zhenglin Du
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
| | - Jingfa Xiao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100049, China
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7
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dos Santos W, dos Reis MB, Porto J, de Carvalho AC, Matsushita M, Oliveira G, Syrjänen K, Reis RM, Guimarães DP. Somatic targeted mutation profiling of colorectal cancer precursor lesions. BMC Med Genomics 2022; 15:143. [PMID: 35761395 PMCID: PMC9238170 DOI: 10.1186/s12920-022-01294-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 06/16/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Most colorectal cancers (CRC) arise from precursor lesions. This study aimed to characterize the mutation profile of colorectal cancer precursor lesions in a Brazilian population.
Methods
In total, 90 formalin-fixed paraffin-embedded colorectal precursor lesions, including 67 adenomas, 7 sessile serrated lesions, and 16 hyperplastic polyps, were analyzed by next-generation sequencing using a panel of 50 oncogenes and tumor suppressor genes. The genetic ancestry of the patients was estimated.
Results
Somatic driver mutations were identified in 66.7% of cases, including alterations in APC (32.2%), TP53 (20.0%), KRAS (18.9%), BRAF (13.3%) and EGFR (7.8%). Adenomas displayed a higher number of mutations, mainly in APC, compared to serrated polyps (73.1% vs. 47.8%, p = 0.026). Advanced adenomas had a significantly higher frequency of mutation in KRAS and a high overall mutation rate than early adenomas (92.9% vs. 59%, p = 0.006). A high degree of ancestry admixture was observed in the population studied, with a predominance of European components (mean of 73%) followed by African (mean of 11.3%). No association between genetic ancestry and type of lesions was found. The mutation profile of Brazilian colorectal precursor lesions exhibits alteration in APC, KRAS, TP53, and BRAF at different frequencies according to lesion type.
Conclusions
These results bestow the knowledge of CRC's biologic history and support the potential of these biomarkers for precursor lesions detection in CRC screening of the Brazilian population.
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Identification of a Genomic Instability-Related Long Noncoding RNA Prognostic Model in Colorectal Cancer Based on Bioinformatic Analysis. DISEASE MARKERS 2022; 2022:4556585. [PMID: 35711569 PMCID: PMC9197617 DOI: 10.1155/2022/4556585] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/17/2022] [Indexed: 11/17/2022]
Abstract
Background. In recent years, a growing body of research has revealed that long noncoding RNAs (lncRNAs) participate in regulating genomic instability. Materials and Methods. We obtained RNA expression profiles, somatic mutation profiles, clinical information, and pathological features of colorectal cancer (CRC) from The Cancer Genome Atlas project. We divided the cohort into two groups based on mutation frequency and identified genomic instability-related lncRNAs (GI-lncRNAs) using R software. We further analyzed the function of identified GI-lncRNAs and established a prognostic model through Cox regression. Using the established prognostic model, we divided the cohort into the high- and low-risk groups and further verified the prognostic differences between the two groups as well as the predictive power of prognosis-related lncRNAs in the genomic instability of CRC. Results. We identified a total of 143 GI-lncRNAs that were differentially expressed between the higher mutation frequency group and the lower mutation frequency group. According to Kyoto Encyclopedia of Genes and Genomes pathway and Gene Ontology analyses, a series of cancer-associated terms were enriched. We further constructed a prognostic model that included five GI-lncRNAs (lncRNA PTPRD-AS1, lncRNA AC009237.14, lncRNA LINC00543, lncRNA AP003555.1, and lncRNA AL109615.3). We confirmed that the expression of the five GI-lncRNAs was associated with prognosis and the mutation of critical genes in the CRC patient cohort. Conclusions. The present research further confirmed the vital function of GI-lncRNAs in the genomic instability of CRC. The five GI-lncRNAs identified in our study are potential biomarkers and need to be studied in more depth.
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Tumor Molecular Profiling in Hispanics: Moving Towards Precision Oncology and Health Equity. J Racial Ethn Health Disparities 2022; 10:1423-1431. [PMID: 35648382 PMCID: PMC10163076 DOI: 10.1007/s40615-022-01328-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Tumor molecular profiling techniques, such as next-generation sequencing (NGS) to identify somatic genetic alterations, allow physicians to have a better understanding of the affected carcinogenic pathways and guide targeted therapy. The objective of our study was to characterize common somatic alterations and carcinogenic pathways among Puerto Rican Hispanics with solid tumors. METHODS We conducted a single-institution, retrospective study to characterize molecular tumor profiles using a 592-gene NGS platform. Actionable mutations with current or developing therapies targeting affected genes/pathways were highlighted. RESULTS Tumors from 50 Hispanic patients were evaluated using CARIS Life Science© NGS testing. The median age of our study population was 55 (range 21-84); 54% (n = 27) were males. The primary tumor sites were colorectal (n = 24), gastric (n = 5), breast (n = 4), and lung (n = 3). The most common genetic mutations identified were in TP53 (44%), APC (38%), and KRAS (32%); followed by alterations in EGFR (4%), HER2 (6%), and homologous recombinant deficiency genes (BRCA2, 6%). Genetic alterations were found in multiple signaling pathways particularly in the cell cycle control pathway, MAPK and Wnt/β-Catenin signaling pathways. Targetable biomarkers were identified in 27/50 (54.0%) of tumors. DISCUSSION Molecular profiling techniques, such as next-generation sequencing, have substantially expanded access to alterations in the cancer genome. Our findings demonstrated important actionable mutations in most of the tumors evaluated and support the integration of somatic mutation profiling in the evaluation of Hispanic cancer patients with advanced cancer to help guide therapeutic options.
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Peng L, Zhao M, Liu T, Chen J, Gao P, Chen L, Xing P, Wang Z, Di J, Xu Q, Qu H, Jiang B, Su X. A stop-gain mutation in GXYLT1 promotes metastasis of colorectal cancer via the MAPK pathway. Cell Death Dis 2022; 13:395. [PMID: 35459861 PMCID: PMC9033806 DOI: 10.1038/s41419-022-04844-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 12/17/2022]
Abstract
Genomic instability plays a key role in the initiation and progression of colorectal cancer (CRC). Although cancer driver genes in CRC have been well characterized, identifying novel genes associated with carcinogenesis and treatment remains challenging because of tumor heterogeneity. Here, we analyzed the genomic alterations of 45 samples from CRC patients in northern China by whole-exome sequencing. In addition to the identification of six well-known CRC driver genes (APC, TP53, KRAS, FBXW7, PIK3CA, and PABPC), two tumor-related genes (MTCH2 and HSPA6) were detected, along with RRP7A and GXYLT1, which have not been previously linked to cancer. GXYLT1 was mutated in 40% (18/45) of the samples in our cohort. Functionally, GXYLT1 promoted migration and invasion in vitro and metastasis in vivo, while the GXYLT1S212* mutant induced significantly greater effect. Furthermore, both GXYLT1 and GXYLT1S212* interacted with ERK2. GXYLT1 induced metastasis via a mechanism involving the Notch and MAPK pathways, whereas the GXYLT1S212* mutant mainly promoted metastasis by activating the MAPK pathway. We propose that GXYLT1 acts as a novel metastasis-associated driver gene and GXYLT1S212* might serve as a potential indicator for therapies targeting the MAPK pathway in CRC.
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Affiliation(s)
- Lin Peng
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Min Zhao
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4556, Australia
| | - Tianqi Liu
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Jiangbo Chen
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Pin Gao
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Lei Chen
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Pu Xing
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Zaozao Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Jiabo Di
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Qiang Xu
- GenomiCare Biotechnology (Shanghai) Co., Ltd, Shanghai, 201210, China
| | - Hong Qu
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, P. R. China.
| | - Beihai Jiang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing, 100142, China.
| | - Xiangqian Su
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, Beijing, 100142, China.
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11
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Zhao S, Wu W, Jiang Z, Tang F, Ding L, Xu W, Ruan L. Roles of ARID1A variations in colorectal cancer: a collaborative review. Mol Med 2022; 28:42. [PMID: 35421925 PMCID: PMC9009033 DOI: 10.1186/s10020-022-00469-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/05/2022] [Indexed: 12/24/2022] Open
Abstract
AbstractColorectal cancer (CRC), a common malignancy, is one of the leading cause of cancer death in adults. AT-rich interaction domain 1A (ARID1A), a critical portion of the SWItch/sucrose non-fermentation (SWI/SNF) chromatin remodeling complexes, shows one of the most frequent mutant genes across different human cancer types. Deleterious variations of ARID1A has been recognized to be correlated the tumorigenesis and the poor prognosis of CRC. Here, we summarize recent advances in the clinical implications and molecular pathogenesis of ARID1A variations in CRC. According to independent data of 23 included studies, ARID1A is mutated in 3.6–66.7%. Consistently, all of the 23 relevant studies report that ARID1A functions as a specific tumor suppressor in CRC. Clinically, ARID1A variation status serves as a biomarker for survival prognosis and various therapies for CRC. Mechanistically, the pathophysiologic impacts of ARID1A variations on CRC may be associated with the co-occurrence variations of other genes (i.e., TP53, KRAS, APC, FBXW7, and PIK3CA) and the regulation of several signaling pathways being affected (i.e., WNT signaling, Akt signaling, and MEK/ERK pathway), leading to cell cycle arrest, chromatin remodeling, chromosome organization, and DNA hypermethylation of the cancer cells. The present review highlights ARID1A serving as a potent tumor suppressor and an important prognostic factor in CRC. ARID1A variations hint towards a promising tool for diagnostic tumor profiling and individualized therapeutic targets for CRC in the future.
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12
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Su MW, Chang CK, Lin CW, Chu HW, Tsai TN, Su WC, Chen YC, Chang TK, Huang CW, Tsai HL, Wu CC, Chou HC, Shiu BH, Wang JY. Genomic and Metabolomic Landscape of Right-Sided and Left-Sided Colorectal Cancer: Potential Preventive Biomarkers. Cells 2022; 11:cells11030527. [PMID: 35159336 PMCID: PMC8834628 DOI: 10.3390/cells11030527] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 12/27/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer worldwide. The incidence and mortality rates of CRC are significantly higher in Taiwan than in other developed countries. Genes involved in CRC tumorigenesis differ depending on whether the tumor occurs on the left or right side of the colon, and genomic analysis is a keystone in the study and treatment of CRC subtypes. However, few studies have focused on the genetic landscape of Taiwanese patients with CRC. This study comprehensively analyzed the genomes of 141 Taiwanese patients with CRC through whole-exome sequencing. Significant genomic differences related to the site of CRC development were observed. Blood metabolomic profiling and polygenic risk score analysis were performed to identify potential biomarkers for the early identification and prevention of CRC in the Taiwanese population. Our findings provide vital clues for establishing population-specific treatments and health policies for CRC prevention in Taiwan.
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Affiliation(s)
- Ming-Wei Su
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan; (M.-W.S.); (C.-K.C.); (C.-W.L.); ho (H.-W.C.)
| | - Chung-Ke Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan; (M.-W.S.); (C.-K.C.); (C.-W.L.); ho (H.-W.C.)
| | - Chien-Wei Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan; (M.-W.S.); (C.-K.C.); (C.-W.L.); ho (H.-W.C.)
| | - Hou-Wei Chu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan; (M.-W.S.); (C.-K.C.); (C.-W.L.); ho (H.-W.C.)
| | - Tsen-Ni Tsai
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (T.-N.T.); (W.-C.S.); (Y.-C.C.); (T.-K.C.); (C.-W.H.); (H.-L.T.)
| | - Wei-Chih Su
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (T.-N.T.); (W.-C.S.); (Y.-C.C.); (T.-K.C.); (C.-W.H.); (H.-L.T.)
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yen-Cheng Chen
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (T.-N.T.); (W.-C.S.); (Y.-C.C.); (T.-K.C.); (C.-W.H.); (H.-L.T.)
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Tsung-Kun Chang
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (T.-N.T.); (W.-C.S.); (Y.-C.C.); (T.-K.C.); (C.-W.H.); (H.-L.T.)
| | - Ching-Wen Huang
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (T.-N.T.); (W.-C.S.); (Y.-C.C.); (T.-K.C.); (C.-W.H.); (H.-L.T.)
- Department of Surgery, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Hsiang-Lin Tsai
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (T.-N.T.); (W.-C.S.); (Y.-C.C.); (T.-K.C.); (C.-W.H.); (H.-L.T.)
- Department of Surgery, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chang-Chieh Wu
- Department of Surgery, Tri-Service General Hospital Keelung Branch, National Defense Medical Center, Keelung 20042, Taiwan;
| | - Huang-Chi Chou
- School of Medicine, Chung Shan Medical University, Taichung 402306, Taiwan; (H.-C.C.); (B.-H.S.)
- Division of Colon and Rectal Surgery, Department of Surgery, Chung Shan Medical University Hospital, Taichung 402306, Taiwan
| | - Bei-Hao Shiu
- School of Medicine, Chung Shan Medical University, Taichung 402306, Taiwan; (H.-C.C.); (B.-H.S.)
- Division of Colon and Rectal Surgery, Department of Surgery, Chung Shan Medical University Hospital, Taichung 402306, Taiwan
| | - Jaw-Yuan Wang
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (T.-N.T.); (W.-C.S.); (Y.-C.C.); (T.-K.C.); (C.-W.H.); (H.-L.T.)
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Surgery, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Center for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Pingtung Hospital, Ministry of Health and Welfare, Pingtung 900, Taiwan
- Correspondence: & ; Tel.: +886-7-312-2805
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Ma L, Lu H, Tian Z, Yang M, Ma J, Shang G, Liu Y, Xie M, Wang G, Wu W, Zhang Z, Dai S, Chen Z. Structural insights into the interactions and epigenetic functions of human nucleic acid repair protein ALKBH6. J Biol Chem 2022; 298:101671. [PMID: 35120926 PMCID: PMC8892091 DOI: 10.1016/j.jbc.2022.101671] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 12/03/2022] Open
Abstract
Human AlkB homolog 6, ALKBH6, plays key roles in nucleic acid damage repair and tumor therapy. However, no precise structural and functional information are available for this protein. In this study, we determined atomic resolution crystal structures of human holo-ALKBH6 and its complex with ligands. AlkB members bind nucleic acids by NRLs (nucleotide recognition lids, also called Flips), which can recognize DNA/RNA and flip methylated lesions. We found that ALKBH6 has unusual Flip1 and Flip2 domains, distinct from other AlkB family members both in sequence and conformation. Moreover, we show that its unique Flip3 domain has multiple unreported functions, such as discriminating against double-stranded nucleic acids, blocking the active center, binding other proteins, and in suppressing tumor growth. Structural analyses and substrate screening reveal how ALKBH6 discriminates between different types of nucleic acids and may also function as a nucleic acid demethylase. Structure-based interacting partner screening not only uncovered an unidentified interaction of transcription repressor ZMYND11 and ALKBH6 in tumor suppression but also revealed cross talk between histone modification and nucleic acid modification in epigenetic regulation. Taken together, these results shed light on the molecular mechanism underlying ALKBH6-associated nucleic acid damage repair and tumor therapy.
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Affiliation(s)
- Lulu Ma
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Hongyun Lu
- School of food and health, Beijing Technology and Business University, No. 11, Fucheng Road, Haidian District, Beijing, 100048, China
| | - Zizi Tian
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Meiting Yang
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jun Ma
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Guohui Shang
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yunlong Liu
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Mengjia Xie
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Guoguo Wang
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Wei Wu
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Shaodong Dai
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
| | - Zhongzhou Chen
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
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Yang Y, Gu X, Li Z, Zheng C, Wang Z, Zhou M, Chen Z, Li M, Li D, Xiang J. Whole-exome sequencing of rectal cancer identifies locally recurrent mutations in the Wnt pathway. Aging (Albany NY) 2021; 13:23262-23283. [PMID: 34642262 PMCID: PMC8544332 DOI: 10.18632/aging.203618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 09/29/2021] [Indexed: 12/29/2022]
Abstract
Locally recurrent rectal cancer (LRRC) leads to a poor prognosis and appears as a clinically predominant pattern of failure. In this research, whole-exome sequencing (WES) was performed on 21 samples from 8 patients to search for the molecular mechanisms of LRRC. The data was analyzed by bioinformatics. Gene Expression Profiling Interactive Analysis (GEPIA) and Human Protein Atlas (HPA) were performed to validate the candidate genes. Immunohistochemistry was used to detect the protein expression of LEF1 and CyclinD1 in LRRC, primary rectal cancer (PRC), and non-recurrent rectal cancer (NRRC) specimens. The results showed that LRRC, PRC, and NRRC had 668, 794, and 190 specific genes, respectively. FGFR1 and MYC have copy number variants (CNVs) in PRC and LRRC, respectively. LRRC specific genes were mainly enriched in positive regulation of transcription from RNA polymerase II promoter, plasma membrane, and ATP binding. The specific signaling pathways of LRRC were Wnt signaling pathway, gap junction, and glucagon signaling pathway, etc. The transcriptional and translational expression levels of genes including NFATC1, PRICKLE1, SOX17, and WNT6 related to Wnt signaling pathway were higher in rectal cancer (READ) tissues than normal rectal tissues. The PRICKLE1 mutation (c.C875T) and WNT6 mutation (c.G629A) were predicted as “D (deleterious)”. Expression levels of LEF1 and cytokinin D1 proteins: LRRC > PRC > NRRC > normal rectal tissue. Gene variants in the Wnt signaling pathway may be critical for the development of LRRC. The present study may provide a basis for the prediction of LRRC and the development of new therapeutic drugs.
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Affiliation(s)
- Yi Yang
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Xiaodong Gu
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Zhenyang Li
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Chuang Zheng
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Zihao Wang
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Minwei Zhou
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Zongyou Chen
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Mengzhen Li
- MyGene Diagnostics Co., Ltd, Guangzhou 510000, China
| | - Dongbing Li
- MyGene Diagnostics Co., Ltd, Guangzhou 510000, China
| | - Jianbin Xiang
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China
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15
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PEG3 mutation is associated with elevated tumor mutation burden and poor prognosis in breast cancer. Biosci Rep 2021; 40:225944. [PMID: 32729618 PMCID: PMC7419805 DOI: 10.1042/bsr20201648] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/22/2020] [Accepted: 07/28/2020] [Indexed: 12/15/2022] Open
Abstract
Background: Breast cancer is the second most common malignancy in women and considered as a severe health burden. PEG3 mutations have been observed in several cancers. However, the associations of PEG3 mutation with tumor mutation burden (TMB) and prognosis in breast cancer have not been investigated. Methods: In our study, the somatic mutation data of 986 breast cancer patients from The Cancer Genome Atlas (TCGA) were analyzed. Results: It showed that PEG3 had a relatively high mutation rate (2%). After calculated the TMB in PEG3 mutant and PEG3 wild-type groups, we found the TMB value was significantly higher in PEG3 mutant samples than that in PEG3 wild-type samples (P = 5.6e-07), which was independent of the confounding factors including age, stage, mutations of BRCA1, BRCA2 and POLE (odd ratio, 0.45; 95% CI, 0.20–0.98; P=0.044). Survival analysis revealed that PEG3 mutant samples had inferior survival outcome compared with the PEG3 wild-type samples after adjusted for the confounding factors above (hazard ratio, 0.27; 95% CI: 0.12–0.57; P<0.001). Conclusion: These results illustrated that PEG3 mutation was associated with high TMB and inferior prognosis, suggesting PEG3 mutation might play a guiding role in prognosis prediction and immunotherapy selection in breast cancer.
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16
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Huang W, Li H, Shi X, Lin M, Liao C, Zhang S, Shi W, Zhang L, Zhang X, Gan J. Characterization of genomic alterations in Chinese colorectal cancer patients. Jpn J Clin Oncol 2021; 51:120-129. [PMID: 33106877 DOI: 10.1093/jjco/hyaa182] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 09/08/2020] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE Colorectal cancer is one of the most prevalent types of cancer worldwide. Right-sided and left-sided colorectal cancer (RCC and LCC) patients respond differently to treatment. We aimed to identify the different mutational profile between RCC and LCC and provided evidence for future precision therapy. METHODS A total of 630 Chinese colorectal cancer patients, including 467 (74.1%) LCC and 163 (25.9%) RCC, were enrolled in this cohort. Both formalin-fixed paraffin-embedded tumor tissues and matching blood samples were collected and deep sequenced targeting 450 cancer genes for genomic alteration analysis. Tumor mutational burden was measured by an algorithm developed in-house. Correlation analysis was performed by Fisher's exact test. RESULTS The most common mutated genes were TP53 (77.0%), APC (71.7%), KRAS (50.0%), SMAD4 (19.8%), PIK3CA (18.3%), FBXW7 (17.5%), TCF7L2 (12.5%), SOX9 (11.3%), LRP1B (10.8%), ARID1A (10.3%) and FAT4 (10.3%). The mutation frequencies of TP53 and APC in LCC were significantly higher than that of RCC, while the mutation frequency of PIK3CA was lower than that of RCC. Six gene fusions were specifically detected in RCC patients. Colorectal cancer sites were associated with gender (P = 4.15 × 10-5) and tumor differentiation (P = 0.059). In LCC, the gender-associated genes were FAT4, EP300, FAT1, LRP1, ARID1B, AR, FYN and TAF1, while in RCC, they were ARID1A, SMARCA4, LRP1 and GRIN2A. The mutations of 18 genes were associated with tumor differentiation (8 for LCC and 10 for RCC). High tumor mutational burden was more common in RCC. Our results implied more potential targeted drug therapy opportunities for RCC. CONCLUSION We describe the different molecular characteristics of LCC and RCC. Our result supported a better prognosis of RCC than LCC in Chinese colorectal cancer patients.
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Affiliation(s)
- Wei Huang
- Department of Colorectal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, P. R. China
| | - Hui Li
- Department of Colorectal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, P. R. China
| | | | - Minglin Lin
- Department of Colorectal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, P. R. China
| | - Cun Liao
- Department of Colorectal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, P. R. China
| | | | | | - Lin Zhang
- Origimed Co. Ltd, Shanghai, P. R. China
| | - Xiaolong Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, P. R. China
| | - Jialiang Gan
- Department of Colorectal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, P. R. China
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McPherson MT, Holub AS, Husbands AY, Petreaca RC. Mutation Spectra of the MRN (MRE11, RAD50, NBS1/NBN) Break Sensor in Cancer Cells. Cancers (Basel) 2020; 12:cancers12123794. [PMID: 33339169 PMCID: PMC7765586 DOI: 10.3390/cancers12123794] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/04/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary A DNA double strand break cuts a chromosome in two and is one of the most dangerous forms of DNA damage. Improper repair can lead to various chromosomal re-arrangements that have been detected in almost all cancer cells. A complex of three proteins (MRE11, RAD50, NBS1 or NBN) detects chromosome breaks and orchestrates repair processes. Mutations in these “break sensor” genes have been described in a multitude of cancers. Here, we provide a comprehensive analysis of reported mutations from data deposited on the Catalogue of Somatic Mutations in Cancer (COSMIC) archive. We also undertake an evolutionary analysis of these genes with the aim to understand whether these mutations preferentially accumulate in conserved residues. Interestingly, we find that mutations are overrepresented in evolutionarily conserved residues of RAD50 and NBS1/NBN but not MRE11. Abstract The MRN complex (MRE11, RAD50, NBS1/NBN) is a DNA double strand break sensor in eukaryotes. The complex directly participates in, or coordinates, several activities at the break such as DNA resection, activation of the DNA damage checkpoint, chromatin remodeling and recruitment of the repair machinery. Mutations in components of the MRN complex have been described in cancer cells for several decades. Using the Catalogue of Somatic Mutations in Cancer (COSMIC) database, we characterized all the reported MRN mutations. This analysis revealed several hotspot frameshift mutations in all three genes that introduce premature stop codons and truncate large regions of the C-termini. We also found through evolutionary analyses that COSMIC mutations are enriched in conserved residues of NBS1/NBN and RAD50 but not in MRE11. Given that all three genes are important to carcinogenesis, we propose these differential enrichment patterns may reflect a more severe pleiotropic role for MRE11.
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Melo-Hanchuk TD, Colleti C, Saito Â, Mendes MCS, Carvalheira JBC, Vassallo J, Kobarg J. Intracellular hyaluronic acid-binding protein 4 (HABP4): a candidate tumor suppressor in colorectal cancer. Oncotarget 2020; 11:4325-4337. [PMID: 33245729 PMCID: PMC7679031 DOI: 10.18632/oncotarget.27804] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023] Open
Abstract
Hyaluronic Acid-binding protein 4 (HABP4) is a regulatory protein of 57 kDa that is functionally involved in transcription regulation and RNA metabolism and shows several characteristics common to oncoproteins or tumor suppressors, including altered expression in cancer tissues, nucleus/cytoplasm shuttling, intrinsic lack of protein structure, complex interactomes and post translational modifications. Its gene has been found in a region on chromosome 9q22.3-31, which contains SNP haplotypes occurring in individuals with a high risk for familial colon cancer. To test a possible role of HABP4 in tumorigenesis we generated knockout mice by the CRISPR/Cas9 method and treated the animals with azoxymethane (AOM)/dextran sodium sulfate (DSS) for induction of colon tumors. HABP4-/- mice, compared to wild type mice, had more and larger tumors, and expressed more of the proliferation marker proteins Cyclin-D1, CDK4 and PCNA. Furthermore, the cells of the bottom of the colon crypts in the HABP4-/- mice divided more rapidly. Next, we generated also HABP4-/- HCT 116 cells, in cell culture and found again an increased proliferation in clonogenic assays in comparison to wild-type cells. Our study of the protein expression levels of HABP4 in human colon cancer samples, through immunohistochemistry assays, showed, that 30% of the tumors analyzed had low expression of HABP4. Our data suggest that HABP4 is involved in proliferation regulation of colon cells in vitro and in vivo and that it is a promising new candidate for a tumor suppressor protein that can be explored both in the diagnosis and possibly therapy of colon cancer.
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Affiliation(s)
- Talita Diniz Melo-Hanchuk
- 2Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, SP, Brazil
- *These authors contributed equally to this work
| | - Carolina Colleti
- 1School of Pharmaceutical Sciences, State University of Campinas (UNICAMP), Campinas, SP, Brazil
- *These authors contributed equally to this work
| | - Ângela Saito
- 3Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
- *These authors contributed equally to this work
| | - Maria Carolina Santos Mendes
- 4Division of Oncology, Department of Internal Medicine, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - José Barreto Campello Carvalheira
- 4Division of Oncology, Department of Internal Medicine, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Jose Vassallo
- 5Laboratory of Investigative Pathology, CIPED, Faculty of Medical Sciences, State University of Campinas, Campinas, SP, Brazil
| | - Jörg Kobarg
- 1School of Pharmaceutical Sciences, State University of Campinas (UNICAMP), Campinas, SP, Brazil
- Correspondence to: Jörg Kobarg, email:
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Siraj S, Masoodi T, Siraj AK, Azam S, Qadri Z, Ahmed SO, AlBalawy WN, Al-Obaisi KA, Parvathareddy SK, AlManea HM, AlHussaini HF, Abduljabbar A, Alhomoud S, Al-Dayel FH, Alkuraya FS, Al-Kuraya KS. Clonal Evolution and Timing of Metastatic Colorectal Cancer. Cancers (Basel) 2020; 12:cancers12102938. [PMID: 33053768 PMCID: PMC7601934 DOI: 10.3390/cancers12102938] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/03/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) is the third most frequently diagnosed cancer worldwide, where ~50% of patients develop metastasis, despite current improved management. Genomic characterisation of metastatic CRC, and elucidating the effects of therapy on the metastatic process, are essential to help guide precision medicine. Multi-region whole-exome sequencing was performed on 191 sampled tumour regions of patient-matched therapy-naïve and treated CRC primary tumours (n = 92 tumour regions) and metastases (n = 99 tumour regions), in 30 patients. Somatic variants were analysed to define the origin, composition, and timing of seeding in the metastatic progression of therapy-naïve and treated metastatic CRC. High concordance, with few genomic differences, was observed between primary CRC and metastases. Most cases supported a late dissemination model, via either monoclonal or polyclonal seeding. Polyclonal seeding appeared more common in therapy-naïve metastases than in treated metastases. Whereby, treatment prompted for the selection of distinct resistant clones, through monoclonal seeding to distant metastatic sites. Overall, this study reinforces the importance of early clinical detection and surgical excision of the CRC tumour, whilst further highlighting the clinical challenges for metastatic CRC with increased intratumour heterogeneity (either due to early dissemination or polyclonal metastatic spread) and the underlying risk of future therapeutic resistance in treated patients.
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Affiliation(s)
- Sarah Siraj
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.O.A.); (W.N.A.); (K.A.A.-O.); (S.K.P.)
| | - Tariq Masoodi
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.O.A.); (W.N.A.); (K.A.A.-O.); (S.K.P.)
| | - Abdul K. Siraj
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.O.A.); (W.N.A.); (K.A.A.-O.); (S.K.P.)
| | - Saud Azam
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.O.A.); (W.N.A.); (K.A.A.-O.); (S.K.P.)
| | - Zeeshan Qadri
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.O.A.); (W.N.A.); (K.A.A.-O.); (S.K.P.)
| | - Saeeda O. Ahmed
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.O.A.); (W.N.A.); (K.A.A.-O.); (S.K.P.)
| | - Wafaa N. AlBalawy
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.O.A.); (W.N.A.); (K.A.A.-O.); (S.K.P.)
| | - Khadija A. Al-Obaisi
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.O.A.); (W.N.A.); (K.A.A.-O.); (S.K.P.)
| | - Sandeep K. Parvathareddy
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.O.A.); (W.N.A.); (K.A.A.-O.); (S.K.P.)
| | - Hadeel M. AlManea
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (H.M.A.); (H.F.A.); (F.H.A.-D.)
| | - Hussah F. AlHussaini
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (H.M.A.); (H.F.A.); (F.H.A.-D.)
| | - Alaa Abduljabbar
- Department of Surgery, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (A.A.); (S.A.)
| | - Samar Alhomoud
- Department of Surgery, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (A.A.); (S.A.)
| | - Fouad H. Al-Dayel
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (H.M.A.); (H.F.A.); (F.H.A.-D.)
| | - Fowzan S. Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia;
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Khawla S. Al-Kuraya
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.O.A.); (W.N.A.); (K.A.A.-O.); (S.K.P.)
- Correspondence: ; Tel.: +966-112-055-2167
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20
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Nelakurti DD, Pappula AL, Rajasekaran S, Miles WO, Petreaca RC. Comprehensive Analysis of MEN1 Mutations and Their Role in Cancer. Cancers (Basel) 2020; 12:cancers12092616. [PMID: 32937789 PMCID: PMC7565326 DOI: 10.3390/cancers12092616] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/04/2020] [Accepted: 09/10/2020] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Cancers are characterized by accumulation of genetic mutations in key cell cycle regulators that alter or disable the function of these genes. Such mutations can be inherited or arise spontaneously during the life of the individual. The MEN1 gene prevents uncontrolled cell division and it is considered a tumor suppressor. Inherited MEN1 mutations are associated with certain parathyroid and pancreatic syndromes while spontaneous mutations have been detected in cancer cells. We investigated whether inherited mutations appear in cancer cells which would suggest that patients with parathyroid and pancreatic syndromes have a predisposition to develop cancer. We find a weak correlation between the spectrum of inherited mutations and those appearing spontaneously. Thus, inherited MEN1 mutations may not be a good predictor of tumorigenesis. Abstract MENIN is a scaffold protein encoded by the MEN1 gene that functions in multiple biological processes, including cell proliferation, migration, gene expression, and DNA damage repair. MEN1 is a tumor suppressor gene, and mutations that disrupts MEN1 function are common to many tumor types. Mutations within MEN1 may also be inherited (germline). Many of these inherited mutations are associated with a number of pathogenic syndromes of the parathyroid and pancreas, and some also predispose patients to hyperplasia. In this study, we cataloged the reported germline mutations from the ClinVar database and compared them with the somatic mutations detected in cancers from the Catalogue of Somatic Mutations in Cancer (COSMIC) database. We then used statistical software to determine the probability of mutations being pathogenic or driver. Our data show that many confirmed germline mutations do not appear in tumor samples. Thus, most mutations that disable MEN1 function in tumors are somatic in nature. Furthermore, of the germline mutations that do appear in tumors, only a fraction has the potential to be pathogenic or driver mutations.
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Affiliation(s)
- Devi D. Nelakurti
- Biomedical Science Undergraduate Program, The Ohio State University Medical School, Columbus, OH 43210, USA;
| | - Amrit L. Pappula
- Computer Science and Engineering Undergraduate Program, The Ohio State University, Columbus, OH 43210, USA;
| | - Swetha Rajasekaran
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA;
| | - Wayne O. Miles
- Department of Cancer Biology and Genetics, The Ohio State University Medical School, Columbus, OH 43210, USA;
| | - Ruben C. Petreaca
- Department of Molecular Genetics, The Ohio State University, Marion, OH 43302, USA
- Correspondence:
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21
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Lei H, Tao K. Somatic mutations in colorectal cancer are associated with the epigenetic modifications. J Cell Mol Med 2020; 24:11828-11836. [PMID: 32865336 PMCID: PMC7579689 DOI: 10.1111/jcmm.15799] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 07/22/2020] [Accepted: 08/09/2020] [Indexed: 01/13/2023] Open
Abstract
Colorectal cancer (CRC) mostly arises from progressive accumulation of somatic mutations within cells. Most commonly mutated genes like TP53, APC and KRAS can promote survival and proliferation of cancer cells. Although the molecular alterations and landscape of some specific mutations in CRC are well known, the presence of a somatic mutation signature related to genomic regions and epigenetic markers remain unclear. To find the signatures from a random distribution of somatic mutations in CRCs, we carried out enrichment analysis in different genomic regions and identified peaks of epigenetic markers. We validated that the mutation frequency in miRNA is dramatically higher than in flanking genomic regions. Moreover, we observed that somatic mutations in CRC and colon cancer cell lines are significantly enriched in CTCF binding sites. We also found these mutations are enriched for H3K27me3 in both normal sigmoid colon and colon cancer cell lines. Taken together, our findings suggest that there are some common somatic mutations signatures which provide new directions to study CRC.
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Affiliation(s)
- Hongwei Lei
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kaixiong Tao
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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22
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Recurrent Neoantigens in Colorectal Cancer as Potential Immunotherapy Targets. BIOMED RESEARCH INTERNATIONAL 2020; 2020:2861240. [PMID: 32733937 PMCID: PMC7383341 DOI: 10.1155/2020/2861240] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 05/26/2020] [Accepted: 06/02/2020] [Indexed: 12/24/2022]
Abstract
This study was aimed at investigating the mutations in colorectal cancer (CRC) for recurrent neoantigen identification. A total of 1779 samples with whole exome sequencing (WES) data were obtained from 7 published CRC cohorts. Common HLA genotypes were used to predict the probability of neoantigens at high-frequency mutants in the dataset. Based on the WES data, we not only obtained the most comprehensive CRC mutation landscape so far but also found 1550 mutations which could be identified in at least 5 patients, including KRAS G12D (8%), KRAS G12V (5.8%), PIK3CA E545K (3.5%), PIK3CA H1047R (2.5%), and BMPR2 N583Tfs∗44 (2.8%). These mutations can also be recognized by multiple common HLA molecules in Chinese and TCGA cohort as potential "public" neoantigens. Many of these mutations also have high mutation rates in metastatic pan-cancers, suggesting their value as therapeutic targets in different cancer types. Overall, our analysis provides recurrent neoantigens as potential cancer immunotherapy targets.
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23
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Ma R, Jing C, Zhang Y, Cao H, Liu S, Wang Z, Chen D, Zhang J, Wu Y, Wu J, Feng J. The somatic mutation landscape of Chinese Colorectal Cancer. J Cancer 2020; 11:1038-1046. [PMID: 31956350 PMCID: PMC6959081 DOI: 10.7150/jca.37017] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 10/27/2019] [Indexed: 01/01/2023] Open
Abstract
Colorectal cancer (CRC) is the fifth leading cause of cancer-related death in China. The incidence of Chinese CRC has increased dramatically with the changes of dietary and lifestyle. However, the genetic landscape of Chinese colorectal cancer mutation is still poorly understood. In this study, we have performed whole exome-sequencing analysis of 63 CRC cases. We found that Chinese CRC were hypermutated, which were enriched in ECM-receptor interaction, antigen processing and presentation, and focal adhesion. Analysis with clinical characteristics indicated that the deficiency of CRC driver gene, FCGBP and NBPF1 conferred CRC development and was showed worse survival rates, which could be the novel regulators and, diagnostic and prognostic biomarkers for Chinese CRC. Taken together, the application of whole exome-sequencing unveiled previously unsuspected somatic mutation landscape in Chinese CRCs, which may expand the understanding of disease mechanisms and provide an alternative personalized treatment for Chinese CRC patients.
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Affiliation(s)
- Rong Ma
- Clinical Cancer Research Center, Jiangsu Cancer Hospital &Jiangsu Institute of Cancer Research &The Affiliated Cancer Hospital of Nanjing Medical University, China
| | - Changwen Jing
- Clinical Cancer Research Center, Jiangsu Cancer Hospital &Jiangsu Institute of Cancer Research &The Affiliated Cancer Hospital of Nanjing Medical University, China
| | - Yuan Zhang
- Clinical Cancer Research Center, Jiangsu Cancer Hospital &Jiangsu Institute of Cancer Research &The Affiliated Cancer Hospital of Nanjing Medical University, China
| | - Haixia Cao
- Clinical Cancer Research Center, Jiangsu Cancer Hospital &Jiangsu Institute of Cancer Research &The Affiliated Cancer Hospital of Nanjing Medical University, China
| | - Siwen Liu
- Clinical Cancer Research Center, Jiangsu Cancer Hospital &Jiangsu Institute of Cancer Research &The Affiliated Cancer Hospital of Nanjing Medical University, China
| | - Zhuo Wang
- Clinical Cancer Research Center, Jiangsu Cancer Hospital &Jiangsu Institute of Cancer Research &The Affiliated Cancer Hospital of Nanjing Medical University, China
| | - Dan Chen
- Clinical Cancer Research Center, Jiangsu Cancer Hospital &Jiangsu Institute of Cancer Research &The Affiliated Cancer Hospital of Nanjing Medical University, China
| | - Junying Zhang
- Clinical Cancer Research Center, Jiangsu Cancer Hospital &Jiangsu Institute of Cancer Research &The Affiliated Cancer Hospital of Nanjing Medical University, China
| | - Yang Wu
- Clinical Cancer Research Center, Jiangsu Cancer Hospital &Jiangsu Institute of Cancer Research &The Affiliated Cancer Hospital of Nanjing Medical University, China
| | - Jianzhong Wu
- Clinical Cancer Research Center, Jiangsu Cancer Hospital &Jiangsu Institute of Cancer Research &The Affiliated Cancer Hospital of Nanjing Medical University, China
| | - Jifeng Feng
- Department of Chemotherapy, Jiangsu Cancer Hospital &Jiangsu Institute of Cancer Research &The Affiliated Cancer Hospital of Nanjing Medical University, China
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24
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Dos Santos W, Sobanski T, de Carvalho AC, Evangelista AF, Matsushita M, Berardinelli GN, de Oliveira MA, Reis RM, Guimarães DP. Mutation profiling of cancer drivers in Brazilian colorectal cancer. Sci Rep 2019; 9:13687. [PMID: 31548566 PMCID: PMC6757044 DOI: 10.1038/s41598-019-49611-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/28/2019] [Indexed: 12/24/2022] Open
Abstract
The molecular basis of colorectal cancer (CRC) can guide patient prognosis and therapy. In Brazil, knowledge on the CRC mutation landscape is limited. Here, we investigated the mutation profile of 150 cancer-related genes by next-generation sequencing and associated with microsatellite instability (MSI) and genetic ancestry in a series of 91 Brazilian CRC patients. Driver mutations were found in the APC (71.4%), TP53 (56.0%), KRAS (52.7%), PIK3CA (15.4%) and FBXW7 (10.9%) genes. Overall, genes in the MAPK/ERK, PIK3/AKT, NOTCH and receptor tyrosine kinase signaling pathways were mutated in 68.0%, 23.1%, 16.5%, and 15.3% of patients, respectively. MSI was found in 13.3% of tumors, most of which were proximal (52.4%, P< 0.001) and had a high mutation burden. European genetic ancestry was predominant (median of 83.1%), followed by Native American (4.1%), Asian (3.4%) and African (3.2%). NF1 and BRAF mutations were associated with African ancestry, while TP53 and PIK3CA mutations were inversely correlated with Native American ancestry. Our study suggests that Brazilian CRC patients exhibit a mutation profile similar to other populations and identify the most frequently mutated genes, which could be useful in future target therapies and molecular cancer screening strategies.
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Affiliation(s)
| | - Thais Sobanski
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | | | | | | | | | | | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.
- Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, 4710-057, Portugal.
- 3ICVS/3B's-PT Government Associate Laboratory, Braga, 4710-057, Portugal.
| | - Denise Peixoto Guimarães
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.
- Department of Endoscopy, Barretos Cancer Hospital, Barretos, Brazil.
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