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Marks SA, Zhou ZX, Lujan SA, Burkholder AB, Kunkel TA. Evidence that DNA polymerase δ proofreads errors made by DNA polymerase α across the Saccharomyces cerevisiae nuclear genome. DNA Repair (Amst) 2024; 143:103768. [PMID: 39332392 DOI: 10.1016/j.dnarep.2024.103768] [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: 07/10/2024] [Revised: 09/09/2024] [Accepted: 09/17/2024] [Indexed: 09/29/2024]
Abstract
We show that the rates of single base substitutions, additions, and deletions across the nuclear genome are strongly increased in a strain harboring a mutator variant of DNA polymerase α combined with a mutation that inactivates the 3´-5´ exonuclease activity of DNA polymerase δ. Moreover, tetrad dissections attempting to produce a haploid triple mutant lacking Msh6, which is essential for DNA mismatch repair (MMR) of base•base mismatches made during replication, result in tiny colonies that grow very slowly and appear to be aneuploid and/or defective in oxidative metabolism. These observations are consistent with the hypothesis that during initiation of nuclear DNA replication, single-base mismatches made by naturally exonuclease-deficient DNA polymerase α are extrinsically proofread by DNA polymerase δ, such that in the absence of this proofreading, the mutation rate is strongly elevated. Several implications of these data are discussed, including that the mutational signature of defective extrinsic proofreading in yeast could appear in human tumors.
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Affiliation(s)
- Sarah A Marks
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, DHHS, Research Triangle Park, NC 27709, USA
| | - Zhi-Xiong Zhou
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, DHHS, Research Triangle Park, NC 27709, USA
| | - Scott A Lujan
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, DHHS, Research Triangle Park, NC 27709, USA
| | - Adam B Burkholder
- Office of Environmental Science Cyberinfrastructure, National Institute of Environmental Health Sciences, National Institutes of Health, DHHS, Research Triangle Park, NC 27709, USA
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, DHHS, Research Triangle Park, NC 27709, USA.
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2
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Su DG, Dhiman A, Bansal VV, Zha Y, Shergill A, Polite B, Alpert L, Turaga KK, Eng OS. Mutational Features and Tumor Microenvironment Alterations in High-Grade Appendiceal Cancers Treated With Iterative Hyperthermic Intraperitoneal Chemotherapy. JCO Precis Oncol 2024; 8:e2400149. [PMID: 39259912 PMCID: PMC11432692 DOI: 10.1200/po.24.00149] [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: 03/06/2024] [Revised: 05/23/2024] [Accepted: 08/06/2024] [Indexed: 09/13/2024] Open
Abstract
PURPOSE High-grade appendiceal adenocarcinomas (HGAA) with peritoneal metastases (PMs) are associated with poor survival. Hyperthermic intraperitoneal chemotherapy (HIPEC) is a novel treatment approach for unresectable HGAA-PM. However, its influence on immunogenomic profiles has not yet been fully explored. MATERIALS AND METHODS We obtained 79 samples of metastatic peritoneal tumor deposits from patients diagnosed with HGAA and performed whole-exome sequencing, RNA sequencing, and immunoprofiling before and after HIPEC. Tumor biopsies were subjected to immunogenomic profiling to detect mutational signatures and immune populations associated with oncologic outcomes. RESULTS Fifteen patients with HGAA-PMs were included in the study. The median progression-free survival (PFS) was 6.7 months (2.7-25.3) and the median overall survival was 11.4 months (4.7-42). Mucin-associated genes (MUC16, MUC3A, and MUC5AC) and titin (TTN) had the highest mutation frequencies. Mutational signatures such as single-base substitution 29 and doublet-base substitution 11 were present in >50% of single-base and double-base mutations. Higher PD-L1 coexpression on CD8+ T cells demonstrated a higher PFS both intratumorally (P = .019) and at the margin (P = .025). CONCLUSION HIPEC-associated mutational signatures were identified in HGAA-PMs. Elevated PD-L1+ cytotoxic T-cell populations after HIPEC had better PFS, offering valuable insights for prognostication in the context of HIPEC treatment.
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Affiliation(s)
- David G Su
- Division of Surgical Oncology, Yale School of Medicine, New Haven, CT
| | - Ankit Dhiman
- Department of Surgery, Medical College of Georgia, Augusta, GA
| | - Varun V Bansal
- Division of Surgical Oncology, Yale School of Medicine, New Haven, CT
| | - Yuanyuan Zha
- Department of Pathology, University of Chicago Medical Center, Chicago, IL
| | - Ardaman Shergill
- Department of Hematology/Oncology, University of Chicago Medical Center, Chicago, IL
| | - Blasé Polite
- Department of Hematology/Oncology, University of Chicago Medical Center, Chicago, IL
| | - Lindsay Alpert
- Department of Pathology, University of Chicago Medical Center, Chicago, IL
| | - Kiran K Turaga
- Division of Surgical Oncology, Yale School of Medicine, New Haven, CT
| | - Oliver S Eng
- Department of Surgery, University of California, Irvine, Orange, CA
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3
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Yang W, Yang T, Huang B, Chen Z, Liu H, Huang C. Berberine improved the microbiota in lung tissue of colon cancer and reversed the bronchial epithelial cell changes caused by cancer cells. Heliyon 2024; 10:e24405. [PMID: 38312643 PMCID: PMC10835176 DOI: 10.1016/j.heliyon.2024.e24405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 12/21/2023] [Accepted: 01/08/2024] [Indexed: 02/06/2024] Open
Abstract
Objective The lung is a common organ for colon cancer metastasis, and the objective of this experiment was to explore the protective effect of berberine on lung tissue or alveolar epithelial cells induced by colon cancer. Methods Thirty-six BALB/c nude mice were used to establish a xenograft model of colon cancer with the HT29 cell line and were treated with berberine and probiotics. Human bronchial epithelial BEAS-2B cells were induced by conditioned medium (CM) from the colon cancer cell lines HT29 and RKO and were treated with berberine. Lung tissues were collected to detect the changes in the microbiota using 16S rDNA sequencing and the expression of inflammatory cytokines. The expression of E-cadherin and N-cadherin in BEAS-2B cells was detected by cellular immunofluorescence. The changes in cell proliferation were detected by the CCK-8 assay. Western blotting was used to detect E-cadherin, N-cadherin, collagen I, fibronectin, PDGF-β, and RAD51 expression in BEAS-2B cells. Results The richness and evenness of the microbiota in the lung tissues of mice with colon cancer were significantly lower than those of the control group. Berberine significantly increased the abundances of Bacteroidetes, Bacteroidia, Bacteroidales, Lactobacillaceae, Lactobacillus and Acinetobacter in the lung tissue of mice with colon cancer, with reduced abundances of Actinobacteria, Bacillales, Staphylococcaceae and Staphylococcus. Berberine or probiotics significantly increased the alpha diversity of the lung microbiota. Compared with probiotics, berberine significantly enhanced the abundance of microbiota involved in the metabolism of lysosomes, flavone and flavonol biosynthesis, glycosaminoglycan degradation, and glycosphingolipid biosynthesis-ganglio. Berberine increased IL-6 and IL-10 and decreased IL-17 and IFN-γ expression in lung tissue (P > 0.05), but berberine-probiotics significantly decreased IL-17 and IFN-γ and increased IL-10 expression (P < 0.05). Colon cancer cells could not induce BEAS-2B proliferation but decreased the expression of the epithelial marker E-cadherin and altered the expression of extracellular matrix-related proteins (collagen I, fibronectin, and PDGF-β), which were reversed by berberine. Berberine increased RAD51 expression in BEAS-2B cells, which had been decreased by HT29 and RKO CM treatment. Conclusion Berberine can selectively regulate the abundance of some microbiomes of lung tissue in colon cancer, improve the inflammatory response in lung tissue, and antagonize the cancerous stimulation of colon cancer cells to lung tissue cells by regulating the bronchial epithelial cell phenotype, extracellular matrix remodelling and the expression of the repair gene RAD51.
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Affiliation(s)
- Wei Yang
- Pediatric Department, The Second Affiliated Hospital of Shenzhen University (People's Hospital of Shenzhen Baoan District), Shenzhen, 518100, China
| | - Ting Yang
- Gastroenterology Department, The Second Affiliated Hospital of Shenzhen University (People's Hospital of Shenzhen Baoan District), Shenzhen, 518100, China
| | - Bo Huang
- General Surgery Department, The Second Affiliated Hospital of Shenzhen University (People's Hospital of Shenzhen Baoan District), Shenzhen, 518100, China
| | - Zhanjun Chen
- Department of Cardiology, The Second Affiliated Hospital of Shenzhen University (People's Hospital of Shenzhen Baoan District), Shenzhen, 518100, China
| | - Haosheng Liu
- Department of Traditional Chinese Medicine, The Second Affiliated Hospital of Shenzhen University (People's Hospital of Shenzhen Baoan District), Shenzhen, 518100, China
| | - Chao Huang
- Department of Traditional Chinese Medicine, The Second Affiliated Hospital of Shenzhen University (People's Hospital of Shenzhen Baoan District), Shenzhen, 518100, China
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4
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Nakano S, Yamaji T, Shiraishi K, Hidaka A, Shimazu T, Kuchiba A, Saito M, Kunishima F, Nakaza R, Kohno T, Sawada N, Inoue M, Tsugane S, Iwasaki M. Smoking and risk of colorectal cancer according to KRAS and BRAF mutation status in a Japanese prospective Study. Carcinogenesis 2023; 44:476-484. [PMID: 37352389 DOI: 10.1093/carcin/bgad046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/21/2023] [Accepted: 06/22/2023] [Indexed: 06/25/2023] Open
Abstract
Although smoking is a major modifiable risk factor for many types of cancer, evidence for colorectal cancer is equivocal in Asian populations. Recent Western studies have proposed that the association between smoking and colorectal cancer is restricted to specific tumor molecular subtypes. However, no studies have evaluated the association according to tumor molecular subtypes in Asian populations. In a Japanese prospective population-based cohort study of 18 773 participants, we collected tumor tissues from incident colorectal cancer cases and evaluated KRAS (Kirsten rat sarcoma viral oncogene homolog) and BRAF (v-raf murine sarcoma viral oncogene homolog B) mutation status using target sequencing. Multivariable-adjusted Cox proportional hazard model was used to estimate the hazard ratios (HRs) and 95% confidence intervals (CIs) for associations of smoking with the risk of overall colorectal cancer and its subtypes defined by KRAS and BRAF mutation status. Among 339 cases, KRAS and BRAF mutations were identified in 164 (48.4%) and 16 (4.7%) cases, respectively. The multivariable-adjusted HR for ever smoking compared with never smoking was 1.24 [95% CI: 0.93-1.66], 1.75 [1.14-2.68], 0.87 [0.59-1.29], 1.24 [0.93-1.67] and 1.22 [0.38-3.93] for overall, KRAS wild-type, KRAS-mutated, BRAF wild-type and BRAF-mutated colorectal cancer, respectively. The statistically significant heterogeneity was indicated between KRAS mutation status (Pheterogeneity = 0.01) but not between BRAF mutation status. This study is the first to demonstrate that smokers have an approximately 2-fold higher risk of KRAS wild-type colorectal cancer than never smokers in an Asian population. Our findings support that smoking is a risk factor for colorectal cancer, especially for its subtype without KRAS mutations, in Asian populations.
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Affiliation(s)
- Shiori Nakano
- Division of Epidemiology, National Cancer Center Institute for Cancer Control, Tokyo, Japan
| | - Taiki Yamaji
- Division of Epidemiology, National Cancer Center Institute for Cancer Control, Tokyo, Japan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Akihisa Hidaka
- Division of Epidemiology, National Cancer Center Institute for Cancer Control, Tokyo, Japan
- Division of Gastroenterology and Hepatology, The Jikei University Daisan Hospital, Tokyo, Japan
| | - Taichi Shimazu
- Division of Behavioral Sciences, National Cancer Center Institute for Cancer Control, Tokyo, Japan
| | - Aya Kuchiba
- Graduate School of Health Innovation, Kanagawa University of Human Services, Kanagawa, Japan
- Division of Biostatistical Research, Institute for Cancer Control/Biostatistics Division, Center for Research Administration and Support, National Cancer Center, Tokyo, Japan
| | - Masahiro Saito
- Department of Diagnostic Pathology, Hiraka General Hospital, Yokote, Akita, Japan
| | - Fumihito Kunishima
- Department of Diagnostic Pathology, Okinawa Prefecture Chubu Hospital, Okinawa, Japan
| | - Ryouji Nakaza
- Department of clinical laboratory, Nakagami Hospital, Okinawa, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Norie Sawada
- Division of Cohort research, National Cancer Center Institute for Cancer Control, Tokyo, Japan
| | - Manami Inoue
- Division of Prevention, National Cancer Center Institute for Cancer Control, Tokyo, Japan
| | - Shoichiro Tsugane
- Division of Cohort research, National Cancer Center Institute for Cancer Control, Tokyo, Japan
- National Institute of Health and Nutrition, National Institutes of Biomedical Innovation, Health and Nutrition, Tokyo, Japan
| | - Motoki Iwasaki
- Division of Epidemiology, National Cancer Center Institute for Cancer Control, Tokyo, Japan
- Division of Cohort research, National Cancer Center Institute for Cancer Control, Tokyo, Japan
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Helderman NC, Van Der Werf-'t Lam AS, Morreau H, Boot A, Van Wezel T, Nielsen M. Molecular Profile of MSH6-Associated Colorectal Carcinomas Shows Distinct Features From Other Lynch Syndrome-Associated Colorectal Carcinomas. Gastroenterology 2023; 165:271-274.e2. [PMID: 36931573 DOI: 10.1053/j.gastro.2023.03.198] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 03/06/2023] [Accepted: 03/09/2023] [Indexed: 03/19/2023]
Affiliation(s)
- Noah C Helderman
- Department of Clinical Genetics Leiden University Medical Center Leiden, The Netherlands
| | | | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Tom Van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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Li DD, Tang YL, Wang X. Challenges and exploration for immunotherapies targeting cold colorectal cancer. World J Gastrointest Oncol 2023; 15:55-68. [PMID: 36684057 PMCID: PMC9850757 DOI: 10.4251/wjgo.v15.i1.55] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/28/2022] [Accepted: 12/07/2022] [Indexed: 01/10/2023] Open
Abstract
In recent years, immune checkpoint inhibitors (ICIs) have made significant breakthroughs in the treatment of various tumors, greatly improving clinical efficacy. As the fifth most common antitumor treatment strategy for patients with solid tumors after surgery, chemotherapy, radiotherapy and targeted therapy, the therapeutic response to ICIs largely depends on the number and spatial distribution of effector T cells that can effectively identify and kill tumor cells, features that are also important when distinguishing malignant tumors from “cold tumors” or “hot tumors”. At present, only a small proportion of colorectal cancer (CRC) patients with deficient mismatch repair (dMMR) or who are microsatellite instability-high (MSI-H) can benefit from ICI treatments because these patients have the characteristics of a “hot tumor”, with a high tumor mutational burden (TMB) and massive immune cell infiltration, making the tumor more easily recognized by the immune system. In contrast, a majority of CRC patients with proficient MMR (pMMR) or who are microsatellite stable (MSS) have a low TMB, lack immune cell infiltration, and have almost no response to immune monotherapy; thus, these tumors are “cold”. The greatest challenge today is how to improve the immunotherapy response of “cold tumor” patients. With the development of clinical research, immunotherapies combined with other treatment strategies (such as targeted therapy, chemotherapy, and radiotherapy) have now become potentially effective clinical strategies and research hotspots. Therefore, the question of how to promote the transformation of “cold tumors” to “hot tumors” and break through the bottleneck of immunotherapy for cold tumors in CRC patients urgently requires consideration. Only by developing an in-depth understanding of the immunotherapy mechanisms of cold CRCs can we screen out the immunotherapy-dominant groups and explore the most suitable treatment options for individuals to improve therapeutic efficacy.
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Affiliation(s)
- Dan-Dan Li
- Department of Abdominal Oncology/Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Yuan-Ling Tang
- Department of Abdominal Oncology/Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Xin Wang
- Department of Abdominal Oncology/Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
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Vickridge E, Faraco CCF, Tehrani PS, Ramdzan ZM, Djerir B, Rahimian H, Leduy L, Maréchal A, Gingras AC, Nepveu A. The DNA repair function of BCL11A suppresses senescence and promotes continued proliferation of triple-negative breast cancer cells. NAR Cancer 2022; 4:zcac028. [PMID: 36186110 PMCID: PMC9516615 DOI: 10.1093/narcan/zcac028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 09/08/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
We identified the BCL11A protein in a proximity-dependent biotinylation screen performed with the DNA glycosylase NTHL1. In vitro, DNA repair assays demonstrate that both BCL11A and a small recombinant BCL11A160-520 protein that is devoid of DNA binding and transcription regulatory domains can stimulate the enzymatic activities of two base excision repair enzymes: NTHL1 and DNA Pol β. Increased DNA repair efficiency, in particular of the base excision repair pathway, is essential for many cancer cells to proliferate in the presence of elevated reactive oxygen species (ROS) produced by cancer-associated metabolic changes. BCL11A is highly expressed in triple-negative breast cancers (TNBC) where its knockdown was reported to reduce clonogenicity and cause tumour regression. We show that BCL11A knockdown in TNBC cells delays repair of oxidative DNA damage, increases the number of oxidized bases and abasic sites in genomic DNA, slows down proliferation and induces cellular senescence. These phenotypes are rescued by ectopic expression of the short BCL11A160-520 protein. We further show that the BCL11A160-520 protein accelerates the repair of oxidative DNA damage and cooperates with RAS in cell transformation assays, thereby enabling cells to avoid senescence and continue to proliferate in the presence of high ROS levels.
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Affiliation(s)
- Elise Vickridge
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Québec H3A 1A3, Canada
| | - Camila C F Faraco
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Québec H3A 1A3, Canada
| | - Payman S Tehrani
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Zubaidah M Ramdzan
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Québec H3A 1A3, Canada
| | - Billel Djerir
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada
| | - Hedyeh Rahimian
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Québec H3A 1A3, Canada
| | - Lam Leduy
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Québec H3A 1A3, Canada
| | - Alexandre Maréchal
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Alain Nepveu
- To whom correspondence should be addressed. Tel: +1 514 398 5839; Fax: +1 514 398 6769;
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8
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Cui G, Wang C, Liu J, Shon K, Gu R, Chang C, Ren L, Wei F, Sun Z. Development of an exosome-related and immune microenvironment prognostic signature in colon adenocarcinoma. Front Genet 2022; 13:995644. [PMID: 36176299 PMCID: PMC9513147 DOI: 10.3389/fgene.2022.995644] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The correlation between exosomes and the tumor immune microenvironment has been proved to affect tumorigenesis and progression of colon adenocarcinoma (COAD). However, it remained unclear whether exosomes had an impact on the prognostic indications of COAD patients.Methods: Expression of exosome-related genes (ERGs) and clinical data were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. The ERGs associated with prognosis were identified and exosome-related prognostic signature was constructed. Patients in two risk groups were classified according to the risk score calculation formula: Risk score = 1.0132 * CCKBR + 0.2416 * HOXC6 + 0.7618 * POU4F1. The expression of three ERGs was investigated by qRT-PCR. After that, we developed a nomogram predicting the likelihood of survival and verified its predictive efficiency. The differences of tumor immune microenvironment, immune cell infiltration, immune checkpoint and sensitivity to drugs in two risk groups were analyzed.Results: A prognostic signature was established based on the three ERGs (CCKBR, HOXC6, and POU4F1) and patients with different risk group were distinguished. Survival analysis revealed the negative associated of risk score and prognosis, ROC curve analyses showed the accuracy of this signature. Three ERGs expression was investigated by qRT-PCR in three colorectal cancer cell lines. Moreover, risk score was positively correlated with tumor mutational burden (TMB), immune activities, microsatellite instability level, the expression of immune checkpoint genes. Meanwhile, the expression level of three ERGs and the risk score were markedly related with the sensitive response to chemotherapy.Conclusion: The novel signature composed of three ERGs with precise predictive capabilities can be used to predict prognosis and provide a promising therapeutic target for improving the efficacy of immunotherapy.
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Affiliation(s)
- Guoliang Cui
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Can Wang
- Department of Colorectal Surgery, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, China
| | - Jinhui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Kinyu Shon
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
- *Correspondence: Fei Wei, ; Zhiguang Sun,
| | - Renjun Gu
- School of Traditional Chinese Medicine and School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Cheng Chang
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Lang Ren
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Fei Wei
- Department of Physiology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
- *Correspondence: Fei Wei, ; Zhiguang Sun,
| | - Zhiguang Sun
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
- *Correspondence: Fei Wei, ; Zhiguang Sun,
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9
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Zhou ZX, Kunkel TA. Extrinsic proofreading. DNA Repair (Amst) 2022; 117:103369. [PMID: 35850061 PMCID: PMC9561950 DOI: 10.1016/j.dnarep.2022.103369] [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: 03/27/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 11/24/2022]
Abstract
The high fidelity of replication of the nuclear DNA genome in eukaryotes involves three processes. Correct rather than incorrect dNTPs are almost always incorporated by the three major replicases, DNA polymerases α, δ and ε. When an incorrect base is occasionally inserted, the latter Pols δ and ε also have a 3 ´ to 5 ´ exonuclease activity that can remove the mismatch to allow correct DNA synthesis to proceed. Lastly, rare mismatches that escape proofreading activity and are present in newly replicated DNA can be removed by DNA mismatch repair. In this review, we consider evidence supporting the hypothesis that the second mechanism, proofreading, can operate in two different ways. Primer terminal mismatches made by either Pol δ or Pol ε can be 'intrinsically' proofread. This mechanism occurs by direct transfer of a misinserted base made at the polymerase active site to the exonuclease active site that is located a short distance away. Intrinsic proofreading allows mismatch excision without intervening enzyme dissociation. Alternatively, considerable evidence suggests that mismatches made by any of the three replicases can also be proofread by 'extrinsic' proofreading by Pol δ. Extrinsic proofreading occurs when a mismatch made by any of the three replicases is initially abandoned, thereby allowing the exonuclease active site of Pol δ to bind directly to and remove the mismatch before replication continues. Here we review the evidence that extrinsic proofreading significantly enhances the fidelity of nuclear DNA replication, and we then briefly consider the implications of this process for evolution and disease.
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Affiliation(s)
- Zhi-Xiong Zhou
- Genome Integrity Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA
| | - Thomas A Kunkel
- Genome Integrity Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA.
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10
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Nunziato M, Di Maggio F, Pensabene M, Esposito MV, Starnone F, De Angelis C, Calabrese A, D’Aiuto M, Botti G, De Placido S, D’Argenio V, Salvatore F. Multi-gene panel testing increases germline predisposing mutations’ detection in a cohort of breast/ovarian cancer patients from Southern Italy. Front Med (Lausanne) 2022; 9:894358. [PMID: 36035419 PMCID: PMC9403188 DOI: 10.3389/fmed.2022.894358] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
Breast cancer is the most common neoplasia in females worldwide, about 10% being hereditary/familial and due to DNA variants in cancer-predisposing genes, such as the highly penetrant BRCA1/BRCA2 genes. However, their variants explain up to 25% of the suspected hereditary/familial cases. The availability of NGS methodologies has prompted research in this field. With the aim to improve the diagnostic sensitivity of molecular testing, a custom designed panel of 44 genes, including also non-coding regions and 5’ and 3’ UTR regions, was set up. Here, are reported the results obtained in a cohort of 64 patients, including also few males, from Southern Italy. All patients had a positive personal and/or familial history for breast and other cancers, but tested negative to routine BRCA analysis. After obtaining their written informed consent, a genomic DNA sample/patient was used to obtain an enriched DNA library, then analyzed by NGS. Sequencing data analysis allowed the identification of pathogenic variants in 12 of tested patients (19%). Interestingly, MUTYH was the most frequently altered gene, followed by RNASEL, ATM, MSH6, MRE11A, and PALB2 genes. The reported resultsreinforce the need for enlarged molecular testing beyond BRCA genes, at least in patients with a personal and familial history, strongly suggestive for a hereditary/familial form. This gives also a hint to pursue more specific precision oncology therapy.
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Affiliation(s)
- Marcella Nunziato
- CEINGE–Biotecnologie Avanzate, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Federica Di Maggio
- CEINGE–Biotecnologie Avanzate, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Matilde Pensabene
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Maria Valeria Esposito
- CEINGE–Biotecnologie Avanzate, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Flavio Starnone
- CEINGE–Biotecnologie Avanzate, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Carmine De Angelis
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
- Department of Oncology and Hematology, Regional Reference Center for Rare Tumors, Azienda Ospedaliera Universitaria (AOU) Federico II of Naples, Naples, Italy
| | - Alessandra Calabrese
- Division of Breast Surgery, Department of Breast Disease, National Cancer Institute, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) “Fondazione G. Pascale,”Naples, Italy
| | - Massimiliano D’Aiuto
- Clinica Villa Fiorita, Aversa, Italy
- Division of Breast Oncology, National Cancer Institute, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) “Fondazione G. Pascale,”Naples, Italy
| | - Gerardo Botti
- Scientific Directorate, National Cancer Institute, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) “Fondazione G. Pascale,”Naples, Italy
| | - Sabino De Placido
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
- Department of Oncology and Hematology, Regional Reference Center for Rare Tumors, Azienda Ospedaliera Universitaria (AOU) Federico II of Naples, Naples, Italy
| | - Valeria D’Argenio
- CEINGE–Biotecnologie Avanzate, Naples, Italy
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Open University, Rome, Italy
- *Correspondence: Valeria D’Argenio,
| | - Francesco Salvatore
- CEINGE–Biotecnologie Avanzate, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
- Francesco Salvatore,
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11
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Gniadecki R, Iyer A, Hennessey D, Khan L, O'Keefe S, Redmond D, Storek J, Durand C, Cohen-Tervaert JW, Osman M. Genomic instability in early systemic sclerosis. J Autoimmun 2022; 131:102847. [PMID: 35803104 DOI: 10.1016/j.jaut.2022.102847] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/03/2022] [Accepted: 06/05/2022] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Systemic sclerosis (SSc) is associated with secondary malignancies. Previous studies have suggested that mutated cancer proteins, such as RNA polymerase III, are autoantigens promoting an inflammatory response in SSc. However, it has never been previously investigated whether non-neoplastic tissue in SSc harbors mutations which may play a role in SSc pathogenesis. METHODS Skin biopsies were obtained from 8 sequential patients with a progressive form of early stage SSc (with severe skin and/or lung involvement). Areas of dermal fibrosis were microdissected and analyzed with deep, whole exome sequencing. Gene mutation patterns were compared to autologous buccal mucosal cells as a control. RESULTS SSc skin biopsies were hypermutated with an average of 58 mutations/106 base pairs. The mutational pattern in all samples exhibited a clock-like signature, which is ubiquitous in cancers and in senescent cells. Of the 1997 genes we identified which were mutated in at least two SSc patients, 39 genes represented cancer drivers (i.e. tumor suppressor genes or oncogenes) which are commonly found in gynecological, squamous and gastrointestinal cancer signatures. Of all the mutations, the most common mutated genes were important in regulating pathways related to epigenetic histone modifications, DNA repair and genome integrity. CONCLUSIONS Somatic hypermutation occurs in fibrotic skin in patients with early progressive SSc. Cancer driver gene mutations may potentially play a fundamental role in the pathogenesis of SSc.
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Affiliation(s)
| | | | | | - Lamia Khan
- Division of Rheumatology, University of Alberta, Edmonton, Canada
| | | | - Desiree Redmond
- Division of Rheumatology, University of Alberta, Edmonton, Canada
| | - Jan Storek
- Division of Hematology, University of Calgary, Canada
| | - Caylib Durand
- Division of Rheumatology, University of Calgary, Canada
| | | | - Mohammed Osman
- Division of Rheumatology, University of Alberta, Edmonton, Canada.
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12
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Vickridge E, Faraco CCF, Nepveu A. Base excision repair accessory factors in senescence avoidance and resistance to treatments. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2022; 5:703-720. [PMID: 36176767 PMCID: PMC9511810 DOI: 10.20517/cdr.2022.36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/20/2022] [Accepted: 05/26/2022] [Indexed: 06/16/2023]
Abstract
Cancer cells, in which the RAS and PI3K pathways are activated, produce high levels of reactive oxygen species (ROS), which cause oxidative DNA damage and ultimately cellular senescence. This process has been documented in tissue culture, mouse models, and human pre-cancerous lesions. In this context, cellular senescence functions as a tumour suppressor mechanism. Some rare cancer cells, however, manage to adapt to avoid senescence and continue to proliferate. One well-documented mode of adaptation involves increased production of antioxidants often associated with inactivation of the KEAP1 tumour suppressor gene and the resulting upregulation of the NRF2 transcription factor. In this review, we detail an alternative mode of adaptation to oxidative DNA damage induced by ROS: the increased activity of the base excision repair (BER) pathway, achieved through the enhanced expression of BER enzymes and DNA repair accessory factors. These proteins, exemplified here by the CUT domain proteins CUX1, CUX2, and SATB1, stimulate the activity of BER enzymes. The ensued accelerated repair of oxidative DNA damage enables cancer cells to avoid senescence despite high ROS levels. As a by-product of this adaptation, these cancer cells exhibit increased resistance to genotoxic treatments including ionizing radiation, temozolomide, and cisplatin. Moreover, considering the intrinsic error rate associated with DNA repair and translesion synthesis, the elevated number of oxidative DNA lesions caused by high ROS leads to the accumulation of mutations in the cancer cell population, thereby contributing to tumour heterogeneity and eventually to the acquisition of resistance, a major obstacle to clinical treatment.
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Affiliation(s)
- Elise Vickridge
- Goodman Cancer Institute, McGill University, 1160 Pine avenue West, Montreal, Québec H3A 1A3, Canada
- These authors contributed equally to this work
| | - Camila C. F. Faraco
- Goodman Cancer Institute, McGill University, 1160 Pine avenue West, Montreal, Québec H3A 1A3, Canada
- Departments of Biochemistry, McGill University, 1160 Pine avenue West, Montreal, Québec H3A 1A3, Canada
- These authors contributed equally to this work
| | - Alain Nepveu
- Goodman Cancer Institute, McGill University, 1160 Pine avenue West, Montreal, Québec H3A 1A3, Canada
- Departments of Biochemistry, McGill University, 1160 Pine avenue West, Montreal, Québec H3A 1A3, Canada
- Medicine, McGill University, 1160 Pine avenue West, Montreal, Québec H3A 1A3, Canada
- Oncology, McGill University, 1160 Pine avenue West, Montreal, Québec H3A 1A3, Canada
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13
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DI Felipe Ávila Alcantara D, Lima Júnior SF, DE Assumpção PP, Lamarão LM, DE Castro Sant'anna C, Moreira-Nunes CA, Burbano RR. Identification of Germline Mutations in Genes Involved in Classic FAP in Patients from Northern Brazil. CANCER DIAGNOSIS & PROGNOSIS 2022; 2:405-410. [PMID: 35530639 PMCID: PMC9066544 DOI: 10.21873/cdp.10123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Colorectal cancer is a common cancer worldwide, with 5-10% of cases being hereditary. Familial adenomatous polyposis syndrome (FAP) is caused by germline mutations in the APC gene or rarely in the MUTYH gene. PATIENTS AND METHODS This work did not identify germline mutations in the MUTYH, NTHL1, POLD1 and POLE genes in 15 individuals belonging to five families with classic FAP, who had the mutation in the APC gene confirmed in a previous study. Our results support mutations in the APC gene as the main genetic contribution of classical FAP with severe phenotype. In the family that had the most aggressive form of the disease, we performed an array-based Comparative Genomic Hybridization analysis and identified the germinal loss of an allele of the NOTCH2 and BMPR2 genes in the mother (proband) and daughter. In order to validate the involvement of these genes in the other four families of this study, we analyzed the DNA copy number variation in the peripheral blood of the 15 participants. RESULTS FAP is a syndrome with considerable genetic and phenotypic heterogeneity and this phenomenon may explain the presence of secondary genetic alterations, such as the allelic loss of NOTCH2 and BMPR2 genes, found only in one family in this study. The CNV analysis confirmed that only the two members of the FAP2 family (patient 02H and 02F) had a deletion of these two genes, as the aCGH methodology had found. The other study participants did not show allelic loss for these two genes. CONCLUSION Validation in a larger number of families could confirm the presence of these new genetic alterations in classic FAP and improve understanding of the different types of aggressiveness of the disease.
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Affiliation(s)
- Diego DI Felipe Ávila Alcantara
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém, Brazil
- Molecular Biology Laboratory, Ophir Loyola Hospital, Belém, Brazil
| | | | | | | | - Carla DE Castro Sant'anna
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém, Brazil
- Molecular Biology Laboratory, Ophir Loyola Hospital, Belém, Brazil
| | - Caroline Aquino Moreira-Nunes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Brazil
| | - Rommel Rodriguez Burbano
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém, Brazil
- Molecular Biology Laboratory, Ophir Loyola Hospital, Belém, Brazil
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Galbraith NJ, Wood C, Steele CW. Targeting Metastatic Colorectal Cancer with Immune Oncological Therapies. Cancers (Basel) 2021; 13:3566. [PMID: 34298779 PMCID: PMC8307556 DOI: 10.3390/cancers13143566] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/08/2021] [Accepted: 07/11/2021] [Indexed: 02/07/2023] Open
Abstract
Metastatic colorectal cancer carries poor prognosis, and current therapeutic regimes convey limited improvements in survival and high rates of detrimental side effects in patients that may not stand to benefit. Immunotherapy has revolutionised cancer treatment by restoring antitumoural mechanisms. However, the efficacy in metastatic colorectal cancer, is limited. A literature search was performed using Pubmed (Medline), Web of Knowledge, and Embase. Search terms included combinations of immunotherapy and metastatic colorectal cancer, primarily focusing on clinical trials in humans. Analysis of these studies included status of MMR/MSS, presence of combination strategies, and disease control rate and median overall survival. Evidence shows that immune checkpoint inhibitors, such as anti-PD1 and anti-PD-L1, show efficacy in less than 10% of patients with microsatellite stable, MMR proficient colorectal cancer. In the small subset of patients with microsatellite unstable, MMR deficient cancers, response rates were 40-50%. Combination strategies with immunotherapy are under investigation but have not yet restored antitumoural mechanisms to permit durable disease regression. Immunotherapy provides the potential to offer additional strategies to established chemotherapeutic regimes in metastatic colorectal cancer. Further research needs to establish which adjuncts to immune checkpoint inhibition can unpick resistance, and better predict which patients are likely to respond to individualised therapies to not just improve response rates but to temper unwarranted side effects.
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Affiliation(s)
- Norman J. Galbraith
- Academic Department of Surgery, University of Glasgow, Level 2 New Lister Building, Glasgow Royal Infirmary, 10-16 Alexandra Parade, Glasgow G31 2ER, UK; (C.W.); (C.W.S.)
| | - Colin Wood
- Academic Department of Surgery, University of Glasgow, Level 2 New Lister Building, Glasgow Royal Infirmary, 10-16 Alexandra Parade, Glasgow G31 2ER, UK; (C.W.); (C.W.S.)
| | - Colin W. Steele
- Academic Department of Surgery, University of Glasgow, Level 2 New Lister Building, Glasgow Royal Infirmary, 10-16 Alexandra Parade, Glasgow G31 2ER, UK; (C.W.); (C.W.S.)
- Institute of Cancer Sciences, Beatson Institute, Garscube Campus, Switchback Road, Bearsden G61 1BD, UK
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