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Yin L, Duan A, Zhang W, Li B, Zhao T, Xu X, Yang L, Nian B, Lu K, Chen S, Li Z, Liu J, Duan Q, Liu D, Chen H, Cui L, Chang Y, Kuang Y, Zhang D, Wang X, Zhang Y. Identification of whole-genome mutations and structural variations of bile cell-free DNA in cholangiocarcinoma. Genomics 2024; 116:110916. [PMID: 39147332 DOI: 10.1016/j.ygeno.2024.110916] [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: 05/01/2024] [Revised: 07/17/2024] [Accepted: 08/02/2024] [Indexed: 08/17/2024]
Abstract
Bile cell-free DNA (cfDNA) has been reported as a promising liquid biopsy tool for cholangiocarcinoma (CCA), however, the whole-genome mutation landscape and structural variants (SVs) of bile cfDNA remains unknown. Here we performed whole-genome sequencing on bile cfDNA and analyzed the correlation between mutation characteristics of bile cfDNA and clinical prognosis. TP53 and KRAS were the most frequently mutated genes, and the RTK/RAS, homologous recombination (HR), and HIPPO were top three pathways containing most gene mutations. Ten overlapping putative driver genes were found in bile cfDNA and tumor tissue. SVs such as chromothripsis and kataegis were identified. Moreover, the hazard ratio of HR pathway mutations were 15.77 (95% CI: 1.571-158.4), patients with HR pathway mutations in bile cfDNA exhibited poorer overall survival (P = 0.0049). Our study suggests that bile cfDNA contains genome mutations and SVs, and HR pathway mutations in bile cfDNA can predict poor outcomes of CCA patients.
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Affiliation(s)
- Lei Yin
- Second Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Anqi Duan
- Second Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Wei Zhang
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Bin Li
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Teng Zhao
- Second Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Xiaoya Xu
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Lixue Yang
- Second Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Baoning Nian
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Kai Lu
- Second Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Sheng Chen
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Zhikuan Li
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Jian Liu
- Second Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Qiaonan Duan
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Dongyu Liu
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Hao Chen
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China
| | - Longjiu Cui
- Second Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Yanxin Chang
- Second Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Yue Kuang
- Second Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Dadong Zhang
- Department of Clinical and Translational Medicine, 3D Medicines Inc., Shanghai, China.
| | - Xiang Wang
- Second Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University (Second Military Medical University), Shanghai, China.
| | - Yongjie Zhang
- Second Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University (Second Military Medical University), Shanghai, China.
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Xu Z, Zhao Y, Zhang Y, Liu X, Song L, Chen M, Xiao G, Ma X, Shi H. Prediction of immunotherapy response of bladder cancer with a pyroptosis-related signature indicating tumor immune microenvironment. Front Pharmacol 2024; 15:1387647. [PMID: 38983908 PMCID: PMC11231188 DOI: 10.3389/fphar.2024.1387647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 06/04/2024] [Indexed: 07/11/2024] Open
Abstract
Background Although prognostic models based on pyroptosis-related genes (PRGs) have been constructed in bladder cancer (BLCA), the comprehensive impact of these genes on tumor microenvironment (TME) and immunotherapeutic response has yet to be investigated. Methods Based on expression profiles of 52 PRGs, we utilized the unsupervised clustering algorithm to identify PRGs subtypes and ssGSEA to quantify immune cells and hallmark pathways. Moreover, we screened feature genes of distinct PRGs subtypes and validated the associations with immune infiltrations in tissue using the multiplex immunofluorescence. Univariate, LASSO, and multivariate Cox regression analyses were employed to construct the scoring scheme. Results Four PRGs clusters were identified, samples in cluster C1 were infiltrated with more immune cells than those in others, implying a favorable response to immunotherapy. While the cluster C2, which shows an extremely low level of most immune cells, do not respond to immunotherapy. CXCL9/CXCL10 and SPINK1/DHSR2 were identified as feature genes of cluster C1 and C2, and the specimen with high CXCL9/CXCL10 was characterized by more CD8 + T cells, macrophages and less Tregs. Based on differentially expressed genes (DEGs) among PRGs subtypes, a predictive model (termed as PRGs score) including five genes (CACNA1D, PTK2B, APOL6, CDK6, ANXA2) was built. Survival probability of patients with low-PRGs score was significantly higher than those with high-PRGs score. Moreover, patients with low-PRGs score were more likely to benefit from anti-PD1/PD-L1 regimens. Conclusion PRGs are closely associated with TME and oncogenic pathways. PRGs score is a promising indicator for predicting clinical outcome and immunotherapy response.
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Affiliation(s)
- Zihan Xu
- Institute for Breast Health Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Yujie Zhao
- Institute for Breast Health Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Yong Zhang
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiaowei Liu
- Institute for Breast Health Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Linlin Song
- Institute for Breast Health Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Meixu Chen
- Institute for Breast Health Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Guixiu Xiao
- Institute for Breast Health Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Xuelei Ma
- Department of Biotherapy, West China Hospital and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China
| | - Hubing Shi
- Institute for Breast Health Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
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3
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Li Y, Zhu R, Jin J, Guo H, Zhang J, He Z, Liang T, Guo L. Exploring the Role of Clustered Mutations in Carcinogenesis and Their Potential Clinical Implications in Cancer. Int J Mol Sci 2024; 25:6744. [PMID: 38928450 PMCID: PMC11203652 DOI: 10.3390/ijms25126744] [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: 04/23/2024] [Revised: 06/07/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Abnormal cell proliferation and growth leading to cancer primarily result from cumulative genome mutations. Single gene mutations alone do not fully explain cancer onset and progression; instead, clustered mutations-simultaneous occurrences of multiple mutations-are considered to be pivotal in cancer development and advancement. These mutations can affect different genes and pathways, resulting in cells undergoing malignant transformation with multiple functional abnormalities. Clustered mutations influence cancer growth rates, metastatic potential, and drug treatment sensitivity. This summary highlights the various types and characteristics of clustered mutations to understand their associations with carcinogenesis and discusses their potential clinical significance in cancer. As a unique mutation type, clustered mutations may involve genomic instability, DNA repair mechanism defects, and environmental exposures, potentially correlating with responsiveness to immunotherapy. Understanding the characteristics and underlying processes of clustered mutations enhances our comprehension of carcinogenesis and cancer progression, providing new diagnostic and therapeutic approaches for cancer.
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Affiliation(s)
- Yi Li
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Rui Zhu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Jiaming Jin
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
| | - Haochuan Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Jiaxi Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Zhiheng He
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
| | - Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Li Guo
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
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Caporale LH. Evolutionary feedback from the environment shapes mechanisms that generate genome variation. J Physiol 2024; 602:2601-2614. [PMID: 38194279 DOI: 10.1113/jp284411] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/14/2023] [Indexed: 01/10/2024] Open
Abstract
Darwin recognized that 'a grand and almost untrodden field of inquiry will be opened, on the causes and laws of variation.' However, because the Modern Synthesis assumes that the intrinsic probability of any individual mutation is unrelated to that mutation's potential adaptive value, attention has been focused on selection rather than on the intrinsic generation of variation. Yet many examples illustrate that the term 'random' mutation, as widely understood, is inaccurate. The probabilities of distinct classes of variation are neither evenly distributed across a genome nor invariant over time, nor unrelated to their potential adaptive value. Because selection acts upon variation, multiple biochemical mechanisms can and have evolved that increase the relative probability of adaptive mutations. In effect, the generation of heritable variation is in a feedback loop with selection, such that those mechanisms that tend to generate variants that survive recurring challenges in the environment would be captured by this survival and thus inherited and accumulated within lineages of genomes. Moreover, because genome variation is affected by a wide range of biochemical processes, genome variation can be regulated. Biochemical mechanisms that sense stress, from lack of nutrients to DNA damage, can increase the probability of specific classes of variation. A deeper understanding of evolution involves attention to the evolution of, and environmental influences upon, the intrinsic variation generated in gametes, in other words upon the biochemical mechanisms that generate variation across generations. These concepts have profound implications for the types of questions that can and should be asked, as omics databases become more comprehensive, detection methods more sensitive, and computation and experimental analyses even more high throughput and thus capable of revealing the intrinsic generation of variation in individual gametes. These concepts also have profound implications for evolutionary theory, which, upon reflection it will be argued, predicts that selection would increase the probability of generating adaptive mutations, in other words, predicts that the ability to evolve itself evolves.
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5
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Rosca OC, Vele OE. Microsatellite Instability, Mismatch Repair, and Tumor Mutation Burden in Lung Cancer. Surg Pathol Clin 2024; 17:295-305. [PMID: 38692812 DOI: 10.1016/j.path.2023.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Since US Food and Drug Administration approval of programmed death ligand 1 (PD-L1) as the first companion diagnostic for immune checkpoint inhibitors (ICIs) in non-small cell lung cancer, many patients have experienced increased overall survival. To improve selection of ICI responders versus nonresponders, microsatellite instability/mismatch repair deficiency (MSI/MMR) and tumor mutation burden (TMB) came into play. Clinical data show PD-L1, MSI/MMR, and TMB are independent predictive immunotherapy biomarkers. Harmonization of testing methodologies, optimization of assay design, and results analysis are ongoing. Future algorithms to determine immunotherapy eligibility might involve complementary use of current and novel biomarkers. Artificial intelligence could facilitate algorithm implementation to convert complex genetic data into recommendations for specific ICIs.
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Affiliation(s)
- Oana C Rosca
- Molecular Pathologist/Cytopathologist, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell; Department of Pathology and Laboratory Medicine, 2200 Northern Boulevard, Suite 104, Greenvale, NY 11548, USA.
| | - Oana E Vele
- Molecular Pathologist/Cytopathologist, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell; Department of Pathology and Laboratory Medicine, Lenox Hill Hospital, New York, NY 10075, USA
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6
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Gustav M, Reitsam NG, Carrero ZI, Loeffler CML, van Treeck M, Yuan T, West NP, Quirke P, Brinker TJ, Brenner H, Favre L, Märkl B, Stenzinger A, Brobeil A, Hoffmeister M, Calderaro J, Pujals A, Kather JN. Deep learning for dual detection of microsatellite instability and POLE mutations in colorectal cancer histopathology. NPJ Precis Oncol 2024; 8:115. [PMID: 38783059 PMCID: PMC11116442 DOI: 10.1038/s41698-024-00592-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/14/2024] [Indexed: 05/25/2024] Open
Abstract
In the spectrum of colorectal tumors, microsatellite-stable (MSS) tumors with DNA polymerase ε (POLE) mutations exhibit a hypermutated profile, holding the potential to respond to immunotherapy similarly to their microsatellite-instable (MSI) counterparts. Yet, due to their rarity and the associated testing costs, systematic screening for these mutations is not commonly pursued. Notably, the histopathological phenotype resulting from POLE mutations is theorized to resemble that of MSI. This resemblance not only could facilitate their detection by a transformer-based Deep Learning (DL) system trained on MSI pathology slides, but also indicates the possibility for MSS patients with POLE mutations to access enhanced treatment options, which might otherwise be overlooked. To harness this potential, we trained a Deep Learning classifier on a large dataset with the ground truth for microsatellite status and subsequently validated its capabilities for MSI and POLE detection across three external cohorts. Our model accurately identified MSI status in both the internal and external resection cohorts using pathology images alone. Notably, with a classification threshold of 0.5, over 75% of POLE driver mutant patients in the external resection cohorts were flagged as "positive" by a DL system trained on MSI status. In a clinical setting, deploying this DL model as a preliminary screening tool could facilitate the efficient identification of clinically relevant MSI and POLE mutations in colorectal tumors, in one go.
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Affiliation(s)
- Marco Gustav
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | | | - Zunamys I Carrero
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Chiara M L Loeffler
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany
- Department of Medicine I, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Marko van Treeck
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Tanwei Yuan
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nicholas P West
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Philip Quirke
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Titus J Brinker
- Digital Biomarkers for Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Loëtitia Favre
- Université Paris Est Créteil, INSERM, IMRB, Créteil, France
- Assistance Publique-Hôpitaux de Paris, Henri Mondor-Albert Chenevier University Hospital, Department of Pathology, Créteil, France
- INSERM, U955, Team Oncogenèse des lymphomes et tumeurs de la Neurofibromatose 1, Créteil, France
| | - Bruno Märkl
- Pathology, Faculty of Medicine, University of Augsburg, Augsburg, Germany
| | | | - Alexander Brobeil
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Tissue Bank of the National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Julien Calderaro
- Université Paris Est Créteil, INSERM, IMRB, Créteil, France
- Assistance Publique-Hôpitaux de Paris, Henri Mondor-Albert Chenevier University Hospital, Department of Pathology, Créteil, France
- INSERM, U955, Team Oncogenèse des lymphomes et tumeurs de la Neurofibromatose 1, Créteil, France
| | - Anaïs Pujals
- Université Paris Est Créteil, INSERM, IMRB, Créteil, France
- Assistance Publique-Hôpitaux de Paris, Henri Mondor-Albert Chenevier University Hospital, Department of Pathology, Créteil, France
- INSERM, U955, Team Oncogenèse des lymphomes et tumeurs de la Neurofibromatose 1, Créteil, France
| | - Jakob Nikolas Kather
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany.
- Department of Medicine I, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom.
- Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, Heidelberg, Germany.
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Shuaibi A, Chitra U, Raphael BJ. A latent variable model for evaluating mutual exclusivity and co-occurrence between driver mutations in cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590995. [PMID: 38712136 PMCID: PMC11071465 DOI: 10.1101/2024.04.24.590995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
A key challenge in cancer genomics is understanding the functional relationships and dependencies between combinations of somatic mutations that drive cancer development. Such driver mutations frequently exhibit patterns of mutual exclusivity or co-occurrence across tumors, and many methods have been developed to identify such dependency patterns from bulk DNA sequencing data of a cohort of patients. However, while mutual exclusivity and co-occurrence are described as properties of driver mutations, existing methods do not explicitly disentangle functional, driver mutations from neutral, passenger mutations. In particular, nearly all existing methods evaluate mutual exclusivity or co-occurrence at the gene level, marking a gene as mutated if any mutation - driver or passenger - is present. Since some genes have a large number of passenger mutations, existing methods either restrict their analyses to a small subset of suspected driver genes - limiting their ability to identify novel dependencies - or make spurious inferences of mutual exclusivity and co-occurrence involving genes with many passenger mutations. We introduce DIALECT, an algorithm to identify dependencies between pairs of driver mutations from somatic mutation counts. We derive a latent variable mixture model for drivers and passengers that combines existing probabilistic models of passenger mutation rates with a latent variable describing the unknown status of a mutation as a driver or passenger. We use an expectation maximization (EM) algorithm to estimate the parameters of our model, including the rates of mutually exclusivity and co-occurrence between drivers. We demonstrate that DIALECT more accurately infers mutual exclusivity and co-occurrence between driver mutations compared to existing methods on both simulated mutation data and somatic mutation data from 5 cancer types in The Cancer Genome Atlas (TCGA).
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8
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Wang S, El Jurdi N, Thyagarajan B, Prizment A, Blaes AH. Accelerated Aging in Cancer Survivors: Cellular Senescence, Frailty, and Possible Opportunities for Interventions. Int J Mol Sci 2024; 25:3319. [PMID: 38542292 PMCID: PMC10970400 DOI: 10.3390/ijms25063319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/08/2024] [Accepted: 03/12/2024] [Indexed: 06/02/2024] Open
Abstract
The population of cancer survivors has markedly increased due to the rapid improvements in cancer treatment. However, cancer survivors experience accelerated aging, which leads to chronic diseases and other age-related conditions, such as frailty. Those conditions may persist years after cancer diagnosis and treatment. Cellular senescence, a hallmark of aging, is one of the mechanisms that contribute to accelerated aging in cancer survivors. Several aging measures, including measures based on clinical markers and biomarkers, have been proposed to estimate the aging process, and some of them have shown associations with mortality and frailty in cancer survivors. Several anti-aging interventions, including lifestyle changes and anti-aging drugs, have been proposed. Future research, particularly in large-scale studies, is needed to determine the efficiency of these aging measures and anti-aging interventions before considering their application in clinics. This review focuses on the mechanisms of cellular senescence and accelerated aging in cancer survivors, assessment of the aging process using clinical markers and biomarkers, and the high prevalence of frailty in that population, as well as possible opportunities for anti-aging interventions. A deeper understanding of aging measures and anti-aging interventions in cancer survivors will contribute to the development of effective strategies to mitigate accelerated aging in cancer survivors and improve their quality of life.
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Affiliation(s)
- Shuo Wang
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Najla El Jurdi
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN 55455, USA
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Anna Prizment
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Anne H. Blaes
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN 55455, USA
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9
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Gonzalez-Cárdenas M, Treviño V. The Impact of Mutational Hotspots on Cancer Survival. Cancers (Basel) 2024; 16:1072. [PMID: 38473427 DOI: 10.3390/cancers16051072] [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: 01/07/2024] [Revised: 02/11/2024] [Accepted: 02/15/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Cofactors, biomarkers, and the mutational status of genes such as TP53, EGFR, IDH1/2, or PIK3CA have been used for patient stratification. However, many genes exhibit recurrent mutational positions known as hotspots, specifically linked to varying degrees of survival outcomes. Nevertheless, few hotspots have been analyzed (e.g., TP53 and EGFR). Thus, many other genes and hotspots remain unexplored. METHODS We systematically screened over 1400 hotspots across 33 TCGA cancer types. We compared the patients carrying a hotspot against (i) all cases, (ii) gene-mutated cases, (iii) other mutated hotspots, or (iv) specific hotspots. Due to the limited number of samples in hotspots and the inherent group imbalance, besides Cox models and the log-rank test, we employed VALORATE to estimate their association with survival precisely. RESULTS We screened 1469 hotspots in 6451 comparisons, where 314 were associated with survival. Many are discussed and linked to the current literature. Our findings demonstrate associations between known hotspots and survival while also revealing more potential hotspots. To enhance accessibility and promote further investigation, all the Kaplan-Meier curves, the log-rank tests, Cox statistics, and VALORATE-estimated null distributions are accessible on our website. CONCLUSIONS Our analysis revealed both known and putatively novel hotspots associated with survival, which can be used as biomarkers. Our web resource is a valuable tool for cancer research.
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Affiliation(s)
- Melissa Gonzalez-Cárdenas
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Ave. Morones Prieto 3000, Monterrey 64710, Nuevo León, Mexico
- Tecnologico de Monterrey, The Institute for Obesity Research, Eugenio Garza Sada Avenue 2501, Monterrey 64849, Nuevo León, Mexico
| | - Víctor Treviño
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Ave. Morones Prieto 3000, Monterrey 64710, Nuevo León, Mexico
- Tecnologico de Monterrey, The Institute for Obesity Research, Eugenio Garza Sada Avenue 2501, Monterrey 64849, Nuevo León, Mexico
- Tecnologico de Monterrey, oriGen Project, Eugenio Garza Sada Avenue 2501, Monterrey 64849, Nuevo León, Mexico
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10
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Khan SU, Fatima K, Aisha S, Malik F. Unveiling the mechanisms and challenges of cancer drug resistance. Cell Commun Signal 2024; 22:109. [PMID: 38347575 PMCID: PMC10860306 DOI: 10.1186/s12964-023-01302-1] [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: 07/01/2023] [Accepted: 08/30/2023] [Indexed: 02/15/2024] Open
Abstract
Cancer treatment faces many hurdles and resistance is one among them. Anti-cancer treatment strategies are evolving due to innate and acquired resistance capacity, governed by genetic, epigenetic, proteomic, metabolic, or microenvironmental cues that ultimately enable selected cancer cells to survive and progress under unfavorable conditions. Although the mechanism of drug resistance is being widely studied to generate new target-based drugs with better potency than existing ones. However, due to the broader flexibility in acquired drug resistance, advanced therapeutic options with better efficacy need to be explored. Combination therapy is an alternative with a better success rate though the risk of amplified side effects is commonplace. Moreover, recent groundbreaking precision immune therapy is one of the ways to overcome drug resistance and has revolutionized anticancer therapy to a greater extent with the only limitation of being individual-specific and needs further attention. This review will focus on the challenges and strategies opted by cancer cells to withstand the current therapies at the molecular level and also highlights the emerging therapeutic options -like immunological, and stem cell-based options that may prove to have better potential to challenge the existing problem of therapy resistance. Video Abstract.
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Affiliation(s)
- Sameer Ullah Khan
- Division of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Holcombe Blvd, Houston, TX, 77030, USA.
- Division of Cancer Pharmacology, CSIR-Indian Institute of Integrative Medicine, Srinagar-190005, Jammu and Kashmir, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India.
| | - Kaneez Fatima
- Division of Cancer Pharmacology, CSIR-Indian Institute of Integrative Medicine, Srinagar-190005, Jammu and Kashmir, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Shariqa Aisha
- Division of Cancer Pharmacology, CSIR-Indian Institute of Integrative Medicine, Srinagar-190005, Jammu and Kashmir, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Fayaz Malik
- Division of Cancer Pharmacology, CSIR-Indian Institute of Integrative Medicine, Srinagar-190005, Jammu and Kashmir, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India.
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11
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He Q, Sun C, Pan Y. Whole‑exome sequencing reveals Lewis lung carcinoma is a hypermutated Kras/Nras-mutant cancer with extensive regional mutation clusters in its genome. Sci Rep 2024; 14:100. [PMID: 38167599 PMCID: PMC10762126 DOI: 10.1038/s41598-023-50703-2] [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: 02/08/2023] [Accepted: 12/23/2023] [Indexed: 01/05/2024] Open
Abstract
Lewis lung carcinoma (LLC), as a widely used preclinical cancer model, has still not been genetically and genomically characterized. Here, we performed a whole-exome sequencing analysis on the LLC cell line to elucidate its molecular characteristics and etiologies. Our data showed that LLC originated from a male mouse belonging to C57BL/6L (a transitional strain between C57BL/6J and C57BL/6N) and contains substantial somatic SNV and InDel mutations (> 20,000). Extensive regional mutation clusters are present in its genome, which were caused mainly by the mutational processes underlying the SBS1, SBS5, SBS15, SBS17a, and SBS21 signatures during frequent structural rearrangements. Thirty three deleterious mutations are present in 30 cancer genes including Kras, Nras, Trp53, Dcc, and Cacna1d. Cdkn2a and Cdkn2b are biallelically deleted from the genome. Five pathways (RTK/RAS, p53, cell cycle, TGFB, and Hippo) are oncogenically deregulated or affected. The major mutational processes in LLC include chromosomal instability, exposure to metabolic mutagens, spontaneous 5-methylcytosine deamination, defective DNA mismatch repair, and reactive oxygen species. Our data also suggest that LLC is a lung cancer similar to human lung adenocarcinoma. This study lays a molecular basis for the more targeted application of LLC in preclinical research.
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Affiliation(s)
- Quan He
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Cuirong Sun
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
| | - Yuanjiang Pan
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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12
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Wu Z, Huang D, Wang J, Zhao Y, Sun W, Shen X. Engineering Heterogeneous Tumor Models for Biomedical Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2304160. [PMID: 37946674 PMCID: PMC10767453 DOI: 10.1002/advs.202304160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/16/2023] [Indexed: 11/12/2023]
Abstract
Tumor tissue engineering holds great promise for replicating the physiological and behavioral characteristics of tumors in vitro. Advances in this field have led to new opportunities for studying the tumor microenvironment and exploring potential anti-cancer therapeutics. However, the main obstacle to the widespread adoption of tumor models is the poor understanding and insufficient reconstruction of tumor heterogeneity. In this review, the current progress of engineering heterogeneous tumor models is discussed. First, the major components of tumor heterogeneity are summarized, which encompasses various signaling pathways, cell proliferations, and spatial configurations. Then, contemporary approaches are elucidated in tumor engineering that are guided by fundamental principles of tumor biology, and the potential of a bottom-up approach in tumor engineering is highlighted. Additionally, the characterization approaches and biomedical applications of tumor models are discussed, emphasizing the significant role of engineered tumor models in scientific research and clinical trials. Lastly, the challenges of heterogeneous tumor models in promoting oncology research and tumor therapy are described and key directions for future research are provided.
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Affiliation(s)
- Zhuhao Wu
- Department of Rheumatology and ImmunologyNanjing Drum Tower HospitalSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjing210096China
| | - Danqing Huang
- Department of Rheumatology and ImmunologyNanjing Drum Tower HospitalSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjing210096China
| | - Jinglin Wang
- Department of Rheumatology and ImmunologyNanjing Drum Tower HospitalSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjing210096China
| | - Yuanjin Zhao
- Department of Rheumatology and ImmunologyNanjing Drum Tower HospitalSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjing210096China
- Department of Gastrointestinal SurgeryThe First Affiliated HospitalWenzhou Medical UniversityWenzhou325035China
| | - Weijian Sun
- Department of Gastrointestinal SurgeryThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityWenzhou325027China
| | - Xian Shen
- Department of Rheumatology and ImmunologyNanjing Drum Tower HospitalSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjing210096China
- Department of Gastrointestinal SurgeryThe First Affiliated HospitalWenzhou Medical UniversityWenzhou325035China
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13
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Gomez F, Fisk B, McMichael JF, Mosior M, Foltz JA, Skidmore ZL, Duncavage EJ, Miller CA, Abel H, Li YS, Russler-Germain DA, Krysiak K, Watkins MP, Ramirez CA, Schmidt A, Martins Rodrigues F, Trani L, Khanna A, Wagner JA, Fulton RS, Fronick CC, O'Laughlin MD, Schappe T, Cashen AF, Mehta-Shah N, Kahl BS, Walker J, Bartlett NL, Griffith M, Fehniger TA, Griffith OL. Ultra-Deep Sequencing Reveals the Mutational Landscape of Classical Hodgkin Lymphoma. CANCER RESEARCH COMMUNICATIONS 2023; 3:2312-2330. [PMID: 37910143 PMCID: PMC10648575 DOI: 10.1158/2767-9764.crc-23-0140] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/27/2023] [Accepted: 10/24/2023] [Indexed: 11/03/2023]
Abstract
The malignant Hodgkin and Reed Sternberg (HRS) cells of classical Hodgkin lymphoma (cHL) are scarce in affected lymph nodes, creating a challenge to detect driver somatic mutations. As an alternative to cell purification techniques, we hypothesized that ultra-deep exome sequencing would allow genomic study of HRS cells, thereby streamlining analysis and avoiding technical pitfalls. To test this, 31 cHL tumor/normal pairs were exome sequenced to approximately 1,000× median depth of coverage. An orthogonal error-corrected sequencing approach verified >95% of the discovered mutations. We identified mutations in genes novel to cHL including: CDH5 and PCDH7, novel stop gain mutations in IL4R, and a novel pattern of recurrent mutations in pathways regulating Hippo signaling. As a further application of our exome sequencing, we attempted to identify expressed somatic single-nucleotide variants (SNV) in single-nuclei RNA sequencing (snRNA-seq) data generated from a patient in our cohort. Our snRNA analysis identified a clear cluster of cells containing a somatic SNV identified in our deep exome data. This cluster has differentially expressed genes that are consistent with genes known to be dysregulated in HRS cells (e.g., PIM1 and PIM3). The cluster also contains cells with an expanded B-cell clonotype further supporting a malignant phenotype. This study provides proof-of-principle that ultra-deep exome sequencing can be utilized to identify recurrent mutations in HRS cells and demonstrates the feasibility of snRNA-seq in the context of cHL. These studies provide the foundation for the further analysis of genomic variants in large cohorts of patients with cHL. SIGNIFICANCE Our data demonstrate the utility of ultra-deep exome sequencing in uncovering somatic variants in Hodgkin lymphoma, creating new opportunities to define the genes that are recurrently mutated in this disease. We also show for the first time the successful application of snRNA-seq in Hodgkin lymphoma and describe the expression profile of a putative cluster of HRS cells in a single patient.
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Affiliation(s)
- Felicia Gomez
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
| | - Bryan Fisk
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Joshua F. McMichael
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Matthew Mosior
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Jennifer A. Foltz
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Zachary L. Skidmore
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Eric J. Duncavage
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - Christopher A. Miller
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Haley Abel
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Yi-Shan Li
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - David A. Russler-Germain
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Kilannin Krysiak
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - Marcus P. Watkins
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Cody A. Ramirez
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Alina Schmidt
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Fernanda Martins Rodrigues
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Lee Trani
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Ajay Khanna
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Julia A. Wagner
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Robert S. Fulton
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Catrina C. Fronick
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Michelle D. O'Laughlin
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Timothy Schappe
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Amanda F. Cashen
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Neha Mehta-Shah
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Brad S. Kahl
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Jason Walker
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Nancy L. Bartlett
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Malachi Griffith
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri
| | - Todd A. Fehniger
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
| | - Obi L. Griffith
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri
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14
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Hudson KM, Klimczak LJ, Sterling JF, Burkholder AB, Kazanov M, Saini N, Mieczkowski PA, Gordenin DA. Glycidamide-induced hypermutation in yeast single-stranded DNA reveals a ubiquitous clock-like mutational motif in humans. Nucleic Acids Res 2023; 51:9075-9100. [PMID: 37471042 PMCID: PMC10516655 DOI: 10.1093/nar/gkad611] [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: 03/19/2023] [Revised: 06/28/2023] [Accepted: 07/10/2023] [Indexed: 07/21/2023] Open
Abstract
Mutagens often prefer specific nucleotides or oligonucleotide motifs that can be revealed by studying the hypermutation spectra in single-stranded (ss) DNA. We utilized a yeast model to explore mutagenesis by glycidamide, a simple epoxide formed endogenously in humans from the environmental toxicant acrylamide. Glycidamide caused ssDNA hypermutation in yeast predominantly in cytosines and adenines. The most frequent mutations in adenines occurred in the nAt→nGt trinucleotide motif. Base substitutions A→G in this motif relied on Rev1 translesion polymerase activity. Inactivating Rev1 did not alter the nAt trinucleotide preference, suggesting it may be an intrinsic specificity of the chemical reaction between glycidamide and adenine in the ssDNA. We found this mutational motif enriched in published sequencing data from glycidamide-treated mouse cells and ubiquitous in human cancers. In cancers, this motif was positively correlated with the single base substitution (SBS) smoking-associated SBS4 signature, with the clock-like signatures SBS1, SBS5, and was strongly correlated with smoking history and with age of tumor donors. Clock-like feature of the motif was also revealed in cells of human skin and brain. Given its pervasiveness, we propose that this mutational motif reflects mutagenic lesions to adenines in ssDNA from a potentially broad range of endogenous and exogenous agents.
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Affiliation(s)
- Kathleen M Hudson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC 27709, USA
| | - Leszek J Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC 27709, USA
| | - Joan F Sterling
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC 27709, USA
| | - Adam B Burkholder
- Office of Environmental Science Cyberinfrastructure, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC 27709, USA
| | - Marat D Kazanov
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, 34956, Turkey
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Natalie Saini
- Department of Biochemistry & Molecular Biology, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Piotr A Mieczkowski
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Dmitry A Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC 27709, USA
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15
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Pužar Dominkuš P, Hudler P. Mutational Signatures in Gastric Cancer and Their Clinical Implications. Cancers (Basel) 2023; 15:3788. [PMID: 37568604 PMCID: PMC10416847 DOI: 10.3390/cancers15153788] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/23/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
Gastric cancer is characterised by high inter- and intratumour heterogeneity. The majority of patients are older than 65 years and the global burden of this disease is increasing due to the aging of the population. The disease is usually diagnosed at advanced stages, which is a consequence of nonspecific symptoms. Few improvements have been made at the level of noninvasive molecular diagnosis of sporadic gastric cancer, and therefore the mortality rate remains high. A new field of mutational signatures has emerged in the past decade with advances in the genome sequencing technology. These distinct mutational patterns in the genome, caused by exogenous and endogenous mutational processes, can be associated with tumour aetiology and disease progression, and could provide novel perception on the treatment possibilities. This review assesses the mutational signatures found in gastric cancer and summarises their potential for use in clinical setting as diagnostic or prognostic biomarkers. Associated treatment options and biomarkers already implemented in clinical use are discussed, together with those that are still being explored or are in clinical studies.
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Affiliation(s)
- Pia Pužar Dominkuš
- Pharmacogenetics Laboratory, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia;
- Medical Centre for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Petra Hudler
- Medical Centre for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
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16
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Vijayraghavan S, Saini N. Aldehyde-Associated Mutagenesis─Current State of Knowledge. Chem Res Toxicol 2023. [PMID: 37363863 DOI: 10.1021/acs.chemrestox.3c00045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Aldehydes are widespread in the environment, with multiple sources such as food and beverages, industrial effluents, cigarette smoke, and additives. The toxic effects of exposure to several aldehydes have been observed in numerous studies. At the molecular level, aldehydes damage DNA, cross-link DNA and proteins, lead to lipid peroxidation, and are associated with increased disease risk including cancer. People genetically predisposed to aldehyde sensitivity exhibit severe health outcomes. In various diseases such as Fanconi's anemia and Cockayne syndrome, loss of aldehyde-metabolizing pathways in conjunction with defects in DNA repair leads to widespread DNA damage. Importantly, aldehyde-associated mutagenicity is being explored in a growing number of studies, which could offer key insights into how they potentially contribute to tumorigenesis. Here, we review the genotoxic effects of various aldehydes, focusing particularly on the DNA adducts underlying the mutagenicity of environmentally derived aldehydes. We summarize the chemical structures of the aldehydes and their predominant DNA adducts, discuss various methodologies, in vitro and in vivo, commonly used in measuring aldehyde-associated mutagenesis, and highlight some recent studies looking at aldehyde-associated mutation signatures and spectra. We conclude the Review with a discussion on the challenges and future perspectives of investigating aldehyde-associated mutagenesis.
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Affiliation(s)
- Sriram Vijayraghavan
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Natalie Saini
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, United States
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17
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Granadillo Rodríguez M, Wong L, Chelico L. Similar deamination activities but different phenotypic outcomes induced by APOBEC3 enzymes in breast epithelial cells. Front Genome Ed 2023; 5:1196697. [PMID: 37324648 PMCID: PMC10267419 DOI: 10.3389/fgeed.2023.1196697] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Abstract
APOBEC3 (A3) enzymes deaminate cytosine to uracil in viral single-stranded DNA as a mutagenic barrier for some viruses. A3-induced deaminations can also occur in human genomes resulting in an endogenous source of somatic mutations in multiple cancers. However, the roles of each A3 are unclear since few studies have assessed these enzymes in parallel. Thus, we developed stable cell lines expressing A3A, A3B, or A3H Hap I using non-tumorigenic MCF10A and tumorigenic MCF7 breast epithelial cells to assess their mutagenic potential and cancer phenotypes in breast cells. The activity of these enzymes was characterized by γH2AX foci formation and in vitro deamination. Cell migration and soft agar colony formation assays assessed cellular transformation potential. We found that all three A3 enzymes had similar γH2AX foci formation, despite different deamination activities in vitro. Notably, in nuclear lysates, the in vitro deaminase activity of A3A, A3B, and A3H did not require digestion of cellular RNA, in contrast to that of A3B and A3H in whole-cell lysates. Their similar activities in cells, nonetheless, resulted in distinct phenotypes where A3A decreased colony formation in soft agar, A3B decreased colony formation in soft agar after hydroxyurea treatment, and A3H Hap I promoted cell migration. Overall, we show that in vitro deamination data do not always reflect cell DNA damage, all three A3s induce DNA damage, and the impact of each is different.
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18
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Naumann JA, Argyris PP, Carpenter MA, Gupta HB, Chen Y, Temiz NA, Zhou Y, Durfee C, Proehl J, Koniar BL, Conticello SG, Largaespada DA, Brown WL, Aihara H, Vogel RI, Harris RS. DNA Deamination Is Required for Human APOBEC3A-Driven Hepatocellular Carcinoma In Vivo. Int J Mol Sci 2023; 24:9305. [PMID: 37298259 PMCID: PMC10253583 DOI: 10.3390/ijms24119305] [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: 04/28/2023] [Revised: 05/20/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
Although the APOBEC3 family of single-stranded DNA cytosine deaminases is well-known for its antiviral factors, these enzymes are rapidly gaining attention as prominent sources of mutation in cancer. APOBEC3's signature single-base substitutions, C-to-T and C-to-G in TCA and TCT motifs, are evident in over 70% of human malignancies and dominate the mutational landscape of numerous individual tumors. Recent murine studies have established cause-and-effect relationships, with both human APOBEC3A and APOBEC3B proving capable of promoting tumor formation in vivo. Here, we investigate the molecular mechanism of APOBEC3A-driven tumor development using the murine Fah liver complementation and regeneration system. First, we show that APOBEC3A alone is capable of driving tumor development (without Tp53 knockdown as utilized in prior studies). Second, we show that the catalytic glutamic acid residue of APOBEC3A (E72) is required for tumor formation. Third, we show that an APOBEC3A separation-of-function mutant with compromised DNA deamination activity and wildtype RNA-editing activity is defective in promoting tumor formation. Collectively, these results demonstrate that APOBEC3A is a "master driver" that fuels tumor formation through a DNA deamination-dependent mechanism.
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Affiliation(s)
- Jordan A. Naumann
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (J.A.N.); (P.P.A.); (W.L.B.); (H.A.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (N.A.T.); (B.L.K.); (D.A.L.); (R.I.V.)
| | - Prokopios P. Argyris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (J.A.N.); (P.P.A.); (W.L.B.); (H.A.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (N.A.T.); (B.L.K.); (D.A.L.); (R.I.V.)
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Division of Oral and Maxillofacial Pathology, College of Dentistry, Ohio State University, Columbus, OH 43210, USA
| | - Michael A. Carpenter
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (M.A.C.); (H.B.G.); (Y.C.); (Y.Z.); (C.D.); (J.P.)
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Harshita B. Gupta
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (M.A.C.); (H.B.G.); (Y.C.); (Y.Z.); (C.D.); (J.P.)
| | - Yanjun Chen
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (M.A.C.); (H.B.G.); (Y.C.); (Y.Z.); (C.D.); (J.P.)
| | - Nuri A. Temiz
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (N.A.T.); (B.L.K.); (D.A.L.); (R.I.V.)
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yufan Zhou
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (M.A.C.); (H.B.G.); (Y.C.); (Y.Z.); (C.D.); (J.P.)
| | - Cameron Durfee
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (M.A.C.); (H.B.G.); (Y.C.); (Y.Z.); (C.D.); (J.P.)
| | - Joshua Proehl
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (M.A.C.); (H.B.G.); (Y.C.); (Y.Z.); (C.D.); (J.P.)
| | - Brenda L. Koniar
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (N.A.T.); (B.L.K.); (D.A.L.); (R.I.V.)
| | - Silvestro G. Conticello
- Core Research Laboratory, ISPRO, 50139 Florence, Italy;
- Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy
| | - David A. Largaespada
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (N.A.T.); (B.L.K.); (D.A.L.); (R.I.V.)
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - William L. Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (J.A.N.); (P.P.A.); (W.L.B.); (H.A.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (N.A.T.); (B.L.K.); (D.A.L.); (R.I.V.)
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (J.A.N.); (P.P.A.); (W.L.B.); (H.A.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (N.A.T.); (B.L.K.); (D.A.L.); (R.I.V.)
| | - Rachel I. Vogel
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; (N.A.T.); (B.L.K.); (D.A.L.); (R.I.V.)
- Department of Obstetrics, Gynecology, and Women’s Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (M.A.C.); (H.B.G.); (Y.C.); (Y.Z.); (C.D.); (J.P.)
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
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Britan-Rosich Y, Ma J, Kotler E, Hassan F, Botvinnik A, Smith Y, Moshel O, Nasereddin A, Sharma G, Pikarsky E, Ross S, Kotler M. APOBEC3G protects the genome of human cultured cells and mice from radiation-induced damage. FEBS J 2023; 290:1822-1839. [PMID: 36325681 PMCID: PMC10079569 DOI: 10.1111/febs.16673] [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: 03/24/2022] [Revised: 09/14/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022]
Abstract
Cytosine deaminases AID/APOBEC proteins act as potent nucleic acid editors, playing important roles in innate and adaptive immunity. However, the mutagenic effects of some of these proteins compromise genomic integrity and may promote tumorigenesis. Here, we demonstrate that human APOBEC3G (A3G), in addition to its role in innate immunity, promotes repair of double-strand breaks (DSBs) in vitro and in vivo. Transgenic mice expressing A3G successfully survived lethal irradiation, whereas wild-type controls quickly succumbed to radiation syndrome. Mass spectrometric analyses identified the differential upregulation of a plethora of proteins involved in DSB repair pathways in A3G-expressing cells early following irradiation to facilitate repair. Importantly, we find that A3G not only accelerates DSB repair but also promotes deamination-dependent error-free rejoining. These findings have two implications: (a) strategies aimed at inhibiting A3G may improve the efficacy of genotoxic therapies used to cure malignant tumours; and (b) enhancing A3G activity may reduce acute radiation syndrome in individuals exposed to ionizing radiation.
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Affiliation(s)
- Yelena Britan-Rosich
- Department of Pathology and Immunology, The Lautenberg Center for Immunology and Cancer Research, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Jing Ma
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, USA
| | - Eran Kotler
- Department of Genetics, Stanford University School of Medicine, Ca, USA
| | - Faizan Hassan
- Department of Pathology and Immunology, The Lautenberg Center for Immunology and Cancer Research, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Alexander Botvinnik
- Department of Pathology and Immunology, The Lautenberg Center for Immunology and Cancer Research, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Yoav Smith
- Genomic Data Analysis, Hadassah Medical School, Hebrew University, Jerusalem, Israel
| | - Ofra Moshel
- Core Research Facility, Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Abed Nasereddin
- Core Research Facility of the Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Gunjan Sharma
- Department of Pathology and Immunology, The Lautenberg Center for Immunology and Cancer Research, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Eli Pikarsky
- Department of Pathology and Immunology, The Lautenberg Center for Immunology and Cancer Research, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Susan Ross
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, USA
| | - Moshe Kotler
- Department of Pathology and Immunology, The Lautenberg Center for Immunology and Cancer Research, The Hebrew University Hadassah Medical School, Jerusalem, Israel
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20
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Calsina B, Piñeiro-Yáñez E, Martínez-Montes ÁM, Caleiras E, Fernández-Sanromán Á, Monteagudo M, Torres-Pérez R, Fustero-Torre C, Pulgarín-Alfaro M, Gil E, Letón R, Jiménez S, García-Martín S, Martin MC, Roldán-Romero JM, Lanillos J, Mellid S, Santos M, Díaz-Talavera A, Rubio Á, González P, Hernando B, Bechmann N, Dona M, Calatayud M, Guadalix S, Álvarez-Escolá C, Regojo RM, Aller J, Del Olmo-Garcia MI, López-Fernández A, Fliedner SMJ, Rapizzi E, Fassnacht M, Beuschlein F, Quinkler M, Toledo RA, Mannelli M, Timmers HJ, Eisenhofer G, Rodríguez-Perales S, Domínguez O, Macintyre G, Currás-Freixes M, Rodríguez-Antona C, Cascón A, Leandro-García LJ, Montero-Conde C, Roncador G, García-García JF, Pacak K, Al-Shahrour F, Robledo M. Genomic and immune landscape Of metastatic pheochromocytoma and paraganglioma. Nat Commun 2023; 14:1122. [PMID: 36854674 PMCID: PMC9975198 DOI: 10.1038/s41467-023-36769-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 02/16/2023] [Indexed: 03/02/2023] Open
Abstract
The mechanisms triggering metastasis in pheochromocytoma/paraganglioma are unknown, hindering therapeutic options for patients with metastatic tumors (mPPGL). Herein we show by genomic profiling of a large cohort of mPPGLs that high mutational load, microsatellite instability and somatic copy-number alteration burden are associated with ATRX/TERT alterations and are suitable prognostic markers. Transcriptomic analysis defines the signaling networks involved in the acquisition of metastatic competence and establishes a gene signature related to mPPGLs, highlighting CDK1 as an additional mPPGL marker. Immunogenomics accompanied by immunohistochemistry identifies a heterogeneous ecosystem at the tumor microenvironment level, linked to the genomic subtype and tumor behavior. Specifically, we define a general immunosuppressive microenvironment in mPPGLs, the exception being PD-L1 expressing MAML3-related tumors. Our study reveals canonical markers for risk of metastasis, and suggests the usefulness of including immune parameters in clinical management for PPGL prognostication and identification of patients who might benefit from immunotherapy.
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Affiliation(s)
- Bruna Calsina
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
| | - Elena Piñeiro-Yáñez
- Bioinformatics Unit, Structural Biology Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ángel M Martínez-Montes
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Eduardo Caleiras
- Histopathology Core Unit, Biotechnology Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ángel Fernández-Sanromán
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - María Monteagudo
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Rafael Torres-Pérez
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Bioinformatics for Genomics and Proteomics, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
| | - Coral Fustero-Torre
- Bioinformatics Unit, Structural Biology Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Marta Pulgarín-Alfaro
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Eduardo Gil
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Rocío Letón
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Scherezade Jiménez
- Monoclonal Antibodies Core Unit, Biotechnology Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Santiago García-Martín
- Bioinformatics Unit, Structural Biology Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Maria Carmen Martin
- Molecular Cytogenetics and Genome Engineering Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Juan María Roldán-Romero
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Javier Lanillos
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Sara Mellid
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - María Santos
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Alberto Díaz-Talavera
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Ángeles Rubio
- Genomics Core Unit, Biotechnology Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Patricia González
- Histopathology Core Unit, Biotechnology Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Barbara Hernando
- Computational Oncology Group, Structural Biology Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Nicole Bechmann
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Margo Dona
- Department of Internal Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - María Calatayud
- Department of Endocrinology, 12 de Octubre University Hospital, Madrid, Spain
| | - Sonsoles Guadalix
- Department of Endocrinology, 12 de Octubre University Hospital, Madrid, Spain
| | | | - Rita M Regojo
- Department of Pathology, La Paz University Hospital, Madrid, Spain
| | - Javier Aller
- Department of Endocrinology, Puerta de Hierro University Hospital, Madrid, Spain
| | | | | | - Stephanie M J Fliedner
- Neuroendocrine Oncology and Metabolism, Medical Department I, Center of Brain, Behavior, and Metabolism, University Medical Center Schleswig-Holstein Lübeck, Lübeck, Germany
| | - Elena Rapizzi
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Martin Fassnacht
- Department of Internal Medicine I, Division of Endocrinology and Diabetes, University Hospital Würzburg, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany
| | - Felix Beuschlein
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Germany
- Klinik für Endokrinologie Diabetologie und Klinische Ernährung, Universitätsspital Zürich (USZ) und Universität Zürich (UZH), Zürich, Switzerland
| | - Marcus Quinkler
- Endocrinology in Charlottenburg Stuttgarter Platz 1, Berlin, Germany
| | - Rodrigo A Toledo
- Gastrointestinal and Endocrine Tumors, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Massimo Mannelli
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Henri J Timmers
- Department of Internal Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Graeme Eisenhofer
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Sandra Rodríguez-Perales
- Molecular Cytogenetics and Genome Engineering Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Orlando Domínguez
- Genomics Core Unit, Biotechnology Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Geoffrey Macintyre
- Computational Oncology Group, Structural Biology Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Maria Currás-Freixes
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Department of Endocrinology, Clínica Universidad de Navarra, Madrid, Spain
| | - Cristina Rodríguez-Antona
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Alberto Cascón
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Luis J Leandro-García
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Cristina Montero-Conde
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Giovanna Roncador
- Monoclonal Antibodies Core Unit, Biotechnology Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | - Karel Pacak
- Section of Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Fátima Al-Shahrour
- Bioinformatics Unit, Structural Biology Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Mercedes Robledo
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Institute of Health Carlos III (ISCIII), Madrid, Spain.
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21
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Tang Q, Zuo W, Wan C, Xiong S, Xu C, Yuan C, Sun Q, Zhou L, Li X. Comprehensive genomic profiling of upper tract urothelial carcinoma and urothelial carcinoma of the bladder identifies distinct molecular characterizations with potential implications for targeted therapy & immunotherapy. Front Immunol 2023; 13:1097730. [PMID: 36818471 PMCID: PMC9936149 DOI: 10.3389/fimmu.2022.1097730] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/19/2022] [Indexed: 02/05/2023] Open
Abstract
Backgrounds Despite the genomic landscape of urothelial carcinomas (UC) patients, especially those with UC of bladder (UCB), has been comprehensively delineated and associated with pathogenetic mechanisms and treatment preferences, the genomic characterization of upper tract UC (UTUC) has yet to be fully elucidated. Materials and methods A total of 131 Chinese UTUC (74 renal pelvis & 57 ureter) and 118 UCB patients were enrolled in the present study, and targeted next-generation sequencing (NGS) of 618 cancer-associated genes were conducted to exhibit the profile of somatic and germline alterations. The COSMIC database, including 30 mutational signatures, were utilized to evaluate the mutational spectrums. Moreover, TCGA-UCB, MSKCC-UCB, and MSKCC-UTUC datasets were retrieved for preforming genomic alterations (GAs) comparison analysis between Western and Chinese UC patients. Results In our cohort, 93.98% and 56.63% of UC patients were identified with oncogenic and actionable somatic alterations, respectively. Meanwhile, 11.24% of Chinese UC patients (of 14.50% and 7.63% of UTUC and UCB cases, respectively) were identified to harbor a total of 32 pathogenic/likely-pathogenic germline variants in 22 genes, with DNA damage repair (DDR)-associated BRCA1 (1.20%) and CHEK2 (1.20%) being the most prevalent. Chinese UTUC and UCB patients possessed distinct somatic genomic characteristics, especially with significantly different prevalence in KMT2D/C/A, GNAQ, ERCC2, RB1, and PPM1D. In addition, we also found notable differences in the prevalence of ELF3, TP53, PMS2, and FAT4 between renal pelvis and ureter carcinomas. Moreover, 22.90% and 33.90% of UTUC and UCB patients, respectively, had at least one deleterious/likely deleterious alteration in DDR related genes/pathways. Subsequently, mutational signature analysis revealed that UC patients with mutational signature 22, irrespective of UTUC or UCB, consistently had the markedly higher level of tumor mutational burden (TMB), which was proved to be positively correlated with the objective complete/partial response rate in the IMvigor210 cohort. By comparison, Chinese and Western UTUC patients also differed regrading GAs in oncogenic-related genes/pathways, especially in TP53, RTK/RAS, and PI3K pathways; besides, more alterations in WNT pathway but less TP53, RTK/RAS, HIPPO, and PI3K pathways were identified in Chinese UCB. Discussions The in-depth analysis of genomic mutational landscapes revealed distinct pathogenetic mechanisms between Chinese UTUC and UCB, and specific genomic characterizations could identify high risk population of UTUC/UCB and provided information regarding the selection of alternative therapeutic regimens.
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Affiliation(s)
- Qi Tang
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Wei Zuo
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Chong Wan
- Precision Medicine Center, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, Zhejiang, China
| | - Shengwei Xiong
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Chunru Xu
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Changwei Yuan
- Department of Urology, Peking University First Hospital, Beijing, China
| | | | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Xuesong Li
- Department of Urology, Peking University First Hospital, Beijing, China
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22
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Chung J, Negm L, Bianchi V, Stengs L, Das A, Liu ZA, Sudhaman S, Aronson M, Brunga L, Edwards M, Forster V, Komosa M, Davidson S, Lees J, Tomboc P, Samuel D, Farah R, Bendel A, Knipstein J, Schneider KW, Reschke A, Zelcer S, Zorzi A, McWilliams R, Foulkes WD, Bedgood R, Peterson L, Rhode S, Van Damme A, Scheers I, Gardner S, Robbins G, Vanan MI, Meyn MS, Auer R, Leach B, Burke C, Villani A, Malkin D, Bouffet E, Huang A, Taylor MD, Durno C, Shlien A, Hawkins C, Getz G, Maruvka YE, Tabori U. Genomic Microsatellite Signatures Identify Germline Mismatch Repair Deficiency and Risk of Cancer Onset. J Clin Oncol 2023; 41:766-777. [PMID: 36240479 PMCID: PMC10489375 DOI: 10.1200/jco.21.02873] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 06/14/2022] [Accepted: 08/02/2022] [Indexed: 02/03/2023] Open
Abstract
PURPOSE Diagnosis of Mismatch Repair Deficiency (MMRD) is crucial for tumor management and early detection in patients with the cancer predisposition syndrome constitutional mismatch repair deficiency (CMMRD). Current diagnostic tools are cumbersome and inconsistent both in childhood cancers and in determining germline MMRD. PATIENTS AND METHODS We developed and analyzed a functional Low-pass Genomic Instability Characterization (LOGIC) assay to detect MMRD. The diagnostic performance of LOGIC was compared with that of current established assays including tumor mutational burden, immunohistochemistry, and the microsatellite instability panel. LOGIC was then applied to various normal tissues of patients with CMMRD with comprehensive clinical data including age of cancer presentation. RESULTS Overall, LOGIC was 100% sensitive and specific in detecting MMRD in childhood cancers (N = 376). It was more sensitive than the microsatellite instability panel (14%, P = 4.3 × 10-12), immunohistochemistry (86%, P = 4.6 × 10-3), or tumor mutational burden (80%, P = 9.1 × 10-4). LOGIC was able to distinguish CMMRD from other cancer predisposition syndromes using blood and saliva DNA (P < .0001, n = 277). In normal cells, MMRDness scores differed between tissues (GI > blood > brain), increased over time in the same individual, and revealed genotype-phenotype associations within the mismatch repair genes. Importantly, increased MMRDness score was associated with younger age of first cancer presentation in individuals with CMMRD (P = 2.2 × 10-5). CONCLUSION LOGIC was a robust tool for the diagnosis of MMRD in multiple cancer types and in normal tissues. LOGIC may inform therapeutic cancer decisions, provide rapid diagnosis of germline MMRD, and support tailored surveillance for individuals with CMMRD.
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Affiliation(s)
- Jiil Chung
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Logine Negm
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Vanessa Bianchi
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Lucie Stengs
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Anirban Das
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Hematology/Oncology, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, ON, Canada
- Department of Pediatric Hematology/Oncology, Tata Medical Centre, Kolkata, India
| | - Zhihui Amy Liu
- Department of Biostatistics, Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Sumedha Sudhaman
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Melyssa Aronson
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, ON, Canada
| | - Ledia Brunga
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Melissa Edwards
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Victoria Forster
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Martin Komosa
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Scott Davidson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jodi Lees
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Patrick Tomboc
- Department of Pediatrics, West Virginia University, Morgantown, WV
| | | | - Roula Farah
- Lebanese American University Medical Center-Rizk, Beirut, Lebanon
| | - Anne Bendel
- Department of Pediatric Hematology-Oncology, Children's Minnesota, Minneapolis, MN
| | - Jeffrey Knipstein
- Division of Pediatric Hematology/Oncology/BMT, Medical College of Wisconsin, Milwaukee, WI
| | - Kami Wolfe Schneider
- Department of Pediatric Hematology-Oncology, Children's Hospital Colorado, Aurora, CO
| | - Agnes Reschke
- Department of Pediatric Hematology/Oncology, Stanford University, Palo Alto, CA
| | - Shayna Zelcer
- Department of Pediatrics, London Health Sciences Centre, London, ON, Canada
| | - Alexandra Zorzi
- Division of Haematology/Oncology, Western University, London, ON, Canada
| | | | - William D. Foulkes
- Departments of Oncology and Human Genetics, McGill University Health Centre, Cancer Genetics Program, Montreal, QC, Canada
| | | | - Lindsay Peterson
- Division of Medical Oncology, Washington University, St Louis, MO
| | - Sara Rhode
- Department of Hematology and Oncology, Cleveland Clinic, Cleveland, OH
| | - An Van Damme
- Pediatric Gastroenterology and Hepatology Unit, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Isabelle Scheers
- Universite Catholique de Louvain La Faculte de Medecine, Bruxelles, Belgium
| | - Sharon Gardner
- Department of Pediatric Hematology-Oncology, NYU Langone Health, New York, NY
| | - Gabriel Robbins
- Department of Pediatric Hematology-Oncology, NYU Langone Health, New York, NY
| | - Magimairajan Issai Vanan
- Department of Pediatric Hematology-Oncology, CancerCare Manitoba, Winnipeg, MB, Canada
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
| | - M. Stephen Meyn
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
- Center for Human Genomics and Precision Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI
| | - Rebecca Auer
- Centre for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Brandie Leach
- Department of Gastroenterology, Hepatology, and Nutrition, Digestive Disease and Surgery Institute, Cleveland Clinic, Cleveland, OH
| | - Carol Burke
- Department of Gastroenterology, Hepatology, and Nutrition, Digestive Disease and Surgery Institute, Cleveland Clinic, Cleveland, OH
| | - Anita Villani
- Division of Hematology/Oncology, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, ON, Canada
| | - David Malkin
- Division of Hematology/Oncology, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, ON, Canada
| | - Eric Bouffet
- Division of Hematology/Oncology, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, ON, Canada
| | - Annie Huang
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Hematology/Oncology, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Michael D. Taylor
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Neurosurgery, The Hospital for Sick Children, Toronto, ON, Canada
| | - Carol Durno
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, ON, Canada
- Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, ON, Canada
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Cynthia Hawkins
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Pathology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, MA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA
- Harvard Medical School, 250 Longwood Avenue, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - Yosef E. Maruvka
- Faculty of Biotechnology and Food Engineering, The Lokey Center for Life Science and Engineering, TECHNION – Israel Institute of Technology, Haifa, Israel
| | - Uri Tabori
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Hematology/Oncology, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, ON, Canada
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23
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Abstract
High-fidelity DNA replication is critical for the faithful transmission of genetic information to daughter cells. Following genotoxic stress, specialized DNA damage tolerance pathways are activated to ensure replication fork progression. These pathways include translesion DNA synthesis, template switching and repriming. In this Review, we describe how DNA damage tolerance pathways impact genome stability, their connection with tumorigenesis and their effects on cancer therapy response. We discuss recent findings that single-strand DNA gap accumulation impacts chemoresponse and explore a growing body of evidence that suggests that different DNA damage tolerance factors, including translesion synthesis polymerases, template switching proteins and enzymes affecting single-stranded DNA gaps, represent useful cancer targets. We further outline how the consequences of DNA damage tolerance mechanisms could inform the discovery of new biomarkers to refine cancer therapies.
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Affiliation(s)
- Emily Cybulla
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
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Sun B, Sherrin M, Roy R. Unscheduled epigenetic modifications cause genome instability and sterility through aberrant R-loops following starvation. Nucleic Acids Res 2022; 51:84-98. [PMID: 36504323 PMCID: PMC9841415 DOI: 10.1093/nar/gkac1155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
During starvation, organisms modify both gene expression and metabolism to adjust to the energy stress. We previously reported that Caenorhabditis elegans lacing AMP-activated protein kinase (AMPK) exhibit transgenerational reproductive defects associated with abnormally elevated trimethylated histone H3 at lysine 4 (H3K4me3) levels in the germ line following recovery from acute starvation. Here, we show that these H3K4me3 marks are significantly increased at promoters, driving aberrant transcription elongation resulting in the accumulation of R-loops in starved AMPK mutants. DNA-RNA immunoprecipitation followed by high-throughput sequencing (DRIP-seq) analysis demonstrated that a significant proportion of the genome was affected by R-loop formation. This was most pronounced in the promoter-transcription start site regions of genes, in which the chromatin was modified by H3K4me3. Like H3K4me3, the R-loops were also found to be heritable, likely contributing to the transgenerational reproductive defects typical of these mutants following starvation. Strikingly, AMPK mutant germ lines show considerably more RAD-51 (the RecA recombinase) foci at sites of R-loop formation, potentially sequestering them from their roles at meiotic breaks or at sites of induced DNA damage. Our study reveals a previously unforeseen role of AMPK in maintaining genome stability following starvation. The downstream effects of R-loops on DNA damage sensitivity and germline stem cell integrity may account for inappropriate epigenetic modification that occurs in numerous human disorders, including various cancers.
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Affiliation(s)
- Bing Sun
- To whom correspondence should be addressed.
| | - McLean Sherrin
- Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada
| | - Richard Roy
- Correspondence may also be addressed to Richard Roy. Tel: +1 514 398 6437;
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25
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Zhang G, Wang Z, Song P, Zhan X. DNA and histone modifications as potent diagnostic and therapeutic targets to advance non-small cell lung cancer management from the perspective of 3P medicine. EPMA J 2022; 13:649-669. [PMID: 36505890 PMCID: PMC9727004 DOI: 10.1007/s13167-022-00300-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/11/2022] [Indexed: 12/12/2022]
Abstract
Lung cancer has a very high mortality in females and males. Most (~ 85%) of lung cancers are non-small cell lung cancers (NSCLC). When lung cancer is diagnosed, most of them have either local or distant metastasis, with a poor prognosis. In order to achieve better outcomes, it is imperative to identify the molecular signature based on genetic and epigenetic variations for different NSCLC subgroups. We hypothesize that DNA and histone modifications play significant roles in the framework of predictive, preventive, and personalized medicine (PPPM; 3P medicine). Epigenetics has a significant impact on tumorigenicity, tumor heterogeneity, and tumor resistance to chemotherapy, targeted therapy, and immunotherapy. An increasing interest is that epigenomic regulation is recognized as a potential treatment option for NSCLC. Most attention has been paid to the epigenetic alteration patterns of DNA and histones. This article aims to review the roles DNA and histone modifications play in tumorigenesis, early detection and diagnosis, and advancements and therapies of NSCLC, and also explore the connection between DNA and histone modifications and PPPM, which may provide an important contribution to improve the prognosis of NSCLC. We found that the success of targeting DNA and histone modifications is limited in the clinic, and how to combine the therapies to improve patient outcomes is necessary in further studies, especially for predictive diagnostics, targeted prevention, and personalization of medical services in the 3P medicine approach. It is concluded that DNA and histone modifications are potent diagnostic and therapeutic targets to advance non-small cell lung cancer management from the perspective of 3P medicine.
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Affiliation(s)
- Guodong Zhang
- Thoracic Surgery Department, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, 440 Jiyan Road, Shandong 250117 Jinan, People’s Republic of China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, 6699 Qingdao Road, Jinan, Shandong 250117 People’s Republic of China
| | - Zhengdan Wang
- Thoracic Surgery Department, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, 440 Jiyan Road, Shandong 250117 Jinan, People’s Republic of China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, 6699 Qingdao Road, Jinan, Shandong 250117 People’s Republic of China
| | - Pingping Song
- Thoracic Surgery Department, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, 440 Jiyan Road, Shandong 250117 Jinan, People’s Republic of China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, 6699 Qingdao Road, Jinan, Shandong 250117 People’s Republic of China
| | - Xianquan Zhan
- Thoracic Surgery Department, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, 440 Jiyan Road, Shandong 250117 Jinan, People’s Republic of China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, 6699 Qingdao Road, Jinan, Shandong 250117 People’s Republic of China
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26
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El-Kafrawy SA, El-Daly MM, Bajrai LH, Alandijany TA, Faizo AA, Mobashir M, Ahmed SS, Ahmed S, Alam S, Jeet R, Kamal MA, Anwer ST, Khan B, Tashkandi M, Rizvi MA, Azhar EI. Genomic profiling and network-level understanding uncover the potential genes and the pathways in hepatocellular carcinoma. Front Genet 2022; 13:880440. [PMID: 36479247 PMCID: PMC9720179 DOI: 10.3389/fgene.2022.880440] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 11/02/2022] [Indexed: 12/11/2023] Open
Abstract
Data integration with phenotypes such as gene expression, pathways or function, and protein-protein interactions data has proven to be a highly promising technique for improving human complex diseases, particularly cancer patient outcome prediction. Hepatocellular carcinoma is one of the most prevalent cancers, and the most common cause is chronic HBV and HCV infection, which is linked to the majority of cases, and HBV and HCV play a role in multistep carcinogenesis progression. We examined the list of known hepatocellular carcinoma biomarkers with the publicly available expression profile dataset of hepatocellular carcinoma infected with HCV from day 1 to day 10 in this study. The study covers an overexpression pattern for the selected biomarkers in clinical hepatocellular carcinoma patients, a combined investigation of these biomarkers with the gathered temporal dataset, temporal expression profiling changes, and temporal pathway enrichment following HCV infection. Following a temporal analysis, it was discovered that the early stages of HCV infection tend to be more harmful in terms of expression shifting patterns, and that there is no significant change after that, followed by a set of genes that are consistently altered. PI3K, cAMP, TGF, TNF, Rap1, NF-kB, Apoptosis, Longevity regulating pathway, signaling pathways regulating pluripotency of stem cells, Cytokine-cytokine receptor interaction, p53 signaling, Wnt signaling, Toll-like receptor signaling, and Hippo signaling pathways are just a few of the most commonly enriched pathways. The majority of these pathways are well-known for their roles in the immune system, infection and inflammation, and human illnesses like cancer. We also find that ADCY8, MYC, PTK2, CTNNB1, TP53, RB1, PRKCA, TCF7L2, PAK1, ITPR2, CYP3A4, UGT1A6, GCK, and FGFR2/3 appear to be among the prominent genes based on the networks of genes and pathways based on the copy number alterations, mutations, and structural variants study.
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Affiliation(s)
- Sherif A. El-Kafrawy
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mai M. El-Daly
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Leena H. Bajrai
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Thamir A. Alandijany
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Arwa A. Faizo
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad Mobashir
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institute, Stockholm, Sweden
- Genome Biology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Sunbul S. Ahmed
- Genome Biology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Sarfraz Ahmed
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Shoaib Alam
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Raja Jeet
- Botany Department, Ganesh Dutt College, Begusarai, Bihar, India
| | - Mohammad Amjad Kamal
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
- Enzymoics, Hebersham, NSW, Australia
- Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| | - Syed Tauqeer Anwer
- Genome Biology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Bushra Khan
- Genome Biology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Manal Tashkandi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Moshahid A. Rizvi
- Genome Biology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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27
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Bukavina L, Bensalah K, Bray F, Carlo M, Challacombe B, Karam JA, Kassouf W, Mitchell T, Montironi R, O'Brien T, Panebianco V, Scelo G, Shuch B, van Poppel H, Blosser CD, Psutka SP. Epidemiology of Renal Cell Carcinoma: 2022 Update. Eur Urol 2022; 82:529-542. [PMID: 36100483 DOI: 10.1016/j.eururo.2022.08.019] [Citation(s) in RCA: 173] [Impact Index Per Article: 86.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 07/27/2022] [Accepted: 08/16/2022] [Indexed: 11/18/2022]
Abstract
CONTEXT International variations in the rates of kidney cancer (KC) are considerable. An understanding of the risk factors for KC development is necessary to generate opportunities to reduce its incidence through prevention and surveillance. OBJECTIVE To retrieve and summarize global incidence and mortality rates of KC and risk factors associated with its development, and to describe known familial syndromes and genetic alterations that represent biologic risk factors. EVIDENCE ACQUISITION A systematic review was conducted via Medline (PubMed) and Scopus to include meta-analyses, reviews, and original studies regarding renal cell carcinoma, epidemiology, and risk factors. EVIDENCE SYNTHESIS Our narrative review provides a detailed analysis of KC incidence and mortality, with significant variations across time, geography, and sex. In particular, while KC incidence has continued to increase, mortality models have leveled off. Among the many risk factors, hypertension, obesity, and smoking are the most well established. The emergence of new genetic data coupled with observational data allows for integrated management and surveillance strategies for KC care. CONCLUSIONS KC incidence and mortality rates vary significantly by geography, sex, and age. Associations of the development of KC with modifiable and fixed risk factors such as obesity, hypertension, smoking, and chronic kidney disease (CKD)/end-stage kidney disease (ESKD) are well described. Recent advances in the genetic characterization of these cancers have led to a better understanding of the germline and somatic mutations that predispose patients to KC development, with potential for identification of therapeutic targets that may improve outcomes for these at-risk patients. PATIENT SUMMARY We reviewed evidence on the occurrence of kidney cancer (KC) around the world. Currently, the main avoidable causes are smoking, obesity, and high blood pressure. Although other risk factors also contribute, prevention and treatment of these three factors provide the best opportunities to reduce the risk of developing KC at present.
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Affiliation(s)
- Laura Bukavina
- Division of Urologic Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA; University Hospitals Cleveland Medical Center, Case Western Reserve School of Medicine, Cleveland, OH, USA
| | - Karim Bensalah
- Department of Urology, University of Rennes, Rennes, France
| | - Freddie Bray
- Cancer Surveillance Section, International Agency for Research on Cancer, Lyon, France
| | - Maria Carlo
- Department of Medical Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ben Challacombe
- Department of Urology, Guy's and St. Thomas Hospitals, London, UK
| | - Jose A Karam
- Departments of Urology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wassim Kassouf
- Division of Adult Urology, McGill University, Montreal, Canada
| | - Thomas Mitchell
- Department of Urology, Wellcome Sanger Institute, Cambridge, UK
| | - Rodolfo Montironi
- Molecular Medicine and Cell Therapy Foundation, Polytechnic University of the Marche Region, Ancona, Italy
| | - Tim O'Brien
- Department of Urology, Guy's and St. Thomas Hospitals, London, UK
| | | | | | - Brian Shuch
- Department of Urology, University of California-Los Angeles, Los Angeles, CA, USA
| | - Hein van Poppel
- Department of Urology, Catholic University of Leuven, Leuven, Belgium
| | - Christopher D Blosser
- Department of Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - Sarah P Psutka
- Department of Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA, USA.
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Kurup HM, Kvach MV, Harjes S, Barzak FM, Jameson GB, Harjes E, Filichev VV. Design, Synthesis, and Evaluation of a Cross-Linked Oligonucleotide as the First Nanomolar Inhibitor of APOBEC3A. Biochemistry 2022; 61:2568-2578. [DOI: 10.1021/acs.biochem.2c00449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Harikrishnan M. Kurup
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Maksim V. Kvach
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Stefan Harjes
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Fareeda M. Barzak
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Geoffrey B. Jameson
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Elena Harjes
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Vyacheslav V. Filichev
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
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29
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Zheng T. DETexT: An SNV detection enhancement for low read depth by integrating mutational signatures into TextCNN. Front Genet 2022; 13:943972. [PMID: 36246660 PMCID: PMC9554618 DOI: 10.3389/fgene.2022.943972] [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: 05/14/2022] [Accepted: 09/06/2022] [Indexed: 12/01/2022] Open
Abstract
Detecting SNV at very low read depths helps to reduce sequencing requirements, lowers sequencing costs, and aids in the early screening, diagnosis, and treatment of cancer. However, the accuracy of SNV detection is significantly reduced at read depths below ×34 due to the lack of a sufficient number of read pairs to help filter out false positives. Many recent studies have revealed the potential of mutational signature (MS) in detecting true SNV, understanding the mutational processes that lead to the development of human cancers, and analyzing the endogenous and exogenous causes. Here, we present DETexT, an SNV detection method better suited to low read depths, which classifies false positive variants by combining MS with deep learning algorithms to mine correlation information around bases in individual reads without relying on the support of duplicate read pairs. We have validated the effectiveness of DETexT on simulated and real datasets and conducted comparative experiments. The source code has been uploaded to https://github.com/TrinaZ/extra-lowRD for academic use only.
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Affiliation(s)
- Tian Zheng
- Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China
- Institute of Data Science and Information Quality, Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Tian Zheng,
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30
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Roemer A, Mohammed L, Strickfaden H, Underhill DA, Hendzel MJ. Mechanisms governing the accessibility of DNA damage proteins to constitutive heterochromatin. Front Genet 2022; 13:876862. [PMID: 36092926 PMCID: PMC9458887 DOI: 10.3389/fgene.2022.876862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/18/2022] [Indexed: 12/05/2022] Open
Abstract
Chromatin is thought to regulate the accessibility of the underlying DNA sequence to machinery that transcribes and repairs the DNA. Heterochromatin is chromatin that maintains a sufficiently high density of DNA packing to be visible by light microscopy throughout the cell cycle and is thought to be most restrictive to transcription. Several studies have suggested that larger proteins and protein complexes are attenuated in their access to heterochromatin. In addition, heterochromatin domains may be associated with phase separated liquid condensates adding further complexity to the regulation of protein concentration within chromocenters. This provides a solvent environment distinct from the nucleoplasm, and proteins that are not size restricted in accessing this liquid environment may partition between the nucleoplasm and heterochromatin based on relative solubility. In this study, we assessed the accessibility of constitutive heterochromatin in mouse cells, which is organized into large and easily identifiable chromocenters, to fluorescently tagged DNA damage response proteins. We find that proteins larger than the expected 10 nm size limit can access the interior of heterochromatin. We find that the sensor proteins Ku70 and PARP1 enrich in mouse chromocenters. At the same time, MRE11 shows variability within an asynchronous population that ranges from depleted to enriched but is primarily homogeneously distribution between chromocenters and the nucleoplasm. While larger downstream proteins such as ATM, BRCA1, and 53BP1 are commonly depleted in chromocenters, they show a wide range of concentrations, with none being depleted beyond approximately 75%. Contradicting exclusively size-dependent accessibility, many smaller proteins, including EGFP, are also depleted in chromocenters. Our results are consistent with minimal size-dependent selectivity but a distinct solvent environment explaining reduced concentrations of diffusing nucleoplasmic proteins within the volume of the chromocenter.
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31
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Biechele-Speziale DJ, Sutton TB, Delaney S. Obstacles and opportunities for base excision repair in chromatin. DNA Repair (Amst) 2022; 116:103345. [PMID: 35689883 PMCID: PMC9253077 DOI: 10.1016/j.dnarep.2022.103345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 01/01/2023]
Abstract
Most eukaryotic DNA is packaged into chromatin, which is made up of tandemly repeating nucleosomes. This packaging of DNA poses a significant barrier to the various enzymes that must act on DNA, including DNA damage response enzymes that interact intimately with DNA to prevent mutations and cell death. To regulate access to certain DNA regions, chromatin remodeling, variant histone exchange, and histone post-translational modifications have been shown to assist several DNA repair pathways including nucleotide excision repair, single strand break repair, and double strand break repair. While these chromatin-level responses have been directly linked to various DNA repair pathways, how they modulate the base excision repair (BER) pathway remains elusive. This review highlights recent findings that demonstrate how BER is regulated by the packaging of DNA into nucleosome core particles (NCPs) and higher orders of chromatin structures. We also summarize the available data that indicate BER may be enabled by chromatin modifications and remodeling.
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Affiliation(s)
| | | | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, RI, USA.
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32
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Ho AT, Hurst LD. Stop codon usage as a window into genome evolution: mutation, selection, biased gene conversion and the TAG paradox. Genome Biol Evol 2022; 14:6648529. [PMID: 35867377 PMCID: PMC9348620 DOI: 10.1093/gbe/evac115] [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] [Accepted: 07/17/2022] [Indexed: 11/16/2022] Open
Abstract
Protein coding genes terminate with one of three stop codons (TAA, TGA, or TAG) that, like synonymous codons, are not employed equally. With TGA and TAG having identical nucleotide content, analysis of their differential usage provides an unusual window into the forces operating on what are ostensibly functionally identical residues. Across genomes and between isochores within the human genome, TGA usage increases with G + C content but, with a common G + C → A + T mutation bias, this cannot be explained by mutation bias-drift equilibrium. Increased usage of TGA in G + C-rich genomes or genomic regions is also unlikely to reflect selection for the optimal stop codon, as TAA appears to be universally optimal, probably because it has the lowest read-through rate. Despite TAA being favored by selection and mutation bias, as with codon usage bias G + C pressure is the prime determinant of between-species TGA usage trends. In species with strong G + C-biased gene conversion (gBGC), such as mammals and birds, the high usage and conservation of TGA is best explained by an A + T → G + C repair bias. How to explain TGA enrichment in other G + C-rich genomes is less clear. Enigmatically, across bacterial and archaeal species and between human isochores TAG usage is mostly unresponsive to G + C pressure. This unresponsiveness we dub the TAG paradox as currently no mutational, selective, or gBGC model provides a well-supported explanation. That TAG does increase with G + C usage across eukaryotes makes the usage elsewhere yet more enigmatic. We suggest resolution of the TAG paradox may provide insights into either an unknown but common selective preference (probably at the DNA/RNA level) or an unrecognized complexity to the action of gBGC.
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Affiliation(s)
- Alexander T Ho
- Milner Centre for Evolution, University of Bath, Bath, UK
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33
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Lim LM, Chung WY, Hwang DY, Yu CC, Ke HL, Liang PI, Lin TW, Cheng SM, Huang AM, Kuo HT. Whole-exome sequencing identified mutational profiles of urothelial carcinoma post kidney transplantation. J Transl Med 2022; 20:324. [PMID: 35864526 PMCID: PMC9301867 DOI: 10.1186/s12967-022-03522-4] [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: 02/11/2022] [Accepted: 07/08/2022] [Indexed: 11/10/2022] Open
Abstract
Kidney transplantation is a lifesaving option for patients with end-stage kidney disease. In Taiwan, urothelial carcinoma (UC) is the most common de novo cancer after kidney transplantation (KT). UC has a greater degree of molecular heterogeneity than do other solid tumors. Few studies have explored genomic alterations in UC after KT. We performed whole-exome sequencing to compare the genetic alterations in UC developed after kidney transplantation (UCKT) and in UC in patients on hemodialysis (UCHD). After mapping and variant calling, 18,733 and 11,093 variants were identified in patients with UCKT and UCHD, respectively. We excluded known single-nucleotide polymorphisms (SNPs) and retained genes that were annotated in the Catalogue of Somatic Mutations in Cancer (COSMIC), in the Integrative Onco Genomic cancer mutations browser (IntOGen), and in the Cancer Genome Atlas (TCGA) database of genes associated with bladder cancer. A total of 14 UCKT-specific genes with SNPs identified in more than two patients were included in further analyses. The single-base substitution (SBS) profile and signatures showed a relative high T > A pattern compared to COMSIC UC mutations. Ingenuity pathway analysis was used to explore the connections among these genes. GNAQ, IKZF1, and NTRK3 were identified as potentially involved in the signaling network of UCKT. The genetic analysis of posttransplant malignancies may elucidate a fundamental aspect of the molecular pathogenesis of UCKT.
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Affiliation(s)
- Lee-Moay Lim
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Division of Nephrology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wen-Yu Chung
- Department of Computer Science and Information Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan
| | - Daw-Yang Hwang
- National Institute of Cancer Research, National Health Research Institute, Tainan, Taiwan
| | - Chih-Chuan Yu
- National Institute of Cancer Research, National Health Research Institute, Tainan, Taiwan
| | - Hung-Lung Ke
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Urology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung, Taiwan.,Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Peir-In Liang
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ting-Wei Lin
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Siao Muk Cheng
- National Institute of Cancer Research, National Health Research Institute, Tainan, Taiwan
| | - A-Mei Huang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan. .,Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan. .,Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan. .,Ph.D. Program in Toxicology, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan. .,Department of Biochemistry, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Hung-Tien Kuo
- Division of Nephrology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan. .,School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
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34
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Saint-Ghislain M, Derrien AC, Geoffrois L, Gastaud L, Lesimple T, Negrier S, Penel N, Kurtz JE, Le Corre Y, Dutriaux C, Gardrat S, Barnhill R, Matet A, Cassoux N, Houy A, Ramtohul T, Servois V, Mariani P, Piperno-Neumann S, Stern MH, Rodrigues M. MBD4 deficiency is predictive of response to immune checkpoint inhibitors in metastatic uveal melanoma patients. Eur J Cancer 2022; 173:105-112. [PMID: 35863105 DOI: 10.1016/j.ejca.2022.06.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/24/2022] [Accepted: 06/17/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND MBD4 mutations have been reported in uveal melanomas, acute myeloid leukemias, colorectal adenocarcinomas, gliomas, and spiradenocarcinomas and cause a hypermutated phenotype. Although metastatic uveal melanomas (mUM) are usually resistant to immune checkpoint inhibitors (ICI), the first reported MBD4-mutated (MBD4m) patient responded to ICI, suggesting that MBD4 mutation may predict response to ICI. METHODS Retrospective cohort of mUM patients treated with ICI. MBD4 was sequenced in a subset of these patients. RESULTS Three hundred mUM patients were included. Median follow-up was 17.3 months. Ten patients with an objective response and 20 cases with stable disease for >12 months were observed, corresponding to an objective response rate of 3.3% and a clinical benefit (i.e., responder patients and stable disease) rate of 10%. Of the 131 tumors sequenced for MBD4, five (3.8%) were mutated. MBD4 mutation was associated with a better objective response rate as three out of five MBD4m versus 4% of MBD4 wild-type patients responded (p < 0.001). Of these five responders, three presented progressive disease at 2.8, 13.9, and 22.3 months. Median PFS was 4.0 months in MBD4 wild-type and 22.3 months in MBD4m patients (HR = 0.22; p = 0.01). Median OS in MBD4def patients was unreached as compared to 16.6 months in MBD4pro (HR = 0.11; 95% CI: 0.02-0.86; log-rank p-test = 0.04; Fig. 2e). CONCLUSIONS In mUM patients, MBD4 mutation is highly predictive for the response, PFS, and overall survival benefit to ICI. MBD4 could be a tissue-agnostic biomarker and should be sequenced in mUM, and other tumor types where MBD4 mutations are reported.
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Affiliation(s)
- Mathilde Saint-Ghislain
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France; INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par La Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France.
| | - Anne-Céline Derrien
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par La Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France.
| | - Lionnel Geoffrois
- Department of Medical Oncology, Institut de Cancérologie de Lorraine - Alexis Vautrin Cancer, Nancy, France.
| | - Lauris Gastaud
- Department of Medical Oncology, Antoine Lacassagne Cancer Centre, 06000 Nice, France.
| | - Thierry Lesimple
- Department of Medical Oncology, Centre Eugène Marquis, Rennes, France.
| | | | - Nicolas Penel
- Department of Medical Oncology, Centre Oscar Lambret, Lille University, Lille, France.
| | - Jean-Emmanuel Kurtz
- Department of Medical Oncology, Strasbourg University Hospital, Strasbourg, France.
| | - Yannick Le Corre
- Department of Dermatology, Angers University Hospital, UNAM, France.
| | - Caroline Dutriaux
- Dermatology Department, CHU de Bordeaux, Hôpital Saint André, Bordeaux, France.
| | - Sophie Gardrat
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France.
| | - Raymond Barnhill
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France; Faculty of Medicine, Université de Paris, Paris, France.
| | - Alexandre Matet
- Department of Ocular Oncology, Institut Curie, PSL Research University, Paris, France; Université de Paris, Paris, France.
| | - Nathalie Cassoux
- Department of Ocular Oncology, Institut Curie, PSL Research University, Paris, France; Université de Paris, Paris, France.
| | - Alexandre Houy
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par La Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France.
| | - Toulsie Ramtohul
- Department of Radiology, Institut Curie, PSL Research University, Paris, France.
| | - Vincent Servois
- Department of Radiology, Institut Curie, PSL Research University, Paris, France.
| | - Pascale Mariani
- Department of Surgical Oncology, Institut Curie, PSL Research University, Paris, France.
| | | | - Marc-Henri Stern
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par La Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France; Department of Genetics, Institut Curie, PSL Research University, Paris, France.
| | - Manuel Rodrigues
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France; INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par La Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France.
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35
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Ma X, Dong L, Liu X, Ou K, Yang L. POLE/POLD1 mutation and tumor immunotherapy. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:216. [PMID: 35780178 PMCID: PMC9250176 DOI: 10.1186/s13046-022-02422-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/17/2022] [Indexed: 12/30/2022]
Abstract
POLE and POLD1 encode the catalytic and proofreading subunits of DNA polymerase ε and polymerase δ, and play important roles in DNA replication and proofreading. POLE/POLD1 exonuclease domain mutations lead to loss of proofreading function, which causes the accumulation of mutant genes in cells. POLE/POLD1 mutations are not only closely related to tumor formation, but are also a potential molecular marker for predicting the efficacy of immunotherapy in pan-carcinomatous species. The association of POLE/POLD1 mutation, ultra-high mutation load, and good prognosis have recently become the focus of clinical research. This article reviews the function of POLE/POLD1, its relationship with deficient mismatch repair/high microsatellite instability, and the role of POLE/POLD1 mutation in the occurrence and development of various tumors.
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Affiliation(s)
- Xiaoting Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Lin Dong
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xiu Liu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Kai Ou
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Lin Yang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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36
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Afify SM, Hassan G, Seno A, Seno M. Cancer-inducing niche: the force of chronic inflammation. Br J Cancer 2022; 127:193-201. [PMID: 35292758 PMCID: PMC9296522 DOI: 10.1038/s41416-022-01775-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 02/10/2022] [Accepted: 02/22/2022] [Indexed: 12/13/2022] Open
Abstract
The growth of cancer tissue is thought to be considered driven by a small subpopulation of cells, so-called cancer stem cells (CSCs). CSCs are located at the apex of a hierarchy in a cancer tissue with self-renewal, differentiation and tumorigenic potential that produce the progeny in the tissue. Although CSCs are generally believed to play a critical role in the growth, metastasis, and recurrence of cancers, the origin of CSCs remains to be reconsidered. We hypothesise that, chronic diseases, including obesity and diabetes, establish the cancer-inducing niche (CIN) that drives the undifferentiated/progenitor cells into CSCs, which then develop malignant tumours in vivo. In this context, a CIN could be traced to chronic inflammation that involves long-lasting tissue damage and repair after being exposed to factors such as cytokines and growth factors. This must be distinguished from the cancer microenvironment, which is responsible for cancer maintenance. The concept of a CIN is most important for cancer prevention as well as cancer therapy.
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Affiliation(s)
- Said M Afify
- Department of Biotechnology and Drug Discovery, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, 700-8530, Japan.
- Division of Biochemistry, Chemistry Department, Faculty of Science, Menoufia University, Shebin El Koum-Menoufia, 32511, Egypt.
| | - Ghmkin Hassan
- Department of Biotechnology and Drug Discovery, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, 700-8530, Japan
| | - Akimasa Seno
- Department of Biotechnology and Drug Discovery, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, 700-8530, Japan
- Okayama University Research Laboratory of Stem Cell Engineering in Detroit, IBio, Wayne State University, Detroit, MI, USA
| | - Masaharu Seno
- Department of Biotechnology and Drug Discovery, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, 700-8530, Japan.
- Okayama University Research Laboratory of Stem Cell Engineering in Detroit, IBio, Wayne State University, Detroit, MI, USA.
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37
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Qian Y, Gong Y, Zou X, Liu Y, Chen Y, Wang R, Dai Z, Tasiheng Y, Lin X, Wang X, Luo G, Yu X, Cheng H, Liu C. Aberrant APOBEC3C expression induces characteristic genomic instability in pancreatic ductal adenocarcinoma. Oncogenesis 2022; 11:35. [PMID: 35750693 PMCID: PMC9232547 DOI: 10.1038/s41389-022-00411-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 06/08/2022] [Accepted: 06/13/2022] [Indexed: 11/12/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a well-known lethal and heterogeneous disease. Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) is an important mutagenic driver that has seldom been investigated in PDAC. Therefore, this study investigated the significance of APOBEC3C in PDAC. First, cytosine deamination-associated mutation signatures were identified in the PDAC cohorts from TCGA and Fudan University Shanghai Cancer Center (FUSCC) datasets, and C > X-enriched kataegis regions were identified in the FUSCC cohort (12 to 27 counts per sample). Patients were stratified according to APOBEC3C expression, and high APOBEC3C expression was found to correlate with a higher motif enrichment score of 5’-CC-3’ and an elevated kataegis count within PCSK5 and NES genes. Second, we compared APOBEC expression in PDAC and normal pancreatic tissues and found that APOBEC3C was substantially upregulated in PDAC. APOBEC3C-overexpressing cell lines were generated to substantiate the effects of APOBEC3C on PDAC genome, including alterations in single-nucleotide variant (SNV) classes (higher proportion of C > T conversions) and the formation of kataegis regions (newly occurring kataegis regions detected in ACHE and MUC6 genes). Three different PDAC cohorts (FUSCC, TCGA, and QCMG) were analysed to evaluate the prognostic value of APOBEC3C, and APOBEC3C overexpression predicted shorter survival. Finally, the APOBEC3C overexpression correalted with the PDAC tumour microenvironment (TME) remodelling, APOBEC3C expression was associated with the invasion of CD4 + T lymphocytes and CD8 + T lymphocytes (cytotoxic T lymphocytes, CTLs), indicating enhanced immune activity and validating the practicality of APOBEC3C for guiding immunotherapy.
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Affiliation(s)
- Yunzhen Qian
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China.,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China
| | - Yitao Gong
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China.,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China
| | - Xuan Zou
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China.,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China
| | - Yu Liu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China.,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China
| | - Yusheng Chen
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China.,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China
| | - Ruijie Wang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China.,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China
| | - Zhengjie Dai
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China.,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China
| | - Yesiboli Tasiheng
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China.,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China
| | - Xuan Lin
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China.,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China
| | - Xu Wang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China.,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China
| | - Guopei Luo
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China.,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China
| | - Xianjun Yu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China. .,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China. .,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China. .,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China.
| | - He Cheng
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China. .,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China. .,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China. .,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China.
| | - Chen Liu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China. .,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China. .,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China. .,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China.
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38
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Chomiak AA, Guo Y, Kopsidas CA, McDaniel DP, Lowe CC, Pan H, Zhou X, Zhou Q, Doughty ML, Feng Y. Nde1 is required for heterochromatin compaction and stability in neocortical neurons. iScience 2022; 25:104354. [PMID: 35601919 PMCID: PMC9121328 DOI: 10.1016/j.isci.2022.104354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 03/28/2022] [Accepted: 04/29/2022] [Indexed: 11/20/2022] Open
Abstract
The NDE1 gene encodes a scaffold protein essential for brain development. Although biallelic NDE1 loss of function (LOF) causes microcephaly with profound mental retardation, NDE1 missense mutations and copy number variations are associated with multiple neuropsychiatric disorders. However, the etiology of the diverse phenotypes resulting from NDE1 aberrations remains elusive. Here we demonstrate Nde1 controls neurogenesis through facilitating H4K20 trimethylation-mediated heterochromatin compaction. This mechanism patterns diverse chromatin landscapes and stabilizes constitutive heterochromatin of neocortical neurons. We demonstrate that NDE1 can undergo dynamic liquid-liquid phase separation, partitioning to the nucleus and interacting with pericentromeric and centromeric satellite repeats. Nde1 LOF results in nuclear architecture aberrations and DNA double-strand breaks, as well as instability and derepression of pericentromeric satellite repeats in neocortical neurons. These findings uncover a pivotal role of NDE1/Nde1 in establishing and protecting neuronal heterochromatin. They suggest that heterochromatin instability predisposes a wide range of brain dysfunction.
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Affiliation(s)
- Alison A. Chomiak
- Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E. Superior Street, Chicago, IL 60611, USA
| | - Yan Guo
- Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E. Superior Street, Chicago, IL 60611, USA
| | - Caroline A. Kopsidas
- Department of Biochemistry and Molecular Biology, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Dennis P. McDaniel
- Biomedical Instrumentation Center, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Clara C. Lowe
- Department of Biochemistry and Molecular Biology, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Hongna Pan
- Department of Biochemistry and Molecular Biology, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Xiaoming Zhou
- Department of Medicine, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Qiong Zhou
- Department of Anatomy, Physiology, and Genetics, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Martin L. Doughty
- Department of Anatomy, Physiology, and Genetics, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Yuanyi Feng
- Department of Biochemistry and Molecular Biology, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
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39
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Ho AT, Hurst LD. Unusual mammalian usage of TGA stop codons reveals that sequence conservation need not imply purifying selection. PLoS Biol 2022; 20:e3001588. [PMID: 35550630 PMCID: PMC9129041 DOI: 10.1371/journal.pbio.3001588] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/24/2022] [Accepted: 04/20/2022] [Indexed: 11/18/2022] Open
Abstract
The assumption that conservation of sequence implies the action of purifying selection is central to diverse methodologies to infer functional importance. GC-biased gene conversion (gBGC), a meiotic mismatch repair bias strongly favouring GC over AT, can in principle mimic the action of selection, this being thought to be especially important in mammals. As mutation is GC→AT biased, to demonstrate that gBGC does indeed cause false signals requires evidence that an AT-rich residue is selectively optimal compared to its more GC-rich allele, while showing also that the GC-rich alternative is conserved. We propose that mammalian stop codon evolution provides a robust test case. Although in most taxa TAA is the optimal stop codon, TGA is both abundant and conserved in mammalian genomes. We show that this mammalian exceptionalism is well explained by gBGC mimicking purifying selection and that TAA is the selectively optimal codon. Supportive of gBGC, we observe (i) TGA usage trends are consistent at the focal stop codon and elsewhere (in UTR sequences); (ii) that higher TGA usage and higher TAA→TGA substitution rates are predicted by a high recombination rate; and (iii) across species the difference in TAA <-> TGA substitution rates between GC-rich and GC-poor genes is largest in genomes that possess higher between-gene GC variation. TAA optimality is supported both by enrichment in highly expressed genes and trends associated with effective population size. High TGA usage and high TAA→TGA rates in mammals are thus consistent with gBGC’s predicted ability to “drive” deleterious mutations and supports the hypothesis that sequence conservation need not be indicative of purifying selection. A general trend for GC-rich trinucleotides to reside at frequencies far above their mutational equilibrium in high recombining domains supports the generality of these results.
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Affiliation(s)
- Alexander Thomas Ho
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
- * E-mail:
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40
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Two-Dimensional Nanomaterial-based catalytic Medicine: Theories, advanced catalyst and system design. Adv Drug Deliv Rev 2022; 184:114241. [PMID: 35367308 DOI: 10.1016/j.addr.2022.114241] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/17/2022] [Accepted: 03/26/2022] [Indexed: 02/06/2023]
Abstract
Two-dimensional nanomaterial-based catalytic medicines that associate the superiorities of novel catalytic mechanisms with nanotechnology have emerged as absorbing therapeutic strategies for cancer therapy. Catalytic medicines featuring high efficiency and selectivity have been widely used as effective anticancer strategies without applying traditional nonselective and highly toxic chemodrugs. Moreover, two-dimensional nanomaterials are characterized by distinctive physicochemical properties, such as a sizeable bandgap, good conductivity, fast electron transfer and photoelectrochemical activity. The introduction of two-dimensional nanomaterials into catalytic medicine provides a more effective, controllable, and precise antitumor strategy. In this review, different types of two-dimensional nanomaterial-based catalytic nanomedicines are generalized, and their catalytic theories, advanced catalytic pathways and catalytic nanosystem design are also discussed in detail. Notably, future challenges and obstacles in the design and further clinical transformation of two-dimensional nanomaterial-based catalytic nanomedicine are prospected.
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41
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Wang Z, Zhang T, Wu W, Wu L, Li J, Huang B, Liang Y, Li Y, Li P, Li K, Wang W, Guo R, Wang Q. Detection and Localization of Solid Tumors Utilizing the Cancer-Type-Specific Mutational Signatures. Front Bioeng Biotechnol 2022; 10:883791. [PMID: 35547159 PMCID: PMC9081532 DOI: 10.3389/fbioe.2022.883791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/07/2022] [Indexed: 11/17/2022] Open
Abstract
Accurate detection and location of tumor lesions are essential for improving the diagnosis and personalized cancer therapy. However, the diagnosis of lesions with fuzzy histology is mainly dependent on experiences and with low accuracy and efficiency. Here, we developed a logistic regression model based on mutational signatures (MS) for each cancer type to trace the tumor origin. We observed MS could distinguish cancer from inflammation and healthy individuals. By collecting extensive datasets of samples from ten tumor types in the training cohort (5,001 samples) and independent testing cohort (2,580 samples), cancer-type-specific MS patterns (CTS-MS) were identified and had a robust performance in distinguishing different types of primary and metastatic solid tumors (AUC:0.76 ∼ 0.93). Moreover, we validated our model in an Asian population and found that the AUC of our model in predicting the tumor origin of the Asian population was higher than 0.7. The metastatic tumor lesions inherited the MS pattern of the primary tumor, suggesting the capability of MS in identifying the tissue-of-origin for metastatic cancers. Furthermore, we distinguished breast cancer and prostate cancer with 90% accuracy by combining somatic mutations and CTS-MS from cfDNA, indicating that the CTS-MS could improve the accuracy of cancer-type prediction by cfDNA. In summary, our study demonstrated that MS was a novel reliable biomarker for diagnosing solid tumors and provided new insights into predicting tissue-of-origin.
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Affiliation(s)
- Ziyu Wang
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Tingting Zhang
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Wei Wu
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Lingxiang Wu
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Jie Li
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Bin Huang
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Yuan Liang
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Yan Li
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Pengping Li
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Kening Li
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
- *Correspondence: Kening Li, ; Wei Wang, ; Renhua Guo, ; Qianghu Wang,
| | - Wei Wang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Kening Li, ; Wei Wang, ; Renhua Guo, ; Qianghu Wang,
| | - Renhua Guo
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Kening Li, ; Wei Wang, ; Renhua Guo, ; Qianghu Wang,
| | - Qianghu Wang
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
- *Correspondence: Kening Li, ; Wei Wang, ; Renhua Guo, ; Qianghu Wang,
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Siraj S, Masoodi T, Siraj AK, Azam S, Qadri Z, Parvathareddy SK, Bu R, Siddiqui KS, Al-Sobhi SS, AlDawish M, Al-Kuraya KS. APOBEC SBS13 Mutational Signature-A Novel Predictor of Radioactive Iodine Refractory Papillary Thyroid Carcinoma. Cancers (Basel) 2022; 14:cancers14061584. [PMID: 35326735 PMCID: PMC8946015 DOI: 10.3390/cancers14061584] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/03/2022] [Accepted: 03/15/2022] [Indexed: 02/04/2023] Open
Abstract
Standard surgery followed by radioactive iodine (131I, RAI) therapy are not curative for 5−20% of papillary thyroid carcinoma (PTC) patients with RAI refractory disease. Early predictors indicating therapeutic response to RAI therapy in PTC are yet to be elucidated. Whole-exome sequencing was performed (at median depth 198x) on 66 RAI-refractory and 92 RAI-avid PTCs with patient-matched germline. RAI-refractory tumors were significantly associated with distinct aggressive clinicopathological features, including positive surgical margins (p = 0.016) and the presence of lymph node metastases at primary diagnosis (p = 0.012); higher nonsilent tumor mutation burden (p = 0.011); TERT promoter (TERTp) mutation (p < 0.0001); and the enrichment of the APOBEC-related single-base substitution (SBS) COSMIC mutational signatures 2 (p = 0.030) and 13 (p < 0.001). Notably, SBS13 (odds ratio [OR] 30.4, 95% confidence intervals [CI] 1.43−647.22) and TERTp mutation (OR 41.3, 95% CI 4.35−391.60) were revealed to be independent predictors of RAI refractoriness in PTC (p = 0.029 and 0.001, respectively). Although SBS13 and TERTp mutations alone highly predicted RAI refractoriness, when combined, they significantly increased the likelihood of predicting RAI refractoriness in PTC. This study highlights the APOBEC SBS13 mutational signature as a novel independent predictor of RAI refractoriness in a distinct subgroup of PTC.
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Affiliation(s)
- Sarah Siraj
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.K.P.); (R.B.)
| | - Tariq Masoodi
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.K.P.); (R.B.)
| | - Abdul K. Siraj
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.K.P.); (R.B.)
| | - Saud Azam
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.K.P.); (R.B.)
| | - Zeeshan Qadri
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.K.P.); (R.B.)
| | - Sandeep K. Parvathareddy
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.K.P.); (R.B.)
| | - Rong Bu
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.K.P.); (R.B.)
| | - Khawar S. Siddiqui
- Department of Pediatric Hematology-Oncology, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, Riyadh 11211, Saudi Arabia;
| | - Saif S. Al-Sobhi
- Department of Surgery, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, Riyadh 11211, Saudi Arabia;
| | - Mohammed AlDawish
- Department of Endocrinology and Diabetes, Prince Sultan Military Medical City, P.O. Box 261370, Riyadh 11342, Saudi Arabia;
| | - Khawla S. Al-Kuraya
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (S.S.); (T.M.); (A.K.S.); (S.A.); (Z.Q.); (S.K.P.); (R.B.)
- Correspondence: ; Tel.: +966-112-055-2167
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Muhammed A, D'Alessio A, Enica A, Talbot T, Fulgenzi CAM, Nteliopoulos G, Goldin RD, Cortellini A, Pinato DJ. Predictive biomarkers of response to immune checkpoint inhibitors in hepatocellular carcinoma. Expert Rev Mol Diagn 2022; 22:253-264. [PMID: 35236211 DOI: 10.1080/14737159.2022.2049244] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Hepatocellular carcinoma (HCC) is the most common primary liver cancer and fourth leading cause of cancer death. While drug discovery to improve disease survival was historically poor, there is now evidence of significant potential for immune checkpoint inhibitors (ICPIs) in treatment of the disease, and indeed such drug approvals are beginning to emerge. AREAS COVERED HCC typically arises in the context of cirrhosis and chronic liver disease (CLD), and HCC exhibits significant biological heterogeneity, in part reflecting the broad range of aetiologies of CLD. Different classes and combinations of ICPI-based therapy exist, but not all patients will respond and predictive biomarkers are not yet available to guide clinician decision making, unlike some other cancer types. In this review, we discuss the emerging biomarkers for ICPI sensitivity in HCC, including tumour genomic features, perturbation of the gut microbiome and systemic inflammatory markers. EXPERT OPINION Additional profiling studies are required to appreciate existing trends with clinical outcome and to further drive clinical studies in disease stratification by response. This will only be possible within collaborative and international efforts, especially regarding biopsy collection. A close collaboration between basic scientists and clinicians will be the key to shape the next future of HCC biomarker research.
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Affiliation(s)
| | - Antonio D'Alessio
- Department of Surgery & Cancer, Imperial College London, UK.,Department of Biomedical Sciences, Humanitas University, Italy
| | - Andrei Enica
- Department of Surgery & Cancer, Imperial College London, UK
| | - Thomas Talbot
- Department of Surgery & Cancer, Imperial College London, UK
| | - Claudia Angela Maria Fulgenzi
- Department of Surgery & Cancer, Imperial College London, UK.,Division of Medical Oncology, Policlinico Universitario Campus Bio-Medico, Rome, Italy
| | | | | | | | - David J Pinato
- Department of Surgery & Cancer, Imperial College London, UK.,Division of Oncology, Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy
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44
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Mammel AE, Hatch EM. Genome instability from nuclear catastrophe and DNA damage. Semin Cell Dev Biol 2022; 123:131-139. [PMID: 33839019 PMCID: PMC8494860 DOI: 10.1016/j.semcdb.2021.03.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/29/2021] [Indexed: 11/28/2022]
Abstract
The nuclear envelope compartmentalizes the eukaryotic genome, provides mechanical resistance, and regulates access to the chromatin. However, recent studies have identified several conditions where the nuclear membrane ruptures during interphase, breaking down this compartmentalization leading to DNA damage, chromothripsis, and kataegis. This review discusses three major circumstances that promote nuclear membrane rupture, nuclear deformation, chromatin bridges, and micronucleation, and how each of these nuclear catastrophes results in DNA damage. In addition, we highlight recent studies that demonstrate a single chromosome missegregation can initiate a cascade of events that lead to accumulating damage and even multiple rounds of chromothripsis.
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Affiliation(s)
- Anna E. Mammel
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Emily M. Hatch
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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45
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Yamaguchi M, Nakaoka H, Suda K, Yoshihara K, Ishiguro T, Yachida N, Saito K, Ueda H, Sugino K, Mori Y, Yamawaki K, Tamura R, Revathidevi S, Motoyama T, Tainaka K, Verhaak RGW, Inoue I, Enomoto T. Spatiotemporal dynamics of clonal selection and diversification in normal endometrial epithelium. Nat Commun 2022; 13:943. [PMID: 35177608 PMCID: PMC8854701 DOI: 10.1038/s41467-022-28568-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 02/02/2022] [Indexed: 12/15/2022] Open
Abstract
It has become evident that somatic mutations in cancer-associated genes accumulate in the normal endometrium, but spatiotemporal understanding of the evolution and expansion of mutant clones is limited. To elucidate the timing and mechanism of the clonal expansion of somatic mutations in cancer-associated genes in the normal endometrium, we sequence 1311 endometrial glands from 37 women. By collecting endometrial glands from different parts of the endometrium, we show that multiple glands with the same somatic mutations occupy substantial areas of the endometrium. We demonstrate that “rhizome structures”, in which the basal glands run horizontally along the muscular layer and multiple vertical glands rise from the basal gland, originate from the same ancestral clone. Moreover, mutant clones detected in the vertical glands diversify by acquiring additional mutations. These results suggest that clonal expansions through the rhizome structures are involved in the mechanism by which mutant clones extend their territories. Furthermore, we show clonal expansions and copy neutral loss-of-heterozygosity events occur early in life, suggesting such events can be tolerated many years in the normal endometrium. Our results of the evolutionary dynamics of mutant clones in the human endometrium will lead to a better understanding of the mechanisms of endometrial regeneration during the menstrual cycle and the development of therapies for the prevention and treatment of endometrium-related diseases. Through regeneration, the endometrium accumulates somatic mutations that can lead to diseases like endometriosis and cancer. Here, the authors use genomics to analyse normal endometrial glands from different patient cohorts, detect rhizome structures with common clonal ancestors and infer clonal expansion dynamics.
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Affiliation(s)
- Manako Yamaguchi
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Hirofumi Nakaoka
- Human Genetics Laboratory, National Institute of Genetics, Mishima, 411-8540, Japan. .,Department of Cancer Genome Research, Sasaki Institute, Sasaki Foundation, Chiyoda-ku, 101-0062, Japan.
| | - Kazuaki Suda
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan.
| | - Tatsuya Ishiguro
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Nozomi Yachida
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Kyota Saito
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Haruka Ueda
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Kentaro Sugino
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Yutaro Mori
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Kaoru Yamawaki
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Ryo Tamura
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | | | - Teiichi Motoyama
- Department of Molecular and Diagnostic Pathology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan
| | - Kazuki Tainaka
- Department of System Pathology for Neurological Disorders, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan.,Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, 565-5241, Japan
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.,Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV, Amsterdam, The Netherlands
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima, 411-8540, Japan.
| | - Takayuki Enomoto
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8510, Japan.
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46
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Wu L, Dias A, Diéguez L. Surface enhanced Raman spectroscopy for tumor nucleic acid: Towards cancer diagnosis and precision medicine. Biosens Bioelectron 2022; 204:114075. [DOI: 10.1016/j.bios.2022.114075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/13/2022] [Accepted: 02/02/2022] [Indexed: 11/25/2022]
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47
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Nambiar TS, Baudrier L, Billon P, Ciccia A. CRISPR-based genome editing through the lens of DNA repair. Mol Cell 2022; 82:348-388. [PMID: 35063100 PMCID: PMC8887926 DOI: 10.1016/j.molcel.2021.12.026] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 01/22/2023]
Abstract
Genome editing technologies operate by inducing site-specific DNA perturbations that are resolved by cellular DNA repair pathways. Products of genome editors include DNA breaks generated by CRISPR-associated nucleases, base modifications induced by base editors, DNA flaps created by prime editors, and integration intermediates formed by site-specific recombinases and transposases associated with CRISPR systems. Here, we discuss the cellular processes that repair CRISPR-generated DNA lesions and describe strategies to obtain desirable genomic changes through modulation of DNA repair pathways. Advances in our understanding of the DNA repair circuitry, in conjunction with the rapid development of innovative genome editing technologies, promise to greatly enhance our ability to improve food production, combat environmental pollution, develop cell-based therapies, and cure genetic and infectious diseases.
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Affiliation(s)
- Tarun S Nambiar
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Lou Baudrier
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N.W., Calgary, Alberta T2N 4N1, Canada
| | - Pierre Billon
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N.W., Calgary, Alberta T2N 4N1, Canada.
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
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48
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Jiang Z, Liao G, Yang Y, Lan Y, Xu L, Yan M, Zhou Y, Zhu J, Liu W, Bai J, Xiao Y, Li X. Analysis of Mutations and Dysregulated Pathways Unravels Carcinogenic Effect and Clinical Actionability of Mutational Processes. Front Cell Dev Biol 2021; 9:768981. [PMID: 34901014 PMCID: PMC8652146 DOI: 10.3389/fcell.2021.768981] [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: 09/01/2021] [Accepted: 11/04/2021] [Indexed: 12/13/2022] Open
Abstract
Somatic mutations accumulate over time in cancer cells as a consequence of mutational processes. However, the role of mutational processes in carcinogenesis remains poorly understood. Here, we infer the causal relationship between mutational processes and somatic mutations in 5,828 samples spanning 34 cancer subtypes. We found most mutational processes cause abundant recurrent mutations in cancer genes, while exceptionally ultraviolet exposure and altered activity of the error-prone polymerase bring a large number of recurrent non-driver mutations. Furthermore, some mutations are specifically induced by a certain mutational process, such as IDH1 p.R132H which is mainly caused by spontaneous deamination of 5-methylcytosine. At the pathway level, clock-like mutational processes extensively trigger mutations to dysregulate cancer signal transduction pathways. In addition, APOBEC mutational process destroys DNA double-strand break repair pathway, and bladder cancer patients with high APOBEC activity, though with homologous recombination proficient, show a significantly longer overall survival with platinum regimens. These findings help to understand how mutational processes act on the genome to promote carcinogenesis, and further, presents novel insights for cancer prevention and treatment, as our results showing, APOBEC mutagenesis and HRD synergistically contributed to the clinical benefits of platinum-based treatment.
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Affiliation(s)
- Zedong Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Gaoming Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yiran Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yujia Lan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Liwen Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Min Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yao Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jiali Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wei Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jing Bai
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.,Key Laboratory of High Throughput Omics Big Data for Cold Region's Major Diseases in Heilongjiang Province, Harbin, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.,Key Laboratory of High Throughput Omics Big Data for Cold Region's Major Diseases in Heilongjiang Province, Harbin, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.,Key Laboratory of High Throughput Omics Big Data for Cold Region's Major Diseases in Heilongjiang Province, Harbin, China
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Impact of the APOBEC3A/B deletion polymorphism on risk of ovarian cancer. Sci Rep 2021; 11:23463. [PMID: 34873230 PMCID: PMC8648731 DOI: 10.1038/s41598-021-02820-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 11/16/2021] [Indexed: 12/24/2022] Open
Abstract
A germline 29.5-kb deletion variant removes the 3’ end of the APOBEC3A gene and a large part of APOBEC3B, creating a hybrid gene that has been linked to increased APOBEC3 activity and DNA damage in human cancers. We genotyped the APOBEC3A/B deletion in hospital-based samples of 1398 Norwegian epithelial ovarian cancer patients without detected BRCA1/2 germline mutations and compared to 1,918 healthy female controls, to assess the potential cancer risk associated with the deletion. We observed an association between APOBEC3A/B status and reduced risk for ovarian cancer (OR = 0.75; CI = 0.61–0.91; p = 0.003) applying the dominant model. Similar results were found in other models. The association was observed both in non-serous and serous cases (dominant model: OR = 0.69; CI = 0.50–0.95; p = 0.018 and OR = 0.77; CI = 0.62–0.96; p = 0.019, respectively) as well as within high-grade serous cases (dominant model: OR = 0.79; CI = 0.59–1.05). For validation purposes, we mined an available large multinational GWAS-based data set of > 18,000 cases and > 26,000 controls for SNP rs12628403, known to be in linkage disequilibrium with the APOBEC3A/B deletion. We found a non-significant trend for SNP rs12628403 being linked to reduced risk of ovarian cancer in general and similar trends for all subtypes. For clear cell cancers, the risk reduction reached significance (OR = 0.85; CI = 0.69–1.00).
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50
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The optimal pH of AID is skewed from that of its catalytic pocket by DNA-binding residues and surface charge. Biochem J 2021; 479:39-55. [PMID: 34870314 DOI: 10.1042/bcj20210529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/02/2021] [Accepted: 12/06/2021] [Indexed: 11/17/2022]
Abstract
Activation-induced cytidine deaminase (AID) is a member of the apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) family of cytidine deaminases. AID mutates immunoglobulin loci to initiate secondary antibody diversification. The APOBEC3 (A3) sub-branch mutates viral pathogens in the cytosol and acidic endosomal compartments. Accordingly, AID functions optimally near neutral pH, while most A3s are acid-adapted (optimal pH 5.5-6.5). To gain a structural understanding for this pH disparity, we constructed high-resolution maps of AID catalytic activity vs pH. We found AID's optimal pH was 7.3 but it retained most (>70%) of the activity at pH 8. Probing of ssDNA-binding residues near the catalytic pocket, key for bending ssDNA into the pocket (e.g R25) yielded mutants with altered pH preference, corroborating previous findings that the equivalent residue in APOBEC3G (H216) underlies its acidic pH preference. AID from bony fish exhibited more basic optimal pH (pH 7.5-8.1) and several R25-equivalent mutants altered pH preference. Comparison of pH optima across the AID/APOBEC3 family revealed an inverse correlation between positive surface charge and overall catalysis. The paralogue with the most robust catalytic activity (APOBEC3A) has the lowest surface charge, most acidic pH preference, while the paralogue with the most lethargic catalytic rate (AID) has the most positive surface charge and highest optimal pH. We suggest one possible mechanism is through surface charge dictating an overall optimal pH that is different from the optimal pH of the catalytic pocket microenvironment. These findings illuminate an additional structural mechanism that regulates AID/APOBEC3 mutagenesis.
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