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Cannataro VL, Glasmacher KA, Hampson CE. Mutations, substitutions, and selection: Linking mutagenic processes to cancer using evolutionary theory. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167268. [PMID: 38823460 DOI: 10.1016/j.bbadis.2024.167268] [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: 02/14/2024] [Revised: 04/25/2024] [Accepted: 05/25/2024] [Indexed: 06/03/2024]
Abstract
Cancers are the product of evolutionary events, where molecular variation occurs and accumulates in tissues and tumors. Sequencing of this molecular variation informs not only which variants are driving tumorigenesis, but also the mechanisms behind what is fueling mutagenesis. Both of these details are crucial for preventing premature deaths due to cancer, whether it is by targeting the variants driving the cancer phenotype or by measures to prevent exogenous mutations from contributing to somatic evolution. Here, we review tools to determine both molecular signatures and cancer drivers, and avenues by which these metrics may be linked.
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Affiliation(s)
| | - Kira A Glasmacher
- Emmanuel College, 400 Fenway, Boston, MA 02115, United States of America
| | - Caralynn E Hampson
- Emmanuel College, 400 Fenway, Boston, MA 02115, United States of America
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2
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Raj A, Petreaca RC, Mirzaei G. Multi-Omics Integration for Liver Cancer Using Regression Analysis. Curr Issues Mol Biol 2024; 46:3551-3562. [PMID: 38666952 PMCID: PMC11049490 DOI: 10.3390/cimb46040222] [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: 02/18/2024] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Genetic biomarkers have played a pivotal role in the classification, prognostication, and guidance of clinical cancer therapies. Large-scale and multi-dimensional analyses of entire cancer genomes, as exemplified by projects like The Cancer Genome Atlas (TCGA), have yielded an extensive repository of data that holds the potential to unveil the underlying biology of these malignancies. Mutations stand out as the principal catalysts of cellular transformation. Nonetheless, other global genomic processes, such as alterations in gene expression and chromosomal re-arrangements, also play crucial roles in conferring cellular immortality. The incorporation of multi-omics data specific to cancer has demonstrated the capacity to enhance our comprehension of the molecular mechanisms underpinning carcinogenesis. This report elucidates how the integration of comprehensive data on methylation, gene expression, and copy number variations can effectively facilitate the unsupervised clustering of cancer samples. We have identified regressors that can effectively classify tumor and normal samples with an optimal integration of RNA sequencing, DNA methylation, and copy number variation while also achieving significant p-values. Further, these regressors were trained using linear and logistic regression with k-means clustering. For comparison, we employed autoencoder- and stacking-based omics integration and computed silhouette scores to evaluate the clusters. The proof of concept is illustrated using liver cancer data. Our analysis serves to underscore the feasibility of unsupervised cancer classification by considering genetic markers beyond mutations, thereby emphasizing the clinical relevance of additional global cellular parameters that contribute to the transformative process in cells. This work is clinically relevant because changes in gene expression and genomic re-arrangements have been shown to be signatures of cellular transformation across cancers, as well as in liver cancers.
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Affiliation(s)
- Aditya Raj
- Department of Electrical and Computer Engineering, The Ohio State University, Columbus, OH 43210, USA;
| | - Ruben C. Petreaca
- Department of Molecular Genetics, The Ohio State University, Marion, OH 43302, USA;
- Cancer Biology Program, The Ohio State University James Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Golrokh Mirzaei
- Department of Computer Science and Engineering, The Ohio State University, Marion, OH 43302, USA
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3
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Sugiyama T, Sanyal MR. Biochemical analysis of H 2O 2-induced mutation spectra revealed that multiple damages were involved in the mutational process. DNA Repair (Amst) 2024; 134:103617. [PMID: 38154332 PMCID: PMC10842480 DOI: 10.1016/j.dnarep.2023.103617] [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: 06/06/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 12/30/2023]
Abstract
Reactive oxygen species (ROS) are a major threat to genomic integrity and believed to be one of the etiologies of cancers. Here we developed a cell-free system to analyze ROS-induced mutagenesis, in which DNA was exposed to H2O2 and then subjected to translesion DNA synthesis by various DNA polymerases. Then, frequencies of mutations on the DNA products were determined by using next-generation sequencing technology. The majority of observed mutations were either C>A or G>A, caused by dAMP insertion at G and C residues, respectively. These mutations showed similar spectra to COSMIC cancer mutational signature 18 and 36, which are proposed to be caused by ROS. The in vitro mutations can be produced by replicative DNA polymerases (yeast DNA polymerase δ and ε), suggesting that ordinary DNA replication is sufficient to produce them. Very little G>A mutation was observed immediately after exposure to H2O2, but the frequency was increased during the 24 h after the ROS was removed, indicating that the initial oxidation product of cytosine needs to be maturated into a mutagenic lesion. Glycosylase-sensitivities of these mutations suggest that the C>A were made on 8-oxoguanine or Fapy-guanine, and that G>A were most likely made on 5-hydroxycytosine modification.
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Affiliation(s)
- Tomohiko Sugiyama
- Department of Biological Sciences, Ohio University, Athens, OH 45701, USA; Molecular and Cellular Biology Graduate Program, Ohio University, Athens, OH 45701, USA.
| | - Mahima R Sanyal
- Department of Biological Sciences, Ohio University, Athens, OH 45701, USA; Molecular and Cellular Biology Graduate Program, Ohio University, Athens, OH 45701, USA
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4
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Becchi T, Beltrame L, Mannarino L, Calura E, Marchini S, Romualdi C. A pan-cancer landscape of pathogenic somatic copy number variations. J Biomed Inform 2023; 147:104529. [PMID: 37858853 DOI: 10.1016/j.jbi.2023.104529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 09/13/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023]
Abstract
OBJECTIVE Copy number variations (CNVs) play crucial roles in physiological and pathological processes, including cancer. However, the functional implications of somatic CNVs in tumor progression and evolution remain unclear. This study focuses on identifying CNV alterations with high pathogenic potential that drive and sustain tumorigenesis, distinguishing them from passenger alterations that accumulate during tumor growth. Our goal is to explore the variability of CNVs across different tumor types and infer their impact on tumor cell functions. METHODS Starting from 7352 copy number profiles across 33 different cancer types, we infer the pathogenicity of each CNV and perform both intra- and inter-tumor analyses to predict the functional impact of different genomic patterns. We evaluate the actionability of genes belonging to altered regions and we correlate the presence of pathogenic regions with genome instability patterns and patients' survival. RESULTS Our analysis uncovered large heterogeneity among different tumors suggesting in many cases distinct genetic drivers of tumorigenesis. Recurrent genomic alterations frequently coincide with dysfunctional homologous recombination pathways and negative regulation of the immune system. In certain tumors, the number of pathogenic CNVs emerged as a prognostic biomarker, highlighting their significance in cancer progression. CONCLUSION This study contributes to elucidate the functional impact of pathogenic CNVs in tumor progression and sheds light on their potential as prognostic markers in specific cancer types.
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Affiliation(s)
- Tommaso Becchi
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Luca Beltrame
- Laboratory of Cancer Pharmacology, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano - Milan, Italy
| | - Laura Mannarino
- Laboratory of Cancer Pharmacology, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano - Milan, Italy; Department of Biomedical Sciences, Humanitas University, via Rita Levi Montalcini 4, 20072 Pieve Emanuele - Milan, Italy
| | - Enrica Calura
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Sergio Marchini
- Laboratory of Cancer Pharmacology, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano - Milan, Italy
| | - Chiara Romualdi
- Department of Biology, University of Padova, 35131 Padova, Italy.
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Li J, Chen Z, Xiao W, Liang H, Liu Y, Hao W, Zhang Y, Wei F. Chromosome instability region analysis and identification of the driver genes of the epithelial ovarian cancer cell lines A2780 and SKOV3. J Cell Mol Med 2023; 27:3259-3270. [PMID: 37525498 PMCID: PMC10623538 DOI: 10.1111/jcmm.17893] [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: 03/30/2023] [Revised: 07/17/2023] [Accepted: 07/22/2023] [Indexed: 08/02/2023] Open
Abstract
Epithelial ovarian cancer (EOC) is one of the most prevalent gynaecological cancers worldwide. The molecular mechanisms of serous ovarian cancer (SOC) remain unclear and not well understood. SOC cases are primarily diagnosed at the late stage, resulting in a poor prognosis. Advances in molecular biology techniques allow us to obtain a better understanding of precise molecular mechanisms and to identify the chromosome instability region and key driver genes in the carcinogenesis and progression of SOC. Whole-exome sequencing was performed on the normal ovarian cell line IOSE80 and the EOC cell lines SKOV3 and A2780. The single-nucleotide variation burden, distribution, frequency and signature followed the known ovarian mutation profiles, without chromosomal bias. Recurrently mutated ovarian cancer driver genes, including LRP1B, KMT2A, ARID1A, KMT2C and ATRX were also found in two cell lines. The genome distribution of copy number alterations was found by copy number variation (CNV) analysis, including amplification of 17q12 and 4p16.1 and deletion of 10q23.33. The CNVs of MED1, GRB7 and MIEN1 located at 17q12 were found to be correlated with the overall survival of SOC patients (MED1: p = 0.028, GRB7: p = 0.0048, MIEN1: p = 0.0051), and the expression of the three driver genes in the ovarian cell line IOSE80 and EOC cell lines SKOV3 and A2780 was confirmed by western blot and cell immunohistochemistry.
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Affiliation(s)
- Jianxiong Li
- Department of GynecologyLonggang District Maternity and Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College)ShenzhenChina
| | - Zexin Chen
- Department of Cell Biology and Medical Genetics, School of Basic Medical SciencesGuangdong Pharmaceutical UniversityGuangzhouChina
| | - Wentao Xiao
- Department of GynecologyLonggang District Maternity and Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College)ShenzhenChina
| | - Huaguo Liang
- Department of Cell Biology and Medical Genetics, School of Basic Medical SciencesGuangdong Pharmaceutical UniversityGuangzhouChina
| | - Yanan Liu
- The Genetics LaboratoryLonggang District Maternity and Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College)ShenzhenChina
| | - Wenqi Hao
- The Genetics LaboratoryLonggang District Maternity and Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College)ShenzhenChina
| | - Yongli Zhang
- Department of Cell Biology and Medical Genetics, School of Basic Medical SciencesGuangdong Pharmaceutical UniversityGuangzhouChina
| | - Fengxiang Wei
- The Genetics LaboratoryLonggang District Maternity and Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College)ShenzhenChina
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Ng AS, Chan DKH. Commonalities and differences in the mutational signature and somatic driver mutation landscape across solid and hollow viscus organs. Oncogene 2023; 42:2713-2724. [PMID: 37573406 PMCID: PMC10491491 DOI: 10.1038/s41388-023-02802-7] [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: 06/08/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/14/2023]
Abstract
Advances in sequencing have revealed a highly variegated landscape of mutational signatures and somatic driver mutations in a range of normal tissues. Normal tissues accumulate mutations at varying rates ranging from 11 per cell per year in the liver, to 1879 per cell per year in the bladder. In addition, some normal tissues are also comprised of a large proportion of cells which possess driver mutations while appearing phenotypically normal, as in the oesophagus where a majority of cells harbour driver mutations. Individual tissue proliferation and mutation rate, unique mutagenic stimuli, and local tissue architecture contribute to this highly variegated landscape which confounds the functional characterization of driver mutations found in normal tissue. In particular, our understanding of the relationship between normal tissue somatic mutations and tumour initiation or future cancer risk remains poor. Here, we describe the mutational signatures and somatic driver mutations in solid and hollow viscus organs, highlighting unique characteristics in a tissue-specific manner, while simultaneously seeking to describe commonalities which can bring forward a basic unified theory on the role of these driver mutations in tumour initiation. We discuss novel findings which can be used to inform future research in this field.
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Affiliation(s)
- Aik Seng Ng
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Dedrick Kok Hong Chan
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Division of Colorectal Surgery, University Surgical Cluster, National University Hospital, Singapore, Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK.
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Laufer VA, Glover TW, Wilson TE. Applications of advanced technologies for detecting genomic structural variation. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108475. [PMID: 37931775 PMCID: PMC10792551 DOI: 10.1016/j.mrrev.2023.108475] [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: 04/26/2023] [Revised: 09/07/2023] [Accepted: 11/02/2023] [Indexed: 11/08/2023]
Abstract
Chromosomal structural variation (SV) encompasses a heterogenous class of genetic variants that exerts strong influences on human health and disease. Despite their importance, many structural variants (SVs) have remained poorly characterized at even a basic level, a discrepancy predicated upon the technical limitations of prior genomic assays. However, recent advances in genomic technology can identify and localize SVs accurately, opening new questions regarding SV risk factors and their impacts in humans. Here, we first define and classify human SVs and their generative mechanisms, highlighting characteristics leveraged by various SV assays. We next examine the first-ever gapless assembly of the human genome and the technical process of assembling it, which required third-generation sequencing technologies to resolve structurally complex loci. The new portions of that "telomere-to-telomere" and subsequent pangenome assemblies highlight aspects of SV biology likely to develop in the near-term. We consider the strengths and limitations of the most promising new SV technologies and when they or longstanding approaches are best suited to meeting salient goals in the study of human SV in population-scale genomics research, clinical, and public health contexts. It is a watershed time in our understanding of human SV when new approaches are expected to fundamentally change genomic applications.
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Affiliation(s)
- Vincent A Laufer
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Thomas W Glover
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Thomas E Wilson
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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Sherwood K, Ward JC, Soriano I, Martin L, Campbell A, Rahbari R, Kafetzopoulos I, Sproul D, Green A, Sampson JR, Donaldson A, Ong KR, Heinimann K, Nielsen M, Thomas H, Latchford A, Palles C, Tomlinson I. Germline de novo mutations in families with Mendelian cancer syndromes caused by defects in DNA repair. Nat Commun 2023; 14:3636. [PMID: 37336879 PMCID: PMC10279637 DOI: 10.1038/s41467-023-39248-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 05/31/2023] [Indexed: 06/21/2023] Open
Abstract
DNA repair defects underlie many cancer syndromes. We tested whether de novo germline mutations (DNMs) are increased in families with germline defects in polymerase proofreading or base excision repair. A parent with a single germline POLE or POLD1 mutation, or biallelic MUTYH mutations, had 3-4 fold increased DNMs over sex-matched controls. POLE had the largest effect. The DNMs carried mutational signatures of the appropriate DNA repair deficiency. No DNM increase occurred in offspring of MUTYH heterozygous parents. Parental DNA repair defects caused about 20-150 DNMs per child, additional to the ~60 found in controls, but almost all extra DNMs occurred in non-coding regions. No increase in post-zygotic mutations was detected, excepting a child with bi-allelic MUTYH mutations who was excluded from the main analysis; she had received chemotherapy and may have undergone oligoclonal haematopoiesis. Inherited DNA repair defects associated with base pair-level mutations increase DNMs, but phenotypic consequences appear unlikely.
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Affiliation(s)
- Kitty Sherwood
- Cancer Research UK Edinburgh Centre and MRC Human Genetics Unit, Institute of Genomics and Cancer, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Joseph C Ward
- Dept of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Ignacio Soriano
- Dept of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Lynn Martin
- Institute of Cancer and Genomic Sciences, University of Birmingham Medical School, Vincent Drive, Edgbaston, Birmingham, B15 2JJ, UK
| | - Archie Campbell
- Centre for Genetics and Experimental Medicine, Institute of Genetics and Cancer, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Raheleh Rahbari
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ioannis Kafetzopoulos
- Cancer Research UK Edinburgh Centre and MRC Human Genetics Unit, Institute of Genomics and Cancer, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Duncan Sproul
- Cancer Research UK Edinburgh Centre and MRC Human Genetics Unit, Institute of Genomics and Cancer, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Andrew Green
- Department of Clinical Genetics, Children's Health Ireland and School of Medicine University College, Dublin, Ireland
| | - Julian R Sampson
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Alan Donaldson
- Bristol Regional Clinical Genetics Service, St Michael's Hospital, Southwell Street, Bristol, BS2 8EG, UK
| | - Kai-Ren Ong
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Karl Heinimann
- Institute for Medical Genetics and Pathology, University Hospital Basel, Basel, BS, Switzerland
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Centre, 2333 ZA, Leiden, the Netherlands
| | - Huw Thomas
- St Mark's Hospital, Watford Road, Harrow, HA1 3UJ, UK
| | | | - Claire Palles
- Institute of Cancer and Genomic Sciences, University of Birmingham Medical School, Vincent Drive, Edgbaston, Birmingham, B15 2JJ, UK.
| | - Ian Tomlinson
- Dept of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.
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Homan EJ, Bremel RD. Determinants of tumor immune evasion: the role of T cell exposed motif frequency and mutant amino acid exposure. Front Immunol 2023; 14:1155679. [PMID: 37215122 PMCID: PMC10196236 DOI: 10.3389/fimmu.2023.1155679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/17/2023] [Indexed: 05/24/2023] Open
Abstract
Few neoepitopes detected in tumor biopsies are immunogenic. Tumor-specific T cell responses require both the presentation of an epitope that differs from wildtype and the presence of T cells with neoepitope-cognate receptors. We show that mutations detected in tumor biopsies result in an increased frequency of rare amino acid combinations compared to the human proteome and gastrointestinal microorganisms. Mutations in a large data set of oncogene and tumor suppressor gene products were compared to wildtype, and to the count of corresponding amino acid motifs in the human proteome and gastrointestinal microbiome. Mutant amino acids in T cell exposed positions of potential neoepitopes consistently generated amino acid motifs that are less common in both proteome reference datasets. Approximately 10% of the mutant amino acid motifs are absent from the human proteome. Motif frequency does not change when mutants were positioned in the MHC anchor positions hidden from T cell receptors. Analysis of neoepitopes in GBM and LUSC cases showed less common T cell exposed motifs, and HLA binding preferentially placing mutant amino acids in an anchor position for both MHC I and MHC II. Cross-presentation of mutant exposed neoepitopes by MHC I and MHC II was particularly uncommon. Review of a tumor mutation dataset known to generate T cell responses showed immunogenic epitopes were those with mutant amino acids exposed to the T cell receptor and with exposed pentamer motifs present in the human and microbiome reference databases. The study illustrates a previously unrecognized mechanism of tumor immune evasion, as rare T cell exposed motifs produced by mutation are less likely to have cognate T cells in the T cell repertoire. The complex interactions of HLA genotype, binding positions, and mutation specific changes in T cell exposed motif underscore the necessity of evaluating potential neoepitopes in each individual patient.
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10
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Ralston NVC. Concomitant selenoenzyme inhibitor exposures as etiologic contributors to disease: Implications for preventative medicine. Arch Biochem Biophys 2023; 733:109469. [PMID: 36423662 DOI: 10.1016/j.abb.2022.109469] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022]
Abstract
The physiological activities of selenium (Se) occur through enzymes that incorporate selenocysteine (Sec), a rare but important amino acid. The human genome includes 25 genes coding for Sec that employ it to catalyze challenging reactions. Selenoenzymes control thyroid hormones, calcium activities, immune responses, and perform other vital roles, but most are devoted to preventing and reversing oxidative damage. As the most potent intracellular nucleophile (pKa 5.2), Sec is vulnerable to binding by metallic and organic soft electrophiles (E*). These electron poor reactants initially form covalent bonds with nucleophiles such as cysteine (Cys) whose thiol (pKa 8.3) forms adducts which function as suicide substrates for selenoenzymes. These adducts orient E* to interact with Sec and since Se has a higher affinity for E* than sulfur, the E* transfers to Sec and irreversibly inhibits the enzyme's activity. Organic electrophiles have lower Se-binding affinities than metallic E*, but exposure sources are more abundant. Individuals with poor Se status are more vulnerable to the toxic effects of high E* exposures. The relative E*:Se stoichiometries remain undefined, but the aggregate effects of multiple E* exposures are predicted to be additive and possibly synergistic under certain conditions. The potential for the combined Se-binding effects of common pharmaceutical, dietary, or environmental E* require study, but even temporary loss of selenoenzyme activities would accentuate oxidative damage to tissues. As various degenerative diseases are associated with accumulating DNA damage, defining the effects of complementary E* exposures on selenoenzyme activities may enhance the ability of preventative medicine to support healthy aging.
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Affiliation(s)
- Nicholas V C Ralston
- Earth System Science and Policy, University of North Dakota, Grand Forks, ND, USA.
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11
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Herrington CS, Poulsom R, Pillay N, Bankhead P, Coates PJ. Recent Advances in Pathology: the 2022 Annual Review Issue of The Journal of Pathology. J Pathol 2022; 257:379-382. [PMID: 35635736 DOI: 10.1002/path.5972] [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] [Received: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 11/10/2022]
Abstract
The 2022 Annual Review Issue of The Journal of Pathology, Recent Advances in Pathology, contains 15 invited reviews on research areas of growing importance in pathology. This year, the articles include those that focus on digital pathology, employing modern imaging techniques and software to enable improved diagnostic and research applications to study human diseases. This subject area includes the ability to identify specific genetic alterations through the morphological changes they induce, as well as integrating digital and computational pathology with 'omics technologies. Other reviews in this issue include an updated evaluation of mutational patterns (mutation signatures) in cancer, the applications of lineage tracing in human tissues, and single cell sequencing technologies to uncover tumour evolution and tumour heterogeneity. The tissue microenvironment is covered in reviews specifically dealing with proteolytic control of epidermal differentiation, cancer-associated fibroblasts, field cancerisation, and host factors that determine tumour immunity. All of the reviews contained in this issue are the work of invited experts selected to discuss the considerable recent progress in their respective fields and are freely available online (https://onlinelibrary.wiley.com/journal/10969896). © 2022 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- C Simon Herrington
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Edinburgh Pathology, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Richard Poulsom
- The Pathological Society of Great Britain and Ireland, London, UK
| | - Nischalan Pillay
- Sarcoma Biology and Genomics Group, UCL Cancer Institute, London, UK
- Department of Histopathology, The Royal National Orthopaedic Hospital NHS Trust, London, UK
| | - Peter Bankhead
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Edinburgh Pathology, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Centre for Genomic & Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Philip J Coates
- RECAMO, Masaryk Memorial Cancer Institute, Brno, Czech Republic
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