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Cata JP, Sessler DI. Lost in Translation: Failure of Preclinical Studies to Accurately Predict the Effect of Regional Analgesia on Cancer Recurrence. Anesthesiology 2024; 140:361-374. [PMID: 38170786 DOI: 10.1097/aln.0000000000004823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The major goal of translational research is to evaluate the efficacy and effectiveness of treatments and interventions that have emerged from exhaustive preclinical evidence. In 2007, a major clinical trial was started to investigate the impact of paravertebral analgesia on breast cancer recurrence. The trial was based on preclinical evidence demonstrating that spinal anesthesia suppressed metastatic dissemination by inhibiting surgical stress, boosting the immunological response, avoiding volatile anesthetics, and reducing opioid use. However, that trial and three more recent randomized trials with a total of 4,770 patients demonstrate that regional analgesia does not improve survival outcomes after breast, lung, and abdominal cancers. An obvious question is why there was an almost complete disconnect between the copious preclinical investigations suggesting benefit and robust clinical trials showing no benefit? The answer is complex but may result from preclinical research being mechanistically driven and based on reductionist models. Both basic scientists and clinical investigators underestimated the limitations of various preclinical models, leading to the apparently incorrect hypothesis that regional anesthesia reduces cancer recurrence. This article reviews factors that contributed to the discordance between the laboratory science, suggesting that regional analgesia might reduce cancer recurrence and clinical trials showing that it does not-and what can be learned from the disconnect.
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Affiliation(s)
- Juan P Cata
- Department of Anesthesiology and Perioperative Medicine, The University of Texas-MD Anderson Cancer Center, Houston, Texas
| | - Daniel I Sessler
- Department of Outcomes Research, Cleveland Clinic, Cleveland, Ohio
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2
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Kozak M, Hu J. DNA Vaccines: Their Formulations, Engineering and Delivery. Vaccines (Basel) 2024; 12:71. [PMID: 38250884 PMCID: PMC10820593 DOI: 10.3390/vaccines12010071] [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: 12/13/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 01/23/2024] Open
Abstract
The concept of DNA vaccination was introduced in the early 1990s. Since then, advancements in the augmentation of the immunogenicity of DNA vaccines have brought this technology to the market, especially in veterinary medicine, to prevent many diseases. Along with the successful COVID mRNA vaccines, the first DNA vaccine for human use, the Indian ZyCovD vaccine against SARS-CoV-2, was approved in 2021. In the current review, we first give an overview of the DNA vaccine focusing on the science, including adjuvants and delivery methods. We then cover some of the emerging science in the field of DNA vaccines, notably efforts to optimize delivery systems, better engineer delivery apparatuses, identify optimal delivery sites, personalize cancer immunotherapy through DNA vaccination, enhance adjuvant science through gene adjuvants, enhance off-target and heritable immunity through epigenetic modification, and predict epitopes with bioinformatic approaches. We also discuss the major limitations of DNA vaccines and we aim to address many theoretical concerns.
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Affiliation(s)
- Michael Kozak
- The Jake Gittlen Laboratories for Cancer Research, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
- The Department of Pathology and Laboratory Medicine, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
| | - Jiafen Hu
- The Jake Gittlen Laboratories for Cancer Research, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
- The Department of Pathology and Laboratory Medicine, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
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3
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Nichols L, Lawrence R, Haboubi H, Al-Sarireh B, Doak S, Jenkins G. Measuring blood cell DNA damage using the PIG-A mutation and CBMN assay in pancreatic cancer patients: a pilot study. Mutagenesis 2023; 38:93-99. [PMID: 37006185 PMCID: PMC10181792 DOI: 10.1093/mutage/gead006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 03/29/2023] [Indexed: 04/04/2023] Open
Abstract
Pancreatic cancer still has one of the worst prognoses of all solid malignancies, despite developments in cancer knowledge and care. Research into pancreatic cancer has not fully translated into clinical improvements and as a result, fewer than 1% of patients survive 10 years post-diagnosis. This bleak outlook for patients could be improved by earlier diagnosis. The human erythrocyte phosphatidylinositol glycan class A (PIG-A) assay monitors the mutation status of the X-linked PIG-A gene by measuring glycosyl phosphatidylinositol (GPI)-anchored proteins on the extracellular surface. We have previously identified an elevated PIG-A mutant frequency in oesophageal adenocarcinoma patients and here investigate whether this could be seen in a pancreatic cancer cohort, given the urgent need for novel pancreatic cancer biomarkers. In our pilot study, an elevated PIG-A mutant frequency (5.775 × 10-6 (95% CI 4.777-10) mutants per million) was seen in pancreatic cancer patients (n = 30) when compared to the non-cancer control group (n = 14) who had an erythrocyte mutant frequency of 4.211 × 10-6 (95% CI 1.39-5.16) mutants per million (p = 0.0052). A cut-off value of 4.7 mutants per million provided an AUROC of 0.7595 with a sensitivity of 70% and specificity of 78.57%. A secondary measure of DNA damage in an alternative blood cell population also showed an increase in peripheral lymphocytes using the cytokinesis-block micronucleus assay (p = 0.0164) (AUROC = 0.77, sensitivity = 72.22%, specificity = 72.73%). The micronucleus frequency and PIG-A status show some potential as blood-based biomarkers of pancreatic cancer, but further investigations of these DNA damage tests are required to assess their utility in pancreatic cancer diagnosis.
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Affiliation(s)
- Lucy Nichols
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, United Kingdom
| | - Rachel Lawrence
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, United Kingdom
| | - Hasan Haboubi
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, United Kingdom
| | - Bilal Al-Sarireh
- Department of Pancreato-biliary surgery, Morriston Hospital, Swansea, United Kingdom
| | - Shareen Doak
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, United Kingdom
| | - Gareth Jenkins
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, United Kingdom
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4
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Homeostasis limits keratinocyte evolution. Proc Natl Acad Sci U S A 2022; 119:e2006487119. [PMID: 35998218 PMCID: PMC9436311 DOI: 10.1073/pnas.2006487119] [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] [Indexed: 12/02/2022] Open
Abstract
Human skin is riddled with mutations creating subclones of variable sizes. Some of these mutations are driver mutations, implicated in cancer development and progression, that appear to be under positive selection due to their relative sizes. We show how these driver and nondriver “passenger” mutations encode their history of division and loss within the tissue using a simple model combined with realistic mutation tracking. Using a three-dimensional in silico homeostatic epidermis model, we reveal that many mutations likely lack functional heterogeneity and are, instead, simply those that arise earlier in life within the basal layer. We use our model to reveal how functional differences conveyed by driver mutations could lead to a persistence phenotype while maintaining homeostasis. Recent studies have revealed that normal human tissues accumulate many somatic mutations. In particular, human skin is riddled with mutations, with multiple subclones of variable sizes. Driver mutations are frequent and tend to have larger subclone sizes, suggesting selection. To begin to understand the histories encoded by these complex somatic mutations, we incorporated genomes into a simple agent-based skin-cell model whose prime directive is homeostasis. In this model, stem-cell survival is random and dependent on proximity to the basement membrane. This simple homeostatic skin model recapitulates the observed log-linear distributions of somatic mutations, where most mutations are found in increasingly smaller subclones that are typically lost with time. Hence, neutral mutations are “passengers” whose fates depend on the random survival of their stem cells, where a rarer larger subclone reflects the survival and spread of mutations acquired earlier in life. The model can also maintain homeostasis and accumulate more frequent and larger driver subclones if these mutations (NOTCH1 and TP53) confer relatively higher persistence in normal skin or during tissue damage (sunlight). Therefore, a relatively simple model of epithelial turnover indicates how observed passenger and driver somatic mutations could accumulate without violating the prime directive of homeostasis in normal human tissues.
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5
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Distinguishing excess mutations and increased cell death based on variant allele frequencies. PLoS Comput Biol 2022; 18:e1010048. [PMID: 35468135 PMCID: PMC9071171 DOI: 10.1371/journal.pcbi.1010048] [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: 07/26/2021] [Revised: 05/05/2022] [Accepted: 03/22/2022] [Indexed: 12/03/2022] Open
Abstract
Tumors often harbor orders of magnitude more mutations than healthy tissues. The increased number of mutations may be due to an elevated mutation rate or frequent cell death and correspondingly rapid cell turnover, or a combination of the two. It is difficult to disentangle these two mechanisms based on widely available bulk sequencing data, where sequences from individual cells are intermixed and, thus, the cell lineage tree of the tumor cannot be resolved. Here we present a method that can simultaneously estimate the cell turnover rate and the rate of mutations from bulk sequencing data. Our method works by simulating tumor growth and finding the parameters with which the observed data can be reproduced with maximum likelihood. Applying this method to a real tumor sample, we find that both the mutation rate and the frequency of death may be high. Tumors frequently harbor an elevated number of mutations, compared to healthy tissue. These extra mutations may be generated either by an increased mutation rate or the presence of cell death resulting in increased cellular turnover and additional cell divisions for tumor growth. Separating the effects of these two factors is a nontrivial problem. Here we present a method which can simultaneously estimate cell turnover rate and genomic mutation rate from bulk sequencing data. Our method is based on the estimation of the parameters of a generative model of tumor growth and mutations. Applying our method to a human hepatocellular carcinoma sample reveals an elevated per cell division mutation rate and high cell turnover.
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6
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Somatic Mutations and Autoimmunity. Cells 2021; 10:cells10082056. [PMID: 34440825 PMCID: PMC8394445 DOI: 10.3390/cells10082056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 11/17/2022] Open
Abstract
Autoimmune diseases are among the most common chronic illness caused by a dysregulated immune response against self-antigens. Close to 5% of the general population in Western countries develops some form of autoimmunity, yet its underlying causes, although intensively studied, are still not fully known, and no curative therapies exist. It is well established that autoimmune diseases have common mechanisms and are caused by both genetic and non-genetic risk factors. One novel risk factor that can contribute to autoimmunity is somatic mutations, in a role parallel to their role in cancer. Somatic mutations are stochastic, de novo, non-inherited mutations. In this hypothesis, the persistent proliferation of self-reactive lymphocytes (that is usually hindered by a series of checkpoints) is permitted, due to somatic mutations in these expanding cells, allowing them to bypass multiple regulatory checkpoints, causing autoimmunity. This novel concept of the contribution of these mutations in non-malignant diseases has recently started to be explored. It proposes a novel paradigm for autoimmunity etiology and could be the missing piece of the autoimmunity puzzle.
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Gopal J, Prakash Sinnarasan VS, Venkatesan A. Identification of Repurpose Drugs by Computational Analysis of Disease-Gene-Drug Associations. J Comput Biol 2021; 28:975-984. [PMID: 34242526 DOI: 10.1089/cmb.2020.0356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Repurposing of marketed drugs to find new indications has become an alternative to circumvent the risk of traditional drug development by its productivity quality. Despite many approaches, computational analysis has great potential to fuel the development of all-rounder drugs to find new classes of medicine for neglected and rare disease. The genes that can explain variations in drug response associated to disease are more important and significant in drug therapeutics necessitate elucidating the relationships of a gene, drug, and disease. The proposed computational analysis facilitates the discovery of knowledge on both target and disease-based relationships from large sources of biomedical literature spread over different platforms. It uses the utility of text mining for automatic extraction of valuable aggregated biomedical entities (disease, gene, and drug) from PubMed to serves as an input to the analysis of association prediction. The top-ranked associations considered for identification of repurposing drugs and also the hidden associations identified using concurrence principle to extrapolate the new relationships. Such findings are reported as novel and contribute to the knowledge base for pharmacogenomics, would immensely support the discovery and progress of novel therapeutic pathways and patient segment biomarkers.
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Affiliation(s)
- Jeyakodi Gopal
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | | | - Amouda Venkatesan
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
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8
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Batool I, Bajcinca N. Evolution of cancer stem cell lineage involving feedback regulation. PLoS One 2021; 16:e0251481. [PMID: 34014979 PMCID: PMC8136751 DOI: 10.1371/journal.pone.0251481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 04/27/2021] [Indexed: 01/16/2023] Open
Abstract
Tumor emergence and progression is a complex phenomenon that assumes special molecular and cellular interactions. The hierarchical structuring and communication via feedback signaling of different cell types, which are categorized as the stem, progenitor, and differentiated cells in dependence of their maturity level, plays an important role. Under healthy conditions, these cells build a dynamical system that is responsible for facilitating the homeostatic regulation of the tissue. Generally, in this hierarchical setting, stem and progenitor cells are yet likely to undergo a mutation, when a cell divides into two daughter cells. This may lead to the development of abnormal characteristics, i.e. mutation in the cell, yielding an unrestrained number of cells. Therefore, the regulation of a stem cell’s proliferation and differentiation rate is crucial for maintaining the balance in the overall cell population. In this paper, a maturity based mathematical model with feedback regulation is formulated for healthy and mutated cell lineages. It is given in the form of coupled ordinary and partial differential equations. The focus is laid on the dynamical effects resulting from acquiring a mutation in the hierarchical structure of stem, progenitor and fully differentiated cells. Additionally, the effects of nonlinear feedback regulation from mature cells into both stem and progenitor cell populations have been inspected. The steady-state solutions of the model are derived analytically. Numerical simulations and results based on a finite volume scheme underpin various expected behavioral patterns of the homeostatic regulation and cancer evolution. For instance, it has been found that the mutated cells can experience significant growth even with a single somatic mutation, but under homeostatic regulation acquire a steady-state and thus, ensuing healthy cell population to either a steady-state or a lower cell concentration. Furthermore, the model behavior has been validated with different experimentally measured tumor values from the literature.
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Affiliation(s)
- Iqra Batool
- Faculty of Mechanical and Process Engineering, Technische Universität Kaiserslautern, Kaiserslautern, Rheinland Pfalz, Germany
| | - Naim Bajcinca
- Faculty of Mechanical and Process Engineering, Technische Universität Kaiserslautern, Kaiserslautern, Rheinland Pfalz, Germany
- * E-mail:
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9
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Kosanke M, Osetek K, Haase A, Wiehlmann L, Davenport C, Schwarzer A, Adams F, Kleppa MJ, Schambach A, Merkert S, Wunderlich S, Menke S, Dorda M, Martin U. Reprogramming enriches for somatic cell clones with small-scale mutations in cancer-associated genes. Mol Ther 2021; 29:2535-2553. [PMID: 33831558 DOI: 10.1016/j.ymthe.2021.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/03/2021] [Accepted: 04/02/2021] [Indexed: 02/06/2023] Open
Abstract
Cellular therapies based on induced pluripotent stem cells (iPSCs) come out of age and an increasing number of clinical trials applying iPSC-based transplants are ongoing or in preparation. Recent studies, however, demonstrated a high number of small-scale mutations in iPSCs. Although the mutational load in iPSCs seems to be largely derived from their parental cells, it is still unknown whether reprogramming may enrich for individual mutations that could lead to loss of functionality and tumor formation from iPSC derivatives. 30 hiPSC lines were analyzed by whole exome sequencing. High accuracy amplicon sequencing showed that all analyzed small-scale variants pre-existed in their parental cells and that individual mutations present in small subpopulations of parental cells become enriched among hiPSC clones during reprogramming. Among those, putatively actionable driver mutations affect genes related to cell-cycle control, cell death, and pluripotency and may confer a selective advantage during reprogramming. Finally, a short hairpin RNA (shRNA)-based experimental approach was applied to provide additional evidence for the individual impact of such genes on the reprogramming efficiency. In conclusion, we show that enriched mutations in curated onco- and tumor suppressor genes may account for an increased tumor risk and impact the clinical value of patient-derived hiPSCs.
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Affiliation(s)
- Maike Kosanke
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Katarzyna Osetek
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Alexandra Haase
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Lutz Wiehlmann
- Research Core Unit Genomics, Hannover Medical School, 30625 Hannover, Germany
| | - Colin Davenport
- Research Core Unit Genomics, Hannover Medical School, 30625 Hannover, Germany
| | - Adrian Schwarzer
- Department of Hematology, Oncology and Stem Cell Transplantation, Institute of Experimental Hematology, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Felix Adams
- Department of Hematology, Oncology and Stem Cell Transplantation, Institute of Experimental Hematology, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Marc-Jens Kleppa
- Department of Hematology, Oncology and Stem Cell Transplantation, Institute of Experimental Hematology, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Axel Schambach
- Department of Hematology, Oncology and Stem Cell Transplantation, Institute of Experimental Hematology, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Sylvia Merkert
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Stephanie Wunderlich
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Sandra Menke
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Marie Dorda
- Research Core Unit Genomics, Hannover Medical School, 30625 Hannover, Germany
| | - Ulrich Martin
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany.
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10
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Li D, Sun X, Yu F, Perle MA, Araten D, Boeke J. Application of counter-selectable marker PIGA in engineering designer deletion cell lines and characterization of CRISPR deletion efficiency. Nucleic Acids Res 2021; 49:2642-2654. [PMID: 33591308 PMCID: PMC7969003 DOI: 10.1093/nar/gkab035] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/11/2021] [Accepted: 02/15/2021] [Indexed: 12/18/2022] Open
Abstract
The CRISPR/Cas9 system is a technology for genome engineering, which has been applied to indel mutations in genes as well as targeted gene deletion and replacement. Here, we describe paired gRNA deletions along the PIGA locus on the human X chromosome ranging from 17 kb to 2 Mb. We found no compelling linear correlation between deletion size and the deletion efficiency, and there is no substantial impact of topologically associating domains on deletion frequency. Using this precise deletion technique, we have engineered a series of designer deletion cell lines, including one with deletions of two X-chromosomal counterselectable (negative selection) markers, PIGA and HPRT1, and additional cell lines bearing each individual deletion. PIGA encodes a component of the glycosylphosphatidylinositol (GPI) anchor biosynthetic apparatus. The PIGA gene counterselectable marker has unique features, including existing single cell level assays for both function and loss of function of PIGA and the existence of a potent counterselectable agent, proaerolysin, which we use routinely for selection against cells expressing PIGA. These designer cell lines may serve as a general platform with multiple selection markers and may be particularly useful for large scale genome engineering projects such as Genome Project-Write (GP-write).
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Affiliation(s)
- Donghui Li
- Institute for Systems Genetics and Department of Biochemistry & Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xiaoji Sun
- Institute for Systems Genetics and Department of Biochemistry & Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Fangzhou Yu
- Institute for Systems Genetics and Department of Biochemistry & Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Mary Ann Perle
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - David Araten
- Division of Hematology, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, and the New York VA Medical Center, New York, NY 10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry & Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn NY 11201, USA
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11
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Noë M, Hong SM, Wood LD, Thompson ED, Roberts NJ, Goggins MG, Klein AP, Eshleman JR, Kern SE, Hruban RH. Pancreatic cancer pathology viewed in the light of evolution. Cancer Metastasis Rev 2021; 40:661-674. [PMID: 33555482 PMCID: PMC8556193 DOI: 10.1007/s10555-020-09953-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/30/2020] [Indexed: 12/14/2022]
Abstract
One way to understand ductal adenocarcinoma of the pancreas (pancreatic cancer) is to view it as unimaginably large numbers of evolving living organisms interacting with their environment. This “evolutionary view” creates both expected and surprising perspectives in all stages of neoplastic progression. Advances in the field will require greater attention to this critical evolutionary prospective.
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Affiliation(s)
- Michaël Noë
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, The Johns Hopkins University School of Medicine, Carnegie 415, 600 North Wolfe Street, Baltimore, MD, 21287, USA
- Sol Goldman Pancreatic Cancer Research Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Seung-Mo Hong
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Laura D Wood
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, The Johns Hopkins University School of Medicine, Carnegie 415, 600 North Wolfe Street, Baltimore, MD, 21287, USA
- Sol Goldman Pancreatic Cancer Research Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Elizabeth D Thompson
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, The Johns Hopkins University School of Medicine, Carnegie 415, 600 North Wolfe Street, Baltimore, MD, 21287, USA
| | - Nicholas J Roberts
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, The Johns Hopkins University School of Medicine, Carnegie 415, 600 North Wolfe Street, Baltimore, MD, 21287, USA
- Sol Goldman Pancreatic Cancer Research Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Michael G Goggins
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, The Johns Hopkins University School of Medicine, Carnegie 415, 600 North Wolfe Street, Baltimore, MD, 21287, USA
- Sol Goldman Pancreatic Cancer Research Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Sol Goldman Pancreatic Cancer Research Center, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Alison P Klein
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, The Johns Hopkins University School of Medicine, Carnegie 415, 600 North Wolfe Street, Baltimore, MD, 21287, USA
- Sol Goldman Pancreatic Cancer Research Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Epidemiology, Bloomberg School of Public Health, The Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - James R Eshleman
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, The Johns Hopkins University School of Medicine, Carnegie 415, 600 North Wolfe Street, Baltimore, MD, 21287, USA
- Sol Goldman Pancreatic Cancer Research Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Scott E Kern
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, The Johns Hopkins University School of Medicine, Carnegie 415, 600 North Wolfe Street, Baltimore, MD, 21287, USA
- Sol Goldman Pancreatic Cancer Research Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Ralph H Hruban
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, The Johns Hopkins University School of Medicine, Carnegie 415, 600 North Wolfe Street, Baltimore, MD, 21287, USA.
- Sol Goldman Pancreatic Cancer Research Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
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12
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Guo SW. Cancer-associated mutations in endometriosis: shedding light on the pathogenesis and pathophysiology. Hum Reprod Update 2020; 26:423-449. [PMID: 32154564 DOI: 10.1093/humupd/dmz047] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 10/22/2019] [Accepted: 11/19/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Endometriosis is a benign gynaecological disease. Thus, it came as a complete surprise when it was reported recently that the majority of deep endometriosis lesions harbour somatic mutations and a sizeable portion of them contain known cancer-associated mutations (CAMs). Four more studies have since been published, all demonstrating the existence of CAMs in different subtypes of endometriosis. While the field is still evolving, the confirmation of CAMs has raised many questions that were previously overlooked. OBJECTIVE AND RATIONALE A comprehensive overview of CAMs in endometriosis has been produced. In addition, with the recently emerged understanding of the natural history of endometriotic lesions as well as CAMs in normal and apparently healthy tissues, this review attempts to address the following questions: Why has there been such a wild discrepancy in reported mutation frequencies? Why does ectopic endometrium have a higher mutation rate than that of eutopic endometrium? Would the presence of CAMs in endometriotic lesions increase the risk of cancer to the bearers? Why do endometriotic epithelial cells have much higher mutation frequencies than their stromal counterpart? What clinical implications, if any, do the CAMs have for the bearers? Do these CAMs tell us anything about the pathogenesis and/or pathophysiology of endometriosis? SEARCH METHODS The PubMed database was searched, from its inception to September 2019, for all papers in English using the term 'endometriosis and CAM', 'endometriosis and cancer-driver mutation', 'somatic mutations', 'fibrosis', 'fibrosis and epigenetic', 'CAMs and tumorigenesis', 'somatic mutation and normal tissues', 'oestrogen receptor and fibrosis', 'oxidative stress and fibrosis', 'ARID1A mutation', and 'Kirsten rat sarcoma mutation and therapeutics'. All retrieved papers were read and, when relevant, incorporated into the review results. OUTCOMES Seven papers that identified CAMs in endometriosis using various sequencing methods were retrieved, and their results were somewhat different. Yet, it is apparent that those using microdissection techniques and more accurate sequencing methods found more CAMs, echoing recent discoveries that apparently healthy tissues also harbour CAMs as a result of the replicative aging process. Hence endometriotic lesions, irrespective of subtype, if left intact, would generate CAMs as part of replicative aging, oxidative stress and perhaps other factors yet to be identified and, in some rare cases, develop cancer. The published data still are unable to paint a clear picture on pathogenesis of endometriosis. However, since endometriotic epithelial cells have a higher turnover than their stromal counterpart due to cyclic bleeding, and since the endometriotic stromal component can be formed by refresh influx of mesenchymal cells through epithelial-mesenchymal transition, endothelial-mesenchymal transition, mesothelial-mesenchymal transition and other processes as well as recruitment of bone-marrow-derived stem cells and outflow due to smooth muscle metaplasia, endometriotic epithelial cells have much higher mutation frequencies than their stromal counterpart. The epithelial and stromal cellular components develop in a dependent and co-evolving manner. Genes involved in CAMs are likely to be active players in lesional fibrogenesis, and hyperestrogenism and oxidative stress are likely drivers of both CAMs and fibrogenesis. Finally, endometriotic lesions harbouring CAMs would conceivably be more refractory to medical treatment, due, in no small part, to their high fibrotic content and reduced vascularity and cellularity. WIDER IMPLICATIONS The accumulating data on CAMs in endometriosis have shed new light on the pathogenesis and pathophysiology of endometriosis. They also suggest new challenges in management. The distinct yet co-evolving developmental trajectories of endometriotic stroma and epithelium underscore the importance of the lesional microenvironment and ever-changing cellular identity. Mutational profiling of normal endometrium from women of different ages and reproductive history is needed in order to gain a deeper understanding of the pathogenesis. Moreover, one area that has conspicuously received scant attention is the epigenetic landscape of ectopic, eutopic and normal endometrium.
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Affiliation(s)
- Sun-Wei Guo
- Shanghai Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, China.,Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Shanghai 200011, China
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13
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Dingli D. Computational and systems biology of cancer. COMPUTATIONAL AND SYSTEMS ONCOLOGY 2020. [DOI: 10.1002/cso2.1005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- David Dingli
- Division of Hematology, Department of Molecular Medicine Mayo Clinic Rochester Minnesota USA
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14
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Giles AR, Calcedo R, Tretiakova AP, Wilson JM. Isolating Human Monoclonal Antibodies Against Adeno-Associated Virus From Donors With Pre-existing Immunity. Front Immunol 2020; 11:1135. [PMID: 32733434 PMCID: PMC7358261 DOI: 10.3389/fimmu.2020.01135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/11/2020] [Indexed: 11/27/2022] Open
Abstract
With the advent of single B-cell cloning technology, we can isolate antibodies against virtually any antigen to study the interaction of a given pathogen with the immune system and develop novel therapeutic strategies. Antibodies directed against the capsid of adeno-associated viruses (AAV) are a significant obstacle to effectively leveraging AAV as a gene-delivery vector in seropositive individuals. In order to design next-generation vectors that can evade neutralization by these antibodies, studies have mapped the epitopes of mouse monoclonal antibodies generated by immunization with AAV. Although these studies provide critical information regarding capsid immunogenicity, they cannot address (1) differences in the antibody repertoire generated in humans following AAV natural infection; or (2) how reactions can vary when generated in response to vector administration. Here, we isolated and evaluated a panel of novel, fully human anti-AAV antibodies by cloning single memory B cells from a seropositive normal donor. We have validated the utility of this approach to study AAV immunology. Our goal is to leverage this knowledge to design novel AAV variants that can effectively transduce target tissues in individuals with AAV-neutralizing antibodies.
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Affiliation(s)
| | | | | | - James M. Wilson
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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15
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Tian X, Chen Y, Nakamura J. Development of a novel PIG-A gene mutation assay based on a GPI-anchored fluorescent protein sensor. Genes Environ 2019; 41:21. [PMID: 31867084 PMCID: PMC6902599 DOI: 10.1186/s41021-019-0135-6] [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: 10/09/2019] [Accepted: 11/14/2019] [Indexed: 11/19/2022] Open
Abstract
Background Accumulation of somatic mutations caused by both endogenous and exogenous exposures is a high risk for human health, in particular, cancer. Efficient detection of somatic mutations is crucial for risk assessment of different types of exposures. Due to its requirement in the process of attaching glycosylphatidylinositol- (GPI-) anchored proteins to the cell surface, the PIG-A gene located on the X-chromosome is used in both in vivo and in vitro mutation assays. Loss-of-function mutations in PIG-A lead to the elimination of GPI-anchored proteins such that they can no longer be detected on the cell surface by antibodies. Historically, mutation assays based on the PIG-A gene rely on the staining of these cell-surface proteins by antibodies; however, as with any antibody-based assay, there are major limitations, especially in terms of variability and lack of specific antibodies. Results In the current study, we developed a modified PIG-A mutation assay that uses the expression of GPI-anchored fluorescent proteins (henceforth referred to as a GPI-sensor), whereby the presence of fluorescence on the cell membrane is dependent on the expression of wild-type PIG-A. Using our modified PIG-A mutation assay, we have achieved complete separation of wild type cells and spontaneously mutated cells, in which the presence of PIG-A mutations has been confirmed via proaerolysin resistance and gene sequencing. Conclusion This study establishes a novel PIG-A mutation assay using GPI-anchored fluorescent protein expression that eliminates the need for antibody-based staining. This GPI-sensor PIG-A mutation assay should be widely applicable for accurate and efficient testing of genotoxicity for use in many mammalian and vertebrate cells.
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Affiliation(s)
- Xu Tian
- 1Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Youjun Chen
- 2Department of Neurology, UNC Neuroscience center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina USA
| | - Jun Nakamura
- 1Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC USA.,3Laboratory of Laboratory Animal Science, Graduate School of Life and Environmental Biosciences, Osaka Prefecture University, Izumisano, Osaka, Japan
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16
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Meynier S, Rieux-Laucat F. FAS and RAS related Apoptosis defects: From autoimmunity to leukemia. Immunol Rev 2019; 287:50-61. [PMID: 30565243 DOI: 10.1111/imr.12720] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 09/09/2018] [Indexed: 02/07/2023]
Abstract
The human adaptive immune system recognizes almost all the pathogens that we encounter and all the tumor antigens that may arise during our lifetime. Primary immunodeficiencies affecting lymphocyte development or function therefore lead to severe infections and tumor susceptibility. Furthermore, the fact that autoimmunity is a frequent feature of primary immunodeficiencies reveals a third function of the adaptive immune system: its self-regulation. Indeed, the generation of a broad repertoire of antigen receptors (via a unique strategy of random somatic rearrangements of gene segments in T cell and B cell receptor loci) inevitably creates receptors with specificity for self-antigens and thus leads to the presence of autoreactive lymphocytes. There are many different mechanisms for controlling the emergence or action of autoreactive lymphocytes, including clonal deletion in the primary lymphoid organs, receptor editing, anergy, suppression of effector lymphocytes by regulatory lymphocytes, and programmed cell death. Here, we review the genetic defects affecting lymphocyte apoptosis and that are associated with lymphoproliferation and autoimmunity, together with the role of somatic mutations and their potential involvement in more common autoimmune diseases.
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Affiliation(s)
- Sonia Meynier
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, INSERM UMR 1163, Paris, France.,Imagine Institute, Paris Descartes-Sorbonne Paris Cité University, Paris, France
| | - Frédéric Rieux-Laucat
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, INSERM UMR 1163, Paris, France.,Imagine Institute, Paris Descartes-Sorbonne Paris Cité University, Paris, France
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17
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Peterson LA, Ignatovich IV, Grill AE, Beauchamp A, Ho YY, DiLernia AS, Zhang L. Individual Differences in the Response of Human β-Lymphoblastoid Cells to the Cytotoxic, Mutagenic, and DNA-Damaging Effects of a DNA Methylating Agent, N-Methylnitrosourethane. Chem Res Toxicol 2019; 32:2214-2226. [PMID: 31589032 DOI: 10.1021/acs.chemrestox.9b00266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Metabolic activation of many carcinogens leads to formation of reactive intermediates that form DNA adducts. These adducts are cytotoxic when they interfere with cell division. They can also cause mutations by miscoding during DNA replication. Therefore, an individual's risk of developing cancer will depend on the balance between these processes as well as their ability to repair the DNA damage. Our hypothesis is that variations of genes participating in DNA damage repair and response pathways play significant roles in an individual's risk of developing tobacco-related cancers. To test this hypothesis, 61 human B-lymphocyte cell lines from the International HapMap project were phenotyped for their sensitivity to the cytotoxic and genotoxic properties of a model methylating agent, N-nitroso-N-methylurethane (NMUr). Cell viability was measured using a luciferase-based assay. Repair of the mutagenic and toxic DNA adduct, O6-methylguanine (O6-mG), was monitored by LC-MS/MS analysis. Genotoxic potential of NMUr was assessed employing a flow-cytometry based in vitro mutagenesis assay in the phosphatidylinositol-glycan biosynthesis class-A (PIG-A) gene. A wide distribution of responses to NMUr was observed with no correlation to gender or ethnicity. While the rate of O6-mG repair partially influenced the toxicity of NMUr, it did not appear to be the major factor affecting individual susceptibility to the mutagenic effects of NMUr. Genome-wide analysis identified several novel single nucleotide polymorphisms to be explored in future functional validation studies for a number of the toxicological end points.
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18
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Tomasetti C, Poling J, Roberts NJ, London NR, Pittman ME, Haffner MC, Rizzo A, Baras A, Karim B, Kim A, Heaphy CM, Meeker AK, Hruban RH, Iacobuzio-Donahue CA, Vogelstein B. Cell division rates decrease with age, providing a potential explanation for the age-dependent deceleration in cancer incidence. Proc Natl Acad Sci U S A 2019; 116:20482-20488. [PMID: 31548407 PMCID: PMC6789572 DOI: 10.1073/pnas.1905722116] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A new evaluation of previously published data suggested to us that the accumulation of mutations might slow, rather than increase, as individuals age. To explain this unexpected finding, we hypothesized that normal stem cell division rates might decrease as we age. To test this hypothesis, we evaluated cell division rates in the epithelium of human colonic, duodenal, esophageal, and posterior ethmoid sinonasal tissues. In all 4 tissues, there was a significant decrease in cell division rates with age. In contrast, cell division rates did not decrease in the colon of aged mice, and only small decreases were observed in their small intestine or esophagus. These results have important implications for understanding the relationship between normal stem cells, aging, and cancer. Moreover, they provide a plausible explanation for the enigmatic age-dependent deceleration in cancer incidence in very old humans but not in mice.
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Affiliation(s)
- Cristian Tomasetti
- Division of Biostatistics and Bioinformatics, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205;
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21205
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205
| | - Justin Poling
- Pathology, Williamson Medical Center, Brentwood, TN 37207
| | - Nicholas J Roberts
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21205
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University, Baltimore, MD 21231
| | - Nyall R London
- Department of Otolaryngology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Meredith E Pittman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065
| | - Michael C Haffner
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21205
- Department of Pathology, The Johns Hopkins University, Baltimore, MD 21231
| | - Anthony Rizzo
- Department of Pathology, The Johns Hopkins University, Baltimore, MD 21231
| | - Alex Baras
- Department of Pathology, The Johns Hopkins University, Baltimore, MD 21231
| | - Baktiar Karim
- Pathology & Histotechnology Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Antonio Kim
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21205
| | - Christopher M Heaphy
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21205
- Department of Pathology, The Johns Hopkins University, Baltimore, MD 21231
| | - Alan K Meeker
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21205
- Department of Pathology, The Johns Hopkins University, Baltimore, MD 21231
| | - Ralph H Hruban
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21205
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University, Baltimore, MD 21231
- Department of Pathology, The Johns Hopkins University, Baltimore, MD 21231
- Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Christine A Iacobuzio-Donahue
- Department of Pathology, Rubenstein Center for Pancreatic Cancer Research, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Bert Vogelstein
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21205;
- Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205
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19
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Bemis JC, Heflich RH. In vitro mammalian cell mutation assays based on the Pig-a gene: A report of the 7th International Workshop on Genotoxicity Testing (IWGT) Workgroup. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2019; 847:403028. [PMID: 31699348 DOI: 10.1016/j.mrgentox.2019.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/29/2019] [Accepted: 03/04/2019] [Indexed: 02/06/2023]
Abstract
Pig-a gene mutation assays enumerate cells with the glycosylphosphatidylinositol (GPI) anchor-deficient phenotype as a reporter of mutation in the endogenous Pig-a gene. Methods for measuring mutation in this gene are quite well established for in vivo systems. This approach to mutagenicity assessment has now been extended to in vitro mammalian cell-based systems. An expert workgroup from the 7th International Workshop on Genotoxicity Testing tasked with assessing the status of in vitro mammalian cell mutation assays has investigated the merits and limitations of in vitro Pig-a gene mutation assays. A review of the current status of these developing methodologies and the formation of consensus statements on the utility and application of these assays were performed to provide guidance for their potential use in genotoxicity hazard identification and risk assessment.
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Affiliation(s)
- J C Bemis
- Litron Laboratories, Rochester, NY, USA.
| | - R H Heflich
- US Food and Drug Administration, National Center for Toxicological Research, Jefferson, AR, USA
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20
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Abstract
Cell reprogramming has been considered a powerful technique in the regenerative medicine field. In addition to diverse its strengths, cell reprogramming technology also has several drawbacks generated during the process of reprogramming. Telomere shortening caused by the cell reprogramming process impedes the efficiency of cell reprogramming. Transcription factors used for reprogramming alter genomic contents and result in genetic mutations. Additionally, defective mitochondria functioning such as excessive mitochondrial fission leads to the limitation of pluripotency and ultimately reduces the efficiency of reprogramming. These problems including genomic instability and impaired mitochondrial dynamics should be resolved to apply cell reprograming in clinical research and to address efficiency and safety concerns. Sirtuin (NAD+-dependent histone deacetylase) has been known to control the chromatin state of the telomere and influence mitochondria function in cells. Recently, several studies reported that Sirtuins could control for genomic instability in cell reprogramming. Here, we review recent findings regarding the role of Sirtuins in cell reprogramming. And we propose that the manipulation of Sirtuins may improve defects that result from the steps of cell reprogramming.
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Affiliation(s)
- Jaein Shin
- Laboratory of Stem Cells and Cell Reprogramming, Department of Biomedical Engineering (BKplus21 team), Dongguk University, Seoul 04620, Korea
| | - Junyeop Kim
- Laboratory of Stem Cells and Cell Reprogramming, Department of Biomedical Engineering (BKplus21 team), Dongguk University, Seoul 04620, Korea
| | - Hanseul Park
- Laboratory of Stem Cells and Cell Reprogramming, Department of Biomedical Engineering (BKplus21 team), Dongguk University, Seoul 04620, Korea
| | - Jongpil Kim
- Laboratory of Stem Cells and Cell Reprogramming, Department of Biomedical Engineering (BKplus21 team), Dongguk University, Seoul 04620, and Department of Chemistry, Dongguk University, Seoul 04620, Korea
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21
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Wojdyla T, Mehta H, Glaubach T, Bertolusso R, Iwanaszko M, Braun R, Corey SJ, Kimmel M. Mutation, drift and selection in single-driver hematologic malignancy: Example of secondary myelodysplastic syndrome following treatment of inherited neutropenia. PLoS Comput Biol 2019; 15:e1006664. [PMID: 30615612 PMCID: PMC6336352 DOI: 10.1371/journal.pcbi.1006664] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/17/2019] [Accepted: 11/19/2018] [Indexed: 12/15/2022] Open
Abstract
Cancer development is driven by series of events involving mutations, which may become fixed in a tumor via genetic drift and selection. This process usually includes a limited number of driver (advantageous) mutations and a greater number of passenger (neutral or mildly deleterious) mutations. We focus on a real-world leukemia model evolving on the background of a germline mutation. Severe congenital neutropenia (SCN) evolves to secondary myelodysplastic syndrome (sMDS) and/or secondary acute myeloid leukemia (sAML) in 30–40%. The majority of SCN cases are due to a germline ELANE mutation. Acquired mutations in CSF3R occur in >70% sMDS/sAML associated with SCN. Hypotheses underlying our model are: an ELANE mutation causes SCN; CSF3R mutations occur spontaneously at a low rate; in fetal life, hematopoietic stem and progenitor cells expands quickly, resulting in a high probability of several tens to several hundreds of cells with CSF3R truncation mutations; therapeutic granulocyte colony-stimulating factor (G-CSF) administration early in life exerts a strong selective pressure, providing mutants with a growth advantage. Applying population genetics theory, we propose a novel two-phase model of disease development from SCN to sMDS. In Phase 1, hematopoietic tissues expand and produce tens to hundreds of stem cells with the CSF3R truncation mutation. Phase 2 occurs postnatally through adult stages with bone marrow production of granulocyte precursors and positive selection of mutants due to chronic G-CSF therapy to reverse the severe neutropenia. We predict the existence of the pool of cells with the mutated truncated receptor before G-CSF treatment begins. The model does not require increase in mutation rate under G-CSF treatment and agrees with age distribution of sMDS onset and clinical sequencing data. Cancer develops by multistep acquisition of mutations in a progenitor cell and its daughter cells. Severe congenital neutropenia (SCN) manifests itself through an inability to produce enough granulocytes to prevent infections. SCN commonly results from a germline ELANE mutation. Large doses of the blood growth factor granulocyte colony-stimulating factor (G-CSF) rescue granulocyte production. However, SCN frequently transforms to a myeloid malignancy, commonly associated with a somatic mutation in CSF3R, the gene encoding the G-CSF Receptor. We built a mathematical model of evolution for CSF3R mutation starting with bone marrow expansion at the fetal development stage and continuing with postnatal competition between normal and malignant bone marrow cells. We employ tools of probability theory such as multitype branching processes and Moran models modified to account for expansion of hematopoiesis during human development. With realistic coefficients, we obtain agreement with the age range at which malignancy arises in patients. In addition, our model predicts the existence of a pool of cells with mutated CSF3R before G-CSF treatment begins. Our findings may be clinically applied to intervene more effectively and selectively in SCN patients.
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Affiliation(s)
- Tomasz Wojdyla
- Systems Engineering Group, Silesian University of Technology, Gliwice, Poland
| | - Hrishikesh Mehta
- Department of Pediatrics, Cleveland Clinic, Cleveland, OH, United States of America
- Department of Cancer Biology, Cleveland Clinic, Cleveland, OH, United States of America
| | - Taly Glaubach
- Clinical Pediatrics, Division of Hospital Medicine, Stony Brook Children's Hospital, Stony Brook, New York
| | - Roberto Bertolusso
- Department of Statistics, Rice University, Houston, TX, United States of America
| | - Marta Iwanaszko
- Systems Engineering Group, Silesian University of Technology, Gliwice, Poland
- Department of Statistics, Rice University, Houston, TX, United States of America
- Department of Preventive Medicine–Division of Biostatistics, Northwestern University, Chicago, IL United States of America
| | - Rosemary Braun
- Department of Preventive Medicine–Division of Biostatistics, Northwestern University, Chicago, IL United States of America
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL United States of America
| | - Seth J. Corey
- Department of Pediatrics, Cleveland Clinic, Cleveland, OH, United States of America
- Department of Cancer Biology, Cleveland Clinic, Cleveland, OH, United States of America
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, United States of America
| | - Marek Kimmel
- Systems Engineering Group, Silesian University of Technology, Gliwice, Poland
- Department of Statistics, Rice University, Houston, TX, United States of America
- Department of Bioengineering, Rice University, Houston, TX, United States of America
- * E-mail:
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22
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Brody Y, Kimmerling RJ, Maruvka YE, Benjamin D, Elacqua JJ, Haradhvala NJ, Kim J, Mouw KW, Frangaj K, Koren A, Getz G, Manalis SR, Blainey PC. Quantification of somatic mutation flow across individual cell division events by lineage sequencing. Genome Res 2018; 28:1901-1918. [PMID: 30459213 PMCID: PMC6280753 DOI: 10.1101/gr.238543.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 10/27/2018] [Indexed: 02/06/2023]
Abstract
Mutation data reveal the dynamic equilibrium between DNA damage and repair processes in cells and are indispensable to the understanding of age-related diseases, tumor evolution, and the acquisition of drug resistance. However, available genome-wide methods have a limited ability to resolve rare somatic variants and the relationships between these variants. Here, we present lineage sequencing, a new genome sequencing approach that enables somatic event reconstruction by providing quality somatic mutation call sets with resolution as high as the single-cell level in subject lineages. Lineage sequencing entails sampling single cells from a population and sequencing subclonal sample sets derived from these cells such that knowledge of relationships among the cells can be used to jointly call variants across the sample set. This approach integrates data from multiple sequence libraries to support each variant and precisely assigns mutations to lineage segments. We applied lineage sequencing to a human colon cancer cell line with a DNA polymerase epsilon (POLE) proofreading deficiency (HT115) and a human retinal epithelial cell line immortalized by constitutive telomerase expression (RPE1). Cells were cultured under continuous observation to link observed single-cell phenotypes with single-cell mutation data. The high sensitivity, specificity, and resolution of the data provide a unique opportunity for quantitative analysis of variation in mutation rate, spectrum, and correlations among variants. Our data show that mutations arrive with nonuniform probability across sublineages and that DNA lesion dynamics may cause strong correlations between certain mutations.
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Affiliation(s)
- Yehuda Brody
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Robert J Kimmerling
- MIT Department of Biological Engineering, Cambridge, Massachusetts 02139, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts 02139, USA
| | - Yosef E Maruvka
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- MGH Cancer Center and Department of Pathology, Boston, Massachusetts 02114, USA
| | - David Benjamin
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Joshua J Elacqua
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- MIT Department of Biological Engineering, Cambridge, Massachusetts 02139, USA
| | - Nicholas J Haradhvala
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- MGH Cancer Center and Department of Pathology, Boston, Massachusetts 02114, USA
| | - Jaegil Kim
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kent W Mouw
- Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Kristjana Frangaj
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Gad Getz
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- MGH Cancer Center and Department of Pathology, Boston, Massachusetts 02114, USA
| | - Scott R Manalis
- MIT Department of Biological Engineering, Cambridge, Massachusetts 02139, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts 02139, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- MIT Department of Biological Engineering, Cambridge, Massachusetts 02139, USA
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23
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Saini N, Gordenin DA. Somatic mutation load and spectra: A record of DNA damage and repair in healthy human cells. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2018; 59:672-686. [PMID: 30152078 PMCID: PMC6188803 DOI: 10.1002/em.22215] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 06/07/2018] [Accepted: 06/11/2018] [Indexed: 05/31/2023]
Abstract
Somatic genome instability is a hallmark of cancer genomes and has been linked to aging and a variety of other pathologies. Large-scale cancer genome and exome sequencing have revealed that mutation load and spectra in cancers can be influenced by environmental exposures, the anatomical site of exposures, and tissue type. There is now an abundance of data favoring the hypothesis that a substantial portion of the mutations in cancers originate prior to carcinogenesis in stem cells of the healthy individual. Rapid advances in sequencing of noncancer cells from healthy humans have shown that their mutation loads and spectra resemble cancer data. Similar to cancer genomes, mutation profiles of healthy cells show marked intra-individual variation, thus providing a metric of the various factors-environmental and endogenous-involved in mutagenesis in these individuals. This review focuses on the current methodologies to measure mutation loads and to determine mutation signatures for evaluating the environmental and endogenous sources of DNA damage in human somatic cells. We anticipate that in future, such large-scale studies aimed at exploring the landscapes of somatic mutations across different cell types in healthy people would provide a valuable resource for designing personalized preventative strategies against diseases associated with somatic genome instability. Environ. Mol. Mutagen. 59:672-686, 2018. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.
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Affiliation(s)
- Natalie Saini
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Dmitry A. Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, USA
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24
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Yuan Y, Tang X, Bai YF, Wang S, An J, Wu Y, Xu ZQD, Zhang YA, Chen Z. Dopaminergic precursors differentiated from human blood-derived induced neural stem cells improve symptoms of a mouse Parkinson's disease model. Theranostics 2018; 8:4679-4694. [PMID: 30279731 PMCID: PMC6160767 DOI: 10.7150/thno.26643] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 08/09/2018] [Indexed: 11/18/2022] Open
Abstract
Autologous neural stem cells (NSCs) may offer a promising source for deriving dopaminergic (DA) cells for treatment of Parkinson's disease (PD). Methods: By using Sendai virus, human peripheral blood mononuclear cells (PBMNCs) were reprogrammed to induced NSCs (iNSCs), which were then differentiated to dopaminergic neurons in vitro. Whole-genome deep sequencing was performed to search for mutations that had accumulated during the reprogramming and expansion processes. To find the optimal differentiation stage of cells for transplantation, DA precursors obtained at various differentiation time points were tested by engraftment into brains of naïve immunodeficient mice. At last, the safety and efficacy of iNSC-derived DA precursors were tested by transplantation into the striatum of immunodeficient PD mouse models. Results: PBMNC-derived iNSCs showed similar characteristics to fetal NSCs, and were able to specifically differentiate to DA neurons with high efficiency in vitro. The sequencing data proved that no harmful SNVs, Indels and CNVs were generated during the reprogramming and expansion processes. DA precursors obtained between differentiation day 10 to 13 in vitro were most suitable for transplantation when a balanced graft survival and maturation were taken into account. Two weeks after transplantation of DA precursors into mouse PD models, the motor functions of PD mice started to improve, and continued to improve until the end of the experiments. No graft overgrowth or tumor was observed, and a significant number of A9-specific midbrain DA neurons were surviving in the striatum. Conclusion: This study confirmed the efficacy of iNSC-derived DA precursors in a mouse PD model, and emphasized the necessity of genomic sequencing and vigorous safety assessment before any clinical translation using iNSCs.
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25
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Lei K, Sun R, Chen LH, Diplas BH, Moure CJ, Wang W, Hansen LJ, Tao Y, Chen X, Chen CPJ, Greer PK, Zhao F, Yan H, Bigner DD, Huang J, He Y. Mutant allele quantification reveals a genetic basis for TP53 mutation-driven castration resistance in prostate cancer cells. Sci Rep 2018; 8:12507. [PMID: 30131529 PMCID: PMC6104024 DOI: 10.1038/s41598-018-30062-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 07/23/2018] [Indexed: 12/02/2022] Open
Abstract
The concept that human cancer is in essence a genetic disease driven by gene mutations has been well established, yet its utilization in functional studies of cancer genes has not been fully explored. Here, we describe a simple genetics-based approach that can quickly and sensitively reveal the effect of the alteration of a gene of interest on the fate of its host cells within a heterogeneous population, essentially monitoring the genetic selection that is associated with and powers the tumorigenesis. Using this approach, we discovered that loss-of-function of TP53 can promote the development of resistance of castration in prostate cancer cells via both transiently potentiating androgen-independent cell growth and facilitating the occurrence of genome instability. The study thus reveals a novel genetic basis underlying the development of castration resistance in prostate cancer cells and provides a facile genetic approach for studying a cancer gene of interest in versatile experimental conditions.
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Affiliation(s)
- Kefeng Lei
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA.,The Preston Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA.,General Surgery, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Zhejiang, 310014, China
| | - Ran Sun
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA.,The Preston Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA.,Scientific Research Center, China-Japan Union Hospital, Jilin University, Jilin, 130033, China
| | - Lee H Chen
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA.,The Preston Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA
| | - Bill H Diplas
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA.,The Preston Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA
| | - Casey J Moure
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA.,The Preston Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA
| | - Wenzhe Wang
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA.,The Preston Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA.,Center for Molecular Medicine, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, 310012, China
| | - Landon J Hansen
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA.,The Preston Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA
| | - Yulei Tao
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Xufeng Chen
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Chin-Pu Jason Chen
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA.,The Preston Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA
| | - Paula K Greer
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA.,The Preston Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA
| | | | - Hai Yan
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA.,The Preston Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA
| | - Darell D Bigner
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA.,The Preston Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA
| | - Jiaoti Huang
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Yiping He
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA. .,The Preston Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA.
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26
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Nicholson AM, Olpe C, Hoyle A, Thorsen AS, Rus T, Colombé M, Brunton-Sim R, Kemp R, Marks K, Quirke P, Malhotra S, Ten Hoopen R, Ibrahim A, Lindskog C, Myers MB, Parsons B, Tavaré S, Wilkinson M, Morrissey E, Winton DJ. Fixation and Spread of Somatic Mutations in Adult Human Colonic Epithelium. Cell Stem Cell 2018; 22:909-918.e8. [PMID: 29779891 PMCID: PMC5989058 DOI: 10.1016/j.stem.2018.04.020] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 02/16/2018] [Accepted: 04/23/2018] [Indexed: 12/21/2022]
Abstract
We investigated the means and timing by which mutations become fixed in the human colonic epithelium by visualizing somatic clones and mathematical inference. Fixation requires two sequential steps. First, one of approximately seven active stem cells residing within each colonic crypt has to be mutated. Second, the mutated stem cell has to replace neighbors to populate the entire crypt in a process that takes several years. Subsequent clonal expansion due to crypt fission is infrequent for neutral mutations (around 0.7% of all crypts undergo fission in a single year). Pro-oncogenic mutations subvert both stem cell replacement to accelerate fixation and clonal expansion by crypt fission to achieve high mutant allele frequencies with age. The benchmarking of these behaviors allows the advantage associated with different gene-specific mutations to be compared irrespective of the cellular mechanisms by which they are conferred.
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Affiliation(s)
- Anna M Nicholson
- Cancer Research-UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Cora Olpe
- Cancer Research-UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK; Wellcome Trust-Medical Research Council, Cambridge Stem Cell Institute, Cambridge, UK
| | - Alice Hoyle
- Cancer Research-UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Ann-Sofie Thorsen
- Cancer Research-UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Teja Rus
- Cancer Research-UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Mathilde Colombé
- Cancer Research-UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | | | - Richard Kemp
- Cancer Research-UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Kate Marks
- Pathology and Tumour Biology, Level 4, Wellcome Trust Brenner Building, St. James University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | - Phil Quirke
- Pathology and Tumour Biology, Level 4, Wellcome Trust Brenner Building, St. James University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | | | | | - Ashraf Ibrahim
- Department of Histopathology, Box 235, CUHFT, Cambridge, UK
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala 751 85, Sweden
| | - Meagan B Myers
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, HFT-120, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Barbara Parsons
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, HFT-120, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Simon Tavaré
- Cancer Research-UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Mark Wilkinson
- Norwich Research Park BioRepository, James Watson Road, Norwich NR4 7UQ, UK
| | - Edward Morrissey
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK.
| | - Douglas J Winton
- Cancer Research-UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
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27
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Teye EK, Sido A, Xin P, Finnberg NK, Gokare P, Kawasawa YI, Salzberg AC, Shimko S, Bayerl M, Ehmann WC, Claxton DF, Rybka WB, Drabick JJ, Wang HG, Abraham T, El-Deiry WS, Brodsky RA, J Hohl R, Pu JJ. PIGN gene expression aberration is associated with genomic instability and leukemic progression in acute myeloid leukemia with myelodysplastic features. Oncotarget 2018; 8:29887-29905. [PMID: 28187452 PMCID: PMC5444711 DOI: 10.18632/oncotarget.15136] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 01/11/2017] [Indexed: 11/26/2022] Open
Abstract
Previous studies have linked increased frequency of glycosylphosphatidylinositol-anchor protein (GPI-AP) deficiency with genomic instability and the risk of carcinogenesis. However, the underlying mechanism is still not clear. A randomForest analysis of the gene expression array data from 55 MDS patients (GSE4619) demonstrated a significant (p = 0.0007) correlation (Pearson r =-0.4068) between GPI-anchor biosynthesis gene expression and genomic instability, in which PIGN, a gene participating in GPI-AP biosynthesis, was ranked as the third most important in predicting risk of MDS progression. Furthermore, we observed that PIGN gene expression aberrations (increased transcriptional activity but diminished to no protein production) were associated with increased frequency of GPI-AP deficiency in leukemic cells during leukemic transformation/progression. PIGN gene expression aberrations were attributed to partial intron retentions between exons 14 and 15 resulting in frameshifts and premature termination which were confirmed by examining the RNA-seq data from a group of AML patients (phs001027.v1.p1). PIGN gene expression aberration correlated with the elevation of genomic instability marker expression that was independent of the TP53 regulatory pathway. Suppression/elimination of PIGN protein expression caused a similar pattern of genomic instability that was rescued by PIGN restoration. Finally, we found that PIGN bound to the spindle assembly checkpoint protein, MAD1, and regulated its expression during the cell cycle. In conclusion, PIGN gene is crucial in regulating mitotic integrity to maintain chromosomal stability and prevents leukemic transformation/progression.
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Affiliation(s)
- Emmanuel K Teye
- Penn State Hershey Cancer Institute and Department of Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - Abigail Sido
- Penn State Hershey Cancer Institute and Department of Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - Ping Xin
- Penn State Hershey Cancer Institute and Department of Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - Niklas K Finnberg
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Prashanth Gokare
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Yuka I Kawasawa
- Institute for Personalized Medicine and Departments of Pharmacology, Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - Anna C Salzberg
- Institute for Personalized Medicine and Departments of Pharmacology, Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - Sara Shimko
- Penn State Hershey Cancer Institute and Department of Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - Michael Bayerl
- Department of Pathology, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - W Christopher Ehmann
- Penn State Hershey Cancer Institute and Department of Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - David F Claxton
- Penn State Hershey Cancer Institute and Department of Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - Witold B Rybka
- Penn State Hershey Cancer Institute and Department of Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA.,Department of Pathology, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - Joseph J Drabick
- Penn State Hershey Cancer Institute and Department of Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - Hong-Gang Wang
- Department of Pediatrics, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - Thomas Abraham
- Department of Neural and Behavioral Science and the Microscopy Imaging Facility, Pennsylvania State University, Hershey, Pennsylvania, USA
| | - Wafik S El-Deiry
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Robert A Brodsky
- Division of Hematology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Raymond J Hohl
- Penn State Hershey Cancer Institute and Department of Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - Jeffrey J Pu
- Penn State Hershey Cancer Institute and Department of Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA.,Department of Pathology, Penn State University College of Medicine, Hershey, Pennsylvania, USA
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28
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Evensen NA, Madhusoodhan PP, Meyer J, Saliba J, Chowdhury A, Araten DJ, Nersting J, Bhatla T, Vincent TL, Teachey D, Hunger SP, Yang J, Schmiegelow K, Carroll WL. MSH6 haploinsufficiency at relapse contributes to the development of thiopurine resistance in pediatric B-lymphoblastic leukemia. Haematologica 2018; 103:830-839. [PMID: 29449434 PMCID: PMC5927991 DOI: 10.3324/haematol.2017.176362] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 07/02/2018] [Indexed: 01/10/2023] Open
Abstract
Survival of children with relapsed acute lymphoblastic leukemia is poor, and understanding mechanisms underlying resistance is essential to developing new therapy. Relapse-specific heterozygous deletions in MSH6, a crucial part of DNA mismatch repair, are frequently detected. Our aim was to determine whether MSH6 deletion results in a hypermutator phenotype associated with generation of secondary mutations involved in drug resistance, or if it leads to a failure to initiate apoptosis directly in response to chemotherapeutic agents. We knocked down MSH6 in mismatch repair proficient cell lines (697 and UOCB1) and showed significant increases in IC50s to 6-thioguanine and 6-mercaptopurine (697: 26- and 9-fold; UOCB1: 5- and 8-fold) in vitro, as well as increased resistance to 6-mercaptopurine treatment in vivo. No shift in IC50 was observed in deficient cells (Reh and RS4;11). 697 MSH6 knockdown resulted in increased DNA thioguanine nucleotide levels compared to non-targeted cells (3070 vs. 1722 fmol/μg DNA) with no difference observed in mismatch repair deficient cells. Loss of MSH6 did not give rise to microsatellite instability in cell lines or clinical samples, nor did it significantly increase mutation rate, but rather resulted in a defect in cell cycle arrest upon thiopurine exposure. MSH6 knockdown cells showed minimal activation of checkpoint regulator CHK1, γH2AX (DNA damage marker) and p53 levels upon treatment with thiopurines, consistent with intrinsic chemoresistance due to failure to recognize thioguanine nucleotide mismatching and initiate mismatch repair. Aberrant MSH6 adds to the list of alterations/mutations associated with acquired resistance to purine analogs emphasizing the importance of thiopurine therapy.
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Affiliation(s)
- Nikki A Evensen
- Departments of Pediatrics and Pathology, Perlmutter Cancer Center, NYU-Langone Medical Center, New York, NY, USA
| | - P Pallavi Madhusoodhan
- Departments of Pediatrics and Pathology, Perlmutter Cancer Center, NYU-Langone Medical Center, New York, NY, USA
| | - Julia Meyer
- Huntsman Cancer Institute, University of Utah Medical Center, Salt Lake City, USA
| | - Jason Saliba
- Departments of Pediatrics and Pathology, Perlmutter Cancer Center, NYU-Langone Medical Center, New York, NY, USA
| | - Ashfiyah Chowdhury
- Departments of Pediatrics and Pathology, Perlmutter Cancer Center, NYU-Langone Medical Center, New York, NY, USA
| | - David J Araten
- Department of Medicine, Perlmutter Cancer Center, NYU-Langone Medical Center, New York NY, USA
| | - Jacob Nersting
- Department of Pediatrics and Adolescent Medicine, The University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Teena Bhatla
- Departments of Pediatrics and Pathology, Perlmutter Cancer Center, NYU-Langone Medical Center, New York, NY, USA
| | - Tiffaney L Vincent
- Department of Pediatrics and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia and The Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA, USA
| | - David Teachey
- Department of Pediatrics and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia and The Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA, USA
| | - Stephen P Hunger
- Department of Pediatrics and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia and The Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA, USA
| | - Jun Yang
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kjeld Schmiegelow
- Department of Pediatrics and Adolescent Medicine, The University Hospital Rigshospitalet, Copenhagen, Denmark
| | - William L Carroll
- Departments of Pediatrics and Pathology, Perlmutter Cancer Center, NYU-Langone Medical Center, New York, NY, USA
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29
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Ortega MA, Poirion O, Zhu X, Huang S, Wolfgruber TK, Sebra R, Garmire LX. Using single-cell multiple omics approaches to resolve tumor heterogeneity. Clin Transl Med 2017; 6:46. [PMID: 29285690 PMCID: PMC5746494 DOI: 10.1186/s40169-017-0177-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 12/06/2017] [Indexed: 12/31/2022] Open
Abstract
It has become increasingly clear that both normal and cancer tissues are composed of heterogeneous populations. Genetic variation can be attributed to the downstream effects of inherited mutations, environmental factors, or inaccurately resolved errors in transcription and replication. When lesions occur in regions that confer a proliferative advantage, it can support clonal expansion, subclonal variation, and neoplastic progression. In this manner, the complex heterogeneous microenvironment of a tumour promotes the likelihood of angiogenesis and metastasis. Recent advances in next-generation sequencing and computational biology have utilized single-cell applications to build deep profiles of individual cells that are otherwise masked in bulk profiling. In addition, the development of new techniques for combining single-cell multi-omic strategies is providing a more precise understanding of factors contributing to cellular identity, function, and growth. Continuing advancements in single-cell technology and computational deconvolution of data will be critical for reconstructing patient specific intra-tumour features and developing more personalized cancer treatments.
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Affiliation(s)
- Michael A. Ortega
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI USA
| | - Olivier Poirion
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI USA
| | - Xun Zhu
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI USA
- Department of Molecular Biosciences and Bioengineering, Honolulu, HI USA
| | - Sijia Huang
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI USA
- Department of Molecular Biosciences and Bioengineering, Honolulu, HI USA
| | - Thomas K. Wolfgruber
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI USA
| | - Robert Sebra
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Lana X. Garmire
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI USA
- Department of Molecular Biosciences and Bioengineering, Honolulu, HI USA
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30
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Martin U. Genome stability of programmed stem cell products. Adv Drug Deliv Rev 2017; 120:108-117. [PMID: 28917518 DOI: 10.1016/j.addr.2017.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 08/31/2017] [Accepted: 09/07/2017] [Indexed: 01/23/2023]
Abstract
Inherited and acquired genomic abnormalities are known to cause genetic diseases and contribute to cancer formation. Recent studies demonstrated a substantial mutational load in mouse and human embryonic and induced pluripotent stem cells (ESCs and iPSCs). Single nucleotide variants, copy number variations, and larger chromosomal abnormalities may influence the differentiation capacity of pluripotent stem cells and the functionality of their derivatives in disease modeling and drug screening, and are considered a serious risk for cellular therapies based on ESC or iPSC derivatives. This review discusses the types and origins of different genetic abnormalities in pluripotent stem cells, methods for their detection, and the mechanisms of development and enrichment during reprogramming and culture expansion.
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Affiliation(s)
- Ulrich Martin
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH Cluster of Excellence, German Center for Lung Research, Hannover Medical School, Germany.
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31
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Axelrod DE, Bravo R. Chemoprevention of colon cancer: advantage of intermittent pulse treatment schedules quantified by computer simulation of human colon crypts. CONVERGENT SCIENCE PHYSICAL ONCOLOGY 2017. [DOI: 10.1088/2057-1739/aa82e6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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32
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Somatic mutations in clonally expanded cytotoxic T lymphocytes in patients with newly diagnosed rheumatoid arthritis. Nat Commun 2017. [PMID: 28635960 PMCID: PMC5482061 DOI: 10.1038/ncomms15869] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Somatic mutations contribute to tumorigenesis. Although these mutations occur in all proliferating cells, their accumulation under non-malignant conditions, such as in autoimmune disorders, has not been investigated. Here, we show that patients with newly diagnosed rheumatoid arthritis have expanded CD8+ T-cell clones; in 20% (5/25) of patients CD8+ T cells, but not CD4+ T cells, harbour somatic mutations. In healthy controls (n=20), only one mutation is identified in the CD8+ T-cell pool. Mutations exist exclusively in the expanded CD8+ effector-memory subset, persist during follow-up, and are predicted to change protein functions. Some of the mutated genes (SLAMF6, IRF1) have previously been associated with autoimmunity. RNA sequencing of mutation-harbouring cells shows signatures corresponding to cell proliferation. Our data provide evidence of accumulation of somatic mutations in expanded CD8+ T cells, which may have pathogenic significance for RA and other autoimmune diseases. Accumulation of somatic mutations in lymphocytes is a feature of some cancers. Here the authors show that patients with recent onset of rheumatoid arthritis also accumulate mutations in their expanded CD8+ effector memory T cell pool independent of cancer association.
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33
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Olsen AK, Dertinger SD, Krüger CT, Eide DM, Instanes C, Brunborg G, Hartwig A, Graupner A. The Pig-a Gene Mutation Assay in Mice and Human Cells: A Review. Basic Clin Pharmacol Toxicol 2017; 121 Suppl 3:78-92. [PMID: 28481423 DOI: 10.1111/bcpt.12806] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 05/01/2017] [Indexed: 01/08/2023]
Abstract
This MiniReview describes the principle of mutation assays based on the endogenous Pig-a gene and summarizes results for two species of toxicological interest, mice and human beings. The work summarized here largely avoids rat-based studies, as are summarized elsewhere. The Pig-a gene mutation assay has emerged as a valuable tool for quantifying in vivo and in vitro mutational events. The Pig-a locus is located at the X-chromosome, giving the advantage that one inactivated allele can give rise to a mutated phenotype, detectable by multicolour flow cytometry. For in vivo studies, only minute blood volumes are required, making it easily incorporated into ongoing studies or experiments with limited biological materials. Low blood volumes also allow individuals to serve as their own controls, providing temporal information of the mutagenic process, and/or outcome of intervention. These characteristics make it a promising exposure marker. To date, the Pig-a gene mutation assay has been most commonly performed in rats, while reports regarding its usefulness in other species are accumulating. Besides its applicability to in vivo studies, it holds promise for genotoxicity testing using cultured cells, as shown in recent studies. In addition to safety assessment roles, it is becoming a valuable tool in basic research to identify mutagenic effects of different interventions or to understand implications of various gene defects by investigating modified mouse models or cell systems. Human blood-based assays are also being developed that may be able to identify genotoxic environmental exposures, treatment- and lifestyle-related factors or endogenous host factors that contribute to mutagenesis.
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Affiliation(s)
- Ann-Karin Olsen
- Department of Molecular Biology, The Norwegian Institute of Public Health, Oslo, Norway.,Centre for Environmental Radioactivity (CERAD CoE), Norway
| | | | - Christopher T Krüger
- Food Chemistry and Toxicology, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Dag M Eide
- Centre for Environmental Radioactivity (CERAD CoE), Norway.,Department of Toxicology and Risk, The Norwegian Institute of Public Health, Oslo, Norway
| | - Christine Instanes
- Department of Molecular Biology, The Norwegian Institute of Public Health, Oslo, Norway.,Centre for Environmental Radioactivity (CERAD CoE), Norway
| | - Gunnar Brunborg
- Department of Molecular Biology, The Norwegian Institute of Public Health, Oslo, Norway.,Centre for Environmental Radioactivity (CERAD CoE), Norway
| | - Andrea Hartwig
- Food Chemistry and Toxicology, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Anne Graupner
- Department of Molecular Biology, The Norwegian Institute of Public Health, Oslo, Norway.,Centre for Environmental Radioactivity (CERAD CoE), Norway
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Affiliation(s)
- Ivana Bozic
- Program for Evolutionary Dynamics and
- Department of Mathematics, Harvard University, Cambridge, Massachusetts 02138
- Department of Applied Mathematics, University of Washington, Seattle, Washington 98195
| | - Martin A. Nowak
- Program for Evolutionary Dynamics and
- Department of Mathematics, Harvard University, Cambridge, Massachusetts 02138
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138
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35
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Sharma A, Ansari AH, Kumari R, Pandey R, Rehman R, Mehani B, Varma B, Desiraju BK, Mabalirajan U, Agrawal A, Mukhopadhyay A. Human brain harbors single nucleotide somatic variations in functionally relevant genes possibly mediated by oxidative stress. F1000Res 2017; 5:2520. [PMID: 28149503 DOI: 10.12688/f1000research.9495.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/08/2016] [Indexed: 12/11/2022] Open
Abstract
Somatic variation in DNA can cause cells to deviate from the preordained genomic path in both disease and healthy conditions. Here, using exome sequencing of paired tissue samples, we show that the normal human brain harbors somatic single base variations measuring up to 0.48% of the total variations. Interestingly, about 64% of these somatic variations in the brain are expected to lead to non-synonymous changes, and as much as 87% of these represent G:C>T:A transversion events. Further, the transversion events in the brain were mostly found in the frontal cortex, whereas the corpus callosum from the same individuals harbors the reference genotype. We found a significantly higher amount of 8-OHdG (oxidative stress marker) in the frontal cortex compared to the corpus callosum of the same subjects (p<0.01), correlating with the higher G:C>T:A transversions in the cortex. We found significant enrichment for axon guidance and related pathways for genes harbouring somatic variations. This could represent either a directed selection of genetic variations in these pathways or increased susceptibility of some loci towards oxidative stress. This study highlights that oxidative stress possibly influence single nucleotide somatic variations in normal human brain.
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Affiliation(s)
- Anchal Sharma
- Genomics & Molceular Medicine Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India
| | - Asgar Hussain Ansari
- Genomics & Molceular Medicine Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India
| | - Renu Kumari
- Genomics & Molceular Medicine Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India
| | - Rajesh Pandey
- CSIR Ayurgenomics Unit- TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Rakhshinda Rehman
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India; Molecular Immunogenetics Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Bharati Mehani
- Genomics & Molceular Medicine Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India
| | - Binuja Varma
- CSIR Ayurgenomics Unit- TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Bapu K Desiraju
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India; Molecular Immunogenetics Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Ulaganathan Mabalirajan
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India; Molecular Immunogenetics Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Anurag Agrawal
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India; Molecular Immunogenetics Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Arijit Mukhopadhyay
- Genomics & Molceular Medicine Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India; School of Environment and Life Sciences, University of Salford, Manchester, UK
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36
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Fortunato A, Boddy A, Mallo D, Aktipis A, Maley CC, Pepper JW. Natural Selection in Cancer Biology: From Molecular Snowflakes to Trait Hallmarks. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a029652. [PMID: 28148564 DOI: 10.1101/cshperspect.a029652] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Evolution by natural selection is the conceptual foundation for nearly every branch of biology and increasingly also for biomedicine and medical research. In cancer biology, evolution explains how populations of cells in tumors change over time. It is a fundamental question whether this evolutionary process is driven primarily by natural selection and adaptation or by other evolutionary processes such as founder effects and drift. In cancer biology, as in organismal evolutionary biology, there is controversy about this question and also about the use of adaptation through natural selection as a guiding framework for research. In this review, we discuss the differences and similarities between evolution among somatic cells versus evolution among organisms. We review what is known about the parameters and rate of evolution in neoplasms, as well as evidence for adaptation. We conclude that adaptation is a useful framework that accurately explains the defining characteristics of cancer. Further, convergent evolution through natural selection provides the only satisfying explanation both for how a group of diverse pathologies have enough in common to usefully share the descriptive label of "cancer" and for why this convergent condition becomes life-threatening.
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Affiliation(s)
- Angelo Fortunato
- Biodesign Center for Personalized Diagnostics, and School of Life Sciences, Arizona State University, Tempe, Arizona 85287
| | - Amy Boddy
- Department of Psychology, Arizona State University, Tempe, Arizona 85287
| | - Diego Mallo
- Biodesign Center for Personalized Diagnostics, and School of Life Sciences, Arizona State University, Tempe, Arizona 85287
| | - Athena Aktipis
- Department of Psychology, Arizona State University, Tempe, Arizona 85287.,Biodesign Center for Evolution and Medicine, Arizona State University, Tempe, Arizona 85287
| | - Carlo C Maley
- Biodesign Center for Personalized Diagnostics, and School of Life Sciences, Arizona State University, Tempe, Arizona 85287.,Centre for Evolution and Cancer, Institute of Cancer Research, London SM2 5NG, United Kingdom
| | - John W Pepper
- Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, Rockville, Maryland 20850.,Santa Fe Institute, Santa Fe, New Mexico 87501
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37
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Krichevsky S, Prus E, Perlman R, Fibach E, Ben-Yehuda D. The JAK2V617F mutation in normal individuals takes place in differentiating cells. Blood Cells Mol Dis 2017; 63:45-51. [PMID: 28126623 DOI: 10.1016/j.bcmd.2017.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 01/05/2017] [Accepted: 01/05/2017] [Indexed: 01/31/2023]
Abstract
The JAK2V617F mutation that results in a hyper-activation of the JAK2 kinase in the erythropoietin pathway is a molecular marker for myeloproliferative neoplasms. Using allele-specific Real-Time PCR, we detected the mutation in the blood of 17.3% (17/98) of normal donors; the mutant allele burden was, however, very low (<0.01% compared to >1% in polycythemia vera). It was much higher in differentiated blood cells in the peripheral blood than in undifferentiated CD34+ cells. Erythropoietin-stimulated differentiation of normal CD34+ cells in liquid culture increased the mutation frequency by 3.34-fold. When progenitors from 9 normal donors were grown in erythropoietin-stimulated semi-solid cultures, the mutation was found in 8.69% of the colonies, but only in <3% of the JAK2 alleles in each positive colony, suggesting that the mutation occurred only in a few cells per colony. In mouse erythroleukemia cells carrying human JAK2 DNA, wild-type or JAK2V617F, the frequencies of mutations from JAK2 wild-type to JAK2V617F and vice versa increased following erythroid differentiation. These results suggest that the mutation occurs and accumulates during differentiation. We hypothesize that genetic stability, which relies on DNA repair, is efficient in normal hematopoietic stem cells but is downgraded in differentiating cells, rendering them susceptible to mutations, including JAK2V617F.
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Affiliation(s)
- Svetlana Krichevsky
- Division of Hematology, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
| | - Eugenia Prus
- Division of Hematology, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
| | - Riki Perlman
- Division of Hematology, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
| | - Eitan Fibach
- Division of Hematology, Hadassah - Hebrew University Medical Center, Jerusalem, Israel.
| | - Dina Ben-Yehuda
- Division of Hematology, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
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38
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Wickliffe JK, Dertinger SD, Torous DK, Avlasevich SL, Simon-Friedt BR, Wilson MJ. Diet-induced obesity increases the frequency of Pig-a mutant erythrocytes in male C57BL/6J mice. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2016; 57:668-677. [PMID: 27739633 PMCID: PMC5118159 DOI: 10.1002/em.22058] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/12/2016] [Accepted: 09/14/2016] [Indexed: 05/10/2023]
Abstract
Obesity increases the risk of a number of chronic diseases in humans including several cancers. Biological mechanisms responsible for such increased risks are not well understood at present. Increases in systemic inflammation and oxidative stress, endogenous production of mutagenic metabolites, altered signaling in proliferative pathways, and increased sensitivity to exogenous mutagens and carcinogens are some of the potential contributing factors. We hypothesize that obesity creates an endogenously mutagenic environment in addition to increasing the sensitivity to environmental mutagens. To test this hypothesis, we examined two in vivo genotoxicity endpoints. Pig-a mutant frequencies and micronucleus frequencies were determined in blood cells in two independent experiments in 30-week old male mice reared on either a high-fat diet (60% calories from fat) that exhibit an obese phenotype or a normal-fat diet (10% calories from fat) that do not exhibit an obese phenotype. Mice were assayed again at 52 weeks of age in one of the experiments. N-ethyl-N-nitrosourea (ENU) was used as a positive mutation control in one experiment. ENU induced a robust Pig-a mutant and micronucleus response in both phenotypes. Obese, otherwise untreated mice, did not differ from non-obese mice with respect to Pig-a mutant frequencies in reticulocytes or micronucleus frequencies. However, such mice, had significantly higher and sustained Pig-a mutant frequencies (increased 2.5-3.7-fold, p < 0.02) in erythrocytes as compared to non-obese mice (based on measurements collected at 30 weeks or 30 and 52 weeks of age). This suggests that obesity, in the absence of exposure to an exogenous mutagen, is itself mutagenic. Environ. Mol. Mutagen. 57:668-677, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Jeffrey K. Wickliffe
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112 USA
| | | | | | | | - Bridget R. Simon-Friedt
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112 USA
| | - Mark J. Wilson
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112 USA
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39
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Saini N, Roberts SA, Klimczak LJ, Chan K, Grimm SA, Dai S, Fargo DC, Boyer JC, Kaufmann WK, Taylor JA, Lee E, Cortes-Ciriano I, Park PJ, Schurman SH, Malc EP, Mieczkowski PA, Gordenin DA. The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts. PLoS Genet 2016; 12:e1006385. [PMID: 27788131 PMCID: PMC5082821 DOI: 10.1371/journal.pgen.1006385] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/23/2016] [Indexed: 12/24/2022] Open
Abstract
Accumulation of somatic changes, due to environmental and endogenous lesions, in the human genome is associated with aging and cancer. Understanding the impacts of these processes on mutagenesis is fundamental to understanding the etiology, and improving the prognosis and prevention of cancers and other genetic diseases. Previous methods relying on either the generation of induced pluripotent stem cells, or sequencing of single-cell genomes were inherently error-prone and did not allow independent validation of the mutations. In the current study we eliminated these potential sources of error by high coverage genome sequencing of single-cell derived clonal fibroblast lineages, obtained after minimal propagation in culture, prepared from skin biopsies of two healthy adult humans. We report here accurate measurement of genome-wide magnitude and spectra of mutations accrued in skin fibroblasts of healthy adult humans. We found that every cell contains at least one chromosomal rearrangement and 600–13,000 base substitutions. The spectra and correlation of base substitutions with epigenomic features resemble many cancers. Moreover, because biopsies were taken from body parts differing by sun exposure, we can delineate the precise contributions of environmental and endogenous factors to the accrual of genetic changes within the same individual. We show here that UV-induced and endogenous DNA damage can have a comparable impact on the somatic mutation loads in skin fibroblasts. Somatic genomes are constantly accumulating changes caused by endogenous lesions, errors in DNA replication and repair, as well as environmental insults. Despite the importance of somatic genome instability in aging and age-related pathologies, including cancers, accurate measurements of mutation loads in healthy cells is still missing. In this study, we developed an experimental approach to accurately determine the somatic genome changes accrued in cell lineages over the lifetime of healthy humans. We show that the amounts and types of mutations in skin cells resemble many cancers, thus indicating that the mechanisms that lead to carcinogenesis are also functional in healthy cells. Moreover, sun-exposed skin cells have a higher mutation load attributable to ultraviolet radiation (UV) unlike cells from hips that were protected by clothing. Our work provides precise measurements of the mutation loads in single cells in human skin. Furthermore our data allowed defining the mutagenic impacts of environmental and endogenous processes within the same individual and led to conclusion that these processes have a comparable impact on the somatic mutation load.
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Affiliation(s)
- Natalie Saini
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
| | - Steven A. Roberts
- School of Molecular Biosciences, Washington State University, Pullman, Washington, United States Of America
| | - Leszek J. Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
| | - Kin Chan
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
| | - Sara A. Grimm
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
| | - Shuangshuang Dai
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
| | - David C. Fargo
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
| | - Jayne C. Boyer
- Department of Environmental Science and Engineering, University of North Carolina, Chapel Hill, North Carolina, United States Of America
| | - William K. Kaufmann
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina, United States Of America
| | - Jack A. Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
| | - Eunjung Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States Of America
- Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States Of America
| | - Isidro Cortes-Ciriano
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States Of America
| | - Peter J. Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States Of America
- Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States Of America
| | - Shepherd H. Schurman
- Clinical Research Unit, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
| | - Ewa P. Malc
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States Of America
| | - Piotr A. Mieczkowski
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States Of America
| | - Dmitry A. Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
- * E-mail:
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40
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Sharma A, Ansari AH, Kumari R, Pandey R, Rehman R, Mehani B, Varma B, Desiraju BK, Mabalirajan U, Agrawal A, Mukhopadhyay A. Human brain harbors single nucleotide somatic variations in functionally relevant genes possibly mediated by oxidative stress. F1000Res 2016; 5:2520. [PMID: 28149503 PMCID: PMC5265704 DOI: 10.12688/f1000research.9495.3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/11/2017] [Indexed: 12/14/2022] Open
Abstract
Somatic variation in DNA can cause cells to deviate from the preordained genomic
path in both disease and healthy conditions. Here, using exome sequencing of
paired tissue samples, we show that the normal human brain harbors somatic
single base variations measuring up to 0.48% of the total variations.
Interestingly, about 64% of these somatic variations in the brain are expected
to lead to non-synonymous changes, and as much as 87% of these represent
G:C>T:A transversion events. Further, the transversion events in the brain
were mostly found in the frontal cortex, whereas the corpus callosum from the
same individuals harbors the reference genotype. We found a significantly higher
amount of 8-OHdG (oxidative stress marker) in the frontal cortex compared to the
corpus callosum of the same subjects (p<0.01), correlating with the higher
G:C>T:A transversions in the cortex. We found significant enrichment for axon
guidance and related pathways for genes harbouring somatic variations. This
could represent either a directed selection of genetic variations in these
pathways or increased susceptibility of some loci towards oxidative stress. This
study highlights that oxidative stress possibly influence single nucleotide
somatic variations in normal human brain.
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Affiliation(s)
- Anchal Sharma
- Genomics & Molceular Medicine Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India
| | - Asgar Hussain Ansari
- Genomics & Molceular Medicine Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India
| | - Renu Kumari
- Genomics & Molceular Medicine Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India
| | - Rajesh Pandey
- CSIR Ayurgenomics Unit- TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Rakhshinda Rehman
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India; Molecular Immunogenetics Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Bharati Mehani
- Genomics & Molceular Medicine Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India
| | - Binuja Varma
- CSIR Ayurgenomics Unit- TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Bapu K Desiraju
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India; Molecular Immunogenetics Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Ulaganathan Mabalirajan
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India; Molecular Immunogenetics Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Anurag Agrawal
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India; Molecular Immunogenetics Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Arijit Mukhopadhyay
- Genomics & Molceular Medicine Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India; School of Environment and Life Sciences, University of Salford, Manchester, UK
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41
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Chen X, Shi X, Hilakivi-Clarke L, Shajahan-Haq AN, Clarke R, Xuan J. PSSV: a novel pattern-based probabilistic approach for somatic structural variation identification. Bioinformatics 2016; 33:177-183. [PMID: 27659451 DOI: 10.1093/bioinformatics/btw605] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 08/30/2016] [Accepted: 09/16/2016] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Whole genome DNA-sequencing (WGS) of paired tumor and normal samples has enabled the identification of somatic DNA changes in an unprecedented detail. Large-scale identification of somatic structural variations (SVs) for a specific cancer type will deepen our understanding of driver mechanisms in cancer progression. However, the limited number of WGS samples, insufficient read coverage, and the impurity of tumor samples that contain normal and neoplastic cells, limit reliable and accurate detection of somatic SVs. RESULTS We present a novel pattern-based probabilistic approach, PSSV, to identify somatic structural variations from WGS data. PSSV features a mixture model with hidden states representing different mutation patterns; PSSV can thus differentiate heterozygous and homozygous SVs in each sample, enabling the identification of those somatic SVs with heterozygous mutations in normal samples and homozygous mutations in tumor samples. Simulation studies demonstrate that PSSV outperforms existing tools. PSSV has been successfully applied to breast cancer data to identify somatic SVs of key factors associated with breast cancer development. AVAILABILITY AND IMPLEMENTATION An R package of PSSV is available at http://www.cbil.ece.vt.edu/software.htm CONTACT: xuan@vt.eduSupplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xi Chen
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Xu Shi
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Leena Hilakivi-Clarke
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Ayesha N Shajahan-Haq
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Robert Clarke
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Jianhua Xuan
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
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42
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Lindsay D, Garvey CM, Mumenthaler SM, Foo J. Leveraging Hypoxia-Activated Prodrugs to Prevent Drug Resistance in Solid Tumors. PLoS Comput Biol 2016; 12:e1005077. [PMID: 27560187 PMCID: PMC4999195 DOI: 10.1371/journal.pcbi.1005077] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/25/2016] [Indexed: 11/21/2022] Open
Abstract
Experimental studies have shown that one key factor in driving the emergence of drug resistance in solid tumors is tumor hypoxia, which leads to the formation of localized environmental niches where drug-resistant cell populations can evolve and survive. Hypoxia-activated prodrugs (HAPs) are compounds designed to penetrate to hypoxic regions of a tumor and release cytotoxic or cytostatic agents; several of these HAPs are currently in clinical trial. However, preliminary results have not shown a survival benefit in several of these trials. We hypothesize that the efficacy of treatments involving these prodrugs depends heavily on identifying the correct treatment schedule, and that mathematical modeling can be used to help design potential therapeutic strategies combining HAPs with standard therapies to achieve long-term tumor control or eradication. We develop this framework in the specific context of EGFR-driven non-small cell lung cancer, which is commonly treated with the tyrosine kinase inhibitor erlotinib. We develop a stochastic mathematical model, parametrized using clinical and experimental data, to explore a spectrum of treatment regimens combining a HAP, evofosfamide, with erlotinib. We design combination toxicity constraint models and optimize treatment strategies over the space of tolerated schedules to identify specific combination schedules that lead to optimal tumor control. We find that (i) combining these therapies delays resistance longer than any monotherapy schedule with either evofosfamide or erlotinib alone, (ii) sequentially alternating single doses of each drug leads to minimal tumor burden and maximal reduction in probability of developing resistance, and (iii) strategies minimizing the length of time after an evofosfamide dose and before erlotinib confer further benefits in reduction of tumor burden. These results provide insights into how hypoxia-activated prodrugs may be used to enhance therapeutic effectiveness in the clinic. It has been suggested that one key factor driving the emergence of drug resistance is the spatial heterogeneity in the distribution of drug and oxygen throughout a tumor due to disorganized tumor vasculatures. Researchers have developed a class of novel drugs that penetrate to hypoxic regions where they are activated to kill tumor cells. The inclusion of these drugs, called hypoxia-activated prodrugs (HAPs) alongside standard therapies in combination may be the key to long-term tumor control or eradication. However, identifying the right timing and administration sequence of combination therapies is an extremely difficult task, and the time and human costs of clinical trials to investigate even a few options is often prohibitive. In this work we design a mathematical model based upon evolutionary principles to investigate the potential of combining HAPs with standard targeted therapy for a specific example in non-small cell lung cancer. We formulate novel toxicity constraints from existing clinical data to estimate the shape of the tolerated drug combination treatment space. We find that (i) combining these therapies delays resistance longer than any monotherapy schedule with either evofosfamide or erlotinib alone, and (ii) the best strategy for combination involves single doses of each drug sequentially administered in an alternating sequence. These model predictions of tumor dynamics during treatment provide insight into the role of the tumor microenvironment in combination therapy and identify treatment hypotheses for further experimental and clinical testing.
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Affiliation(s)
- Danika Lindsay
- School of Mathematics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Colleen M. Garvey
- Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Shannon M. Mumenthaler
- Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, California, United States of America
- * E-mail: (SMM); (JF)
| | - Jasmine Foo
- School of Mathematics, University of Minnesota, Minneapolis, Minnesota, United States of America
- * E-mail: (SMM); (JF)
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Shahriyari L, Komarova NL, Jilkine A. The role of cell location and spatial gradients in the evolutionary dynamics of colon and intestinal crypts. Biol Direct 2016; 11:42. [PMID: 27549762 PMCID: PMC4994304 DOI: 10.1186/s13062-016-0141-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 07/15/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Colon and intestinal crypts serve as an important model system for adult stem cell proliferation and differentiation. We develop a spatial stochastic model to study the rate of somatic evolution in a normal crypt, focusing on the production of two-hit mutants that inactivate a tumor suppressor gene. We investigate the effect of cell division pattern along the crypt on mutant production, assuming that the division rate of each cell depends on its location. RESULTS We find that higher probability of division at the bottom of the crypt, where the stem cells are located, leads to a higher rate of double-hit mutant production. The optimal case for delaying mutations occurs when most of the cell divisions happen at the top of the crypt. We further consider an optimization problem where the "evolutionary" penalty for double-hit mutant generation is complemented with a "functional" penalty that assures that fully differentiated cells at the top of the crypt cannot divide. CONCLUSION The trade-off between the two types of objectives leads to the selection of an intermediate division pattern, where the cells in the middle of the crypt divide with the highest rate. This matches the pattern of cell divisions obtained experimentally in murine crypts. REVIEWERS This article was reviewed by David Axelrod (nominated by an Editorial Board member, Marek Kimmel), Yang Kuang and Anna Marciniak-Czochra. For the full reviews, please go to the Reviewers' comments section.
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Affiliation(s)
- Leili Shahriyari
- Mathematical Biosciences Institute, The Ohio State University, 1735 Neil Ave, Columbus, 43210, USA
| | - Natalia L Komarova
- Department of Mathematics, University of California Irvine, 340 Rowland Hall, Irvine, 92697, USA.
| | - Alexandra Jilkine
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, 153 Hurley Hall, Notre Dame, 46556, USA.
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Abstract
The large number of cell divisions required to make a human body inevitably leads to the accumulation of somatic mutations. Such mutations cause individuals to be somatic mosaics. Recent advances in genomic technology now allow measurement of somatic diversity. Initial studies confirmed the expected high levels of somatic mutations within individuals. Going forward, the big questions concern the degree to which those somatic mutations influence disease. Theory predicts that the frequency of mutant cells should vary greatly between individuals. Such somatic mutational variability between individuals could explain much of the diversity in the risk of disease. But how variable is mosaicism between individuals in reality? What is the relation between the fraction of cells carrying a predisposing mutation and the risk of disease? What kinds of heritable somatic change lead to disease besides classical DNA mutations? What molecular processes connect a predisposing somatic change to disease? We know that predisposing somatic mutations strongly influence the onset of cancer. Likewise, neurodegenerative diseases may often begin from somatically mutated cells. If so, both neurodegeneration and cancer may be diseases of later life for which much of the risk may be set by early life somatic mutations.
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Pu J, Deng Y, Tan X, Chen G, Zhu C, Qi N, Wen H, Guo J, Wang X, Qiu Y, Liang J, Fu X, Hu Y, Song J, Geng X, Wang C, Zhang L, Huang Z, Li B, Wang X. The in vivo Pig-a gene mutation assay is applied to study the genotoxicity of procarbazine hydrochloride in Sprague-Dawley rats. ACTA ACUST UNITED AC 2016. [DOI: 10.2131/fts.3.167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Jiang Pu
- National Centre for Safety Evaluation of Drugs, National Institutes for Food and Drug Control, China
- Sun Yat-sen University, China
| | - Yuanyuan Deng
- National Centre for Safety Evaluation of Drugs, National Institutes for Food and Drug Control, China
- National Centre for Safety Evaluation of Drugs, China
| | - Xiaoyan Tan
- National Centre for Safety Evaluation of Drugs, National Institutes for Food and Drug Control, China
- Sun Yat-sen University, China
| | - Gaofeng Chen
- National Centre for Safety Evaluation of Drugs, National Institutes for Food and Drug Control, China
- Sun Yat-sen University, China
| | - Cong Zhu
- National Centre for Safety Evaluation of Drugs, National Institutes for Food and Drug Control, China
- Sun Yat-sen University, China
| | - Naisong Qi
- National Centre for Safety Evaluation of Drugs, National Institutes for Food and Drug Control, China
| | - Hairuo Wen
- National Centre for Safety Evaluation of Drugs, National Institutes for Food and Drug Control, China
| | - Jun Guo
- National Centre for Safety Evaluation of Drugs, National Institutes for Food and Drug Control, China
| | - Xin Wang
- National Centre for Safety Evaluation of Drugs, National Institutes for Food and Drug Control, China
| | | | | | | | - Yanping Hu
- National Centre for Safety Evaluation of Drugs, National Institutes for Food and Drug Control, China
| | - Jie Song
- National Centre for Safety Evaluation of Drugs, National Institutes for Food and Drug Control, China
| | - Xingchao Geng
- National Centre for Safety Evaluation of Drugs, National Institutes for Food and Drug Control, China
| | - Chao Wang
- National Centre for Safety Evaluation of Drugs, National Institutes for Food and Drug Control, China
| | - Lin Zhang
- National Centre for Safety Evaluation of Drugs, National Institutes for Food and Drug Control, China
| | | | - Bo Li
- National Centre for Safety Evaluation of Drugs, National Institutes for Food and Drug Control, China
| | - Xue Wang
- National Centre for Safety Evaluation of Drugs, National Institutes for Food and Drug Control, China
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Infection of a Single Cell Line with Distinct Strains of Human Cytomegalovirus Can Result in Large Variations in Virion Production and Facilitate Efficient Screening of Virus Protein Function. J Virol 2015; 90:2523-35. [PMID: 26676783 DOI: 10.1128/jvi.01762-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 12/11/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Previously, we reported that the absence of the ataxia telangiectasia mutated (ATM) kinase, a critical DNA damage response (DDR) signaling component for double-strand breaks, caused no change in HCMV Towne virion production. Later, others reported decreased AD169 viral titers in the absence of ATM. To address this discrepancy, human foreskin fibroblasts (HFF) and three ATM(-) lines (GM02530, GM05823, and GM03395) were infected with both Towne and AD169. Two additional ATM(-) lines (GM02052 and GM03487) were infected with Towne. Remarkably, both previous studies' results were confirmed. However, the increased number of cell lines and infections with both lab-adapted strains confirmed that ATM was not necessary to produce wild-type-level titers in fibroblasts. Instead, interactions between individual virus strains and the cellular microenvironment of the individual ATM(-) line determined efficiency of virion production. Surprisingly, these two commonly used lab-adapted strains produced drastically different titers in one ATM(-) cell line, GM05823. The differences in titer suggested a rapid method for identifying genes involved in differential virion production. In silico comparison of the Towne and AD169 genomes determined a list of 28 probable candidates responsible for the difference. Using serial iterations of an experiment involving virion entry and input genome nuclear trafficking with a panel of related strains, we reduced this list to four (UL129, UL145, UL147, and UL148). As a proof of principle, reintroduction of UL148 largely rescued genome trafficking. Therefore, use of a battery of related strains offers an efficient method to narrow lists of candidate genes affecting various virus life cycle checkpoints. IMPORTANCE Human cytomegalovirus (HCMV) infection of multiple cell lines lacking ataxia telangiectasia mutated (ATM) protein produced wild-type levels of infectious virus. Interactions between virus strains and the microenvironment of individual ATM(-) lines determined the efficiency of virion production. Infection of one ATM(-) cell line, GM05823, produced large titer differentials dependent on the strain used, Towne or AD169. This discrepancy resolved a disagreement in the literature of a requirement for ATM expression and HCMV reproduction. The titer differentials in GM08523 cells were due, in part, to a decreased capacity of AD169 virions to enter the cell and traffic genomes to the nucleus. In silico comparison of the Towne, AD169, and related variant strains' genomes was coupled with serial iterations of a virus entry experiment, narrowing 28 candidate proteins responsible for the phenotype down to 4. Reintroduction of UL148 significantly rescued genome trafficking. Differential behavior of virus strains can be exploited to elucidate gene function.
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Fang LT, Afshar PT, Chhibber A, Mohiyuddin M, Fan Y, Mu JC, Gibeling G, Barr S, Asadi NB, Gerstein MB, Koboldt DC, Wang W, Wong WH, Lam HYK. An ensemble approach to accurately detect somatic mutations using SomaticSeq. Genome Biol 2015; 16:197. [PMID: 26381235 PMCID: PMC4574535 DOI: 10.1186/s13059-015-0758-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 08/20/2015] [Indexed: 12/03/2022] Open
Abstract
SomaticSeq is an accurate somatic mutation detection pipeline implementing a stochastic boosting algorithm to produce highly accurate somatic mutation calls for both single nucleotide variants and small insertions and deletions. The workflow currently incorporates five state-of-the-art somatic mutation callers, and extracts over 70 individual genomic and sequencing features for each candidate site. A training set is provided to an adaptively boosted decision tree learner to create a classifier for predicting mutation statuses. We validate our results with both synthetic and real data. We report that SomaticSeq is able to achieve better overall accuracy than any individual tool incorporated.
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Affiliation(s)
- Li Tai Fang
- Bina Technologies, Roche Sequencing, Redwood City, 94065, CA, USA. li\
| | | | - Aparna Chhibber
- Bina Technologies, Roche Sequencing, Redwood City, 94065, CA, USA.
| | | | - Yu Fan
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA.
| | - John C Mu
- Bina Technologies, Roche Sequencing, Redwood City, 94065, CA, USA.
| | - Greg Gibeling
- Bina Technologies, Roche Sequencing, Redwood City, 94065, CA, USA.
| | - Sharon Barr
- Bina Technologies, Roche Sequencing, Redwood City, 94065, CA, USA.
| | | | - Mark B Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, 06520, CT, USA.
| | - Daniel C Koboldt
- The Genome Institute, Washington University in St Louis, St Louis, 63108, MO, USA.
| | - Wenyi Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA.
| | - Wing H Wong
- Department of Statistics, Stanford University, Stanford, 94305, CA, USA.
- Department of Health Research and Policy, Stanford University, Stanford, 94305, CA, USA.
| | - Hugo Y K Lam
- Bina Technologies, Roche Sequencing, Redwood City, 94065, CA, USA.
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Affiliation(s)
- Lucio Luzzatto
- From the Istituto Toscano Tumori and University of Firenze, Florence, Italy (L.L.); and the Cancer Research Institute and Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston (P.P.P.)
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Sanal MG. Cell therapy from bench to bedside: Hepatocytes from fibroblasts - the truth and myth of transdifferentiation. World J Gastroenterol 2015; 21:6427-6433. [PMID: 26074681 PMCID: PMC4458753 DOI: 10.3748/wjg.v21.i21.6427] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 03/24/2015] [Accepted: 05/07/2015] [Indexed: 02/06/2023] Open
Abstract
Hepatocyte transplantation is an alternative to liver transplantation in certain disorders such as inherited liver diseases and liver failure. It is a relatively less complicated surgical procedure, and has the advantage that it can be repeated several times if unsuccessful. Another advantage is that hepatocytes can be isolated from partly damaged livers which are not suitable for liver transplantation. Despite these advantages hepatocyte transplantation is less popular. Important issues are poor engraftment of the transplanted cells and the scarcity of donor hepatocytes. Generation of “hepatocyte like cells”/iHeps from embryonic stem cells (ES) and induced pluripotent stem cells (iPSCs) by directed differentiation is an emerging solution to the latter issue. Direct conversation or trans-differentiation of fibroblasts to “hepatocyte like cells” is another way which is, being explored. However this method has several inherent and technical disadvantages compared to the directed differentiation from ES or iPSC. There are several methods claiming to be “highly efficient” for generating “highly functional”“hepatocyte like cells”. Currently different groups are working independently and coming up with differentiation protocols and each group claiming an advantage for their protocol. Directed differentiation protocols need to be designed, compared, analyzed and tweaked systematically and logically than empirically. There is a need for a well-coordinated global initiative comparable to the Human Genome Project to achieve this goal in the near future.
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Exome Sequencing and Epigenetic Analysis of Twins Who Are Discordant for Congenital Cataract. Twin Res Hum Genet 2015; 18:393-8. [PMID: 26045100 DOI: 10.1017/thg.2015.34] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
PURPOSE To further understand genetic factors that contribute to congenital cataracts, we sought to identify early post-twinning mutational and epigenetic events that may account for the discordant phenotypes of a twin pair. METHODS A patient with a congenital cataract and her twin sister were assessed for genetic factors that might contribute to their discordant phenotypes by mutation screening of 11 candidate genes (CRYGC, CRYGD, CRYAA, CRYAB, CRYBA1, CRYBB1, CRYBB2, MIP, HSF4, GJA3, and GJA8), exome analysis followed by Sanger sequencing of 10 additional candidate genes (PLEKHO2, FRYL, RBP3, P2RX2, GSR, TRAM1, VEGFA, NARS2, CADPS, and TEKT4), and promoter methylation analysis of five representative genes (TRAM1, CRYAA, HSF4, VEGFA, GJA3, DCT) plus one additional candidate gene (FTL). RESULTS Mutation screening revealed no gene mutation differences between the patient and her twin sister for the 11 candidate genes. Exome sequencing analysis revealed variations between the twins in 442 genes, 10 of which are expressed in the eye. However, these differential variants could not be confirmed by Sanger sequencing. Furthermore, epigenetic discordance was not detected in the twin pair. CONCLUSIONS The genomic DNA mutational and epigenetic events assessed in this study could not explain the discordance in the development of phenotypic differences between the twin pair, suggesting the possible involvement of somatic mutations or environmental factors. Identification of possible causes requires further research.
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