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Acurzio B, Cecere F, Giaccari C, Verma A, Russo R, Valletta M, Hay Mele B, Angelini C, Chambery A, Riccio A. The mismatch-repair proteins MSH2 and MSH6 interact with the imprinting control regions through the ZFP57-KAP1 complex. Epigenetics Chromatin 2022; 15:27. [PMID: 35918739 PMCID: PMC9344765 DOI: 10.1186/s13072-022-00462-7] [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: 06/13/2022] [Accepted: 07/25/2022] [Indexed: 11/21/2022] Open
Abstract
Background Imprinting Control Regions (ICRs) are CpG-rich sequences acquiring differential methylation in the female and male germline and maintaining it in a parental origin-specific manner in somatic cells. Despite their expected high mutation rate due to spontaneous deamination of methylated cytosines, ICRs show conservation of CpG-richness and CpG-containing transcription factor binding sites in mammalian species. However, little is known about the mechanisms contributing to the maintenance of a high density of methyl CpGs at these loci. Results To gain functional insights into the mechanisms for maintaining CpG methylation, we sought to identify the proteins binding the methylated allele of the ICRs by determining the interactors of ZFP57 that recognizes a methylated hexanucleotide motif of these DNA regions in mouse ESCs. By using a tagged approach coupled to LC–MS/MS analysis, we identified several proteins, including factors involved in mRNA processing/splicing, chromosome organization, transcription and DNA repair processes. The presence of the post-replicative mismatch-repair (MMR) complex components MSH2 and MSH6 among the identified ZFP57 interactors prompted us to investigate their DNA binding profile by chromatin immunoprecipitation and sequencing. We demonstrated that MSH2 was enriched at gene promoters overlapping unmethylated CpG islands and at repeats. We also found that both MSH2 and MSH6 interacted with the methylated allele of the ICRs, where their binding to DNA was mediated by the ZFP57/KAP1 complex. Conclusions Our findings show that the MMR complex is concentrated on gene promoters and repeats in mouse ESCs, suggesting that maintaining the integrity of these regions is a primary function of highly proliferating cells. Furthermore, the demonstration that MSH2/MSH6 are recruited to the methylated allele of the ICRs through interaction with ZFP57/KAP1 suggests a role of the MMR complex in the maintenance of the integrity of these regulatory regions and evolution of genomic imprinting in mammalian species. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-022-00462-7.
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Affiliation(s)
- Basilia Acurzio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy.,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), 80131, Naples, Italy
| | - Francesco Cecere
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy.,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), 80131, Naples, Italy
| | - Carlo Giaccari
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy.,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), 80131, Naples, Italy
| | - Ankit Verma
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy.,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), 80131, Naples, Italy
| | - Rosita Russo
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Mariangela Valletta
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Bruno Hay Mele
- Department of Biology, Università Degli Studi Di Napoli "Federico II", 80126, Naples, Italy
| | - Claudia Angelini
- Istituto Per Le Applicazioni del Calcolo "Mauro Picone" (IAC), CNR, 80131, Naples, Italy
| | - Angela Chambery
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy. .,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), 80131, Naples, Italy.
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2
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Shrestha KS, Tuominen MM, Kauppi L. Mlh1 heterozygosity and promoter methylation associates with microsatellite instability in mouse sperm. Mutagenesis 2021; 36:237-244. [PMID: 33740045 PMCID: PMC8262379 DOI: 10.1093/mutage/geab010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 03/17/2021] [Indexed: 11/13/2022] Open
Abstract
DNA mismatch repair (MMR) proteins play an important role in maintaining genome stability, both in somatic and in germline cells. Loss of MLH1, a central MMR protein, leads to infertility and to microsatellite instability (MSI) in spermatocytes, however, the effect of Mlh1 heterozygosity on germline genome stability remains unexplored. To test the effect of Mlh1 heterozygosity on MSI in mature sperm, we combined mouse genetics with single-molecule PCR that detects allelic changes at unstable microsatellites. We discovered 4.5% and 5.9% MSI in sperm of 4- and 12-month-old Mlh1+/− mice, respectively, and that Mlh1 promoter methylation in Mlh1+/− sperm correlated with higher MSI. No such elevated MSI was seen in non-proliferating somatic cells. Additionally, we show contrasting dynamics of deletions versus insertions at unstable microsatellites (mononucleotide repeats) in sperm.
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Affiliation(s)
- Kul S Shrestha
- Systems Oncology (ONCOSYS) Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8 (PO Box 63), FI-00014 Helsinki, Finland.,Doctoral Program in Integrative Life Sciences, University of Helsinki, Viikinkaari 1 (PO Box 65), FI-00014 Helsinki, Finland
| | - Minna M Tuominen
- Systems Oncology (ONCOSYS) Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8 (PO Box 63), FI-00014 Helsinki, Finland
| | - Liisa Kauppi
- Systems Oncology (ONCOSYS) Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8 (PO Box 63), FI-00014 Helsinki, Finland.,Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8 (PO Box 63), FI-00014 Helsinki, Finland
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3
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banimohamad-shotorbani B, Kahroba H, Sadeghzadeh H, Wilson DM, Maadi H, Samadi N, Hejazi MS, Farajpour H, Onari BN, Sadeghi MR. DNA damage repair response in mesenchymal stromal cells: From cellular senescence and aging to apoptosis and differentiation ability. Ageing Res Rev 2020; 62:101125. [PMID: 32683038 DOI: 10.1016/j.arr.2020.101125] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 07/04/2020] [Accepted: 07/10/2020] [Indexed: 12/12/2022]
Abstract
Mesenchymal stromal cells (MSCs) are heterogeneous and contain several populations, including stem cells. MSCs' secretome has the ability to induce proliferation, differentiation, chemo-attraction, anti-apoptosis, and immunomodulation activities in stem cells. Moreover, these cells recognize tissue damage caused by drugs, radiation (e.g., Ultraviolet, infra-red) and oxidative stress, and respond in two ways: either MSCs differentiate into particular cell lineages to preserve tissue homeostasis, or they release a regenerative secretome to activate tissue repairing mechanisms. The maintenance of MSCs in quiescence can increase the incidence and accumulation of various forms of genomic modifications, particularly upon environmental insults. Thus, dysregulated DNA repair pathways can predispose MSCs to senescence or apoptosis, reducing their stemness and self-renewal properties. For instance, DNA damage can impair telomere replication, activating DNA damage checkpoints to maintain MSC function. In this review, we aim to summarize the role of DNA damage and associated repair responses in MSC senescence, differentiation and programmed cell death.
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4
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Sex in Symbiodiniaceae dinoflagellates: genomic evidence for independent loss of the canonical synaptonemal complex. Sci Rep 2020; 10:9792. [PMID: 32555361 PMCID: PMC7299967 DOI: 10.1038/s41598-020-66429-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 05/19/2020] [Indexed: 01/07/2023] Open
Abstract
Dinoflagellates of the Symbiodiniaceae family encompass diverse symbionts that are critical to corals and other species living in coral reefs. It is well known that sexual reproduction enhances adaptive evolution in changing environments. Although genes related to meiotic functions were reported in Symbiodiniaceae, cytological evidence of meiosis and fertilisation are however yet to be observed in these taxa. Using transcriptome and genome data from 21 Symbiodiniaceae isolates, we studied genes that encode proteins associated with distinct stages of meiosis and syngamy. We report the absence of genes that encode main components of the synaptonemal complex (SC), a protein structure that mediates homologous chromosomal pairing and class I crossovers. This result suggests an independent loss of canonical SCs in the alveolates, that also includes the SC-lacking ciliates. We hypothesise that this loss was due in part to permanently condensed chromosomes and repeat-rich sequences in Symbiodiniaceae (and other dinoflagellates) which favoured the SC-independent class II crossover pathway. Our results reveal novel insights into evolution of the meiotic molecular machinery in the ecologically important Symbiodiniaceae and in other eukaryotes.
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5
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Gonzalez V, Spampinato CP. The mismatch repair protein MSH6 regulates somatic recombination in Arabidopsis thaliana. DNA Repair (Amst) 2020; 87:102789. [PMID: 31945543 DOI: 10.1016/j.dnarep.2020.102789] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 11/29/2019] [Accepted: 01/08/2020] [Indexed: 11/28/2022]
Abstract
The mismatch repair (MMR) pathway promotes genome stability by controlling the fidelity of replication and recombination. The first step of the pathway involves recognition of the mismatch by heterodimers composed of MutS homologs (MSH). Although MSH6 has been well characterized in yeasts and humans, the role of the plant protein has not been extensively studied. We first analyzed gene expression in Arabidopsis thaliana. The use of transgenic plants expressing the β-glucuronidase (GUS) reporter gene under the control of approximately 1-kb region upstream of the start codon of the AtMSH6 gene demonstrated that MSH6 is preferentially expressed in undifferentiated cells with an intense cell division rate. We then examined protein function in meiotic and somatic recombination. Suppression of AtMSH6 did not affect the rate of meiotic recombination, but increased the frequency of recombination between two homeologous repeats of a marker gene by 3-fold relative to wild-type plants. Expression of the AtMSH6 gene under the control of its own promoter in msh6 homozygous mutant plants rescued the altered somatic recombination phenotype. We conclude that MSH6 shows a functional conservation across different biological kingdoms and a functional specificity in plants.
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Affiliation(s)
- Valentina Gonzalez
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Claudia P Spampinato
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina.
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6
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Stringer JM, Winship A, Liew SH, Hutt K. The capacity of oocytes for DNA repair. Cell Mol Life Sci 2018; 75:2777-2792. [PMID: 29748894 PMCID: PMC11105623 DOI: 10.1007/s00018-018-2833-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/27/2018] [Accepted: 05/02/2018] [Indexed: 12/18/2022]
Abstract
Female fertility and offspring health are critically dependent on the maintenance of an adequate supply of high-quality oocytes. Like somatic cells, oocytes are subject to a variety of different types of DNA damage arising from endogenous cellular processes and exposure to exogenous genotoxic stressors. While the repair of intentionally induced DNA double strand breaks in gametes during meiotic recombination is well characterised, less is known about the ability of oocytes to repair pathological DNA damage and the relative contribution of DNA repair to oocyte quality is not well defined. This review will discuss emerging data suggesting that oocytes are in fact capable of efficient DNA repair and that DNA repair may be an important mechanism for ensuring female fertility, as well as the transmission of high-quality genetic material to subsequent generations.
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Affiliation(s)
- Jessica M Stringer
- Ovarian Biology Laboratory, Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Amy Winship
- Ovarian Biology Laboratory, Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Seng H Liew
- Ovarian Biology Laboratory, Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Karla Hutt
- Ovarian Biology Laboratory, Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia.
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7
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Maletzki C, Beyrich F, Hühns M, Klar E, Linnebacher M. The mutational profile and infiltration pattern of murine MLH1-/- tumors: concurrences, disparities and cell line establishment for functional analysis. Oncotarget 2018; 7:53583-53598. [PMID: 27447752 PMCID: PMC5288207 DOI: 10.18632/oncotarget.10677] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/06/2016] [Indexed: 12/21/2022] Open
Abstract
Mice lines homozygous negative for one of the four DNA mismatch repair (MMR) genes (MLH1, MSH2, PMS2, MSH6) were generated as models for MMR deficient (MMR-D) diseases. Clinically, hereditary forms of MMR-D include Lynch syndrome (characterized by a germline MMR gene defect) and constitutional MMR-D, the biallelic form. MMR-D knockout mice may be representative for both diseases. Here, we aimed at characterizing the MLH1-/- model focusing on tumor-immune microenvironment and identification of coding microsatellite mutations in lymphomas and gastrointestinal tumors (GIT). All tumors showed microsatellite instability (MSI) in non-coding mononucleotide markers. Mutational profiling of 26 coding loci in MSI+ GIT and lymphomas revealed instability in half of the microsatellites, two of them (Rfc3 and Rasal2) shared between both entities. MLH1-/- tumors of both entities displayed a similar phenotype (high CD71, FasL, PD-L1 and CTLA-4 expression). Additional immunofluorescence verified the tumors’ natural immunosuppressive character (marked CD11b/CD200R infiltration). Vice versa, CD3+ T cells as well as immune checkpoints molecules were detectable, indicative for an active immune microenvironment. For functional analysis, a permanent cell line from an MLH1-/- GIT was established. The newly developed MLH1-/- A7450 cells exhibit stable in vitro growth, strong invasive potential and heterogeneous drug response. Moreover, four additional MSI target genes (Nktr1, C8a, Taf1b, and Lig4) not recognized in the primary were identified in this cell line. Summing up, molecular and immunological mechanisms of MLH1-/- driven carcinogenesis correlate well with clinical features of MMR-D. MLH1-/- knockout mice combine characteristics of Lynch syndrome and constitutional MMR-D, making them suitable models for preclinical research aiming at MMR-D related diseases.
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Affiliation(s)
- Claudia Maletzki
- Molecular Oncology and Immunotherapy, Department of General Surgery, University of Rostock, 18057 Rostock, Germany
| | - Franziska Beyrich
- Molecular Oncology and Immunotherapy, Department of General Surgery, University of Rostock, 18057 Rostock, Germany
| | - Maja Hühns
- Institute of Pathology, University of Rostock, 18057 Rostock, Germany
| | - Ernst Klar
- Department of General Surgery, University of Rostock, 18057 Rostock, Germany
| | - Michael Linnebacher
- Molecular Oncology and Immunotherapy, Department of General Surgery, University of Rostock, 18057 Rostock, Germany
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8
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Risks at the DNA Replication Fork: Effects upon Carcinogenesis and Tumor Heterogeneity. Genes (Basel) 2017; 8:genes8010046. [PMID: 28117753 PMCID: PMC5295039 DOI: 10.3390/genes8010046] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/09/2017] [Accepted: 01/17/2017] [Indexed: 12/27/2022] Open
Abstract
The ability of all organisms to copy their genetic information via DNA replication is a prerequisite for cell division and a biological imperative of life. In multicellular organisms, however, mutations arising from DNA replication errors in the germline and somatic cells are the basis of genetic diseases and cancer, respectively. Within human tumors, replication errors additionally contribute to mutator phenotypes and tumor heterogeneity, which are major confounding factors for cancer therapeutics. Successful DNA replication involves the coordination of many large-scale, complex cellular processes. In this review, we focus on the roles that defects in enzymes that normally act at the replication fork and dysregulation of enzymes that inappropriately damage single-stranded DNA at the fork play in causing mutations that contribute to carcinogenesis. We focus on tumor data and experimental evidence that error-prone variants of replicative polymerases promote carcinogenesis and on research indicating that the primary target mutated by APOBEC (apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like) cytidine deaminases is ssDNA present at the replication fork. Furthermore, we discuss evidence from model systems that indicate replication stress and other cancer-associated metabolic changes may modulate mutagenic enzymatic activities at the replication fork.
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9
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Wang KY, Chen CC, Tsai SF, Shen CKJ. Epigenetic Enhancement of the Post-replicative DNA Mismatch Repair of Mammalian Genomes by a Hemi- mCpG-Np95-Dnmt1 Axis. Sci Rep 2016; 6:37490. [PMID: 27886214 PMCID: PMC5122852 DOI: 10.1038/srep37490] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 10/26/2016] [Indexed: 01/02/2023] Open
Abstract
DNA methylation at C of CpG dyads (mCpG) in vertebrate genomes is essential for gene regulation, genome stability and development. We show in this study that proper functioning of post-replicative DNA mismatch repair (MMR) in mammalian cells relies on the presence of genomic mCpG, as well as on the maintenance DNA methyltransferase Dnmt1 independently of its catalytic activity. More importantly, high efficiency of mammalian MMR surveillance is achieved through a hemi-mCpG-Np95(Uhrf1)-Dnmt1 axis, in which the MMR surveillance complex(es) is recruited to post-replicative DNA by Dnmt1, requiring its interactions with MutSα, as well as with Np95 bound at the hemi-methylated CpG sites. Thus, efficiency of MMR surveillance over the mammalian genome in vivo is enhanced at the epigenetic level. This synergy endows vertebrate CpG methylation with a new biological significance and, consequently, an additional mechanism for the maintenance of vertebrate genome stability.
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Affiliation(s)
- Keh-Yang Wang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Chun-Chang Chen
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Shih-Feng Tsai
- Genome Research Center, National Yang-Ming University, Taipei 11221, Taiwan.,Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 11221, Taiwan.,Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Che-Kun James Shen
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan
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10
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Abstract
As many as 5% of human cancers appear to be of hereditable etiology. Of the more than 50 characterized familial cancer syndromes, most involve disease affecting multiple organs and many can be traced to one or more abnormalities in specific genes. Studying these syndromes in humans is a difficult task, especially when it comes to genes that may manifest themselves early in gestation. It has been made somewhat easier with the development of genetically engineered mice (GEM) that phenotypically mimic many of these inheritable human cancers. The past 15 years has seen the establishment of mouse lines heterozygous or homozygous null for genes known or suspected of being involved in human cancer syndromes, including APC, ATM, BLM, BRCA1, BRCA2, LKB1, MEN1, MLH, MSH, NF1, TP53, PTEN, RB1, TSC1, TSC2, VHL, and XPA. These lines not only provide models for clinical disease and pathology, but also provide avenues to investigate molecular pathology, gene-gene and protein-tissue interaction, and, ultimately, therapeutic intervention. Possibly of even greater importance, they provide a means of looking at placental and fetal tissues, where genetic abnormalities are often first detected and where they may be most easily corrected. We will review these mouse models, examine their usefulness in medical research, and furnish sources of animals and references.
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Affiliation(s)
- Jerrold M Ward
- Veterinary and Tumor Pathology Section, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, USA.
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11
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Kloor M, von Knebel Doeberitz M. The Immune Biology of Microsatellite-Unstable Cancer. Trends Cancer 2016; 2:121-133. [PMID: 28741532 DOI: 10.1016/j.trecan.2016.02.004] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/03/2016] [Accepted: 02/09/2016] [Indexed: 12/16/2022]
Abstract
Deficient DNA mismatch repair (MMR) boosts the accumulation of frameshift mutations in genes encompassing coding microsatellites (cMS). This results in the translation of proteins with mutation-induced frameshift peptides (neoantigens) rendering microsatellite-unstable (MSI) cancers highly immunogenic. MSI cancers express a defined set of neoantigens resulting from functionally relevant driver mutations, which are shared by most MSI cancers. Patients with MSI cancers and healthy individuals affected by Lynch syndrome, an inherited predisposition for MSI cancers, develop specific immune responses against these neoantigens. In this review, we summarize our current understanding of the immune biology of MSI cancers and outline new concepts and research directions to develop not only therapeutic treatments, but also preventive vaccines based on the MSI cancer genome landscapes.
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Affiliation(s)
- Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Clinical Cooperation Unit (CCU 105) of the German Cancer Research Center and Molecular Medicine Partner Unit (MMPU) of the European Molecular Biology Laboratory, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany.
| | - Magnus von Knebel Doeberitz
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Clinical Cooperation Unit (CCU 105) of the German Cancer Research Center and Molecular Medicine Partner Unit (MMPU) of the European Molecular Biology Laboratory, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany.
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12
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Kadyrova LY, Kadyrov FA. Endonuclease activities of MutLα and its homologs in DNA mismatch repair. DNA Repair (Amst) 2016; 38:42-49. [PMID: 26719141 PMCID: PMC4820397 DOI: 10.1016/j.dnarep.2015.11.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 08/26/2015] [Accepted: 11/30/2015] [Indexed: 12/28/2022]
Abstract
MutLα is a key component of the DNA mismatch repair system in eukaryotes. The DNA mismatch repair system has several genetic stabilization functions. Of these functions, DNA mismatch repair is the major one. The loss of MutLα abolishes DNA mismatch repair, thereby predisposing humans to cancer. MutLα has an endonuclease activity that is required for DNA mismatch repair. The endonuclease activity of MutLα depends on the DQHA(X)2E(X)4E motif which is a part of the active site of the nuclease. This motif is also present in many bacterial MutL and eukaryotic MutLγ proteins, DNA mismatch repair system factors that are homologous to MutLα. Recent studies have shown that yeast MutLγ and several MutL proteins containing the DQHA(X)2E(X)4E motif possess endonuclease activities. Here, we review the endonuclease activities of MutLα and its homologs in the context of DNA mismatch repair.
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Affiliation(s)
- Lyudmila Y Kadyrova
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Farid A Kadyrov
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.
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13
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Jackstadt R, Sansom OJ. Mouse models of intestinal cancer. J Pathol 2016; 238:141-51. [PMID: 26414675 PMCID: PMC4832380 DOI: 10.1002/path.4645] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 09/21/2015] [Accepted: 09/23/2015] [Indexed: 12/19/2022]
Abstract
Murine models of intestinal cancer are powerful tools to recapitulate human intestinal cancer, understand its biology and test therapies. With recent developments identifying the importance of the tumour microenvironment and the potential for immunotherapy, autochthonous genetically engineered mouse models (GEMMs) will remain an important part of preclinical studies for the foreseeable future. This review will provide an overview of the current mouse models of intestinal cancer, from the Apc(Min/+) mouse, which has been used for over 25 years, to the latest 'state-of-the-art' organoid models. We discuss here how these models have been used to define fundamental processes involved in tumour initiation and the attempts to generate metastatic models, which is the ultimate cause of cancer mortality. Together these models will provide key insights to understand this complex disease and hopefully will lead to the discovery of new therapeutic strategies.
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14
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Ferguson LR, Chen H, Collins AR, Connell M, Damia G, Dasgupta S, Malhotra M, Meeker AK, Amedei A, Amin A, Ashraf SS, Aquilano K, Azmi AS, Bhakta D, Bilsland A, Boosani CS, Chen S, Ciriolo MR, Fujii H, Guha G, Halicka D, Helferich WG, Keith WN, Mohammed SI, Niccolai E, Yang X, Honoki K, Parslow VR, Prakash S, Rezazadeh S, Shackelford RE, Sidransky D, Tran PT, Yang ES, Maxwell CA. Genomic instability in human cancer: Molecular insights and opportunities for therapeutic attack and prevention through diet and nutrition. Semin Cancer Biol 2015; 35 Suppl:S5-S24. [PMID: 25869442 PMCID: PMC4600419 DOI: 10.1016/j.semcancer.2015.03.005] [Citation(s) in RCA: 188] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 03/08/2015] [Accepted: 03/13/2015] [Indexed: 02/06/2023]
Abstract
Genomic instability can initiate cancer, augment progression, and influence the overall prognosis of the affected patient. Genomic instability arises from many different pathways, such as telomere damage, centrosome amplification, epigenetic modifications, and DNA damage from endogenous and exogenous sources, and can be perpetuating, or limiting, through the induction of mutations or aneuploidy, both enabling and catastrophic. Many cancer treatments induce DNA damage to impair cell division on a global scale but it is accepted that personalized treatments, those that are tailored to the particular patient and type of cancer, must also be developed. In this review, we detail the mechanisms from which genomic instability arises and can lead to cancer, as well as treatments and measures that prevent genomic instability or take advantage of the cellular defects caused by genomic instability. In particular, we identify and discuss five priority targets against genomic instability: (1) prevention of DNA damage; (2) enhancement of DNA repair; (3) targeting deficient DNA repair; (4) impairing centrosome clustering; and, (5) inhibition of telomerase activity. Moreover, we highlight vitamin D and B, selenium, carotenoids, PARP inhibitors, resveratrol, and isothiocyanates as priority approaches against genomic instability. The prioritized target sites and approaches were cross validated to identify potential synergistic effects on a number of important areas of cancer biology.
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Affiliation(s)
| | - Helen Chen
- Department of Pediatrics, University of British Columbia, Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Vancouver, Canada
| | - Andrew R Collins
- Department of Nutrition, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Marisa Connell
- Department of Pediatrics, University of British Columbia, Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Vancouver, Canada
| | - Giovanna Damia
- Department of Oncology, Instituti di Ricovero e Cura a Carattere Scientifico-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Santanu Dasgupta
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, United States
| | | | - Alan K Meeker
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Amr Amin
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates; Faculty of Science, Cairo University, Cairo, Egypt
| | - S Salman Ashraf
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Katia Aquilano
- Department of Biology, Università di Roma Tor Vergata, Rome, Italy
| | - Asfar S Azmi
- Department of Biology, University of Rochester, Rochester, United States
| | - Dipita Bhakta
- School of Chemical and BioTechnology, SASTRA University, Thanjavur, Tamil Nadu, India
| | - Alan Bilsland
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Chandra S Boosani
- Department of BioMedical Sciences, Creighton University, Omaha, NE, United States
| | - Sophie Chen
- Department of Research & Development, Ovarian and Prostate Cancer Research Trust Laboratory, Guildford, Surrey, United Kingdom
| | | | - Hiromasa Fujii
- Department of Orthopaedic Surgery, Nara Medical University, Kashihara, Nara, Japan
| | - Gunjan Guha
- School of Chemical and BioTechnology, SASTRA University, Thanjavur, Tamil Nadu, India
| | | | - William G Helferich
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - W Nicol Keith
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Sulma I Mohammed
- Department of Comparative Pathobiology and Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, United States
| | - Elena Niccolai
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Xujuan Yang
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Kanya Honoki
- Department of Orthopaedic Surgery, Nara Medical University, Kashihara, Nara, Japan
| | | | - Satya Prakash
- School of Pharmacy, University College Cork, Cork, Ireland
| | - Sarallah Rezazadeh
- Department of Biology, University of Rochester, Rochester, United States
| | - Rodney E Shackelford
- Department of Pathology, Louisiana State University Health Shreveport, Shreveport, LA, United States
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Phuoc T Tran
- Departments of Radiation Oncology & Molecular Radiation Sciences, Oncology and Urology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Eddy S Yang
- Department of Radiation Oncology, University of Alabama at Birmingham School of Medicine, Birmingham, AL, United States
| | - Christopher A Maxwell
- Department of Pediatrics, University of British Columbia, Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Vancouver, Canada.
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Cheah CY, Dsouza L, Taggart MW, Schlette EJ, Turturro F. Diffuse large B-cell lymphoma with microsatellite instability developing in the setting of Muir-Torre variant hereditary non-polyposis colon cancer. J Clin Pathol 2015; 68:755-7. [PMID: 26008772 DOI: 10.1136/jclinpath-2015-203039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 05/04/2015] [Indexed: 02/03/2023]
Affiliation(s)
- Chan Yoon Cheah
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ly Dsouza
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Melissa W Taggart
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ellen J Schlette
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Francesco Turturro
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Colon cancer-associated mutator DNA polymerase δ variant causes expansion of dNTP pools increasing its own infidelity. Proc Natl Acad Sci U S A 2015; 112:E2467-76. [PMID: 25827231 DOI: 10.1073/pnas.1422934112] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Defects in DNA polymerases δ (Polδ) and ε (Polε) cause hereditary colorectal cancer and have been implicated in the etiology of some sporadic colorectal and endometrial tumors. We previously reported that the yeast pol3-R696W allele mimicking a human cancer-associated variant, POLD1-R689W, causes a catastrophic increase in spontaneous mutagenesis. Here, we describe the mechanism of this extraordinary mutator effect. We found that the mutation rate increased synergistically when the R696W mutation was combined with defects in Polδ proofreading or mismatch repair, indicating that pathways correcting DNA replication errors are not compromised in pol3-R696W mutants. DNA synthesis by purified Polδ-R696W was error-prone, but not to the extent that could account for the unprecedented mutator phenotype of pol3-R696W strains. In a search for cellular factors that augment the mutagenic potential of Polδ-R696W, we discovered that pol3-R696W causes S-phase checkpoint-dependent elevation of dNTP pools. Abrogating this elevation by strategic mutations in dNTP metabolism genes eliminated the mutator effect of pol3-R696W, whereas restoration of high intracellular dNTP levels restored the mutator phenotype. Further, the use of dNTP concentrations present in pol3-R696W cells for in vitro DNA synthesis greatly decreased the fidelity of Polδ-R696W and produced a mutation spectrum strikingly similar to the spectrum observed in vivo. The results support a model in which (i) faulty synthesis by Polδ-R696W leads to a checkpoint-dependent increase in dNTP levels and (ii) this increase mediates the hypermutator effect of Polδ-R696W by facilitating the extension of mismatched primer termini it creates and by promoting further errors that continue to fuel the mutagenic pathway.
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Kane DP, Shcherbakova PV. A common cancer-associated DNA polymerase ε mutation causes an exceptionally strong mutator phenotype, indicating fidelity defects distinct from loss of proofreading. Cancer Res 2014; 74:1895-901. [PMID: 24525744 DOI: 10.1158/0008-5472.can-13-2892] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Exonucleolytic proofreading and DNA mismatch repair (MMR) act in series to maintain high-fidelity DNA replication and to avoid mutagenesis. MMR defects elevate the overall mutation rate and are associated with increased cancer incidence. Hypermutable colorectal and endometrial tumors with functional MMR were recently reported to carry amino acid substitutions in the exonuclease domain of DNA polymerase ε (Polε). This created a notion that loss of the proofreading activity of Polε is an initiating cause of some sporadic human cancers. In this study, we identified a somatic P286R substitution in the conserved ExoI motif of Polε in a collection of 52 sporadic colorectal tumor specimens. This change has been repeatedly observed in colorectal and endometrial tumors in previous studies despite many possible ways to inactivate Polε proofreading. To understand the reasons for the recurrent appearance of the P286R variant, we characterized its functional consequences using the yeast model system. An analogous substitution in the yeast Polε produced an unusually strong mutator phenotype exceeding that of proofreading-deficient mutants by two orders of magnitude. This argues that the P286R mutation acts at some level other than loss of exonuclease to elevate cancer risk. Heterozygosity for the variant allele caused a strong mutator effect comparable with that of complete MMR deficiency, providing an explanation for why loss of heterozygosity is not required for the development of Polε-mutant human tumors.
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Affiliation(s)
- Daniel P Kane
- Authors' Affiliation: Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
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18
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Colon and rectal cancer. Mol Oncol 2013. [DOI: 10.1017/cbo9781139046947.048] [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
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19
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Chapal-Ilani N, Maruvka YE, Spiro A, Reizel Y, Adar R, Shlush LI, Shapiro E. Comparing algorithms that reconstruct cell lineage trees utilizing information on microsatellite mutations. PLoS Comput Biol 2013; 9:e1003297. [PMID: 24244121 PMCID: PMC3828138 DOI: 10.1371/journal.pcbi.1003297] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Accepted: 09/09/2013] [Indexed: 11/18/2022] Open
Abstract
Organism cells proliferate and die to build, maintain, renew and repair it. The cellular history of an organism up to any point in time can be captured by a cell lineage tree in which vertices represent all organism cells, past and present, and directed edges represent progeny relations among them. The root represents the fertilized egg, and the leaves represent extant and dead cells. Somatic mutations accumulated during cell division endow each organism cell with a genomic signature that is unique with a very high probability. Distances between such genomic signatures can be used to reconstruct an organism's cell lineage tree. Cell populations possess unique features that are absent or rare in organism populations (e.g., the presence of stem cells and a small number of generations since the zygote) and do not undergo sexual reproduction, hence the reconstruction of cell lineage trees calls for careful examination and adaptation of the standard tools of population genetics. Our lab developed a method for reconstructing cell lineage trees by examining only mutations in highly variable microsatellite loci (MS, also called short tandem repeats, STR). In this study we use experimental data on somatic mutations in MS of individual cells in human and mice in order to validate and quantify the utility of known lineage tree reconstruction algorithms in this context. We employed extensive measurements of somatic mutations in individual cells which were isolated from healthy and diseased tissues of mice and humans. The validation was done by analyzing the ability to infer known and clear biological scenarios. In general, we found that if the biological scenario is simple, almost all algorithms tested can infer it. Another somewhat surprising conclusion is that the best algorithm among those tested is Neighbor Joining where the distance measure used is normalized absolute distance. We include our full dataset in Tables S1, S2, S3, S4, S5 to enable further analysis of this data by others.
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Affiliation(s)
- Noa Chapal-Ilani
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
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20
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Mismatch repair genes Mlh1 and Mlh3 modify CAG instability in Huntington's disease mice: genome-wide and candidate approaches. PLoS Genet 2013; 9:e1003930. [PMID: 24204323 PMCID: PMC3814320 DOI: 10.1371/journal.pgen.1003930] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 09/15/2013] [Indexed: 11/19/2022] Open
Abstract
The Huntington's disease gene (HTT) CAG repeat mutation undergoes somatic expansion that correlates with pathogenesis. Modifiers of somatic expansion may therefore provide routes for therapies targeting the underlying mutation, an approach that is likely applicable to other trinucleotide repeat diseases. Huntington's disease HdhQ111 mice exhibit higher levels of somatic HTT CAG expansion on a C57BL/6 genetic background (B6.HdhQ111) than on a 129 background (129.HdhQ111). Linkage mapping in (B6x129).HdhQ111 F2 intercross animals identified a single quantitative trait locus underlying the strain-specific difference in expansion in the striatum, implicating mismatch repair (MMR) gene Mlh1 as the most likely candidate modifier. Crossing B6.HdhQ111 mice onto an Mlh1 null background demonstrated that Mlh1 is essential for somatic CAG expansions and that it is an enhancer of nuclear huntingtin accumulation in striatal neurons. HdhQ111 somatic expansion was also abolished in mice deficient in the Mlh3 gene, implicating MutLγ (MLH1–MLH3) complex as a key driver of somatic expansion. Strikingly, Mlh1 and Mlh3 genes encoding MMR effector proteins were as critical to somatic expansion as Msh2 and Msh3 genes encoding DNA mismatch recognition complex MutSβ (MSH2–MSH3). The Mlh1 locus is highly polymorphic between B6 and 129 strains. While we were unable to detect any difference in base-base mismatch or short slipped-repeat repair activity between B6 and 129 MLH1 variants, repair efficiency was MLH1 dose-dependent. MLH1 mRNA and protein levels were significantly decreased in 129 mice compared to B6 mice, consistent with a dose-sensitive MLH1-dependent DNA repair mechanism underlying the somatic expansion difference between these strains. Together, these data identify Mlh1 and Mlh3 as novel critical genetic modifiers of HTT CAG instability, point to Mlh1 genetic variation as the likely source of the instability difference in B6 and 129 strains and suggest that MLH1 protein levels play an important role in driving of the efficiency of somatic expansions. The expansion of a CAG repeat underlies Huntington's disease (HD), with longer CAG tracts giving rise to earlier onset and more severe disease. In individuals harboring a CAG expansion the repeat undergoes further somatic expansion over time, particularly in brain cells most susceptible to disease pathogenesis. Preventing this repeat lengthening may delay disease onset and/or slow progression. We are using mouse models of HD to identify the factors that modify the somatic expansion of the HD CAG repeat, as these may provide novel targets for therapeutic intervention. To identify genetic modifiers of somatic expansion in HD mouse models we have used both an unbiased genetic mapping approach in inbred mouse strains that exhibit different levels of somatic expansion, as well as targeted gene knockout approaches. Our results demonstrate that: 1) Mlh1 and Mlh3 genes, encoding components of the DNA mismatch repair pathway, are critical for somatic CAG expansion; 2) in the absence of somatic expansion the pathogenic process in the mouse is slowed; 3) MLH1 protein levels are likely to be a driver of the efficiency of somatic expansion. Together, our data provide new insight into the factors underlying the process of somatic expansion of the HD CAG repeat.
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21
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Emergence of DNA polymerase ε antimutators that escape error-induced extinction in yeast. Genetics 2013; 193:751-70. [PMID: 23307893 DOI: 10.1534/genetics.112.146910] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA polymerases (Pols) ε and δ perform the bulk of yeast leading- and lagging-strand DNA synthesis. Both Pols possess intrinsic proofreading exonucleases that edit errors during polymerization. Rare errors that elude proofreading are extended into duplex DNA and excised by the mismatch repair (MMR) system. Strains that lack Pol proofreading or MMR exhibit a 10- to 100-fold increase in spontaneous mutation rate (mutator phenotype), and inactivation of both Pol δ proofreading (pol3-01) and MMR is lethal due to replication error-induced extinction (EEX). It is unclear whether a similar synthetic lethal relationship exists between defects in Pol ε proofreading (pol2-4) and MMR. Using a plasmid-shuffling strategy in haploid Saccharomyces cerevisiae, we observed synthetic lethality of pol2-4 with alleles that completely abrogate MMR (msh2Δ, mlh1Δ, msh3Δ msh6Δ, or pms1Δ mlh3Δ) but not with partial MMR loss (msh3Δ, msh6Δ, pms1Δ, or mlh3Δ), indicating that high levels of unrepaired Pol ε errors drive extinction. However, variants that escape this error-induced extinction (eex mutants) frequently emerged. Five percent of pol2-4 msh2Δ eex mutants encoded second-site changes in Pol ε that reduced the pol2-4 mutator phenotype between 3- and 23-fold. The remaining eex alleles were extragenic to pol2-4. The locations of antimutator amino-acid changes in Pol ε and their effects on mutation spectra suggest multiple mechanisms of mutator suppression. Our data indicate that unrepaired leading- and lagging-strand polymerase errors drive extinction within a few cell divisions and suggest that there are polymerase-specific pathways of mutator suppression. The prevalence of suppressors extragenic to the Pol ε gene suggests that factors in addition to proofreading and MMR influence leading-strand DNA replication fidelity.
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22
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Couronné L, Ruminy P, Waultier-Rascalou A, Rainville V, Cornic M, Picquenot JM, Figeac M, Bastard C, Tilly H, Jardin F. Mutation mismatch repair gene deletions in diffuse large B-cell lymphoma. Leuk Lymphoma 2012; 54:1079-86. [DOI: 10.3109/10428194.2012.739687] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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23
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Tian S, Roepman P, Popovici V, Michaut M, Majewski I, Salazar R, Santos C, Rosenberg R, Nitsche U, Mesker WE, Bruin S, Tejpar S, Delorenzi M, Bernards R, Simon I. A robust genomic signature for the detection of colorectal cancer patients with microsatellite instability phenotype and high mutation frequency. J Pathol 2012; 228:586-95. [PMID: 22926706 PMCID: PMC3532622 DOI: 10.1002/path.4092] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 08/14/2012] [Accepted: 08/15/2012] [Indexed: 01/05/2023]
Abstract
Microsatellite instability (MSI) occurs in 10-20% of colorectal tumours and is associated with good prognosis. Here we describe the development and validation of a genomic signature that identifies colorectal cancer patients with MSI caused by DNA mismatch repair deficiency with high accuracy. Microsatellite status for 276 stage II and III colorectal tumours has been determined. Full-genome expression data was used to identify genes that correlate with MSI status. A subset of these samples (n = 73) had sequencing data for 615 genes available. An MSI gene signature of 64 genes was developed and validated in two independent validation sets: the first consisting of frozen samples from 132 stage II patients; and the second consisting of FFPE samples from the PETACC-3 trial (n = 625). The 64-gene MSI signature identified MSI patients in the first validation set with a sensitivity of 90.3% and an overall accuracy of 84.8%, with an AUC of 0.942 (95% CI, 0.888-0.975). In the second validation, the signature also showed excellent performance, with a sensitivity 94.3% and an overall accuracy of 90.6%, with an AUC of 0.965 (95% CI, 0.943-0.988). Besides correct identification of MSI patients, the gene signature identified a group of MSI-like patients that were MSS by standard assessment but MSI by signature assessment. The MSI-signature could be linked to a deficient MMR phenotype, as both MSI and MSI-like patients showed a high mutation frequency (8.2% and 6.4% of 615 genes assayed, respectively) as compared to patients classified as MSS (1.6% mutation frequency). The MSI signature showed prognostic power in stage II patients (n = 215) with a hazard ratio of 0.252 (p = 0.0145). Patients with an MSI-like phenotype had also an improved survival when compared to MSS patients. The MSI signature was translated to a diagnostic microarray and technically and clinically validated in FFPE and frozen samples.
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Affiliation(s)
- Sun Tian
- Agendia NV, Amsterdam, The Netherlands; and Agendia Inc., Irvine, CA, USA
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24
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Kovalenko M, Dragileva E, St. Claire J, Gillis T, Guide JR, New J, Dong H, Kucherlapati R, Kucherlapati MH, Ehrlich ME, Lee JM, Wheeler VC. Msh2 acts in medium-spiny striatal neurons as an enhancer of CAG instability and mutant huntingtin phenotypes in Huntington's disease knock-in mice. PLoS One 2012; 7:e44273. [PMID: 22970194 PMCID: PMC3436885 DOI: 10.1371/journal.pone.0044273] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 07/31/2012] [Indexed: 11/19/2022] Open
Abstract
The CAG trinucleotide repeat mutation in the Huntington's disease gene (HTT) exhibits age-dependent tissue-specific expansion that correlates with disease onset in patients, implicating somatic expansion as a disease modifier and potential therapeutic target. Somatic HTT CAG expansion is critically dependent on proteins in the mismatch repair (MMR) pathway. To gain further insight into mechanisms of somatic expansion and the relationship of somatic expansion to the disease process in selectively vulnerable MSNs we have crossed HTT CAG knock-in mice (HdhQ111) with mice carrying a conditional (floxed) Msh2 allele and D9-Cre transgenic mice, in which Cre recombinase is expressed specifically in MSNs within the striatum. Deletion of Msh2 in MSNs eliminated Msh2 protein in those neurons. We demonstrate that MSN-specific deletion of Msh2 was sufficient to eliminate the vast majority of striatal HTT CAG expansions in HdhQ111 mice. Furthermore, MSN-specific deletion of Msh2 modified two mutant huntingtin phenotypes: the early nuclear localization of diffusely immunostaining mutant huntingtin was slowed; and the later development of intranuclear huntingtin inclusions was dramatically inhibited. Therefore, Msh2 acts within MSNs as a genetic enhancer both of somatic HTT CAG expansions and of HTT CAG-dependent phenotypes in mice. These data suggest that the selective vulnerability of MSNs may be at least in part contributed by the propensity for somatic expansion in these neurons, and imply that intervening in the expansion process is likely to have therapeutic benefit.
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Affiliation(s)
- Marina Kovalenko
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Ella Dragileva
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Jason St. Claire
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Tammy Gillis
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Jolene R. Guide
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Jaclyn New
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Hualing Dong
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Raju Kucherlapati
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Melanie H. Kucherlapati
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Michelle E. Ehrlich
- Farber Institute for Neurosciences, Thomas Jefferson University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jong-Min Lee
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Vanessa C. Wheeler
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- * E-mail:
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25
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Aberdein D, Munday J, Howe L, French A, Gibson I. Widespread Mismatch Repair Expression in Feline Small Intestinal Lymphomas. J Comp Pathol 2012; 147:24-30. [DOI: 10.1016/j.jcpa.2011.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 08/05/2011] [Accepted: 08/19/2011] [Indexed: 02/02/2023]
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26
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Perspectives for tailored chemoprevention and treatment of colorectal cancer in Lynch syndrome. Crit Rev Oncol Hematol 2011; 80:264-77. [DOI: 10.1016/j.critrevonc.2010.11.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 11/03/2010] [Accepted: 11/18/2010] [Indexed: 12/22/2022] Open
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27
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Lang WH, Coats JE, Majka J, Hura GL, Lin Y, Rasnik I, McMurray CT. Conformational trapping of mismatch recognition complex MSH2/MSH3 on repair-resistant DNA loops. Proc Natl Acad Sci U S A 2011; 108:E837-44. [PMID: 21960445 PMCID: PMC3198364 DOI: 10.1073/pnas.1105461108] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Insertion and deletion of small heteroduplex loops are common mutations in DNA, but why some loops are prone to mutation and others are efficiently repaired is unknown. Here we report that the mismatch recognition complex, MSH2/MSH3, discriminates between a repair-competent and a repair-resistant loop by sensing the conformational dynamics of their junctions. MSH2/MSH3 binds, bends, and dissociates from repair-competent loops to signal downstream repair. Repair-resistant Cytosine-Adenine-Guanine (CAG) loops adopt a unique DNA junction that traps nucleotide-bound MSH2/MSH3, and inhibits its dissociation from the DNA. We envision that junction dynamics is an active participant and a conformational regulator of repair signaling, and governs whether a loop is removed by MSH2/MSH3 or escapes to become a precursor for mutation.
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Affiliation(s)
- Walter H. Lang
- Lawrence Berkeley National Laboratory, Life Sciences Division, 1 Cyclotron Road, Berkeley, CA 94720
| | - Julie E. Coats
- Department of Physics, Emory University, 400 Dowman Drive, MSC N214, Atlanta, GA 30322
| | - Jerzy Majka
- Lawrence Berkeley National Laboratory, Life Sciences Division, 1 Cyclotron Road, Berkeley, CA 94720
| | - Greg L. Hura
- Lawrence Berkeley National Laboratory, Life Sciences Division, 1 Cyclotron Road, Berkeley, CA 94720
| | - Yuyen Lin
- Department of Physics, Emory University, 400 Dowman Drive, MSC N214, Atlanta, GA 30322
| | - Ivan Rasnik
- Department of Physics, Emory University, 400 Dowman Drive, MSC N214, Atlanta, GA 30322
| | - Cynthia T. McMurray
- Lawrence Berkeley National Laboratory, Life Sciences Division, 1 Cyclotron Road, Berkeley, CA 94720
- Department of Molecular Pharmacology and Experimental Therapeutics
- Department of Biochemistry and Molecular Biology, Mayo Foundation, 200 First Street, Rochester, MN 55905; and
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Herr AJ, Ogawa M, Lawrence NA, Williams LN, Eggington JM, Singh M, Smith RA, Preston BD. Mutator suppression and escape from replication error-induced extinction in yeast. PLoS Genet 2011; 7:e1002282. [PMID: 22022273 PMCID: PMC3188538 DOI: 10.1371/journal.pgen.1002282] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 07/21/2011] [Indexed: 11/23/2022] Open
Abstract
Cells rely on a network of conserved pathways to govern DNA replication fidelity. Loss of polymerase proofreading or mismatch repair elevates spontaneous mutation and facilitates cellular adaptation. However, double mutants are inviable, suggesting that extreme mutation rates exceed an error threshold. Here we combine alleles that affect DNA polymerase δ (Pol δ) proofreading and mismatch repair to define the maximal error rate in haploid yeast and to characterize genetic suppressors of mutator phenotypes. We show that populations tolerate mutation rates 1,000-fold above wild-type levels but collapse when the rate exceeds 10−3 inactivating mutations per gene per cell division. Variants that escape this error-induced extinction (eex) rapidly emerge from mutator clones. One-third of the escape mutants result from second-site changes in Pol δ that suppress the proofreading-deficient phenotype, while two-thirds are extragenic. The structural locations of the Pol δ changes suggest multiple antimutator mechanisms. Our studies reveal the transient nature of eukaryotic mutators and show that mutator phenotypes are readily suppressed by genetic adaptation. This has implications for the role of mutator phenotypes in cancer. Organisms strike a balance between genetic continuity and change. Most cells are well adapted to their niches and therefore invest heavily in mechanisms that maintain accurate DNA replication. When cell populations are confronted with changing environmental conditions, “mutator” clones with high mutation rates emerge and readily adapt to the new conditions by rapidly acquiring beneficial mutations. However, deleterious mutations also accumulate, raising the question: what level of mutational burden can cell populations sustain before collapsing? Here we experimentally determine the maximal mutation rate in haploid yeast. We observe that yeast can withstand a 1,000-fold increase in mutation rate without losing colony forming capacity. Yet no strains survive a 10,000-fold increase in mutation rate. Escape mutants with an “anti-mutator” phenotype frequently emerge from cell populations undergoing this error-induced extinction. The diversity of antimutator changes suggests that strong mutator phenotypes in nature may be inherently transient, ensuring that rapid adaptation is followed by genetic attenuation which preserves the beneficial, adaptive mutations. These observations are relevant to microbial populations during infection as well as the somatic evolution of cancer cells.
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Affiliation(s)
- Alan J. Herr
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Masanori Ogawa
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Nicole A. Lawrence
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Lindsey N. Williams
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Julie M. Eggington
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Mallika Singh
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Robert A. Smith
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Bradley D. Preston
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
- * E-mail: E-mail:
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29
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The mismatch repair pathway functions normally at a non-AID target in germinal center B cells. Blood 2011; 118:3013-8. [DOI: 10.1182/blood-2011-03-345991] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Abstract
Deficiency in Msh2, a component of the mismatch repair (MMR) system, leads to an approximately 10-fold increase in the mutation frequency in most tissues. By contrast, Msh2 deficiency in germinal center (GC) B cells decreases the mutation frequency at the IgH V region as a dU:dG mismatch produced by AID initiates modifications by MMR, resulting in mutations at nearby A:T base pairs. This raises the possibility that GC B cells express a factor that converts MMR into a globally mutagenic pathway. To test this notion, we investigated whether MMR corrects mutations in GC B cells at a gene that is not mutated by AID. Strikingly, we found that GC B cells accumulate 5 times more mutations at a reporter gene than during the development of the mouse. Notably, the mutation frequency at this reporter gene was approximately 10 times greater in Msh2−/− compared with wild-type GC B cells cells. In contrast to the V region, the increased level of mutations at A:T base pairs in GC B cells was not caused by MMR. These results show that in GC B cells, (1) MMR functions normally at an AID-insensitive gene and (2) the frequency of background mutagenesis is greater in GC B cells than in their precursor follicular B cells.
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Transient suppression of MLH1 allows effective single-nucleotide substitution by single-stranded DNA oligonucleotides. Mutat Res 2011; 715:52-60. [PMID: 21801734 DOI: 10.1016/j.mrfmmm.2011.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 07/11/2011] [Accepted: 07/12/2011] [Indexed: 01/27/2023]
Abstract
Short synthetic single-stranded oligodeoxyribonucleotides (ssODNs) can be used to introduce subtle modifications into the genome of mouse embryonic stem cells (ESCs). We have previously shown that effective application of ssODN-mediated gene targeting in ESC requires (transient) suppression of DNA mismatch repair (MMR). However, whereas transient down-regulation of the mismatch recognition protein MSH2 allowed substitution of 3 or 4 nucleotides, 1 or 2 nucleotide substitutions were still suppressed. We now demonstrate that single- or dinucleotide substitution can effectively be achieved by transient down-regulation of the downstream MMR protein MLH1. By exploiting highly specific real-time PCR, we demonstrate the feasibility of substituting a single basepair in a non-selectable gene. However, disabling the MMR machinery may lead to inadvertent mutations. To obtain insight into the mutation rate associated with transient MMR suppression, we have compared the impact of transient and constitutive MMR deficiency on the repair of frameshift intermediates at mono- and dinucleotide repeats. Repair at these repeats relied on the substrate specificity and functional redundancy of the MSH2/MSH6 and MSH2/MSH3 MMR complexes. MLH1 knockdown increased the level of spontaneous mutagenesis, but modified ESCs remained germ line competent. Thus, transient MLH1 suppression provides a valuable extension of the MSH2 knockdown strategy, allowing rapid generation of mice carrying single basepair alterations in their genome.
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31
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Kovtun IV, Harris KJ, Jatoi A, Jevremovic D. Increased incidence of endometrioid tumors caused by aberrations in E-cadherin promoter of mismatch repair-deficient mice. Carcinogenesis 2011; 32:1085-92. [PMID: 21551128 PMCID: PMC3128562 DOI: 10.1093/carcin/bgr080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 04/15/2011] [Accepted: 04/19/2011] [Indexed: 01/05/2023] Open
Abstract
Loss of E-cadherin expression is a critical step in the development and progression of gynecological tumors. Study of the precise role of E-cadherin has been hampered by the lack of satisfactory mouse model for E-cadherin deficiency. Likewise, DNA mismatch repair (MMR) is implicated in gynecological tumorigenesis, but knockout of MMR in mice predominantly causes hematologic neoplasms. Here, we show that combined disruption of E-cadherin and DNA MMR pathways increases incidence of endometrioid tumors in mice. Twenty percent of mice knockout for Msh2 enzyme and hemizygous for E-cadherin [Msh2(-/-)/Cdh1(+/-)] developed endometrioid-like tumors in the ovary, uterus and genital area. Characteristic of these tumors was a complete loss of E-cadherin expression. Sequence analysis of E-cadherin promoter region demonstrated that the loss of E-cadherin expression is caused by inactivating mutations, implying that E-cadherin is a mutational target in Msh2-deficient mice. In addition, Msh2(-/-)/Cdh1(+/-) mice showed a reduction in overall survival as compared with their Msh2(-/-) counterparts due to the development of more aggressive lymphomas, suggesting a specific role of E-cadherin in lymphomagenesis. In conclusion, Msh2(-/-)/Cdh1(+/-) mice provide a good model of gynecological tumorigenesis and may be useful for testing molecular target-specific therapies.
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Affiliation(s)
- Irina V Kovtun
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic and Foundation, 200 First Street SW, Rochester, MN 55905, USA.
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32
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Young LC, Bone KM, Wang P, Wu F, Adam BA, Hegazy S, Gelebart P, Holovati J, Li L, Andrew SE, Lai R. Fusion tyrosine kinase NPM-ALK Deregulates MSH2 and suppresses DNA mismatch repair function novel insights into a potent oncoprotein. THE AMERICAN JOURNAL OF PATHOLOGY 2011; 179:411-21. [PMID: 21703420 DOI: 10.1016/j.ajpath.2011.03.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 02/09/2011] [Accepted: 03/10/2011] [Indexed: 11/17/2022]
Abstract
The fusion tyrosine kinase NPM-ALK is central to the pathogenesis of ALK-positive anaplastic large cell lymphoma (ALK(+)ALCL). We recently identified that MSH2, a key DNA mismatch repair (MMR) protein integral to the suppression of tumorigenesis, is an NPM-ALK-interacting protein. In this study, we found in vitro evidence that enforced expression of NPM-ALK in HEK293 cells suppressed MMR function. Correlating with these findings, six of nine ALK(+)ALCL tumors displayed evidence of microsatellite instability, as opposed to none of the eight normal DNA control samples (P = 0.007, Student's t-test). Using co-immunoprecipitation, we found that increasing levels of NPM-ALK expression in HEK293 cells resulted in decreased levels of MSH6 bound to MSH2, whereas MSH2·NPM-ALK binding was increased. The NPM-ALK·MSH2 interaction was dependent on the activation/autophosphorylation of NPM-ALK, and the Y191 residue of NPM-ALK was a crucial site for this interaction and NPM-ALK-mediated MMR suppression. MSH2 was found to be tyrosine phosphorylated in the presence of NPM-ALK. Finally, NPM-ALK impeded the expected DNA damage-induced translocation of MSH2 out of the cytoplasm. To conclude, our data support a model in which the suppression of MMR by NPM-ALK is attributed to its ability to interfere with normal MSH2 biochemistry and function.
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MESH Headings
- Cytoplasm/metabolism
- DNA Damage
- DNA Mismatch Repair
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Humans
- Immunoenzyme Techniques
- Immunoprecipitation
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/metabolism
- Lymphoma, Large B-Cell, Diffuse/pathology
- Lymphoma, Large-Cell, Anaplastic/genetics
- Lymphoma, Large-Cell, Anaplastic/metabolism
- Lymphoma, Large-Cell, Anaplastic/pathology
- Microsatellite Instability
- MutS Homolog 2 Protein/genetics
- MutS Homolog 2 Protein/metabolism
- Phosphorylation
- Protein Multimerization
- Protein Transport
- Protein-Tyrosine Kinases/genetics
- Protein-Tyrosine Kinases/metabolism
- Tumor Cells, Cultured
- Tyrosine/metabolism
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Affiliation(s)
- Leah C Young
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
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Abstract
Animal models of cancer have been instrumental in understanding the progression and therapy of hereditary cancer syndromes. The ability to alter the genome of an individual mouse cell in both constitutive and inducible approaches has led to many novel insights into their human counterparts. In this review, knockout mouse models of inherited human cancer syndromes are presented and insights from the study of these models are highlighted.
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Affiliation(s)
- Sohail Jahid
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
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34
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Selective induction of DNA repair pathways in human B cells activated by CD4+ T cells. PLoS One 2010; 5:e15549. [PMID: 21179576 PMCID: PMC3002972 DOI: 10.1371/journal.pone.0015549] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Accepted: 11/11/2010] [Indexed: 11/26/2022] Open
Abstract
Greater than 75% of all hematologic malignancies derive from germinal center (GC) or post-GC B cells, suggesting that the GC reaction predisposes B cells to tumorigenesis. Because GC B cells acquire expression of the highly mutagenic enzyme activation-induced cytidine deaminase (AID), GC B cells may require additional DNA repair capacity. The goal of this study was to investigate whether normal human B cells acquire enhanced expression of DNA repair factors upon AID induction. We first demonstrated that several DNA mismatch repair, homologous recombination, base excision repair, and ATR signaling genes were overexpressed in GC B cells relative to naïve and memory B cells, reflecting activation of a process we have termed somatic hyperrepair (SHR). Using an in vitro system, we next characterized activation signals required to induce AID expression and SHR. Although AID expression was induced by a variety of polyclonal activators, SHR induction strictly required signals provided by contact with activated CD4+ T cells, and B cells activated in this manner displayed reduced levels of DNA damage-induced apoptosis. We further show the induction of SHR is independent of AID expression, as GC B cells from AID -/- mice retained heightened expression of SHR proteins. In consideration of the critical role that CD4+ T cells play in inducing the SHR process, our data suggest a novel role for CD4+ T cells in the tumor suppression of GC/post-GC B cells.
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35
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Aarts M, te Riele H. Progress and prospects: oligonucleotide-directed gene modification in mouse embryonic stem cells: a route to therapeutic application. Gene Ther 2010; 18:213-9. [PMID: 21160530 DOI: 10.1038/gt.2010.161] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Gene targeting by single-stranded oligodeoxyribonucleotides (ssODNs) is a promising technique for introducing site-specific sequence alterations without affecting the genomic organization of the target locus. Here, we discuss the significant progress that has been made over the last 5 years in unraveling the mechanisms and reaction parameters underlying ssODN-mediated gene targeting. We will specifically focus on ssODN-mediated gene targeting in murine embryonic stem cells (ESCs) and the impact of the DNA mismatch repair (MMR) system on the targeting process. Implications of novel findings for routine application of ssODN-mediated gene targeting and challenges that need to be overcome for future therapeutic applications are highlighted.
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Affiliation(s)
- M Aarts
- Division of Molecular Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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36
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Preston BD, Albertson TM, Herr AJ. DNA replication fidelity and cancer. Semin Cancer Biol 2010; 20:281-93. [PMID: 20951805 PMCID: PMC2993855 DOI: 10.1016/j.semcancer.2010.10.009] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2010] [Accepted: 10/07/2010] [Indexed: 12/14/2022]
Abstract
Cancer is fueled by mutations and driven by adaptive selection. Normal cells avoid deleterious mutations by replicating their genomes with extraordinary accuracy. Here we review the pathways governing DNA replication fidelity and discuss evidence implicating replication errors (point mutation instability or PIN) in carcinogenesis.
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Affiliation(s)
- Bradley D Preston
- Department of Pathology, University of Washington, Seattle, WA 98195, USA.
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37
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Arana ME, Holmes SF, Fortune JM, Moon AF, Pedersen LC, Kunkel TA. Functional residues on the surface of the N-terminal domain of yeast Pms1. DNA Repair (Amst) 2010; 9:448-57. [PMID: 20138591 DOI: 10.1016/j.dnarep.2010.01.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2009] [Revised: 01/07/2010] [Accepted: 01/07/2010] [Indexed: 01/21/2023]
Abstract
Saccharomyces cerevisiae MutLalpha is a heterodimer of Mlh1 and Pms1 that participates in DNA mismatch repair (MMR). Both proteins have weakly conserved C-terminal regions (CTDs), with the CTD of Pms1 harboring an essential endonuclease activity. These proteins also have conserved N-terminal domains (NTDs) that bind and hydrolyze ATP and bind to DNA. To better understand Pms1 functions and potential interactions with DNA and/or other proteins, we solved the 2.5A crystal structure of yeast Pms1 (yPms1) NTD. The structure is similar to the homologous NTDs of Escherichia coli MutL and human PMS2, including the site involved in ATP binding and hydrolysis. The structure reveals a number of conserved, positively charged surface residues that do not interact with other residues in the NTD and are therefore candidates for interactions with DNA, with the CTD and/or with other proteins. When these were replaced with glutamate, several replacements resulted in yeast strains with elevated mutation rates. Two replacements also resulted in NTDs with decreased DNA binding affinity in vitro, suggesting that these residues contribute to DNA binding that is important for mismatch repair. Elevated mutation rates also resulted from surface residue replacements that did not affect DNA binding, suggesting that these conserved residues serve other functions, possibly involving interactions with other MMR proteins.
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Affiliation(s)
- Mercedes E Arana
- Laboratory of Molecular Genetics, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, United States
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38
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Roa S, Li Z, Peled JU, Zhao C, Edelmann W, Scharff MD. MSH2/MSH6 complex promotes error-free repair of AID-induced dU:G mispairs as well as error-prone hypermutation of A:T sites. PLoS One 2010; 5:e11182. [PMID: 20567595 PMCID: PMC2887398 DOI: 10.1371/journal.pone.0011182] [Citation(s) in RCA: 32] [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: 05/11/2010] [Accepted: 05/21/2010] [Indexed: 12/05/2022] Open
Abstract
Mismatch repair of AID-generated dU:G mispairs is critical for class switch recombination (CSR) and somatic hypermutation (SHM) in B cells. The generation of a previously unavailable Msh2−/−Msh6−/− mouse has for the first time allowed us to examine the impact of the complete loss of MutSα on lymphomagenesis, CSR and SHM. The onset of T cell lymphomas and the survival of Msh2−/−Msh6−/− and Msh2−/−Msh6−/−Msh3−/− mice are indistinguishable from Msh2−/− mice, suggesting that MSH2 plays the critical role in protecting T cells from malignant transformation, presumably because it is essential for the formation of stable MutSα heterodimers that maintain genomic stability. The similar defects on switching in Msh2−/−, Msh2−/−Msh6−/− and Msh2−/−Msh6−/−Msh3−/− mice confirm that MutSα but not MutSβ plays an important role in CSR. Analysis of SHM in Msh2−/−Msh6−/− mice not only confirmed the error-prone role of MutSα in the generation of strand biased mutations at A:T bases, but also revealed an error-free role of MutSα when repairing some of the dU:G mispairs generated by AID on both DNA strands. We propose a model for the role of MutSα at the immunoglobulin locus where the local balance of error-free and error-prone repair has an impact in the spectrum of mutations introduced during Phase 2 of SHM.
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Affiliation(s)
- Sergio Roa
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, United States of America
| | - Ziqiang Li
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, United States of America
| | - Jonathan U. Peled
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, United States of America
| | - Chunfang Zhao
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, United States of America
| | - Winfried Edelmann
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, United States of America
| | - Matthew D. Scharff
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, United States of America
- * E-mail:
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39
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Abstract
Mouse models of human cancer have played a vital role in understanding tumorigenesis and answering experimental questions that other systems cannot address. Advances continue to be made that allow better understanding of the mechanisms of tumor development, and therefore the identification of better therapeutic and diagnostic strategies. We review major advances that have been made in modeling cancer in the mouse and specific areas of research that have been explored with mouse models. For example, although there are differences between mice and humans, new models are able to more accurately model sporadic human cancers by specifically controlling timing and location of mutations, even within single cells. As hypotheses are developed in human and cell culture systems, engineered mice provide the most tractable and accurate test of their validity in vivo. For example, largely through the use of these models, the microenvironment has been established to play a critical role in tumorigenesis, since tumor development and the interaction with surrounding stroma can be studied as both evolve. These mouse models have specifically fueled our understanding of cancer initiation, immune system roles, tumor angiogenesis, invasion, and metastasis, and the relevance of molecular diversity observed among human cancers. Currently, these models are being designed to facilitate in vivo imaging to track both primary and metastatic tumor development from much earlier stages than previously possible. Finally, the approaches developed in this field to achieve basic understanding are emerging as effective tools to guide much needed development of treatment strategies, diagnostic strategies, and patient stratification strategies in clinical research.
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Affiliation(s)
- Jessica C Walrath
- Mouse Cancer Genetics Program, National Cancer Institute, Frederick, Maryland, USA
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40
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Msh2-dependent DNA repair mitigates a unique susceptibility of B cell progenitors to c-Myc-induced lymphomas. Proc Natl Acad Sci U S A 2009; 106:18698-703. [PMID: 19837692 DOI: 10.1073/pnas.0905965106] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
C-Myc is one of the most common targets of genetic alterations in human cancers. Although overexpression of c-Myc in the B cell compartment predisposes to lymphomas, secondary mutations are required for disease manifestation. In this article, we show that genetic deficiencies causing arrested B cell development and accumulation of B cell progenitors lead to accelerated lymphomagenesis in Emu c-myc transgenic mice. This result suggests that B cell progenitors are more prone than their mature counterparts to developing secondary oncogenic lesions that complement c-Myc in promoting transformation. To investigate the nature of these oncogenic lesions, we examined Emu c-myc mice deficient in mismatch repair function. We report that Msh2(-/-) Emu c-myc and Msh2(G674A/G674A) Emu c-myc mice rapidly succumb to pro-B cell stage lymphomas, indicating that Msh2-dependent mismatch repair function actively suppresses c-Myc-associated oncogenesis during early B cell development.
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41
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DNA polymerase epsilon and delta proofreading suppress discrete mutator and cancer phenotypes in mice. Proc Natl Acad Sci U S A 2009; 106:17101-4. [PMID: 19805137 DOI: 10.1073/pnas.0907147106] [Citation(s) in RCA: 171] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Organisms require faithful DNA replication to avoid deleterious mutations. In yeast, replicative leading- and lagging-strand DNA polymerases (Pols epsilon and delta, respectively) have intrinsic proofreading exonucleases that cooperate with each other and mismatch repair to limit spontaneous mutation to less than 1 per genome per cell division. The relationship of these pathways in mammals and their functions in vivo are unknown. Here we show that mouse Pol epsilon and delta proofreading suppress discrete mutator and cancer phenotypes. We found that inactivation of Pol epsilon proofreading elevates base-substitution mutations and accelerates a unique spectrum of spontaneous cancers; the types of tumors are entirely different from those triggered by loss of Pol delta proofreading. Intercrosses of Pol epsilon-, Pol delta-, and mismatch repair-mutant mice show that Pol epsilon and delta proofreading act in parallel pathways to prevent spontaneous mutation and cancer. These findings distinguish Pol epsilon and delta functions in vivo and reveal tissue-specific requirements for DNA replication fidelity.
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42
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Russo MT, De Luca G, Casorelli I, Degan P, Molatore S, Barone F, Mazzei F, Pannellini T, Musiani P, Bignami M. Role of MUTYH and MSH2 in the Control of Oxidative DNA Damage, Genetic Instability, and Tumorigenesis. Cancer Res 2009; 69:4372-9. [DOI: 10.1158/0008-5472.can-08-3292] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Mismatch repair is the major pathway controlling genetic stability by removing mispairs caused by faulty replication and/or mismatches containing oxidized bases. Thus, inactivation of the Msh2 mismatch repair gene is associated with a mutator phenotype and increased cancer susceptibility. The base excision repair gene Mutyh is also involved in the maintenance of genomic integrity by repairing premutagenic lesions induced by oxidative DNA damage. Because evidence in bacteria suggested that Msh2 and Mutyh repair factors might have some overlapping functions, we investigated the biological consequences of their single and double inactivation in vitro and in vivo. Msh2−/− mouse embryo fibroblasts (MEF) showed a strong mutator phenotype at the hprt gene, whereas Mutyh inactivation was associated with a milder phenotype (2.9 × 10−6 and 3.3 × 10−7 mutation/cell/generation, respectively). The value of 2.7 × 10−6 mutation/cell/generation in Msh2−/−Mutyh−/− MEFs did not differ significantly from Msh2−/− cells. When steady-state levels of DNA 8-oxo-7,8-dihydroguanine (8-oxoG) were measured in MEFs of different genotypes, single gene inactivation resulted in increases similar to those observed in doubly defective cells. In contrast, a synergistic accumulation of 8-oxoG was observed in several organs of Msh2−/−Mutyh−/− animals, suggesting that in vivo Msh2 and Mutyh provide separate repair functions and contribute independently to the control of oxidative DNA damage. Finally, a strong delay in lymphomagenesis was observed in Msh2−/−Mutyh−/− when compared with Msh2−/− animals. The immunophenotype of these tumors indicate that both genotypes develop B-cell lymphoblastic lymphomas displaying microsatellite instability. This suggests that a large fraction of the cancer-prone phenotype of Msh2−/− mice depends on Mutyh activity. [Cancer Res 2009;69(10):4372–9]
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Affiliation(s)
- Maria Teresa Russo
- 1Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
| | - Gabriele De Luca
- 1Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
| | - Ida Casorelli
- 1Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
| | - Paolo Degan
- 2Department of Translational Oncology, Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Sara Molatore
- 3Department of Genetics and Microbiology, University of Pavia, Pavia, Italy; and
| | - Flavia Barone
- 1Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
| | - Filomena Mazzei
- 1Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
| | - Tania Pannellini
- 4Centro Studi per l'Invecchiamento, Università degli Studi “G. d'Annunzio,” Chieti-Pescara, Italy
| | - Piero Musiani
- 4Centro Studi per l'Invecchiamento, Università degli Studi “G. d'Annunzio,” Chieti-Pescara, Italy
| | - Margherita Bignami
- 1Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
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43
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The nucleotide binding dynamics of human MSH2-MSH3 are lesion dependent. Nat Struct Mol Biol 2009; 16:550-7. [PMID: 19377479 DOI: 10.1038/nsmb.1596] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Accepted: 03/30/2009] [Indexed: 01/12/2023]
Abstract
Here we report that the human DNA mismatch complex MSH2-MSH3 recognizes small loops by a mechanism different from that of MSH2-MSH6 for single-base mismatches. The subunits MSH2 and MSH3 can bind either ADP or ATP with similar affinities. Upon binding to a DNA loop, however, MSH2-MSH3 adopts a single 'nucleotide signature', in which the MSH2 subunit is occupied by an ADP molecule and the MSH3 subunit is empty. Subsequent ATP binding and hydrolysis in the MSH3 subunit promote ADP-ATP exchange in the MSH2 subunit to yield a hydrolysis-independent ATP-MSH2-MSH3-ADP intermediate. Human MSH2-MSH3 and yeast Msh2-Msh6 both undergo ADP-ATP exchange in the Msh2 subunit but, apparently, have opposite requirements for ATP hydrolysis: ADP release from DNA-bound Msh2-Msh6 requires ATP stabilization in the Msh6 subunit, whereas ADP release from DNA-bound MSH2-MSH3 requires ATP hydrolysis in the MSH3 subunit. We propose a model in which lesion binding converts MSH2-MSH3 into a distinct nucleotide-bound form that is poised to be a molecular sensor for lesion specificity.
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Interactions of Transposons with the Cellular DNA Repair Machinery. TRANSPOSONS AND THE DYNAMIC GENOME 2009. [DOI: 10.1007/7050_2008_043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Busuttil RA, Muñoz DP, Garcia AM, Rodier F, Kim WH, Suh Y, Hasty P, Campisi J, Vijg J. Effect of Ku80 deficiency on mutation frequencies and spectra at a LacZ reporter locus in mouse tissues and cells. PLoS One 2008; 3:e3458. [PMID: 18941635 PMCID: PMC2565499 DOI: 10.1371/journal.pone.0003458] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2008] [Accepted: 09/19/2008] [Indexed: 01/08/2023] Open
Abstract
Non-homologous end joining (NHEJ) is thought to be an important mechanism for preventing the adverse effects of DNA double strand breaks (DSBs) and its absence has been associated with premature aging. To investigate the effect of inactivated NHEJ on spontaneous mutation frequencies and spectra in vivo and in cultured cells, we crossed a Ku80-deficient mouse with mice harboring a lacZ-plasmid-based mutation reporter. We analyzed various organs and tissues, as well as cultured embryonic fibroblasts, for mutations at the lacZ locus. When comparing mutant with wild-type mice, we observed a significantly higher number of genome rearrangements in liver and spleen and a significantly lower number of point mutations in liver and brain. The reduced point mutation frequency was not due to a decrease in small deletion mutations thought to be a hallmark of NHEJ, but could be a consequence of increased cellular responses to unrepaired DSBs. Indeed, we found a substantial increase in persistent 53BP1 and γH2AX DNA damage foci in Ku80−/− as compared to wild-type liver. Treatment of cultured Ku80-deficient or wild-type embryonic fibroblasts, either proliferating or quiescent, with hydrogen peroxide or bleomycin showed no differences in the number or type of induced genome rearrangements. However, after such treatment, Ku80-deficient cells did show an increased number of persistent DNA damage foci. These results indicate that Ku80-dependent repair of DNA damage is predominantly error-free with the effect of alternative more error-prone pathways creating genome rearrangements only detectable after extended periods of time, i.e., in young adult animals. The observed premature aging likely results from a combination of increased cellular senescence and an increased load of stable, genome rearrangements.
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Affiliation(s)
- Rita A. Busuttil
- Buck Institute for Age Research, Novato, California, United States of America
| | - Denise P. Muñoz
- Buck Institute for Age Research, Novato, California, United States of America
| | - Ana Maria Garcia
- Department of Biology, University of Texas at San Antonio, San Antonio, Texas, United States of America
| | - Francis Rodier
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Woo Ho Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Yousin Suh
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Paul Hasty
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas, United States of America
| | - Judith Campisi
- Buck Institute for Age Research, Novato, California, United States of America
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Jan Vijg
- Buck Institute for Age Research, Novato, California, United States of America
- * E-mail:
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Abstract
The zebrafish has developed into an important model organism for biomedical research over the last decades. Although the main focus of zebrafish research has traditionally been on developmental biology, keeping and observing zebrafish in the lab led to the identification of diseases similar to humans, such as cancer, which subsequently became a subject for study. As a result, about 50 articles have been published since 2000 in which zebrafish were used as a cancer model. Strategies used include carcinogenic treatments, transplantation of mammalian cancer cells, forward genetic screens for proliferation or genomic instability, reverse genetic target-selected mutagenesis to inactivate known tumor suppressor genes, and the generation of transgenics to express human oncogenes. Zebrafish have been found to develop almost any tumor type known from human, with similar morphology and, according to gene expression array studies, comparable signaling pathways. However, tumor incidences are relatively low, albeit highly comparable between different mutants, and tumors develop late in life. In addition, tumor spectra are sometimes different when compared with mice and humans. Nevertheless, the zebrafish model has created its own niche in cancer research, complementing existing models with its specific experimental advantages and characteristics. Examples of these are imaging of tumor progression in living fish by fluorescence, treatment with chemical compounds, and screening possibilities not only for chemical modifiers but also for genetic enhancers and suppressors. This review aims to provide a comprehensive overview of the state of the art of zebrafish as a model in cancer research. (Mol Cancer Res 2008;6(5):685-94).
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Affiliation(s)
- Harma Feitsma
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
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47
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Abstract
The depth of a cell of a multicellular organism is the number of cell divisions it underwent since the zygote, and knowing this basic cell property would help address fundamental problems in several areas of biology. At present, the depths of the vast majority of human and mouse cell types are unknown. Here, we show a method for estimating the depth of a cell by analyzing somatic mutations in its microsatellites, and provide to our knowledge for the first time reliable depth estimates for several cells types in mice. According to our estimates, the average depth of oocytes is 29, consistent with previous estimates. The average depth of B cells ranges from 34 to 79, linearly related to the mouse age, suggesting a rate of one cell division per day. In contrast, various types of adult stem cells underwent on average fewer cell divisions, supporting the notion that adult stem cells are relatively quiescent. Our method for depth estimation opens a window for revealing tissue turnover rates in animals, including humans, which has important implications for our knowledge of the body under physiological and pathological conditions. All the cells in our body are descendants of a single cell – the fertilized egg. Some cells are relatively close descendants, having undergone a small number of cell divisions, while other cells may be hundreds or even thousands of divisions deep. So far, science was unable to provide even gross estimates for the depths of the vast majority of human and mouse cells. In this study, we show that precise depth estimates of cells can be obtained from the analysis of non-hazardous mutations that spontaneously accumulate during normal development. The concept behind the method is simple: deeper cells tend to acquire more mutations and “drift away” from the original DNA sequence of the fertilized egg. Knowing how deep cells are is the key to many fundamental open questions in biology and medicine, such as whether neurons in our brain can regenerate, or whether new eggs are created in adult females.
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van Boxtel R, Toonen PW, van Roekel HS, Verheul M, Smits BMG, Korving J, de Bruin A, Cuppen E. Lack of DNA mismatch repair protein MSH6 in the rat results in hereditary non-polyposis colorectal cancer-like tumorigenesis. Carcinogenesis 2008; 29:1290-7. [DOI: 10.1093/carcin/bgn094] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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49
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Wasserstrom A, Adar R, Shefer G, Frumkin D, Itzkovitz S, Stern T, Shur I, Zangi L, Kaplan S, Harmelin A, Reisner Y, Benayahu D, Tzahor E, Segal E, Shapiro E. Reconstruction of cell lineage trees in mice. PLoS One 2008; 3:e1939. [PMID: 18398465 PMCID: PMC2276688 DOI: 10.1371/journal.pone.0001939] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Accepted: 02/25/2008] [Indexed: 12/27/2022] Open
Abstract
The cell lineage tree of a multicellular organism represents its history of cell divisions from the very first cell, the zygote. A new method for high-resolution reconstruction of parts of such cell lineage trees was recently developed based on phylogenetic analysis of somatic mutations accumulated during normal development of an organism. In this study we apply this method in mice to reconstruct the lineage trees of distinct cell types. We address for the first time basic questions in developmental biology of higher organisms, namely what is the correlation between the lineage relation among cells and their (1) function, (2) physical proximity and (3) anatomical proximity. We analyzed B-cells, kidney-, mesenchymal- and hematopoietic-stem cells, as well as satellite cells, which are adult skeletal muscle stem cells isolated from their niche on the muscle fibers (myofibers) from various skeletal muscles. Our results demonstrate that all analyzed cell types are intermingled in the lineage tree, indicating that none of these cell types are single exclusive clones. We also show a significant correlation between the physical proximity of satellite cells within muscles and their lineage. Furthermore, we show that satellite cells obtained from a single myofiber are significantly clustered in the lineage tree, reflecting their common developmental origin. Lineage analysis based on somatic mutations enables performing high resolution reconstruction of lineage trees in mice and humans, which can provide fundamental insights to many aspects of their development and tissue maintenance.
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Affiliation(s)
- Adam Wasserstrom
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Rivka Adar
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Gabi Shefer
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Dan Frumkin
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Shalev Itzkovitz
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Tomer Stern
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | | | - Lior Zangi
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Shai Kaplan
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Harmelin
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Yair Reisner
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Dafna Benayahu
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Eldad Tzahor
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Ehud Shapiro
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
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Scott RH, Homfray T, Huxter NL, Mitton SG, Nash R, Potter MN, Lancaster D, Rahman N. Familial T-cell non-Hodgkin lymphoma caused by biallelic MSH2 mutations. J Med Genet 2008; 44:e83. [PMID: 17601929 PMCID: PMC2597999 DOI: 10.1136/jmg.2007.048942] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Familial non-Hodgkin lymphoma (NHL) is rare and in most cases, no underlying cause is identifiable. We report homozygous truncating mutations in the mismatch repair gene MSH2 (226C-->T; Q76X) in three siblings who each developed T-cell NHL in early childhood. All three children had hyperpigmented and hypopigmented skin lesions. Constitutional biallelic MSH2 mutations have previously been reported in five individuals, all of whom developed malignancy in childhood. Familial lymphoma has not been reported in this context or in association with biallelic mutations in the other mismatch repair genes MLH1, MSH6 or PMS2. In addition, hypopigmented skin lesions have not previously been reported in biallelic MSH2 carriers. Our findings therefore expand the spectrum of phenotypes associated with biallelic MSH2 mutations and identify a new cause of familial lymphoma. Moreover, the diagnosis has important management implications as it allows the avoidance of chemotherapeutic agents likely to be ineffective and mutagenic in the proband, and the provision of cascade genetic testing and tumour screening for relatives.
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Affiliation(s)
- Richard H Scott
- Section of Cancer Genetics, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, UK, SM2 5NG.
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