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Maimaiti A, Liu Y, Abulaiti A, Wang X, Feng Z, Wang J, Mijiti M, Turhon M, Alimu N, Wang Y, Liang W, Jiang L, Pei Y. Genomic Profiling of Lower-Grade Gliomas Subtype with Distinct Molecular and Clinicopathologic Characteristics via Altered DNA-Damage Repair Features. J Mol Neurosci 2023; 73:269-286. [PMID: 37067735 DOI: 10.1007/s12031-023-02116-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 03/30/2023] [Indexed: 04/18/2023]
Abstract
Lower WHO grade II and III gliomas (LGGs) exhibit significant genetic and transcriptional heterogeneity, and the heterogeneity of DNA damage repair (DDR) and its relationship to tumor biology, transcriptome, and tumor microenvironment (TME) remains poorly understood. In this study, we conducted multi-omics data integration to investigate DDR alterations in LGG. Based on clinical parameters and molecular characteristics, LGG patients were categorized into distinct DDR subtypes, namely, DDR-activated and DDR-suppressed subtypes. We compared gene mutation, immune spectrum, and immune cell infiltration between the two subtypes. DDR scores were generated to classify LGG patients based on DDR subtype features, and the results were validated using a multi-layer data cohort. We found that DDR activation was associated with poorer overall survival and that clinicopathological features of advanced age and higher grade were more common in the DDR-activated subtype. DDR-suppressed subtypes exhibited more frequent mutations in IDH1. In addition, we observed significant upregulation of activated immune cells in the DDR-activated subgroup, which suggests that immune cell infiltration significantly influences tumor progression and immunotherapeutic responses. Furthermore, we constructed a DDR signature for LGG using six DDR genes, which allowed for the division of patients into low- and high-risk groups. Quantitative real-time PCR results showed that CDK1, CDK2, TYMS, SMC4, and WEE1 were significantly upregulated in LGG samples compared to normal brain tissue samples. Overall, our study sheds light on DDR heterogeneity in LGG and provides insight into the molecular pathways of DDR involved in LGG development.
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Affiliation(s)
- Aierpati Maimaiti
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, 830054, Urumqi, Xinjiang, China
| | - Yanwen Liu
- Department of Medical Laboratory, Xinjiang Production and Construction Corps Hospital, 830002, Urumqi, Xinjiang, China
| | - Aimitaji Abulaiti
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, 830054, Urumqi, Xinjiang, China
| | - Xixian Wang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, 830054, Urumqi, Xinjiang, China
| | - Zhaohai Feng
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, 830054, Urumqi, Xinjiang, China
| | - Jiaming Wang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, 830054, Urumqi, Xinjiang, China
| | - Maimaitili Mijiti
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, 830054, Urumqi, Xinjiang, China
| | - Mirzat Turhon
- Department of Neurointerventional Surgery, Beijing Neurosurgical Institute, Capital Medical University, 100070, Beijing, China
- Department of Neurointerventional Surgery, Beijing Tiantan Hospital, Capital Medical University, 100070, Beijing, China
| | - Nilipaer Alimu
- Department of Otorhinolaryngology, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, 830054, Urumqi, Xinjiang, China
| | - Yongxin Wang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, 830054, Urumqi, Xinjiang, China
| | - Wenbao Liang
- Department of Neurosurgery, The Fourth Affiliated Hospital of Xinjiang Medical University, No. 116, Huanghe Road, Shaibak District, 830000, Urumqi, Xinjiang, China.
| | - Lei Jiang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, 830054, Urumqi, Xinjiang, China.
| | - Yinan Pei
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, 830054, Urumqi, Xinjiang, China.
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Pfeifer M, Brem R, Lippert TP, Boulianne B, Ho HN, Robinson ME, Stebbing J, Feldhahn N. SSB1/SSB2 Proteins Safeguard B Cell Development by Protecting the Genomes of B Cell Precursors. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2019; 202:3423-3433. [PMID: 31085591 PMCID: PMC6545462 DOI: 10.4049/jimmunol.1801618] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 04/12/2019] [Indexed: 12/22/2022]
Abstract
Induction of programmed DNA damage and its recognition and repair are fundamental for B cell development. The ssDNA-binding protein SSB1 has been described in human cells as essential for the recognition and repair of DNA damage. To study its relevance for B cells, we recently developed Ssb1 -/- and conditional Ssb1 -/- mice. Although SSB1 loss did not affect B cell development, Ssb1 -/- cells exhibited compensatory expression of its homolog SSB2. We have now generated Ssb2 -/- mice and show in this study that SSB2 is also dispensable for B cell development and DNA damage response activation. In contrast to the single loss of Ssb1 or Ssb2, however, combined SSB1/2 deficiency caused a defect in early B cell development. We relate this to the sensitivity of B cell precursors as mature B cells largely tolerated their loss. Toxicity of combined genetic SSB1/2 loss can be rescued by ectopic expression of either SSB1 or SSB2, mimicked by expression of SSB1 ssDNA-binding mutants, and attenuated by BCL2-mediated suppression of apoptosis. SSB1/2 loss in B cell precursors further caused increased exposure of ssDNA associated with disruption of genome fragile sites, inefficient cell cycle progression, and increased DNA damage if apoptosis is suppressed. As such, our results establish SSB1/2 as safeguards of B cell development and unveil their differential requirement in immature and mature B lymphocytes.
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Affiliation(s)
- Matthias Pfeifer
- Centre for Hematology, Department of Medicine, Imperial College London, W12 0NN London, United Kingdom; and
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, W12 0NN London, United Kingdom
| | - Reto Brem
- Centre for Hematology, Department of Medicine, Imperial College London, W12 0NN London, United Kingdom; and
| | - Timothy P Lippert
- Centre for Hematology, Department of Medicine, Imperial College London, W12 0NN London, United Kingdom; and
| | - Bryant Boulianne
- Centre for Hematology, Department of Medicine, Imperial College London, W12 0NN London, United Kingdom; and
| | - Howin Ng Ho
- Centre for Hematology, Department of Medicine, Imperial College London, W12 0NN London, United Kingdom; and
| | - Mark E Robinson
- Centre for Hematology, Department of Medicine, Imperial College London, W12 0NN London, United Kingdom; and
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, W12 0NN London, United Kingdom
| | - Justin Stebbing
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, W12 0NN London, United Kingdom
| | - Niklas Feldhahn
- Centre for Hematology, Department of Medicine, Imperial College London, W12 0NN London, United Kingdom; and
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Frankenberger S, Davari K, Fischer-Burkart S, Böttcher K, Tomi NS, Zimber-Strobl U, Jungnickel B. Checkpoint kinase 1 negatively regulates somatic hypermutation. Nucleic Acids Res 2014; 42:3666-74. [PMID: 24423870 PMCID: PMC3973322 DOI: 10.1093/nar/gkt1378] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Immunoglobulin (Ig) diversification by somatic hypermutation in germinal center B cells is instrumental for maturation of the humoral immune response, but also bears the risk of excessive or aberrant genetic changes. Thus, introduction of DNA damage by activation-induced cytidine deaminase as well as DNA repair by multiple pathways need to be tightly regulated during the germinal center response to prevent lymphomagenesis. In the present study, we show that DNA damage checkpoint signaling via checkpoint kinase 1 (Chk1) negatively regulates somatic hypermutation. Chk1 inhibition in human B cell lymphoma lines as well as inactivation of Chk1 alleles by gene targeting in DT40 B cells leads to increased somatic hypermutation. This is apparently due to changes in DNA repair pathways regulated by Chk1, such as a decreased homologous recombination efficiency that also leads to decreased Ig gene conversion in DT40. Our data show that Chk1 signaling plays a crucial role in regulation of Ig diversification and sheds unexpected light on potential origins of aberrant somatic hypermutation in B cell lymphomagenesis.
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Affiliation(s)
- Samantha Frankenberger
- Institute of Clinical and Molecular Biology, Helmholtz Center Munich, Marchioninistrasse 25, 81377 Munich, Germany, Department of Cell Biology, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich-Schiller University Jena, Hans-Knoell-Strasse 2, 07745 Jena, Germany and Department of Gene Vectors, Helmholtz Center Munich, Marchioninistrasse 25, 81377 Munich, Germany
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Haque S, Yan XJ, Rosen L, McCormick S, Chiorazzi N, Mongini PKA. Effects of prostaglandin E2 on p53 mRNA transcription and p53 mutagenesis during T-cell-independent human B-cell clonal expansion. FASEB J 2013; 28:627-43. [PMID: 24145719 DOI: 10.1096/fj.13-237792] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Within T-cell-dependent germinal centers, p53 gene transcription is repressed by Bcl-6 and is thus less vulnerable to mutation. Malignant lymphomas within inflamed extranodal sites exhibit a relatively high incidence of p53 mutations. The latter might originate from normal B-cell clones manifesting activation-induced cytosine deaminase (AID) and up-regulated p53 following T-cell-independent (TI) stimulation. We here examine p53 gene transcription in such TI clones, with a focus on modulatory effects of prostaglandin E2 (PGE2), and evaluate progeny for p53 mutations. Resting IgM(+)IgD(+)CD27(-) B cells from human tonsils were labeled with CFSE and stimulated in vitro with complement-coated antigen surrogate, IL-4, and BAFF ± exogenous PGE2 (50 nM) or an analog specific for the EP2 PGE2 receptor. We use flow cytometry to measure p53 and AID protein within variably divided blasts, qRT-PCR of p53 mRNA from cultures with or without actinomycin D to monitor mRNA transcription/stability, and single-cell p53 RT-PCR/sequencing to assess progeny for p53 mutations. We report that EP2 signaling triggers increased p53 gene transcriptional activity in AID(+) cycling blasts (P<0.01). Progeny exhibit p53 mutations at a frequency (8.5 × 10(-4)) greater than the baseline error rate (<0.8 × 10(-4)). We conclude that, devoid of the repressive influences of Bcl-6, dividing B lymphoblasts in inflamed tissues should display heightened p53 transcription and increased risk of p53 mutagenesis.
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Affiliation(s)
- Shabirul Haque
- 1Laboratory of B-Cell Biology, Karches Center for CLL Research and Center for Autoimmunity and Musculoskeletal Diseases, Feinstein Institute for Medical Research, 350 Community Dr., Manhasset, NY 11030, USA.
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Pei H, Wu X, Liu T, Yu K, Jelinek DF, Lou Z. The histone methyltransferase MMSET regulates class switch recombination. THE JOURNAL OF IMMUNOLOGY 2012; 190:756-63. [PMID: 23241889 DOI: 10.4049/jimmunol.1201811] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Wolf-Hirschhorn syndrome (WHS) is a genetic disease with characteristic facial features and developmental disorders. Of interest, loss of the MMSET gene (also known as WHSC1) is considered to be responsible for the core phenotypes of this disease. Patients with WHS also display Ab deficiency, although the underlying cause of this deficiency is unclear. Recent studies suggest that the histone methyltransferase activity of MMSET plays an important role in the DNA damage response by facilitating the recruitment of 53BP1 to sites of DNA damage. We hypothesize that MMSET also regulates class switch recombination (CSR) through its effect on 53BP1. In this study, we show that MMSET indeed plays an important role in CSR through its histone methyltransferase activity. Knocking down MMSET expression impaired 53BP1 recruitment as well as the germline transcription of the Igh switch regions, resulting in defective CSR but no effect on cell growth and viability. These results suggest that defective CSR caused by MMSET deficiency could be a cause of Ab deficiency in WHS patients.
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Affiliation(s)
- Huadong Pei
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
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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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