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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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Nousiainen A, Schenkwein D, Ylä-Herttuala S. Characterization of a new IN-I-PpoI fusion protein and a homology-arm containing transgene cassette that improve transgene expression persistence and 28S rRNA gene-targeted insertion of lentiviral vectors. PLoS One 2023; 18:e0280894. [PMID: 36662822 PMCID: PMC9858087 DOI: 10.1371/journal.pone.0280894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 01/10/2023] [Indexed: 01/21/2023] Open
Abstract
Targeting transgene integration into a safe genomic locus would be very important for gene therapy. We have generated lentivirus vectors containing the ribosomal RNA-recognising I-PpoI endonuclease fused to viral integrase, and transgene cassettes with target site homology arms to enhance insertion targeting. These new vectors were characterised with respect to the persistence of transgene expression, insertion targeting efficiency and chromosomal integrity of the transduced cells. The aim was to find an optimally safe and effective vector for human gene therapy. Fusion protein vectors with high endonuclease activity were the most effective in the accurate targeting of transgene insertion. The homology construct increased the insertion targeting efficiency to 28% in MRC-5 cells. However, karyotyping analysis showed that the high endonuclease activity induced the formation of derivative chromosomes in as many as 24% of the analysed primary T lymphocytes. The persistence of transgene expression was excellent in homology arm-containing fusion protein vectors with reduced endonuclease activity, and these fusion proteins did not cause any detectable chromosomal rearrangements attributable to the endonuclease activity. We thus conclude that instead of the fusion protein vectors that carry a highly active endonuclease, our vectors with the ability to tether the lentivirus preintegration complex to benign loci in the genome without high ribosomal DNA cleavage activity are better suited for lentivirus-based gene therapy applications.
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Affiliation(s)
- Alisa Nousiainen
- A. I. Virtanen Institute, University of Eastern Finland, Kuopio, Finland
| | - Diana Schenkwein
- A. I. Virtanen Institute, University of Eastern Finland, Kuopio, Finland
| | - Seppo Ylä-Herttuala
- A. I. Virtanen Institute, University of Eastern Finland, Kuopio, Finland
- Heart Center and Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland
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Jones CL, Degasperi A, Grandi V, Amarante TD, Mitchell TJ, Nik-Zainal S, Whittaker SJ. Spectrum of mutational signatures in T-cell lymphoma reveals a key role for UV radiation in cutaneous T-cell lymphoma. Sci Rep 2021; 11:3962. [PMID: 33597573 PMCID: PMC7889847 DOI: 10.1038/s41598-021-83352-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 01/27/2021] [Indexed: 12/02/2022] Open
Abstract
T-cell non-Hodgkin's lymphomas develop following transformation of tissue resident T-cells. We performed a meta-analysis of whole exome sequencing data from 403 patients with eight subtypes of T-cell non-Hodgkin's lymphoma to identify mutational signatures and associated recurrent gene mutations. Signature 1, indicative of age-related deamination, was prevalent across all T-cell lymphomas, reflecting the derivation of these malignancies from memory T-cells. Adult T-cell leukemia-lymphoma was specifically associated with signature 17, which was found to correlate with the IRF4 K59R mutation that is exclusive to Adult T-cell leukemia-lymphoma. Signature 7, implicating UV exposure was uniquely identified in cutaneous T-cell lymphoma (CTCL), contributing 52% of the mutational burden in mycosis fungoides and 23% in Sezary syndrome. Importantly this UV signature was observed in CD4 + T-cells isolated from the blood of Sezary syndrome patients suggesting extensive re-circulation of these T-cells through skin and blood. Analysis of non-Hodgkin's T-cell lymphoma cases submitted to the national 100,000 WGS project confirmed that signature 7 was only identified in CTCL strongly implicating UV radiation in the pathogenesis of cutaneous T-cell lymphoma.
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MESH Headings
- CD4-Positive T-Lymphocytes/metabolism
- Databases, Genetic
- Humans
- Interferon Regulatory Factors
- Lymphoma, T-Cell/etiology
- Lymphoma, T-Cell/genetics
- Lymphoma, T-Cell/metabolism
- Lymphoma, T-Cell/pathology
- Lymphoma, T-Cell, Cutaneous/etiology
- Lymphoma, T-Cell, Cutaneous/genetics
- Lymphoma, T-Cell, Cutaneous/pathology
- Mutation/genetics
- Sezary Syndrome/blood
- Skin Neoplasms/pathology
- Ultraviolet Rays/adverse effects
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Affiliation(s)
- Christine L Jones
- St. John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, Guy's Hospital, London, SE1 9RT, UK
| | - Andrea Degasperi
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
- Academic Laboratory of Medical Genetics, Lv 6 Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Box 238, Cambridge, CB2 0QQ, UK
| | - Vieri Grandi
- St. John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, Guy's Hospital, London, SE1 9RT, UK
| | - Tauanne D Amarante
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
- Academic Laboratory of Medical Genetics, Lv 6 Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Box 238, Cambridge, CB2 0QQ, UK
| | - Tracey J Mitchell
- St. John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, Guy's Hospital, London, SE1 9RT, UK
| | - Serena Nik-Zainal
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
- Academic Laboratory of Medical Genetics, Lv 6 Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Box 238, Cambridge, CB2 0QQ, UK
| | - Sean J Whittaker
- St. John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, Guy's Hospital, London, SE1 9RT, UK.
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Amaral T, Schulze M, Sinnberg T, Nieser M, Martus P, Battke F, Garbe C, Biskup S, Forschner A. Are Pathogenic Germline Variants in Metastatic Melanoma Associated with Resistance to Combined Immunotherapy? Cancers (Basel) 2020; 12:cancers12051101. [PMID: 32354124 PMCID: PMC7281129 DOI: 10.3390/cancers12051101] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 01/10/2023] Open
Abstract
Background: Combined immunotherapy has significantly improved survival of patients with advanced melanoma, but there are still patients that do not benefit from it. Early biomarkers that indicate potential resistance would be highly relevant for these patients. Methods: We comprehensively analyzed tumor and blood samples from patients with advanced melanoma, treated with combined immunotherapy and performed descriptive and survival analysis. Results: Fifty-nine patients with a median follow-up of 13 months (inter quartile range (IQR) 11–15) were included. Interestingly, nine patients were found to have pathogenic or likely pathogenic (P/LP) germline variants in one of these genes: BRCA2, POLE, WRN, FANCI, CDKN2A, BAP1, PALB2 and RAD54B. Most of them are involved in DNA repair mechanisms. Patients with P/LP germline variants had a significantly shorter progression-free survival (PFS) and melanoma specific survival (MSS) compared to patients without P/LP germline variants (HR = 2.16; 95% CI: 1.01–4.64; p = 0.048 and HR = 3.21; 95% CI: 1.31–7.87; p = 0.011, respectively). None of the patients with a P/LP germline variant responded to combined immunotherapy. In the multivariate Cox-regression analysis, presence of a P/LP germline variant, S100B and lactate dehydrogenase (LDH) remained independently significant factors for MSS (p = 0.036; p = 0.044 and p = 0.001, respectively). Conclusions: The presence of P/LP germline variants was associated with resistance to combined immunotherapy in our cohort. As genes involved in DNA repair mechanisms are also involved in lymphocyte development and T-cell differentiation, a P/LP germline variant in these genes may preclude an antitumor immune response.
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Affiliation(s)
- Teresa Amaral
- Center for Dermatooncology, Department of Dermatology, University Hospital Tuebingen, Eberhard Karls University, 72076 Tuebingen, Germany; (T.A.); (T.S.); (C.G.)
- Portuguese Air Force, Health Care Direction, 1649-020 Lisbon, Portugal
| | - Martin Schulze
- Practice for Human Genetics, 72076 Tuebingen, Germany; (M.S.); (M.N.); (S.B.)
| | - Tobias Sinnberg
- Center for Dermatooncology, Department of Dermatology, University Hospital Tuebingen, Eberhard Karls University, 72076 Tuebingen, Germany; (T.A.); (T.S.); (C.G.)
| | - Maike Nieser
- Practice for Human Genetics, 72076 Tuebingen, Germany; (M.S.); (M.N.); (S.B.)
| | - Peter Martus
- Institute for Clinical Epidemiology and applied Biostatistics (IKEaB), Eberhard Karls University, 72076 Tuebingen, Germany;
| | - Florian Battke
- Center for Genomics and Transcriptomics (CeGaT) GmbH, 72076 Tuebingen, Germany;
| | - Claus Garbe
- Center for Dermatooncology, Department of Dermatology, University Hospital Tuebingen, Eberhard Karls University, 72076 Tuebingen, Germany; (T.A.); (T.S.); (C.G.)
| | - Saskia Biskup
- Practice for Human Genetics, 72076 Tuebingen, Germany; (M.S.); (M.N.); (S.B.)
- Center for Genomics and Transcriptomics (CeGaT) GmbH, 72076 Tuebingen, Germany;
| | - Andrea Forschner
- Center for Dermatooncology, Department of Dermatology, University Hospital Tuebingen, Eberhard Karls University, 72076 Tuebingen, Germany; (T.A.); (T.S.); (C.G.)
- Correspondence: ; Tel.: +49-(0)-7071-29 84555; Fax: +49-(0)-7071-29-4599
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5
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Batich KA, Reap EA, Archer GE, Sanchez-Perez L, Nair SK, Schmittling RJ, Norberg P, Xie W, Herndon JE, Healy P, McLendon RE, Friedman AH, Friedman HS, Bigner D, Vlahovic G, Mitchell DA, Sampson JH. Long-term Survival in Glioblastoma with Cytomegalovirus pp65-Targeted Vaccination. Clin Cancer Res 2017; 23:1898-1909. [PMID: 28411277 PMCID: PMC5559300 DOI: 10.1158/1078-0432.ccr-16-2057] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/09/2016] [Accepted: 01/29/2017] [Indexed: 01/12/2023]
Abstract
Purpose: Patients with glioblastoma have less than 15-month median survival despite surgical resection, high-dose radiation, and chemotherapy with temozolomide. We previously demonstrated that targeting cytomegalovirus pp65 using dendritic cells (DC) can extend survival and, in a separate study, that dose-intensified temozolomide (DI-TMZ) and adjuvant granulocyte macrophage colony-stimulating factor (GM-CSF) potentiate tumor-specific immune responses in patients with glioblastoma. Here, we evaluated pp65-specific cellular responses following DI-TMZ with pp65-DCs and determined the effects on long-term progression-free survival (PFS) and overall survival (OS).Experimental Design: Following standard-of-care, 11 patients with newly diagnosed glioblastoma received DI-TMZ (100 mg/m2/d × 21 days per cycle) with at least three vaccines of pp65 lysosome-associated membrane glycoprotein mRNA-pulsed DCs admixed with GM-CSF on day 23 ± 1 of each cycle. Thereafter, monthly DI-TMZ cycles and pp65-DCs were continued if patients had not progressed.Results: Following DI-TMZ cycle 1 and three doses of pp65-DCs, pp65 cellular responses significantly increased. After DI-TMZ, both the proportion and proliferation of regulatory T cells (Tregs) increased and remained elevated with serial DI-TMZ cycles. Median PFS and OS were 25.3 months [95% confidence interval (CI), 11.0-∞] and 41.1 months (95% CI, 21.6-∞), exceeding survival using recursive partitioning analysis and matched historical controls. Four patients remained progression-free at 59 to 64 months from diagnosis. No known prognostic factors [age, Karnofsky performance status (KPS), IDH-1/2 mutation, and MGMT promoter methylation] predicted more favorable outcomes for the patients in this cohort.Conclusions: Despite increased Treg proportions following DI-TMZ, patients receiving pp65-DCs showed long-term PFS and OS, confirming prior studies targeting cytomegalovirus in glioblastoma. Clin Cancer Res; 23(8); 1898-909. ©2017 AACR.
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Affiliation(s)
- Kristen A Batich
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina
- Department of Pathology, Duke University Medical Center, Durham, North Carolina
| | - Elizabeth A Reap
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina
| | - Gary E Archer
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina
- Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina
| | - Luis Sanchez-Perez
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina
| | - Smita K Nair
- Division of Surgical Sciences, Department of Surgery, Duke University Medical Center, Durham, North Carolina
| | - Robert J Schmittling
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina
| | - Pam Norberg
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina
| | - Weihua Xie
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina
| | - James E Herndon
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina
| | - Patrick Healy
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina
| | - Roger E McLendon
- Department of Pathology, Duke University Medical Center, Durham, North Carolina
- Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina
| | - Allan H Friedman
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina
- Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina
| | - Henry S Friedman
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina
- Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina
| | - Darell Bigner
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina
- Department of Pathology, Duke University Medical Center, Durham, North Carolina
- Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina
| | - Gordana Vlahovic
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina
- Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina
| | - Duane A Mitchell
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina.
- Department of Pathology, Duke University Medical Center, Durham, North Carolina
- Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina
| | - John H Sampson
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina.
- Department of Pathology, Duke University Medical Center, Durham, North Carolina
- Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina
- Department of Immunology, Duke University Medical Center, Durham, North Carolina
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
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