1
|
Higuchi F, Uzuka T, Matsuda H, Sumi T, Iwata K, Namatame T, Shin M, Akutsu H, Ueki K. Rise of oligodendroglioma hypermutator phenotype from a subclone harboring TP53 mutation after TMZ treatment. Brain Tumor Pathol 2024; 41:80-84. [PMID: 38294664 DOI: 10.1007/s10014-024-00477-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/05/2024] [Indexed: 02/01/2024]
Abstract
Oligodendrogliomas characterized and defined by 1p/19q co-deletion are slowly growing tumors showing better prognosis than astrocytomas. TP53 mutation is rare in oligodendrogliomas while the vast majority of astrocytomas harbor the mutation, making TP53 mutation mutually exclusive with 1p/19q codeletion in lower grade gliomas virtually. We report a case of 51-year-old woman with a left fronto-temporal oligodendroglioma that contained a small portion with a TP53 mutation, R248Q, at the initial surgery. On a first, slow-growing recurrence 29 months after radiation and nitrosourea-based chemotherapy, the patient underwent TMZ chemotherapy. The recurrent tumor responded well to TMZ but developed a rapid progression after 6 cycles as a malignant hypermutator tumor with a MSH6 mutation. Most of the recurrent tumor lacked typical oligodendroglioma morphology that was observed in the primary tumor, while it retained the IDH1 mutation and 1p/19q co-deletion. The identical TP53 mutation observed in the small portion of the primary tumor was universal in the recurrence. This case embodied the theoretically understandable clonal expansion of the TP53 mutation with additional mismatch repair gene dysfunction leading to hypermutator phenotype. It thus indicated that TP53 mutation in oligodendroglioma, although not common, may play a critical role in the development of hypermutator after TMZ treatment.
Collapse
Affiliation(s)
- Fumi Higuchi
- Department of Neurosurgery, Dokkyo Medical University, Kitakobayashi880, Mibu , Tochigi, 321-0293, Japan.
- Department of Neurosurgery, Teikyo University School of Medicine, Kaga 2-11-1, Itabashi, Tokyo, 173-8606, Japan.
| | - Takeo Uzuka
- Department of Neurosurgery, Dokkyo Medical University, Kitakobayashi880, Mibu , Tochigi, 321-0293, Japan
| | - Hadzki Matsuda
- Department of Diagnostic Pathology, Dokkyo Medical University, Kitakobayashi880, Mibu, Tochigi, 321-0293, Japan
| | - Takuma Sumi
- Department of Neurosurgery, Dokkyo Medical University, Kitakobayashi880, Mibu , Tochigi, 321-0293, Japan
| | - Kayoko Iwata
- Department of Neurosurgery, Dokkyo Medical University, Kitakobayashi880, Mibu , Tochigi, 321-0293, Japan
| | - Takashi Namatame
- Clinical Research Center, Dokkyo Medical University, Kitakobayashi880, Mibu, Tochigi, 321-0293, Japan
| | - Masahiro Shin
- Department of Neurosurgery, Teikyo University School of Medicine, Kaga 2-11-1, Itabashi, Tokyo, 173-8606, Japan
| | - Hiroyoshi Akutsu
- Department of Neurosurgery, Dokkyo Medical University, Kitakobayashi880, Mibu , Tochigi, 321-0293, Japan
| | - Keisuke Ueki
- Department of Neurosurgery, Dokkyo Medical University, Kitakobayashi880, Mibu , Tochigi, 321-0293, Japan
| |
Collapse
|
2
|
Hadad S, Gupta R, Oberheim Bush NA, Taylor JW, Villanueva-Meyer JE, Young JS, Wu J, Ravindranathan A, Zhang Y, Warrier G, McCoy L, Shai A, Pekmezci M, Perry A, Bollen AW, Phillips JJ, Braunstein SE, Raleigh DR, Theodosopoulos P, Aghi MK, Chang EF, Hervey-Jumper SL, Costello JF, de Groot J, Butowski NA, Clarke JL, Chang SM, Berger MS, Molinaro AM, Solomon DA. "De novo replication repair deficient glioblastoma, IDH-wildtype" is a distinct glioblastoma subtype in adults that may benefit from immune checkpoint blockade. Acta Neuropathol 2023; 147:3. [PMID: 38079020 PMCID: PMC10713691 DOI: 10.1007/s00401-023-02654-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 12/18/2023]
Abstract
Glioblastoma is a clinically and molecularly heterogeneous disease, and new predictive biomarkers are needed to identify those patients most likely to respond to specific treatments. Through prospective genomic profiling of 459 consecutive primary treatment-naïve IDH-wildtype glioblastomas in adults, we identified a unique subgroup (2%, 9/459) defined by somatic hypermutation and DNA replication repair deficiency due to biallelic inactivation of a canonical mismatch repair gene. The deleterious mutations in mismatch repair genes were often present in the germline in the heterozygous state with somatic inactivation of the remaining allele, consistent with glioblastomas arising due to underlying Lynch syndrome. A subset of tumors had accompanying proofreading domain mutations in the DNA polymerase POLE and resultant "ultrahypermutation". The median age at diagnosis was 50 years (range 27-78), compared with 63 years for the other 450 patients with conventional glioblastoma (p < 0.01). All tumors had histologic features of the giant cell variant of glioblastoma. They lacked EGFR amplification, lacked combined trisomy of chromosome 7 plus monosomy of chromosome 10, and only rarely had TERT promoter mutation or CDKN2A homozygous deletion, which are hallmarks of conventional IDH-wildtype glioblastoma. Instead, they harbored frequent inactivating mutations in TP53, NF1, PTEN, ATRX, and SETD2 and recurrent activating mutations in PDGFRA. DNA methylation profiling revealed they did not align with known reference adult glioblastoma methylation classes, but instead had unique globally hypomethylated epigenomes and mostly classified as "Diffuse pediatric-type high grade glioma, RTK1 subtype, subclass A". Five patients were treated with immune checkpoint blockade, four of whom survived greater than 3 years. The median overall survival was 36.8 months, compared to 15.5 months for the other 450 patients (p < 0.001). We conclude that "De novo replication repair deficient glioblastoma, IDH-wildtype" represents a biologically distinct subtype in the adult population that may benefit from prospective identification and treatment with immune checkpoint blockade.
Collapse
Affiliation(s)
- Sara Hadad
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Rohit Gupta
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Nancy Ann Oberheim Bush
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Jennie W Taylor
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Javier E Villanueva-Meyer
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA, USA
| | - Jacob S Young
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Jasper Wu
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Ajay Ravindranathan
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Yalan Zhang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Gayathri Warrier
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Lucie McCoy
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Anny Shai
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Melike Pekmezci
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Arie Perry
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Andrew W Bollen
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Steve E Braunstein
- Department of Radiation Oncology, University of California, San Francisco, CA, USA
| | - David R Raleigh
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Radiation Oncology, University of California, San Francisco, CA, USA
| | - Philip Theodosopoulos
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Manish K Aghi
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Edward F Chang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Shawn L Hervey-Jumper
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - John de Groot
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Nicholas A Butowski
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Jennifer L Clarke
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Annette M Molinaro
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA.
| | - David A Solomon
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA.
| |
Collapse
|
3
|
Wood MD, Beadling C, Neff T, Moore S, Harrington CA, Baird L, Corless C. Molecular profiling of pre- and post-treatment pediatric high-grade astrocytomas reveals acquired increased tumor mutation burden in a subset of recurrences. Acta Neuropathol Commun 2023; 11:143. [PMID: 37670377 PMCID: PMC10481558 DOI: 10.1186/s40478-023-01644-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/25/2023] [Indexed: 09/07/2023] Open
Abstract
Diffuse gliomas are a heterogeneous category of primary central nervous system tumors. Due to their infiltrative growth precluding complete surgical resection, most diffuse high-grade gliomas are treated with adjuvant chemotherapy and radiation. Recurrent/progressive diffuse gliomas may show genetic differences when compared to the primary tumors, giving insight into their molecular evolution and mechanisms of treatment resistance. In adult-type diffuse gliomas with or without isocitrate dehydrogenase gene mutations, tumor recurrence/progression can be associated with mutations in genes encoding DNA mismatch repair proteins, leading to a dramatic increase in tumor mutation burden. This phenomenon is closely linked to treatment with the DNA alkylating agent temozolomide, a mainstay of adult diffuse glioma chemotherapeutic management. Post-treatment mismatch repair deficiency and acquired high tumor mutation burden is relatively unexplored in pediatric patients who have recurrent high-grade gliomas. Here, we report a molecular and histological analysis of an institutional cohort of eleven pediatric patients with paired initial and recurrent high-grade astrocytoma samples with intervening temozolomide treatment. We identified three cases with evidence for increased tumor mutation burden at recurrence, including two cases of diffuse hemispheric glioma H3 G34-mutant (one previously reported). We also show that molecular analysis by next-generation DNA sequencing and DNA methylation-based profiling enabled an integrated diagnosis per 2021 World Health Organization criteria in 10 of 11 cases (91%). Our findings indicate that increased tumor mutation burden at post-treatment recurrence is relevant in pediatric-type diffuse high-grade gliomas. Diffuse hemispheric glioma H3 G34-mutant may be particularly susceptible to this phenomenon.
Collapse
Affiliation(s)
- Matthew D Wood
- Department of Pathology and Laboratory Medicine, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, L-113, Portland, OR, 97239, USA.
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
| | - Carol Beadling
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Tanaya Neff
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Steve Moore
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Christina A Harrington
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
- Integrated Genomics Laboratory, Oregon Health & Science University, Portland, OR, USA
| | - Lissa Baird
- Department of Neurological Surgery, Oregon Health & Science University, Portland, OR, USA
- Boston Children's Hospital, Boston, MA, USA
| | - Christopher Corless
- Department of Pathology and Laboratory Medicine, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, L-113, Portland, OR, 97239, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| |
Collapse
|
4
|
Imamura T, Okamura Y, Ohshima K, Uesaka K, Sugiura T, Ito T, Yamamoto Y, Ashida R, Ohgi K, Otsuka S, Ohnami S, Nagashima T, Hatakeyama K, Sugino T, Urakami K, Akiyama Y, Yamaguchi K. Overview and clinical significance of multiple mutations in individual genes in hepatocellular carcinoma. BMC Cancer 2022; 22:1046. [PMID: 36199046 PMCID: PMC9535898 DOI: 10.1186/s12885-022-10143-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/28/2022] [Indexed: 12/24/2022] Open
Abstract
Background Multiple mutation (MM) within a single gene has recently been reported as a mechanism involved in carcinogenesis. The present study investigated the clinical significance of MMs in hepatocellular carcinoma (HCC). Methods Two hundred twenty-three surgically resected HCCs were subjected to gene expression profiling and whole-exome sequencing. Results MMs in individual genes were detected in 178 samples (MM tumors: 79.8%). The remaining samples all carried a single mutation (SM tumors: 20.2%). Recurrence-free survival in the MM group was significantly worse in comparison to the SM group (P = 0.012). A Cox proportional hazard analysis revealed that MM tumor was an independent predictor for worse a prognosis (hazard ratio, 1.72; 95% confidence interval, 1.01–3.17; P = 0.045). MMs were frequently observed across in various genes, especially MUC16 (15% of samples had at least one mutation in the gene) and CTNNB1 (14%). Although the MUC16 mRNA expression of MUC16 wild-type and MUC16 SM tumors did not differ to a statistically significant extent, the expression in MUC16 MM tumors was significantly enhanced in comparison to MUC16 SM tumors (P < 0.001). In MUC16, MMs were associated with viral hepatitis, higher tumor marker levels and vascular invasion. The MUC16 MMs group showed significantly worse recurrence-free survival in comparison to the MUC16 SM group (P = 0.022), while no significant difference was observed between the MUC16 SM group and the MUC16 wild-type group (P = 0.324). Conclusions MM was a relatively common event that may occur selectively in specific oncogenes and is involved in aggressive malignant behavior. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-10143-z.
Collapse
Affiliation(s)
- Taisuke Imamura
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Sunto-Nagaizumi, Shizuoka, 4118777, Japan
| | - Yukiyasu Okamura
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Sunto-Nagaizumi, Shizuoka, 4118777, Japan. .,Department of Digestive Surgery, Nihon University School of Medicine, Tokyo, Japan.
| | - Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Katsuhiko Uesaka
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Sunto-Nagaizumi, Shizuoka, 4118777, Japan
| | - Teiichi Sugiura
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Sunto-Nagaizumi, Shizuoka, 4118777, Japan
| | - Takaaki Ito
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Sunto-Nagaizumi, Shizuoka, 4118777, Japan
| | - Yusuke Yamamoto
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Sunto-Nagaizumi, Shizuoka, 4118777, Japan
| | - Ryo Ashida
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Sunto-Nagaizumi, Shizuoka, 4118777, Japan
| | - Katsuhisa Ohgi
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Sunto-Nagaizumi, Shizuoka, 4118777, Japan
| | - Shimpei Otsuka
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Sunto-Nagaizumi, Shizuoka, 4118777, Japan
| | - Sumiko Ohnami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Takeshi Nagashima
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan.,SRL, Inc., Tokyo, Japan
| | - Keiichi Hatakeyama
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Takashi Sugino
- Division of Pathology, Shizuoka Cancer Center, Shizuoka, Japan
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Yasuto Akiyama
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Ken Yamaguchi
- Shizuoka Cancer Center Hospital and Research Institute, Shizuoka, Japan
| |
Collapse
|
5
|
Saint-Ghislain M, Derrien AC, Geoffrois L, Gastaud L, Lesimple T, Negrier S, Penel N, Kurtz JE, Le Corre Y, Dutriaux C, Gardrat S, Barnhill R, Matet A, Cassoux N, Houy A, Ramtohul T, Servois V, Mariani P, Piperno-Neumann S, Stern MH, Rodrigues M. MBD4 deficiency is predictive of response to immune checkpoint inhibitors in metastatic uveal melanoma patients. Eur J Cancer 2022; 173:105-112. [PMID: 35863105 DOI: 10.1016/j.ejca.2022.06.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/24/2022] [Accepted: 06/17/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND MBD4 mutations have been reported in uveal melanomas, acute myeloid leukemias, colorectal adenocarcinomas, gliomas, and spiradenocarcinomas and cause a hypermutated phenotype. Although metastatic uveal melanomas (mUM) are usually resistant to immune checkpoint inhibitors (ICI), the first reported MBD4-mutated (MBD4m) patient responded to ICI, suggesting that MBD4 mutation may predict response to ICI. METHODS Retrospective cohort of mUM patients treated with ICI. MBD4 was sequenced in a subset of these patients. RESULTS Three hundred mUM patients were included. Median follow-up was 17.3 months. Ten patients with an objective response and 20 cases with stable disease for >12 months were observed, corresponding to an objective response rate of 3.3% and a clinical benefit (i.e., responder patients and stable disease) rate of 10%. Of the 131 tumors sequenced for MBD4, five (3.8%) were mutated. MBD4 mutation was associated with a better objective response rate as three out of five MBD4m versus 4% of MBD4 wild-type patients responded (p < 0.001). Of these five responders, three presented progressive disease at 2.8, 13.9, and 22.3 months. Median PFS was 4.0 months in MBD4 wild-type and 22.3 months in MBD4m patients (HR = 0.22; p = 0.01). Median OS in MBD4def patients was unreached as compared to 16.6 months in MBD4pro (HR = 0.11; 95% CI: 0.02-0.86; log-rank p-test = 0.04; Fig. 2e). CONCLUSIONS In mUM patients, MBD4 mutation is highly predictive for the response, PFS, and overall survival benefit to ICI. MBD4 could be a tissue-agnostic biomarker and should be sequenced in mUM, and other tumor types where MBD4 mutations are reported.
Collapse
Affiliation(s)
- Mathilde Saint-Ghislain
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France; INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par La Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France.
| | - Anne-Céline Derrien
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par La Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France.
| | - Lionnel Geoffrois
- Department of Medical Oncology, Institut de Cancérologie de Lorraine - Alexis Vautrin Cancer, Nancy, France.
| | - Lauris Gastaud
- Department of Medical Oncology, Antoine Lacassagne Cancer Centre, 06000 Nice, France.
| | - Thierry Lesimple
- Department of Medical Oncology, Centre Eugène Marquis, Rennes, France.
| | | | - Nicolas Penel
- Department of Medical Oncology, Centre Oscar Lambret, Lille University, Lille, France.
| | - Jean-Emmanuel Kurtz
- Department of Medical Oncology, Strasbourg University Hospital, Strasbourg, France.
| | - Yannick Le Corre
- Department of Dermatology, Angers University Hospital, UNAM, France.
| | - Caroline Dutriaux
- Dermatology Department, CHU de Bordeaux, Hôpital Saint André, Bordeaux, France.
| | - Sophie Gardrat
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France.
| | - Raymond Barnhill
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France; Faculty of Medicine, Université de Paris, Paris, France.
| | - Alexandre Matet
- Department of Ocular Oncology, Institut Curie, PSL Research University, Paris, France; Université de Paris, Paris, France.
| | - Nathalie Cassoux
- Department of Ocular Oncology, Institut Curie, PSL Research University, Paris, France; Université de Paris, Paris, France.
| | - Alexandre Houy
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par La Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France.
| | - Toulsie Ramtohul
- Department of Radiology, Institut Curie, PSL Research University, Paris, France.
| | - Vincent Servois
- Department of Radiology, Institut Curie, PSL Research University, Paris, France.
| | - Pascale Mariani
- Department of Surgical Oncology, Institut Curie, PSL Research University, Paris, France.
| | | | - Marc-Henri Stern
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par La Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France; Department of Genetics, Institut Curie, PSL Research University, Paris, France.
| | - Manuel Rodrigues
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France; INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par La Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France.
| |
Collapse
|
6
|
Molina RS, Rix G, Mengiste AA, Alvarez B, Seo D, Chen H, Hurtado J, Zhang Q, Donato García-García J, Heins ZJ, Almhjell PJ, Arnold FH, Khalil AS, Hanson AD, Dueber JE, Schaffer DV, Chen F, Kim S, Ángel Fernández L, Shoulders MD, Liu CC. In vivo hypermutation and continuous evolution. Nat Rev Methods Primers 2022; 2:37. [PMID: 37073402 PMCID: PMC10108624 DOI: 10.1038/s43586-022-00130-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rosana S. Molina
- Department of Biomedical Engineering, University of California, Irvine, CA 92617, USA
| | - Gordon Rix
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Amanuella A. Mengiste
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Beatriz Alvarez
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Daeje Seo
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Haiqi Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Juan Hurtado
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Qiong Zhang
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Jorge Donato García-García
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Av. General Ramon Corona 2514, Nuevo Mexico, C.P. 45138, Zapopan, Jalisco, Mexico
| | - Zachary J. Heins
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Patrick J. Almhjell
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Frances H. Arnold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ahmad S. Khalil
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Andrew D. Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - John E. Dueber
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley and San Francisco, Berkeley, CA, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David V. Schaffer
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley and San Francisco, Berkeley, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Fei Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Seokhee Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Matthew D. Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Chang C. Liu
- Department of Biomedical Engineering, University of California, Irvine, CA 92617, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
- Department of Chemistry, University of California, Irvine, CA 92617, USA
| |
Collapse
|
7
|
Schulz D, Piontek G, Zissler UM, Multhoff G, Wirth M, Pickhard A. MEK1/2 regulates APOBEC3B and polymerase iota-induced mutagenesis in head and neck cancer cells. Am J Cancer Res 2021; 11:5581-5590. [PMID: 34873481 PMCID: PMC8640808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023] Open
Abstract
Resistance to chemotherapy provides a major challenge in treatment of metastatic cancer. Prolonged exposure to almost any drug regimen leads to the formation of resistant subclones in almost all advanced solid tumors. Tumor heterogeneity because of intrinsic genetic instability is seen as one of the major contributing factors. In this work, we present evidence that genetic instability measured by mutation frequency is induced by treatment with the EGFR inhibitor afatinib or cisplatin in head and neck squamous cancer cells. We find that APOBEC3B and polymerase iota are upregulated, and inhibition of MEK1/2 by U0126 leads to downregulation on the protein level. Costimulation of afatnib and cisplatin with U0126 leads to a significantly lower mutation frequency. These findings may represent a molecular mechanism for dynamically controlling genetic instability during chemotherapy in head and neck squamous cell carcinoma (HNSCC) cancer cells.
Collapse
Affiliation(s)
- Dominik Schulz
- Department of Internal Medicine II, Klinikum Rechts der IsarIsmaninger Straße 22, Munich 81675, Germany
| | - Guido Piontek
- Institute of Pathology, Ludwig Maximilians University of MunichMunich 81377, Germany
| | - Ulrich M Zissler
- Center of Allergy & Environment (ZAUM), German Research Center for Environmental Health, Member of The German Center for Lung Research (DZL), Helmholtz Center Munich, Technical University of Munich (TUM)Biedersteiner Street 29, Munich 80333, Germany
| | - Gabriele Multhoff
- Department of Radiotherapy, Technical University of MunichIsmaninger Straße 22, Munich 80333, Germany
| | - Markus Wirth
- Department of Head and Neck Surgery, Klinikum Rechts der IsarIsmaninger Straße 22, Munich 81675, Germany
| | - Anja Pickhard
- Department of Head and Neck Surgery, Klinikum Rechts der IsarIsmaninger Straße 22, Munich 81675, Germany
| |
Collapse
|
8
|
Davila JI, Chanana P, Sarangi V, Fogarty ZC, Weroha SJ, Guo R, Goode EL, Huang Y, Wang C. Frequent POLE-driven hypermutation in ovarian endometrioid cancer revealed by mutational signatures in RNA sequencing. BMC Med Genomics 2021; 14:165. [PMID: 34158040 PMCID: PMC8218518 DOI: 10.1186/s12920-021-01017-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/13/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA polymerase epsilon (POLE) is encoded by the POLE gene, and POLE-driven tumors are characterized by high mutational rates. POLE-driven tumors are relatively common in endometrial and colorectal cancer, and their presence is increasingly recognized in ovarian cancer (OC) of endometrioid type. POLE-driven cases possess an abundance of TCT > TAT and TCG > TTG somatic mutations characterized by mutational signature 10 from the Catalog of Somatic Mutations in Cancer (COSMIC). By quantifying the contribution of COSMIC mutational signature 10 in RNA sequencing (RNA-seq) we set out to identify POLE-driven tumors in a set of unselected Mayo Clinic OC. METHODS Mutational profiles were calculated using expressed single-nucleotide variants (eSNV) in the Mayo Clinic OC tumors (n = 195), The Cancer Genome Atlas (TCGA) OC tumors (n = 419), and the Genotype-Tissue Expression (GTEx) normal ovarian tissues (n = 84). Non-negative Matrix Factorization (NMF) of the mutational profiles inferred the contribution per sample of four distinct mutational signatures, one of which corresponds to COSMIC mutational signature 10. RESULTS In the Mayo Clinic OC cohort we identified six tumors with a predicted contribution from COSMIC mutational signature 10 of over five mutations per megabase. These six cases harbored known POLE hotspot mutations (P286R, S297F, V411L, and A456P) and were of endometrioid histotype (P = 5e-04). These six tumors had an early onset (average age of patients at onset, 48.33 years) when compared to non-POLE endometrioid OC cohort (average age at onset, 60.13 years; P = .008). Samples from TCGA and GTEx had a low COSMIC signature 10 contribution (median 0.16 mutations per megabase; maximum 1.78 mutations per megabase) and carried no POLE hotspot mutations. CONCLUSIONS From the largest cohort of RNA-seq from endometrioid OC to date (n = 53), we identified six hypermutated samples likely driven by POLE (frequency, 11%). Our result suggests the clinical need to screen for POLE driver mutations in endometrioid OC, which can guide enrollment in immunotherapy clinical trials.
Collapse
Affiliation(s)
- Jaime I Davila
- Department of Mathematics, Statistics and Computer Science, St Olaf College, Northfield, MN, USA. .,Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.
| | - Pritha Chanana
- Division of Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Zachary C Fogarty
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - S John Weroha
- Division of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | - Ruifeng Guo
- Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Ellen L Goode
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Yajue Huang
- Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Chen Wang
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.
| |
Collapse
|
9
|
Yu Y, Villanueva-Meyer J, Grimmer MR, Hilz S, Solomon DA, Choi S, Wahl M, Mazor T, Hong C, Shai A, Phillips JJ, Wainer BH, McDermott M, Haas-Kogan D, Taylor JW, Butowski N, Clarke JL, Berger MS, Molinaro AM, Chang SM, Costello JF, Oberheim Bush NA. Temozolomide-induced hypermutation is associated with distant recurrence and reduced survival after high-grade transformation of low-grade IDH-mutant gliomas. Neuro Oncol 2021; 23:1872-1884. [PMID: 33823014 DOI: 10.1093/neuonc/noab081] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Chemotherapy improves overall survival after surgery and radiotherapy for newly diagnosed high-risk IDH-mutant low-grade gliomas, but a proportion of patients treated with temozolomide (TMZ) will develop recurrent tumors with TMZ-induced hypermutation. We aimed to determine the prevalence of TMZ-induced hypermutation at recurrence and prognostic implications. METHODS We sequenced recurrent tumors from 82 patients with initially low-grade IDH-mutant gliomas who underwent re-operation and correlated hypermutation status with grade at recurrence and subsequent clinical outcomes. RESULTS Hypermutation was associated with high-grade disease at the time of re-operation (OR 12.0 95% CI 2.5-115.5, p=0.002) and was identified at transformation in 57% of recurrent LGGs previously exposed to TMZ. After anaplastic (grade III) transformation, hypermutation was associated with shorter survival on univariate and multivariate analysis (HR 3.4, 95% CI 1.2-9.9, p=0.024), controlling for tumor grade, subtype, age, and prior radiotherapy. The effect of hypermutation on survival after transformation was validated in an independent, published dataset. Hypermutated (HM) tumors were more likely to develop discontiguous foci of disease in the brain and spine (p=0.003). To estimate the overall incidence of high-grade transformation among low-grade IDH-mutant tumors, data from a phase II trial of TMZ for LGG were analyzed. 8-year transformation-free survival was 53.8% (95% CI 42.8-69.2) and 61% of analyzed transformed cases were HM. CONCLUSIONS TMZ-induced hypermutation is a common event in transformed LGG previously treated with TMZ, and is associated with worse prognosis and development of discontiguous disease after recurrence. These findings impact tumor classification at recurrence, prognostication, and clinical trial design.
Collapse
Affiliation(s)
- Yao Yu
- Department of Radiation Oncology, Memorial Sloan Kettering, New York City, NY USA
| | - Javier Villanueva-Meyer
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | - Matthew R Grimmer
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Stephanie Hilz
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - David A Solomon
- Division of Neuropathology, Department of Pathology, University of California, San Francisco, CA, USA
| | - Serah Choi
- Department of Radiation Oncology, University Hospitals, Cleveland, OH, USA
| | - Michael Wahl
- Department of Radiation Oncology Samaritan Pastega Regional Cancer Center, Corvallis, OR, USA
| | - Tali Mazor
- Department of Computational Biology, Dana Farber/Harvard Cancer Center, Boston, MA, USA
| | - Chibo Hong
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Anny Shai
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California, San Francisco, CA, USA.,Division of Neuropathology, Department of Pathology, University of California, San Francisco, CA, USA
| | | | - Michael McDermott
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Daphne Haas-Kogan
- Department of Radiation Oncology, Dana Farber/Harvard Cancer Center, Boston, MA, USA
| | - Jennie W Taylor
- Department of Neurological Surgery, University of California, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, CA, USA
| | - Nicholas Butowski
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Jennifer L Clarke
- Department of Neurological Surgery, University of California, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, CA, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Annette M Molinaro
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Nancy Ann Oberheim Bush
- Department of Neurological Surgery, University of California, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, CA, USA
| |
Collapse
|
10
|
Rix G, Liu CC. Systems for in vivo hypermutation: a quest for scale and depth in directed evolution. Curr Opin Chem Biol 2021; 64:20-6. [PMID: 33784581 DOI: 10.1016/j.cbpa.2021.02.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/18/2021] [Accepted: 02/20/2021] [Indexed: 12/14/2022]
Abstract
Traditional approaches to the directed evolution of genes of interest (GOIs) place constraints on the scale of experimentation and depth of evolutionary search reasonably achieved. Engineered genetic systems that dramatically elevate the mutation of target GOIs in vivo relieve these constraints by enabling continuous evolution, affording new strategies in the exploration of sequence space and fitness landscapes for GOIs. We describe various in vivo hypermutation systems for continuous evolution, discuss how different architectures for in vivo hypermutation facilitate evolutionary search scale and depth in their application to problems in protein evolution and engineering, and outline future opportunities for the field.
Collapse
|
11
|
Wood MD, Neff T, Nickerson JP, Sayama C, Raslan AM, Ambady P, Corless CL, Nazemi KJ. Post-treatment hypermutation in a recurrent diffuse glioma with H3.3 p.G34 Mutation. Neuropathol Appl Neurobiol 2020; 47:460-463. [PMID: 33296093 DOI: 10.1111/nan.12679] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/16/2020] [Accepted: 11/27/2020] [Indexed: 12/01/2022]
Affiliation(s)
- Matthew D Wood
- Department of Pathology, Oregon Health & Science University, Portland, OR, USA.,Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Tanaya Neff
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Joshua P Nickerson
- Department of Diagnostic Radiology, Oregon Health & Science University, Portland, OR, USA
| | - Christina Sayama
- Department of Neurological Surgery, Oregon Health & Science University, Portland, OR, USA
| | - Ahmed M Raslan
- Department of Neurological Surgery, Oregon Health & Science University, Portland, OR, USA
| | - Prakash Ambady
- Department of Neurology, Oregon Health & Science University, Portland, OR, USA
| | - Christopher L Corless
- Department of Pathology, Oregon Health & Science University, Portland, OR, USA.,Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Kellie J Nazemi
- Department of Pediatrics, Doernbecher Children's Hospital, Oregon Health & Science University, Portland, OR, USA
| |
Collapse
|
12
|
Abstract
Regions of genomic DNA can become single-stranded in the course of normal replication and transcription as well as during DNA repair. Abnormal repair and replication intermediates can contain large stretches of persistent single-stranded DNA, which is extremely vulnerable to DNA damaging agents and hypermutation. Since such single-stranded DNA spans only a fraction of the genome at a given instance, hypermutation in these regions leads to tightly-spaced mutation clusters. This phenomenon of hypermutation in single-stranded DNA has been documented in several experimental models as well as in cancer genomes. Recently, hypermutated single-stranded RNA viral genomes also have been documented. Moreover, indications of hypermutation in single-stranded DNA may also be found in the human germline. This review will summarize key current knowledge and the recent developments in understanding the diverse mechanisms and sources of ssDNA hypermutation.
Collapse
Affiliation(s)
- Natalie Saini
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC, USA
| | - Dmitry A Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC, USA.
| |
Collapse
|
13
|
Ridderberg W, Jensen Handberg K, Nørskov-Lauritsen N. Prevalence of hypermutator isolates of Achromobacter spp. from cystic fibrosis patients. Int J Med Microbiol 2020; 310:151393. [PMID: 31969255 DOI: 10.1016/j.ijmm.2020.151393] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 10/30/2019] [Accepted: 12/04/2019] [Indexed: 01/26/2023] Open
Abstract
Bacteria colonising the lungs of cystic fibrosis (CF) patients encounter high selective pressures. Hypermutation facilitates adaptation to fluctuating environments, and hypermutator strains are frequently isolated from CF patients. We investigated the prevalence of hypermutator isolates of Achromobacter spp. among patients affiliated with the CF Centre in Aarhus, Denmark. By exposure to rifampicin, the mutation frequency was determined for 90 isolates of Achromobacter spp. cultured from 42 CF patients; 20 infections were categorised as chronic, 22 as intermittent. The genetic mechanisms of hypermutation were examined by comparing DNA repair gene sequences from hypermutator and normomutator isolates. Achromobacter spp. cultured from 11 patients were categorised as hypermutators, and this phenotype was exclusively associated with chronic infections. Isolates of the Danish epidemic strain (DES) of Achromobacter ruhlandii cultured from patients from both Danish CF centres showed elevated mutation frequencies. The hypermutator state of Achromobacter spp. was most commonly associated with nonsynonymous mutations in the DNA mismatch repair gene mutS; a single clone had developed a substitution in the S-adenosyl-L-methionine-dependent methyltransferase putatively involved in DNA repair mechanisms, but not previously linked to the hypermutator phenotype. Hypermutation is prevalent among clinical isolates of Achromobacter spp. and could be a key determinant for the extraordinary adaptation and persistence of DES.
Collapse
|
14
|
Bóka B, Manczinger L, Kocsubé S, Shine K, Alharbi NS, Khaled JM, Münsterkötter M, Vágvölgyi C, Kredics L. Genome analysis of a Bacillus subtilis strain reveals genetic mutations determining biocontrol properties. World J Microbiol Biotechnol 2019; 35:52. [PMID: 30868269 PMCID: PMC6435635 DOI: 10.1007/s11274-019-2625-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/01/2019] [Indexed: 11/03/2022]
Abstract
Several Bacillus strains are used as biocontrol agents, as they frequently have strong antagonistic effects against microbial plant pathogens. Bacillus strain SZMC 6179J, isolated from tomato rhizosphere, was previously shown to have excellent in vitro antagonistic properties against the most important fungal pathogens of tomato (Alternaria solani, Botrytis cinerea, Phytophthora infestans and Sclerotinia sclerotiorum) as well as several Fusarium species. Taxonomic investigations revealed that it is a member of the B. subtilis subsp. subtilis group and very closely related with the reference type strain B. subtilis subsp. subtilis 168. The sequenced genome of strain SZMC 6179J contains the genes responsible for the synthesis of the extracellular antibiotics surfactin, fengycin and bacilysin. Compared to strain 168, a prophage-like region is missing from the genome of SZMC 6179J, while there are 106 single nucleotide polymorphisms and 23 deletion-insertion polymorphisms. The high biocontrol potential of strain SZMC 6179J may results from a single base deletion in the sfp gene encoding the transcription factor of the surfactin and fengycin operons. Hypermutated regions reflecting short-time evolutionary processes could be detected in SZMC 6179J. The deletion-insertion polymorphism in the sfp gene and the detected hypermutations can be suggested as genetic determinants of biocontrol features in B. subtilis.
Collapse
Affiliation(s)
- Bettina Bóka
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary
| | - László Manczinger
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary
| | - Sándor Kocsubé
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary
| | - Kadaikunnan Shine
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Naiyf S Alharbi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Jamal M Khaled
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Martin Münsterkötter
- Functional Genomics and Bioinformatics Group, Research Center for Forestry and Wood Industry, University of Sopron, Bajcsy-Zsilinszky u. 4, Sopron, 9401, Hungary
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary.
| |
Collapse
|
15
|
Abstract
The DNA mutagenic enzyme known as APOBEC3G (A3G) plays a critical role in innate immunity to Human Immunodeficiency Virus-1 (HIV-1 ). A3G is a zinc-dependent enzyme that mutates select deoxycytidines (dC) to deoxyuridine (dU) through deamination within nascent single stranded DNA (ssDNA) during HIV reverse transcription. This activity requires that the enzyme be delivered to viral replication complexes by redistributing from the cytoplasm of infected cells to budding virions through what appears to be an RNA-dependent process. Once inside infected cells, A3G must bind to nascent ssDNA reverse transcripts for dC to dU base modification gene editing. In this chapter we will discuss data indicating that ssDNA deaminase activity of A3G is regulated by RNA binding to A3G and ribonucleoprotein complex formation along with evidence suggesting that RNA-selective interactions with A3G are temporally and mechanistically important in this process.
Collapse
Affiliation(s)
- Jason D Salter
- OyaGen, Inc, 77 Ridgeland Road, Rochester, NY, 14623, USA
| | - Bogdan Polevoda
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, 601 Elmwood Ave, Rochester, NY, 14642, USA
| | - Ryan P Bennett
- OyaGen, Inc, 77 Ridgeland Road, Rochester, NY, 14623, USA
| | - Harold C Smith
- OyaGen, Inc, 77 Ridgeland Road, Rochester, NY, 14623, USA. .,Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, 601 Elmwood Ave, Rochester, NY, 14642, USA.
| |
Collapse
|
16
|
Wakai T, Prasoon P, Hirose Y, Shimada Y, Ichikawa H, Nagahashi M. Next-generation sequencing-based clinical sequencing: toward precision medicine in solid tumors. Int J Clin Oncol 2018; 24:115-122. [PMID: 30515675 DOI: 10.1007/s10147-018-1375-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 11/26/2018] [Indexed: 12/14/2022]
Abstract
Numerous technical and functional advances in next-generation sequencing (NGS) have led to the adoption of this technique in conventional clinical practice. Recently, large-scale genomic research and NGS technological innovation have revealed many more details of somatic and germline mutations in solid tumors. This development is allowing for the classification of tumor type sub-categories based on genetic alterations in solid tumors, and based on this information, new drugs and targeted therapies are being administered to patients. This has largely been facilitated by gene panel testing, which allows for a better understanding of the genetic basis for an individual's response to therapy. NGS-based comprehensive gene panel testing is a clinically useful approach to investigate genomic mechanisms, including therapy-related signaling pathways, microsatellite instability, hypermutated phenotypes, and tumor mutation burden. In this review, we describe the concept of precision medicine in solid tumors using NGS-based comprehensive gene panel testing, as well as the importance of quality control of tissue sample handling in routine NGS-based genomic testing, and we discuss issues for the future adoption of this technique in Japan.
Collapse
Affiliation(s)
- Toshifumi Wakai
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, Niigata, 951-8510, Japan.
| | - Pankaj Prasoon
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, Niigata, 951-8510, Japan
| | - Yuki Hirose
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, Niigata, 951-8510, Japan
| | - Yoshifumi Shimada
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, Niigata, 951-8510, Japan
| | - Hiroshi Ichikawa
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, Niigata, 951-8510, Japan
| | - Masayuki Nagahashi
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, Niigata, 951-8510, Japan
| |
Collapse
|
17
|
Boi S, Ferrell ME, Zhao M, Hasenkrug KJ, Evans LH. Mouse APOBEC3 expression in NIH 3T3 cells mediates hypermutation of AKV murine leukemia virus. Virology 2018; 518:377-384. [PMID: 29605684 DOI: 10.1016/j.virol.2018.03.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 03/13/2018] [Accepted: 03/15/2018] [Indexed: 11/18/2022]
Abstract
Mouse APOBEC3 (mA3) is a cytidine deaminase that can act on the single-stranded DNA reverse transcripts of retroviruses resulting in G→A hypermutation of proviral DNA. Many mA3 studies have used NIH 3T3 cells assuming that endogenous mA3 production was negligible. We developed a monoclonal antibody specific for mA3 that reveals detectable mA3 in NIH 3T3 cells and we demonstrate that AKV released from the cells undergoes G→A hypermutation. Inactivation of the mA3 gene abolished the deamination confirming that AKV hypermutation was mediated by mA3. The G→A mutations in AKV viral transcripts deviated from a normal distribution with all the mutations contained within only 20% of the transcripts. Single cell analyses revealed that the expression of mA3 in NIH 3T3 cells was limited to 20% of the cells, which likely accounted for the abnormal distribution of mutations. Endogenous NIH 3T3 mA3 was found to restrict AKV replication.
Collapse
Affiliation(s)
- Stefano Boi
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA.
| | - Morgan E Ferrell
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA
| | - Ming Zhao
- Protein Chemistry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kim J Hasenkrug
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA
| | - Leonard H Evans
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA.
| |
Collapse
|
18
|
Rogozin IB, Goncearenco A, Lada AG, De S, Yurchenko V, Nudelman G, Panchenko AR, Cooper DN, Pavlov YI. DNA polymerase η mutational signatures are found in a variety of different types of cancer. Cell Cycle 2018; 17:348-355. [PMID: 29139326 DOI: 10.1080/15384101.2017.1404208] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
DNA polymerase (pol) η is a specialized error-prone polymerase with at least two quite different and contrasting cellular roles: to mitigate the genetic consequences of solar UV irradiation, and promote somatic hypermutation in the variable regions of immunoglobulin genes. Misregulation and mistargeting of pol η can compromise genome integrity. We explored whether the mutational signature of pol η could be found in datasets of human somatic mutations derived from normal and cancer cells. A substantial excess of single and tandem somatic mutations within known pol η mutable motifs was noted in skin cancer as well as in many other types of human cancer, suggesting that somatic mutations in A:T bases generated by DNA polymerase η are a common feature of tumorigenesis. Another peculiarity of pol ηmutational signatures, mutations in YCG motifs, led us to speculate that error-prone DNA synthesis opposite methylated CpG dinucleotides by misregulated pol η in tumors might constitute an additional mechanism of cytosine demethylation in this hypermutable dinucleotide.
Collapse
Affiliation(s)
- Igor B Rogozin
- a National Center for Biotechnology Information, National Library of Medicine , National Institutes of Health , Bethesda , MD , USA
| | - Alexander Goncearenco
- a National Center for Biotechnology Information, National Library of Medicine , National Institutes of Health , Bethesda , MD , USA
| | - Artem G Lada
- b Department Microbiology and Molecular Genetics , University of California , Davis , CA , USA
| | - Subhajyoti De
- c Rutgers Cancer Institute of New Jersey , Rutgers University , New Brunswick , NJ , USA
| | - Vyacheslav Yurchenko
- d Life Science Research Center , University of Ostrava, 71000 Ostrava , Czech Republic
| | - German Nudelman
- e Systems Biology Center , Icahn School of Medicine at Mount Sinai , New York , New York 10029 , USA
| | - Anna R Panchenko
- a National Center for Biotechnology Information, National Library of Medicine , National Institutes of Health , Bethesda , MD , USA
| | - David N Cooper
- f Institute of Medical Genetics, School of Medicine , Cardiff University , UK
| | - Youri I Pavlov
- g Eppley Institute for Research in Cancer and Allied Diseases , University of Nebraska Medical Center , Omaha , NE 68198, USA.,h Departments of Microbiology and Pathology , University of Nebraska Medical Center , Omaha , NE , USA.,i Biochemistry and Molecular Biology , University of Nebraska Medical Center , Omaha , NE , USA.,j Genetics, Cell Biology and Anatomy , University of Nebraska Medical Center , Omaha , NE , USA
| |
Collapse
|
19
|
Clutterbuck AJ. Genomic CG dinucleotide deficiencies associated with transposable element hypermutation in Basidiomycetes, some lower fungi, a moss and a clubmoss. Fungal Genet Biol 2017; 104:16-28. [PMID: 28438577 DOI: 10.1016/j.fgb.2017.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/10/2017] [Accepted: 04/17/2017] [Indexed: 12/15/2022]
Abstract
Many Basidiomycete genomes include substantial fractions that are deficient in CG dinucleotides, in extreme cases amounting to 70% of the genome. CG deficiency is variable and correlates with genome size and, more closely, with transposable element (TE) content. Many species have limited CG deficiency; it is therefore likely that there are other mechanisms that can control TE proliferation. Examination of TEs confirms that C-to-T transition mutations in CG dinucleotides may comprise a conspicuous proportion of differences between paired elements, however transition/transversion ratios are never as high as those due to RIP in some Ascomycetes, suggesting that repeat-associated CG mutation is not totally pervasive. This has allowed gene family expansion in Basidiomycetes, although CG transition differences are often prominent in paired gene family members, and are evidently responsible for destruction of some copies. A few lower fungal genomes exhibit similar evidence of repeat-associated CG mutation, as do the genomes of the two lower plants Physcomitrella patens and Selaginella moellendorffii, in both of which mutation parallels published methylation of CHG as well as CG nucleotides. In Basidiomycete DNA methylation has been reported to be largely confined to CG dinucleotides in repetitive DNA, but while methylation and mutation are evidently associated, it is not clear which is cause and which effect.
Collapse
Affiliation(s)
- A John Clutterbuck
- Wolfson Link Building, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, UK.
| |
Collapse
|
20
|
Miyagi E, Kao S, Fumitaka M, Buckler-White A, Plishka R, Strebel K. Long-term passage of Vif-null HIV-1 in CD4 + T cells expressing sub-lethal levels of APOBEC proteins fails to develop APOBEC resistance. Virology 2017; 504:1-11. [PMID: 28131088 DOI: 10.1016/j.virol.2017.01.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 01/19/2017] [Accepted: 01/21/2017] [Indexed: 10/20/2022]
Abstract
APOBEC3G (A3G) is a cytidine deaminase with potent antiviral activity that is antagonized by Vif. A3G is expressed in a cell type-specific manner and some semi-permissive cells, including A3.01, express A3G but fail to block replication of Vif-null HIV-1. Here we explored the semi-permissive nature of A3.01 cells and found it to be defined exclusively by the levels of A3G. Indeed, minor changes in A3G levels rendered A3.01 cells either fully permissive or non-permissive for Vif-null HIV-1. Our data indicate that A3.01 cells express sub-lethal levels of catalytically active A3G that affects Vif-null HIV-1 at the proviral level but does not completely block virus replication due to purifying selection. Attempts to use the selective pressure exerted by such sub-lethal levels of A3G to select for APOBEC-resistant Vif-null virus capable of replicating in H9 cells failed despite passaging virus for five months, demonstrating that Vif is a critical viral accessory protein.
Collapse
Affiliation(s)
- Eri Miyagi
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bldg. 4, Room 312, 4 Center Drive, MSC 0460, Bethesda, MD 20892, United States
| | - Sandra Kao
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bldg. 4, Room 312, 4 Center Drive, MSC 0460, Bethesda, MD 20892, United States
| | - Miyoshi Fumitaka
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bldg. 4, Room 312, 4 Center Drive, MSC 0460, Bethesda, MD 20892, United States
| | - Alicia Buckler-White
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bldg. 4, Room 312, 4 Center Drive, MSC 0460, Bethesda, MD 20892, United States
| | - Ron Plishka
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bldg. 4, Room 312, 4 Center Drive, MSC 0460, Bethesda, MD 20892, United States
| | - Klaus Strebel
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bldg. 4, Room 312, 4 Center Drive, MSC 0460, Bethesda, MD 20892, United States.
| |
Collapse
|
21
|
Nagahashi M, Wakai T, Shimada Y, Ichikawa H, Kameyama H, Kobayashi T, Sakata J, Yagi R, Sato N, Kitagawa Y, Uetake H, Yoshida K, Oki E, Kudo SE, Izutsu H, Kodama K, Nakada M, Tse J, Russell M, Heyer J, Powers W, Sun R, Ring JE, Takabe K, Protopopov A, Ling Y, Okuda S, Lyle S. Genomic landscape of colorectal cancer in Japan: clinical implications of comprehensive genomic sequencing for precision medicine. Genome Med 2016; 8:136. [PMID: 28007036 PMCID: PMC5180401 DOI: 10.1186/s13073-016-0387-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 12/01/2016] [Indexed: 12/18/2022] Open
Abstract
Background Comprehensive genomic sequencing (CGS) has the potential to revolutionize precision medicine for cancer patients across the globe. However, to date large-scale genomic sequencing of cancer patients has been limited to Western populations. In order to understand possible ethnic and geographic differences and to explore the broader application of CGS to other populations, we sequenced a panel of 415 important cancer genes to characterize clinically actionable genomic driver events in 201 Japanese patients with colorectal cancer (CRC). Methods Using next-generation sequencing methods, we examined all exons of 415 known cancer genes in Japanese CRC patients (n = 201) and evaluated for concordance among independent data obtained from US patients with CRC (n = 108) and from The Cancer Genome Atlas-CRC whole exome sequencing (WES) database (n = 224). Mutation data from non-hypermutated Japanese CRC patients were extracted and clustered by gene mutation patterns. Two different sets of genes from the 415-gene panel were used for clustering: 61 genes with frequent alteration in CRC and 26 genes that are clinically actionable in CRC. Results The 415-gene panel is able to identify all of the critical mutations in tumor samples as well as WES, including identifying hypermutated tumors. Although the overall mutation spectrum of the Japanese patients is similar to that of the Western population, we found significant differences in the frequencies of mutations in ERBB2 and BRAF. We show that the 415-gene panel identifies a number of clinically actionable mutations in KRAS, NRAS, and BRAF that are not detected by hot-spot testing. We also discovered that 26% of cases have mutations in genes involved in DNA double-strand break repair pathway. Unsupervised clustering revealed that a panel of 26 genes can be used to classify the patients into eight different categories, each of which can optimally be treated with a particular combination therapy. Conclusions Use of a panel of 415 genes can reliably identify all of the critical mutations in CRC patients and this information of CGS can be used to determine the most optimal treatment for patients of all ethnicities. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0387-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Masayuki Nagahashi
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata City, Niigata, 951-8510, Japan
| | - Toshifumi Wakai
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata City, Niigata, 951-8510, Japan.
| | - Yoshifumi Shimada
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata City, Niigata, 951-8510, Japan
| | - Hiroshi Ichikawa
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata City, Niigata, 951-8510, Japan
| | - Hitoshi Kameyama
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata City, Niigata, 951-8510, Japan
| | - Takashi Kobayashi
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata City, Niigata, 951-8510, Japan
| | - Jun Sakata
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata City, Niigata, 951-8510, Japan
| | - Ryoma Yagi
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata City, Niigata, 951-8510, Japan
| | - Nobuaki Sato
- Niigata Cancer Center Hospital, 15-3 Kawagishi-cho 2-Chome, Chuo-ku, Niigata City, Niigata, 951-8566, Japan
| | - Yuko Kitagawa
- Department of Surgery, Keio University School of Medicine, 35 Shinano-machi, Shinjyuku-ku, Tokyo, 160-8582, Japan
| | - Hiroyuki Uetake
- Department of Chemotherapy and Oncosurgery, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Kazuhiro Yoshida
- Department of Surgical Oncology, Gifu University School of Medicine, 1-1 Yanagido, Gifu, 501-1194, Japan
| | - Eiji Oki
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Shin-Ei Kudo
- Digestive Disease Center, Showa University Northern Yokohama Hospital, 35-1 Chigasaki-chuo, Tsuzuki-ku, Yokohama, 224-8503, Japan
| | - Hiroshi Izutsu
- Diagnostics Research Department, Life innovation Research Institute, Denka innovation center, Denka Co., Ltd., 3-5-1 Asahi-Machi, Machida-City, Tokyo, 194-8560, Japan
| | - Keisuke Kodama
- Diagnostics Research Department, Life innovation Research Institute, Denka innovation center, Denka Co., Ltd., 3-5-1 Asahi-Machi, Machida-City, Tokyo, 194-8560, Japan
| | - Mitsutaka Nakada
- Diagnostics Research Department, Life innovation Research Institute, Denka innovation center, Denka Co., Ltd., 3-5-1 Asahi-Machi, Machida-City, Tokyo, 194-8560, Japan
| | - Julie Tse
- KEW, Inc, 840 Memorial Drive, 4th floor, Cambridge, MA, 02139, USA
| | - Meaghan Russell
- KEW, Inc, 840 Memorial Drive, 4th floor, Cambridge, MA, 02139, USA
| | - Joerg Heyer
- KEW, Inc, 840 Memorial Drive, 4th floor, Cambridge, MA, 02139, USA
| | - Winslow Powers
- KEW, Inc, 840 Memorial Drive, 4th floor, Cambridge, MA, 02139, USA
| | - Ruobai Sun
- KEW, Inc, 840 Memorial Drive, 4th floor, Cambridge, MA, 02139, USA
| | - Jennifer E Ring
- KEW, Inc, 840 Memorial Drive, 4th floor, Cambridge, MA, 02139, USA
| | - Kazuaki Takabe
- Breast Surgery, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, NY, 14263, USA.,Department of Surgery, University at Buffalo, The State University of New York, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA
| | | | - Yiwei Ling
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata City, Niigata, 951-8510, Japan
| | - Shujiro Okuda
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata City, Niigata, 951-8510, Japan.
| | - Stephen Lyle
- KEW, Inc, 840 Memorial Drive, 4th floor, Cambridge, MA, 02139, USA. .,University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA.
| |
Collapse
|
22
|
Nicolas E, Golemis EA, Arora S. POLD1: Central mediator of DNA replication and repair, and implication in cancer and other pathologies. Gene 2016; 590:128-41. [PMID: 27320729 PMCID: PMC4969162 DOI: 10.1016/j.gene.2016.06.031] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/10/2016] [Accepted: 06/14/2016] [Indexed: 02/06/2023]
Abstract
The evolutionarily conserved human polymerase delta (POLD1) gene encodes the large p125 subunit which provides the essential catalytic activities of polymerase δ (Polδ), mediated by 5′–3′ DNA polymerase and 3′–5′ exonuclease moieties. POLD1 associates with three smaller subunits (POLD2, POLD3, POLD4), which together with Replication Factor C and Proliferating Nuclear Cell Antigen constitute the polymerase holoenzyme. Polδ function is essential for replication, with a primary role as the replicase for the lagging strand. Polδ also has an important proofreading ability conferred by the exonuclease activity, which is critical for ensuring replicative fidelity, but also serves to repair DNA lesions arising as a result of exposure to mutagens. Polδ has been shown to be important for multiple forms of DNA repair, including nucleotide excision repair, double strand break repair, base excision repair, and mismatch repair. A growing number of studies in the past decade have linked germline and sporadic mutations in POLD1 and the other subunits of Polδ with human pathologies. Mutations in Polδ in mice and humans lead to genomic instability, mutator phenotype and tumorigenesis. The advent of genome sequencing techniques has identified damaging mutations in the proofreading domain of POLD1 as the underlying cause of some inherited cancers, and suggested that mutations in POLD1 may influence therapeutic management. In addition, mutations in POLD1 have been identified in the developmental disorders of mandibular hypoplasia, deafness, progeroid features and lipodystrophy and atypical Werner syndrome, while changes in expression or activity of POLD1 have been linked to senescence and aging. Intriguingly, some recent evidence suggests that POLD1 function may also be altered in diabetes. We provide an overview of critical Polδ activities in the context of these pathologic conditions.
Collapse
Affiliation(s)
- Emmanuelle Nicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Erica A Golemis
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Sanjeevani Arora
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
| |
Collapse
|
23
|
Smith T, Ho G, Christodoulou J, Price EA, Onadim Z, Gauthier-Villars M, Dehainault C, Houdayer C, Parfait B, van Minkelen R, Lohman D, Eyre-Walker A. Extensive Variation in the Mutation Rate Between and Within Human Genes Associated with Mendelian Disease. Hum Mutat 2016; 37:488-94. [PMID: 26857394 DOI: 10.1002/humu.22967] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/25/2016] [Indexed: 01/05/2023]
Abstract
We have investigated whether the mutation rate varies between genes and sites using de novo mutations (DNMs) from three genes associated with Mendelian diseases (RB1, NF1, and MECP2). We show that the relative frequency of mutations at CpG dinucleotides relative to non-CpG sites varies between genes and relative to the genomic average. In particular we show that the rate of transition mutation at CpG sites relative to the rate of non-CpG transversion is substantially higher in our disease genes than amongst DNMs in general; the rate of CpG transition can be several hundred-fold greater than the rate of non-CpG transversion. We also show that the mutation rate varies significantly between sites of a particular mutational type, such as non-CpG transversion, within a gene. We estimate that for all categories of sites, except CpG transitions, there is at least a 30-fold difference in the mutation rate between the 10% of sites with the highest and lowest mutation rates. However, our best estimate is that the mutation rate varies by several hundred-fold variation. We suggest that the presence of hypermutable sites may be one reason certain genes are associated with disease.
Collapse
Affiliation(s)
- Thomas Smith
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Gladys Ho
- NSW Centre for Rett Syndrome Research, Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney, Australia
| | - John Christodoulou
- NSW Centre for Rett Syndrome Research, Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney, Australia.,Disciplines of Paediatrics and Child Health and Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, Australia
| | - Elizabeth Ann Price
- Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust, The Royal London Hospital, 80 Newark Street, London, United Kingdom
| | - Zerrin Onadim
- Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust, The Royal London Hospital, 80 Newark Street, London, United Kingdom
| | | | | | - Claude Houdayer
- Service de Génétique, Institut Curie, Paris, France.,INSERM U830, centre de recherche de l'Institut Curie, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Beatrice Parfait
- EA7331, Faculté de Pharmacie de Paris, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Service de Biochimie et de Génétique Moléculaire, Hôpital Cochin, AP-HP, Paris, France
| | - Rick van Minkelen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, Netherlands
| | - Dietmar Lohman
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| |
Collapse
|
24
|
Qiao Y, Han X, Guan G, Wu N, Sun J, Pak V, Liang G. TGF-β triggers HBV cccDNA degradation through AID-dependent deamination. FEBS Lett 2016; 590:419-27. [PMID: 26867650 DOI: 10.1002/1873-3468.12058] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 12/18/2015] [Accepted: 10/23/2015] [Indexed: 01/05/2023]
Abstract
The covalently closed circular DNA (cccDNA) of hepatitis B virus (HBV) is a viral center molecule for HBV infection and persistence. However, the cellular restriction factors of HBV cccDNA are not well understood. Here, we show that TGF-β can induce nuclear viral cccDNA degradation and hypermutation via activation-induced cytidine deaminase (AID) deamination activity in hepatocytes. This suppression by TGF-β is abrogated when AID or the activity of uracil-DNA glycosylase (UNG) is absent, which indicates that AID deamination and the UNG-mediated excision of uracil act in concert to degrade viral cccDNA. Moreover, the HBV core protein promotes the interaction between AID and viral cccDNA. Overall, our results indicate a novel molecular mechanism that allows cytokine TGF-β to restrict viral nuclear cccDNA in innate immunity, thereby suggesting a novel method for potentially eliminating cccDNA.
Collapse
Affiliation(s)
- Ying Qiao
- The Core Laboratory for Public Health Science and Practice, The First Affiliated Hospital, China Medical University, Shenyang, China
| | - Xiaoxu Han
- Key Laboratory of AIDS Immunology of the National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, Shenyang, China
| | - Gefei Guan
- Department of Neurosurgery, The First Affiliated Hospital, China Medical University, Shenyang, China
| | - Na Wu
- The Core Laboratory for Public Health Science and Practice, The First Affiliated Hospital, China Medical University, Shenyang, China
| | - Jianbo Sun
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
| | - Vladimir Pak
- Department of Medicine, Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Guoxin Liang
- Key Laboratory of AIDS Immunology of the National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, Shenyang, China
| |
Collapse
|
25
|
Wakae K, Aoyama S, Wang Z, Kitamura K, Liu G, Monjurul AM, Koura M, Imayasu M, Sakamoto N, Nakamura M, Kyo S, Kondo S, Fujiwara H, Yoshizaki T, Kukimoto I, Yamaguchi K, Shigenobu S, Nishiyama T, Muramatsu M. Detection of hypermutated human papillomavirus type 16 genome by Next-Generation Sequencing. Virology 2015; 485:460-6. [PMID: 26356796 DOI: 10.1016/j.virol.2015.08.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 08/16/2015] [Accepted: 08/17/2015] [Indexed: 11/28/2022]
Abstract
Human papillomavirus type 16 (HPV16) is a major cause of cervical cancer. We previously demonstrated that C-to-T and G-to-A hypermutations accumulated in the HPV16 genome by APOBEC3 expression in vitro. To investigate in vivo characteristics of hypermutation, differential DNA denaturation-PCR (3D-PCR) was performed using three clinical specimens obtained from HPV16-positive cervical dysplasia, and detected hypermutation from two out of three specimens. One sample accumulating hypermutations in both E2 and the long control region (LCR) was further subjected to Next-Generation Sequencing, revealing that hypermutations spread across the LCR and all early genes. Notably, hypermutation was more frequently observed in the LCR, which contains a viral replication origin and the early promoter. APOBEC3 expressed abundantly in an HPV16-positive cervix, suggesting that single-stranded DNA exposed during viral replication and transcription may be efficient targets for deamination. The results further strengthen a role of APOBEC3 in introducing HPV16 hypermutation in vivo.
Collapse
Affiliation(s)
- Kousho Wakae
- Department of Molecular Genetics, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan
| | - Satoru Aoyama
- Department of Molecular Genetics, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan; Tokyo Medical and Dental University Hospital Faculty of Medicine, Tokyo 113-8510, Japan
| | - Zhe Wang
- Department of Molecular Genetics, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan; Division of Medical Oncology, Affiliated Zhongshan Hospital of Dalian University, 116001, China
| | - Kouichi Kitamura
- Department of Molecular Genetics, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan
| | - Guangyan Liu
- Department of Molecular Genetics, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan
| | - Ahasan Md Monjurul
- Department of Molecular Genetics, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan
| | - Miki Koura
- Department of Molecular Genetics, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan
| | - Mieko Imayasu
- Department of Molecular Genetics, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan
| | - Naoya Sakamoto
- Department of Molecular Genetics, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan
| | - Mitsuhiro Nakamura
- Department of Obstetrics and Gynecology, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan
| | - Satoru Kyo
- Department of Obstetrics and Gynecology, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan; Department of Obstetrics and Gynecology, Shimane University Faculty of Medicine, Izumo, Shimane 693-8501, Japan
| | - Satoru Kondo
- Division of Otorhinolaryngology and Head and Neck Surgery, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan
| | - Hiroshi Fujiwara
- Department of Obstetrics and Gynecology, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan
| | - Tomokazu Yoshizaki
- Division of Otorhinolaryngology and Head and Neck Surgery, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan
| | - Iwao Kukimoto
- Pathogen Genomics Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashi-murayama, Tokyo 208-0011, Japan
| | - Katsushi Yamaguchi
- Functional Genomic Facility, National Institute of Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Shuji Shigenobu
- Functional Genomic Facility, National Institute of Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Tomoaki Nishiyama
- Advanced Science Research Center, Kanazawa University, Kanazawa, Ishikawa 920-8640, Japan.
| | - Masamichi Muramatsu
- Department of Molecular Genetics, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan.
| |
Collapse
|
26
|
Alinejad-Rokny H, Ebrahimi D. A method to avoid errors associated with the analysis of hypermutated viral sequences by alignment-based methods. J Biomed Inform 2015; 58:220-225. [PMID: 26494601 DOI: 10.1016/j.jbi.2015.10.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 09/30/2015] [Accepted: 10/15/2015] [Indexed: 12/17/2022]
Abstract
The human genome encodes for a family of editing enzymes known as APOBEC3 (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like3). They induce context dependent G-to-A changes, referred to as "hypermutation", in the genome of viruses such as HIV, SIV, HBV and endogenous retroviruses. Hypermutation is characterized by aligning affected sequences to a reference sequence. We show that indels (insertions/deletions) in the sequences lead to an incorrect assignment of APOBEC3 targeted and non-target sites. This can result in an incorrect identification of hypermutated sequences and erroneous biological inferences made based on hypermutation analysis.
Collapse
Affiliation(s)
| | - Diako Ebrahimi
- Department of Biochemistry, Molecular Biology and Biophysics; Masonic Cancer Center; Institute for Molecular Virology; University of Minnesota, MN, USA.
| |
Collapse
|
27
|
Barrett BS, Guo K, Harper MS, Li SX, Heilman KJ, Davidson NO, Santiago ML. Reassessment of murine APOBEC1 as a retrovirus restriction factor in vivo. Virology 2014; 468-470:601-608. [PMID: 25303118 DOI: 10.1016/j.virol.2014.09.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 09/02/2014] [Accepted: 09/06/2014] [Indexed: 12/21/2022]
Abstract
APOBEC1 is a cytidine deaminase involved in cholesterol metabolism that has been linked to retrovirus restriction, analogous to the evolutionarily-related APOBEC3 proteins. In particular, murine APOBEC1 was shown to inhibit Friend retrovirus (FV) in vitro, generating high levels of C-to-T and G-to-A mutations. These observations raised the possibility that FV infection might be altered in APOBEC1-null mice. To examine this question directly, we infected wild-type and APOBEC1-null mice with FV complex and evaluated acute infection levels. Surprisingly, APOBEC1-null mice exhibited similar cellular infection levels and plasma viremia relative to wild-type mice. Moreover, next-generation sequencing analyses revealed that in contrast to APOBEC3, APOBEC1 did not enhance retroviral C-to-T and G-to-A mutational frequencies in genomic DNA. Thus, APOBEC1 neither inhibited nor significantly drove the molecular evolution of FV in vivo. Our findings reinforce that not all retrovirus restriction factors characterized as potent in vitro may be functionally relevant in vivo.
Collapse
Affiliation(s)
- Bradley S Barrett
- Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
| | - Kejun Guo
- Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
| | - Michael S Harper
- Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA; Department of Immunology and Microbiology, University of Colorado Denver, Aurora, CO 80045, USA
| | - Sam X Li
- Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA; Department of Immunology and Microbiology, University of Colorado Denver, Aurora, CO 80045, USA
| | - Karl J Heilman
- Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
| | - Nicholas O Davidson
- Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Mario L Santiago
- Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA; Department of Immunology and Microbiology, University of Colorado Denver, Aurora, CO 80045, USA.
| |
Collapse
|
28
|
Martina P, Feliziani S, Juan C, Bettiol M, Gatti B, Yantorno O, Smania AM, Oliver A, Bosch A. Hypermutation in Burkholderia cepacia complex is mediated by DNA mismatch repair inactivation and is highly prevalent in cystic fibrosis chronic respiratory infection. Int J Med Microbiol 2014; 304:1182-91. [PMID: 25217078 DOI: 10.1016/j.ijmm.2014.08.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 08/15/2014] [Accepted: 08/18/2014] [Indexed: 11/25/2022] Open
Abstract
The Burkholderia cepacia complex (Bcc) represents an important group of pathogens involved in long-term lung infection in cystic fibrosis (CF) patients. A positive selection of hypermutators, linked to antimicrobial resistance development, has been previously reported for Pseudomonas aeruginosa in this chronic infection setting. Hypermutability, however, has not yet been systematically evaluated in Bcc species. A total of 125 well characterized Bcc isolates recovered from 48 CF patients, 10 non-CF patients and 15 environmental samples were analyzed. In order to determine the prevalence of mutators their spontaneous mutation rates to rifampicin resistance were determined. In addition, the genetic basis of the mutator phenotypes was investigated by sequencing the mutS and mutL genes, the main components of the mismatch repair system (MRS). The overall prevalence of hypermutators in the collection analyzed was 13.6%, with highest occurrence (40.7%) among the chronically infected CF patients, belonging mainly to B. cenocepacia, B. multivorans, B. cepacia, and B. contaminans -the most frequently recovered Bcc species from CF patients worldwide. Thirteen (76.5%) of the hypermutators were defective in mutS and/or mutL. Finally, searching for a possible association between antimicrobial resistance and hypermutability, the resistance-profiles to 17 antimicrobial agents was evaluated. High antimicrobial resistance rates were documented for all the Bcc species recovered from CF patients, but, except for ciprofloxacin, a significant association with hypermutation was not detected. In conclusion, in the present study we demonstrate for the first time that, MRS-deficient Bcc species mutators are highly prevalent and positively selected in CF chronic lung infections. Hypermutation therefore, might be playing a key role in increasing bacterial adaptability to the CF-airway environment, facilitating the persistence of chronic lung infections.
Collapse
Affiliation(s)
- Pablo Martina
- CINDEFI-CONICET-CCT La Plata, Centro de Biotecnología Aplicada, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, 1900 La Plata, Argentina
| | - Sofía Feliziani
- CIQUIBIC-CONICET, Centro de Investigaciones en Química Biológica de Córdoba, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina
| | - Carlos Juan
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), 07010 Palma de Mallorca, Spain
| | - Marisa Bettiol
- Sala de Microbiología, Hospital de Niños de La Plata "Sor María Ludovica", 1900 La Plata, Argentina
| | - Blanca Gatti
- Sala de Microbiología, Hospital de Niños de La Plata "Sor María Ludovica", 1900 La Plata, Argentina
| | - Osvaldo Yantorno
- CINDEFI-CONICET-CCT La Plata, Centro de Biotecnología Aplicada, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, 1900 La Plata, Argentina
| | - Andrea M Smania
- CIQUIBIC-CONICET, Centro de Investigaciones en Química Biológica de Córdoba, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina
| | - Antonio Oliver
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), 07010 Palma de Mallorca, Spain.
| | - Alejandra Bosch
- CINDEFI-CONICET-CCT La Plata, Centro de Biotecnología Aplicada, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, 1900 La Plata, Argentina.
| |
Collapse
|
29
|
Bélanger K, Savoie M, Aydin H, Renner TM, Montazeri Z, Langlois MA. Deamination intensity profiling of human APOBEC3 protein activity along the near full-length genomes of HIV-1 and MoMLV by HyperHRM analysis. Virology 2014; 448:168-75. [PMID: 24314647 DOI: 10.1016/j.virol.2013.10.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 09/15/2013] [Accepted: 10/04/2013] [Indexed: 12/17/2022]
Abstract
Enzymatic deamination of cytidines in DNA is an intrinsic component of antibody maturation and retroviral resistance, but can also be a source of HIV drug resistance and cancer-causing mutations. Here, we developed a high-throughput method based on high resolution melt (HRM) analysis called HyperHRM that can screen genomic DNA for rare hypermutated proviral sequences and accurately quantify the number of C-to-T or G-to-A mutations in each sequence. We demonstrate the effectiveness of the approach by profiling in parallel the intensity of the DNA mutator activity of all seven human APOBEC3 proteins on the near full-length sequence of HIV-1 and the Moloney murine leukemia virus. Additionally, HRM was successfully used to identify hypermutated proviral sequences in peripheral blood mononuclear cells from an HIV-1 patient. These results exemplify the effectiveness of HRM-based approaches for hypermutation quantification and for the detection of hypermutated DNA sequences potentially associated with disease or retroviral drug resistance.
Collapse
Affiliation(s)
- Kasandra Bélanger
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | | | | | | | | | | |
Collapse
|
30
|
Eyzaguirre LM, Charurat M, Redfield RR, Blattner WA, Carr JK, Sajadi MM. Elevated hypermutation levels in HIV-1 natural viral suppressors. Virology 2013; 443:306-12. [PMID: 23791226 DOI: 10.1016/j.virol.2013.05.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 04/05/2013] [Accepted: 05/10/2013] [Indexed: 12/28/2022]
Abstract
Mutations in the HIV-1 proviral genomes delay the progression of the disease. We compared the mutation status in full-length proviral genomes of 23 HIV-infected patients with undetectable viral loads in the absence of therapy named natural viral suppressors (NVS) or Elite Controllers with 23 HIV-infected controls (10 patients on HAART treatment and 13 untreated patients). Provirus DNA was extracted from PBMC for amplification and sequencing to determine the mutation status. Nine (39 %) of the 23 NVS patients had defective proviral genomes, compared to 4 of the treated controls (40%, p = 0.96) and only one of the untreated controls (8%, p = 0.059). Most of the defective genomes resulted from Gto-A hypermutation. Among patients with hypermutation, the rate ratio for mutation was significantly higher for the NVS compared to treated controls (p = 0.043). Our data suggests that inactivation of the virus through the APOBEC3G system may contribute to the NVS phenotype.
Collapse
Affiliation(s)
- Lindsay M Eyzaguirre
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, United States 725 West Lombard Street Baltimore, MD 21201, USA.
| | | | | | | | | | | |
Collapse
|
31
|
Taylor BJ, Nik-Zainal S, Wu YL, Stebbings LA, Raine K, Campbell PJ, Rada C, Stratton MR, Neuberger MS. DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis. eLife 2013; 2:e00534. [PMID: 23599896 PMCID: PMC3628087 DOI: 10.7554/elife.00534] [Citation(s) in RCA: 269] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 03/09/2013] [Indexed: 01/15/2023] Open
Abstract
Breast cancer genomes have revealed a novel form of mutation showers (kataegis) in which multiple same-strand substitutions at C:G pairs spaced one to several hundred nucleotides apart are clustered over kilobase-sized regions, often associated with sites of DNA rearrangement. We show kataegis can result from AID/APOBEC-catalysed cytidine deamination in the vicinity of DNA breaks, likely through action on single-stranded DNA exposed during resection. Cancer-like kataegis can be recapitulated by expression of AID/APOBEC family deaminases in yeast where it largely depends on uracil excision, which generates an abasic site for strand breakage. Localized kataegis can also be nucleated by an I-SceI-induced break. Genome-wide patterns of APOBEC3-catalyzed deamination in yeast reveal APOBEC3B and 3A as the deaminases whose mutational signatures are most similar to those of breast cancer kataegic mutations. Together with expression and functional assays, the results implicate APOBEC3B/A in breast cancer hypermutation and give insight into the mechanism of kataegis. DOI:http://dx.doi.org/10.7554/eLife.00534.001 The genomes of cancer cells contain mutations that are not present in normal cells. Some of these prevent cells from repairing their DNA, while others give rise to tumours by causing cells to multiply uncontrollably. Moreover, some of the mutations in breast cancer cells occur in clusters—a phenomenon known as kataegis (from the Greek for ‘thunderstorm’). Kataegic mutations occur almost exclusively at a cytosine preceded by a thymine. This suggests that a family of proteins called AID/APOBEC enzymes—which remove amine groups from cytosines—may be involved in generating these mutations. In this study, Taylor et al. confirm this possibility by showing that expressing individual members of the AID/APOBEC family of enzymes in yeast cells increases the mutation frequency and induces kataegis. The kataegis triggered by the AID/APOBEC enzymes could be localised through the introduction of double-stranded breaks into the DNA: Taylor et al. suggest that this might happen because repairing the breaks exposes single-stranded DNA, which the AID/APOBEC enzymes then act upon. By comparing the mutations induced in the yeast cells with those observed in breast cancer cells, Taylor et al. identified APOBEC3B as the enzyme most likely to be responsible for kataegis in breast cancer (with APOBEC3A also a strong candidate in some cancers). Moreover, they showed that APOBEC3B was highly expressed in breast cancer cell lines, and that APOBEC3B and APOBEC3A can also cause DNA damage in human cells. Taken together, the findings provide key insights into the mechanism by which kataegis arises, and identify two proteins likely to contribute to the mutations seen in breast cancer. Further work is now required to determine whether these enzymes also give rise to mutations in other forms of cancer. DOI:http://dx.doi.org/10.7554/eLife.00534.002
Collapse
Affiliation(s)
- Benjamin Jm Taylor
- Protein and Nucleic Acid Chemistry Division , Medical Research Council Laboratory of Molecular Biology , Cambridge , United Kingdom
| | | | | | | | | | | | | | | | | |
Collapse
|