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Vallarelli AF, Rachakonda PS, André J, Heidenreich B, Riffaud L, Bensussan A, Kumar R, Dumaz N. TERT promoter mutations in melanoma render TERT expression dependent on MAPK pathway activation. Oncotarget 2018; 7:53127-53136. [PMID: 27449293 PMCID: PMC5288173 DOI: 10.18632/oncotarget.10634] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [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: 03/18/2016] [Accepted: 07/09/2016] [Indexed: 11/25/2022] Open
Abstract
The mechanism of telomerase re-activation in cancer had remained elusive until the discovery of frequent mutations in the promoter of the TERT gene that encodes the catalytic reverse transcriptase subunit of telomerase. We investigated the regulation of TERT expression in melanoma cell lines and our results show that promoter mutations render TERT expression dependent on MAPK activation due to oncogenic BRAF or NRAS mutations. Mutations in the TERT promoter create binding sites for ETS transcription factors. ETS1, expressed in melanoma cell lines, undergoes activating phosphorylation by ERK at Thr38 residue as a consequence of constitutively activated MAPK pathway. We demonstrate that ETS1 binds on the mutated TERT promoter leading to the re-expression of the gene. The inhibition of ETS1 resulted in reduced TERT expression. We provide evidence that the TERT promoter mutations provide a direct link between TERT expression and MAPK pathway activation due to BRAF or NRAS mutations via the transcription factor ETS1.
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Affiliation(s)
- Andrelou F Vallarelli
- INSERM, U976, Skin Research Centre, Hôpital Saint-Louis, Paris, F-75010, France.,Université Paris Diderot, Sorbonne Paris Cité, UMRS976, Paris, F-75010, France.,Department of Internal Medicine, School of Medicine Sciences, State University of Campinas (UNICAMP), 13083-970, Campinas, SP, Brazil
| | | | - Jocelyne André
- INSERM, U976, Skin Research Centre, Hôpital Saint-Louis, Paris, F-75010, France.,Université Paris Diderot, Sorbonne Paris Cité, UMRS976, Paris, F-75010, France
| | - Barbara Heidenreich
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Laurence Riffaud
- INSERM, U976, Skin Research Centre, Hôpital Saint-Louis, Paris, F-75010, France.,Université Paris Diderot, Sorbonne Paris Cité, UMRS976, Paris, F-75010, France
| | - Armand Bensussan
- INSERM, U976, Skin Research Centre, Hôpital Saint-Louis, Paris, F-75010, France.,Université Paris Diderot, Sorbonne Paris Cité, UMRS976, Paris, F-75010, France
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Nicolas Dumaz
- INSERM, U976, Skin Research Centre, Hôpital Saint-Louis, Paris, F-75010, France.,Université Paris Diderot, Sorbonne Paris Cité, UMRS976, Paris, F-75010, France
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2
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Xie H, Rachakonda PS, Heidenreich B, Nagore E, Sucker A, Hemminki K, Schadendorf D, Kumar R. Mapping of deletion breakpoints at the CDKN2A locus in melanoma: detection of MTAP-ANRIL fusion transcripts. Oncotarget 2017; 7:16490-504. [PMID: 26909863 PMCID: PMC4941330 DOI: 10.18632/oncotarget.7503] [Citation(s) in RCA: 17] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 02/11/2016] [Indexed: 12/17/2022] Open
Abstract
Genomic locus at chromosome 9p21 that contains the CDKN2A and CDKN2B tumor suppressor genes is inactivated through mutations, deletions and promoter methylation in multiple human cancers. Additionally, the locus encodes an anti-sense RNA (ANRIL). Both hemizygous and homozygous deletions at the locus targeting multiple genes are fairly common in different cancers. We in this study investigated breakpoints in five melanoma cell lines, derived from metastasized tumors, with previously identified homozygous deletions using array comparative genomic hybridization (aCGH). For breakpoint mapping, we used primer approximation multiplex PCR (PAMP) and inverse PCR techniques. Our results showed that three cell lines carried complex rearrangements. In two other cell lines, with focal deletions of 141 kb and 181 kb, we identified fusion gene products, involving MTAP and ANRIL. We also confirmed the complex rearrangements and focal deletions in DNA from tumor tissues corresponding to three cell lines. The rapid amplification of 3′cDNA ends (3′RACE) carried out on transcripts resulted in identification of three isoforms of MTAP-ANRIL fusion gene. Screening of cDNA from 64 melanoma cell lines resulted in detection of fusion transcripts in 13 (20%) cell lines that involved exons 4-7 of the MTAP and exon 2 or 5 of the ANRIL genes. We also detected fusion transcripts involving MTAP and ANRIL in two of the seven primary melanoma tumors with focal deletion at the locus. The results from the study, besides identifying complex rearrangements involving CDKN2A locus, show frequent occurrence of fusion transcripts involving MTAP and ANRIL genes.
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Affiliation(s)
- Huaping Xie
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | | | - Barbara Heidenreich
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Eduardo Nagore
- Department of Dermatology, Instituto Valenciano de Oncologia, Valencia, Spain
| | - Antje Sucker
- Department of Dermatology, University Hospital Essen, Essen, Germany
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany.,Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen, Essen, Germany.,German Cancer Consortium (DKTK), Essen, Germany
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
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3
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Vijayakrishnan J, Kumar R, Henrion MYR, Moorman AV, Rachakonda PS, Hosen I, da Silva Filho MI, Holroyd A, Dobbins SE, Koehler R, Thomsen H, Irving JA, Allan JM, Lightfoot T, Roman E, Kinsey SE, Sheridan E, Thompson PD, Hoffmann P, Nöthen MM, Heilmann-Heimbach S, Jöckel KH, Greaves M, Harrison CJ, Bartram CR, Schrappe M, Stanulla M, Hemminki K, Houlston RS. A genome-wide association study identifies risk loci for childhood acute lymphoblastic leukemia at 10q26.13 and 12q23.1. Leukemia 2017; 31:573-579. [PMID: 27694927 PMCID: PMC5336191 DOI: 10.1038/leu.2016.271] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 08/26/2016] [Accepted: 09/06/2016] [Indexed: 02/08/2023]
Abstract
Genome-wide association studies (GWASs) have shown that common genetic variation contributes to the heritable risk of childhood acute lymphoblastic leukemia (ALL). To identify new susceptibility loci for the largest subtype of ALL, B-cell precursor ALL (BCP-ALL), we conducted a meta-analysis of two GWASs with imputation using 1000 Genomes and UK10K Project data as reference (totaling 1658 cases and 7224 controls). After genotyping an additional 2525 cases and 3575 controls, we identify new susceptibility loci for BCP-ALL mapping to 10q26.13 (rs35837782, LHPP, P=1.38 × 10-11) and 12q23.1 (rs4762284, ELK3, P=8.41 × 10-9). We also provide confirmatory evidence for the existence of independent risk loci at 9p21.3, but show that the association marked by rs77728904 can be accounted for by linkage disequilibrium with the rare high-impact CDKN2A p.Ala148Thr variant rs3731249. Our data provide further insights into genetic susceptibility to ALL and its biology.
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Affiliation(s)
- J Vijayakrishnan
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - R Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - M Y R Henrion
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - A V Moorman
- Leukemia Research Group, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - P S Rachakonda
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - I Hosen
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - M I da Silva Filho
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - A Holroyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - S E Dobbins
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - R Koehler
- Department of Human Genetics, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - H Thomsen
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - J A Irving
- Leukemia Research Group, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - J M Allan
- Leukemia Research Group, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - T Lightfoot
- Department of Health Sciences, Epidemiology and Cancer Statistics Group, University of York, York, UK
| | - E Roman
- Department of Health Sciences, Epidemiology and Cancer Statistics Group, University of York, York, UK
| | - S E Kinsey
- Department of Paediatric and Adolescent Haematology and Oncology, Leeds General Infirmary, Leeds, UK
| | - E Sheridan
- Medical Genetics Research Group, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, UK
| | - P D Thompson
- Paediatric and Familial Cancer Research Group, Institute of Cancer Sciences, University of Manchester, St Mary's Hospital, Manchester, UK
| | - P Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Biomedicine, Human Genomics Research Group, University Hospital Basel, Basel, Switzerland
| | - M M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | | | - K H Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Essen, Germany
| | - M Greaves
- Haemato-Oncology Research Unit, Division of Molecular Pathology, Institute of Cancer Research, Sutton, UK
| | - C J Harrison
- Leukemia Research Group, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - C R Bartram
- Department of Human Genetics, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - M Schrappe
- General Paediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - M Stanulla
- Department of Paediatric Haematology and Oncology, Hannover Medical School, Hannover, Germany
| | - K Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | - R S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
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4
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Willmes C, Kumar R, Becker JC, Fried I, Rachakonda PS, Poppe LM, Hesbacher S, Schadendorf D, Sucker A, Schrama D, Ugurel S. SERPINB1 expression is predictive for sensitivity and outcome of cisplatin-based chemotherapy in melanoma. Oncotarget 2017; 7:10117-32. [PMID: 26799424 PMCID: PMC4891108 DOI: 10.18632/oncotarget.6956] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 04/10/2015] [Accepted: 12/26/2015] [Indexed: 12/02/2022] Open
Abstract
Despite of highly effective new therapeutic strategies, chemotherapy still is an important treatment option in metastatic melanoma. Since predictors of chemotherapy response are rare, drugs and regimens are currently chosen arbitrarily. The present study was aimed at the identification of molecular markers predicting the outcome of chemotherapy in melanoma. Tumor biopsies from metastatic lesions were collected from 203 stage IV melanoma patients prior to chemotherapy onset and used for gene expression profiling (n = 6; marker identification set), quantitative real-time PCR (n = 127; validation set 1), and immunohistochemistry on tissue microarrays (n = 70; validation set 2). The results were correlated to the tumors' in-vitro chemosensitivity and to the patients' in-vivo chemotherapy outcome. SERPINB1 was found to correlate to the in-vitro sensitivity to cisplatin-containing chemotherapy regimens (p = 0.005). High SERPINB1 gene expression was associated with favorable tumor response (p = 0.012) and prolonged survival (p = 0.081) under cisplatin-based chemotherapy. High SERPINB1 protein expression in tumor tissue from cisplatin-treated patients was associated with a favorable survival (p = 0.011), and proved as an independent predictor of survival (p = 0.008) by multivariate analysis. We conclude, that SERPINB1 expression, although not functionally involved, is predictive for the outcome of cisplatin-based chemotherapy in melanoma, and thus may be useful to personalize melanoma chemotherapy.
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Affiliation(s)
- Christoph Willmes
- Department of Dermatology, University Hospital Würzburg, Würzburg, Germany
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Jürgen C Becker
- Translational Skin Cancer Research, Deutsches Konsortium für Translationale Krebsforschung (DKTK), Essen, Germany.,Department of Dermatology, University Duisburg-Essen, Essen, Germany
| | - Isabella Fried
- Department of Dermatology, Medical University of Graz, Graz, Austria
| | | | - Lidia M Poppe
- Department of Dermatology, University Hospital Würzburg, Würzburg, Germany
| | - Sonja Hesbacher
- Department of Dermatology, University Hospital Würzburg, Würzburg, Germany
| | - Dirk Schadendorf
- Department of Dermatology, University Duisburg-Essen, Essen, Germany
| | - Antje Sucker
- Department of Dermatology, University Duisburg-Essen, Essen, Germany
| | - David Schrama
- Department of Dermatology, University Hospital Würzburg, Würzburg, Germany
| | - Selma Ugurel
- Department of Dermatology, University Hospital Würzburg, Würzburg, Germany.,Department of Dermatology, University Duisburg-Essen, Essen, Germany
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5
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Denisova E, Heidenreich B, Nagore E, Rachakonda PS, Hosen I, Akrap I, Traves V, García-Casado Z, López-Guerrero JA, Requena C, Sanmartin O, Serra-Guillén C, Llombart B, Guillén C, Ferrando J, Gimeno E, Nordheim A, Hemminki K, Kumar R. Frequent DPH3 promoter mutations in skin cancers. Oncotarget 2016; 6:35922-30. [PMID: 26416425 PMCID: PMC4742151 DOI: 10.18632/oncotarget.5771] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [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: 08/10/2015] [Accepted: 09/12/2015] [Indexed: 12/24/2022] Open
Abstract
Recent reports suggested frequent occurrence of cancer associated somatic mutations within regulatory elements of the genome. Based on initial exome sequencing of 21 melanomas, we report frequent somatic mutations in skin cancers in a bidirectional promoter of diphthamide biosynthesis 3 (DPH3) and oxidoreductase NAD-binding domain containing 1 (OXNAD1) genes. The UV-signature mutations occurred at sites adjacent and within a binding motif for E-twenty six/ternary complex factors (Ets/TCF), at -8 and -9 bp from DPH3 transcription start site. Follow up screening of 586 different skin lesions showed that the DPH3 promoter mutations were present in melanocytic nevi (2/114; 2%), melanoma (30/304; 10%), basal cell carcinoma of skin (BCC; 57/137; 42%) and squamous cell carcinoma of skin (SCC; 12/31; 39%). Reporter assays carried out in one melanoma cell line for DPH3 and OXNAD1 orientations showed statistically significant increased promoter activity due to -8/-9CC > TT tandem mutations; although, no effect of the mutations on DPH3 and OXNAD1 transcription in tumors was observed. The results from this study show occurrence of frequent somatic non-coding mutations adjacent to a pre-existing binding site for Ets transcription factors within the directional promoter of DPH3 and OXNAD1 genes in three major skin cancers. The detected mutations displayed typical UV signature; however, the functionality of the mutations remains to be determined.
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Affiliation(s)
- Evgeniya Denisova
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Barbara Heidenreich
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Eduardo Nagore
- Department of Dermatology, Instituto Valenciano de Oncologia, Valencia, Spain
| | | | - Ismail Hosen
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Ivana Akrap
- Interfaculty Institute of Cell Biology, Tuebingen University, and IMPRS ("From Molecules to Organisms"), Tuebingen, Germany
| | - Víctor Traves
- Department of Pathology, Instituto Valenciano de Oncologia, Valencia, Spain
| | - Zaida García-Casado
- Laboratory of Molecular Biology, Instituto Valenciano de Oncologia, Valencia, Spain
| | | | - Celia Requena
- Department of Dermatology, Instituto Valenciano de Oncologia, Valencia, Spain
| | - Onofre Sanmartin
- Department of Dermatology, Instituto Valenciano de Oncologia, Valencia, Spain
| | | | - Beatriz Llombart
- Department of Dermatology, Instituto Valenciano de Oncologia, Valencia, Spain
| | - Carlos Guillén
- Department of Dermatology, Instituto Valenciano de Oncologia, Valencia, Spain
| | - Jose Ferrando
- Departments of Pathology & Dermatology, Hospital Arnau de Vilanova, Valencia, Spain
| | - Enrique Gimeno
- Departments of Pathology & Dermatology, Hospital Arnau de Vilanova, Valencia, Spain
| | - Alfred Nordheim
- Interfaculty Institute of Cell Biology, Tuebingen University, and IMPRS ("From Molecules to Organisms"), Tuebingen, Germany.,German Cancer Consortium (DKTK/DKFZ), Heidelberg, Germany
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany.,Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
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6
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Laugier F, Finet-Benyair A, André J, Rachakonda PS, Kumar R, Bensussan A, Dumaz N. RICTOR involvement in the PI3K/AKT pathway regulation in melanocytes and melanoma. Oncotarget 2016; 6:28120-31. [PMID: 26356562 PMCID: PMC4695048 DOI: 10.18632/oncotarget.4866] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 08/17/2015] [Indexed: 01/16/2023] Open
Abstract
Several studies have highlighted the importance of the PI3K pathway in melanocytes and its frequent over-activation in melanoma. However, little is known about regulation of the PI3K pathway in melanocytic cells. We showed that normal human melanocytes are less sensitive to selective PI3K or mTOR inhibitors than to dual PI3K/mTOR inhibitors. The resistance to PI3K inhibitor was due to a rapid AKT reactivation limiting the inhibitor effect on proliferation. Reactivation of AKT was linked to a feedback mechanism involving the mTORC2 complex and in particular its scaffold protein RICTOR. RICTOR overexpression in melanocytes disrupted the negative feedback, activated the AKT pathway and stimulated clonogenicity highlighting the importance of this feedback to restrict melanocyte proliferation. We found that the RICTOR locus is frequently amplified and overexpressed in melanoma and that RICTOR over-expression in NRAS-transformed melanocytes stimulates their clonogenicity, demonstrating that RICTOR amplification can cooperate with NRAS mutation to stimulate melanoma proliferation. These results show that RICTOR plays a central role in PI3K pathway negative feedback in melanocytes and that its deregulation could be involved in melanoma development.
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Affiliation(s)
- Florence Laugier
- INSERM, U976, Centre de Recherche sur la Peau, Hôpital Saint-Louis, Paris, F-75010, France.,Université Paris Diderot, Sorbonne Paris Cité, UMRS976, Paris, F-75010, France
| | - Adeline Finet-Benyair
- INSERM, U976, Centre de Recherche sur la Peau, Hôpital Saint-Louis, Paris, F-75010, France.,Université Paris Diderot, Sorbonne Paris Cité, UMRS976, Paris, F-75010, France
| | - Jocelyne André
- INSERM, U976, Centre de Recherche sur la Peau, Hôpital Saint-Louis, Paris, F-75010, France.,Université Paris Diderot, Sorbonne Paris Cité, UMRS976, Paris, F-75010, France
| | | | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, 69120, Heidelberg, Germany
| | - Armand Bensussan
- INSERM, U976, Centre de Recherche sur la Peau, Hôpital Saint-Louis, Paris, F-75010, France.,Université Paris Diderot, Sorbonne Paris Cité, UMRS976, Paris, F-75010, France
| | - Nicolas Dumaz
- INSERM, U976, Centre de Recherche sur la Peau, Hôpital Saint-Louis, Paris, F-75010, France.,Université Paris Diderot, Sorbonne Paris Cité, UMRS976, Paris, F-75010, France
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7
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Heidenreich B, Rachakonda PS, Hosen I, Volz F, Hemminki K, Weyerbrock A, Kumar R. TERT promoter mutations and telomere length in adult malignant gliomas and recurrences. Oncotarget 2015; 6:10617-33. [PMID: 25797251 PMCID: PMC4496380 DOI: 10.18632/oncotarget.3329] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 02/09/2015] [Indexed: 02/03/2023] Open
Abstract
In this report on 303 gliomas we show the highest frequency of TERT promoter mutations in gliobastomas (80%) followed by oligodendrogliomas (70%) and astrocytomas (39%). We observed positive association between TERT promoter and IDH mutations in oligodendroglial tumors (OR = 26.3; 95% CI 2.5-250.2) and inverse association in primary glioblastomas (OR = 0.13; 95% CI 0.03-0.58). Tumors with TERT promoter mutations compared to those without showed increased TERT transcription; we also showed difference in the transcription levels due to the two main mutations. Tumors with TERT promoter mutations had shorter telomeres than those without. The patients with only TERT promoter mutations showed worst survival (median survival 14.6 months) and patients with both IDH and TERT promoter mutations showed best survival (246.5 months). In patients with astrocytoma, the TERT promoter mutations only associated with poor survival (P < 0.0001); IDH mutations and 1p/19q deletions associated with increased survival (P = 0.0004). TERT promoter mutations in low grade gliomas associated with reduced progression free survival (HR 10.2; 95% CI 1.9 - 55.9). While our data affirm the role of TERT promoter mutations in glial tumors, effects on transcription and telomere length emphasise the importance of telomere biology in disease genesis and outcome.
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Affiliation(s)
- Barbara Heidenreich
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg 69120, Germany
| | | | - Ismail Hosen
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg 69120, Germany
| | - Florian Volz
- Department of Neurosurgery, University Medical Center Freiburg, Freiburg 79106, Germany
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg 69120, Germany
- Center for Primary Health Care Research, Lund University, Malmö, Lund 22100, Sweden
| | - Astrid Weyerbrock
- Department of Neurosurgery, University Medical Center Freiburg, Freiburg 79106, Germany
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg 69120, Germany
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8
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Hosen I, Rachakonda PS, Heidenreich B, de Verdier PJ, Ryk C, Steineck G, Hemminki K, Kumar R. Mutations in TERT promoter and FGFR3 and telomere length in bladder cancer. Int J Cancer 2015; 137:1621-9. [PMID: 25809917 DOI: 10.1002/ijc.29526] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [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: 11/19/2014] [Revised: 02/23/2015] [Accepted: 03/13/2015] [Indexed: 01/09/2023]
Abstract
Mutations in the promoter of the telomerase reverse transcriptase (TERT) and fibroblast growth factor receptor 3 (FGFR3) genes constitute the most recurrent somatic alterations in urothelial carcinoma of bladder. In this study, we screened DNA from 327 urothelial bladder carcinomas from well-documented patients, with different stages and grades and known TERT promoter mutational status, for FGFR3 alterations and measured relative telomere length (RTL). Although, the frequency of the TERT promoter mutations was higher than those in FGFR3; however, the alterations at the two loci occurred together more frequently than per chance [Odds ratio (OR) = 4.93, 95% CI = 2.72-8.92, p < 0.0001]. While tumors with TERT promoter and FGFR3 mutations had shorter RTL than those without mutations (p < 0.0001), the TERT promoter mutations in conjunction with the common allele of the rs2853669 polymorphism defined sub-group of patients with an observed decreased overall survival (OR = 2.15, 95% CI = 1.00-4.61) and increased recurrence in patients with TaG1+TaG2 disease categories (OR = 3.68, 95%CI = 1.12-12.05). The finding of shorter telomeres in tumors with TERT promoter and/or FGFR3 mutations than without mutations implies mechanistic relevance of telomere biology in cancer progression. The observed association with recurrence and survival shows that the TERT promoter mutations can potentially be used as markers to refine selection of patients for different treatments. The overwhelming frequency of the TERT promoter mutations also represents a case for development of an eventual therapeutic target.
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Affiliation(s)
- Ismail Hosen
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | | | - Barbara Heidenreich
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Petra J de Verdier
- Division of Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Charlotta Ryk
- Department of Urology, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Urology Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Gunnar Steineck
- Division of Clinical Cancer Epidemiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Cancer Epidemiology, Karolinska Intstitutet, Stockholm, Sweden
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany.,Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
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9
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Hosen I, Rachakonda PS, Heidenreich B, Sitaram RT, Ljungberg B, Roos G, Hemminki K, Kumar R. TERT promoter mutations in clear cell renal cell carcinoma. Int J Cancer 2014; 136:2448-52. [PMID: 25331263 DOI: 10.1002/ijc.29279] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [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: 09/01/2014] [Accepted: 10/07/2014] [Indexed: 01/22/2023]
Abstract
We screened promoter region of the telomerase reverse transcriptase (TERT) for activating somatic mutations in 188 tumors from patients with clear cell renal cell carcinoma (ccRCC). Twelve tumors (6.4%) carried a mutation within the core promoter region of the gene. The mutations were less frequent in high grade tumors compared to low grade tumors [odds ratio (OR) = 0.15, 95% confidence interval (CI) = 0.03-0.72, p = 0.02]. Multivariate analysis for cause specific survival showed statistically significant poor outcome in patients with TERT promoter mutations [hazard ratio (HR) = 2.90, 95% CI = 1.13-7.39, p = 0.03]. A common polymorphism (rs2853669) within the locus seemed to act as a modifier of the effect of the mutations on patient survival as the noncarriers of the variant allele with the TERT promoter mutations showed worst survival (HR = 3.34, 95% CI = 1.24-8.98, p = 0.02). We also measured relative telomere length (RTL) in tumors and difference between tumors with and without the TERT promoter mutations was not statistically significant. Similarly, no difference in patient survival based on RTL in tumors was observed. Our study showed a relatively low frequency of TERT promoter mutations in ccRCC. Nevertheless, patients with the mutations, particularly in the absence of the rs2853669 variant showed the worst disease-specific survival. Thus, it is possible that the TERT promoter mutations define a small subset of tumors with an aggressive behavior.
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Affiliation(s)
- Ismail Hosen
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
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10
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Davies JR, Jewell R, Affleck P, Anic GM, Randerson-Moor J, Ozola A, Egan KM, Elliott F, García-Casado Z, Hansson J, Harland M, Höiom V, Jian G, Jönsson G, Kumar R, Nagore E, Wendt J, Olsson H, Park JY, Patel P, Pjanova D, Puig S, Schadendorf D, Sivaramakrishna Rachakonda P, Snowden H, Stratigos AJ, Bafaloukos D, Ogbah Z, Sucker A, Van den Oord JJ, Van Doorn R, Walker C, Okamoto I, Wolter P, Barrett JH, Timothy Bishop D, Newton-Bishop J. Inherited variation in the PARP1 gene and survival from melanoma. Int J Cancer 2014; 135:1625-33. [PMID: 24535833 PMCID: PMC4106984 DOI: 10.1002/ijc.28796] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [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: 10/01/2013] [Accepted: 12/17/2013] [Indexed: 12/20/2022]
Abstract
We report the association of an inherited variant located upstream of the poly(adenosine diphosphate-ribose) polymerase 1 (PARP1) gene (rs2249844), with survival in 11 BioGenoMEL melanoma cohorts. The gene encodes a protein involved in a number of cellular processes including single-strand DNA repair. Survival analysis was conducted for each cohort using proportional hazards regression adjusting for factors known to be associated with survival. Survival was measured as overall survival (OS) and, where available, melanoma-specific survival (MSS). Results were combined using random effects meta-analysis. Evidence for a role of the PARP1 protein in melanoma ulceration and survival was investigated by testing gene expression levels taken from formalin-fixed paraffin-embedded tumors. A significant association was seen for inheritance of the rarer variant of PARP1, rs2249844 with OS (hazard ratio (HR) = 1.16 per allele, 95% confidence interval (CI) 1.04–1.28, p = 0.005, eleven cohorts) and MSS (HR = 1.20 per allele, 95% CI 1.01–1.39, p = 0.03, eight cohorts). We report bioinformatic data supportive of a functional effect for rs2249844. Higher levels of PARP1 gene expression in tumors were shown to be associated with tumor ulceration and poorer OS.
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Affiliation(s)
- John R Davies
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
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11
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Davies JR, Field S, Randerson-Moor J, Harland M, Kumar R, Anic GM, Nagore E, Hansson J, Höiom V, Jönsson G, Gruis NA, Park JY, Guan J, Sivaramakrishna Rachakonda P, Wendt J, Pjanova D, Puig S, Schadendorf D, Okamoto I, Olsson H, Affleck P, García-Casado Z, Puig-Butille JA, Stratigos AJ, Kodela E, Donina S, Sucker A, Hosen I, Egan KM, Barrett JH, van Doorn R, Bishop DT, Newton-Bishop J. An inherited variant in the gene coding for vitamin D-binding protein and survival from cutaneous melanoma: a BioGenoMEL study. Pigment Cell Melanoma Res 2014; 27:234-43. [PMID: 24219834 PMCID: PMC4065372 DOI: 10.1111/pcmr.12193] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [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: 08/13/2013] [Accepted: 11/11/2013] [Indexed: 01/05/2023]
Abstract
An association between low serum vitamin D levels and poorer melanoma survival has been reported. We have studied inheritance of a polymorphism of the GC gene, rs2282679, coding for the vitamin D-binding protein, which is associated with lower serum levels of vitamin D, in a meta-analysis of 3137 melanoma patients. The aim was to investigate evidence for a causal relationship between vitamin D and outcome (Mendelian randomization). The variant was not associated with reduced overall survival (OS) in the UK cohort, per-allele hazard ratio (HR) for death 1.23 (95% confidence interval (CI) 0.93, 1.64). In the smaller cohorts, HR in OS analysis was 1.07 (95% CI 0.88, 1.3) and for all cohorts combined, HR for OS was 1.09 (95% CI 0.93, 1.29). There was evidence of increased melanoma-specific deaths in the seven cohorts for which these data were available. The lack of unequivocal findings despite the large sample size illustrates the difficulties of implementing Mendelian randomization.
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Affiliation(s)
- John R Davies
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
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12
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Heidenreich B, Nagore E, Rachakonda PS, Garcia-Casado Z, Requena C, Traves V, Becker J, Soufir N, Hemminki K, Kumar R. Telomerase reverse transcriptase promoter mutations in primary cutaneous melanoma. Nat Commun 2014; 5:3401. [PMID: 24569790 DOI: 10.1038/ncomms4401] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 02/06/2014] [Indexed: 01/06/2023] Open
Abstract
We previously reported a disease segregating causal germline mutation in a melanoma family and recurrent somatic mutations in metastasized tumours from unrelated patients in the core promoter region of the telomerase reverse transcriptase (TERT) gene. Here we show that the TERT promoter mutations, besides causing an increased gene expression, associate with increased patient age, increased Breslow thickness and tumour ulceration in 287 primary melanomas. The mutations are more frequent at both intermittently and chronically sun-exposed sites than non-exposed sites and tend to co-occur with BRAF and CDKN2A alterations. The association with parameters generally connected with poor outcome, coupled with high recurrence and mechanistic relevance, raises the possibility of the eventual use of TERT promoter mutations in the disease management.
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Affiliation(s)
- Barbara Heidenreich
- 1] Division of Molecular Genetic Epidemiology, German Cancer Research Center, 69120 Heidelberg, Germany [2]
| | - Eduardo Nagore
- 1] Department of Dermatology, Instituto Valenciano de Oncologia, Valencia 46009, Spain [2] Universidad Catolica de Valencia, Valencia 46001, Spain [3]
| | | | - Zaida Garcia-Casado
- Laboratory of Molecular Biology, Instituto Valenciano de Oncologia, Valencia 46009, Spain
| | - Celia Requena
- Department of Dermatology, Instituto Valenciano de Oncologia, Valencia 46009, Spain
| | - Victor Traves
- Department of Pathology, Instituto Valenciano de Oncologia, Valencia 46009, Spain
| | - Jürgen Becker
- Department of General Dermatology, Medical University of Graz, Graz 8036, Austria
| | - Nadem Soufir
- Departement de Genetique, Hôpital Bichat-Claude Bernard, APHP, Paris 75877, France
| | - Kari Hemminki
- 1] Division of Molecular Genetic Epidemiology, German Cancer Research Center, 69120 Heidelberg, Germany [2] Center for Primary Health Care Research, Lund University, Malmö, Lund 221 00, Sweden
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, 69120 Heidelberg, Germany
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13
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Heidenreich B, Rachakonda PS, Hemminki K, Kumar R. TERT promoter mutations in cancer development. Curr Opin Genet Dev 2013; 24:30-7. [PMID: 24657534 DOI: 10.1016/j.gde.2013.11.005] [Citation(s) in RCA: 175] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 10/18/2013] [Accepted: 11/03/2013] [Indexed: 12/20/2022]
Abstract
Human telomerase reverse transcriptase (TERT) encodes a rate-limiting catalytic subunit of telomerase that maintains genomic integrity. TERT expression is mostly repressed in somatic cells with exception of proliferative cells in self-renewing tissues and cancer. Immortality associated with cancer cells has been attributed to telomerase over-expression. The precise mechanism behind the TERT activation in cancers has mostly remained unknown. The newly described germline and recurrent somatic mutations in melanoma and other cancers in the TERT promoter that create de novo E-twenty six/ternary complex factors (Ets/TCF) binding sites, provide an insight into the possible cause of tumor-specific increased TERT expression. In this review we discuss the discovery and possible implications of the TERT promoter mutations in melanoma and other cancers.
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Affiliation(s)
- Barbara Heidenreich
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - P Sivaramakrishna Rachakonda
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany.
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14
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Dutruel C, Bergmann F, Rooman I, Zucknick M, Weichenhan D, Geiselhart L, Kaffenberger T, Rachakonda PS, Bauer A, Giese N, Hong C, Xie H, Costello JF, Hoheisel J, Kumar R, Rehli M, Schirmacher P, Werner J, Plass C, Popanda O, Schmezer P. Early epigenetic downregulation of WNK2 kinase during pancreatic ductal adenocarcinoma development. Oncogene 2013; 33:3401-10. [PMID: 23912455 DOI: 10.1038/onc.2013.312] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 05/16/2013] [Accepted: 06/13/2013] [Indexed: 12/11/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is usually incurable. Contrary to genetic mechanisms involved in PDAC pathogenesis, epigenetic alterations are ill defined. Here, we determine the contribution of epigenetically silenced genes to the development of PDAC. We analyzed enriched, highly methylated DNAs from PDACs, chronic pancreatitis (CP) and normal tissues using CpG island microarrays and identified WNK2 as a prominent candidate tumor suppressor gene being downregulated early in PDAC development. WNK2 was further investigated in tissue microarrays, methylation analysis of early pancreatic intraepithelial neoplasia (PanIN), mouse models for PDAC and pancreatitis, re-expression studies after demethylation, and cell growth assays using WNK2 overexpression. Demethylation assays confirmed the link between methylation and expression. WNK2 hypermethylation was higher in tumor than in surrounding inflamed tissues and was observed in PanIN lesions as well as in a PDAC mouse model. WNK2 mRNA and protein expressions were lower in PDAC and CP compared with normal tissues both in patients and mouse models. Overexpression of WNK2 led to reduced cell growth, and WNK2 expression in tissues correlated negatively with pERK1/2 expression, a downstream target of WNK2 responsible for cell proliferation. Downregulation of WNK2 by promoter hypermethylation occurs early in PDAC pathogenesis and may support tumor cell growth via the ERK-MAPK pathway.
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Affiliation(s)
- C Dutruel
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - F Bergmann
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - I Rooman
- Cancer Research Program, Garvan Institute of Medical Research, Darlinghurst, Australia
| | - M Zucknick
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - D Weichenhan
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - L Geiselhart
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - T Kaffenberger
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - P S Rachakonda
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - A Bauer
- Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - N Giese
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - C Hong
- Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, USA
| | - H Xie
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - J F Costello
- Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, USA
| | - J Hoheisel
- Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - R Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - M Rehli
- Department of Hematology and Oncology, University Hospital Regensburg, Regensburg, Germany
| | - P Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - J Werner
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - C Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - O Popanda
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - P Schmezer
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
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15
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Rachakonda PS, Bauer AS, Xie H, Campa D, Rizzato C, Canzian F, Beghelli S, Greenhalf W, Costello E, Schanne M, Heller A, Scarpa A, Neoptolemos JP, Werner J, Büchler M, Hoheisel JD, Hemminki K, Giese N, Kumar R. Somatic mutations in exocrine pancreatic tumors: association with patient survival. PLoS One 2013; 8:e60870. [PMID: 23565280 PMCID: PMC3614935 DOI: 10.1371/journal.pone.0060870] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 03/04/2013] [Indexed: 12/12/2022] Open
Abstract
KRAS mutations are major factors involved in initiation and maintenance of pancreatic tumors. The impact of different mutations on patient survival has not been clearly defined. We screened tumors from 171 pancreatic cancer patients for mutations in KRAS and CDKN2A genes. Mutations in KRAS were detected in 134 tumors, with 131 in codon 12 and only 3 in codon 61. The GGT>GAT (G12D) was the most frequent mutation and was present in 60% (80/134). Deletions and mutations in CDKN2A were detected in 43 tumors. Analysis showed that KRAS mutations were associated with reduced patient survival in both malignant exocrine and ductal adenocarcinomas (PDAC). Patients with PDACs that had KRAS mutations showed a median survival of 17 months compared to 30 months for those without mutations (log-rank P = 0.07) with a multivariate hazard ratio (HR) of 2.19 (95%CI 1.09-4.42). The patients with G12D mutation showed a median survival of 16 months (log-rank-test P = 0.03) and an associated multivariate HR 2.42 (95%CI 1.14-2.67). Although, the association of survival in PDAC patients with CDKN2A aberrations in tumors was not statistically significant, the sub-group of patients with concomitant KRAS mutations and CDKN2A alterations in tumors were associated with a median survival of 13.5 months compared to 22 months without mutation (log-rank-test P = 0.02) and a corresponding HR of 3.07 (95%CI 1.33-7.10). Our results are indicative of an association between mutational status and survival in PDAC patients, which if confirmed in subsequent studies can have potential clinical application.
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16
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Horn S, Figl A, Rachakonda PS, Fischer C, Sucker A, Gast A, Kadel S, Moll I, Nagore E, Hemminki K, Schadendorf D, Kumar R. TERT promoter mutations in familial and sporadic melanoma. Science 2013; 339:959-61. [PMID: 23348503 DOI: 10.1126/science.1230062] [Citation(s) in RCA: 1315] [Impact Index Per Article: 119.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cutaneous melanoma occurs in both familial and sporadic forms. We investigated a melanoma-prone family through linkage analysis and high-throughput sequencing and identified a disease-segregating germline mutation in the promoter of the telomerase reverse transcriptase (TERT) gene, which encodes the catalytic subunit of telomerase. The mutation creates a new binding motif for Ets transcription factors and ternary complex factors (TCFs) near the transcription start and, in reporter gene assays, caused up to twofold increase in transcription. We then screened the TERT promoter in sporadic melanoma and observed recurrent ultraviolet signature somatic mutations in 125 of 168 (74%) of human cell lines derived from metastatic melanomas, 45 of 53 corresponding metastatic tumor tissues (85%), and 25 of 77 (33%) primary melanomas. The majority of those mutations occurred at two positions in the TERT promoter and also generated binding motifs for Ets/TCF transcription factors.
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Affiliation(s)
- Susanne Horn
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
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17
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Maccioni L, Rachakonda PS, Scherer D, Bermejo JL, Planelles D, Requena C, Hemminki K, Nagore E, Kumar R. Variants at chromosome 20 (ASIP locus) and melanoma risk. Int J Cancer 2012; 132:42-54. [PMID: 22628150 DOI: 10.1002/ijc.27648] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 05/07/2012] [Indexed: 02/04/2023]
Abstract
Agouti signaling protein (ASIP) locus on chromosome 20q11 is implicated, as shown by genome-wide association studies, in phenotype variation and melanoma risk. We genotyped 837 melanoma cases and 1,154 controls for 21 single nucleotide polymorphisms (SNPs) informative for 495 polymorphisms at the locus. Our data showed an increased risk of melanoma (odds ratio [OR] 1.27, 95% confidence interval [95% CI] 1.03-1.57) in carriers of the rs4911414 variant, located 120 kb upstream of ASIP. The main effect of rs4911414, as reported previously, was in tandem with a 10 kb adjacent polymorphism rs1015362; two constituted risk-associated haplotype/diplotype. Except for rs1015363, none of the 12 tagging SNPs, genotyped to cover 239.9 kb region with polymorphisms linked to rs4911414 and rs1015362, were associated with melanoma. Our data confirmed a previous association of melanoma risk (OR 1.82, 95% CI 1.37-2.41) with rs4911442, located in intron 5 of the nuclear receptor coactivator 6 (NCOA6) gene. The rs910871, one of the six variants, genotyped to cover NCOA6, showed an association with melanoma risk (OR 1.33, 95% CI 1.04-1.70). Both, rs4911442 and rs910871 were in moderate linkage with a, previously reported, risk-associated rs910873 polymorphism. A haplotype from the variants within NCOA6 showed an association with risk of melanoma (OR 1.49, 95% CI 1.17-1.88). Interaction between risk-associated polymorphisms and previously genotyped melanocortin receptor 1 (MC1R) variants, in our study, was not statistically significant. Nevertheless, the carriers of the variant alleles over the background of MC1R variants were at a higher risk than the carriers not enriched for MC1R variants. Our data confirmed the association of different variants at chromosome 20q11 with melanoma risk.
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Affiliation(s)
- Livia Maccioni
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
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18
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Mair C, Rachakonda PS, Korte T, Herrmann A. Influence of Salt Bridges in the Avian Influenza Virus HA on Acid-Induced Membrane Fusion and Pathogenicity. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.3291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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19
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Rizzato C, Campa D, Giese N, Werner J, Rachakonda PS, Kumar R, Schanné M, Greenhalf W, Costello E, Khaw KT, Key TJ, Siddiq A, Lorenzo-Bermejo J, Burwinkel B, Neoptolemos JP, Büchler MW, Hoheisel JD, Bauer A, Canzian F. Pancreatic cancer susceptibility loci and their role in survival. PLoS One 2011; 6:e27921. [PMID: 22125638 PMCID: PMC3220706 DOI: 10.1371/journal.pone.0027921] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 10/27/2011] [Indexed: 12/15/2022] Open
Abstract
Pancreatic cancer has one of the worst mortality rates of all cancers. Little is known about its etiology, particularly regarding inherited risk. The PanScan project, a genome-wide association study, identified several common polymorphisms affecting pancreatic cancer susceptibility. Single nucleotide polymorphisms (SNPs) in ABO, sonic hedgehog (SHH), telomerase reverse transcriptase (TERT), nuclear receptor subfamily 5, group A, member 2 (NR5A2) were found to be associated with pancreatic cancer risk. Moreover the scan identified loci on chromosomes 13q22.1 and 15q14, to which no known genes or other functional elements are mapped. We sought to replicate these observations in two additional, independent populations (from Germany and the UK), and also evaluate the possible impact of these SNPs on patient survival. We genotyped 15 SNPs in 690 cases of pancreatic ductal adenocarcinoma (PDAC) and in 1277 healthy controls. We replicated several associations between SNPs and PDAC risk. Furthermore we found that SNP rs8028529 was weakly associated with a better overall survival (OS) in both populations. We have also found that NR5A2 rs12029406_T allele was associated with a shorter survival in the German population. In conclusion, we found that rs8028529 could be, if these results are replicated, a promising marker for both risk and prognosis for this lethal disease.
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Affiliation(s)
| | - Daniele Campa
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nathalia Giese
- Clinic for General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Jens Werner
- Clinic for General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | | | - Rajiv Kumar
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - William Greenhalf
- Pancreas Biomedical Research Unit and the Liverpool Experimental Cancer Medicine Centre, National Institute for Health Research, Liverpool, United Kingdom
| | - Eithne Costello
- Pancreas Biomedical Research Unit and the Liverpool Experimental Cancer Medicine Centre, National Institute for Health Research, Liverpool, United Kingdom
| | - Kay-tee Khaw
- University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Tim J. Key
- Cancer Epidemiology Unit, University of Oxford, Oxford, United Kingdom
| | | | - Justo Lorenzo-Bermejo
- Institute of Medical Biometry and Informatics, University Hospital Heidelberg, Heidelberg, Germany
| | - Barbara Burwinkel
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany
| | - John P. Neoptolemos
- Pancreas Biomedical Research Unit and the Liverpool Experimental Cancer Medicine Centre, National Institute for Health Research, Liverpool, United Kingdom
| | - Markus W. Büchler
- Clinic for General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | | | - Andrea Bauer
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Federico Canzian
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- * E-mail:
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20
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Ott K, Rachakonda PS, Panzram B, Keller G, Lordick F, Becker K, Langer R, Buechler M, Hemminki K, Kumar R. DNA repair gene and MTHFR gene polymorphisms as prognostic markers in locally advanced adenocarcinoma of the esophagus or stomach treated with cisplatin and 5-fluorouracil-based neoadjuvant chemotherapy. Ann Surg Oncol 2011; 18:2688-98. [PMID: 21347786 DOI: 10.1245/s10434-011-1601-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Indexed: 01/08/2023]
Abstract
BACKGROUND DNA repair plays an important role in chemoresistance to platinum-based therapy, and therefore polymorphisms in the genes may modulate therapeutic response. We assessed 12 polymorphisms in 7 DNA repair genes and 2 polymorphisms in the MTHFR gene for association with disease response and prognosis. METHODS A total of 258 patients included in the study had adenocarcinoma of the esophagus (n = 114) or gastric cancer (n = 144), at stage cT3/4 and cM0, and had been treated with platinum-based neoadjuvant polychemotherapy. The patients were genotyped for polymorphisms in the XPC, XPD, XPG, APEX, XRCC1, NBS1, XRCC3, and MTHFR genes by the allelic discrimination method and the data correlated with various clinical parameters. RESULTS None of the investigated polymorphisms was associated with histopathological response. XRCC3 polymorphisms rs861539 (P = 0.02) and rs861530 (P = 0.05) showed association with clinical response in gastric cancer. The variants in XRCC3 (rs861539, P = 0.05; rs1799794, P = 0.03) and MTHFR (rs1801131, P = 0.02) were associated with survival in esophageal and gastric cancer, respectively. In R0 resected patients, XRCC3 variants (rs861539, P = 0.04; rs861530, P = 0.02) in esophageal cancer, and XRCC3 (rs1799794, P = 0.02) and MTHFR (rs1801131, P = 0.005) in gastric cancer predicted survival. Cox regression revealed ypT category (P = 0.001) and lymphatic vessel invasion (P = 0.03) to be independent prognostic factors for esophageal cancer, and histopathological response (P = 0.01), MTHFR variant (rs1801131, P = 0.002), and ypN category (P = 0.02) to be prognostic factors for gastric cancer. CONCLUSION In gastric cancer patients, MTHFR variant (rs1801131) could serve as a potential prognostic marker. In esophageal cancer patients, none of the polymorphisms studied had conclusive results in multivariate analysis, although XRCC3 variant (rs861539) showed an effect on survival in Kaplan-Meier univariate analysis.
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Affiliation(s)
- Katja Ott
- Department of Surgery, University Hospital Heidelberg, Heidelberg, Germany
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Manning K, Rachakonda PS, Rai MF, Schmidt MFG. Co-expression of insulin-like growth factor-1 and interleukin-4 in an in vitro inflammatory model. Cytokine 2010; 50:297-305. [PMID: 20188584 DOI: 10.1016/j.cyto.2010.01.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Revised: 11/16/2009] [Accepted: 01/26/2010] [Indexed: 10/19/2022]
Abstract
The ailment osteoarthritis (OA) has two aspects - inflammation and cartilage degradation - where combined transgene expression may offer an effective gene therapy. Our present study focuses on the co-expression of interleukin-4 (IL-4) and insulin-like-growth factor-1 (IGF-1), which specifically target inflammation and cartilage repair, respectively. In this study, we analyze the expression of IGF-1 and IL-4 from a single plasmid vector, where each gene is expressed through an independent promoter and enhancer sequence. Regenerative and anti-inflammatory effects of IGF-1 alone and of both IGF-1 and IL-4 were analyzed in an in vitro chondrocyte inflammatory model. Co-expression of both transgenes in primary chondrocytes was ascertained by immunoassays. Following stimulation with IL-1beta and TNFalpha, pro-inflammatory mediators as well as IGF-binding proteins were down-regulated more effectively in the presence of both genes to levels comparable to the non-stimulated control. Further, cartilage regeneration proteins type II collagen and proteoglycans were up-regulated in stimulated cells transfected with IGF-1 alone and in combination with IL-4. The co-expression of IGF-1 and IL-4 shows that both transgenes complement each other by effectively triggering cartilage regeneration and reducing inflammation. Use of combinatorial transgene expression offers a promising avenue in the area of gene therapy in OA.
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Affiliation(s)
- Kizzie Manning
- Institute of Immunology and Molecular Biology, Freie Universität Berlin, Philippstrasse 13, 10115 Berlin, Germany
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Rai MF, Rachakonda PS, Manning K, Palissa C, Sittinger M, Ringe J, Schmidt MFG. Molecular and phenotypic modulations of primary and immortalized canine chondrocytes in different culture systems. Res Vet Sci 2009; 87:399-407. [PMID: 19439332 DOI: 10.1016/j.rvsc.2009.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Revised: 03/24/2009] [Accepted: 04/14/2009] [Indexed: 11/24/2022]
Abstract
This study was conducted to determine physiological and functional features of primary and immortalized canine chondrocytes. Chondrocytes were immortalized by introducing the catalytic component of human telomerase namely human telomerase reverse transcriptase (hTERT). Primary chondrocytes lost their characteristic phenotype and growth properties whereas the immortalized cells remained polygonal with rapid growth rate. The expression of chondrocyte-specific markers decreased many-fold whereas that of chondrocyte-non-specific gene increased in primary chondrocytes. The immortalized cells did not express chondrocyte-specific genes in monolayers. Both primary and immortalized cells were encapsulated in alginate microspheres to construct three-dimensional (3D) culture system. As the primary chondrocytes, also the telomerase-transfected cells adopted a chondrocyte-specific gene expression pattern in alginate culture. Thus, the expression of telomerase represents possibility to expand chondrocytes without limitation while maintaining the chondrocyte-specific phenotype in 3D cultures. Use of such cells provides a standardized tool for testing different tissue engineering applications in canine model.
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Affiliation(s)
- Muhammad Farooq Rai
- Institute of Immunology and Molecular Biology, Faculty of Veterinary Medicine, Freie Universität, House 18, Philippstrasse 13, D-10115 Berlin, Germany
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Huang Q, Korte T, Rachakonda PS, Knapp EW, Herrmann A. Energetics of the loop-to-helix transition leading to the coiled-coil structure of influenza virus hemagglutinin HA2 subunits. Proteins 2009; 74:291-303. [DOI: 10.1002/prot.22157] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Rachakonda PS, Rai MF, Manning K, Schmidt MF. Expression of canine interleukin-4 in canine chondrocytes inhibits inflammatory cascade through STAT6. Cytokine 2008; 44:179-84. [DOI: 10.1016/j.cyto.2008.07.470] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2008] [Revised: 06/17/2008] [Accepted: 07/30/2008] [Indexed: 12/28/2022]
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Rachakonda PS, Rai MF, Schmidt MFG. Application of inflammation‐responsive promoter for an in vitro arthritis model. ACTA ACUST UNITED AC 2008; 58:2088-97. [DOI: 10.1002/art.23598] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Rachakonda PS, Veit M, Korte T, Ludwig K, Böttcher C, Huang Q, Schmidt MFG, Herrmann A. The relevance of salt bridges for the stability of the influenza virus hemagglutinin. FASEB J 2007; 21:995-1002. [PMID: 17218542 DOI: 10.1096/fj.06-7052hyp] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Hemagglutinin (HA) of influenza virus undergoes an irreversible conformational change at acidic pH, mediating viral fusion with the host endosomal membrane. To unravel the molecular basis of the pH-dependent stability of HA, we demonstrate by mutagenesis of the prototype HA of virus strain X31 (H3 subtype) that salt bridges, especially a tetrad salt bridge within the monomers, are crucial for folding and stability of the trimeric ectodomain. This complex (tetrad) salt bridge is highly conserved among influenza virus subtypes. Introducing additional sites of electrostatic attraction between monomers in the distal region enhanced the stability of ectodomain at low pH mimicking the natural variant H2 subtype. We propose that distinct salt bridges in the distal domain may contribute to the enhanced stability of HA of natural virus variants. This hypothesis may provide clues to understanding adaptations of virus strains (for example, avian influenza viruses) in order to preserve stability of the protein in the host-specific environment.
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Affiliation(s)
- P Sivaramakrishna Rachakonda
- Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, Institut für Biologie/Biophysik, Invalidenstr. 43, D-10115 Berlin, Germany
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Korte T, Ludwig K, Huang Q, Rachakonda PS, Herrmann A. Conformational change of influenza virus hemagglutinin is sensitive to ionic concentration. Eur Biophys J 2007; 36:327-35. [PMID: 17211621 DOI: 10.1007/s00249-006-0116-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2006] [Revised: 11/03/2006] [Accepted: 11/17/2006] [Indexed: 11/29/2022]
Abstract
The homotrimeric spike glycoprotein hemagglutinin (HA) of influenza virus undergoes a low pH-mediated conformational change which mediates the fusion of the viral envelope with the target membrane. Previous approaches predict that the interplay of electrostatic interactions between and within HA subunits, HA 1 and HA2, are essential for the metastability of the HA ectodomain. Here, we show that suspension media of low ionic concentration promote fusion of fluorescent labelled influenza virus X31 with erythrocyte ghosts and with ganglioside containing liposomes. By measuring the low pH mediated inactivation of the fusion competence of HA and the Proteinase K sensitivity of low pH incubated HA we show that the conformational change is promoted by low ionic concentration. We surmise that electrostatic attraction within the HA ectodomain is weakened by lowering the ionic concentration facilitating the conformational change at low pH.
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Affiliation(s)
- Thomas Korte
- Institute of Biology, Molecular Biophysics, Humboldt University, Berlin 10115, Germany
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