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Montero‐Conde C, Graña‐Castro O, Martín‐Serrano G, Martínez‐Montes ÁM, Zarzuela E, Muñoz J, Torres‐Perez R, Pita G, Cordero‐Barreal A, Leandro‐García LJ, Letón R, López de Silanes I, Guadalix S, Pérez‐Barrios A, Hawkins F, Guerrero‐Álvarez A, Álvarez‐Escolá C, Regojo‐Zapata RM, Calsina B, Remacha L, Roldán‐Romero JM, Santos M, Lanillos J, Jordá M, Riesco‐Eizaguirre G, Zafon C, González‐Neira A, Blasco MA, Al‐Shahrour F, Rodríguez‐Antona C, Cascón A, Robledo M. Hsa‐miR‐139‐5p is a prognostic thyroid cancer marker involved in HNRNPF‐mediated alternative splicing. Int J Cancer 2019; 146:521-530. [DOI: 10.1002/ijc.32622] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/12/2019] [Accepted: 07/30/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Cristina Montero‐Conde
- Hereditary Endocrine Cancer GroupSpanish National Cancer Research Centre (CNIO) Madrid Spain
| | | | | | | | - Eduardo Zarzuela
- Proteomics Core Unit and Proteored‐ISCIIISpanish National Cancer Research Centre (CNIO) Madrid Spain
| | - Javier Muñoz
- Proteomics Core Unit and Proteored‐ISCIIISpanish National Cancer Research Centre (CNIO) Madrid Spain
| | - Rafael Torres‐Perez
- Hereditary Endocrine Cancer GroupSpanish National Cancer Research Centre (CNIO) Madrid Spain
| | - Guillermo Pita
- CEGEN UnitSpanish National Cancer Research Centre (CNIO) Madrid Spain
| | - Alfonso Cordero‐Barreal
- Hereditary Endocrine Cancer GroupSpanish National Cancer Research Centre (CNIO) Madrid Spain
| | - Luis J. Leandro‐García
- Hereditary Endocrine Cancer GroupSpanish National Cancer Research Centre (CNIO) Madrid Spain
| | - Rocío Letón
- Hereditary Endocrine Cancer GroupSpanish National Cancer Research Centre (CNIO) Madrid Spain
| | | | - Sonsoles Guadalix
- Endocrinology and Nutrition DepartmentHospital Universitario 12 de Octubre Madrid Spain
| | | | - Federico Hawkins
- Endocrinology and Nutrition DepartmentHospital Universitario 12 de Octubre Madrid Spain
| | | | | | | | - Bruna Calsina
- Hereditary Endocrine Cancer GroupSpanish National Cancer Research Centre (CNIO) Madrid Spain
| | - Laura Remacha
- Hereditary Endocrine Cancer GroupSpanish National Cancer Research Centre (CNIO) Madrid Spain
| | - Juan M. Roldán‐Romero
- Hereditary Endocrine Cancer GroupSpanish National Cancer Research Centre (CNIO) Madrid Spain
| | - María Santos
- Hereditary Endocrine Cancer GroupSpanish National Cancer Research Centre (CNIO) Madrid Spain
| | - Javier Lanillos
- Hereditary Endocrine Cancer GroupSpanish National Cancer Research Centre (CNIO) Madrid Spain
| | - Mireia Jordá
- Program for Predictive and Personalized Medicine of CancerGermans Trias i Pujol Research Institute Barcelona Spain
| | - Garcilaso Riesco‐Eizaguirre
- Endocrinology and Nutrition DepartmentHospital Universitario de Móstoles Madrid Spain
- Biomedical Research Networking Centre in Oncology (CIBERONC)Institute of Health Carlos III Madrid Spain
- Universidad Francisco de Vitoria Madrid Spain
| | - Carles Zafon
- Diabetes and Metabolism Research Unit and Endocrinology DepartmentHospital Universitari Vall d'Hebron Barcelona Spain
- Biomedical Research Networking Centre on Diabetes and Associated Metabolic Diseases (CIBERDEM)Institute of Health Carlos III Madrid Spain
| | | | - Maria A. Blasco
- Telomeres and Telomerase GroupSpanish National Cancer Research Centre (CNIO) Madrid Spain
| | - Fátima Al‐Shahrour
- Bioinformatics UnitSpanish National Cancer Research Centre (CNIO) Madrid Spain
| | | | - Alberto Cascón
- Hereditary Endocrine Cancer GroupSpanish National Cancer Research Centre (CNIO) Madrid Spain
| | - Mercedes Robledo
- Hereditary Endocrine Cancer GroupSpanish National Cancer Research Centre (CNIO) Madrid Spain
- Biomedical Research Networking Centre on Rare Diseases (CIBERER)Institute of Health Carlos III Madrid Spain
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Calsina B, Castro-Vega LJ, Torres-Pérez R, Inglada-Pérez L, Currás-Freixes M, Roldán-Romero JM, Mancikova V, Letón R, Remacha L, Santos M, Burnichon N, Lussey-Lepoutre C, Rapizzi E, Graña O, Álvarez-Escolá C, de Cubas AA, Lanillos J, Cordero-Barreal A, Martínez-Montes ÁM, Bellucci A, Amar L, Fernandes-Rosa FL, Calatayud M, Aller J, Lamas C, Sastre-Marcos J, Canu L, Korpershoek E, Timmers HJ, Lenders JWM, Beuschlein F, Fassnacht-Capeller M, Eisenhofer G, Mannelli M, Al-Shahrour F, Favier J, Rodríguez-Antona C, Cascón A, Montero-Conde C, Gimenez-Roqueplo AP, Robledo M. Integrative multi-omics analysis identifies a prognostic miRNA signature and a targetable miR-21-3p/TSC2/mTOR axis in metastatic pheochromocytoma/paraganglioma. Am J Cancer Res 2019; 9:4946-4958. [PMID: 31410193 PMCID: PMC6691382 DOI: 10.7150/thno.35458] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 05/09/2019] [Indexed: 12/14/2022] Open
Abstract
Rationale: Pheochromocytomas and paragangliomas (PPGLs) are rare neuroendocrine tumors that present variable outcomes. To date, no effective therapies or reliable prognostic markers are available for patients who develop metastatic PPGL (mPPGL). Our aim was to discover robust prognostic markers validated through in vitro models, and define specific therapeutic options according to tumor genomic features. Methods: We analyzed three PPGL miRNome datasets (n=443), validated candidate markers and assessed them in serum samples (n=36) to find a metastatic miRNA signature. An integrative study of miRNome, transcriptome and proteome was performed to find miRNA targets, which were further characterized in vitro. Results: A signature of six miRNAs (miR-21-3p, miR-183-5p, miR-182-5p, miR-96-5p, miR-551b-3p, and miR-202-5p) was associated with metastatic risk and time to progression. A higher expression of five of these miRNAs was also detected in PPGL patients' liquid biopsies compared with controls. The combined expression of miR-21-3p/miR-183-5p showed the best power to predict metastasis (AUC=0.804, P=4.67·10-18), and was found associated in vitro with pro-metastatic features, such as neuroendocrine-mesenchymal transition phenotype, and increased cell migration rate. A pan-cancer multi-omic integrative study correlated miR-21-3p levels with TSC2 expression, mTOR pathway activation, and a predictive signature for mTOR inhibitor-sensitivity in PPGLs and other cancers. Likewise, we demonstrated in vitro a TSC2 repression and an enhanced rapamycin sensitivity upon miR-21-3p expression. Conclusions: Our findings support the assessment of miR-21-3p/miR-183-5p, in tumors and liquid biopsies, as biomarkers for risk stratification to improve the PPGL patients' management. We propose miR-21-3p to select mPPGL patients who may benefit from mTOR inhibitors.
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Remacha L, Pirman D, Mahoney CE, Coloma J, Calsina B, Currás-Freixes M, Letón R, Torres-Pérez R, Richter S, Pita G, Herráez B, Cianchetta G, Honrado E, Maestre L, Urioste M, Aller J, García-Uriarte Ó, Gálvez MÁ, Luque RM, Lahera M, Moreno-Rengel C, Eisenhofer G, Montero-Conde C, Rodríguez-Antona C, Llorca Ó, Smolen GA, Robledo M, Cascón A. Recurrent Germline DLST Mutations in Individuals with Multiple Pheochromocytomas and Paragangliomas. Am J Hum Genet 2019; 104:1008-1010. [PMID: 31051110 DOI: 10.1016/j.ajhg.2019.04.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Remacha L, Pirman D, Mahoney CE, Coloma J, Calsina B, Currás-Freixes M, Letón R, Torres-Pérez R, Richter S, Pita G, Herráez B, Cianchetta G, Honrado E, Maestre L, Urioste M, Aller J, García-Uriarte Ó, Gálvez MÁ, Luque RM, Lahera M, Moreno-Rengel C, Eisenhofer G, Montero-Conde C, Rodríguez-Antona C, Llorca Ó, Smolen GA, Robledo M, Cascón A. Recurrent Germline DLST Mutations in Individuals with Multiple Pheochromocytomas and Paragangliomas. Am J Hum Genet 2019; 104:651-664. [PMID: 30929736 PMCID: PMC6451733 DOI: 10.1016/j.ajhg.2019.02.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [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: 07/26/2018] [Accepted: 02/14/2019] [Indexed: 12/21/2022] Open
Abstract
Pheochromocytomas and paragangliomas (PPGLs) provide some of the clearest genetic evidence for the critical role of metabolism in the tumorigenesis process. Approximately 40% of PPGLs are caused by driver germline mutations in 16 known susceptibility genes, and approximately half of these genes encode members of the tricarboxylic acid (TCA) cycle. Taking as a starting point the involvement of the TCA cycle in PPGL development, we aimed to identify unreported mutations that occurred in genes involved in this key metabolic pathway and that could explain the phenotypes of additional individuals who lack mutations in known susceptibility genes. To accomplish this, we applied a targeted sequencing of 37 TCA-cycle-related genes to DNA from 104 PPGL-affected individuals with no mutations in the major known predisposing genes. We also performed omics-based analyses, TCA-related metabolite determination, and 13C5-glutamate labeling assays. We identified five germline variants affecting DLST in eight unrelated individuals (∼7%); all except one were diagnosed with multiple PPGLs. A recurrent variant, c.1121G>A (p.Gly374Glu), found in four of the eight individuals triggered accumulation of 2-hydroxyglutarate, both in tumors and in a heterologous cell-based assay designed to functionally evaluate DLST variants. p.Gly374Glu-DLST tumors exhibited loss of heterozygosity, and their methylation and expression profiles are similar to those of EPAS1-mutated PPGLs; this similarity suggests a link between DLST disruption and pseudohypoxia. Moreover, we found positive DLST immunostaining exclusively in tumors carrying TCA-cycle or EPAS1 mutations. In summary, this study reveals DLST as a PPGL-susceptibility gene and further strengthens the relevance of the TCA cycle in PPGL development.
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Affiliation(s)
- Laura Remacha
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre, Madrid, Madrid 28029, Spain
| | - David Pirman
- Agios Pharmaceuticals, 88 Sidney Street, Cambridge, MA 02139, USA
| | | | - Javier Coloma
- Structural Biology Programme, Spanish National Cancer Research Centre, Madrid, Madrid 28029, Spain
| | - Bruna Calsina
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre, Madrid, Madrid 28029, Spain
| | - Maria Currás-Freixes
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre, Madrid, Madrid 28029, Spain
| | - Rocío Letón
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre, Madrid, Madrid 28029, Spain
| | - Rafael Torres-Pérez
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre, Madrid, Madrid 28029, Spain
| | - Susan Richter
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Freistaat Sachsen 01069, Germany
| | - Guillermo Pita
- Human Genotyping Unit-CeGen, Human Cancer Genetics Programme, Spanish National Cancer Research Centre, Madrid, Madrid 28029, Spain
| | - Belén Herráez
- Human Genotyping Unit-CeGen, Human Cancer Genetics Programme, Spanish National Cancer Research Centre, Madrid, Madrid 28029, Spain
| | | | - Emiliano Honrado
- Anatomical Pathology Service, Hospital of León, León, Castilla y León 24071, Spain
| | - Lorena Maestre
- Monoclonal Antibodies Unit, Biotechnology Programme, Spanish National Cancer Research Centre, Madrid, Madrid 28029, Spain
| | - Miguel Urioste
- Familial Cancer Clinical Unit, Spanish National Cancer Research Centre, Madrid, Madrid 28029, Spain
| | - Javier Aller
- Department of Endocrinology, University Hospital Puerta de Hierro, Majadahonda, Madrid 28222, Spain
| | - Óscar García-Uriarte
- Nephrology Department, University Hospital of Araba, Vitoria, País Vasco 01009, Spain
| | - María Ángeles Gálvez
- Service of Endocrinology and Nutrition, University Hospital Reina Sofía, Córdoba, Andalucía 14004, Spain; Maimónides Institute of Biomedical Research of Cordoba, Córdoba, Andalucía 14004, Spain
| | - Raúl M Luque
- Hormones and Cancer Group, Maimónides Institute of Biomedical Research of Córdoba, Córdoba, Andalucía 14004, Spain
| | - Marcos Lahera
- Endocrinology and Nutrition Department, La Princesa University Hospital, Madrid, Madrid 28006, Spain
| | - Cristina Moreno-Rengel
- Department of Endocrinology and Nutrition, University Hospital of Basurto, Bilbao 48013, Spain
| | - Graeme Eisenhofer
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Freistaat Sachsen 01069, Germany
| | - Cristina Montero-Conde
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre, Madrid, Madrid 28029, Spain
| | - Cristina Rodríguez-Antona
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre, Madrid, Madrid 28029, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Madrid 28029, Spain
| | - Óscar Llorca
- Structural Biology Programme, Spanish National Cancer Research Centre, Madrid, Madrid 28029, Spain
| | | | - Mercedes Robledo
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre, Madrid, Madrid 28029, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Madrid 28029, Spain
| | - Alberto Cascón
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre, Madrid, Madrid 28029, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Madrid 28029, Spain.
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5
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Sánchez-Barroso L, Apellaniz-Ruiz M, Gutiérrez-Gutiérrez G, Santos M, Roldán-Romero JM, Curras M, Remacha L, Calsina B, Calvo I, Sereno M, Merino M, García-Donas J, Castelo B, Guerra E, Letón R, Montero-Conde C, Cascón A, Inglada-Pérez L, Robledo M, Rodríguez-Antona C. Concomitant Medications and Risk of Chemotherapy-Induced Peripheral Neuropathy. Oncologist 2018; 24:e784-e792. [PMID: 30470691 DOI: 10.1634/theoncologist.2018-0418] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 07/17/2018] [Accepted: 10/16/2018] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Peripheral neuropathy is the dose-limiting toxicity of many oncology drugs, including paclitaxel. There is large interindividual variability in the neuropathy, and several risk factors have been proposed; however, many have not been replicated. Here we present a comprehensive study aimed at identifying treatment and physiopathology-related paclitaxel-induced neuropathy risk factors in a large cohort of well-characterized patients. PATIENTS AND METHODS Analyses included 503 patients with breast or ovarian cancer who received paclitaxel treatment. Paclitaxel dose modifications caused by the neuropathy were extracted from medical records and patients self-reported neuropathy symptoms were collected. Multivariate logistic regression analyses were performed to identify concomitant medications and comorbidities associated with paclitaxel-induced neuropathy. RESULTS Older patients had higher neuropathy: for each increase of 1 year of age, the risk of dose modifications and grade 3 neuropathy increased 4% and 5%, respectively. Cardiovascular drugs increased the risk of paclitaxel dose reductions (odds ratio [OR], 2.51; p = .006), with a stronger association for beta-adrenergic antagonists. The total number of concomitant medications also showed an association with dose modifications (OR, 1.25; p = .012 for each concomitant drug increase). A dose modification predictive model that included the new identified factors gave an area under the curve of 0.74 (p = 1.07 × 10-10). Preexisting nerve compression syndromes seemed to increase neuropathy risk. CONCLUSION Baseline characteristics of the patients, including age and concomitant medications, could be used to identify individuals at high risk of neuropathy, personalizing chemotherapy treatment and reducing the risk of severe neuropathy. IMPLICATIONS FOR PRACTICE Peripheral neuropathy is a common adverse effect of many cancer drugs, including chemotherapeutics, targeted therapies, and immune checkpoint inhibitors. About 40% of survivors of cancer have functional deficits caused by this toxicity, some of them irreversible. Currently, there are no effective treatments to prevent or treat this neuropathy. This study, performed in a large cohort of well-characterized patients homogenously treated with paclitaxel, identified concomitant medications, comorbidities, and demographic factors associated with peripheral neuropathy. These factors could serve to identify patients at high risk of severe neuropathy for whom alternative non-neurotoxic alternatives may be considered.
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Affiliation(s)
- Lara Sánchez-Barroso
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Madrid, Spain
| | - Maria Apellaniz-Ruiz
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | - María Santos
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Juan M Roldán-Romero
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Maria Curras
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Laura Remacha
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Bruna Calsina
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Isabel Calvo
- Medical Oncology Department, Hospital Montepríncipe, Madrid, Spain
- Medical Oncology Department, Centro Integral Oncológico Clara Campal, Madrid, Spain
| | - María Sereno
- Medical Oncology Department, Hospital Universitario Infanta Sofía, Madrid, Spain
| | - María Merino
- Medical Oncology Department, Hospital Universitario Infanta Sofía, Madrid, Spain
| | - Jesús García-Donas
- Genitourinary Tumors Programme, Centro Integral Oncológico Clara Campal, Madrid, Spain
| | - Beatriz Castelo
- Medical Oncology Department, Hospital Universitario La Paz, Madrid, Spain
| | - Eva Guerra
- Medical Oncology Department, Hospital Universitario Ramon y Cajal, Madrid, Spain
| | - Rocio Letón
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Cristina Montero-Conde
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Alberto Cascón
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- ISCIII Center for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Lucía Inglada-Pérez
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- ISCIII Center for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Mercedes Robledo
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- ISCIII Center for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Cristina Rodríguez-Antona
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- ISCIII Center for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain
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6
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Remacha L, Comino-Méndez I, Richter S, Contreras L, Currás-Freixes M, Pita G, Letón R, Galarreta A, Torres-Pérez R, Honrado E, Jiménez S, Maestre L, Moran S, Esteller M, Satrústegui J, Eisenhofer G, Robledo M, Cascón A. Targeted Exome Sequencing of Krebs Cycle Genes Reveals Candidate Cancer-Predisposing Mutations in Pheochromocytomas and Paragangliomas. Clin Cancer Res 2017; 23:6315-6324. [PMID: 28720665 DOI: 10.1158/1078-0432.ccr-16-2250] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 05/22/2017] [Accepted: 07/12/2017] [Indexed: 11/16/2022]
Abstract
Purpose: Mutations in Krebs cycle genes are frequently found in patients with pheochromocytomas/paragangliomas. Disruption of SDH, FH or MDH2 enzymatic activities lead to accumulation of specific metabolites, which give rise to epigenetic changes in the genome that cause a characteristic hypermethylated phenotype. Tumors showing this phenotype, but no alterations in the known predisposing genes, could harbor mutations in other Krebs cycle genes.Experimental Design: We used downregulation and methylation of RBP1, as a marker of a hypermethylation phenotype, to select eleven pheochromocytomas and paragangliomas for targeted exome sequencing of a panel of Krebs cycle-related genes. Methylation profiling, metabolite assessment and additional analyses were also performed in selected cases.Results: One of the 11 tumors was found to carry a known cancer-predisposing somatic mutation in IDH1 A variant in GOT2, c.357A>T, found in a patient with multiple tumors, was associated with higher tumor mRNA and protein expression levels, increased GOT2 enzymatic activity in lymphoblastic cells, and altered metabolite ratios both in tumors and in GOT2 knockdown HeLa cells transfected with the variant. Array methylation-based analysis uncovered a somatic epigenetic mutation in SDHC in a patient with multiple pheochromocytomas and a gastrointestinal stromal tumor. Finally, a truncating germline IDH3B mutation was found in a patient with a single paraganglioma showing an altered α-ketoglutarate/isocitrate ratio.Conclusions: This study further attests to the relevance of the Krebs cycle in the development of PCC and PGL, and points to a potential role of other metabolic enzymes involved in metabolite exchange between mitochondria and cytosol. Clin Cancer Res; 23(20); 6315-24. ©2017 AACR.
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Affiliation(s)
- Laura Remacha
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Iñaki Comino-Méndez
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Susan Richter
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Laura Contreras
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma de Madrid and Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | - María Currás-Freixes
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Guillermo Pita
- Human Genotyping Unit-CeGen, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Rocío Letón
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Antonio Galarreta
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Rafael Torres-Pérez
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | - Scherezade Jiménez
- Monoclonal Antibodies Unit, Biotechnology Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Lorena Maestre
- Monoclonal Antibodies Unit, Biotechnology Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Sebastian Moran
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Spain
| | - Jorgina Satrústegui
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma de Madrid and Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | - Graeme Eisenhofer
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Mercedes Robledo
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Alberto Cascón
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
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7
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Currás-Freixes M, Piñeiro-Yañez E, Montero-Conde C, Apellániz-Ruiz M, Calsina B, Mancikova V, Remacha L, Richter S, Ercolino T, Rogowski-Lehmann N, Deutschbein T, Calatayud M, Guadalix S, Álvarez-Escolá C, Lamas C, Aller J, Sastre-Marcos J, Lázaro C, Galofré JC, Patiño-García A, Meoro-Avilés A, Balmaña-Gelpi J, De Miguel-Novoa P, Balbín M, Matías-Guiu X, Letón R, Inglada-Pérez L, Torres-Pérez R, Roldán-Romero JM, Rodríguez-Antona C, Fliedner SMJ, Opocher G, Pacak K, Korpershoek E, de Krijger RR, Vroonen L, Mannelli M, Fassnacht M, Beuschlein F, Eisenhofer G, Cascón A, Al-Shahrour F, Robledo M. PheoSeq: A Targeted Next-Generation Sequencing Assay for Pheochromocytoma and Paraganglioma Diagnostics. J Mol Diagn 2017; 19:575-588. [PMID: 28552549 DOI: 10.1016/j.jmoldx.2017.04.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [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: 02/10/2017] [Accepted: 04/07/2017] [Indexed: 12/26/2022] Open
Abstract
Genetic diagnosis is recommended for all pheochromocytoma and paraganglioma (PPGL) cases, as driver mutations are identified in approximately 80% of the cases. As the list of related genes expands, genetic diagnosis becomes more time-consuming, and targeted next-generation sequencing (NGS) has emerged as a cost-effective tool. This study aimed to optimize targeted NGS in PPGL genetic diagnostics. A workflow based on two customized targeted NGS assays was validated to study the 18 main PPGL genes in germline and frozen tumor DNA, with one of them specifically directed toward formalin-fixed paraffin-embedded tissue. The series involved 453 unrelated PPGL patients, of whom 30 had known mutations and were used as controls. Partial screening using Sanger had been performed in 275 patients. NGS results were complemented with the study of gross deletions. NGS assay showed a sensitivity ≥99.4%, regardless of DNA source. We identified 45 variants of unknown significance and 89 pathogenic mutations, the latter being germline in 29 (7.2%) and somatic in 58 (31.7%) of the 183 tumors studied. In 37 patients previously studied by Sanger sequencing, the causal mutation could be identified. We demonstrated that both assays are an efficient and accurate alternative to conventional sequencing. Their application facilitates the study of minor PPGL genes, and enables genetic diagnoses in patients with incongruent or missing clinical data, who would otherwise be missed.
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Affiliation(s)
- Maria Currás-Freixes
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - Elena Piñeiro-Yañez
- Translational Bioinformatics Unit, Spanish National Cancer Research Centre, Madrid, Spain
| | - Cristina Montero-Conde
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - María Apellániz-Ruiz
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - Bruna Calsina
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - Veronika Mancikova
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - Laura Remacha
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - Susan Richter
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Medical Faculty Carl Gustav Carus, Technische Universitat Dresden, Dresden, Germany
| | - Tonino Ercolino
- Department of Experimental and Clinical Biomedical Sciences Mario Serio, University of Florence and Istituto Toscano Tumori, Florence, Italy
| | - Natalie Rogowski-Lehmann
- Department of Internal Medicine IV Campus Innenstadt, University-Hospital, Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Timo Deutschbein
- Department of Internal Medicine I, Division of Endocrinology and Diabetes, University Hospital, University of Würzburg, Würzburg, Germany
| | - María Calatayud
- Department of Endocrinology and Nutrition Service, University Hospital 12 de Octubre, Madrid, Spain
| | - Sonsoles Guadalix
- Department of Endocrinology and Nutrition Service, University Hospital 12 de Octubre, Madrid, Spain
| | | | - Cristina Lamas
- Department of Endocrinology, Albacete University Hospital Complex, Albacete, Spain
| | - Javier Aller
- Department of Endocrinology, University Hospital Puerta de Hierro, Madrid, Spain
| | - Julia Sastre-Marcos
- Department of Endocrinology, Virgen de la Salud Hospital-Toledo Hospital Complex, Toledo, Spain
| | - Conxi Lázaro
- Molecular Diagnostics Units of the Hereditary Cancer Program at the Catalan Institute of Oncology, Barcelona, Spain
| | - Juan C Galofré
- Department of Endocrinology, University of Navarra Clinic, Navarra, Spain
| | - Ana Patiño-García
- Department of Pediatrics and Clinical Genetics Unit, University of Navarra Clinic, Navarra, Spain
| | | | - Judith Balmaña-Gelpi
- High Risk and Cancer Prevention Group, Medical Oncology Department, Vall d'Hebron University Hospital and Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Milagros Balbín
- Department of Molecular Oncology, Central University Hospital of Asturias and University Institute of Oncology of Asturias, University of Oviedo, Oviedo, Spain
| | - Xavier Matías-Guiu
- Department of Endocrinology and Nutrition, University Hospital Arnau de Vilanova, IRBLLEIDA, Lleida, Spain; Department of Pathology, Hospital Universitari de Bellvitge, IDIBELL, Barcelona, Spain
| | - Rocío Letón
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - Lucía Inglada-Pérez
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre, Madrid, Spain; Biomedical Research Networking Center on Rare Diseases (CIBERER), Madrid, Spain
| | - Rafael Torres-Pérez
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - Juan M Roldán-Romero
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - Cristina Rodríguez-Antona
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre, Madrid, Spain; Biomedical Research Networking Center on Rare Diseases (CIBERER), Madrid, Spain
| | - Stephanie M J Fliedner
- 1st Department of Medicine, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Giuseppe Opocher
- Department of Endocrinology, Department of Medical and Surgical Sciences University of Padova, Padova, Italy
| | - Karel Pacak
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland
| | - Esther Korpershoek
- Department of Pathology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Ronald R de Krijger
- Department of Pathology, Erasmus University Medical Center, Rotterdam, the Netherlands; Department of Pathology, Reinier de Graaf Hospital, Delft, the Netherlands
| | - Laurent Vroonen
- Department of Endocrinology, Centre Hospitalier Universitaire de Liège, Liège, Belgium
| | - Massimo Mannelli
- Department of Experimental and Clinical Biomedical Sciences Mario Serio, University of Florence and Istituto Toscano Tumori, Florence, Italy
| | - Martin Fassnacht
- Department of Internal Medicine I, Division of Endocrinology and Diabetes, University Hospital, University of Würzburg, Würzburg, Germany
| | - Felix Beuschlein
- Department of Internal Medicine IV Campus Innenstadt, University-Hospital, Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Graeme Eisenhofer
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Medical Faculty Carl Gustav Carus, Technische Universitat Dresden, Dresden, Germany; Department of Medicine III, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Alberto Cascón
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre, Madrid, Spain; Biomedical Research Networking Center on Rare Diseases (CIBERER), Madrid, Spain
| | - Fátima Al-Shahrour
- Translational Bioinformatics Unit, Spanish National Cancer Research Centre, Madrid, Spain
| | - Mercedes Robledo
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre, Madrid, Spain; Biomedical Research Networking Center on Rare Diseases (CIBERER), Madrid, Spain.
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8
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Comino-Méndez I, Tejera ÁM, Currás-Freixes M, Remacha L, Gonzalvo P, Tonda R, Letón R, Blasco MA, Robledo M, Cascón A. ATRX driver mutation in a composite malignant pheochromocytoma. Cancer Genet 2016; 209:272-7. [PMID: 27209355 DOI: 10.1016/j.cancergen.2016.04.058] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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: 01/11/2016] [Revised: 04/01/2016] [Accepted: 04/23/2016] [Indexed: 12/19/2022]
Abstract
Pheochromocytomas (PCCs) and paragangliomas (PGLs) are tumors arising from the adrenal medulla and sympathetic/parasympathetic paraganglia, respectively. Approximately 40% of PCCs/PGLs are due to germline mutations in one of 16 susceptibility genes, and a further 30% are due to somatic alterations in 5 main genes. Recently, somatic ATRX mutations have been found in succinate dehydrogenase (SDH)-associated hereditary PCCs/PGLs. In the present study we applied whole-exome sequencing to the germline and tumor DNA of a patient with metastatic composite PCC and no alterations in known PCC/PGL susceptibility genes. A somatic loss-of-function mutation affecting ATRX was identified in tumor DNA. Transcriptional profiling analysis classified the tumor within cluster 2 of PCCs/PGLs (without SDH gene mutations) and identified downregulation of genes involved in neuronal development and homeostasis (NLGN4, CD99 and CSF2RA) as well as upregulation of Drosha, an important gene involved in miRNA and rRNA processing. CpG island methylator phenotype typical of SDH gene-mutated tumors was ruled out, and SNP array data revealed a unique profile of gains and losses. Finally, we demonstrated the presence of alternative lengthening of telomeres in the tumor, probably associated with the failure of ATRX functions. In conclusion, somatic variants affecting ATRX may play a driver role in sporadic PCC/PGL.
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Affiliation(s)
- Iñaki Comino-Méndez
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Águeda M Tejera
- Telomeres and Telomerase Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - María Currás-Freixes
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Laura Remacha
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Pablo Gonzalvo
- Department of Anatomical Pathology, Cabueñes Hospital, Gijón, Spain
| | - Raúl Tonda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Rocío Letón
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - María A Blasco
- Telomeres and Telomerase Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Mercedes Robledo
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Alberto Cascón
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.
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