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Moratalla-Navarro F, Díez-Villanueva A, Garcia-Serrano A, Closa A, Cordero D, Solé X, Guinó E, Sanz-Pamplona R, Sanjuan X, Santos C, Biondo S, Salazar R, Moreno V. Identification of a Twelve-microRNA Signature with Prognostic Value in Stage II Microsatellite Stable Colon Cancer. Cancers (Basel) 2023; 15:3301. [PMID: 37444411 DOI: 10.3390/cancers15133301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
We aimed to identify and validate a set of miRNAs that could serve as a prognostic signature useful to determine the recurrence risk for patients with COAD. Small RNAs from tumors of 100 stage II, untreated, MSS colon cancer patients were sequenced for the discovery step. For this purpose, we built an miRNA score using an elastic net Cox regression model based on the disease-free survival status. Patients were grouped into high or low recurrence risk categories based on the median value of the score. We then validated these results in an independent sample of stage II microsatellite stable tumor tissues, with a hazard ratio of 3.24, (CI95% = 1.05-10.0) and a 10-year area under the receiver operating characteristic curve of 0.67. Functional analysis of the miRNAs present in the signature identified key pathways in cancer progression. In conclusion, the proposed signature of 12 miRNAs can contribute to improving the prediction of disease relapse in patients with stage II MSS colorectal cancer, and might be useful in deciding which patients may benefit from adjuvant chemotherapy.
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Affiliation(s)
- Ferran Moratalla-Navarro
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO), 08908 Barcelona, Spain
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona (UB), 08907 Barcelona, Spain
| | - Anna Díez-Villanueva
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO), 08908 Barcelona, Spain
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain
| | - Ainhoa Garcia-Serrano
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, 14186 Stockholm, Sweden
| | - Adrià Closa
- Department of Pathology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - David Cordero
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO), 08908 Barcelona, Spain
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain
| | - Xavier Solé
- Molecular Biology CORE, Center for Biomedical Diagnostics, Hospital Clinic de Barcelona, 08036 Barcelona, Spain
- Translational Genomic and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - Elisabet Guinó
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO), 08908 Barcelona, Spain
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain
| | - Rebeca Sanz-Pamplona
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO), 08908 Barcelona, Spain
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- Lozano Blesa University Hospital, Aragon Health Research Institute (IISA), Aragon I+D Foundation (ARAID), Government of Aragon, 50009 Zaragoza, Spain
| | - Xavier Sanjuan
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain
- Department of Pathology, Bellvitge University Hospital, 08907 Barcelona, Spain
| | - Cristina Santos
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain
- Oncology Service, Catalan Institute of Oncology (ICO), 08908 Barcelona, Spain
- Consortium for Biomedical Research in Oncology (CIBERONC), 28029 Madrid, Spain
| | - Sebastiano Biondo
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona (UB), 08907 Barcelona, Spain
- Department of General and Digestive Surgery, Bellvitge University Hospital, 08907 Barcelona, Spain
| | - Ramón Salazar
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona (UB), 08907 Barcelona, Spain
- Oncology Service, Catalan Institute of Oncology (ICO), 08908 Barcelona, Spain
- Consortium for Biomedical Research in Oncology (CIBERONC), 28029 Madrid, Spain
| | - Victor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO), 08908 Barcelona, Spain
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona (UB), 08907 Barcelona, Spain
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Ferre-Martinez A, Miguel-Pérez M, Möller I, Ortiz-Miguel S, Pérez-Bellmunt A, Ruiz N, Sanjuan X, Agullo J, Ortiz-Sagristà J, Martinoli C. Possible Points of Ulnar Nerve Entrapment in the Arm and Forearm: An Ultrasound, Anatomical, and Histological Study. Diagnostics (Basel) 2023; 13:diagnostics13071332. [PMID: 37046548 PMCID: PMC10093241 DOI: 10.3390/diagnostics13071332] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/21/2023] [Accepted: 03/31/2023] [Indexed: 04/07/2023] Open
Abstract
Background: Ulnar nerve entrapment is one of the most common entrapment neuropathies, usually occurring in the cubital tunnel of the elbow and in Guyon’s canal of the wrist. However, it can also occur at other anatomical locations. Purpose: Our aim was to review other possible locations of ulnar nerve entrapment in an ultrasound and anatomical study. Material and Methods: Eleven upper limbs from eight adult corpses were ultrasonographically examined and subsequently dissected in a dissection laboratory. Four specific anatomical points were analysed, and any anatomical variations were documented. Moreover, six samples of the nerve were taken for histological analysis. Results: Distinct anatomical relationships were observed during ultrasound and dissection between the ulnar nerve and the medial intermuscular septum, the triceps aponeurosis, Osborne’s fascia at the elbow, the arcuate ligament of Osborne and the intermuscular aponeurosis between the flexor carpi ulnaris and the flexor digitorum superficialis muscles. A statistical study showed that these locations are potential areas for ulnar nerve compression. In addition, a fourth head of the triceps brachii muscle was found in some specimens. Conclusion: Results demonstrate that ultrasound is a good tool to investigate ulnar nerve entrapment neuropathy and to identify other anatomical points where the nerve can remain compressed.
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Affiliation(s)
- Andrea Ferre-Martinez
- Unit of Human Anatomy and Embryology, Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences (Bellvitge Campus), University of Barcelona, 08907 Barcelona, Spain
| | - Maribel Miguel-Pérez
- Unit of Human Anatomy and Embryology, Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences (Bellvitge Campus), University of Barcelona, 08907 Barcelona, Spain
| | - Ingrid Möller
- Unit of Human Anatomy and Embryology, Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences (Bellvitge Campus), University of Barcelona, 08907 Barcelona, Spain
| | - Sara Ortiz-Miguel
- Unit of Human Anatomy and Embryology, Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences (Bellvitge Campus), University of Barcelona, 08907 Barcelona, Spain
- Basic Sciences Department, Universitat Internacional de Catalunya, 08017 Barcelona, Spain
| | - Albert Pérez-Bellmunt
- Basic Sciences Department, Universitat Internacional de Catalunya, 08017 Barcelona, Spain
| | - Núria Ruiz
- Unit of Human Anatomy and Embryology, Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences (Bellvitge Campus), University of Barcelona, 08907 Barcelona, Spain
- Department of Pathology, University Hospital of Bellvitge, 08907 Barcelona, Spain
| | - Xavier Sanjuan
- Department of Pathology, University Hospital of Bellvitge, 08907 Barcelona, Spain
- Unit of Pathological Anatomy, Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences (Bellvitge Campus), University of Barcelona, 08907 Barcelona, Spain
| | - Jose Agullo
- Unit of Human Anatomy and Embryology, Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences (Bellvitge Campus), University of Barcelona, 08907 Barcelona, Spain
| | | | - Carlo Martinoli
- Cattedra di Radiologia “R”-DICMI, Universita di Genova, 16126 Genoa, Italy
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Díez-Villanueva A, Sanz-Pamplona R, Solé X, Cordero D, Crous-Bou M, Guinó E, Lopez-Doriga A, Berenguer A, Aussó S, Paré-Brunet L, Obón-Santacana M, Moratalla-Navarro F, Salazar R, Sanjuan X, Santos C, Biondo S, Diez-Obrero V, Garcia-Serrano A, Alonso MH, Carreras-Torres R, Closa A, Moreno V. COLONOMICS - integrative omics data of one hundred paired normal-tumoral samples from colon cancer patients. Sci Data 2022; 9:595. [PMID: 36182938 PMCID: PMC9526730 DOI: 10.1038/s41597-022-01697-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/16/2022] [Indexed: 11/29/2022] Open
Abstract
Colonomics is a multi-omics dataset that includes 250 samples: 50 samples from healthy colon mucosa donors and 100 paired samples from colon cancer patients (tumor/adjacent). From these samples, Colonomics project includes data from genotyping, DNA methylation, gene expression, whole exome sequencing and micro-RNAs (miRNAs) expression. It also includes data from copy number variation (CNV) from tumoral samples. In addition, clinical data from all these samples is available. The aims of the project were to explore and integrate these datasets to describe colon cancer at molecular level and to compare normal and tumoral tissues. Also, to improve screening by finding biomarkers for the diagnosis and prognosis of colon cancer. This project has its own website including four browsers allowing users to explore Colonomics datasets. Since generated data could be reuse for the scientific community for exploratory or validation purposes, here we describe omics datasets included in the Colonomics project as well as results from multi-omics layers integration.
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Affiliation(s)
- Anna Díez-Villanueva
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Rebeca Sanz-Pamplona
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Xavier Solé
- Molecular Biology CORE, Center for Biomedical Diagnostics, Hospital Clínic de Barcelona, 08036, Barcelona, Spain
- Translational Genomic and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036, Barcelona, Spain
| | - David Cordero
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Marta Crous-Bou
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO) - Bellvitge Biomedical Research Institute (IDIBELL). L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Elisabet Guinó
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Adriana Lopez-Doriga
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Antoni Berenguer
- Rheumatology Department - Parc Taulí Research and Innovation Institute (I3PT), Barcelona, Spain
| | - Susanna Aussó
- TIC Salut Social Foundation. Ministry of Health of Generalitat de Catalunya, Barcelona, Spain
| | | | - Mireia Obón-Santacana
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Ferran Moratalla-Navarro
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
| | - Ramon Salazar
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
- Medical Oncology Department. Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Oncology (CIBERONC), Madrid, Spain
| | - Xavier Sanjuan
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
- Pathology Service, Bellvitge University Hospital (HUB), Hospitalet de Llobregat, Barcelona, Spain
| | - Cristina Santos
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
- Medical Oncology Department. Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Oncology (CIBERONC), Madrid, Spain
| | - Sebastiano Biondo
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
- Digestive Surgery Service, Bellvitge University Hospital (HUB). Hospitalet de Llobregat, Barcelona, Spain
| | - Virginia Diez-Obrero
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
| | - Ainhoa Garcia-Serrano
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Maria Henar Alonso
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
| | - Robert Carreras-Torres
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Adria Closa
- The John Curtin School of Medical Research, Australian National University, Canberra, Australia
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, Australia
| | - Víctor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain.
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain.
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain.
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain.
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4
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Lanuza PM, Alonso MH, Hidalgo S, Uranga-Murillo I, García-Mulero S, Arnau R, Santos C, Sanjuan X, Santiago L, Comas L, Redrado S, Pazo-Cid R, Agustin-Ferrández MJ, Jaime-Sánchez P, Pesini C, Gálvez EM, Ramírez-Labrada A, Arias M, Sanz-Pamplona R, Pardo J. Adoptive NK Cell Transfer as a Treatment in Colorectal Cancer Patients: Analyses of Tumour Cell Determinants Correlating With Efficacy In Vitro and In Vivo. Front Immunol 2022; 13:890836. [PMID: 35747143 PMCID: PMC9210952 DOI: 10.3389/fimmu.2022.890836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
Background Colorectal cancer (CRC) is a heterogeneous disease with variable mutational profile and tumour microenvironment composition that influence tumour progression and response to treatment. While chemoresistant and poorly immunogenic CRC remains a challenge, the development of new strategies guided by biomarkers could help stratify and treat patients. Allogeneic NK cell transfer emerges as an alternative against chemoresistant and poorly immunogenic CRC. Methods NK cell-related immunological markers were analysed by transcriptomics and immunohistochemistry in human CRC samples and correlated with tumour progression and overall survival. The anti-tumour ability of expanded allogeneic NK cells using a protocol combining cytokines and feeder cells was analysed in vitro and in vivo and correlated with CRC mutational status and the expression of ligands for immune checkpoint (IC) receptors regulating NK cell activity. Results HLA-I downmodulation and NK cell infiltration correlated with better overall survival in patients with a low-stage (II) microsatellite instability-high (MSI-H) CRC, suggesting a role of HLA-I as a prognosis biomarker and a potential benefit of NK cell immunotherapy. Activated allogeneic NK cells were able to eliminate CRC cultures without PD-1 and TIM-3 restriction but were affected by HLA-I expression. In vivo experiments confirmed the efficacy of the therapy against both HLA+ and HLA− CRC cell lines. Concomitant administration of pembrolizumab failed to improve tumour control. Conclusions Our results reveal an immunological profile of CRC tumours in which immunogenicity (MSI-H) and immune evasion mechanisms (HLA downmodulation) favour NK cell immunosurveillance at early disease stages. Accordingly, we have shown that allogeneic NK cell therapy can target tumours expressing mutations conferring poor prognosis regardless of the expression of T cell-related inhibitory IC ligands. Overall, this study provides a rationale for a new potential basis for CRC stratification and NK cell-based therapy.
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Affiliation(s)
- Pilar M. Lanuza
- Aragón Health Research Institute (IIS Aragón), Biomedical Research Centre of Aragón (CIBA), Zaragoza, Spain
- *Correspondence: Pilar M. Lanuza,
| | - M. Henar Alonso
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, Hospitalet de Llobregat, Barcelona, Spain
| | - Sandra Hidalgo
- Aragón Health Research Institute (IIS Aragón), Biomedical Research Centre of Aragón (CIBA), Zaragoza, Spain
- Department of Microbiology, Radiology, Pediatry and Public Health, University of Zaragoza, Zaragoza, Spain
| | - Iratxe Uranga-Murillo
- Aragón Health Research Institute (IIS Aragón), Biomedical Research Centre of Aragón (CIBA), Zaragoza, Spain
- Department of Microbiology, Radiology, Pediatry and Public Health, University of Zaragoza, Zaragoza, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Sandra García-Mulero
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, Hospitalet de Llobregat, Barcelona, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Raquel Arnau
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, Hospitalet de Llobregat, Barcelona, Spain
| | - Cristina Santos
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL)-CIBERONC, L’Hospitalet de Llobregat, Barcelona, Spain
| | - Xavier Sanjuan
- Department of Pathology, University Hospital Bellvitge (HUB-IDIBELL), L’Hospitalet de Llobregat, Barcelona, Spain
| | - Llipsy Santiago
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Oncology and Pharmacology Units, HUMSICB-CSIC, Instituto de Carboquímica ICB-CSIC, Zaragoza, Spain
| | - Laura Comas
- Oncology and Pharmacology Units, HUMSICB-CSIC, Instituto de Carboquímica ICB-CSIC, Zaragoza, Spain
| | - Sergio Redrado
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Oncology and Pharmacology Units, HUMSICB-CSIC, Instituto de Carboquímica ICB-CSIC, Zaragoza, Spain
| | | | | | - Paula Jaime-Sánchez
- Aragón Health Research Institute (IIS Aragón), Biomedical Research Centre of Aragón (CIBA), Zaragoza, Spain
| | - Cecilia Pesini
- Aragón Health Research Institute (IIS Aragón), Biomedical Research Centre of Aragón (CIBA), Zaragoza, Spain
| | - Eva M. Gálvez
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Oncology and Pharmacology Units, HUMSICB-CSIC, Instituto de Carboquímica ICB-CSIC, Zaragoza, Spain
| | - Ariel Ramírez-Labrada
- Unidad de Nanotoxicología e Inmunotoxicología (UNATI), Aragón Health Research Institute (IIS Aragón), Biomedical Research Centre of Aragón (CIBA), Zaragoza, Spain
| | - Maykel Arias
- Aragón Health Research Institute (IIS Aragón), Biomedical Research Centre of Aragón (CIBA), Zaragoza, Spain
- Department of Microbiology, Radiology, Pediatry and Public Health, University of Zaragoza, Zaragoza, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Rebeca Sanz-Pamplona
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, Hospitalet de Llobregat, Barcelona, Spain
- ARAID Foundation, Aragon Health Research Institute (IIS Aragón), Zaragoza, Spain
| | - Julián Pardo
- Aragón Health Research Institute (IIS Aragón), Biomedical Research Centre of Aragón (CIBA), Zaragoza, Spain
- Department of Microbiology, Radiology, Pediatry and Public Health, University of Zaragoza, Zaragoza, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- ARAID Foundation, Aragon Health Research Institute (IIS Aragón), Zaragoza, Spain
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Díez-Villanueva A, Jordà M, Carreras-Torres R, Alonso H, Cordero D, Guinó E, Sanjuan X, Santos C, Salazar R, Sanz-Pamplona R, Moreno V. Identifying causal models between genetically regulated methylation patterns and gene expression in healthy colon tissue. Clin Epigenetics 2021; 13:162. [PMID: 34419169 PMCID: PMC8380335 DOI: 10.1186/s13148-021-01148-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 04/13/2021] [Accepted: 08/07/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND DNA methylation is involved in the regulation of gene expression and phenotypic variation, but the inter-relationship between genetic variation, DNA methylation and gene expression remains poorly understood. Here we combine the analysis of genetic variants related to methylation markers (methylation quantitative trait loci: mQTLs) and gene expression (expression quantitative trait loci: eQTLs) with methylation markers related to gene expression (expression quantitative trait methylation: eQTMs), to provide novel insights into the genetic/epigenetic architecture of colocalizing molecular markers. RESULTS Normal mucosa from 100 patients with colon cancer and 50 healthy donors included in the Colonomics project have been analyzed. Linear models have been used to find mQTLs and eQTMs within 1 Mb of the target gene. From 32,446 eQTLs previously detected, we found a total of 6850 SNPs, 114 CpGs and 52 genes interrelated, generating 13,987 significant combinations of co-occurring associations (meQTLs) after Bonferromi correction. Non-redundant meQTLs were 54, enriched in genes involved in metabolism of glucose and xenobiotics and immune system. SNPs in meQTLs were enriched in regulatory elements (enhancers and promoters) compared to random SNPs within 1 Mb of genes. Three colorectal cancer GWAS SNPs were related to methylation changes, and four SNPs were related to chemerin levels. Bayesian networks have been used to identify putative causal relationships among associated SNPs, CpG and gene expression triads. We identified that most of these combinations showed the canonical pathway of methylation markers causes gene expression variation (60.1%) or non-causal relationship between methylation and gene expression (33.9%); however, in up to 6% of these combinations, gene expression was causing variation in methylation markers. CONCLUSIONS In this study we provided a characterization of the regulation between genetic variants and inter-dependent methylation markers and gene expression in a set of 150 healthy colon tissue samples. This is an important finding for the understanding of molecular susceptibility on colon-related complex diseases.
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Affiliation(s)
- Anna Díez-Villanueva
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Av Gran Via 199-203, 08907, L'Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Mireia Jordà
- Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP), Badalona, Barcelona, Spain
| | - Robert Carreras-Torres
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Av Gran Via 199-203, 08907, L'Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Henar Alonso
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Av Gran Via 199-203, 08907, L'Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - David Cordero
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Av Gran Via 199-203, 08907, L'Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Elisabet Guinó
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Av Gran Via 199-203, 08907, L'Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Xavier Sanjuan
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Pathology Department, University Hospital Bellvitge (HUB), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Cristina Santos
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Medical Oncology Service, Catalan Institute of Oncology (ICO), Barcelona, Spain
- Biomedical Research Centre Network for Oncology (CIBERONC), Madrid, Spain
| | - Ramón Salazar
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- Medical Oncology Service, Catalan Institute of Oncology (ICO), Barcelona, Spain
- Biomedical Research Centre Network for Oncology (CIBERONC), Madrid, Spain
| | - Rebeca Sanz-Pamplona
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Av Gran Via 199-203, 08907, L'Hospitalet de Llobregat, Barcelona, Spain.
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain.
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain.
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO), Av Gran Via 199-203, 08907, L'Hospitalet de Llobregat, Barcelona, Spain.
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain.
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain.
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain.
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Machado I, Cruz J, Righi A, Gambarotti M, Ferrari C, Ruengwanichayakun P, Giner F, Rausell N, Lavernia J, Sugita S, Najera L, Suarez L, Sanjuan X, García JAN, García Del Muro FJ, Gómez-Mateo MC, Valladares MM, Ramos-Oliver I, Romagosa C, Parafioriti A, Elisabetta A, di Bernardo A, Navarro S, Hasegawa T, Arana E, Llombart-Bosch A. Ki-67 immunoexpression and radiological assessment of necrosis improves accuracy of conventional and modified core biopsy systems in predicting the final grade assigned to adult-soft tissue sarcomas. An international collaborative study. Pathol Res Pract 2021; 225:153562. [PMID: 34329836 DOI: 10.1016/j.prp.2021.153562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 07/18/2021] [Accepted: 07/20/2021] [Indexed: 10/20/2022]
Abstract
Based on the French Federation Nationale des Centers de Lutte Contre le Cancer (FNCLCC) grading system, this study assesses the accuracy of conventional and modified core biopsy (CB) systems in predicting the final grade (low vs high) assigned to the resected specimen. Substituting Ki-67 immunoexpression for mitotic count, and radiological for histological assessment of necrosis, we used two modified FNCLCC CB grading systems: (1) Ki-67 immunoexpression alone, and (2) Ki-67 plus radiological assessment of necrosis. We graded 199 soft tissue sarcomas (STS) from nine centers, and compared the results for the conventional (obtained from local histopathology reports) and modified CB systems with the final FNCLCC grading of the corresponding resected specimens. Due to insufficient sample quality or lack of available radiologic data, five cases were not evaluated for Ki67 or radiological assessment of necrosis. The conventional FNCLCC CB grading system accurately identified 109 of the 130 high-grade cases (83.8%). The CB grading matched the final FNCLCC grading (low vs high) in 175 (87.9%) of the 199 resected tumors; overestimating the final grade in three cases and underestimating in 21 cases. Modified system 1 (Ki-67) accurately identified 117 of the 130 high-grade cases (90.0%). The CB grading matched the final FNCLCC grading (low vs high) in 175 (89.7%) of the 195 evaluated cases; overestimating seven and underestimating 13 cases. Modified system 2 (Ki-67 plus radiological necrosis) accurately identified 120 of the 130 high-grade cases (92.3%). This last matched the final FNCLCC grading (low vs high) in 177 (91.2%) of the 194 evaluated cases; overestimating seven and underestimating 10 cases. Modified system 2 obtained highest area under ROC curves, although not statistically significant. Underestimated CB grades did not correlate with histological subtypes, although many of the discrepant cases were myxoid tumors (myxofibrosarcomas or myxoid liposarcomas), leiomyosarcomas or undifferentiated pleomorphic/spindle cell sarcomas. Using modified FNCLCC CB grading systems to replace conventional mitotic count and histologic assessment of necrosis may improve the distinction between low and high-grade STS on CB. Our study confirms that classifying grade 1 as low grade and grades 2 and 3 as high grade improves correlation between CB and final grade by up to 21%, irrespective of CB system used. A higher than expected Ki-67 score in a low-grade sarcoma diagnosed on CB should raise concern that a higher-grade component may not have been sampled. Furthermore, correlation of all clinicopathological and radiological findings at multidisciplinary meetings is essential to assess the histological grade on CB as accurately as possible.
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Affiliation(s)
- Isidro Machado
- Pathology Department, Instituto Valenciano de Oncología, Valencia, Spain; Pathology Department, Patologika, Hospital Quirón-Salud, Valencia, Spain.
| | - Julia Cruz
- Pathology Department, Instituto Valenciano de Oncología, Valencia, Spain
| | - Alberto Righi
- Pathology Department, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Marco Gambarotti
- Pathology Department, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Cristina Ferrari
- Pathology Department, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | | | - Francisco Giner
- Pathology Department, University Hospital La Fe, Valencia, Spain
| | - Nuria Rausell
- Pathology Department, University Hospital La Fe, Valencia, Spain
| | - Javier Lavernia
- Oncology Department, Instituto Valenciano de Oncología, Valencia, Spain
| | - Shintaro Sugita
- Department of Surgical Pathology, Sapporo Medical University, School of Medicine. Japan
| | - Laura Najera
- Pathology Department, University Hospital Puerta de Hierro, Madrid, Spain
| | - Lola Suarez
- Pathology Department, University Hospital Puerta de Hierro, Madrid, Spain
| | - Xavier Sanjuan
- Pathology Department, Hospital Universitari de Bellvitge, Barcelona, Spain
| | | | | | | | | | | | - Cleofe Romagosa
- Pathology Department, Hospital Vall d'Hebron, Barcelona, Spain; Vall d'Hebron Research Institut (VHIR), Universitat Autónoma de Barcelona, Spain; Centro de Investigación Biomédica en RED (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Antonina Parafioriti
- Pathology Department, ASST Centro Specialistico Ortopedico Traumatologico Gaetano Pini-CTO, Milan, Italy
| | - Armiraglio Elisabetta
- Pathology Department, ASST Centro Specialistico Ortopedico Traumatologico Gaetano Pini-CTO, Milan, Italy
| | - Andrea di Bernardo
- Pathology Department, ASST Centro Specialistico Ortopedico Traumatologico Gaetano Pini-CTO, Milan, Italy
| | - Samuel Navarro
- Pathology Department, University of Valencia, Valencia, Spain
| | - Tadashi Hasegawa
- Department of Surgical Pathology, Sapporo Medical University, School of Medicine. Japan
| | - Estanislao Arana
- Radiology Department, Instituto Valenciano de Oncología, Valencia, Spain
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García-Mulero S, Alonso MH, Pardo J, Santos C, Sanjuan X, Salazar R, Moreno V, Piulats JM, Sanz-Pamplona R. Lung metastases share common immune features regardless of primary tumor origin. J Immunother Cancer 2021; 8:jitc-2019-000491. [PMID: 32591432 PMCID: PMC7319789 DOI: 10.1136/jitc-2019-000491] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [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] [Accepted: 05/12/2020] [Indexed: 01/13/2023] Open
Abstract
Background Only certain disseminated cells are able to grow in secondary organs to create a metastatic tumor. Under the hypothesis that the immune microenvironment of the host tissue may play an important role in this process, we have categorized metastatic samples based on their immune features. Methods Gene expression data of metastatic samples (n=374) from four secondary sites (brain, bone, liver and lung) were used to characterize samples based on their immune and stromal infiltration using gene signatures and cell quantification tools. A clustering analysis was done that separated metastatic samples into three different immune categories: high, medium and low. Results Significant differences were found between the immune profiles of samples metastasizing in distinct organs. Metastases in lung showed a higher immunogenic score than metastases in brain, liver or bone, regardless of their primary site of origin. Also, they preferentially clustered in the high immune group. Samples in this cluster exhibited a clear inflammatory phenotype, higher levels of immune infiltrate, overexpression of programmed death-ligand 1 (PD-L1) and cytotoxic T-lymphocyte-associated protein 4 (CTLA4) pathways and upregulation of genes predicting clinical response to programmed cell death protein 1 (PD-1) blockade (T-cell inflammatory signature). A decision tree algorithm was used to select CD74 as a biomarker that identify samples belonging to this high-immune subtype of metastases, having specificity of 0.96 and sensitivity of 1. Conclusions We have found a group of lung-enriched metastases showing an inflammatory phenotype susceptible to be treated with immunotherapy.
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Affiliation(s)
- Sandra García-Mulero
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain.,Department of Clinical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - M Henar Alonso
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain.,Department of Clinical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - Julián Pardo
- Immunotherapy, Inflammation and Cancer Group, Aragón Health Research Institute (IIS Aragón), Aragón i + D Foundation (ARAID), Zaragoza, Spain
| | - Cristina Santos
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL)-CIBERONC, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Xavier Sanjuan
- Department of Pathology, University Hospital Bellvitge (HUB-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ramón Salazar
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL)-CIBERONC, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain.,Department of Clinical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - Josep María Piulats
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL)-CIBERONC, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Rebeca Sanz-Pamplona
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
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8
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Sanz-Pamplona R, Melas M, Maoz A, Schmit SL, Rennert H, Lejbkowicz F, Greenson JK, Sanjuan X, Lopez-Zambrano M, Alonso MH, Qu C, McDonnell KJ, Idos GE, Vignali M, Emerson R, Fields P, Guinó E, Santos C, Salazar R, Robins HS, Rennert G, Gruber SB, Moreno V. Lymphocytic infiltration in stage II microsatellite stable colorectal tumors: A retrospective prognosis biomarker analysis. PLoS Med 2020; 17:e1003292. [PMID: 32970670 PMCID: PMC7514069 DOI: 10.1371/journal.pmed.1003292] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 08/14/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Identifying stage II patients with colorectal cancer (CRC) at higher risk of progression is a clinical priority in order to optimize the advantages of adjuvant chemotherapy while avoiding unnecessary toxicity. Recently, the intensity and the quality of the host immune response in the tumor microenvironment have been reported to have an important role in tumorigenesis and an inverse association with tumor progression. This association is well established in microsatellite instable CRC. In this work, we aim to assess the usefulness of measures of T-cell infiltration as prognostic biomarkers in 640 stage II, CRC tumors, 582 of them confirmed microsatellite stable. METHODS AND FINDINGS We measured both the quantity and clonality index of T cells by means of T-cell receptor (TCR) immunosequencing in a discovery dataset (95 patients with colon cancer diagnosed at stage II and microsatellite stable, median age 67, 30% women) and replicated the results in 3 additional series of stage II patients from 2 countries. Series 1 and 2 were recruited in Barcelona, Spain and included 112 fresh frozen (FF, median age 69, 44% women) and 163 formalin-fixed paraffin-embedded (FFPE, median age 67, 39% women) samples, respectively. Series 3 included 270 FFPE samples from patients recruited in Haifa, Northern Israel, as part of a large case-control study of CRC (median age 73, 46% women). Median follow-up time was 81.1 months. Cox regression models were fitted to evaluate the prognostic value of T-cell abundance and Simpson clonality of TCR variants adjusting by sex, age, tumor location, and stage (IIA and IIB). In the discovery dataset, higher TCR abundance was associated with better prognosis (hazard ratio [HR] for ≥Q1 = 0.25, 95% CI 0.10-0.63, P = 0.003). A functional analysis of gene expression on these tumors revealed enrichment in pathways related to immune response. Higher values of clonality index (lower diversity) were not associated with worse disease-free survival, though the HR for ≥Q3 was 2.32 (95% CI 0.90-5.97, P = 0.08). These results were replicated in an independent FF dataset (TCR abundance: HR = 0.30, 95% CI 0.12-0.72, P = 0.007; clonality: HR = 3.32, 95% CI 1.38-7.94, P = 0.007). Also, the association with prognosis was tested in 2 independent FFPE datasets. The same association was observed with TCR abundance (HR = 0.41, 95% CI 0.18-0.93, P = 0.03 and HR = 0.56, 95% CI 0.31-1, P = 0.042, respectively, for each FFPE dataset). However, the clonality index was associated with prognosis only in the FFPE dataset from Israel (HR = 2.45, 95% CI 1.39-4.32, P = 0.002). Finally, a combined analysis combining all microsatellite stable (MSS) samples demonstrated a clear prognosis value both for TCR abundance (HR = 0.39, 95% CI 0.26-0.57, P = 1.3e-06) and the clonality index (HR = 2.13, 95% CI 1.44-3.15, P = 0.0002). These associations were also observed when variables were considered continuous in the models (HR per log2 of TCR abundance = 0.85, 95% CI 0.78-0.93, P = 0.0002; HR per log2 or clonality index = 1.16, 95% CI 1.03-1.31, P = 0.016). LIMITATIONS This is a retrospective study, and samples had been preserved with different methods. Validation series lack complete information about microsatellite instability (MSI) status and pathology assessment. The Molecular Epidemiology of Colorectal Cancer (MECC) study had information about overall survival instead of progression-free survival. CONCLUSION Results from this study demonstrate that tumor lymphocytes, assessed by TCR repertoire quantification based on a sequencing method, are an independent prognostic factor in microsatellite stable stage II CRC.
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Affiliation(s)
- Rebeca Sanz-Pamplona
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Spain
| | - Marilena Melas
- Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Asaf Maoz
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Stephanie L. Schmit
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Hedy Rennert
- Carmel Medical Center, and Technion, Haifa, Israel
| | | | - Joel K. Greenson
- University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Xavier Sanjuan
- University Hospital Bellvitge (HUB-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Maria Lopez-Zambrano
- University Hospital Bellvitge (HUB-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - M. Henar Alonso
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Chenxu Qu
- City of Hope National Medical Center, Duarte, California, United States of America
| | - Kevin J. McDonnell
- City of Hope National Medical Center, Duarte, California, United States of America
| | - Gregory E. Idos
- City of Hope National Medical Center, Duarte, California, United States of America
| | - Marissa Vignali
- Adaptive Biotechnologies, Seattle, Washington, United States of America
| | - Ryan Emerson
- Adaptive Biotechnologies, Seattle, Washington, United States of America
| | - Paul Fields
- Adaptive Biotechnologies, Seattle, Washington, United States of America
| | - Elisabet Guinó
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Spain
| | - Cristina Santos
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Oncology (CIBERONC), Spain
| | - Ramon Salazar
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Oncology (CIBERONC), Spain
| | - Harlan S. Robins
- Adaptive Biotechnologies, Seattle, Washington, United States of America
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail: (VM); (SBG); (GR); (HSR)
| | - Gad Rennert
- Carmel Medical Center, and Technion, Haifa, Israel
- * E-mail: (VM); (SBG); (GR); (HSR)
| | - Stephen B. Gruber
- City of Hope National Medical Center, Duarte, California, United States of America
- * E-mail: (VM); (SBG); (GR); (HSR)
| | - Victor Moreno
- Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- * E-mail: (VM); (SBG); (GR); (HSR)
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Dumbović G, Sanjuan X, Perucho M, Forcales SV. Stimulated emission depletion (STED) super resolution imaging of RNA- and protein-containing domains in fixed cells. Methods 2020; 187:68-76. [PMID: 32360441 DOI: 10.1016/j.ymeth.2020.04.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/25/2020] [Accepted: 04/26/2020] [Indexed: 12/20/2022] Open
Abstract
Super resolution microscopy has changed our capability to visualize and understand spatial arrangements of RNA- and protein-containing domains in individual cells. In a previous study, we described a novel lncRNA, Tumor-associated NBL2 transcript (TNBL), which originates from a primate specific macrosatellite repeat. We aimed to describe several aspects of TNBL lncRNA, with one focus being pinpointing its precise location in the nucleus, as well as visualizing its interactions with proteins to deduce its functionality. Using a combination of STimulated Emission Depletion (STED) super resolution microscopy, single molecule RNA (smRNA) FISH against TNBL, and immunofluorescence against SAM68 perinucleolar body, we resolved the spatial complexity of the interaction between TNBL aggregates and SAM68 bodies at the perinucleolar region. Here, we describe protocols for a step-by-step optimized smRNA FISH/IF and STED imaging, detailing parameter settings, and three-dimensional data analysis of spatial positioning of subnuclear structures. These protocols can be employed for single-cell imaging of complex nuclear RNA-protein structures.
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Affiliation(s)
- Gabrijela Dumbović
- BioFrontiers Institute, University of Colorado at Boulder, Boulder, CO, USA.
| | - Xavier Sanjuan
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain; Advanced Light Microscopy Unit, Center for Genomic Regulation, Barcelona, Spain
| | - Manuel Perucho
- Cancer Genetics and Epigenetics, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Health Science Research Institute Germans Trias i Pujol (IGTP), Badalona, Spain; Tumor Initiation and Maintenance Program, Sanford Burnham Prebys (SBP) Medical Discovery Institute, La Jolla, CA, USA
| | - Sonia-V Forcales
- Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences, University of Barcelona, L' Hospitalet de Llobregat, Barcelona, Spain.
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10
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Azuara D, Aussó S, Rodriguez-Moranta F, Guardiola J, Sanjuan X, Lobaton T, Boadas J, Piqueras M, Monfort D, Guinó E, Moreno V, Capellá G, de Oca J. New Methylation Biomarker Panel for Early Diagnosis of Dysplasia or Cancer in High-Risk Inflammatory Bowel Disease Patients. Inflamm Bowel Dis 2018; 24:2555-2564. [PMID: 30099509 DOI: 10.1093/ibd/izy255] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND The risk of developing colorectal cancer (CRC) is increased in patients with inflammatory bowel disease (IBD) of the colon. The aim of the study was to evaluate the effectiveness of selected methylation gene panel for the early detection of CRC in high-risk IBD patients. METHODS In a discovery phase, 73 biopsies of 48 IBD patients (associated or not to CRC) were analyzed from genome-wide DNA methylation analysis using the Illumina Human Methylation 450K BeadChip. The panel of 5 genes selected (EYA4, SLIT2, FLI1, USP44, and SND1) was validated prospectively using methylation-specific melting curve analysis in biopsies of diseased and adjacent healthy tissue of 203 patients: 38 with IBD and associated neoplasia, 81 patients with IBD (25 of them with high risk), 48 with sporadic CRC, and 36 healthy controls. RESULTS The prevalence of methylation was higher in patients with IBD and associated neoplasia (both in diseased and adjacent healthy tissue, 71% and 52%, respectively) than in healthy controls (2/36, 6%; P = 6.72E-05). Methylation in IBD patients at high risk of dysplasia or cancer was more frequently detected than in patients at low risk (92% vs 57%; odds ratio, 8.63; P = 0.001). EYA4 and SLIT2 were the markers most frequently methylated. Differences in methylation levels were more evident in healthy mucosa (82% vs 15% high vs low risk, respectively; P = 1.25E-05). CONCLUSIONS Analysis of this panel of methylation markers may help in the early identification of colorectal dysplasia or cancer in high-risk IBD patients.
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Affiliation(s)
- Daniel Azuara
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL)-CIBERONC, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Susanna Aussó
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, ICO-IDIBELL and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Francisco Rodriguez-Moranta
- Department of Gastroenterology, University Hospital Bellvitge (HUB-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Jordi Guardiola
- Department of Gastroenterology, University Hospital Bellvitge (HUB-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Xavier Sanjuan
- Department of Pathology, University Hospital Bellvitge (HUB-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Triana Lobaton
- Department of Gastroenterology, Germans Trias i Pujol University Hospital, Badalona, Barcelona, Spain
| | - Jaume Boadas
- Department of Gastroenterology, Hospital of Terrassa, Terrassa Health Consortium (CST), Terrassa, Barcelona, Spain
| | - Marta Piqueras
- Department of Gastroenterology, Hospital of Terrassa, Terrassa Health Consortium (CST), Terrassa, Barcelona, Spain
| | - David Monfort
- Department of Gastroenterology, Hospital of Terrassa, Terrassa Health Consortium (CST), Terrassa, Barcelona, Spain
| | - Elisabet Guinó
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, ICO-IDIBELL and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, ICO-IDIBELL and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Gabriel Capellá
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL)-CIBERONC, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Javier de Oca
- Department of General and Digestive Surgery, Colorectal Unit, University Hospital Bellvitge (HUB-IDIBELL)-CIBERONC, L'Hospitalet de Llobregat, Barcelona, Spain
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Lopez-Doriga A, Valle L, Alonso MH, Aussó S, Closa A, Sanjuan X, Barquero D, Rodríguez-Moranta F, Sanz-Pamplona R, Moreno V. Telomere length alterations in microsatellite stable colorectal cancer and association with the immune response. Biochim Biophys Acta Mol Basis Dis 2018; 1864:2992-3000. [DOI: 10.1016/j.bbadis.2018.06.010] [Citation(s) in RCA: 3] [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: 12/19/2017] [Revised: 06/12/2018] [Accepted: 06/12/2018] [Indexed: 02/07/2023]
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12
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Vecchione L, Beumer I, Snel M, Salazar R, Pietrantonio F, Loupakis F, Vivas CS, Martinez-Villacampa MM, Sanjuan X, Martinetti A, Fuca' G, Schirripa M, Fassan M, Bernards R. Abstract 206: The Consensus Molecular Classification (CMS) of primary colorectal tumors and their matched liver metastasis: Investigating the concordance. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background The Consensus Molecular Subtypes (CMS) identified four different molecular groups in colorectal cancer (1). Coding mutations are concordant between primary tumors (PT) and matched metastasis (MM) while gene copy numbers seem highly discordant (2). This could somehow influence the molecular classification of PT and MM. We therefore aimed to investigate the concordance of the CMS between PT and MM.
Material and methods We retrospectively collected 25 fresh matched samples of primary (P) and synchronous liver metastasis (LM) (discovery cohort) and 50 formalin-fixed-paraffin embedded (FFPE) samples of P and synchronous LM (validation cohort) of chemonaive metastatic colorectal cancer patients. All samples contained at least 30% of tumor cells. RNA was extracted from four sections of 5-μm by using the RNeasy FFPE kit (Qiagen). RNA yield was quantified using a NanoDrop spectrophotometer. Extracted RNA was amplified using a TransPLEX C-WTA whole-transcriptome amplification kit. Amplified cDNA was labeled using the Genomic DNA Enzymatic Labeling Kit and hybridized onto Agendia's full genome arrays both according to the manufacturer's instructions. For FFPE samples, no reference channel was used. Gene expression intensities were normalized using Lowess normalization method implemented in Matlab software version R2012a, and the CMS classification was applied as in Guinney et al (1).
Results and conclusion Clinical data were currently available for 66% of patients. Median age at the diagnosis was 64 (35-76), 30% of patients were female and 70% were male. 42% of PT were right side located and 58% were left side located. 42% of tumors were well differentiated, 40% moderately differentiated, 15% poorly differentiated and 3% were not classified. 3% of tumors were MSI, 45% were MSS. No data on the MMR status was available (NA) for 52% of the tumors. Mutations in KRAS were detected in 18% of the tumors while 30% were wild type (WT) and 52% NA. BRAF(V600E) mutation was detected in 3% of tumors, 39% were WT and 58 NA. 73% of patients received surgery of both P and LM simultaneously and before starting a systemic treatment. 72% of patients received a first line treatment. The results of the molecular classification will be presented at the conference.
References 1. Guinney J et al. The consensus molecular subtypes of colorectal cancer Nat Med. 2015 Nov;21(11):1350-62. 2.Mamlouk S et al. DNA copy number changes define spatial patterns of heterogeneity in colorectal cancer. Nat Commun. 2017 Jan 25;8:14093
Citation Format: Loredana Vecchione, Ines Beumer, Mireille Snel, Ramon Salazar, Filippo Pietrantonio, Fotios Loupakis, Cristina Santos Vivas, Maria Mercedes Martinez-Villacampa, Xavier Sanjuan, Antonia Martinetti, Giovanni Fuca', Marta Schirripa, Matteo Fassan, Rene' Bernards. The Consensus Molecular Classification (CMS) of primary colorectal tumors and their matched liver metastasis: Investigating the concordance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 206.
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Affiliation(s)
| | | | | | - Ramon Salazar
- 3Catalan Institute of Oncology, IDIBELL, Barcelona, Spain
| | | | | | | | | | | | | | - Giovanni Fuca'
- 4Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Milan, Italy
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13
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Gonçalves-Ribeiro S, Sanz-Pamplona R, Vidal A, Sanjuan X, Guillen Díaz-Maroto N, Soriano A, Guardiola J, Albert N, Martínez-Villacampa M, López I, Santos C, Serra-Musach J, Salazar R, Capellà G, Villanueva A, Molleví DG. Prediction of pathological response to neoadjuvant treatment in rectal cancer with a two-protein immunohistochemical score derived from stromal gene-profiling. Ann Oncol 2018; 28:2160-2168. [PMID: 28911071 DOI: 10.1093/annonc/mdx293] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background Preoperative chemoradiotherapy followed by surgical mesorectal resection is the standard of care for locally advanced rectal carcinomas. Yet, predicting that patients will respond to treatment remains an unmet clinical challenge. Experimental design Using laser-capture microdissection we isolated RNA from stroma and tumour glands from prospective pre-treatment samples (n = 15). Transcriptomic profiles were obtained hybridising PrimeView Affymetrix arrays. We modelled a carcinoma-associated fibroblast-specific genes filtering data using GSE39396. Results The analysis of differentially expressed genes of stroma/tumour glands from responder and non-responder patients shows that most changes were associated with the stromal compartment; codifying mainly for extracellular matrix and ribosomal components. We built a carcinoma-associated fibroblast (CAF) specific classifier with genes showing changes in expression according to the tumour regression grade (FN1, COL3A1, COL1A1, MMP2 and IGFBP5). We assessed these five genes at the protein level by means of immunohistochemical staining in a patient's cohort (n = 38). For predictive purposes we used a leave-one-out cross-validated model with a positive predictive value (PPV) of 83.3%. Random Forest identified FN1 and COL3A1 as the best predictors. Rebuilding the leave-one-out cross-validated regression model improved the classification performance with a PPV of 93.3%. An independent cohort was used for classifier validation (n = 36), achieving a PPV of 88.2%. In a multivariate analysis, the two-protein classifier proved to be the only independent predictor of response. Conclusion We developed a two-protein immunohistochemical classifier that performs well at predicting the non-response to neoadjuvant treatment in rectal cancer.
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Affiliation(s)
| | - R Sanz-Pamplona
- Program of Prevention and Cancer Control, Biomarkers Unit, Catalan Institute of Oncology
| | | | | | | | - A Soriano
- Department of Gastroenterology Endoscopy Unit, Hospital Universitari de Bellvitge
| | - J Guardiola
- Department of Gastroenterology Endoscopy Unit, Hospital Universitari de Bellvitge
| | - N Albert
- Program Against Cancer Therapeutic Resistance
| | | | - I López
- Department of Medical Oncology
| | | | | | | | - G Capellà
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Catalonia, Spain
| | | | - D G Molleví
- Program Against Cancer Therapeutic Resistance
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14
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Vargas-Parra GM, González-Acosta M, Thompson BA, Gómez C, Fernández A, Dámaso E, Pons T, Morak M, Del Valle J, Iglesias S, Velasco À, Solanes A, Sanjuan X, Padilla N, de la Cruz X, Valencia A, Holinski-Feder E, Brunet J, Feliubadaló L, Lázaro C, Navarro M, Pineda M, Capellá G. Elucidating the molecular basis of MSH2-deficient tumors by combined germline and somatic analysis. Int J Cancer 2017; 141:1365-1380. [PMID: 28577310 DOI: 10.1002/ijc.30820] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 05/06/2017] [Accepted: 05/16/2017] [Indexed: 12/20/2022]
Abstract
In a proportion of patients presenting mismatch repair (MMR)-deficient tumors, no germline MMR mutations are identified, the so-called Lynch-like syndrome (LLS). Recently, MMR-deficient tumors have been associated with germline mutations in POLE and MUTYH or double somatic MMR events. Our aim was to elucidate the molecular basis of MSH2-deficient LS-suspected cases using a comprehensive analysis of colorectal cancer (CRC)-associated genes at germline and somatic level. Fifty-eight probands harboring MSH2-deficient tumors were included. Germline mutational analysis of MSH2 (including EPCAM deletions) and MSH6 was performed. Pathogenicity of MSH2 variants was assessed by RNA analysis and multifactorial likelihood calculations. MSH2 cDNA and methylation of MSH2 and MSH6 promoters were studied. Matched blood and tumor DNA were analyzed using a customized next generation sequencing panel. Thirty-five individuals were carriers of pathogenic or probably pathogenic variants in MSH2 and EPCAM. Five patients harbored 4 different MSH2 variants of unknown significance (VUS) and one had 2 novel MSH6 promoter VUS. Pathogenicity assessment allowed the reclassification of the 4 MSH2 VUS and 6 probably pathogenic variants as pathogenic mutations, enabling a total of 40 LS diagnostics. Predicted pathogenic germline variants in BUB1, SETD2, FAN1 and MUTYH were identified in 5 cases. Three patients had double somatic hits in MSH2 or MSH6, and another 2 had somatic alterations in other MMR genes and/or proofreading polymerases. In conclusion, our comprehensive strategy combining germline and somatic mutational status of CRC-associated genes by means of a subexome panel allows the elucidation of up to 86% of MSH2-deficient suspected LS tumors.
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Affiliation(s)
- Gardenia M Vargas-Parra
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Maribel González-Acosta
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Bryony A Thompson
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT.,Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Carolina Gómez
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Anna Fernández
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Estela Dámaso
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Tirso Pons
- Structural Biology and Biocomputing Program, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Monika Morak
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. Germany MGZ-Medizinisch Genetisches Zentrum, Munich, Germany.,MGZ-Medizinisch Genetisches Zentrum, Munich, Germany
| | - Jesús Del Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Silvia Iglesias
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Àngela Velasco
- Hereditary Cancer Program, Catalan Institute of Oncology, IdIBGI, Girona, Spain
| | - Ares Solanes
- Hereditary Cancer Program, Catalan Institute of Oncology, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Xavier Sanjuan
- Pathology Department, Hospital Universitari de Bellvitge-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Natàlia Padilla
- Research Unit in Translational Bioinformatics, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Xavier de la Cruz
- Research Unit in Translational Bioinformatics, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Alfonso Valencia
- Structural Biology and Biocomputing Program, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. Germany MGZ-Medizinisch Genetisches Zentrum, Munich, Germany.,MGZ-Medizinisch Genetisches Zentrum, Munich, Germany
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, IdIBGI, Girona, Spain
| | - Lídia Feliubadaló
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Matilde Navarro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain.,Hereditary Cancer Program, Catalan Institute of Oncology, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Spain
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15
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Gausachs M, Borras E, Chang K, Gonzalez S, Azuara D, Delgado Amador A, Lopez-Doriga A, San Lucas FA, Sanjuan X, Paules MJ, Taggart MW, Davies GE, Ehli EA, Fowler J, Moreno V, Pineda M, You YN, Lynch PM, Lazaro C, Navin NE, Scheet PA, Hawk ET, Capella G, Vilar E. Mutational Heterogeneity in APC and KRAS Arises at the Crypt Level and Leads to Polyclonality in Early Colorectal Tumorigenesis. Clin Cancer Res 2017. [PMID: 28645942 DOI: 10.1158/1078-0432.ccr-17-0821] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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
Purpose: The majority of genomic alterations causing intratumoral heterogeneity (ITH) in colorectal cancer are thought to arise during early stages of carcinogenesis as a burst but only after truncal mutations in APC have expanded a single founder clone. We have investigated if the initial source of ITH is consequent to multiple independent lineages derived from different crypts harboring distinct truncal APC and driver KRAS mutations, thus challenging the prevailing monoclonal monocryptal model.Experimental Design: High-depth next-generation sequencing and SNP arrays were performed in whole-lesion extracts of 37 familial adenomatous polyposis colorectal adenomas. Also, ultrasensitive genotyping of hotspot mutations of APC and KRAS was performed using nanofluidic PCRs in matched bulk biopsies (n = 59) and crypts (n = 591) from 18 adenomas and seven carcinomas and adjacent normal tissues.Results: Multiple co-occurring truncal APC and driver KRAS alterations were uncovered in whole-lesion extracts from adenomas and subsequently confirmed to belong to multiple clones. Ultrasensitive genotyping of bulk biopsies and crypts revealed novel undetected APC mutations that were prominent among carcinomas, whereas abundant wild-type APC crypts were detected in adenomas. KRAS mutational heterogeneity within crypts was evident in both adenomas and carcinomas with a higher degree of concordance between biopsy and crypt genotyping in carcinomas. Nonrandom heterogeneity among crypts was also observed.Conclusions: The striking degree of nonrandom intercrypt heterogeneity in truncal and driver gene mutations observed in adenomas and carcinomas is consistent with a polycryptal model derived from multiple independent initiation linages as the source of early ITH in colorectal carcinogenesis. Clin Cancer Res; 23(19); 5936-47. ©2017 AACR.
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Affiliation(s)
- Mireia Gausachs
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO - IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ester Borras
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kyle Chang
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sara Gonzalez
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO - IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.,CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Daniel Azuara
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO - IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.,CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Axel Delgado Amador
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Adriana Lopez-Doriga
- Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO-IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - F Anthony San Lucas
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xavier Sanjuan
- Department of Pathology, University Hospital Bellvitge (HUB - IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Maria J Paules
- Department of Pathology, University Hospital Bellvitge (HUB - IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Melissa W Taggart
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gareth E Davies
- Avera Institute for Human Genetics, Sioux Falls, South Dakota
| | - Erik A Ehli
- Avera Institute for Human Genetics, Sioux Falls, South Dakota
| | - Jerry Fowler
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Victor Moreno
- Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO-IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain.,Department of Clinical Sciences, Medical School, University of Barcelona, Barcelona, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO - IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.,CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Y Nancy You
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Patrick M Lynch
- Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Conxi Lazaro
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO - IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.,CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Nicholas E Navin
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Paul A Scheet
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ernest T Hawk
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gabriel Capella
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO - IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain. .,CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas. .,Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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16
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Santos C, Azuara D, Garcia-Carbonero R, Alfonso PG, Carrato A, Elez ME, Gomez A, Losa F, Montagut C, Massuti B, Navarro V, Varela M, Lopez-Doriga A, Moreno V, Valladares M, Manzano JL, Vieitez JM, Aranda E, Sanjuan X, Tabernero J, Capella G, Salazar R. Optimization of RAS/BRAF Mutational Analysis Confirms Improvement in Patient Selection for Clinical Benefit to Anti-EGFR Treatment in Metastatic Colorectal Cancer. Mol Cancer Ther 2017. [DOI: 10.1158/1535-7163.mct-17-0153] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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17
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González-Acosta M, Del Valle J, Navarro M, Thompson BA, Iglesias S, Sanjuan X, Paúles MJ, Padilla N, Fernández A, Cuesta R, Teulé À, Plotz G, Cadiñanos J, de la Cruz X, Balaguer F, Lázaro C, Pineda M, Capellá G. Elucidating the clinical significance of two PMS2 missense variants coexisting in a family fulfilling hereditary cancer criteria. Fam Cancer 2017; 16:501-507. [PMID: 28365877 DOI: 10.1007/s10689-017-9981-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The clinical spectrum of germline mismatch repair (MMR) gene variants continues increasing, encompassing Lynch syndrome, Constitutional MMR Deficiency (CMMRD), and the recently reported MSH3-associated polyposis. Genetic diagnosis of these hereditary cancer syndromes is often hampered by the presence of variants of unknown significance (VUS) and overlapping phenotypes. Two PMS2 VUS, c.2149G>A (p.V717M) and c.2444C>T (p.S815L), were identified in trans in one individual diagnosed with early-onset colorectal cancer (CRC) who belonged to a family fulfilling clinical criteria for hereditary cancer. Clinico-pathological data, multifactorial likelihood calculations and functional analyses were used to refine their clinical significance. Likelihood analysis based on cosegregation and tumor data classified the c.2444C>T variant as pathogenic, which was supported by impaired MMR activity associated with diminished protein expression in functional assays. Conversely, the c.2149G>A variant displayed MMR proficiency and protein stability. These results, in addition to the conserved PMS2 expression in normal tissues and the absence of germline microsatellite instability (gMSI) in the biallelic carrier ruled out a CMMRD diagnosis. The use of comprehensive strategies, including functional and clinico-pathological information, is mandatory to improve the clinical interpretation of naturally occurring MMR variants. This is critical for appropriate clinical management of cancer syndromes associated to MMR gene mutations.
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Affiliation(s)
- Maribel González-Acosta
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Jesús Del Valle
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Matilde Navarro
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Bryony A Thompson
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA.,Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Sílvia Iglesias
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Xavier Sanjuan
- Pathology Department, Hospital Universitari de Bellvitge, IDIBELL, Hospitalet de Llobregat (Barcelona), Spain
| | - María José Paúles
- Pathology Department, Hospital Universitari de Bellvitge, IDIBELL, Hospitalet de Llobregat (Barcelona), Spain
| | - Natàlia Padilla
- Research Unit in Translational Bioinformatics, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Anna Fernández
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Raquel Cuesta
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Àlex Teulé
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Guido Plotz
- Medical Clinic 1, Johann Wolfgang Goethe-University, Frankfurt, Germany
| | - Juan Cadiñanos
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA), Oviedo, Spain
| | - Xavier de la Cruz
- Research Unit in Translational Bioinformatics, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Francesc Balaguer
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBERehd), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), IDIBELL and CIBERONC, Av. Gran Via de l'Hospitalet, 199-203, 08908, Hospitalet de Llobregat (Barcelona), Spain.
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18
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Manchon-Walsh P, Aliste L, Espinàs J, Prades J, Guarga A, Balart J, Biondo S, Castells A, Sanjuan X, Tabernero J, Borras J, Biondo S, Cambray M, Castells A, Codina A, Espín E, Musulen E, Pozuelo A, Saigi E, Sala J, Salas A, Salazar R, Sanjuán X, Tabernero J, Targarona E. Improving survival and local control in rectal cancer in Catalonia (Spain) in the context of centralisation: A full cycle audit assessment. Eur J Surg Oncol 2016; 42:1873-1880. [DOI: 10.1016/j.ejso.2016.08.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/29/2016] [Accepted: 08/04/2016] [Indexed: 01/27/2023] Open
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19
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Azuara D, Garcia-Carbonero R, Alfonso PG, Santos-Vivas C, Navarro V, Varela M, Carrato A, Elez E, Cano M, Losa F, Montagut C, Sureda BM, Manzano J, Vieitez J, Valladares-Ayerbes M, Sanjuan X, Capellá G, Tabernero J, Aranda E, Salazar R. Extended genotyping of RAS/BRAF for improved selection of metastatic CRC patients to anti-EGFR therapy: Comparison of three platforms. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw363.05] [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: 11/13/2022] Open
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Maurel J, López-Pousa A, Calabuig S, Bagué S, Del Muro XG, Sanjuan X, Rubió-Casadevall J, Cuatrecasas M, Martinez-Trufero J, Horndler C, Fra J, Valverde C, Redondo A, Poveda A, Sevilla I, Lainez N, Rubini M, García-Albéniz X, Martín-Broto J, de Alava E. Phosphorylated-insulin growth factor I receptor (p-IGF1R) and metalloproteinase-3 (MMP3) expression in advanced gastrointestinal stromal tumors (GIST). A GEIS 19 study. Clin Sarcoma Res 2016; 6:10. [PMID: 27358721 PMCID: PMC4926286 DOI: 10.1186/s13569-016-0050-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/13/2016] [Indexed: 01/04/2023] Open
Abstract
Background Most GISTs have mutations in KIT or PDGFRA. Patients with advanced GIST with KIT exon 9, PDGFRA mutation or WT for KIT and PDGFRA have a worse progression-free survival (PFS) compared to patients with KIT exon 11 mutated tumors. We evaluated the immunohistochemical (IHC) expression of p-IGF1R (Y1316) and MMP3 as predictors of PFS or overall survival (OS). Methods Ninety-two advanced GIST patients included in GEIS-16 study with KIT and PDGFRA mutational information were examined for p-IGF1R (Y1316) and MMP3 expression in a tissue micro-array. To study activation of the IGF1R system, we have used an antibody (anti-pY1316) that specifically recognizes the active phosphorylated form of the IGF1R. DNA was extracted from paraffin-embedded tissues and intronic PCR primers were used to amplify exons 9, 11, 13 and 17 of KIT, 12 and 18 of PDGFRA. Bidirectional sequencing with specific primers was performed on a ABI3100 sequencer using the Big Dye Terminator v3.1 kit. Multivariate model was built using a stepwise automated variable selection approach with criterion to enter the variable in the model of p < 0.10 and criterion to keep the variable in the model of p < 0.05. PFS was computed as the date of imatinib initiation to progression or death. Overall survival was defined as the time from imatinib initiation to death. Results Phospho-IGF1R was expressed only in 9 % (2/22) of cases without KIT mutation. MMP3 expression was detected in 2/5 patients (40 %) with PDGFRA mutation, 1/16 patients (6 %) with WT genotype and 7/71 patients (10 %) of KIT mutant patients. At univariate analysis KIT exon 11/13 mutation had better PFS than patients with exon 9 mutation, PDGFRA mutation or WT genotype (p = 0.021; HR: 0.46; 95 %CI (0.28–0.76). Less than 24 months disease free-interval (HR 24.2, 95 % CI 10.5–55.8), poor performance status (PS) (HR 6.3, 95 % CI 2.5–15.9), extension of disease; >1 organ (HR 1.89; 95 % CI 1.03–3.4) and genotype analysis (HR 0.57, 95 % CI 0.37–0.97) but not immunophenotype analysis (HR 1.53; 95 % CI 0.76–3.06) were the strongest prognostic factors for PFS in the multivariate analysis. Conclusions Our results do not support p-IGF-1R and MMP3 evaluation in non-selected GIST patients but evaluation of this immunophenotype in WT and mutant PDGFR mutation in larger group of GIST patients, deserve merits.
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Affiliation(s)
- Joan Maurel
- Department of Medical Oncology, Hospital Clinic, CIBERehd, Translational Genomics and Targeted Therapeutics in Solid Tumors (IDIBAPS), Barcelona, Spain
| | - Antonio López-Pousa
- Department of Medical Oncology, Hospital Universitario Sant Pau, Barcelona, Spain
| | - Silvia Calabuig
- Molecular Oncology Laboratory, Fundación de Investigación del Hospital General Universitario de Valencia, Valencia, Spain
| | - Silvia Bagué
- Pathology Department, Hospital Universitario Sant Pau, Barcelona, Spain
| | - Xavier Garcia Del Muro
- Department of Medical Oncology, Institut Català d'Oncologia L'Hospitalet, Barcelona, Spain
| | - Xavier Sanjuan
- Pathology Department, Institut Català d'Oncologia L'Hospitalet, Barcelona, Spain
| | | | - Miriam Cuatrecasas
- Pathology Department, Hospital Clínic, CIBERehd, IDIBAPS, Barcelona, Spain
| | | | - Carlos Horndler
- Pathology Department, Hospital Universitario Miguel Servet, Saragossa, Spain
| | - Joaquin Fra
- Department of Medical Oncology, Hospital Central de Asturias, Oviedo, Spain
| | - Claudia Valverde
- Department of Medical Oncology, Hospital Universitario Vall d'Hebron, Barcelona, Spain
| | | | - Andrés Poveda
- Department of Medical Oncology, Fundación Instituto Valenciano de Oncología, Valencia, Spain
| | - Isabel Sevilla
- Department of Medical Oncology, Hospital Universitario Virgen de la Victoria y Regional de Málaga, Málaga, Spain
| | - Nuria Lainez
- Department of Medical Oncology, Hospital de Navarra, Pamplona, Spain
| | - Michele Rubini
- Department of Experimental and Diagnostic Medicine, Department of Epidemiology, University of Ferrara (UNIFE), Emilia-Romagna, Italy
| | | | - Javier Martín-Broto
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - Enrique de Alava
- Pathology Department, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
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Domenech Viñolas M, Santos C, Pérez Martín Francisco J, Varela M, Merche M, Grasselli J, Teule A, Soler G, Mulet Margalef N, Bergamino Sirven M, Ortega Franco A, Sanjuan X, Salazar R. P-160 Impact of KRAS mutation on patterns of metastasis in a series of colorectal cancer patients. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw199.154] [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: 11/13/2022] Open
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Santos C, Garcia-Carbonero R, Garcia Alfonso P, Azuara D, Varela M, Navarro-Perez V, Carrato A, Elez E, Gomez-España M, Losa F, Montagut C, Massuti B, Manzano JL, Vieitez JM, Valladares M, Sanjuan X, Capella G, Aranda E, Tabernero J, Salazar R. Comparison of three molecular methods to detect mutations in KRAS, NRAS, BRAF and PIK3CA in metastatic colorectal cancer (mCRC). J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.3559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Cristina Santos
- Translational Research Laboratory and Department of Medical Oncology, Institut Català d'Oncologia-IDIBELL, L'Hospitalet de Llobregat, Spain
| | | | | | - Daniel Azuara
- Translational Research Laboratory, Institut Catala d'Oncologia-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Mar Varela
- ICO. H.ospital Duran i Reynals, Barcelona, Spain
| | - Valentín Navarro-Perez
- Clinical Research Unit, Catalan Institute of Oncology-IDIBELL, Hospitalet (Barcelona), Spain
| | - Alfredo Carrato
- Medical Oncology Department, Ramon y Cajal University Hospital, Madrid, Spain
| | - Elena Elez
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - M.Auxiliadora Gomez-España
- Reina Sofia Hospital, University of Cordoba, Maimonides Institute of Biomedical Research (IMIBIC). Spanish Cancer Network (RTICC), Instituto de Salud Carlos III, Cordoba, Spain
| | | | - Clara Montagut
- Cancer Research Program, IMIM (Hospital del Mar Research Institute), Medical Oncology Department, Hospital del Mar, Barcelona, Spain
| | | | - Jose Luis Manzano
- Institut Català d'Oncologia, Hospital Universitario German Trias i Pujol, Badalona, Spain
| | - Jose M Vieitez
- Hospital Universitario Central de Asturias, Oviedo, Spain
| | | | - Xavier Sanjuan
- Department of Pathology, Hospital Universitari Bellvitge-IDIBELL, Hospitalet de Llobregat, Spain
| | | | - Enrique Aranda
- Reina Sofia Hospital, University of Cordoba, Maimonides Institute of Biomedical Research, Spanish Cancer Network, Instituto de Salud Carlos III, Córdoba, Spain
| | - Josep Tabernero
- Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology, Barcelona, Spain, Barcelona, Spain
| | - Ramon Salazar
- Institut Català d'Oncologia-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
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Azuara D, Santos C, Lopez-Doriga A, Grasselli J, Nadal M, Sanjuan X, Marin F, Vidal J, Montal R, Moreno V, Bellosillo B, Argiles G, Elez E, Dienstmann R, Montagut C, Tabernero J, Capellá G, Salazar R. Nanofluidic Digital PCR and Extended Genotyping of RAS and BRAF for Improved Selection of Metastatic Colorectal Cancer Patients for Anti-EGFR Therapies. Mol Cancer Ther 2016; 15:1106-12. [PMID: 27037411 DOI: 10.1158/1535-7163.mct-15-0820] [Citation(s) in RCA: 14] [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: 10/06/2015] [Accepted: 02/17/2016] [Indexed: 11/16/2022]
Abstract
The clinical significance of low-frequent RAS pathway-mutated alleles and the optimal sensitivity cutoff value in the prediction of response to anti-EGFR therapy in metastatic colorectal cancer (mCRC) patients remains controversial. We aimed to evaluate the added value of genotyping an extended RAS panel using a robust nanofluidic digital PCR (dPCR) approach. A panel of 34 hotspots, including RAS (KRAS and NRAS exons 2/3/4) and BRAF (V600E), was analyzed in tumor FFPE samples from 102 mCRC patients treated with anti-EGFR therapy. dPCR was compared with conventional quantitative PCR (qPCR). Response rates, progression-free survival (PFS), and overall survival (OS) were correlated to the mutational status and the mutated allele fraction. Tumor response evaluations were not available in 9 patients and were excluded for response rate analysis. Twenty-two percent of patients were positive for one mutation with qPCR (mutated alleles ranged from 2.1% to 66.6%). Analysis by dPCR increased the number of positive patients to 47%. Mutated alleles for patients only detected by dPCR ranged from 0.04% to 10.8%. An inverse correlation between the fraction of mutated alleles and radiologic response was observed. ROC analysis showed that a fraction of 1% or higher of any mutated alleles offered the best predictive value for all combinations of RAS and BRAF analysis. In addition, this threshold also optimized prediction both PFS and OS. We conclude that mutation testing using an extended gene panel, including RAS and BRAF with a threshold of 1% improved prediction of response to anti-EGFR therapy. Mol Cancer Ther; 15(5); 1106-12. ©2016 AACR.
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Affiliation(s)
- Daniel Azuara
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Cristina Santos
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain. Department of Medical Oncology, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Adriana Lopez-Doriga
- Unit of Biomarkers and Susceptibility, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Julieta Grasselli
- Department of Medical Oncology, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain. Department of Medical Oncology, Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marga Nadal
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Xavier Sanjuan
- Department of Pathology, University Hospital Bellvitge (HUB-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Fátima Marin
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Joana Vidal
- Department of Medical Oncology, Hospital Universitari del Mar, Barcelona, Spain
| | - Robert Montal
- Department of Medical Oncology, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Beatriz Bellosillo
- Department of Pathology, Hospital Universitari del Mar, Barcelona, Spain
| | - Guillem Argiles
- Department of Medical Oncology, Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Elena Elez
- Department of Medical Oncology, Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Rodrigo Dienstmann
- Department of Medical Oncology, Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Clara Montagut
- Department of Medical Oncology, Hospital Universitari del Mar, Barcelona, Spain
| | - Josep Tabernero
- Department of Medical Oncology, Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Gabriel Capellá
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.
| | - Ramon Salazar
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain. Department of Medical Oncology, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.
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Sanz-Pamplona R, Lopez-Doriga A, Paré-Brunet L, Lázaro K, Bellido F, Alonso MH, Aussó S, Guinó E, Beltrán S, Castro-Giner F, Gut M, Sanjuan X, Closa A, Cordero D, Morón-Duran FD, Soriano A, Salazar R, Valle L, Moreno V. Exome Sequencing Reveals AMER1 as a Frequently Mutated Gene in Colorectal Cancer. Clin Cancer Res 2015; 21:4709-18. [PMID: 26071483 DOI: 10.1158/1078-0432.ccr-15-0159] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Accepted: 05/17/2015] [Indexed: 12/30/2022]
Abstract
PURPOSE Somatic mutations occur at early stages of adenoma and accumulate throughout colorectal cancer progression. The aim of this study was to characterize the mutational landscape of stage II tumors and to search for novel recurrent mutations likely implicated in colorectal cancer tumorigenesis. EXPERIMENTAL DESIGN The exomic DNA of 42 stage II, microsatellite-stable colon tumors and their paired mucosae were sequenced. Other molecular data available in the discovery dataset [gene expression, methylation, and copy number variations (CNV)] were used to further characterize these tumors. Additional datasets comprising 553 colorectal cancer samples were used to validate the discovered mutations. RESULTS As a result, 4,886 somatic single-nucleotide variants (SNV) were found. Almost all SNVs were private changes, with few mutations shared by more than one tumor, thus revealing tumor-specific mutational landscapes. Nevertheless, these diverse mutations converged into common cellular pathways, such as cell cycle or apoptosis. Among this mutational heterogeneity, variants resulting in early stop codons in the AMER1 (also known as FAM123B or WTX) gene emerged as recurrent mutations in colorectal cancer. Losses of AMER1 by other mechanisms apart from mutations such as methylation and copy number aberrations were also found. Tumors lacking this tumor suppressor gene exhibited a mesenchymal phenotype characterized by inhibition of the canonical Wnt pathway. CONCLUSIONS In silico and experimental validation in independent datasets confirmed the existence of functional mutations in AMER1 in approximately 10% of analyzed colorectal cancer tumors. Moreover, these tumors exhibited a characteristic phenotype.
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Affiliation(s)
- Rebeca Sanz-Pamplona
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Adriana Lopez-Doriga
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Laia Paré-Brunet
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Kira Lázaro
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Fernando Bellido
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - M Henar Alonso
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Susanna Aussó
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Elisabet Guinó
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Sergi Beltrán
- Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain
| | | | - Marta Gut
- Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain
| | - Xavier Sanjuan
- Pathology Service, University Hospital Bellvitge (HUB-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Adria Closa
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - David Cordero
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Francisco D Morón-Duran
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Antonio Soriano
- Gastroenterology Service, University Hospital Bellvitge (HUB-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ramón Salazar
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain. Translational Research Laboratory, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain. Department of Clinical Sciences, Faculty of Medicine, University of Barcelona (UB), Barcelona, Spain.
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Montal R, Merche MV, Anta B, Martínez N, Santos C, Sanjuan X, Paúles M, Pérez Martín F, Azuara D, Salazar R, Rojas J. P-195 SPRY2 and response to FOLFOX/CAPOX in metastatic KRAS mutated colorectal cancer. Ann Oncol 2015. [DOI: 10.1093/annonc/mdv233.193] [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: 11/12/2022] Open
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Azuara D, Santos C, Lopez-Doriga A, Grasselli J, Nadal M, Sanjuan X, Marin F, Morell M, Montal R, Moreno V, Montagut C, Bellosillo B, Argiles G, Elez E, Tabernero J, Capellá G, Salazar R. O-012 Nanofluidic digital PCR and extended genotyping of RAS, BRAF and PI3KCA for improved selection of metastatic colorectal cancer patients to anti-EGFR therapies. Ann Oncol 2015. [DOI: 10.1093/annonc/mdv235.11] [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: 11/13/2022] Open
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27
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Santos C, Navarro-Perez V, Fernandez MEE, Massuti B, Valladares Ayerbes M, Vieitez de Prado JM, Mozo JLM, Gallego Plazas J, Gravalos Castro C, Carrato A, Varela M, Safont MJ, Alonso V, Falco E, Escudero MP, Sanjuan X, Tabernero J, Capella G, Salazar R, Aranda E. Comparison of three different molecular methods to detect mutations in KRAS, NRAS, BRAF and PIK3CA in metastatic colorectal cancer samples (mCRC): Interim analysis of a Spanish cohort. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.e14613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Cristina Santos
- Translational Research Laboratory and Department of Medical Oncology, Institut Català d'Oncologia-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Valentín Navarro-Perez
- Clinical Research Unit, Institut Català d'Oncologia, IDIBELL, Hospitalet de Llobrega, Barcelona, Spain
| | | | | | | | | | | | | | | | - Alfredo Carrato
- Ramon y Cajal University Hospital, Medical Oncology Department, Madrid, Spain
| | - Mar Varela
- ICO. H.ospital Duran i Reynals, Barcelona, Spain
| | | | | | | | | | - Xavier Sanjuan
- Department of Pathology, Hospital Universitari Bellvitge-IDIBELL, Hospitalet de Llobregat, Spain
| | | | | | - Ramon Salazar
- Institut Català d'Oncologia-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Enrique Aranda
- Reina Sofía Hospital, University of Córdoba, Maimonides Institute of Biomedical Research (IMIBIC). Spanish Cancer Network (RTICC), Instituto de Salud Carlos III, Córdoba, Spain
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Pérez-Vilaró G, Fernández-Carrillo C, Mensa L, Miquel R, Sanjuan X, Forns X, Pérez-del-Pulgar S, Díez J. Hepatitis C virus infection inhibits P-body granule formation in human livers. J Hepatol 2015; 62:785-90. [PMID: 25463546 DOI: 10.1016/j.jhep.2014.11.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 10/28/2014] [Accepted: 11/06/2014] [Indexed: 12/04/2022]
Abstract
BACKGROUND & AIMS Decoding the myriad of interactions that hepatitis C virus (HCV) establishes with infected cells is mandatory to obtain a complete understanding of HCV biology and its associated pathogenesis. We and others have previously found that HCV infection disrupts the formation of P-bodies in cell culture. These are cytoplasmic RNA granules with key roles in post-transcriptional regulation of gene expression. Therefore, P-body disruption might have consequences beyond viral propagation. However, whether P-body disruption occurs also in vivo is unknown. Aim of this study was to address this important issue. METHODS Formalin-fixed paraffin-embedded liver biopsies from four groups of patients (healthy donors, patients with non-virus related liver inflammation, HCV- and HBV-infected patients) were immunostained to detect DDX6 and Dcp1, two core P-body components. Changes in the localization of these proteins were assessed by confocal microscopy. RESULTS HCV specifically inhibited P-body formation in hepatocytes from human livers regardless of viral genotype, inflammation grade or whether the infection was recent or long established. Importantly, this alteration was reversed once HCV was eliminated by therapy. Furthermore, we observed in vivo an unexpected heterogeneity in P-body composition, which might reflect functional specializations. CONCLUSIONS This is the first comprehensive in vivo P-body analysis that links a pathogenic condition to P-body alterations. Because of their role in gene expression, the alteration of P-bodies should be further studied to understand fully complex HCV-associated pathologies.
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Affiliation(s)
| | | | - Laura Mensa
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, Barcelona, Spain
| | - Rosa Miquel
- Pathology Department, Hospital Clínic, Barcelona, Spain
| | - Xavier Sanjuan
- Scientific and Technical Services, Universitat Pompeu Fabra, Barcelona, Spain; Advanced Light Microscopy Unit, Center for Genomic Regulation, Barcelona, Spain
| | - Xavier Forns
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, Barcelona, Spain
| | | | - Juana Díez
- Molecular Virology, Universitat Pompeu Fabra, Barcelona, Spain.
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Guardiola J, Lobatón T, Rodríguez-Alonso L, Ruiz-Cerulla A, Arajol C, Loayza C, Sanjuan X, Sánchez E, Rodríguez-Moranta F. Fecal level of calprotectin identifies histologic inflammation in patients with ulcerative colitis in clinical and endoscopic remission. Clin Gastroenterol Hepatol 2014; 12:1865-70. [PMID: 24993368 DOI: 10.1016/j.cgh.2014.06.020] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 06/03/2014] [Accepted: 06/05/2014] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Histologic recovery of patients with ulcerative colitis (UC) often is incomplete, even among those in clinical and endoscopic remission. Persistent active microscopic inflammation is associated with an increased risk of relapse and colorectal neoplasia. A high level of fecal calprotectin (FC) is a reliable marker of endoscopic lesions in patients with UC. We evaluated the accuracy of FC in identifying patients with UC in clinical and endoscopic remission who still have histologic features of inflammation. METHODS We performed a prospective observational study of 59 patients with UC in clinical and endoscopic remission undergoing colonoscopy. Several biopsy specimens were collected from each colonic segment. Endoscopic remission was defined as a Mayo endoscopic subscore with a grade of 0 or 1. Active histologic inflammation was defined by the presence of neutrophils infiltrating crypt epithelial cells. FC was determined by enzyme-linked immunosorbent assay analysis. RESULTS Eighteen patients (30.5%) showed evidence of active histologic inflammation. Patients with active histologic inflammation had a significantly higher median level of FC (278 μg/g; interquartile range, 136-696 μg/g) than those without active histologic inflammation (68 μg/g; interquartile range, 30-172 μg/g) (P = .002). In multivariate analysis, the FC and Mayo endoscopic subscore (0 or 1) were each independent predictors of histologic inflammation. The level of FC identified active histologic inflammation in patients in clinical and endoscopic remission, with an area under the receiver operator characteristic curve value of 0.754. CONCLUSIONS Histologic inflammation is common among patients with UC in clinical and endoscopic remission. Patients with histologic features of inflammation can be identified reliably based on their fecal level of calprotectin.
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Affiliation(s)
- Jordi Guardiola
- Department of Gastroenterology, Hospital Universitari de Bellvitge-Institut d'Investigació Biomédica de Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain.
| | - Triana Lobatón
- Department of Gastroenterology, Hospital Universitari de Bellvitge-Institut d'Investigació Biomédica de Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Lorena Rodríguez-Alonso
- Department of Gastroenterology, Hospital Universitari de Bellvitge-Institut d'Investigació Biomédica de Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Alexandra Ruiz-Cerulla
- Department of Gastroenterology, Hospital Universitari de Bellvitge-Institut d'Investigació Biomédica de Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Claudia Arajol
- Department of Gastroenterology, Hospital Universitari de Bellvitge-Institut d'Investigació Biomédica de Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Carolina Loayza
- Department of Pathology, Hospital Universitari de Bellvitge-Institut d'Investigació Biomédica de Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Xavier Sanjuan
- Department of Pathology, Hospital Universitari de Bellvitge-Institut d'Investigació Biomédica de Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Elena Sánchez
- Department of Gastroenterology, Hospital Universitari de Bellvitge-Institut d'Investigació Biomédica de Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Francisco Rodríguez-Moranta
- Department of Gastroenterology, Hospital Universitari de Bellvitge-Institut d'Investigació Biomédica de Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
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Jové M, Mora J, Sanjuan X, Rodriguez E, Robledo M, Farran L, Garcia del Muro X. Simultaneous KIT mutation and succinate dehydrogenase (SDH) deficiency in a patient with a gastrointestinal stromal tumour and Carney-Stratakis syndrome: a case report. Histopathology 2014; 65:712-7. [DOI: 10.1111/his.12506] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria Jové
- Department of Medical Oncology; Institut Català d'Oncologia; L'Hospitalet de Llobregat; Barcelona Spain
| | - Jaume Mora
- Department of Pediatric Oncology; Hospital Sant Joan de Déu (HSJD); Barcelona Spain
| | - Xavier Sanjuan
- Department of Pathology; Hospital Universitari de Bellvitge; L'Hospitalet de Llobregat; Barcelona Spain
| | - Eva Rodriguez
- Department of Pediatric Oncology; Hospital Sant Joan de Déu (HSJD); Barcelona Spain
| | - Mercedes Robledo
- Hereditary Endocrine Cancer, Group Leader, Human Cancer Genetics Programme; Spanish National Cancer Centre (CNIO); Madrid Spain
| | - Leandre Farran
- Department of Surgery; Hospital Universitari de Bellvitge; L'Hospitalet de Llobregat; Barcelona Spain
| | - Xavier Garcia del Muro
- Department of Medical Oncology; Institut Català d'Oncologia; L'Hospitalet de Llobregat; Barcelona Spain
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Boni V, De La Portilla F, Cubillo A, Gil-Martin M, Calvo E, Salazar R, Santos C, Sanchez-Gastaldo A, Prados S, Sanjuan X, Bozada J, Duran H, Jurado M, Ellis C, Alvis S, Beadle J, Fisher K, Blanc C, Garcia-Carbonero R. A Phase 1 Mechanism of Action Study of Intra-Tumoural (It) or Intravenous (Iv) Administration of Enadenotucirev, an Oncolytic Ad11/Ad3 Chimeric Group B Adenovirus in Colon Cancer Patients Undergoing Resection of Primary Tumour. Ann Oncol 2014. [DOI: 10.1093/annonc/mdu342.21] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Maurel J, Lopez-Pousa A, Calabuig S, Bagué S, Del Muro XG, Sanjuan X, Rubió J, Cuatrecasas M, Martinez-Trufero J, Horndler C, Fra J, Morales CV, Redondo A, Poveda A, Sevilla I, Lainez N, Rubini M, Albéniz XG, Broto JM, De Álava E. Prognosis of Phosphorylated-Insulin Growth Factor Receptor (P-Igf-1R) and Metalloproteinase-3 (Mmp3) Expression in Advanced Gastrointestinal Stromal Tumors (Gist) Patients Treated with Imatinib. a Geis Study. Ann Oncol 2014. [DOI: 10.1093/annonc/mdu326.61] [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: 11/14/2022] Open
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33
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Lobatón T, Azuara D, Rodríguez-Moranta F, Loayza C, Sanjuan X, de Oca J, Fernández-Robles A, Guardiola J, Capellá G. Relationship between methylation and colonic inflammation in inflammatory bowel disease. World J Gastroenterol 2014; 20:10591-10598. [PMID: 25132780 PMCID: PMC4130871 DOI: 10.3748/wjg.v20.i30.10591] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 04/23/2014] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the relationship between the methylation status in the SLIT2 and TGFB2 promoters and colonic inflammation in inflammatory bowel disease patients.
METHODS: We evaluated the methylation status of 2 genes (SLIT2 and TGFB2) in 226 biopsies taken from 62 colonoscopies of 38 patients (29 ulcerative colitis and 9 Crohn’s colitis) using methylation-specific melting curve analysis. The relationships between methylation status and clinical, biological, endoscopic and histological activities were evaluated. Twenty-three of the 38 patients had a second colonoscopy and were included in a longitudinal analysis. Numerical results were given as the means ± SD of the sample and range, except when specified. Student t analysis, U Mann Whitney and ANOVA factor were used to compare the means. Qualitative results were based on the χ2 test.
RESULTS: SLIT2 methylation was more frequent in samples with endoscopic activity than with endoscopic remission (55% vs 18%, P < 0.001). SLIT2 methylation was also higher in samples with acute inflammation (56.5%) than in samples with chronic (24%) or absent inflammation (15%) (P < 0.001). For TGFB2 methylation, the correlation was only significant with endoscopic activity. Methylation was higher in the distal colon for both genes (P < 0.001 for SLIT2 and P = 0.022 for TGFB2). In the multivariate analysis, only inflammation status (and not disease duration or extension) was independently associated with SLIT2 methylation [OR = 6.6 (95%CI: 1.65-27.36), P = 0.009]. In the longitudinal analysis, the maintenance of endoscopic remission was protective for methylation.
CONCLUSION: Endoscopic and histological inflammation are predictive for SLIT2 methylation.
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Garcia-Carbonero R, Gil-Martin M, Calvo E, Prados S, De la Portilla F, Salazar R, Santos C, Sanchez-Gastaldo A, Duran H, Sanjuan X, Bozada JM, Boni V, Jurado M, Ellis C, Alvis S, Beadle JW, Fisher K, Blanc C, Cubillo A. A phase 1 mechanism of action study of intratumoral or intravenous administration of enadenotucirev, an oncolytic Ad11/Ad3 chimeric group B adenovirus in colon cancer patients undergoing resection of primary tumor. J Clin Oncol 2014. [DOI: 10.1200/jco.2014.32.15_suppl.tps3112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Rocio Garcia-Carbonero
- Hospital Universitario Virgen del Rocio, Instituto de Biomedicina de Sevilla, Sevilla, Spain
| | - Marta Gil-Martin
- Early Clinical Research Unit, Institut Català d'Oncologia, L´Hospitalet-Barcelona, Spain
| | | | - Susana Prados
- Centro Integral Oncológico Clara Campal, Madrid, Spain
| | | | - Ramon Salazar
- Early Clinical Research Unit, Institut Català d'Oncologia, L´Hospitalet-Barcelona, Spain
| | - Cristina Santos
- Translational Research Laboratory and Department of Medical Oncology, Institut Català d'Oncologia-IDIBELL, L'Hospitalet de Llobregat, Spain
| | | | | | - Xavier Sanjuan
- Department of Pathology, Hospital Universitari Bellvitge-IDIBELL, Hospitalet de Llobregat, Spain
| | - Juan M. Bozada
- Gastroenterology Department, Hospital Universitario Virgen del Rocio, Sevilla, Spain
| | - Valentina Boni
- START Madrid, Centro Integral Oncológico Clara Campal, Madrid, Spain
| | | | | | | | | | | | | | - Antonio Cubillo
- START Madrid, Centro Integral Oncológico Clara Campal, Madrid, Spain
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35
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Garcia del Muro X, Lopez-Pousa A, Martinez-Trufero J, Martin Broto J, Cubedo R, Lavernia J, Redondo A, Lopez-Martin JA, Mulet-Margalef N, Sanjuan X, M. Tirado O. Phase II study of gemcitabine (GEM) plus sirolimus (SIR) in previously treated patients with advanced soft tissue sarcoma (STS): A Spanish Group for Research on Sarcomas (GEIS) study. J Clin Oncol 2014. [DOI: 10.1200/jco.2014.32.15_suppl.10594] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Xavier Sanjuan
- Department of Pathology, Hospital Universitari Bellvitge-IDIBELL, Hospitalet de Llobregat, Spain
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Berdiel-Acer M, Cuadras D, Díaz-Maroto NG, Sanjuan X, Serrano T, Berenguer A, Moreno V, Gonçalves-Ribeiro S, Salazar R, Villanueva A, Molleví DG. A monotonic and prognostic genomic signature from fibroblasts for colorectal cancer initiation, progression, and metastasis. Mol Cancer Res 2014; 12:1254-66. [PMID: 24829396 DOI: 10.1158/1541-7786.mcr-14-0121] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
UNLABELLED The differential gene expression patterns between normal colonic fibroblasts (NCF), carcinoma-associated fibroblasts from primary tumors (CAF-PT), and CAFs from hepatic metastasis (CAF-LM) are hypothesized to be useful for predicting relapse in primary tumors. A transcriptomic profile of NCF (n = 9), CAF-PT (n = 14), and CAF-LM (n = 11) was derived. Prediction Analysis of Microarrays (PAM) was used to obtain molecular details for each fibroblast class, and differentially expressed transcripts were used to classify patients according to recurrence status. A number of transcripts (n = 277) were common to all three types of fibroblasts and whose expression level was sequentially deregulated according to the transition: NCF→CAF-PT→CAF-LM. Importantly, the gene signature was able to accurately classify patients with primary tumors according to their prognosis. This capacity was exploited to obtain a refined 19-gene classifier that predicted recurrence with high accuracy in two independent datasets of patients with colorectal cancer and correlates with fibroblast migratory potential. The prognostic power of this genomic signature is strong evidence of the link between the tumor-stroma microenvironment and cancer progression. Furthermore, the 19-gene classifier was able to identify low-risk patients very accurately, which is of particular importance for stage II patients, who would benefit from the omission of chemotherapy, especially T4N0 patients, who are clinically classified as being at high risk. IMPLICATIONS A defined stromal gene expression signature predicts relapse in patients with colorectal cancer.
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Affiliation(s)
- Mireia Berdiel-Acer
- Translational Research Laboratory, Department of Medicine, Autonomous University of Barcelona, Bellaterra, Barcelona, Catalonia, Spain
| | | | | | - Xavier Sanjuan
- Pathology Department, Hospital Universitari de Bellvitge-IDIBELL, IDIBELL, Barcelona; and
| | - Teresa Serrano
- Pathology Department, Hospital Universitari de Bellvitge-IDIBELL, IDIBELL, Barcelona; and
| | | | | | | | - Ramon Salazar
- Medical Oncology Department, Institut Català d'Oncologia-ICO
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37
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Berdiel-Acer M, Sanz-Pamplona R, Calon A, Cuadras D, Berenguer A, Sanjuan X, Paules MJ, Salazar R, Moreno V, Batlle E, Villanueva A, Molleví DG. Differences between CAFs and their paired NCF from adjacent colonic mucosa reveal functional heterogeneity of CAFs, providing prognostic information. Mol Oncol 2014; 8:1290-305. [PMID: 24839936 DOI: 10.1016/j.molonc.2014.04.006] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [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: 02/10/2014] [Revised: 04/14/2014] [Accepted: 04/15/2014] [Indexed: 12/18/2022] Open
Abstract
Little is known about the difference in gene expression between carcinoma-associated fibroblasts (CAFs) and paired normal colonic fibroblasts (NCFs) in colorectal cancer. Paired CAFs and NCFs were isolated from eight primary human colorectal carcinoma specimens. In culture conditions, soluble factors secreted by CAFs in the conditioned media increased clonogenicity and migration of epithelial cancer cells lines to a greater extent than did NCF. In vivo, CAFs were more competent as tumour growth enhancers than paired NCFs when co-inoculated with colorectal cell lines. Gene expression analysis of microarrays of CAF and paired NCF populations enabled us to identify 108 deregulated genes (38 upregulated and 70 downregulated genes). Most of those genes are fibroblast-specific. This has been validated in silico in dataset GSE39396 and by qPCR in selected genes. GSEA analysis revealed a differential transcriptomic profile of CAFs, mainly involving the Wnt signallingsignalling pathway, focal adhesion and cell cycle. Both deregulated genes and biological processes involved depicted a considerable degree of overlap with deregulated genes reported in breast, lung, oesophagus and prostate CAFs. These observations suggest that similar transcriptomic programs may be active in the transition from normal fibroblast in adjacent tissues to CAFs, independently of their anatomic demarcation. Additionally NCF already depicted an activated pattern associated with inflammation. The deregulated genes signature score seemed to correlate with CAF tumour promoter abilities in vitro, suggesting a high degree of heterogeneity between CAFs, and it has also prognostic value in two independent datasets. Further characterization of the roles these biomarkers play in cancer will reveal how CAFs provide cancer cells with a suitable microenvironment and may help in the development of new therapeutic targets for cancer treatment.
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Affiliation(s)
- Mireia Berdiel-Acer
- Translational Research Laboratory, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, 08908 Catalonia, Spain
| | - Rebeca Sanz-Pamplona
- Biomarkers and Susceptibility Unit, Cancer Prevention and Monitoring Programme, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Catalonia, Spain
| | - Alexandre Calon
- Oncology Programme, Institute for Research in Biomedicine IRB, Barcelona, Catalonia, Spain
| | - Daniel Cuadras
- Biomarkers and Susceptibility Unit, Cancer Prevention and Monitoring Programme, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Catalonia, Spain
| | - Antoni Berenguer
- Biomarkers and Susceptibility Unit, Cancer Prevention and Monitoring Programme, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Catalonia, Spain
| | - Xavier Sanjuan
- Pathology Department, Hospital Universitari de Bellvitge, IDIBELL, L'Hospitalet de Llobregat, Catalonia, Spain
| | - Maria José Paules
- Pathology Department, Hospital Universitari de Bellvitge, IDIBELL, L'Hospitalet de Llobregat, Catalonia, Spain
| | - Ramon Salazar
- Medical Oncology Department, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Catalonia, Spain
| | - Victor Moreno
- Biomarkers and Susceptibility Unit, Cancer Prevention and Monitoring Programme, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Catalonia, Spain
| | - Eduard Batlle
- Oncology Programme, Institute for Research in Biomedicine IRB, Barcelona, Catalonia, Spain
| | - Alberto Villanueva
- Translational Research Laboratory, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, 08908 Catalonia, Spain
| | - David G Molleví
- Translational Research Laboratory, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, 08908 Catalonia, Spain.
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38
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Lopez-Serra P, Marcilla M, Villanueva A, Ramos-Fernandez A, Palau A, Leal L, Wahi JE, Setien-Baranda F, Szczesna K, Moutinho C, Martinez-Cardus A, Heyn H, Sandoval J, Puertas S, Vidal A, Sanjuan X, Martinez-Balibrea E, Viñals F, Perales JC, Bramsem JB, Ørntoft TF, Andersen CL, Tabernero J, McDermott U, Boxer MB, Heiden MGV, Albar JP, Esteller M. A DERL3-associated defect in the degradation of SLC2A1 mediates the Warburg effect. Nat Commun 2014; 5:3608. [PMID: 24699711 PMCID: PMC3988805 DOI: 10.1038/ncomms4608] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [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: 10/24/2013] [Accepted: 03/10/2014] [Indexed: 01/03/2023] Open
Abstract
Cancer cells possess aberrant proteomes that can arise by the disruption of genes involved in physiological protein degradation. Here we demonstrate the presence of promoter CpG island hypermethylation-linked inactivation of DERL3 (Derlin-3), a key gene in the endoplasmic reticulum-associated protein degradation pathway, in human tumours. The restoration of in vitro and in vivo DERL3 activity highlights the tumour suppressor features of the gene. Using the stable isotopic labelling of amino acids in cell culture workflow for differential proteome analysis, we identify SLC2A1 (glucose transporter 1, GLUT1) as a downstream target of DERL3. Most importantly, SLC2A1 overexpression mediated by DERL3 epigenetic loss contributes to the Warburg effect in the studied cells and pinpoints a subset of human tumours with greater vulnerability to drugs targeting glycolysis.
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Affiliation(s)
- Paula Lopez-Serra
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | - Miguel Marcilla
- Proteomics Unit, Spanish National Biotechnology Centre (CNB), CSIC, 28049 Madrid, Spain
| | - Alberto Villanueva
- Translational Research Laboratory, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | | | - Anna Palau
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | - Lucía Leal
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | - Jessica E. Wahi
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | - Fernando Setien-Baranda
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | - Karolina Szczesna
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | - Catia Moutinho
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | - Anna Martinez-Cardus
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | - Holger Heyn
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | - Juan Sandoval
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | - Sara Puertas
- Translational Research Laboratory, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | - August Vidal
- Bellvitge Biomedical Research Institute (IDIBELL), Department of Pathology, Bellvitge University Hospital, L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | - Xavier Sanjuan
- Bellvitge Biomedical Research Institute (IDIBELL), Department of Pathology, Bellvitge University Hospital, L'Hospitalet, Barcelona, 08908 Catalonia, Spain
| | - Eva Martinez-Balibrea
- Medical Oncology Service, Catalan Institute of Oncology (ICO), l'Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Hospital Germans Trias I Pujol, Badalona, Barcelona, 08916 Catalonia, Spain
| | - Francesc Viñals
- Translational Research Laboratory, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, 08036 Barcelona, Spain
| | - Jose C. Perales
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, 08036 Barcelona, Spain
| | - Jesper B. Bramsem
- Department of Molecular Medicine, Aarhus University Hospital, Brendstrupgaardsvej 100, Aarhus N, DK-8200 Aarhus, Denmark
| | - Torben F. Ørntoft
- Department of Molecular Medicine, Aarhus University Hospital, Brendstrupgaardsvej 100, Aarhus N, DK-8200 Aarhus, Denmark
| | - Claus L. Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Brendstrupgaardsvej 100, Aarhus N, DK-8200 Aarhus, Denmark
| | - Josep Tabernero
- Medical Oncology Department, Vall d’Hebron University Hospital, Barcelona, 08035 Catalonia, Spain
| | - Ultan McDermott
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Matthew B. Boxer
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20891-4874, USA
| | - Matthew G. Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Juan Pablo Albar
- Proteomics Unit, Spanish National Biotechnology Centre (CNB), CSIC, 28049 Madrid, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, 08908 Catalonia, Spain
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, 08036 Barcelona, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, 08010 Catalonia, Spain
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Sanz-Pamplona R, Berenguer A, Cordero D, Molleví DG, Crous-Bou M, Sole X, Paré-Brunet L, Guino E, Salazar R, Santos C, de Oca J, Sanjuan X, Rodriguez-Moranta F, Moreno V. Aberrant gene expression in mucosa adjacent to tumor reveals a molecular crosstalk in colon cancer. Mol Cancer 2014; 13:46. [PMID: 24597571 PMCID: PMC4023701 DOI: 10.1186/1476-4598-13-46] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 02/19/2014] [Indexed: 01/01/2023] Open
Abstract
Background A colorectal tumor is not an isolated entity growing in a restricted location of the body. The patient’s gut environment constitutes the framework where the tumor evolves and this relationship promotes and includes a complex and tight correlation of the tumor with inflammation, blood vessels formation, nutrition, and gut microbiome composition. The tumor influence in the environment could both promote an anti-tumor or a pro-tumor response. Methods A set of 98 paired adjacent mucosa and tumor tissues from colorectal cancer (CRC) patients and 50 colon mucosa from healthy donors (246 samples in total) were included in this work. RNA extracted from each sample was hybridized in Affymetrix chips Human Genome U219. Functional relationships between genes were inferred by means of systems biology using both transcriptional regulation networks (ARACNe algorithm) and protein-protein interaction networks (BIANA software). Results Here we report a transcriptomic analysis revealing a number of genes activated in adjacent mucosa from CRC patients, not activated in mucosa from healthy donors. A functional analysis of these genes suggested that this active reaction of the adjacent mucosa was related to the presence of the tumor. Transcriptional and protein-interaction networks were used to further elucidate this response of normal gut in front of the tumor, revealing a crosstalk between proteins secreted by the tumor and receptors activated in the adjacent colon tissue; and vice versa. Remarkably, Slit family of proteins activated ROBO receptors in tumor whereas tumor-secreted proteins transduced a cellular signal finally activating AP-1 in adjacent tissue. Conclusions The systems-level approach provides new insights into the micro-ecology of colorectal tumorogenesis. Disrupting this intricate molecular network of cell-cell communication and pro-inflammatory microenvironment could be a therapeutic target in CRC patients.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain.
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Grünberg R, Burnier JV, Ferrar T, Beltran-Sastre V, Stricher F, van der Sloot AM, Garcia-Olivas R, Mallabiabarrena A, Sanjuan X, Zimmermann T, Serrano L. Engineering of weak helper interactions for high-efficiency FRET probes. Nat Methods 2013; 10:1021-7. [PMID: 23995386 DOI: 10.1038/nmeth.2625] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [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: 04/09/2013] [Accepted: 07/20/2013] [Indexed: 12/19/2022]
Abstract
Fluorescence resonance energy transfer (FRET)-based detection of protein interactions is limited by the very narrow range of FRET-permitting distances. We show two different strategies for the rational design of weak helper interactions that co-recruit donor and acceptor fluorophores for a more robust detection of bimolecular FRET: (i) in silico design of electrostatically driven encounter complexes and (ii) fusion of tunable domain-peptide interaction modules based on WW or SH3 domains. We tested each strategy for optimization of FRET between (m)Citrine and mCherry, which do not natively interact. Both approaches yielded comparable and large increases in FRET efficiencies with little or no background. Helper-interaction modules can be fused to any pair of fluorescent proteins and could, we found, enhance FRET between mTFP1 and mCherry as well as between mTurquoise2 and mCitrine. We applied enhanced helper-interaction FRET (hiFRET) probes to study the binding between full-length H-Ras and Raf1 as well as the drug-induced interaction between Raf1 and B-Raf.
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Affiliation(s)
- Raik Grünberg
- 1] EMBL/CRG Systems Biology Research Unit, Center for Genomic Regulation, Barcelona, Spain. [2] Pompeu Fabra University, Barcelona, Spain. [3] Institut de Recherche en Immunologie et en Cancérologie, Université de Montréal, Montréal, Canada
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Azuara D, Santos C, Lopez-Doriga A, Montal R, Nadal M, Sanjuan X, Moreno V, Tabernero J, Montagut C, Salazar R, Capellá G. Nanofluidic Digital PCR for Improved Selection of Metastatic Colorectal Cancer Patients to Anti-EGFR Therapies. Ann Oncol 2013. [DOI: 10.1093/annonc/mdt201.11] [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: 11/13/2022] Open
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Santos C, Terricabras M, Lopez-Doriga A, Gonzalez S, Fernández A, Martinez-Iniesta M, Sanjuan X, García-Molleví D, Villanueva A, Teule A, Merche MV, Soler G, Kreisler E, Moreno V, Biondo S, Capellá G, Salazar R. Prognostic Biomarkers in a Series of Stage II Colon Cancer. Ann Oncol 2013. [DOI: 10.1093/annonc/mdt202.4] [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: 11/14/2022] Open
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Borràs E, Pineda M, Cadiñanos J, Del Valle J, Brieger A, Hinrichsen I, Cabanillas R, Navarro M, Brunet J, Sanjuan X, Musulen E, van der Klift H, Lázaro C, Plotz G, Blanco I, Capellá G. Refining the role of PMS2 in Lynch syndrome: germline mutational analysis improved by comprehensive assessment of variants. J Med Genet 2013; 50:552-63. [PMID: 23709753 DOI: 10.1136/jmedgenet-2012-101511] [Citation(s) in RCA: 42] [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] [Indexed: 12/21/2022]
Abstract
BACKGROUND AND AIM The majority of mismatch repair (MMR) gene mutations causing Lynch syndrome (LS) occur either in MLH1 or MSH2. However, the relative contribution of PMS2 is less well defined. The aim of this study was to evaluate the role of PMS2 in LS by assessing the pathogenicity of variants of unknown significance (VUS) detected in the mutational analysis of PMS2 in a series of Spanish patients. METHODS From a cohort of 202 LS suspected patients, 13 patients showing loss of PMS2 expression in tumours were screened for germline mutations in PMS2, using a long range PCR based strategy and multiplex ligation dependent probe amplification (MLPA). Pathogenicity assessment of PMS2 VUS was performed evaluating clinicopathological data, frequency in control population and in silico and in vitro analyses at the RNA and protein level. RESULTS Overall 25 different PMS2 DNA variants were detected. Fourteen were classified as polymorphisms. Nine variants were classified as pathogenic: seven alterations based on their molecular nature and two after demonstrating a functional defect (c.538-3C>G affected mRNA processing and c.137G>T impaired MMR activity). The c.1569C>G variant was classified as likely neutral while the c.384G>A remained as a VUS. We have also shown that the polymorphic variant c.59G>A is MMR proficient. CONCLUSIONS Pathogenic PMS2 mutations were detected in 69% of patients harbouring LS associated tumours with loss of PMS2 expression. In all, PMS2 mutations account for 6% of the LS cases identified. The comprehensive functional analysis shown here has been useful in the classification of PMS2 VUS and contributes to refining the role of PMS2 in LS.
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Affiliation(s)
- Ester Borràs
- Hereditary Cancer Program, Catalan Institute of Oncology, ICO-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
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Santos C, Terricabras M, Lopez-Doriga A, Gonzalez S, Fernandez A, Martinez Iniesta M, Sanjuan X, Garcia-Molleva D, Villanueva A, Moreno V, Biondo S, Kreisler E, Capella G, Salazar R. Prognostic biomarkers in a series of stage II colon cancer. J Clin Oncol 2013. [DOI: 10.1200/jco.2013.31.15_suppl.3629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3629 Background: Different clinico-pathological factors are used to define a group of patients with high-risk stage II colon cancer (CC) that may benefit of adjuvant treatment. Moreover, several molecular markers, such as microsatellite instability (MSI) and BRAF, have been widely investigated as prognostic factors. Recently a high stroma component (EMT+ subtypes) has also been associated with poor outcome. The aim of the study is to analyze the prognostic value of MSI, BRAF and tumor-stroma ratio in a prospective series of stage II CC patients. Methods: FFPE tissue from 432 stage II CC patients operated at Hospital Universitari de Bellvitge (1996 - 2006) were included in the study. MSI status was assessed by the analysis of 5 mononucleotide repeat markers (BAT-25, BAT-26, NR-21, NR-24 and MONO-27). BRAF V600E mutation was analyzed by single strand conformation polymorphism technique. Tumor-stroma ratio was analyzed by immunohistochemistry. Associations between molecular factors and clinical features were assessed by Chi-Squared (X2) tests. A Cox regression model was used to evaluate the Relapse Free (RFS) and the Colon Cancer specific Survival. Results: MSI status could be determined in 350 patients. 48 (14%) had MSI high (MSI-H) tumor. BRAF status could be assessed in 380 cases. 58 (15%) cases were BRAF mutated. Tumor-stroma ratio was analyzed in 407 tumor samples. 176 (43%) tumors had more than 50% intra-tumor stroma and were classified as stroma-high. MSI-H tumors were significantly located in right colon (X2 p-value = 1.03e-5), were poorly differentiated (X2 p-value = 0.003) and had more than 12 lymph nodes resected (X2 p-value = 0.037). MSI-H tumors were associated with BRAF mutation (X2 p-value = 0.02) and stroma-low (X2 p-value = 0.0005). When a molecular prognostic risk classification was performed, patients with MSI-H /stroma-low suggested a low risk of relapse comparing to MSI-H/stroma-high, microsatellite stable (MSS)/stroma-low and MSS/stroma-high patients (HR = 3.15; 95 CI, 0.76 – 13.1, p-value = 0.0602). Conclusions: MSI-H tumors have BRAF mutation as well as low intra-tumor stroma. Our results suggest that tumor-stroma ratio can explain differential prognosis in MSI-H stage II tumors.
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Affiliation(s)
- Cristina Santos
- Department of Medical Oncology, Institut Català d'Oncologia-IDIBELL, L'Hospitalet de LLobregat, Spain
| | - Marta Terricabras
- Department of Pathology, Hospital Universitari de Bellvitge-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Adriana Lopez-Doriga
- Biomarkers and Susceptibility Unit, Institut Català d'Oncologia-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Sara Gonzalez
- Translational Research Laboratory, Institut Català d'Oncologia-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Anna Fernandez
- Translational Research Laboratory, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Maria Martinez Iniesta
- Translational Research Laboratory, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Xavier Sanjuan
- Department of Pathology, Hospital Universitari Bellvitge-IDIBELL, Hospitalet de Llobregat, Spain
| | - David Garcia-Molleva
- Translational Research Laboratory, Institut Catala d'Oncologia-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Alberto Villanueva
- Translational Research Laboratory, Institut Català d'Oncologia-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Victor Moreno
- IDIBELL, Institut Catala d'Oncologia, L'Hospitalet de Llobregat, Spain
| | - Sebastiano Biondo
- Surgery Department, Hospital Universitari de Bellvitge-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Esther Kreisler
- Surgery Department, Hospital Universitari de Bellvitge-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Gabriel Capella
- Translational Research Laboratory, Institut Català d´Oncologia-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Ramon Salazar
- Translational Research Laboratory, Institut Catala d'Oncologia - IDIBELL, L'Hospitalet de Llobregat, Spain
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Santos C, López-Doriga A, Navarro M, Mateo J, Biondo S, Martínez Villacampa M, Soler G, Sanjuan X, Paules MJ, Laquente B, Guinó E, Kreisler E, Frago R, Germà JR, Moreno V, Salazar R. Clinicopathological risk factors of Stage II colon cancer: results of a prospective study. Colorectal Dis 2013; 15:414-22. [PMID: 22974322 DOI: 10.1111/codi.12028] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
AIM Adjuvant 5-fluorouracil based chemotherapy has demonstrated benefit in Stage III colon cancer but still remains controversial in Stage II. The aim of this study was to analyse the prognostic impact of clinicopathological factors that may help guide treatment decisions in Stage II colon cancer. METHOD Between 1996 and 2006 data from patients diagnosed with colorectal cancer at Hospital Universitari Bellvitge and its referral comprehensive cancer centre Institut Català d'Oncologia/L'Hospitalet were prospectively included in a database. We identified 432 patients with Stage II colon cancer operated on at Hospital Universitari Bellvitge. The 5-year relapse-free survival (RFS) and colon-cancer-specific survival (CCSS) were determined. RESULTS The 5-year RFS and CCSS were 83% and 88%, respectively. Lymphovascular or perineural invasion was associated with RFS [hazard ratio (HR) 1.84; 95% CI 1.01-3.35]. Gender (women, HR 0.48; 95% CI 0.23-1) and lymphovascular or perineural invasion (HR 3.51; 95% CI 1.86-6.64) together with pT4 (HR 2.79; 95% CI 1.44-5.41) influenced CCSS. In multivariate analysis pT4 and lymphovascular or perineural invasion remained significantly associated with CCSS. We performed a risk index with these factors with prognostic impact. Patients with pT4 tumours and lymphovascular or perineural invasion had a 5-year CCSS of 61%vs the 93% (HR 5.87; 95 CI 2.46-13.97) of those without any of these factors. CONCLUSION pT4 and lymphatic, venous or perineural invasion are confirmed as significant prognostic factors in Stage II colon cancer and should be taken into account in the clinical validation process of new molecular prognostic factors.
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Affiliation(s)
- C Santos
- Department of Medical Oncology, Institut Català d'Oncologia - Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
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Azuara D, Rodriguez-Moranta F, de Oca J, Sanjuan X, Guardiola J, Lobaton T, Wang A, Boadas J, Piqueras M, Monfort D, Galter S, Esteller M, Moreno V, Capellá G. Novel methylation panel for the early detection of neoplasia in high-risk ulcerative colitis and Crohn's colitis patients. Inflamm Bowel Dis 2013; 19:165-73. [PMID: 22532293 DOI: 10.1002/ibd.22994] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Patients with ulcerative colitis and Crohn's colonic disease are at increased risk of developing colorectal cancer (CRC). The aim of the study was to analyze the methylation status of selected genes as a risk marker for CRC in inflammatory bowel disease (IBD) patients. METHODS We evaluated the methylation status of four genes (TGFB2, SLIT2, HS3ST2, and TMEFF2) in biopsies of four groups of patients: 60 patients with sporadic CRC, 32 patients with IBD-associated neoplasia, 85 patients with IBD without associated neoplasia (20 at high risk and 65 at low risk), and 28 healthy controls. Methylation-specific melting curve analysis (MS-MCA) was used. Methylation status of these genes was also assessed in stool DNA from 60 IBD patients without neoplasia. RESULTS Methylation of the panel of genes analyzed was a very common phenomenon (78%) in IBD-associated neoplasia. The prevalence of methylation in adjacent nonneoplastic mucosa was also high (12/30). This prevalence was higher than in mucosa from healthy controls (2/28;7.1%; P < 0.05). Methylation of SLIT2 and TMEFF2 was more frequently detected in the mucosa of IBD patients at high risk of dysplasia or cancer (15/20) than patients at low risk (32/63) (P = 0.05 and P = 0.03, respectively). When stool samples were assessed, only SLIT2 gene methylation was more frequently methylated in the group of patients at high risk of dysplasia or cancer (4/16) compared to low risk (0/37) (P = 0.006). CONCLUSIONS Analysis of a panel of methylation markers may help in the early identification of colorectal dysplasia or cancer in high-risk IBD patients.
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Affiliation(s)
- Daniel Azuara
- Translational Research Laboratory, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
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Sanz-Pamplona R, Berenguer A, Cordero D, Riccadonna S, Solé X, Crous-Bou M, Guinó E, Sanjuan X, Biondo S, Soriano A, Jurman G, Capella G, Furlanello C, Moreno V. Clinical value of prognosis gene expression signatures in colorectal cancer: a systematic review. PLoS One 2012; 7:e48877. [PMID: 23145004 PMCID: PMC3492249 DOI: 10.1371/journal.pone.0048877] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 10/02/2012] [Indexed: 12/01/2022] Open
Abstract
Introduction The traditional staging system is inadequate to identify those patients with stage II colorectal cancer (CRC) at high risk of recurrence or with stage III CRC at low risk. A number of gene expression signatures to predict CRC prognosis have been proposed, but none is routinely used in the clinic. The aim of this work was to assess the prediction ability and potential clinical usefulness of these signatures in a series of independent datasets. Methods A literature review identified 31 gene expression signatures that used gene expression data to predict prognosis in CRC tissue. The search was based on the PubMed database and was restricted to papers published from January 2004 to December 2011. Eleven CRC gene expression datasets with outcome information were identified and downloaded from public repositories. Random Forest classifier was used to build predictors from the gene lists. Matthews correlation coefficient was chosen as a measure of classification accuracy and its associated p-value was used to assess association with prognosis. For clinical usefulness evaluation, positive and negative post-tests probabilities were computed in stage II and III samples. Results Five gene signatures showed significant association with prognosis and provided reasonable prediction accuracy in their own training datasets. Nevertheless, all signatures showed low reproducibility in independent data. Stratified analyses by stage or microsatellite instability status showed significant association but limited discrimination ability, especially in stage II tumors. From a clinical perspective, the most predictive signatures showed a minor but significant improvement over the classical staging system. Conclusions The published signatures show low prediction accuracy but moderate clinical usefulness. Although gene expression data may inform prognosis, better strategies for signature validation are needed to encourage their widespread use in the clinic.
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Affiliation(s)
- Rebeca Sanz-Pamplona
- Unit of Biomarkers and Susceptibility (UBS), Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), and CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain
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Garcia del Muro X, Lopez-Pousa A, Flor MJ, Redondo A, Jurado JC, Andres R, Casado A, Fra J, Lopez-Martin JA, Maurel J, Valverde CM, Gallego O, Narvaez JA, Bague S, Sanjuan X, Vinyals JM. Phase II study of neoadjuvant high-dose ifosfamide with concurrent radiotherapy followed by surgical resection in high-risk soft tissue sarcoma: A Spanish Group for Research on Sarcomas (GEIS) study. J Clin Oncol 2012. [DOI: 10.1200/jco.2012.30.15_suppl.10052] [Citation(s) in RCA: 3] [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] [Indexed: 11/20/2022] Open
Abstract
10052 Background: High-dose ifosfamide (HDI) has shown promising activity as single agent in first-line chemotherapy for advanced soft tissue sarcoma (STS). The purpose of this study was to assess the activity and toxicity of a preoperative doxorubicin-free regimen of HDI given concurrently with radiotherapy (RT) and followed by surgery in patients (pts) with localized high-risk STS. Methods: Pts with localized > 5 cm grade 2-3 and deep STS of the extremities and trunk wall, ≤65 years, no prior chemotherapy and ECOG PS 0-1 were enrolled in this multicenter phase II study. Pts received 3 cycles of preoperative HDI at a dose of 12 gr/m2 by continuous infusion over 5 days every 3 weeks, with mesna and prophylactic GCSF support, and concomitant external beam RT to a total dose of 50 Gy, followed by surgical resection. Postoperatively, pts with pathological response received 2 cycles of HDI and those with positive surgical margins 16 Gy of RT. The primary study endpoint was pathologic response (≥ 95% pathologic necrosis). A Simon 2-stage design (response rate P0=15%, P1=35%, α=0.10, β=0.10) required at least 2 responses in the first 17 pts to expand to a second cohort, and 7/32 responses to be considered of positive. Results: From March 08 to December 10, 34 pts were included. Two pts were ineligible. Median age was 54 (18-65). Tumor location was extremity (28 pts) and trunk wall (4). Preoperative planned treatment was completed in 87.5% pts. HDI was completed in 87.5% pts while RT in 94% pts. Grade 3-4 toxicities included neutropenic fever (3 pts), anemia (4), asthenia (2), infection (2) and radiation dermatitis (2). 31 pts underwent surgery: 27 were R0 resections, of which 2 were amputations, and 4 were R1 resections. Pathologic response was ≥ 95% necrosis in 9 pts (28%) and 50%-94% necrosis in 12 pts. After a median follow-up of 21 months, estimated 2-year rates for disease-free survival and overall survival were 58% (95%CI, 40%-77%) and 77% (95%CI, 61%-93%), respectively. Conclusions: Preoperative treatment with HDI given concurrently with RT in pts with high-risk STS is feasible and safe, yielding promising pathologic response rates.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Juan Maurel
- Hospital Clinic i Provincial, Barcelona, Spain
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Sanz-Pamplona R, Cordero D, Berenguer A, Lejbkowicz F, Rennert H, Salazar R, Biondo S, Sanjuan X, Pujana MA, Rozek L, Giordano TJ, Ben-Izhak O, Cohen HI, Trougouboff P, Bejhar J, Sova Y, Rennert G, Gruber SB, Moreno V. Gene expression differences between colon and rectum tumors. Clin Cancer Res 2011; 17:7303-12. [PMID: 21976543 DOI: 10.1158/1078-0432.ccr-11-1570] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE Colorectal cancer studies typically include both colon and rectum tumors as a common entity, though this assumption is controversial and only minor differences have been reported at the molecular and epidemiologic level. We conducted a molecular study based on gene expression data of tumors from colon and rectum to assess the degree of similarity between these cancer sites at transcriptomic level. EXPERIMENTAL DESIGN A pooled analysis of 460 colon tumors and 100 rectum tumors from four data sets belonging to three independent studies was conducted. Microsatellite instable tumors were excluded as these are known to have a different expression profile and have a preferential proximal colon location. Expression differences were assessed with linear models, and significant genes were identified using adjustment for multiple comparisons. RESULTS Minor differences at a gene expression level were found between tumors arising in the proximal colon, distal colon, or rectum. Only several HOX genes were found to be associated with tumor location. More differences were found between proximal and distal colon than between distal colon and rectum. CONCLUSIONS Microsatellite stable colorectal cancers do not show major transcriptomic differences for tumors arising in the colon or rectum. The small but consistent differences observed are largely driven by the HOX genes. These results may have important implications in the design and interpretation of studies in colorectal cancer.
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Affiliation(s)
- Rebeca Sanz-Pamplona
- Unit of Biomarkers and Susceptibility, Catalan Institute of Oncology, IDIBELL, and CIBERESP, Barcelona, Spain
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Sáinz-Jaspeado M, Lagares-Tena L, Lasheras J, Navid F, Rodriguez-Galindo C, Mateo-Lozano S, Notario V, Sanjuan X, Garcia Del Muro X, Fabra A, Tirado OM. Caveolin-1 modulates the ability of Ewing's sarcoma to metastasize. Mol Cancer Res 2011; 8:1489-500. [PMID: 21106507 DOI: 10.1158/1541-7786.mcr-10-0060] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Metastasis is the final stage of tumor progression and is thought to be responsible for up to 90% of deaths associated with solid tumors. Caveolin-1 (CAV1) regulates multiple cancer-associated processes related to malignant tumor progression. In the present study, we tested the hypothesis that CAV1 modulates the metastatic ability of cells from the Ewing's sarcoma family of tumors (ESFT). First, we analyzed the expression of CAV1 by immunostaining a tissue microarray containing 43 paraffin-embedded ESFT tumors with known EWS translocations. Even though no evidence was found for a significant association between CAV1 expression and stage, size or tumor site, all metastatic samples (10 of 10) had significantly high CAV1 expression, suggesting that high CAV1 content could positively contribute to enhance ESFT metastasis. To determine the effect of CAV1 on the migratory and invasive capabilities of ESFT cells, we knocked down CAV1 expression in TC252 and A673 cells by stably transfecting a previously validated shRNA construct. In vitro, migration and invasion assays showed that for both cell lines, CAV1 knocked-down cells migrated and invaded significantly less (P ≤ 0.01) than control cells. Moreover, control A673 cells introduced into BALB/c nude mice by tail vein injection strongly colonized the lungs. In contrast, animals injected with CAV1 knocked-down cells showed either no incidence of metastasis or developed lung metastases after a significant delay (P < 0.0001). Finally, we show that the molecular mechanisms by which CAV1 carries out its key role in regulating ESFT metastasis involve matrix metalloproteinase production and activation as well as the control of the expression of SPARC, a known determinant of lung colonization.
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Affiliation(s)
- Miguel Sáinz-Jaspeado
- Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospital Duran i Reynals-3 Planta Gran via s/n Km. 2, 7, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
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