1
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Segalés L, Juanpere N, Gallarín N, Lorenzo M, López D, Perera-Bel J, Rodriguez-Vida A, Fumadó L, Cecchini L, Bellmunt J, Lloreta-Trull J, Hernández-Llodrà S. Immunohistochemical markers as predictors of prognosis in multifocal prostate cancer. Virchows Arch 2023:10.1007/s00428-023-03699-z. [PMID: 38017230 DOI: 10.1007/s00428-023-03699-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/09/2023] [Accepted: 11/04/2023] [Indexed: 11/30/2023]
Abstract
The impact of tumor focality on prostate cancer (PCa) prognosis has been addressed in several studies with conflicting results. Tumor foci from multifocal (MF) PCa can show highly heterogeneous molecular features. Our aim was to analyze the protein expression of PTEN, SPOP, SLC45A3, ETV1, ERG and the "triple hit" (ERG overexpression, PTEN plus SLC45A3 loss) in unifocal (UF) and MF PCa, to evaluate their value as prognostic markers according to focality, and the role of tumor heterogeneity in MF disease. PTEN, SPOP, SLC45A3, ETV1 and ERG immunohistochemical expression was evaluated in 185 PCa from 9 TMAs, 51 UF and 134 MF. In a subset of 69 MF cases, the dominant and secondary foci (DF and SF) were compared. Heterogeneity was considered when both tumor foci presented different expression patterns. Relationship with clinicopathological features was also analyzed. MF PCa was diagnosed in significantly younger patients when compared to UF ones (p = 0.007). ETV1 overexpression was associated with UF disease (p = 0.028). A shorter time to PSA recurrence was related to SLC45A3 wt expression in UF PCa (p = 0.052), and to SPOP expression loss (p = 0.043) or "triple hit" phenotype in MF PCa (p = 0.041). In MF cases, PTEN loss, SLC45A3 loss and "triple hit" phenotype were associated with the DF and had significant heterogeneity. In conclusion, our results indicate that UF and MF PCa have relevant and consistent molecular differences. The analysis of an immunohistochemical panel, composed by PTEN, SPOP, SLC45A3, ETV1 and ERG, could be useful to predict outcome in MF cases.
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Affiliation(s)
- Laura Segalés
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nuria Juanpere
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Department of Pathology, Hospital del Mar, Barcelona, Spain
| | | | - Marta Lorenzo
- Department of Pathology, Hospital del Mar, Barcelona, Spain
| | - David López
- Department of Pathology, Hospital del Mar, Barcelona, Spain
| | | | - Alejo Rodriguez-Vida
- Hospital del Mar Research Institute, Barcelona, Spain
- Department of Medical Oncology, Hospital del Mar, CIBERONC, Barcelona, Spain
| | - Lluís Fumadó
- Department of Urology, Hospital del Mar, Barcelona, Spain
| | - Lluís Cecchini
- Department of Urology, Hospital del Mar, Barcelona, Spain
| | - Joaquim Bellmunt
- Hospital del Mar Research Institute, Barcelona, Spain
- Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Josep Lloreta-Trull
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Department of Pathology, Hospital del Mar, Barcelona, Spain
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2
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Boll LM, Perera-Bel J, Rodriguez-Vida A, Arpí O, Rovira A, Juanpere N, Vázquez Montes de Oca S, Hernández-Llodrà S, Lloreta J, Albà MM, Bellmunt J. The impact of mutational clonality in predicting the response to immune checkpoint inhibitors in advanced urothelial cancer. Sci Rep 2023; 13:15287. [PMID: 37714872 PMCID: PMC10504302 DOI: 10.1038/s41598-023-42495-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/11/2023] [Indexed: 09/17/2023] Open
Abstract
Immune checkpoint inhibitors (ICI) have revolutionized cancer treatment and can result in complete remissions even at advanced stages of the disease. However, only a small fraction of patients respond to the treatment. To better understand which factors drive clinical benefit, we have generated whole exome and RNA sequencing data from 27 advanced urothelial carcinoma patients treated with anti-PD-(L)1 monoclonal antibodies. We assessed the influence on the response of non-synonymous mutations (tumor mutational burden or TMB), clonal and subclonal mutations, neoantigen load and various gene expression markers. We found that although TMB is significantly associated with response, this effect can be mostly explained by clonal mutations, present in all cancer cells. This trend was validated in an additional cohort. Additionally, we found that responders with few clonal mutations had abnormally high levels of T and B cell immune markers, suggesting that a high immune cell infiltration signature could be a better predictive biomarker for this subset of patients. Our results support the idea that highly clonal cancers are more likely to respond to ICI and suggest that non-additive effects of different signatures should be considered for predictive models.
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Affiliation(s)
| | | | - Alejo Rodriguez-Vida
- Hospital del Mar Research Institute, Barcelona, Spain
- Medical Oncology Department, Hospital del Mar, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Oncología (CIBERONC-ISCIII), Barcelona, Spain
| | - Oriol Arpí
- Hospital del Mar Research Institute, Barcelona, Spain
| | - Ana Rovira
- Hospital del Mar Research Institute, Barcelona, Spain
- Medical Oncology Department, Hospital del Mar, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Oncología (CIBERONC-ISCIII), Barcelona, Spain
| | | | | | | | - Josep Lloreta
- Hospital del Mar Research Institute, Barcelona, Spain
- Department of Medicine and Life Science, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - M Mar Albà
- Hospital del Mar Research Institute, Barcelona, Spain.
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain.
| | - Joaquim Bellmunt
- Hospital del Mar Research Institute, Barcelona, Spain.
- Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
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3
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Rocha P, Rodrigo M, Moliner L, Menendez S, Masfarré L, Navarro N, Del Rey-Vergara R, Galindo-Campos M, Taus Á, Giner M, Sanchez I, Rodríguez-Fuster A, Aguiló R, Chalela R, Sánchez-Font A, Belda J, Curull V, Pijuan L, Casadevall D, Clavé S, Bellosillo B, Perera-Bel J, Comerma L, Arriola E. Pre-existing tumor host immunity characterization in resected non-small cell lung cancer. Lung Cancer 2023; 181:107257. [PMID: 37263182 DOI: 10.1016/j.lungcan.2023.107257] [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: 12/21/2022] [Revised: 04/28/2023] [Accepted: 05/17/2023] [Indexed: 06/03/2023]
Abstract
INTRODUCTION Neoadjuvant and adjuvant immune checkpoint blockade (ICB) have recently become standard of care in resectable non-small cell lung cancer (NSCLC). Yet, biomarkers that inform patients who benefit from this approach remain largely unknown. Here, we interrogated the tumor immune microenvironment (TIME) in early-stage NSCLC patients that underwent up-front surgery. METHODS A total of 185 treatment-naïve patients with early-stage NSCLC, that underwent up-front surgical treatment between 2006 and 2018 at Hospital del Mar were included. 124 lung adenocarcinomas (LUADs), and 61 squamous cell carcinoma (LUSCs) were included in a tissue microarray. Immunohistochemistry for CD3, CD4, CD8, CD68, CD80, CD103, FOXP3, PD-1, PD-L1, PD-L2 and HLA class II were evaluated by digital image analysis (QuPath software). TIME was categorized into four groups using PD-L1 expression in tumor cells (<1 % or ≥1 %) and tumor resident memory (CD103+) immune cells (using the median as cut-off). We explored the association between different TIME dimensions and patient's clinicopathological features and outcomes. RESULTS We found increased levels of T cell markers (CD3+, CD4+, CD8+ cells), functional immune markers (FOXP3+ cells) as well as, higher HLA-II tumor membrane expression in LUADs compared to LUSCs (p < 0.05 for all). In contrast, LUSCs displayed higher percentage of intratumor macrophages (CD68+ cells) as well as, higher PD-L1 and PD-L2 tumor membrane expression (p < 0.05 for all). Unsupervised analysis revealed three different tumor subsets characterized by membrane tumor expression of PD-L1, PD-L2 and HLA-class II. Enrichment of T cells (CD3+, CD8+ cells), regulatory T cells (FOXP3+ cells) and macrophages (CD68+ cells) was observed in the CD103+/PD-L1+ group (p < 0.05 for all). Multivariate analysis showed that infiltration by CD103+ immune cells was associated with improved OS (p = 0.009). CONCLUSIONS TIME analysis in resected NSCLC highlighted differences by histology, PD-L1 expression and molecular subgroups. Biomarker studies using IHC might aid to individually tailor adjuvant treatment in early-stage NSCLC.
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Affiliation(s)
- Pedro Rocha
- Medical Oncology Department, Hospital del Mar - CIBERONC, Barcelona, Spain; IMIM (Instituto Hospital del Mar de Investigaciones Médicas), Barcelona, Spain
| | - Maite Rodrigo
- Pathology Department, Hospital del Mar, Barcelona, Spain
| | - Laura Moliner
- Medical Oncology Department, Hospital del Mar - CIBERONC, Barcelona, Spain; Medical Oncology Department, Catalan Institute of Oncology (ICO), Barcelona, Spain
| | - Silvia Menendez
- IMIM (Instituto Hospital del Mar de Investigaciones Médicas), Barcelona, Spain
| | - Laura Masfarré
- Medical Oncology Department, Hospital del Mar - CIBERONC, Barcelona, Spain
| | - Nil Navarro
- Medical Oncology Department, Hospital del Mar - CIBERONC, Barcelona, Spain
| | | | | | - Álvaro Taus
- Medical Oncology Department, Hospital del Mar - CIBERONC, Barcelona, Spain; IMIM (Instituto Hospital del Mar de Investigaciones Médicas), Barcelona, Spain
| | - Mario Giner
- Pathology Department, Hospital del Mar, Barcelona, Spain
| | | | - Alberto Rodríguez-Fuster
- IMIM (Instituto Hospital del Mar de Investigaciones Médicas), Barcelona, Spain; Thoracic Surgery Department, Hospital del Mar, Barcelona, Spain; Centro de Investigación en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), Barcelona, Spain
| | - Rafael Aguiló
- Thoracic Surgery Department, Hospital del Mar, Barcelona, Spain
| | - Roberto Chalela
- IMIM (Instituto Hospital del Mar de Investigaciones Médicas), Barcelona, Spain; Pulmonology Department, Hospital del Mar, Barcelona, Spain
| | - Albert Sánchez-Font
- IMIM (Instituto Hospital del Mar de Investigaciones Médicas), Barcelona, Spain; Centro de Investigación en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), Barcelona, Spain; Pulmonology Department, Hospital del Mar, Barcelona, Spain
| | - Josep Belda
- Thoracic Surgery Department, Hospital del Mar, Barcelona, Spain
| | - Victor Curull
- IMIM (Instituto Hospital del Mar de Investigaciones Médicas), Barcelona, Spain; Thoracic Surgery Department, Hospital del Mar, Barcelona, Spain; Centro de Investigación en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), Barcelona, Spain
| | - Lara Pijuan
- Pathology Department, Hospital del Mar, Barcelona, Spain
| | - David Casadevall
- Medical Oncology Department, Hospital del Mar - CIBERONC, Barcelona, Spain; IMIM (Instituto Hospital del Mar de Investigaciones Médicas), Barcelona, Spain
| | - Sergi Clavé
- Pathology Department, Hospital del Mar, Barcelona, Spain
| | | | | | - Laura Comerma
- Pathology Department, Hospital del Mar, Barcelona, Spain
| | - Edurne Arriola
- Medical Oncology Department, Hospital del Mar - CIBERONC, Barcelona, Spain; IMIM (Instituto Hospital del Mar de Investigaciones Médicas), Barcelona, Spain.
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Rombauts A, Bódalo Torruella M, Abelenda-Alonso G, Perera-Bel J, Ferrer-Salvador A, Acedo-Terrades A, Gabarrós-Subirà M, Oriol I, Gudiol C, Nonell L, Carratalà J. Dynamics of Gene Expression Profiling and Identification of High-Risk Patients for Severe COVID-19. Biomedicines 2023; 11:biomedicines11051348. [PMID: 37239019 DOI: 10.3390/biomedicines11051348] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/28/2023] [Accepted: 05/01/2023] [Indexed: 05/28/2023] Open
Abstract
The clinical manifestations of SARS-CoV-2 infection vary widely, from asymptomatic infection to the development of acute respiratory distress syndrome (ARDS) and death. The host response elicited by SARS-CoV-2 plays a key role in determining the clinical outcome. We hypothesized that determining the dynamic whole blood transcriptomic profile of hospitalized adult COVID-19 patients and characterizing the subgroup that develops severe disease and ARDS would broaden our understanding of the heterogeneity in clinical outcomes. We recruited 60 hospitalized patients with RT-PCR-confirmed SARS-CoV-2 infection, among whom 19 developed ARDS. Peripheral blood was collected using PAXGene RNA tubes within 24 h of admission and on day 7. There were 2572 differently expressed genes in patients with ARDS at baseline and 1149 at day 7. We found a dysregulated inflammatory response in COVID-19 ARDS patients, with an increased expression of genes related to pro-inflammatory molecules and neutrophil and macrophage activation at admission, in addition to an immune regulation loss. This led, in turn, to a higher expression of genes related to reactive oxygen species, protein polyubiquitination, and metalloproteinases in the latter stages. Some of the most significant differences in gene expression found between patients with and without ARDS corresponded to long non-coding RNA involved in epigenetic control.
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Affiliation(s)
- Alexander Rombauts
- Department of Infectious Diseases, Hospital Universitari de Bellvitge-IDIBELL, 08908 Barcelona, Spain
| | | | - Gabriela Abelenda-Alonso
- Department of Infectious Diseases, Hospital Universitari de Bellvitge-IDIBELL, 08908 Barcelona, Spain
| | - Júlia Perera-Bel
- MARGenomics, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
| | - Anna Ferrer-Salvador
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | | | - Maria Gabarrós-Subirà
- MARGenomics, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
| | - Isabel Oriol
- Department of Infectious Diseases, Hospital Universitari de Bellvitge-IDIBELL, 08908 Barcelona, Spain
| | - Carlota Gudiol
- Department of Infectious Diseases, Hospital Universitari de Bellvitge-IDIBELL, 08908 Barcelona, Spain
- Department of Medicine, Universitat de Barcelona, 08007 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Lara Nonell
- MARGenomics, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain
| | - Jordi Carratalà
- Department of Infectious Diseases, Hospital Universitari de Bellvitge-IDIBELL, 08908 Barcelona, Spain
- Department of Medicine, Universitat de Barcelona, 08007 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
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5
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Kurz NS, Perera-Bel J, Höltermann C, Tucholski T, Yang J, Beissbarth T, Dönitz J. Identifying Actionable Variants in Cancer - The Dual Web and Batch Processing Tool MTB-Report. Stud Health Technol Inform 2022; 296:73-80. [PMID: 36073491 DOI: 10.3233/shti220806] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Next-generation sequencing methods continuously provide clinicians and researchers in precision oncology with growing numbers of genomic variants found in cancer. However, manually interpreting the list of variants to identify reliable targets is an inefficient and cumbersome process that does not scale with the increasing number of cases. Support by computer systems is needed for the analysis of large scale experiments and clinical studies to identify new targets and therapies, and user-friendly applications are needed in molecular tumor boards to support clinicians in their decision-making processes. The MTB-Report tool annotates, filters and sorts genetic variants with information from public databases, providing evidence on actionable variants in both scenarios. A web interface supports medical doctors in the tumor board, and a command line mode allows batch processing of large datasets. The MTB-Report tool is available as an R implementation as well as a Docker image to provide a tool that runs out-of-the-box. Moreover, containerization ensures a stable application that delivers reproducible results over time. A public version of the web interface is available at: http://mtb.bioinf.med.uni-goettingen.de/mtb-report.
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Affiliation(s)
- Nadine S Kurz
- Dept. of Medical Bioinformatics, University Medical Center Göttingen, Germany
| | - Júlia Perera-Bel
- MARGenomics, Hospital del Mar Medical Research Institute (IMIM), Spain
| | | | - Tim Tucholski
- Dept. of Medical Bioinformatics, University Medical Center Göttingen, Germany
| | - Jingyu Yang
- Dept. of Medical Bioinformatics, University Medical Center Göttingen, Germany
| | - Tim Beissbarth
- Dept. of Medical Bioinformatics, University Medical Center Göttingen, Germany
| | - Jürgen Dönitz
- Dept. of Medical Bioinformatics, University Medical Center Göttingen, Germany
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6
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Perera-Bel J, Bellmunt J. Reply to Anirban P. Mitra, Tanner Miest, and Colin P.N. Dinney's Words of Wisdom re: Genomic Predictors of Good Outcome, Recurrence, or Progression in High-Grade T1 Non-Muscle-Invasive Bladder Cancer. Eur Urol 2021;79:428-9. Eur Urol 2021; 79:e119-e120. [PMID: 33419679 DOI: 10.1016/j.eururo.2020.12.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 12/23/2020] [Indexed: 11/19/2022]
Affiliation(s)
- Júlia Perera-Bel
- IMIM-Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Joaquim Bellmunt
- IMIM-Hospital del Mar Medical Research Institute, Barcelona, Spain; Beth Israel Deaconess Medical Center, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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7
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Bellmunt J, Kim J, Reardon B, Perera-Bel J, Orsola A, Rodriguez-Vida A, Wankowicz SA, Bowden M, Barletta JA, Morote J, de Torres I, Juanpere N, Lloreta-Trull J, Hernandez S, Mouw KW, Taplin ME, Cejas P, Long HW, Van Allen EM, Getz G, Kwiatkowski DJ. Genomic Predictors of Good Outcome, Recurrence, or Progression in High-Grade T1 Non-Muscle-Invasive Bladder Cancer. Cancer Res 2020; 80:4476-4486. [PMID: 32868381 DOI: 10.1158/0008-5472.can-20-0977] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/27/2020] [Accepted: 08/20/2020] [Indexed: 11/16/2022]
Abstract
High-grade T1 (HGT1) bladder cancer is the highest risk subtype of non-muscle-invasive bladder cancer with unpredictable outcome and poorly understood risk factors. Here, we examined the association of somatic mutation profiles with nonrecurrent disease (GO, good outcome), recurrence (R), or progression (PD) in a cohort of HGT1 patients. Exome sequencing was performed on 62 HGT1 and 15 matched normal tissue samples. Both tumor only (TO) and paired analyses were performed, focusing on 95 genes known to be mutated in bladder cancer. Somatic mutations, copy-number alterations, mutation load, and mutation signatures were studied. Thirty-three GO, 10 R, 18 PD, and 1 unknown outcome patients were analyzed. Tumor mutational burden (TMB) was similar to muscle-invasive disease and was highest in GO, intermediate in PD, and lowest in R patients (P = 0.017). DNA damage response gene mutations were associated with higher TMB (P < 0.0001) and GO (P = 0.003). ERCC2 and BRCA2 mutations were associated with GO. TP53, ATM, ARID1A, AHR, and SMARCB1 mutations were more frequent in PD. Focal copy-number gain in CCNE1 and CDKN2A deletion was enriched in PD or R (P = 0.047; P = 0.06). APOBEC (46%) and COSMIC5 (34%) signatures were most frequent. APOBEC-A and ERCC2 mutant tumors (COSMIC5) were associated with GO (P = 0.047; P = 0.0002). pT1b microstaging was associated with a genomic cluster (P = 0.05) with focal amplifications of E2F3/SOX4, PVRL4, CCNE1, and TP53 mutations. Findings were validated using external public datasets. These findings require confirmation but suggest that management of HGT1 bladder cancer may be improved via molecular characterization to predict outcome. SIGNIFICANCE: Detailed genetic analyses of HGT1 bladder tumors identify features that correlate with outcome, e.g., high mutational burden, ERCC2 mutations, and high APOBEC-A/ERCC2 mutation signatures were associated with good outcome.
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Affiliation(s)
- Joaquim Bellmunt
- Beth Israel Deaconess Medical Center, Boston, Massachusetts. .,Harvard Medical School University, Boston, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,IMIM-Hospital del Mar Medical Research Institute; Hospital del Mar, Barcelona, Spain
| | - Jaegil Kim
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Brendan Reardon
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Júlia Perera-Bel
- IMIM-Hospital del Mar Medical Research Institute; Hospital del Mar, Barcelona, Spain
| | - Anna Orsola
- IMIM-Hospital del Mar Medical Research Institute; Hospital del Mar, Barcelona, Spain
| | - Alejo Rodriguez-Vida
- IMIM-Hospital del Mar Medical Research Institute; Hospital del Mar, Barcelona, Spain
| | - Stephanie A Wankowicz
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Michaela Bowden
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Justine A Barletta
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Juan Morote
- Department of Urology, University Hospital Valle de Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Inés de Torres
- Department of Pathology, University Hospital Valle de Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Nuria Juanpere
- Department of Pathology, University Hospital del Mar, Pompeu Fabra University, Barcelona, Spain
| | - Josep Lloreta-Trull
- Department of Pathology, University Hospital del Mar, Pompeu Fabra University, Barcelona, Spain
| | - Silvia Hernandez
- Department of Pathology, University Hospital del Mar, Pompeu Fabra University, Barcelona, Spain
| | - Kent W Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts
| | - Mary-Ellen Taplin
- Harvard Medical School University, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Henry W Long
- Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Eliezer M Van Allen
- Harvard Medical School University, Boston, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts.,Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - David J Kwiatkowski
- Harvard Medical School University, Boston, Massachusetts. .,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
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8
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Perera-Bel J, Hutter B, Heining C, Bleckmann A, Fröhlich M, Fröhling S, Glimm H, Brors B, Beißbarth T. From somatic variants towards precision oncology: Evidence-driven reporting of treatment options in molecular tumor boards. Genome Med 2018; 10:18. [PMID: 29544535 PMCID: PMC5856211 DOI: 10.1186/s13073-018-0529-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 02/28/2018] [Indexed: 01/11/2023] Open
Abstract
Background A comprehensive understanding of cancer has been furthered with technological improvements and decreasing costs of next-generation sequencing (NGS). However, the complexity of interpreting genomic data is hindering the implementation of high-throughput technologies in the clinical context: increasing evidence on gene–drug interactions complicates the task of assigning clinical significance to genomic variants. Methods Here we present a method that automatically matches patient-specific genomic alterations to treatment options. The method relies entirely on public knowledge of somatic variants with predictive evidence on drug response. The output report is aimed at supporting clinicians in the task of finding the clinical meaning of genomic variants. We applied the method to 1) The Cancer Genome Atlas (TCGA) and Genomics Evidence Neoplasia Information Exchange (GENIE) cohorts and 2) 11 patients from the NCT MASTER trial whose treatment discussions included information on their genomic profiles. Results Our reporting strategy showed a substantial number of patients with actionable variants in the analyses of TCGA and GENIE samples. Notably, it was able to reproduce experts’ treatment suggestions in a retrospective study of 11 patients from the NCT MASTER trial. Our results establish a proof of concept for comprehensive, evidence-based reports as a supporting tool for discussing treatment options in tumor boards. Conclusions We believe that a standardized method to report actionable somatic variants will smooth the incorporation of NGS in the clinical context. We anticipate that tools like the one we present here will become essential in summarizing for clinicians the growing evidence in the field of precision medicine. The R code of the presented method is provided in Additional file 6 and available at https://github.com/jperera-bel/MTB-Report. Electronic supplementary material The online version of this article (10.1186/s13073-018-0529-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Júlia Perera-Bel
- Department of Medical Statistics, University Medical Center Göttingen, 37073, Göttingen, Germany
| | - Barbara Hutter
- Division Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120, Heidelberg, Germany
| | - Christoph Heining
- Division Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Annalen Bleckmann
- Department of Medical Statistics, University Medical Center Göttingen, 37073, Göttingen, Germany.,Department of Hematology and Medical Oncology, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Martina Fröhlich
- Division Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120, Heidelberg, Germany
| | - Stefan Fröhling
- Division Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| | - Hanno Glimm
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany.,Department of Translational Medical Oncology, NCT-Dresden, University Hospital, Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden and DKFZ, Heidelberg, 69120, Germany
| | - Benedikt Brors
- Division Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120, Heidelberg, Germany
| | - Tim Beißbarth
- Department of Medical Statistics, University Medical Center Göttingen, 37073, Göttingen, Germany.
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9
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Wolff A, Perera-Bel J, Schildhaus HU, Homayounfar K, Schatlo B, Bleckmann A, Beißbarth T. Using RNA-Seq Data for the Detection of a Panel of Clinically Relevant Mutations. Stud Health Technol Inform 2018; 253:217-221. [PMID: 30147077] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Somatic single nucleotide variants (SNVs) are genomic events with increasing implications in cancer treatment. The clinical standard for SNVs detection is whole genome/exome sequencing (WGS/WES) in matched tumor-normal samples. Yet, this is a very costly approach both economically and biologically and very often only tumor samples are sequenced. On the other hand, RNA sequencing (RNA-Seq) is the most popular technology to study gene expression, and has also the potential for a cost-effective identification of SNVs as an alternative to tumor-only WES. Here we present a method for the identification of SNVs in tumor-only RNA-Seq data putting a special focus on a small panel of clinically relevant SNVs. For evaluation purposeswe analyzed matched tumor-normal WEStumor-only RNA-Seq data from 14 cancer patients. We compared SNVs detected in i) RNA-Seq by our method, ii) WES tumor-only by Mutect2 and iii) WES matched tumor-normal by Mutect2. We did a detailed evaluation for a reduced panel of clinically relevant SNVs and reliably identified in RNA-Seq data a subset of mutations for which we had pathological annotation. Hence, RNA-Seq rises as a cost-effective option to detect in parallel gene expression as well as a small panel of clinically relevant SNVs in research.
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Affiliation(s)
- Alexander Wolff
- Department of Medical Statistics, University Medical Center Göttingen
| | - Júlia Perera-Bel
- Department of Medical Statistics, University Medical Center Göttingen
| | | | - Kia Homayounfar
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen
| | | | - Annalen Bleckmann
- Department of Medical Statistics, University Medical Center Göttingen
| | - Tim Beißbarth
- Department of Medical Statistics, University Medical Center Göttingen
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Pernice MC, Giner CR, Logares R, Perera-Bel J, Acinas SG, Duarte CM, Gasol JM, Massana R. Large variability of bathypelagic microbial eukaryotic communities across the world's oceans. ISME J 2015; 10:945-58. [PMID: 26451501 DOI: 10.1038/ismej.2015.170] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 07/30/2015] [Accepted: 08/13/2015] [Indexed: 01/26/2023]
Abstract
In this work, we study the diversity of bathypelagic microbial eukaryotes (0.8-20 μm) in the global ocean. Seawater samples from 3000 to 4000 m depth from 27 stations in the Atlantic, Pacific and Indian Oceans were analyzed by pyrosequencing the V4 region of the 18S ribosomal DNA. The relative abundance of the most abundant operational taxonomic units agreed with the results of a parallel metagenomic analysis, suggesting limited PCR biases in the tag approach. Although rarefaction curves for single stations were seldom saturated, the global analysis of all sequences together suggested an adequate recovery of bathypelagic diversity. Community composition presented a large variability among samples, which was poorly explained by linear geographic distance. In fact, the similarity between communities was better explained by water mass composition (26% of the variability) and the ratio in cell abundance between prokaryotes and microbial eukaryotes (21%). Deep diversity appeared dominated by four taxonomic groups (Collodaria, Chrysophytes, Basidiomycota and MALV-II) appearing in different proportions in each sample. Novel diversity amounted to 1% of the pyrotags and was lower than expected. Our study represents an essential step in the investigation of bathypelagic microbial eukaryotes, indicating dominating taxonomic groups and suggesting idiosyncratic assemblages in distinct oceanic regions.
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Affiliation(s)
- Massimo C Pernice
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Caterina R Giner
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Ramiro Logares
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Júlia Perera-Bel
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Carlos M Duarte
- Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.,IMEDEA (UiB-CSIC), Department of Global Change Research, Institut Mediterraneo de Estudios Avanzados, Esporles, Spain
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
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