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Saillard C, Delecourt F, Schmauch B, Moindrot O, Svrcek M, Bardier-Dupas A, Emile JF, Ayadi M, Rebours V, de Mestier L, Hammel P, Neuzillet C, Bachet JB, Iovanna J, Dusetti N, Blum Y, Richard M, Kermezli Y, Paradis V, Zaslavskiy M, Courtiol P, Kamoun A, Nicolle R, Cros J. Pacpaint: a histology-based deep learning model uncovers the extensive intratumor molecular heterogeneity of pancreatic adenocarcinoma. Nat Commun 2023; 14:3459. [PMID: 37311751 DOI: 10.1038/s41467-023-39026-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 05/25/2023] [Indexed: 06/15/2023] Open
Abstract
Two tumor (Classical/Basal) and stroma (Inactive/active) subtypes of Pancreatic adenocarcinoma (PDAC) with prognostic and theragnostic implications have been described. These molecular subtypes were defined by RNAseq, a costly technique sensitive to sample quality and cellularity, not used in routine practice. To allow rapid PDAC molecular subtyping and study PDAC heterogeneity, we develop PACpAInt, a multi-step deep learning model. PACpAInt is trained on a multicentric cohort (n = 202) and validated on 4 independent cohorts including biopsies (surgical cohorts n = 148; 97; 126 / biopsy cohort n = 25), all with transcriptomic data (n = 598) to predict tumor tissue, tumor cells from stroma, and their transcriptomic molecular subtypes, either at the whole slide or tile level (112 µm squares). PACpAInt correctly predicts tumor subtypes at the whole slide level on surgical and biopsies specimens and independently predicts survival. PACpAInt highlights the presence of a minor aggressive Basal contingent that negatively impacts survival in 39% of RNA-defined classical cases. Tile-level analysis ( > 6 millions) redefines PDAC microheterogeneity showing codependencies in the distribution of tumor and stroma subtypes, and demonstrates that, in addition to the Classical and Basal tumors, there are Hybrid tumors that combine the latter subtypes, and Intermediate tumors that may represent a transition state during PDAC evolution.
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Affiliation(s)
| | - Flore Delecourt
- Université Paris Cité, Dpt of Pathology - FHU MOSAIC, Beaujon Hospital, INSERM U1149, Clichy, France
| | | | | | - Magali Svrcek
- Dpt of Pathology, Saint-Antoine Hospital - Sorbonne Universités, Paris, France
| | | | - Jean Francois Emile
- Dpt of Pathology, Ambroise Paré Hospital - Université Saint Quentin en Yvelines, Paris, France
| | - Mira Ayadi
- Integragen, Genomic Services & Precision Medicine, Paris, France
| | - Vinciane Rebours
- Université Paris Cité, Dpt of Pancreatology - FHU MOSAIC, Beaujon Hospital, INSERM U1149, Clichy, France
| | - Louis de Mestier
- Université Paris Cité, Dpt of Pancreatology - FHU MOSAIC, Beaujon Hospital, INSERM U1149, Clichy, France
| | - Pascal Hammel
- Dpt of Medical oncology, Paul Brousse Hospital, Villejuif, France
| | | | - Jean Baptiste Bachet
- Dpt of Gastroenterology, Pitié-Salpêtrière Hospital - Sorbonne Universités, Paris, France
| | - Juan Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, Institut Paoli-Calmettes, Aix Marseille Université, CNRS UMR 7258, Marseille, France
| | - Nelson Dusetti
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, Institut Paoli-Calmettes, Aix Marseille Université, CNRS UMR 7258, Marseille, France
| | - Yuna Blum
- Institut Génétique et Développement de Rennes (IGDR), CNRS, Université de Rennes 1, UMR 6290, Rennes, France
| | - Magali Richard
- Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications Grenoble (TIMC-IMAG), CNRS, Université Grenoble-Alpes, UMR5525, Grenoble, France
| | - Yasmina Kermezli
- Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications Grenoble (TIMC-IMAG), CNRS, Université Grenoble-Alpes, UMR5525, Grenoble, France
| | - Valerie Paradis
- Université Paris Cité, Dpt of Pathology - FHU MOSAIC, Beaujon Hospital, INSERM U1149, Clichy, France
| | | | | | | | - Remy Nicolle
- Université Paris Cité, FHU MOSAIC, Centre de Recherche sur l'Inflammation (CRI), INSERM, U1149, CNRS, ERL 8252, F-75018, Paris, France
| | - Jerome Cros
- Université Paris Cité, Dpt of Pathology - FHU MOSAIC, Beaujon Hospital, INSERM U1149, Clichy, France.
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Lansbergen MF, Khelil M, Etten-Jamaludin FSV, Bijlsma MF, van Laarhoven HWM. Poor-prognosis molecular subtypes in adenocarcinomas of pancreato-biliary and gynecological origin: A systematic review. Crit Rev Oncol Hematol 2023; 185:103982. [PMID: 37004743 DOI: 10.1016/j.critrevonc.2023.103982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 04/03/2023] Open
Abstract
Pancreato-biliary and gynecological adenocarcinomas need better tools to predict clinical outcome. Potential prognostic mesenchymal(-like) transcriptome-based subtypes have been identified in these cancers. In this systematic review, we include studies into molecular subtyping and summarize biological and clinical features of the subtypes within and across sites of origin, searching for suggestions to improve classification and prognostication. PubMed and Embase were searched for original research articles describing potential mesenchymal(-like) mRNA-based subtypes in pancreato-biliary or gynecological adenocarcinomas. Studies limited to supervised clustering were excluded. Fourty-four studies, discussing cholangiocarcinomas, gallbladder, ampullary, pancreatic, ovarian, and endometrial adenocarcinomas were included. There was overlap in molecular and clinical features in mesenchymal(-like) subtypes across all adenocarcinomas. Approaches including microdissection were more likely to identify prognosis-associating subtypes. To conclude, molecular subtypes in pancreato-biliary and gynecological adenocarcinomas share biological and clinical characteristics. Furthermore, separation of stromal and epithelial signals should be applied in future studies into biliary and gynecological adenocarcinomas.
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Affiliation(s)
- Marjolein F Lansbergen
- Amsterdam UMC location University of Amsterdam, Medical Oncology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam UMC location University of Amsterdam, Center for Experimental Molecular Medicine, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, the Netherlands.
| | - Maryam Khelil
- University of Amsterdam, Spui 21, 1012 WX Amsterdam, the Netherlands
| | - Faridi S van Etten-Jamaludin
- Amsterdam UMC location University of Amsterdam, Research Support Medical Library, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Maarten F Bijlsma
- Amsterdam UMC location University of Amsterdam, Center for Experimental Molecular Medicine, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, the Netherlands; Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands
| | - Hanneke W M van Laarhoven
- Amsterdam UMC location University of Amsterdam, Medical Oncology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV Amsterdam, the Netherlands
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3
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Philip PA. Pancreatic cancer: why we must be optimistic? Cancer Metastasis Rev 2021; 40:659-660. [PMID: 34611795 DOI: 10.1007/s10555-021-09994-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Philip A Philip
- Departments of Oncology and Pharmacology, Karmanos Cancer Institute, Wayne State University, School of Medicine, Detroit, MI, USA.
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4
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Zhao S, Nicolle R, Augustin J, Svrcek M, de Mestier L, Le Corre D, Pietrasz D, Caliez O, Cros J, Laurent-Puig P, Bachet JB. Prognostic Relevance of Pancreatic Adenocarcinoma Whole-Tumor Transcriptomic Subtypes and Components. Clin Cancer Res 2021; 27:6491-6499. [PMID: 34518308 DOI: 10.1158/1078-0432.ccr-21-1907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/15/2021] [Accepted: 09/03/2021] [Indexed: 12/09/2022]
Abstract
PURPOSE Our team previously defined six quantitative transcriptomic components, and a classification in five subtypes by association of these components. In this study, we compared the robustness of quantitative components and qualitative classifications from different transcriptomic profiling techniques, investigated their clinical relevance, and proposed a new prognostic model. EXPERIMENTAL DESIGN A total of 210 patients from a multicentric cohort and 149 patients from a monocentric cohort were included in this study. RNA microarray profiles were obtained from 165 patients of the multicentric cohort. RNA sequencing (RNA-seq) profiles were obtained from all the patients. RESULTS For the patients with both RNA microarray and RNA-seq profiles, the concordance in subtype assignment was partial with an 82.4% coherence rate. The correlation between the two technique projections of the six components ranged from 0.85 to 0.95, demonstrating an advantage of robustness. On the basis of the Akaike information criterion, the RNA components showed more prognostic value in univariate or multivariate models than the subtypes. Using the monocentric cohort for training, we developed a multivariate Cox regression model using all six components and clinicopathologic characteristics (node invasion and resection margins) on disease-free survival (DFS). This prognostic model was highly associated with DFS (P < 0.001). The evaluation of the model in the multicentric cohort showed significant association with DFS and overall survival (P < 0.001). CONCLUSIONS We described the advantage of the prognostic value and robustness of the whole-tumor transcriptomic components than subtypes. We created and validated a new DFS-based multivariate Cox regression prognostic model, including six pancreatic adenocarcinoma transcriptomic component levels and pathologic characteristics.
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Affiliation(s)
- Shulin Zhao
- Centre de Recherche des Cordeliers, INSERM UMRS1138, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale contre le cancer, CNRS SNC 5096, Paris, France.,Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Rémy Nicolle
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre le Cancer, Paris, France
| | - Jérémy Augustin
- Sorbonne Université, Assistance Publique - Hôpitaux de Paris, Department of Pathology, Groupe Hospitalier Pitié Salpêtrière, Paris, France
| | - Magali Svrcek
- Sorbonne Université, UPMC Université, IUC, Paris, France.,Assistance Publique - Hôpitaux de Paris, Department of pathology, Hôpital Saint Antoine, Paris, France
| | - Louis de Mestier
- Assistance Publique - Hôpitaux de Paris, Department of Gastroenterology and Pancreatology, and INSERM U1149, Hôpital Beaujon, Clichy, France
| | - Delphine Le Corre
- Centre de Recherche des Cordeliers, INSERM UMRS1138, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale contre le cancer, CNRS SNC 5096, Paris, France
| | - Daniel Pietrasz
- Centre de Recherche des Cordeliers, INSERM UMRS1138, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale contre le cancer, CNRS SNC 5096, Paris, France.,Paris-Saclay University, Assistance Publique - Hôpitaux de Paris, Department of digestive surgery, Paul Brousse Hospital, Villejuif, France
| | - Olivier Caliez
- Centre de Recherche des Cordeliers, INSERM UMRS1138, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale contre le cancer, CNRS SNC 5096, Paris, France.,Sorbonne Université, UPMC Université, IUC, Paris, France.,Assistance Publique - Hôpitaux de Paris, Department of Hepato-gastroenterology, Groupe Hospitalier Pitié Salpêtrière, Paris, France
| | - Jérôme Cros
- Assistance Publique - Hôpitaux de Paris, INSERM, Université de Paris, Department of Pathology, Hôpital Beaujon, Clichy, France
| | - Pierre Laurent-Puig
- Centre de Recherche des Cordeliers, INSERM UMRS1138, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale contre le cancer, CNRS SNC 5096, Paris, France.,Assistance Publique - Hôpitaux de Paris, Department of biochemistry, Hôpital Européen Georges Pompidou, Paris, France
| | - Jean-Baptiste Bachet
- Centre de Recherche des Cordeliers, INSERM UMRS1138, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale contre le cancer, CNRS SNC 5096, Paris, France. .,Sorbonne Université, UPMC Université, IUC, Paris, France.,Assistance Publique - Hôpitaux de Paris, Department of Hepato-gastroenterology, Groupe Hospitalier Pitié Salpêtrière, Paris, France
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Huang CT, Liang YJ. Anti-tumor effect of statin on pancreatic adenocarcinoma: From concept to precision medicine. World J Clin Cases 2021; 9:4500-4505. [PMID: 34222418 PMCID: PMC8223840 DOI: 10.12998/wjcc.v9.i18.4500] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/11/2021] [Accepted: 03/31/2021] [Indexed: 02/06/2023] Open
Abstract
A statin is a cholesterol-lowering agent, which inhibits HMG-CoA (3-hydroxy-3-methylglutaryl-coenzyme A) reductase and subsequently reduces the cholesterol precursor, and was first used commercially in 1987. The concept of cholesterol restriction leading to cancer cell dysfunction was proposed in 1992. The interruption of different signaling pathways has been proved in preclinical experiments to elucidate the anti-tumor mechanism of statins in pancreatic adenocarcinoma. Observational studies have shown that the clinical use of statins is beneficial in patients with pancreatic adenocarcinoma, including a chemoprevention effect, post-surgical resection follow-up and therapeutic prognosis of advanced cancer stage. Arrest of the cancer cell cycle by the combined use of gemcitabine and statin was observed in a cell line study. The effect of microbiota on the tumor microenvironment of pancreatic adenocarcinoma is a new therapeutic approach as statins can modulate the gut microbiota. Hence, further randomized trials of statins in pancreatic adenocarcinoma treatment will be warranted with application of precision medicine from microbiota-derived, cell cycle-based and signaling pathway-targeted research.
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Affiliation(s)
- Chung-Tsui Huang
- Department of Gastroenterology and Hepatology, Far Eastern Memorial Hospital, New Taipei 220, Taiwan
| | - Yao-Jen Liang
- Graduate Institute of Applied Science and Engineering, Department and Institute of Life Science, Fu-Jen University, New Taipei 242, Taiwan
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