1
|
Cyrta J, Dermawan JK, Tauziède-Espariat A, Liu T, Rosenblum M, Shroff S, Katabi N, Cardoen L, Guillemot D, Masliah-Planchon J, Hoare O, Delattre O, Bale T, Bourdeaut F, Antonescu CR. Expanding the clinicopathologic spectrum and genomic landscape of tumors with SMARCA2/4::CREM fusions. J Pathol 2024; 264:305-317. [PMID: 39344423 DOI: 10.1002/path.6350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 07/13/2024] [Accepted: 08/14/2024] [Indexed: 10/01/2024]
Abstract
CREB gene family (ATF1, CREB1, CREM) fusions with either EWSR1 or FUS gene partners drive the pathogenesis of a wide range of neoplasms, including various soft tissue tumors, intracranial myxoid mesenchymal tumors (IMMTs), hyalinizing clear cell carcinoma (HCCC), and rare mesotheliomas. Recently, a SMARCA2::CREM fusion was reported in one case each of IMMT and HCCC. In this study, we expand the clinicopathologic and molecular spectrum of these neoplasms by describing three additional cases with SMARCA2::CREM and one with a novel SMARCA4::CREM fusion, highlighting the recurrent potential of additional CREB gene fusion partners beyond FET family members. To evaluate if these fusions define a new pathologic entity, we performed a comprehensive genomic and methylation analysis and compared the results to other related tumors. Tumors occurred in children and young adults (median age 20 years) and spanned a broad anatomic distribution, including soft tissue, intracranial, head and neck, and prostatic urethra. Microscopically, the tumors shared an undifferentiated round to epithelioid cell phenotype and a hyalinized fibrous stroma. Immunohistochemically, a polyphenotypic profile was observed, with variable expression of SOX10, desmin, and/or epithelial markers. No targetable genomic alterations were found using panel-based DNA sequencing. By DNA methylation and transcriptomic analyses, tumors grouped closely to FET::CREB entities, but not with SMARCA4/SMARCB1-deficient tumors. High expression of CREM by immunohistochemistry was also documented in these tumors. Patients experienced local recurrence (n = 2), locoregional lymph node metastases (n = 2), and an isolated visceral metastasis (n = 1). Overall, our study suggests that SMARCA2/4::CREM fusions define a distinct group of neoplasms with round cell to epithelioid histology, a variable immunoprofile, and a definite risk of malignancy. Larger studies are needed to further explore the pathogenetic relationship with the FET::CREB family of tumors. © 2024 The Pathological Society of Great Britain and Ireland.
Collapse
Affiliation(s)
- Joanna Cyrta
- Department of Pathology, Institut Curie, PSL Research University, Paris, France
| | - Josephine K Dermawan
- Department of Pathology and Laboratory Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Arnault Tauziède-Espariat
- Department of Neuropathology, GHU Paris Psychiatry and Neurosciences, Sainte-Anne Hospital, Paris, France
| | - Ting Liu
- Department of Pathology, University of Utah/ARUP Laboratories, Salt Lake City, UT, USA
| | - Marc Rosenblum
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Seema Shroff
- Department of Pathology, Advent Health, Orlando, FL, USA
| | - Nora Katabi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Delphine Guillemot
- Genetics Unit, Department of Tumor Biology, Institut Curie, PSL Research University, Paris, France
| | - Julien Masliah-Planchon
- Genetics Unit, Department of Tumor Biology, Institut Curie, PSL Research University, Paris, France
| | - Owen Hoare
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, Paris Cité University, Paris, France
| | - Olivier Delattre
- Genetics Unit, Department of Tumor Biology, Institut Curie, PSL Research University, Paris, France
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, Paris Cité University, Paris, France
| | - Tejus Bale
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Franck Bourdeaut
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, Paris Cité University, Paris, France
| | - Cristina R Antonescu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| |
Collapse
|
2
|
Gehrmann J, Soenarto DJ, Hidayat K, Beyer M, Quakulinski L, Alkarkoukly S, Berressem S, Gundert A, Butler M, Grönke A, Lennartz S, Persigehl T, Zander T, Beyan O. Seeing the primary tumor because of all the trees: Cancer type prediction on low-dimensional data. Front Med (Lausanne) 2024; 11:1396459. [PMID: 39257886 PMCID: PMC11385615 DOI: 10.3389/fmed.2024.1396459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 08/06/2024] [Indexed: 09/12/2024] Open
Abstract
The Cancer of Unknown Primary (CUP) syndrome is characterized by identifiable metastases while the primary tumor remains hidden. In recent years, various data-driven approaches have been suggested to predict the location of the primary tumor (LOP) in CUP patients promising improved diagnosis and outcome. These LOP prediction approaches use high-dimensional input data like images or genetic data. However, leveraging such data is challenging, resource-intensive and therefore a potential translational barrier. Instead of using high-dimensional data, we analyzed the LOP prediction performance of low-dimensional data from routine medical care. With our findings, we show that such low-dimensional routine clinical information suffices as input data for tree-based LOP prediction models. The best model reached a mean Accuracy of 94% and a mean Matthews correlation coefficient (MCC) score of 0.92 in 10-fold nested cross-validation (NCV) when distinguishing four types of cancer. When considering eight types of cancer, this model achieved a mean Accuracy of 85% and a mean MCC score of 0.81. This is comparable to the performance achieved by approaches using high-dimensional input data. Additionally, the distribution pattern of metastases appears to be important information in predicting the LOP.
Collapse
Affiliation(s)
- Julia Gehrmann
- Institute for Biomedical Informatics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Devina Johanna Soenarto
- Institute for Biomedical Informatics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Kevin Hidayat
- Institute for Biomedical Informatics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Maria Beyer
- Institute for Biomedical Informatics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Lars Quakulinski
- Institute for Biomedical Informatics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Samer Alkarkoukly
- Institute for Biomedical Informatics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Medical Data Integration Center (MeDIC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Scarlett Berressem
- Department of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), Aachen, Germany
| | - Anna Gundert
- Department of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), Aachen, Germany
| | - Michael Butler
- Department of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), Aachen, Germany
| | - Ana Grönke
- Medical Data Integration Center (MeDIC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Simon Lennartz
- Institute for Diagnostic and Interventional Radiology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Thorsten Persigehl
- Institute for Diagnostic and Interventional Radiology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Thomas Zander
- Department of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), Aachen, Germany
| | - Oya Beyan
- Institute for Biomedical Informatics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Medical Data Integration Center (MeDIC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Department of Data Science and Artificial Intelligence, Fraunhofer FIT, Sankt Augustin, Germany
| |
Collapse
|
3
|
Jacquin N, Flippot R, Masliah-Planchon J, Grisay G, Brillet R, Dupain C, Kamal M, Guillou I, Gruel N, Servant N, Gestraud P, Wong J, Cockenpot V, Goncalves A, Selves J, Blons H, Rouleau E, Delattre O, Gervais C, Le Tourneau C, Bièche I, Allory Y, Albigès L, Watson S. Metastatic renal cell carcinoma with occult primary: a multicenter prospective cohort. NPJ Precis Oncol 2024; 8:147. [PMID: 39025947 PMCID: PMC11258290 DOI: 10.1038/s41698-024-00648-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 07/09/2024] [Indexed: 07/20/2024] Open
Abstract
Metastatic carcinoma of presumed renal origin (rCUP) has recently emerged as a new entity within the heterogeneous entity of Cancers of Unknown Primary (CUP) but their biological features and optimal therapeutic management remain unknown. We report the molecular characteristics and clinical outcome of a series of 25 rCUP prospectively identified within the French National Multidisciplinary Tumor Board for CUP. This cohort strongly suggests that rCUP share similarities with common RCC subtypes and benefit from renal-tailored systemic treatment. This study highlights the importance of integrating clinical and molecular data for optimal diagnosis and management of CUP.
Collapse
Affiliation(s)
- Nicolas Jacquin
- INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Center, Paris, France
- Department of Medical Oncology, Institut Godinot, Reims, France
| | - Ronan Flippot
- Department of Cancer Medicine, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | | | - Guillaume Grisay
- Department of Cancer Medicine, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Riwan Brillet
- Clinical Bioinformatic Unit, Department of Diagnostic and Theragnostic Medicine, Institut Curie Hospital, Paris, France
| | - Célia Dupain
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | - Maud Kamal
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | - Isabelle Guillou
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | - Nadège Gruel
- INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Center, Paris, France
- Department of Translational Research, Institut Curie Hospital, Paris, France
| | - Nicolas Servant
- INSERM U900, CBIO-Centre for Computational Biology, Institut Curie Research Center, Mines ParisTech, Paris, France
| | - Pierre Gestraud
- INSERM U900, CBIO-Centre for Computational Biology, Institut Curie Research Center, Mines ParisTech, Paris, France
| | - Jennifer Wong
- Somatic Genetic Unit, Department of Genetics, Institut Curie Hospital, Paris, France
| | | | | | - Janick Selves
- Department of Pathology, University Hospital of Toulouse (IUCT), Toulouse, France
| | - Hélène Blons
- Department of Biochemistry, Pharmacogenetics and Molecular Oncology, Georges Pompidou European Hospital, APHP, Paris, France
| | - Etienne Rouleau
- PRISM Center for personalized medicine, Gustave Roussy Cancer Center, Villejuif, France
| | - Olivier Delattre
- INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Center, Paris, France
- Somatic Genetic Unit, Department of Genetics, Institut Curie Hospital, Paris, France
| | - Claire Gervais
- Department of Medical Oncology, Georges Pompidou European Hospital, APHP, Paris, France
| | - Christophe Le Tourneau
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
- INSERM U900, Institut Curie, Saint-Cloud, France
- Paris-Saclay University, Paris, France
| | - Ivan Bièche
- Department of Genetics, Institut Curie Hospital, INSERM U1016, Université Paris Cité, Paris, France
| | - Yves Allory
- Department of Pathology, Institut Curie Hospital, Saint-Cloud, France.
- Université Versailles St-Quentin, Université Paris-Saclay, Montigny-le-Bretonneux, France.
| | - Laurence Albigès
- Department of Cancer Medicine, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France.
| | - Sarah Watson
- INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Center, Paris, France.
- Department of Medical Oncology, Institut Curie Hospital, Paris, France.
| |
Collapse
|
4
|
de Traux De Wardin H, Cyrta J, Dermawan JK, Guillemot D, Orbach D, Aerts I, Pierron G, Antonescu CR. FGFR1 fusions as a novel molecular driver in rhabdomyosarcoma. Genes Chromosomes Cancer 2024; 63:e23232. [PMID: 38607246 PMCID: PMC11385681 DOI: 10.1002/gcc.23232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/17/2024] [Accepted: 03/21/2024] [Indexed: 04/13/2024] Open
Abstract
The wide application of RNA sequencing in clinical practice has allowed the discovery of novel fusion genes, which have contributed to a refined molecular classification of rhabdomyosarcoma (RMS). Most fusions in RMS result in aberrant transcription factors, such as PAX3/7::FOXO1 in alveolar RMS (ARMS) and fusions involving VGLL2 or NCOA2 in infantile spindle cell RMS. However, recurrent fusions driving oncogenic kinase activation have not been reported in RMS. Triggered by an index case of an unclassified RMS (overlapping features between ARMS and sclerosing RMS) with a novel FGFR1::ANK1 fusion, we reviewed our molecular files for cases harboring FGFR1-related fusions. One additional case with an FGFR1::TACC1 fusion was identified in a tumor resembling embryonal RMS (ERMS) with anaplasia, but with no pathogenic variants in TP53 or DICER1 on germline testing. Both cases occurred in males, aged 7 and 24, and in the pelvis. The 2nd case also harbored additional alterations, including somatic TP53 and TET2 mutations. Two additional RMS cases (one unclassified, one ERMS) with FGFR1 overexpression but lacking FGFR1 fusions were identified by RNA sequencing. These two cases and the FGFR1::TACC1-positive case clustered together with the ERMS group by RNAseq. This is the first report of RMS harboring recurrent FGFR1 fusions. However, it remains unclear if FGFR1 fusions define a novel subset of RMS or alternatively, whether this alteration can sporadically drive the pathogenesis of known RMS subtypes, such as ERMS. Additional larger series with integrated genomic and epigenetic datasets are needed for better subclassification, as the resulting oncogenic kinase activation underscores the potential for targeted therapy.
Collapse
Affiliation(s)
- Henry de Traux De Wardin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Pediatrics, Brussels University Hospital, Academic Children's Hospital Queen Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Joanna Cyrta
- Department of Pathology, Institut Curie, PSL University, Paris, France
| | - Josephine K Dermawan
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | | | - Daniel Orbach
- SIREDO Oncology Center (Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer), PSL University, Institut Curie, Paris, France
| | - Isabelle Aerts
- SIREDO Oncology Center (Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer), PSL University, Institut Curie, Paris, France
| | - Gaelle Pierron
- Unité de Génétique Somatique, Institut Curie, Paris, France
| | - Cristina R Antonescu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| |
Collapse
|
5
|
Guérin J, Nahid A, Tassy L, Deloger M, Bocquet F, Thézenas S, Desandes E, Le Deley MC, Durando X, Jaffré A, Es-Saad I, Crochet H, Le Morvan M, Lion F, Raimbourg J, Khay O, Craynest F, Giro A, Laizet Y, Bertaut A, Joly F, Livartowski A, Heudel P. Consore: A Powerful Federated Data Mining Tool Driving a French Research Network to Accelerate Cancer Research. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2024; 21:189. [PMID: 38397680 PMCID: PMC10887639 DOI: 10.3390/ijerph21020189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/28/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024]
Abstract
BACKGROUND Real-world data (RWD) related to the health status and care of cancer patients reflect the ongoing medical practice, and their analysis yields essential real-world evidence. Advanced information technologies are vital for their collection, qualification, and reuse in research projects. METHODS UNICANCER, the French federation of comprehensive cancer centres, has innovated a unique research network: Consore. This potent federated tool enables the analysis of data from millions of cancer patients across eleven French hospitals. RESULTS Currently operational within eleven French cancer centres, Consore employs natural language processing to structure the therapeutic management data of approximately 1.3 million cancer patients. These data originate from their electronic medical records, encompassing about 65 million medical records. Thanks to the structured data, which are harmonized within a common data model, and its federated search tool, Consore can create patient cohorts based on patient or tumor characteristics, and treatment modalities. This ability to derive larger cohorts is particularly attractive when studying rare cancers. CONCLUSIONS Consore serves as a tremendous data mining instrument that propels French cancer centres into the big data era. With its federated technical architecture and unique shared data model, Consore facilitates compliance with regulations and acceleration of cancer research projects.
Collapse
Affiliation(s)
| | - Amine Nahid
- Coexya, 69370 Saint-Didier-au-Mont-d’Or, France; (A.N.); (F.J.)
| | - Louis Tassy
- Institut Paoli-Calmettes, 13009 Marseille, France; (L.T.); (M.L.M.)
| | - Marc Deloger
- Gustave Roussy, 94805 Villejuif, France; (M.D.); (F.L.)
| | - François Bocquet
- Data Factory & Analytics Department, Institut de Cancérologie de l’Ouest, 44805 Nantes-Angers, France (J.R.)
| | - Simon Thézenas
- Institut Régional du Cancer de Montpellier, 34090 Montpellier, France;
| | - Emmanuel Desandes
- Institut de Cancérologie de Lorraine, 54519 Nancy, France; (E.D.); (O.K.)
| | | | - Xavier Durando
- Centre Jean Perrin, 63011 Clermont Ferrand, France; (X.D.); (A.G.)
| | - Anne Jaffré
- Institut Bergonié, 33076 Bordeaux, France; (A.J.); (Y.L.)
| | - Ikram Es-Saad
- Centre Georges Francois Leclerc, 21000 Dijon, France; (I.E.-S.); (A.B.)
| | | | - Marie Le Morvan
- Institut Paoli-Calmettes, 13009 Marseille, France; (L.T.); (M.L.M.)
| | - François Lion
- Gustave Roussy, 94805 Villejuif, France; (M.D.); (F.L.)
| | - Judith Raimbourg
- Data Factory & Analytics Department, Institut de Cancérologie de l’Ouest, 44805 Nantes-Angers, France (J.R.)
| | - Oussama Khay
- Institut de Cancérologie de Lorraine, 54519 Nancy, France; (E.D.); (O.K.)
| | - Franck Craynest
- Centre Oscar Lambret, 59000 Lille, France; (M.-C.L.D.); (F.C.)
| | - Alexia Giro
- Centre Jean Perrin, 63011 Clermont Ferrand, France; (X.D.); (A.G.)
| | - Yec’han Laizet
- Institut Bergonié, 33076 Bordeaux, France; (A.J.); (Y.L.)
| | - Aurélie Bertaut
- Centre Georges Francois Leclerc, 21000 Dijon, France; (I.E.-S.); (A.B.)
| | - Frederik Joly
- Coexya, 69370 Saint-Didier-au-Mont-d’Or, France; (A.N.); (F.J.)
| | | | | |
Collapse
|
6
|
Ma W, Wu H, Chen Y, Xu H, Jiang J, Du B, Wan M, Ma X, Chen X, Lin L, Su X, Bao X, Shen Y, Xu N, Ruan J, Jiang H, Ding Y. New techniques to identify the tissue of origin for cancer of unknown primary in the era of precision medicine: progress and challenges. Brief Bioinform 2024; 25:bbae028. [PMID: 38343328 PMCID: PMC10859692 DOI: 10.1093/bib/bbae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 12/10/2023] [Accepted: 01/11/2024] [Indexed: 02/15/2024] Open
Abstract
Despite a standardized diagnostic examination, cancer of unknown primary (CUP) is a rare metastatic malignancy with an unidentified tissue of origin (TOO). Patients diagnosed with CUP are typically treated with empiric chemotherapy, although their prognosis is worse than those with metastatic cancer of a known origin. TOO identification of CUP has been employed in precision medicine, and subsequent site-specific therapy is clinically helpful. For example, molecular profiling, including genomic profiling, gene expression profiling, epigenetics and proteins, has facilitated TOO identification. Moreover, machine learning has improved identification accuracy, and non-invasive methods, such as liquid biopsy and image omics, are gaining momentum. However, the heterogeneity in prediction accuracy, sample requirements and technical fundamentals among the various techniques is noteworthy. Accordingly, we systematically reviewed the development and limitations of novel TOO identification methods, compared their pros and cons and assessed their potential clinical usefulness. Our study may help patients shift from empirical to customized care and improve their prognoses.
Collapse
Affiliation(s)
- Wenyuan Ma
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hui Wu
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yiran Chen
- Department of Surgical Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hongxia Xu
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, China
| | - Junjie Jiang
- Department of Gastroenterology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bang Du
- Real Doctor AI Research Centre, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Mingyu Wan
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaolu Ma
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoyu Chen
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lili Lin
- Department of Nuclear Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinhui Su
- Department of Nuclear Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xuanwen Bao
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yifei Shen
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Nong Xu
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jian Ruan
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haiping Jiang
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yongfeng Ding
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| |
Collapse
|
7
|
Chen C, Lu C, Viswanathan V, Maveal B, Maheshwari B, Willis J, Madabhushi A. Identifying primary tumor site of origin for liver metastases via a combination of handcrafted and deep learning features. J Pathol Clin Res 2024; 10:e344. [PMID: 37822044 PMCID: PMC10766034 DOI: 10.1002/cjp2.344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 08/14/2023] [Accepted: 08/28/2023] [Indexed: 10/13/2023]
Abstract
Liver is one of the most common sites for metastases, which can occur on account of primary tumors from multiple sites of origin. Identifying the primary site of origin (PSO) of a metastasis can help in guiding therapeutic options for liver metastases. In this pilot study, we hypothesized that computer extracted handcrafted (HC) histomorphometric features can be utilized to identify the PSO of liver metastases. Cellular features, including tumor nuclei morphological and graph features as well as cytoplasm texture features, were extracted by computer algorithms from 175 slides (114 patients). The study comprised three experiments: (1) comparing and (2) fusing a machine learning (ML) model trained with HC pathomic features and deep learning (DL)-based classifiers to predict site of origin; (3) identifying the section of the primary tumor from which metastases were derived. For experiment 1, we divided the cohort into training sets composed of primary and matched liver metastases [60 patients, 121 whole slide images (WSIs)], and a hold-out validation set (54 patients, 54 WSIs) composed solely of liver metastases of known site of origin. Using the extracted HC features of the training set, a combination of supervised machine classifiers and unsupervised clustering was applied to identify the PSO. A random forest classifier achieved areas under the curve (AUCs) of 0.83, 0.64, 0.82, and 0.64 in classifying the metastatic tumor from colon, esophagus, breast, and pancreas on the validation set. The top features related to nuclear and peri-nuclear shape and textural attributes. We also trained a DL network to serve as a direct comparison to our method. The DL model achieved AUCs for colon: 0.94, esophagus: 0.66, breast: 0.79, and pancreas: 0.67 in identifying PSO. A decision fusion-based strategy was deployed to fuse the trained ML and DL classifiers and achieved slightly better results than ML or DL classifier alone (colon: 0.93, esophagus: 0.68, breast: 0.81, and pancreas: 0.69). For the third experiment, WSI-level attention maps were also generated using a trained DL network to generate a composite feature similarity heat map between paired primaries and their associated metastases. Our experiments revealed that epithelium-rich and moderately differentiated tumor regions of primary tumors were quantitatively similar to paired metastatic tumors. Our findings suggest that a combination of HC and DL features could potentially help identify the PSO for liver metastases while at the same time also potentially identify the spatial sites of origin for the metastases within primary tumors.
Collapse
Affiliation(s)
- Chuheng Chen
- Department of Biomedical EngineeringCase Western Reserve UniversityClevelandOHUSA
| | - Cheng Lu
- Department of Biomedical EngineeringCase Western Reserve UniversityClevelandOHUSA
| | - Vidya Viswanathan
- Wallace H. Coulter Department of Biomedical EngineeringGeorgia Institute of Technology and Emory UniversityAtlantaGAUSA
| | - Brandon Maveal
- Department of PathologyUniversity Hospitals Cleveland Medical Center and Case Western Reserve UniversityClevelandOHUSA
| | - Bhunesh Maheshwari
- Department of PathologyUniversity Hospitals Cleveland Medical Center and Case Western Reserve UniversityClevelandOHUSA
| | - Joseph Willis
- Department of Biomedical EngineeringCase Western Reserve UniversityClevelandOHUSA
- Department of PathologyUniversity Hospitals Cleveland Medical Center and Case Western Reserve UniversityClevelandOHUSA
| | - Anant Madabhushi
- Wallace H. Coulter Department of Biomedical EngineeringGeorgia Institute of Technology and Emory UniversityAtlantaGAUSA
- Radiology and Imaging Sciences, Biomedical Informatics (BMI) and PathologyGeorgia Institute of Technology and Emory UniversityAtlantaGAUSA
- Atlanta Veterans Administration Medical CenterAtlantaGAUSA
| |
Collapse
|
8
|
Štancl P, Karlić R. Machine learning for pan-cancer classification based on RNA sequencing data. Front Mol Biosci 2023; 10:1285795. [PMID: 38028533 PMCID: PMC10667476 DOI: 10.3389/fmolb.2023.1285795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023] Open
Abstract
Despite recent improvements in cancer diagnostics, 2%-5% of all malignancies are still cancers of unknown primary (CUP), for which the tissue-of-origin (TOO) cannot be determined at the time of presentation. Since the primary site of cancer leads to the choice of optimal treatment, CUP patients pose a significant clinical challenge with limited treatment options. Data produced by large-scale cancer genomics initiatives, which aim to determine the genomic, epigenomic, and transcriptomic characteristics of a large number of individual patients of multiple cancer types, have led to the introduction of various methods that use machine learning to predict the TOO of cancer patients. In this review, we assess the reproducibility, interpretability, and robustness of results obtained by 20 recent studies that utilize different machine learning methods for TOO prediction based on RNA sequencing data, including their reported performance on independent data sets and identification of important features. Our review investigates the strengths and weaknesses of different methods, checks the correspondence of their results, and identifies potential issues with datasets used for model training and testing, assessing their potential usefulness in a clinical setting and suggesting future improvements.
Collapse
Affiliation(s)
| | - Rosa Karlić
- Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| |
Collapse
|
9
|
Edsjö A, Holmquist L, Geoerger B, Nowak F, Gomon G, Alix-Panabières C, Ploeger C, Lassen U, Le Tourneau C, Lehtiö J, Ott PA, von Deimling A, Fröhling S, Voest E, Klauschen F, Dienstmann R, Alshibany A, Siu LL, Stenzinger A. Precision cancer medicine: Concepts, current practice, and future developments. J Intern Med 2023; 294:455-481. [PMID: 37641393 DOI: 10.1111/joim.13709] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Precision cancer medicine is a multidisciplinary team effort that requires involvement and commitment of many stakeholders including the society at large. Building on the success of significant advances in precision therapy for oncological patients over the last two decades, future developments will be significantly shaped by improvements in scalable molecular diagnostics in which increasingly complex multilayered datasets require transformation into clinically useful information guiding patient management at fast turnaround times. Adaptive profiling strategies involving tissue- and liquid-based testing that account for the immense plasticity of cancer during the patient's journey and also include early detection approaches are already finding their way into clinical routine and will become paramount. A second major driver is the development of smart clinical trials and trial concepts which, complemented by real-world evidence, rapidly broaden the spectrum of therapeutic options. Tight coordination with regulatory agencies and health technology assessment bodies is crucial in this context. Multicentric networks operating nationally and internationally are key in implementing precision oncology in clinical practice and support developing and improving the ecosystem and framework needed to turn invocation into benefits for patients. The review provides an overview of the diagnostic tools, innovative clinical studies, and collaborative efforts needed to realize precision cancer medicine.
Collapse
Affiliation(s)
- Anders Edsjö
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
- Division of Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
- Genomic Medicine Sweden (GMS), Kristianstad, Sweden
| | - Louise Holmquist
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
- Genomic Medicine Sweden (GMS), Kristianstad, Sweden
| | - Birgit Geoerger
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | | | - Georgy Gomon
- Department of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
- Department of Medical Oncology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Catherine Alix-Panabières
- Laboratory of Rare Human Circulating Cells, University Medical Center of Montpellier, Montpellier, France
- CREEC, MIVEGEC, University of Montpellier, Montpellier, France
| | - Carolin Ploeger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Centers for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Ulrik Lassen
- Department of Oncology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Christophe Le Tourneau
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
- INSERM U900 Research Unit, Saint-Cloud, France
- Faculty of Medicine, Paris-Saclay University, Paris, France
| | - Janne Lehtiö
- Department of Oncology Pathology, Karolinska Institutet, Science for Life Laboratory, Stockholm, Sweden
| | - Patrick A Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan Fröhling
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Emile Voest
- Department of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Frederick Klauschen
- Institute of Pathology, Charite - Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- BIFOLD - Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
- Institute of Pathology, Ludwig-Maximilians-University, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Munich Partner Site, Heidelberg, Germany
| | | | | | - Lillian L Siu
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Centers for Personalized Medicine (ZPM), Heidelberg, Germany
| |
Collapse
|
10
|
de Traux de Wardin H, Dermawan JK, Merlin MS, Wexler LH, Orbach D, Vanoli F, Schleiermacher G, Geoerger B, Ballet S, Guillemot D, Frouin E, Cyrille S, Delattre O, Pierron G, Antonescu CR. Sequential genomic analysis using a multisample/multiplatform approach to better define rhabdomyosarcoma progression and relapse. NPJ Precis Oncol 2023; 7:96. [PMID: 37730754 PMCID: PMC10511463 DOI: 10.1038/s41698-023-00445-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/30/2023] [Indexed: 09/22/2023] Open
Abstract
The genomic spectrum of rhabdomyosarcoma (RMS) progression from primary to relapse is not fully understood. In this pilot study, we explore the sensitivity of various targeted and whole-genome NGS platforms in order to assess the best genomic approach of using liquid biopsy in future prospective clinical trials. Moreover, we investigate 35 paired primary/relapsed RMS from two contributing institutions, 18 fusion-positive (FP-RMS) and 17 fusion-negative RMS (FN-RMS) by either targeted DNA or whole exome sequencing (WES). In 10 cases, circulating tumor DNA (ctDNA) from multiple timepoints through clinical care and progression was analyzed for feasibility of liquid biopsy in monitoring treatment response/relapse. ctDNA alterations were evaluated using a targeted 36-gene custom RMS panel at high coverage for single-nucleotide variation and fusion detection, and a shallow whole-genome sequencing for copy number variation. FP-RMS have a stable genome with relapse, with common secondary alterations CDKN2A/B, MYCN, and CDK4 present at diagnosis and impacting survival. FP-RMS lacking major secondary events at baseline acquire recurrent MYCN and AKT1 alterations. FN-RMS acquire a higher number of new alterations, most commonly SMARCA2 missense mutations. ctDNA analyses detect pathognomonic variants in all RMS patients within our collection at diagnosis, regardless of type of alterations, and confirmed at relapse in 86% of FP-RMS and 100% FN-RMS. Moreover, a higher number of fusion reads is detected with increased disease burden and at relapse in patients following a fatal outcome. These results underscore patterns of tumor progression and provide rationale for using liquid biopsy to monitor treatment response.
Collapse
Affiliation(s)
- Henry de Traux de Wardin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Unit of Somatic Genetics, Institut Curie, Paris, France
| | - Josephine K Dermawan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marie-Sophie Merlin
- University of Lorraine, Centre Hospitalier Régional Universitaire (CHRU), Childrens' Hospital, Department of Pediatric Oncology, Vandoeuvre-lès-Nancy, France
| | - Leonard H Wexler
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Orbach
- SIREDO Oncology Center (Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer), PSL University, Institut Curie, Paris, France
| | - Fabio Vanoli
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gudrun Schleiermacher
- SIREDO Oncology Center (Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer), PSL University, Institut Curie, Paris, France
- U830 INSERM, Paris, France
| | - Birgit Geoerger
- Gustave Roussy Cancer Center, Department of Pediatric and Adolescent Oncology, Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Université Paris-Saclay, Villejuif, 94805, France
| | - Stelly Ballet
- Unit of Somatic Genetics, Institut Curie, Paris, France
| | | | | | - Stacy Cyrille
- Department of Biometrics, Institut Curie, Paris, France
| | - Olivier Delattre
- SIREDO Oncology Center (Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer), PSL University, Institut Curie, Paris, France
- U830 INSERM, Paris, France
| | - Gaelle Pierron
- Unit of Somatic Genetics, Institut Curie, Paris, France.
| | - Cristina R Antonescu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
11
|
Kazdal D, Menzel M, Budczies J, Stenzinger A. [Molecular tumor diagnostics as the driving force behind precision oncology]. Dtsch Med Wochenschr 2023; 148:1157-1165. [PMID: 37657453 DOI: 10.1055/a-1937-0347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
Molecular pathological diagnostics plays a central role in personalized oncology and requires multidisciplinary teamwork. It is just as relevant for the individual patient who is being treated with an approved therapy method or an individual treatment attempt as it is for prospective clinical studies that require the identification of specific therapeutic target structures or complex biomarkers for study inclusion. It is also of crucial importance for the generation of real-world data, which is becoming increasingly important for drug development. Future developments will be significantly shaped by improvements in scalable molecular diagnostics, in which increasingly complex and multi-layered data sets must be quickly converted into clinically useful information. One focus will be on the development of adaptive diagnostic strategies in order to be able to depict the enormous plasticity of a cancer disease over time.
Collapse
|
12
|
Michuda J, Breschi A, Kapilivsky J, Manghnani K, McCarter C, Hockenberry AJ, Mineo B, Igartua C, Dudley JT, Stumpe MC, Beaubier N, Shirazi M, Jones R, Morency E, Blackwell K, Guinney J, Beauchamp KA, Taxter T. Validation of a Transcriptome-Based Assay for Classifying Cancers of Unknown Primary Origin. Mol Diagn Ther 2023; 27:499-511. [PMID: 37099070 PMCID: PMC10300170 DOI: 10.1007/s40291-023-00650-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2023] [Indexed: 04/27/2023]
Abstract
INTRODUCTION Cancers assume a variety of distinct histologies, and may originate from a myriad of sites including solid organs, hematopoietic cells, and connective tissue. Clinical decision-making based on consensus guidelines such as the National Comprehensive Cancer Network (NCCN) is often predicated on a specific histologic and anatomic diagnosis, supported by clinical features and pathologist interpretation of morphology and immunohistochemical (IHC) staining patterns. However, in patients with nonspecific morphologic and IHC findings-in addition to ambiguous clinical presentations such as recurrence versus new primary-a definitive diagnosis may not be possible, resulting in the patient being categorized as having a cancer of unknown primary (CUP). Therapeutic options and clinical outcomes are poor for patients with CUP, with a median survival of 8-11 months. METHODS Here, we describe and validate the Tempus Tumor Origin (Tempus TO) assay, an RNA-sequencing-based machine learning classifier capable of discriminating between 68 clinically relevant cancer subtypes. Model accuracy was assessed using primary and/or metastatic samples with known subtype. RESULTS We show that the Tempus TO model is 91% accurate when assessed on both a retrospectively held out cohort and a set of samples sequenced after model freeze that collectively contained 9210 total samples with known diagnoses. When evaluated on a cohort of CUPs, the model recapitulated established associations between genomic alterations and cancer subtype. DISCUSSION Combining diagnostic prediction tests (e.g., Tempus TO) with sequencing-based variant reporting (e.g., Tempus xT) may expand therapeutic options for patients with cancers of unknown primary or uncertain histology.
Collapse
|
13
|
Mahadevia H, Kujtan L, Roth M, Sharma P, Buckley JR, Ewing E, Bansal D. Utility of RNA Expression to Determine the Tissue of Origin of Malignancies with an Inconclusive Histopathology. Case Rep Oncol 2023; 16:784-790. [PMID: 37900851 PMCID: PMC10603602 DOI: 10.1159/000533376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/26/2023] [Indexed: 10/31/2023] Open
Abstract
We present 2 cases of cancer of unknown origin in which RNA-based cancer classification testing provided vital insight and directed treatment management. The tissue of origin could not be determined in both of these patients utilizing morphology and immunohistochemical analysis of the tissue samples. Next-generation sequencing and tumor-of-origin testing using an RNA-based molecular cancer classifier were performed to elucidate the possible tissue of origin. A 61-year-old male with a history of localized basal cell carcinoma presented with a 4.4-cm axillary lymph node in addition to upper extremity edema and supraclavicular lymphadenopathy. RNA-based tumor origin testing revealed skin basal or squamous cell carcinoma as the likely tissue of origin, with a probability of 97%. He received vismodegib, a hedgehog inhibitor, after progression on cemiplimab and experienced a partial response by RECIST criteria, which is currently ongoing for over a year. A 74-year-old female patient with a remote history of ovarian cancer for which she underwent resection and adjuvant chemotherapy presented 15 years later with abdominal pain. The diagnostic workup revealed a 2-cm pancreatic mass and enlarged peritoneal lymph nodes. RNA sequencing revealed a 99% likelihood of the tissue of origin being serous ovarian carcinoma. Subsequently, she underwent surgery and adjuvant chemotherapy and is currently in remission with letrozole maintenance. Genomic data already plays a crucial role in therapeutic decision-making for individuals with cancer. These cases highlight the complementary role of genomic data in the diagnostic workup of cancer, leading to favorable patient outcomes.
Collapse
Affiliation(s)
- Himil Mahadevia
- Internal Medicine, University of Missouri, Kansas City, MO, USA
| | - Lara Kujtan
- Hematology/Oncology, University of Missouri, Kansas City, MO, USA
| | - Marc Roth
- Hematology/Oncology, Saint Luke’s Hospital, Kansas City, MO, USA
| | - Parth Sharma
- Internal Medicine, University of Missouri, Kansas City, MO, USA
| | | | | | - Dhruv Bansal
- Hematology/Oncology, Saint Luke’s Hospital, Kansas City, MO, USA
| |
Collapse
|
14
|
Nourieh M, Vibert R, Saint-Ghislain M, Cyrta J, Vincent-Salomon A. Next-generation sequencing in breast pathology: real impact on routine practice over a decade since its introduction. Histopathology 2023; 82:162-169. [PMID: 36482269 PMCID: PMC10108312 DOI: 10.1111/his.14794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/08/2022] [Accepted: 09/11/2022] [Indexed: 12/13/2022]
Abstract
The diagnosis, histomolecular classes of breast cancers (luminal A, luminal B, HER2-enriched, and basal-like), and accurate prediction of prognosis are commonly determined using morphological and phenotypical analyses in clinical practice worldwide. Therapeutic strategies are mostly based on the disease stage and molecular subclasses of breast cancer. Targeted therapies, such as anti-HER2s, poly-ADP ribose polymerase inhibitors or, to a lesser extent, phosphatidylinositol 3 kinase inhibitors, have substantially improved breast cancer patient prognosis over the past decades. Human epidermal growth factor receptor 2 (HER2) overexpression is widely determined based on immunohistochemistry, while next-generation sequencing (NGS) is currently employed to assess the presence of molecular alterations, including breast cancer gene 1 (BRCA1) and 2 or phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) mutations, which are targets of these new approved therapies. In addition, next-generation sequencing (NGS) can aid the pathologist in challenging situations, such as a diagnostic workup for a metastatic carcinoma in lymph nodes of unknown origin, differential diagnosis of spindle cell tumourtumor in the breast between metaplastic carcinoma, malignant PT and sarcoma, o, as well as determining relatedness between primary breast cancers and recurrences. NGS offers a powerful tool that enables the pathologist to combine morphological analyses together with molecular alterations in challenging diagnostic situations.
Collapse
Affiliation(s)
- Maya Nourieh
- Department of Diagnostic and Theranostic Medicine, Versailles Saint Quentin University UVSQ, Institut CURIE, Saint-Cloud, France
| | - Roseline Vibert
- Department of Diagnostic and Theranostic Medicine, Paris Sciences Lettres University PSL, Institut CURIE, Paris, France
| | - Mathilde Saint-Ghislain
- Department of Medical Oncology, Paris Sciences Lettres University PSL, Institut CURIE, Paris, France
| | - Joanna Cyrta
- Department of Diagnostic and Theranostic Medicine, Paris Sciences Lettres University PSL, Institut CURIE, Paris, France
| | - Anne Vincent-Salomon
- Department of Diagnostic and Theranostic Medicine, Paris Sciences Lettres University PSL, Institut CURIE, Paris, France
| |
Collapse
|
15
|
Ngo C, Verret B, Vibert J, Cotteret S, Levy A, Pechoux CL, Haddag-Miliani L, Honore C, Faron M, Quinquis F, Cesne AL, Scoazec JY, Pierron G. A novel fusion variant LSM14A::NR4A3 in extraskeletal myxoid chondrosarcoma. Genes Chromosomes Cancer 2023; 62:52-56. [PMID: 35932215 DOI: 10.1002/gcc.23090] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 11/12/2022] Open
Abstract
Extraskeletal myxoid chondrosarcoma (EMC) is a rare soft tissue neoplasm of uncertain lineage characterized by the pathognomonic rearrangement of the NR4A3 gene, which in most cases is fused with EWSR1. Other NR4A3 fusion partners have been described, namely TAF15, FUS, TCF12, and TGF. Some studies suggest that EMCs with non-EWSR1 variant fusion are associated with high-grade morphology and worst clinical behavior compared to EWSR1::NR4A3 tumors, supporting the potential significance of particular fusion variant in EMC. We report a case of a 34-year-old male who presented with calf EMC and subsequently developed a slowly progressive metastatic disease 3 years after diagnosis. Whole-transcriptome analysis with total RNA sequencing enabled identification of a novel fusion transcript LSM14A::NR4A3, expanding the molecular spectrum of EMC.
Collapse
Affiliation(s)
- Carine Ngo
- Department of Pathology and Biology, Gustave Roussy, Villejuif, France
| | | | - Julien Vibert
- Department of Medicine, Gustave Roussy, Villejuif, France
| | - Sophie Cotteret
- Department of Pathology and Biology, Gustave Roussy, Villejuif, France
| | - Antonin Levy
- Department of Radiation Oncology, Gustave Roussy, Villejuif, France
| | | | | | - Charles Honore
- Department of Surgery, Gustave Roussy, Villejuif, France
| | - Matthieu Faron
- Department of Surgery, Gustave Roussy, Villejuif, France
| | | | - Axel Le Cesne
- Department of Medicine, Gustave Roussy, Villejuif, France
| | - Jean-Yves Scoazec
- Department of Pathology and Biology, Gustave Roussy, Villejuif, France
| | | |
Collapse
|