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Wang Z, Yuan X, Jiang G, Li Y, Yang F, Wang J, Chen K. Towards the molecular era of discriminating multiple lung cancers. EBioMedicine 2023; 90:104508. [PMID: 36958271 PMCID: PMC10040518 DOI: 10.1016/j.ebiom.2023.104508] [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: 10/22/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 03/25/2023] Open
Abstract
In the era of histopathology-based diagnosis, the discrimination between multiple lung cancers (MLCs) poses significant uncertainties and has thus become a clinical dilemma. However, recent significant advances and increased application of molecular technologies in clonal relatedness assessment have led to more precision in distinguishing between multiple primary lung cancers (MPLCs) and intrapulmonary metastasis (IPMs). This review summarizes recent advances in the molecular identification of MLCs and compares various methods based on somatic mutations, chromosome alterations, microRNAs, and tumor microenvironment markers. The paper also discusses current challenges at the forefront of genomics-based discrimination, including the selection of detection technology, application of next-generation sequencing, and intratumoral heterogeneity (ITH). In summary, this paper highlights an entrance into the primary stage of molecule-based diagnostics.
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Affiliation(s)
- Ziyang Wang
- Thoracic Oncology Institute and Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Xiaoqiu Yuan
- Peking University Health Science Center, Beijing, 100191, China
| | - Guanchao Jiang
- Thoracic Oncology Institute and Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Yun Li
- Thoracic Oncology Institute and Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Fan Yang
- Thoracic Oncology Institute and Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Jun Wang
- Thoracic Oncology Institute and Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Kezhong Chen
- Thoracic Oncology Institute and Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China.
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2
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Warrick JI, Hu W, Yamashita H, Walter V, Shuman L, Craig JM, Gellert LL, Castro MAA, Robertson AG, Kuo F, Ostrovnaya I, Sarungbam J, Chen YB, Gopalan A, Sirintrapun SJ, Fine SW, Tickoo SK, Kim K, Thomas J, Karan N, Gao SP, Clinton TN, Lenis AT, Chan TA, Chen Z, Rao M, Hollman TJ, Li Y, Socci ND, Chavan S, Viale A, Mohibullah N, Bochner BH, Pietzak EJ, Teo MY, Iyer G, Rosenberg JE, Bajorin DF, Kaag M, Merrill SB, Joshi M, Adam R, Taylor JA, Clark PE, Raman JD, Reuter VE, Chen Y, Funt SA, Solit DB, DeGraff DJ, Al-Ahmadie HA. FOXA1 repression drives lineage plasticity and immune heterogeneity in bladder cancers with squamous differentiation. Nat Commun 2022; 13:6575. [PMID: 36323682 PMCID: PMC9630410 DOI: 10.1038/s41467-022-34251-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
Cancers arising from the bladder urothelium often exhibit lineage plasticity with regions of urothelial carcinoma adjacent to or admixed with regions of divergent histomorphology, most commonly squamous differentiation. To define the biologic basis for and clinical significance of this morphologic heterogeneity, here we perform integrated genomic analyses of mixed histology bladder cancers with separable regions of urothelial and squamous differentiation. We find that squamous differentiation is a marker of intratumoral genomic and immunologic heterogeneity in patients with bladder cancer and a biomarker of intrinsic immunotherapy resistance. Phylogenetic analysis confirms that in all cases the urothelial and squamous regions are derived from a common shared precursor. Despite the presence of marked genomic heterogeneity between co-existent urothelial and squamous differentiated regions, no recurrent genomic alteration exclusive to the urothelial or squamous morphologies is identified. Rather, lineage plasticity in bladder cancers with squamous differentiation is associated with loss of expression of FOXA1, GATA3, and PPARG, transcription factors critical for maintenance of urothelial cell identity. Of clinical significance, lineage plasticity and PD-L1 expression is coordinately dysregulated via FOXA1, with patients exhibiting morphologic heterogeneity pre-treatment significantly less likely to respond to immune checkpoint inhibitors.
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Affiliation(s)
- Joshua I Warrick
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Wenhuo Hu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hironobu Yamashita
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Vonn Walter
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Lauren Shuman
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Jenna M Craig
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Lan L Gellert
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mauro A A Castro
- Bioinformatics and Systems Biology Laboratory, Federal University of Parana, Curitiba, Paraná, Brazil
| | - A Gordon Robertson
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Fengshen Kuo
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Judy Sarungbam
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ying-Bei Chen
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anuradha Gopalan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sahussapont J Sirintrapun
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samson W Fine
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Satish K Tickoo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kwanghee Kim
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jasmine Thomas
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nagar Karan
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sizhi Paul Gao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy N Clinton
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew T Lenis
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ziyu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Manisha Rao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Travis J Hollman
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yanyun Li
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicholas D Socci
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shweta Chavan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Agnes Viale
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Neeman Mohibullah
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bernard H Bochner
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eugene J Pietzak
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Min Yuen Teo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gopa Iyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonathan E Rosenberg
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dean F Bajorin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew Kaag
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Suzanne B Merrill
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Monika Joshi
- Department of Medicine, Division of Hematology-Oncology, Penn State Cancer Institute, Hershey, PA, USA
| | - Rosalyn Adam
- Department of Urology, Boston Children's Hospital, Boston, MA, USA
| | - John A Taylor
- Department of Urology, University of Kansas Medical Center, Kansas City, MO, USA
| | - Peter E Clark
- Levine Cancer Institute, Atrium Health, Charlotte, NC, USA
| | - Jay D Raman
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Victor E Reuter
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel A Funt
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David J DeGraff
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA.
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, USA.
- Deparment of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, USA.
| | - Hikmat A Al-Ahmadie
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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3
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Lips EH, Kumar T, Megalios A, Visser LL, Sheinman M, Fortunato A, Shah V, Hoogstraat M, Sei E, Mallo D, Roman-Escorza M, Ahmed AA, Xu M, van den Belt-Dusebout AW, Brugman W, Casasent AK, Clements K, Davies HR, Fu L, Grigoriadis A, Hardman TM, King LM, Krete M, Kristel P, de Maaker M, Maley CC, Marks JR, Menegaz BA, Mulder L, Nieboer F, Nowinski S, Pinder S, Quist J, Salinas-Souza C, Schaapveld M, Schmidt MK, Shaaban AM, Shami R, Sridharan M, Zhang J, Stobart H, Collyar D, Nik-Zainal S, Wessels LFA, Hwang ES, Navin NE, Futreal PA, Thompson AM, Wesseling J, Sawyer EJ. Genomic analysis defines clonal relationships of ductal carcinoma in situ and recurrent invasive breast cancer. Nat Genet 2022; 54:850-860. [PMID: 35681052 PMCID: PMC9197769 DOI: 10.1038/s41588-022-01082-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 04/22/2022] [Indexed: 11/29/2022]
Abstract
Ductal carcinoma in situ (DCIS) is the most common form of preinvasive breast cancer and, despite treatment, a small fraction (5-10%) of DCIS patients develop subsequent invasive disease. A fundamental biologic question is whether the invasive disease arises from tumor cells in the initial DCIS or represents new unrelated disease. To address this question, we performed genomic analyses on the initial DCIS lesion and paired invasive recurrent tumors in 95 patients together with single-cell DNA sequencing in a subset of cases. Our data show that in 75% of cases the invasive recurrence was clonally related to the initial DCIS, suggesting that tumor cells were not eliminated during the initial treatment. Surprisingly, however, 18% were clonally unrelated to the DCIS, representing new independent lineages and 7% of cases were ambiguous. This knowledge is essential for accurate risk evaluation of DCIS, treatment de-escalation strategies and the identification of predictive biomarkers.
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Affiliation(s)
- Esther H Lips
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tapsi Kumar
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Anargyros Megalios
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Lindy L Visser
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Michael Sheinman
- Division of Molecular Carcinogenesis, Oncode Institute and The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Angelo Fortunato
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Biocomputing, Security and Society, Arizona State University, Tempe, AZ, USA
| | - Vandna Shah
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Marlous Hoogstraat
- Division of Molecular Carcinogenesis, Oncode Institute and The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Emi Sei
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Diego Mallo
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Biocomputing, Security and Society, Arizona State University, Tempe, AZ, USA
| | - Maria Roman-Escorza
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Ahmed A Ahmed
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Mingchu Xu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Wim Brugman
- Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anna K Casasent
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Karen Clements
- Screening Quality Assurance Service, Public Health England, London, UK
| | - Helen R Davies
- Early Cancer Unit, Hutchison/MRC Research Centre and Academic Department of Medical Genetics, Cambridge Biomedical Research Campus, University of Cambridge, Cambridge, UK
| | - Liping Fu
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anita Grigoriadis
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Timothy M Hardman
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Lorraine M King
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Marielle Krete
- Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Petra Kristel
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Michiel de Maaker
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Carlo C Maley
- Biodesign Center for Biocomputing, Security and Society, Arizona State University, Tempe, AZ, USA
| | - Jeffrey R Marks
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Brian A Menegaz
- Department of Surgery, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Lennart Mulder
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Frank Nieboer
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Salpie Nowinski
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Sarah Pinder
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Jelmar Quist
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Carolina Salinas-Souza
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Michael Schaapveld
- Division of Psychosocial research and Epidemiology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Abeer M Shaaban
- Queen Elizabeth Hospital Birmingham and University of Birmingham, Birmingham, UK
| | - Rana Shami
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Mathini Sridharan
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - John Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Serena Nik-Zainal
- Early Cancer Unit, Hutchison/MRC Research Centre and Academic Department of Medical Genetics, Cambridge Biomedical Research Campus, University of Cambridge, Cambridge, UK
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute and The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University of Technology, Delft, The Netherlands
| | - E Shelley Hwang
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Nicholas E Navin
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alastair M Thompson
- Department of Surgery, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Jelle Wesseling
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Divisions of Diagnostic Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Elinor J Sawyer
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK.
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Cyrta J, Prandi D, Arora A, Hovelson DH, Sboner A, Rodriguez A, Fedrizzi T, Beltran H, Robinson DR, Gopalan A, True L, Nelson PS, Robinson BD, Mosquera JM, Tomlins SA, Shen R, Demichelis F, Rubin MA. Comparative genomics of primary prostate cancer and paired metastases: insights from 12 molecular case studies. J Pathol 2022; 257:274-284. [PMID: 35220606 PMCID: PMC9311708 DOI: 10.1002/path.5887] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 02/09/2022] [Accepted: 02/23/2022] [Indexed: 11/25/2022]
Abstract
Primary prostate cancer (PCa) can show marked molecular heterogeneity. However, systematic analyses comparing primary PCa and matched metastases in individual patients are lacking. We aimed to address the molecular aspects of metastatic progression while accounting for the heterogeneity of primary PCa. In this pilot study, we collected 12 radical prostatectomy (RP) specimens from men who subsequently developed metastatic castration‐resistant prostate cancer (mCRPC). We used histomorphology (Gleason grade, focus size, stage) and immunohistochemistry (IHC) (ERG and p53) to identify independent tumors and/or distinct subclones of primary PCa. We then compared molecular profiles of these primary PCa areas to matched metastatic samples using whole‐exome sequencing (WES) and amplicon‐based DNA and RNA sequencing. Based on combined pathology and molecular analysis, seven (58%) RP specimens harbored monoclonal and topographically continuous disease, albeit with some degree of intratumor heterogeneity; four (33%) specimens showed true multifocal disease; and one displayed monoclonal disease with discontinuous topography. Early (truncal) events in primary PCa included SPOP p.F133V (one patient), BRAF p.K601E (one patient), and TMPRSS2:ETS rearrangements (eight patients). Activating AR alterations were seen in nine (75%) mCRPC patients, but not in matched primary PCa. Hotspot TP53 mutations, found in metastases from three patients, were readily present in matched primary disease. Alterations in genes encoding epigenetic modifiers were observed in several patients (either shared between primary foci and metastases or in metastatic samples only). WES‐based phylogenetic reconstruction and/or clonality scores were consistent with the index focus designated by pathology review in six out of nine (67%) cases. The three instances of discordance pertained to monoclonal, topographically continuous tumors, which would have been considered as unique disease in routine practice. Overall, our results emphasize pathologic and molecular heterogeneity of primary PCa, and suggest that comprehensive IHC‐assisted pathology review and genomic analysis are highly concordant in nominating the ‘index’ primary PCa area. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Joanna Cyrta
- Department of Pathology and Laboratory Medicine Weill Cornell Medicine New York NY USA
- Englander Institute for Precision Medicine Weill Cornell Medicine New York NY USA
- Department for BioMedical Research University of Bern Bern Switzerland
| | - Davide Prandi
- Department of Cellular Computational and Integrative Biology, University of Trento Trento Italy
| | - Arshi Arora
- Department of Epidemiology and Biostatistics Memorial Sloan‐Kettering Cancer Center New York NY USA
| | - Daniel H. Hovelson
- Center for Computational Medicine and Bioinformatics Univ. Michigan Ann Arbor MA USA
| | - Andrea Sboner
- Englander Institute for Precision Medicine Weill Cornell Medicine New York NY USA
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA
| | - Antonio Rodriguez
- Department for BioMedical Research University of Bern Bern Switzerland
- Institute of Pathology University of Bern Bern Switzerland
| | - Tarcisio Fedrizzi
- Department of Epidemiology and Biostatistics Memorial Sloan‐Kettering Cancer Center New York NY USA
| | - Himisha Beltran
- Department of Medicine Division of Medical Oncology, Weill Cornell Medicine New York NY USA
- Department of Medical Oncology Dana Farber Cancer Institute Boston MA USA
| | - Dan R. Robinson
- Department of Pathology University of Michigan Ann Arbor MI USA
| | - Anurandha Gopalan
- Department of Pathology Memorial Sloan Kettering Cancer Center New York NY USA
| | - Lawrence True
- Department of Pathology Univ. of Washington Seattle WA USA
| | | | - Brian D. Robinson
- Department of Pathology and Laboratory Medicine Weill Cornell Medicine New York NY USA
- Englander Institute for Precision Medicine Weill Cornell Medicine New York NY USA
| | - Juan Miguel Mosquera
- Department of Pathology and Laboratory Medicine Weill Cornell Medicine New York NY USA
- Englander Institute for Precision Medicine Weill Cornell Medicine New York NY USA
| | | | - Ronglai Shen
- Department of Epidemiology and Biostatistics Memorial Sloan‐Kettering Cancer Center New York NY USA
| | - Francesca Demichelis
- Englander Institute for Precision Medicine Weill Cornell Medicine New York NY USA
- Department of Cellular Computational and Integrative Biology, University of Trento Trento Italy
| | - Mark A. Rubin
- Department of Pathology and Laboratory Medicine Weill Cornell Medicine New York NY USA
- Englander Institute for Precision Medicine Weill Cornell Medicine New York NY USA
- Department for BioMedical Research University of Bern Bern Switzerland
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5
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Goodwin D, Rathi V, Conron M, Wright GM. Genomic and Clinical Significance of Multiple Primary Lung Cancers as Determined by Next-Generation Sequencing. J Thorac Oncol 2021; 16:1166-1175. [PMID: 33845213 DOI: 10.1016/j.jtho.2021.03.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 02/17/2021] [Accepted: 03/19/2021] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Marked variations in survival rates have brought into question whether standard clinicopathologic classification should be applied to patients presenting with multiple primary lung cancers (MPLCs). This study investigated the genetic profiles of MPLCs in a cohort of patients using next-generation sequencing and correlated results to clinicopathologic data and patient outcome. METHODS Patients treated surgically with curative intent for two putative primaries of similar histopathology from January 2000 to December 2019 at St Vincent's Hospital Melbourne. DNA and RNA was extracted from formalin-fixed, paraffin-embedded tumor tissue and sequenced on an Ion Torrent Personal Genome Machine system. Patient outcome was determined by overall survival and disease-free survival. RESULTS A total of 40 cases fulfilled the inclusion criteria. Mutational profiling was concordant with clinicopathologic diagnosis in most cases; however, seven cases (17.5%) revealed shared mutations suggesting metastatic disease and this was associated with a substantial reduction in overall survival (p < 0.05). CONCLUSIONS Our results suggest that gene sequencing technologies are potentially a more accurate diagnostic and prognostic tool compared with traditional histopathologic evaluation in patients presenting with suspected MPLCs, which could better guide management and predict outcomes.
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Affiliation(s)
- Daryn Goodwin
- Department of Surgery, St Vincent's Hospital Melbourne, The University of Melbourne, Fitzroy, Australia; Alfred Hospital, Melbourne, Australia
| | - Vivek Rathi
- Department of Anatomical Pathology, St Vincent's Hospital Melbourne, The University of Melbourne, Fitzroy, Australia
| | - Matthew Conron
- Department of Respiratory and Sleep Medicine, St Vincent's Hospital Melbourne, The University of Melbourne, Fitzroy, Australia
| | - Gavin M Wright
- Department of Surgery, St Vincent's Hospital Melbourne, The University of Melbourne, Fitzroy, Australia; Research and Education Lead Program, Victorian Comprehensive Cancer Centre, Parkville, Australia; Division of Cancer Surgery, Peter MacCallum Cancer Centre, Parkville, Australia.
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6
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Simmer F, van der Linden RLA, Ligtenberg MJL, Ylstra B, van der Post RS, Nagtegaal ID. Multifocal Colorectal Cancer-Do Intraluminal Metastases Occur? Gastroenterology 2021; 160:1853-1855. [PMID: 33316233 DOI: 10.1053/j.gastro.2020.12.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/20/2020] [Accepted: 12/05/2020] [Indexed: 01/24/2023]
Affiliation(s)
- Femke Simmer
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands.
| | - Ragna L A van der Linden
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands; Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Bauke Ylstra
- The Tumor Genome Analysis Core, Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Rachel S van der Post
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Iris D Nagtegaal
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
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7
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van Doeveren T, Nakauma-Gonzalez JA, Mason AS, van Leenders GJLH, Zuiverloon TCM, Zwarthoff EC, Meijssen IC, van der Made AC, van der Heijden AG, Hendricksen K, van Rhijn BWG, Voskuilen CS, van Riet J, Dinjens WNM, Dubbink HJ, van de Werken HJG, Boormans JL. The clonal relation of primary upper urinary tract urothelial carcinoma and paired urothelial carcinoma of the bladder. Int J Cancer 2020; 148:981-987. [PMID: 33006377 PMCID: PMC7821318 DOI: 10.1002/ijc.33327] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/11/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022]
Abstract
The risk of developing urothelial carcinoma of the bladder (UCB) in patients treated by radical nephroureterectomy (RNU) for an upper urinary tract urothelial carcinoma (UTUC) is 22% to 47% in the 2 years after surgery. Subject of debate remains whether UTUC and the subsequent UCB are clonally related or represent separate origins. To investigate the clonal relationship between both entities, we performed targeted DNA sequencing of a panel of 41 genes on matched normal and tumor tissue of 15 primary UTUC patients treated by RNU who later developed 19 UCBs. Based on the detected tumor‐specific DNA aberrations, the paired UTUC and UCB(s) of 11 patients (73.3%) showed a clonal relation, whereas in four patients the molecular results did not indicate a clear clonal relationship. Our results support the hypothesis that UCBs following a primary surgically resected UTUC are predominantly clonally derived recurrences and not separate entities. What's new? Patients treated by radical nephroureterectomy for upper urinary tract cancer have an increased risk of developing bladder carcinoma following surgery. It remains unclear, however, whether the upper urinary tract cancer and subsequent bladder carcinoma are clonally related or have separate origins. This targeted DNA sequencing study shows that almost 75% of patients have tumors that are clonally related, suggesting that seeding of tumor cells is the main mechanism of bladder carcinoma development following radical nephroureterectomy. This result underscores the need to minimalize the risk of seeding during surgery and/or diagnostic ureterorenoscopy plus biopsy, and to apply peri‐operative intravesical instillations with chemotherapy.
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Affiliation(s)
- Thomas van Doeveren
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Jose A Nakauma-Gonzalez
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands.,Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands.,Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Andrew S Mason
- Jack Birch Unit for Molecular Carcinogenesis, Department of Biology, The University of York, York, UK.,York Biomedical Research Institute, The University of York, York, UK
| | - Geert J L H van Leenders
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Tahlita C M Zuiverloon
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Ellen C Zwarthoff
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Isabelle C Meijssen
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Angelique C van der Made
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Antoine G van der Heijden
- Department of Urology, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Kees Hendricksen
- Department of Urology, Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Bas W G van Rhijn
- Department of Urology, Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands.,Department of Urology, Caritas St. Josef Medical Center, University of Regensburg, Regensburg, Germany
| | - Charlotte S Voskuilen
- Department of Urology, Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Job van Riet
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands.,Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Hendrikus J Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Harmen J G van de Werken
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands.,Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Joost L Boormans
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
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8
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Yuan Z, Huo X, Jiang D, Yu M, Cao D, Wu H, Shen K, Yang J, Zhang Y, Zhou H, Wang Y. Clinical Characteristics and Mutation Analyses of Ovarian Sertoli-Leydig Cell Tumors. Oncologist 2020; 25:e1396-e1405. [PMID: 32557933 PMCID: PMC7485360 DOI: 10.1634/theoncologist.2020-0110] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/28/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND There are limited studies on Sertoli-Leydig cell tumors (SLCTs) and no data in the population of Chinese patients with SLCTs from the genetic level. In addition, previous studies on SLCTs have focused exclusively on mutations in the DICER1 gene and no data exists on the genetic landscape of SLCTs. METHODS Patients with moderately or poorly differentiated SLCTs who underwent surgical resection between January 2012 and October 2018 in our institution were recruited. Whole exome sequencing was performed on formalin-fixed, paraffin-embedded tumor tissue and peripheral blood or normal tissue samples. RESULTS Seventeen patients were recruited with 19 tumor samples. The rate of tumor-associated germline mutations was 6 of 17 (35.3%), and that of DICER1 germline mutations was 4 of 17 (23.5%). Regarding clinical relapse, patients with germline tumor-associated mutations had significantly poorer prognosis than those without (p = .007), and those with germline DICER1 mutations were relatively more likely to exhibit clinical relapse, although not to a significant degree (p = .069). Regarding somatic mutations, firstly, the subclone evolution analysis demonstrated that the two tumors on the contralateral ovary were primary tumors, respectively. Secondly, somatic mutations were most commonly found in CDC27 (10/19, 52.6%), DICER1 (4/19, 21.1%), and MUC22 (4/19, 21.1%). And the analysis of cancer cell fractions showed that DICER1 mutations were correlated with tumorigenesis of SLCTs. The rates of germline and somatic DICER1 mutations were higher in patients who were younger than 18 years than those in older patients (p = .022 and p = .001, respectively). CONCLUSION Our study indicates that genetic testing may have important clinical significance for patients with SLCTs, particularly for younger patients. IMPLICATIONS FOR PRACTICE Bilateral ovarian Sertoli-Leydig cell tumors were verified to be primary tumors from the genetic perspective. The rates of germline and somatic DICER1 mutations were 4 of 17 (23.5%) and 4 of 19 (21.1%), respectively. The rates of germline and somatic DICER1 mutations were higher in patients who were younger than 18 years than those in older patients (p = .022 and p = .001, respectively).
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Affiliation(s)
- Zhen Yuan
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical SciencesBeijingPeople's Republic of China
| | - Xiao Huo
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical SciencesBeijingPeople's Republic of China
| | - Dezhi Jiang
- Department of Bioinformatics, Berry Oncology CorporationBeijingPeople's Republic of China
| | - Mei Yu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical SciencesBeijingPeople's Republic of China
| | - Dongyan Cao
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical SciencesBeijingPeople's Republic of China
| | - Huanwen Wu
- Department of Pathology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical SciencesBeijingPeople's Republic of China
| | - Keng Shen
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical SciencesBeijingPeople's Republic of China
| | - Jiaxin Yang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical SciencesBeijingPeople's Republic of China
| | - Ying Zhang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical SciencesBeijingPeople's Republic of China
| | - Huimei Zhou
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical SciencesBeijingPeople's Republic of China
| | - Yao Wang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical SciencesBeijingPeople's Republic of China
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9
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Mauguen A, Seshan VE, Begg CB, Ostrovnaya I. Testing clonal relatedness of two tumors from the same patient based on their mutational profiles: update of the Clonality R package. Bioinformatics 2020; 35:4776-4778. [PMID: 31198957 DOI: 10.1093/bioinformatics/btz486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/04/2019] [Accepted: 06/10/2019] [Indexed: 11/13/2022] Open
Abstract
SUMMARY The Clonality R package is a practical tool to assess the clonal relatedness of two tumors from the same patient. We have previously presented its functionality for testing tumors using loss of heterozygosity data or copy number arrays. Since then somatic mutation data have been more widely available through next generation sequencing and we have developed new methodology for comparing the tumors' mutational profiles. We thus extended the package to include these two new methods for comparing tumors as well as the mutational frequency estimation from external data required for their implementation. The first method is a likelihood ratio test that is readily available on a patient by patient basis. The second method employs a random-effects model to estimate both the population and individual probabilities of clonal relatedness from a group of patients with pairs of tumors. The package is available on Bioconductor. AVAILABILITY AND IMPLEMENTATION Bioconductor (http://bioconductor.org/packages/release/bioc/html/Clonality.html). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Audrey Mauguen
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY 10017, USA
| | - Venkatraman E Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY 10017, USA
| | - Colin B Begg
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY 10017, USA
| | - Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY 10017, USA
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10
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Synchronous and metachronous urothelial carcinoma of the upper urinary tract and the bladder: Are they clonally related? A systematic review. Urol Oncol 2020; 38:590-598. [DOI: 10.1016/j.urolonc.2020.01.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 12/17/2022]
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11
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Ostrovnaya I, Mauguen A, Seshan VE, Begg CB. Testing tumors from different anatomic sites for clonal relatedness using somatic mutation data. Biometrics 2020; 77:283-292. [PMID: 32135575 DOI: 10.1111/biom.13256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 12/13/2019] [Accepted: 02/18/2020] [Indexed: 11/27/2022]
Abstract
A common task for the cancer pathologist is to determine, in a patient suffering from cancer, whether a new tumor in a distinct anatomic site from the primary is an independent occurrence of cancer or a metastasis. As mutational profiling of tumors becomes more widespread in routine clinical practice, this diagnostic task can be greatly enhanced by comparing mutational profiles of the tumors to determine if they are sufficiently similar to conclude that the tumors are clonally related, that is, one is a metastasis of the other. We present here a likelihood ratio test for clonal relatedness in this setting and provide evidence of its validity. The test is unusual in that there are two possible alternative hypotheses, representing the two anatomic sites from which the single clonal cell could have initially emerged. Although evidence for clonal relatedness is largely provided by the presence of exact mutational matches in the two tumors, we show that it is possible to observe data where the test is statistically significant even when no matches are observed. This can occur when the mutational profile of one of the tumors is closely aligned with the anatomic site of the other tumor, suggesting indirectly that the tumor originated in that other site. We exhibit examples of this phenomenon and recommend a strategy for interpreting the results of these tests in practice.
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Affiliation(s)
- Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Audrey Mauguen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Venkatraman E Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Colin B Begg
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
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12
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Using somatic variant richness to mine signals from rare variants in the cancer genome. Nat Commun 2019; 10:5506. [PMID: 31796730 PMCID: PMC6890761 DOI: 10.1038/s41467-019-13402-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 11/04/2019] [Indexed: 12/19/2022] Open
Abstract
To date, the vast preponderance of somatic variants observed in the cancer genome have been rare variants, and it is common in practice to encounter in a new tumor variants that have not been observed previously. Here we focus on probability estimation for encountering such hitherto unseen variants. We draw upon statistical methodology that has been developed in other fields of study, notably in species estimation in ecology, and word frequency estimation in computational linguistics. Analysis of whole-exome and targeted panel sequencing data sets reveal substantial variability in variant “richness” between genes that could be harnessed for clinically relevant problems. We quantify the variant-tissue association and show a strong gene-specific, lineage-dependent pattern of encountering new variants. This variability is largely determined by the proportion of observed variants that are rare. Our findings suggest that variants that occur at very low frequencies can harbor important signals that are clinically consequential. Sequencing cancer genomes reveals low frequency novel somatic variants without known function. Here, the authors leverage statistical methodology from the fields of computational linguistics and ecology to highlight the potentially important signals harboured by these novel variants that are often dismissed.
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13
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Chang JC, Alex D, Bott M, Tan KS, Seshan V, Golden A, Sauter JL, Buonocore DJ, Vanderbilt CM, Gupta S, Desmeules P, Bodd FM, Riely GJ, Rusch VW, Jones DR, Arcila ME, Travis WD, Ladanyi M, Rekhtman N. Comprehensive Next-Generation Sequencing Unambiguously Distinguishes Separate Primary Lung Carcinomas From Intrapulmonary Metastases: Comparison with Standard Histopathologic Approach. Clin Cancer Res 2019; 25:7113-7125. [PMID: 31471310 PMCID: PMC7713586 DOI: 10.1158/1078-0432.ccr-19-1700] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/30/2019] [Accepted: 08/26/2019] [Indexed: 12/24/2022]
Abstract
PURPOSE In patients with >1 non-small cell lung carcinoma (NSCLC), the distinction between separate primary lung carcinomas (SPLCs) and intrapulmonary metastases (IPMs) is a common diagnostic dilemma with critical staging implications. Here, we compared the performance of comprehensive next-generation sequencing (NGS) with standard histopathologic approaches for distinguishing NSCLC clonal relationships in clinical practice. EXPERIMENTAL DESIGN We queried 4,119 NSCLCs analyzed by 341-468 gene MSK-IMPACT NGS assay for patients with >1 surgically resected tumor profiled by NGS. Tumor relatedness predicted by prospective histopathologic assessment was contrasted with comparative genomic profiling by subsequent NGS. RESULTS Sixty patients with NGS performed on >1 NSCLCs were identified, yielding 76 tumor pairs. NGS classified tumor pairs into 51 definite SPLCs (median, 14; up to 72 unique somatic mutations per pair), and 25 IPMs (24 definite, one high probability; median, 5; up to 16 shared somatic mutations per pair). Prospective histologic prediction was discordant with NGS in 17 cases (22%), particularly in the prediction of IPMs (44% discordant). Retrospective review highlighted several histologic challenges, including morphologic progression in some IPMs. We subsampled MSK-IMPACT data to model the performance of less comprehensive assays, and identified several clinicopathologic differences between NGS-defined tumor pairs, including increased risk of subsequent recurrence for IPMs. CONCLUSIONS Comprehensive NGS allows unambiguous delineation of clonal relationship among NSCLCs. In comparison, standard histopathologic approach is adequate in most cases, but has notable limitations in the recognition of IPMs. Our results support the adoption of broad panel NGS to supplement histology for robust discrimination of NSCLC clonal relationships in clinical practice.
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Affiliation(s)
- Jason C Chang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Deepu Alex
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Matthew Bott
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kay See Tan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Venkatraman Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrew Golden
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jennifer L Sauter
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Darren J Buonocore
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chad M Vanderbilt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sounak Gupta
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Patrice Desmeules
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Francis M Bodd
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gregory J Riely
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Valerie W Rusch
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David R Jones
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William D Travis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Natasha Rekhtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
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14
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de Bitter TJJ, van der Linden RLA, van Vliet S, Weren F, Sie D, Ylstra B, van der Linden HC, Knijn N, Ligtenberg MJL, van der Post RS, Simmer F, Nagtegaal ID. Colorectal metastasis to the gallbladder mimicking a primary gallbladder malignancy: histopathological and molecular characteristics. Histopathology 2019; 75:394-404. [PMID: 31044440 PMCID: PMC6794645 DOI: 10.1111/his.13892] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/25/2019] [Accepted: 04/28/2019] [Indexed: 12/29/2022]
Abstract
AIMS Outcomes of colorectal cancer (CRC) treatment and survival have steadily improved during the past decades, accompanied by an increased risk of developing second primary tumours and metastatic tumours at unusual sites. Metastatic CRC can show mucosal colonisation, thereby mimicking a second primary tumour. This potential confusion could lead to incorrect diagnosis and consequently inadequate treatment of the patient. The aim of this study was to differentiate between metastatic CRC and a second primary (gallbladder cancer, GBC) using a combination of standard histopathology and molecular techniques. METHODS AND RESULTS Ten consecutive patients with both CRC and GBC were identified in our region using the Dutch National Pathology Archive (PALGA). Two patients served as negative controls. Histology of GBC was reviewed by nine pathologists. A combination of immunohistochemistry, microsatellite analysis, genomewide DNA copy number analysis and targeted somatic mutation analysis was used to aid in differential diagnosis. In two patients, CRC and GBC were clonally related, as confirmed by somatic mutation analysis. For one case, this was confirmed by genomewide DNA copy number analysis. However, in both cases, pathologists initially considered the GBC as a second primary tumour. CONCLUSIONS Metastatic CRC displaying mucosal colonisation is often misinterpreted as a second primary tumour. A combination of traditional histopathology and molecular techniques improves this interpretation, and lowers the risk of inadequate treatment.
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Affiliation(s)
- Tessa J J de Bitter
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Shannon van Vliet
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Fieke Weren
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Daoud Sie
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Bauke Ylstra
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | | | - Nikki Knijn
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rachel S van der Post
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Femke Simmer
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Iris D Nagtegaal
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
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15
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Audenet F, Isharwal S, Cha EK, Donoghue MTA, Drill EN, Ostrovnaya I, Pietzak EJ, Sfakianos JP, Bagrodia A, Murugan P, Dalbagni G, Donahue TF, Rosenberg JE, Bajorin DF, Arcila ME, Hechtman JF, Berger MF, Taylor BS, Al-Ahmadie H, Iyer G, Bochner BH, Coleman JA, Solit DB. Clonal Relatedness and Mutational Differences between Upper Tract and Bladder Urothelial Carcinoma. Clin Cancer Res 2019; 25:967-976. [PMID: 30352907 PMCID: PMC6359971 DOI: 10.1158/1078-0432.ccr-18-2039] [Citation(s) in RCA: 159] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/20/2018] [Accepted: 10/19/2018] [Indexed: 12/23/2022]
Abstract
PURPOSE To investigate genomic differences between urothelial carcinomas of the upper tract (UTUC) and bladder (UCB), with a focus on defining the clonal relatedness of temporally distinct tumors. EXPERIMENTAL DESIGN We prospectively sequenced tumors and matched germline DNA using targeted next-generation sequencing methods. The cohort included 195 UTUC patients and 454 UCB patients. For a subgroup of 29 patients with UTUC and a history of a subsequent UCB, both tumors were analyzed to assess their clonal relatedness. RESULTS With the progression to higher UTUC clinical state, there were fewer alterations in the RTK/RAS pathway but more alterations in TP53/MDM2. Compared with UCB, TP53, RB1, and ERBB2 were less frequently altered in UTUC (26% vs. 46%, 3% vs. 20%, 8% vs. 19%, respectively; Q < 0.001), whereas FGFR3 and HRAS were more frequently altered (40% vs. 26%, 12% vs. 4%, respectively; Q < 0.001). On the basis of an integrated analysis of tumor mutational burden, MSIsensor score and mutational signature, 7.2% of UTUC tumors were classified as MSI-high/MMR-deficient (MSI-H/dMMR). The risk of bladder recurrence after UTUC was significantly associated with mutations in FGFR3, KDM6A, CCND1, and TP53. Comparison of UCB with corresponding UTUC tumors from the same patient supports their clonal relatedness. CONCLUSIONS UTUC and UCB exhibit significant differences in the prevalence of common genomic alterations. In individual patients with a history of both tumors, UCB and UTUC were always clonally related. Genomic characterization of UTUC provides information regarding the risk of bladder recurrence and can identify tumors associated with Lynch syndrome.
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Affiliation(s)
- François Audenet
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Sumit Isharwal
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eugene K Cha
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark T A Donoghue
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Esther N Drill
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eugene J Pietzak
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Aditya Bagrodia
- Department of Urology, UT Southwestern Medical Center, Dallas, Texas
| | - Paari Murugan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | - Guido Dalbagni
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Timothy F Donahue
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jonathan E Rosenberg
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dean F Bajorin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Barry S Taylor
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hikmat Al-Ahmadie
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gopa Iyer
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Weil Cornell Medical College, New York, New York
| | - Bernard H Bochner
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Weil Cornell Medical College, New York, New York
| | - Jonathan A Coleman
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - David B Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Weil Cornell Medical College, New York, New York
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16
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Perea J, García JL, Corchete L, Lumbreras E, Arriba M, Rueda D, Tapial S, Pérez J, Vieiro V, Rodríguez Y, Brandáriz L, García-Arranz M, García-Olmo D, Goel A, Urioste M, Sarmiento RG. Redefining synchronous colorectal cancers based on tumor clonality. Int J Cancer 2018; 144:1596-1608. [PMID: 30151896 DOI: 10.1002/ijc.31761] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/14/2018] [Accepted: 07/13/2018] [Indexed: 12/19/2022]
Abstract
To analyze the possible clonal origin of a part of Synchronous colorectal cancer (SCRC), we studied 104 paired-SCRCs from 52 consecutive patients without hereditary forms of CRC. We used a Single-Nucleotide Polymorphism array to characterize the genomic profiles, and subsequently used a statistical application to define them according to clonality within the same individual. We categorized the ensuing groups according to colonic location to identify differential phenotypes. The SCRC Monoclonal group (M) (19 cases) was divided into Monosegmental (MM) and Pancolonic (MP) groups. The SCRC Polyclonal group (P) (33 cases) was also divided into Monosegmental (PM) and Pancolonic (PP), the first exhibiting preference for left colon. The MM group showed a high rate of mucinous tumors, the lowest mean-number of tumors and associated-polyps, and the worst prognosis. The MP group included the largest mean-number of associated-polyps, best prognosis and familial cancer component. The PM group seemed to be a "frontier" group. Finally, the PP group also exhibited a mucin component, the highest mean-number of tumors (4.6) compared with the mean-number of polyps (7.7), poor prognosis and sporadic cases. Most relevant differential genomic regions within M groups were gains on 1q24 and 8q24, and deletions on 1p21 and 1p23 for MM, while within P were the gains on 7q36 and deletions on 1p36 for PM. The statistical application employed seems to define clonality more accurately in SCRC -more likely to be polyclonal in origin-, and together with the tumor locations, helped us to configure a classification with prognostic and clinical value.
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Affiliation(s)
- José Perea
- Surgery Department, Fundación Jiménez Díaz University Hospital, Madrid, Spain.,Health Research Institute Fundación Jiménez Díaz, Madrid, Spain
| | - Juan L García
- Biomedical Research Institute of Salamanca (IBSAL), University Hospital of Salamanca-USAL-CSIC, Salamanca, Spain.,Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-CSIC, Salamanca, Spain
| | - Luis Corchete
- Biomedical Research Institute of Salamanca (IBSAL), University Hospital of Salamanca-USAL-CSIC, Salamanca, Spain.,Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-CSIC, Salamanca, Spain
| | - Eva Lumbreras
- Biomedical Research Institute of Salamanca (IBSAL), University Hospital of Salamanca-USAL-CSIC, Salamanca, Spain.,Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-CSIC, Salamanca, Spain
| | - María Arriba
- Biochemistry Department, Gregorio Marañón University Hospital, Madrid, Spain
| | - Daniel Rueda
- Centre for Biomedical Research of the 12 de Octubre University Hospital, Madrid, Spain.,Molecular Biology Laboratory, 12 de Octubre University Hospital, Madrid, Spain
| | - Sandra Tapial
- Centre for Biomedical Research of the 12 de Octubre University Hospital, Madrid, Spain
| | - Jessica Pérez
- Biomedical Research Institute of Salamanca (IBSAL), University Hospital of Salamanca-USAL-CSIC, Salamanca, Spain.,Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-CSIC, Salamanca, Spain
| | - Victoria Vieiro
- Surgery Department, 12 de Octubre University Hospital, Madrid, Spain
| | - Yolanda Rodríguez
- Department of Pathology, 12 de Octubre University Hospital, Madrid, Spain
| | - Lorena Brandáriz
- Surgery Department, Fundación Jiménez Díaz University Hospital, Madrid, Spain.,Health Research Institute Fundación Jiménez Díaz, Madrid, Spain
| | | | - Damián García-Olmo
- Surgery Department, Fundación Jiménez Díaz University Hospital, Madrid, Spain.,Health Research Institute Fundación Jiménez Díaz, Madrid, Spain
| | - Ajay Goel
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute, Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX
| | - Miguel Urioste
- Familial Cancer Clinical Unit, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain
| | - Rogelio González Sarmiento
- Biomedical Research Institute of Salamanca (IBSAL), University Hospital of Salamanca-USAL-CSIC, Salamanca, Spain.,Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-CSIC, Salamanca, Spain
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17
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Biermann J, Parris TZ, Nemes S, Danielsson A, Engqvist H, Werner Rönnerman E, Forssell-Aronsson E, Kovács A, Karlsson P, Helou K. Clonal relatedness in tumour pairs of breast cancer patients. Breast Cancer Res 2018; 20:96. [PMID: 30092821 PMCID: PMC6085699 DOI: 10.1186/s13058-018-1022-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 07/18/2018] [Indexed: 01/18/2023] Open
Abstract
Background Molecular classification of tumour clonality is currently not evaluated in multiple invasive breast carcinomas, despite evidence suggesting common clonal origins. There is no consensus about which type of data (e.g. copy number, mutation, histology) and especially which statistical method is most suitable to distinguish clonal recurrences from independent primary tumours. Methods Thirty-seven invasive breast tumour pairs were stratified according to laterality and time interval between the diagnoses of the two tumours. In a multi-omics approach, tumour clonality was analysed by integrating clinical characteristics (n = 37), DNA copy number (n = 37), DNA methylation (n = 8), gene expression microarray (n = 7), RNA sequencing (n = 3), and SNP genotyping data (n = 3). Different statistical methods, e.g. the diagnostic similarity index (SI), were used to classify the tumours as clonally related recurrences or independent primary tumours. Results The SI and hierarchical clustering showed similar tendencies and the highest concordance with the other methods. Concordant evidence for tumour clonality was found in 46% (17/37) of patients. Notably, no association was found between the current clinical guidelines and molecular tumour features. Conclusions A more accurate classification of clonal relatedness between multiple breast tumours may help to mitigate treatment failure and relapse by integrating tumour-associated molecular features, clinical parameters, and statistical methods. Guidelines need to be defined with exact thresholds to standardise clonality testing in a routine diagnostic setting. Electronic supplementary material The online version of this article (10.1186/s13058-018-1022-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jana Biermann
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, Box 425, SE-405 30, Gothenburg, Sweden.
| | - Toshima Z Parris
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, Box 425, SE-405 30, Gothenburg, Sweden
| | - Szilárd Nemes
- Swedish Hip Arthroplasty Register, 405 30, Gothenburg, Sweden
| | - Anna Danielsson
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, Box 425, SE-405 30, Gothenburg, Sweden
| | - Hanna Engqvist
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, Box 425, SE-405 30, Gothenburg, Sweden
| | - Elisabeth Werner Rönnerman
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, Box 425, SE-405 30, Gothenburg, Sweden.,Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Eva Forssell-Aronsson
- Department of Radiation Physics, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, 405 30, Gothenburg, Sweden
| | - Anikó Kovács
- Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Per Karlsson
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, Box 425, SE-405 30, Gothenburg, Sweden
| | - Khalil Helou
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, Box 425, SE-405 30, Gothenburg, Sweden
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18
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Begg CB, Ostrovnaya I, Geyer FC, Papanastasiou AD, Ng CKY, Sakr R, Bernstein JL, Burke KA, King TA, Piscuoglio S, Mauguen A, Orlow I, Weigelt B, Seshan VE, Morrow M, Reis-Filho JS. Contralateral breast cancers: Independent cancers or metastases? Int J Cancer 2018; 142:347-356. [PMID: 28921573 PMCID: PMC5749409 DOI: 10.1002/ijc.31051] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/24/2017] [Accepted: 08/30/2017] [Indexed: 12/24/2022]
Abstract
A cancer in the contralateral breast in a woman with a previous or synchronous breast cancer is typically considered to be an independent primary tumor. Emerging evidence suggests that in a small subset of these cases the second tumor represents a metastasis. We sought to investigate the issue using massively parallel sequencing targeting 254 genes recurrently mutated in breast cancer. We examined the tumor archives at Memorial Sloan Kettering Cancer Center for the period 1995-2006 to identify cases of contralateral breast cancer where surgery for both tumors was performed at the Center. We report results from 49 patients successfully analyzed by a targeted massively parallel sequencing assay. Somatic mutations and copy number alterations were defined by state-of-the-art algorithms. Clonal relatedness was evaluated by statistical tests specifically designed for this purpose. We found evidence that the tumors in contralateral breasts were clonally related in three cases (6%) on the basis of matching mutations at codons where somatic mutations are rare. Clinical data and the presence of similar patterns of gene copy number alterations were consistent with metastasis for all three cases. In three additional cases, there was a solitary matching mutation at a common PIK3CA locus. The results suggest that a subset of contralateral breast cancers represent metastases rather than independent primary tumors. Massively parallel sequencing analysis can provide important evidence to clarify the diagnosis. However, given the inter-tumor mutational heterogeneity in breast cancer, sufficiently large gene panels need to be employed to define clonality convincingly in all cases.
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Affiliation(s)
- Colin B Begg
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Felipe C Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anastasios D Papanastasiou
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Metaxa Cancer Hospital/University of Patras, Patras, Greece
| | - Charlotte KY Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Institute of Pathology, University Hospital Basel, Switzerland
| | - Rita Sakr
- Breast Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonine L Bernstein
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kathleen A Burke
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- IBM Watson Health, Cambridge, MA USA
| | - Tari A King
- Dana-Farber Cancer Institute/Brigham and Women’s Hospital, Boston, MA USA
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Institute of Pathology, University Hospital Basel, Switzerland
| | - Audrey Mauguen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Venkatraman E Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Monica Morrow
- Breast Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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19
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Mauguen A, Seshan VE, Ostrovnaya I, Begg CB. Estimating the probability of clonal relatedness of pairs of tumors in cancer patients. Biometrics 2017; 74:321-330. [PMID: 28482133 DOI: 10.1111/biom.12710] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 03/01/2017] [Accepted: 03/01/2017] [Indexed: 12/31/2022]
Abstract
Next generation sequencing panels are being used increasingly in cancer research to study tumor evolution. A specific statistical challenge is to compare the mutational profiles in different tumors from a patient to determine the strength of evidence that the tumors are clonally related, that is, derived from a single, founder clonal cell. The presence of identical mutations in each tumor provides evidence of clonal relatedness, although the strength of evidence from a match is related to how commonly the mutation is seen in the tumor type under investigation. This evidence must be weighed against the evidence in favor of independent tumors from non-matching mutations. In this article, we frame this challenge in the context of diagnosis using a novel random effects model. In this way, by analyzing a set of tumor pairs, we can estimate the proportion of cases that are clonally related in the sample as well as the individual diagnostic probabilities for each case. The method is illustrated using data from a study to determine the clonal relationship of lobular carcinoma in situ with subsequent invasive breast cancers, where each tumor in the pair was subjected to whole exome sequencing. The statistical properties of the method are evaluated using simulations, demonstrating that the key model parameters are estimated with only modest bias in small samples in most configurations.
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Affiliation(s)
- Audrey Mauguen
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, 485 Lexington Avenue, 2nd Floor, New York, New York 10017, U.S.A
| | - Venkatraman E Seshan
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, 485 Lexington Avenue, 2nd Floor, New York, New York 10017, U.S.A
| | - Irina Ostrovnaya
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, 485 Lexington Avenue, 2nd Floor, New York, New York 10017, U.S.A
| | - Colin B Begg
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, 485 Lexington Avenue, 2nd Floor, New York, New York 10017, U.S.A
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20
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Begg CB, Ostrovnaya I, Carniello JVS, Sakr RA, Giri D, Towers R, Schizas M, De Brot M, Andrade VP, Mauguen A, Seshan VE, King TA. Clonal relationships between lobular carcinoma in situ and other breast malignancies. Breast Cancer Res 2016; 18:66. [PMID: 27334989 PMCID: PMC4918003 DOI: 10.1186/s13058-016-0727-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 06/05/2016] [Indexed: 11/29/2022] Open
Abstract
Background Recent evidence suggests that lobular carcinoma in situ (LCIS) can be a clonal precursor of invasive breast cancers of both the ductal and lobular phenotypes. We sought to confirm these findings with an extensive study of fresh frozen breast specimens from women undergoing mastectomy. Methods Patients with a history of LCIS presenting for therapeutic mastectomy were identified prospectively. Frozen tissue blocks were collected, screened for lesions of interest, and subjected to microdissection and DNA extraction. Copy number profiling, whole-exome sequencing, or both were performed. Clonal relatedness was assessed using specialized statistical techniques developed for this purpose. Results After exclusions for genotyping failure, a total of 84 lesions from 30 patients were evaluated successfully. Strong evidence of clonal relatedness was observed between an LCIS lesion and the invasive cancer for the preponderance of cases with lobular carcinoma. Anatomically distinct in situ lesions of both ductal and lobular histology were also shown to be frequently clonally related. Conclusions These data derived from women with LCIS with or without invasive cancer confirm that LCIS is commonly the clonal precursor of invasive lobular carcinoma and that distinct foci of LCIS frequently share a clonal origin, as do foci of LCIS and ductal carcinoma in situ. Electronic supplementary material The online version of this article (doi:10.1186/s13058-016-0727-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Colin B Begg
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
| | - Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Jose V Scarpa Carniello
- Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Rita A Sakr
- Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Dilip Giri
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Russell Towers
- Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Michail Schizas
- Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Marina De Brot
- Department of Pathology, Federal University of Minas Gerais, Avenida Presidente Antônio Carlos, 6627 - Pampulha, Belo Horizonte, MG, 31270-901, Brazil
| | - Victor P Andrade
- Department of Pathology, AC Camargo Cancer Center, Rua Professor Antônio Prudente, 211, Liberdade, São Paulo, SP, CEP 01509 - 010, Sao Paulo, Brazil
| | - Audrey Mauguen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Venkatraman E Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Tari A King
- Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
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