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Selenica P, Conlon N, Gonzalez C, Frosina D, Jungbluth AA, Beets-Tan RGH, Rao MK, Zhang Y, Benayed R, Ladanyi M, Solit DB, Chiang S, Hyman DM, Hensley ML, Soslow RA, Weigelt B, Murali R. Genomic Profiling Aids Classification of Diagnostically Challenging Uterine Mesenchymal Tumors With Myomelanocytic Differentiation. Am J Surg Pathol 2021; 45:77-92. [PMID: 32889887 PMCID: PMC8276853 DOI: 10.1097/pas.0000000000001572] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Although diagnosis of high-grade uterine mesenchymal tumors (UMTs) exhibiting classic morphologic features is straightforward, diagnosis is more challenging in tumors in which prototypical features are poorly developed, focal, and/or coexist with features seen in other neoplasms. Here, we sought to define the repertoire of somatic genetic alterations in diagnostically challenging UMTs with myomelanocytic differentiation, including some reported as perivascular epithelioid cell tumors (PEComas). In 17 samples from 15 women, the tumors were histologically heterogenous. Immunohistochemical expression of at least 1 melanocytic marker (HMB45, Melan-A, or MiTF) was identified in all tumors, and of myogenic markers (desmin or smooth muscle actin) in most tumors. Targeted massively parallel sequencing revealed several genetic alterations, most commonly in TP53 (41% mutation, 12% deletion), TSC2 (29% mutation, 6% deletion), RB1 (18% deletion), ATRX (24% mutation), MED12 (12% mutation), BRCA2 (12% deletion), CDKN2A (6% deletion) as well as FGFR3, NTRK1, and ERBB3 amplification (each 6%). Gene rearrangements (JAZF1-SUZ12; DNAJB6-PLAG1; and SFPQ-TFE3) were identified in 3 tumors. Integrating histopathologic, immunohistochemical, and genetic findings, tumors from 4 patients were consistent with malignant PEComa (1 TFE3-rearranged); 6 were classified as leiomyosarcomas; 3 showed overlapping features of PEComa and other sarcoma types (leiomyosarcoma or low-grade endometrial stromal sarcoma); and 2 were classified as sarcoma, not otherwise specified. Our findings suggest that diagnostically challenging UMTs with myomelanocytic differentiation represent a heterogenous group of neoplasms which harbor a diverse repertoire of somatic genetic alterations; these genetic alterations can aid classification.
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Affiliation(s)
- Pier Selenica
- Departments of Pathology
- GROW School for Oncology and Developmental Biology
| | - Niamh Conlon
- Departments of Pathology
- Department of Pathology, Cork University Hospital, Cork, Ireland
| | | | | | | | - Regina G. H. Beets-Tan
- GROW School for Oncology and Developmental Biology
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | - David B. Solit
- Department of Radiology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Medicine
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Yadav S, Kasi PM, Bamlet WR, Ho TP, Polley EC, Hu C, Hart SN, Rabe KG, Boddicker NJ, Gnanaolivu RD, Lee KY, Lindstrom TH, Petersen GM, Couch FJ, McWilliams RR. Effect of Germline Mutations in Homologous Recombination Repair Genes on Overall Survival of Patients with Pancreatic Adenocarcinoma. Clin Cancer Res 2020; 26:6505-6512. [PMID: 33028596 PMCID: PMC9063708 DOI: 10.1158/1078-0432.ccr-20-1788] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/20/2020] [Accepted: 09/28/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE To compare the clinical characteristics and overall survival (OS) of germline mutation carriers in homologous recombination repair (HRR) genes and noncarriers with pancreatic ductal adenocarcinoma (PDAC). EXPERIMENTAL DESIGN Germline DNA from 3,078 patients with PDAC enrolled in a prospective registry at Mayo Clinic between 2000 and 2017 was analyzed for mutations in 37 cancer predisposition genes. Characteristics and OS of patients with mutations in eight genes (ATM, BARD1, BRCA1, BRCA2, BRIP1, PALB2, RAD51C, and RAD51D) involved in HRR were compared with patients testing negative for mutations in all 37 genes. RESULTS The 175 HRR mutation carriers and 2,730 noncarriers in the study had a median duration of follow-up of 9.9 years. HRR mutation carriers were younger (median age at diagnosis: 63 vs. 66 years, P < 0.001) and more likely to have metastatic disease at diagnosis (46% vs. 36%, P = 0.004). In a multivariable model adjusting for sex, age at diagnosis, and tumor staging, patients with germline HRR mutations had a significantly longer OS compared with noncarriers [HR, 0.83; 95% confidence interval (CI), 0.70-0.97; P = 0.02]. Further gene-level analysis demonstrated that germline ATM mutation carriers had longer OS compared with patients without germline mutations in any of the 37 genes (HR, 0.72; 95% CI, 0.55-0.94; P = 0.01). CONCLUSIONS This study demonstrates that germline mutation carrier status in PDAC is associated with longer OS compared with noncarriers. Further research into tumor biology and response to platinum-based chemotherapy in germline mutation carriers with PDAC are needed to better understand the association with longer OS.
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Affiliation(s)
| | - Pashtoon M Kasi
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa
| | - William R Bamlet
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Thanh P Ho
- Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Eric C Polley
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Chunling Hu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Steven N Hart
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Kari G Rabe
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | | | - Rohan D Gnanaolivu
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Kun Y Lee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Tricia H Lindstrom
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
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D'Alfonso TM, Pareja F, Da Cruz Paula A, Vahdatinia M, Gazzo A, Ferrando L, da Silva EM, Cheng E, Sclafani L, Chandarlapaty S, Zhang H, Hoda SA, Wen HY, Brogi E, Weigelt B, Reis-Filho JS. Whole-exome sequencing analysis of juvenile papillomatosis and coexisting breast carcinoma. JOURNAL OF PATHOLOGY CLINICAL RESEARCH 2020; 7:113-120. [PMID: 33263939 PMCID: PMC7869928 DOI: 10.1002/cjp2.190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/08/2020] [Accepted: 10/16/2020] [Indexed: 12/18/2022]
Abstract
Juvenile papillomatosis (JP) of the breast is a rare benign mass‐forming lesion occurring in young women, which is histologically characterized by a constellation of proliferative changes and large cysts, giving it the gross appearance of Swiss cheese. A subset of patients with JP report a family history of breast carcinoma and/or coexisting or subsequent breast carcinoma. We performed whole‐exome sequencing of the hyperplastic epithelial component of three JPs, including one with coexisting ductal carcinoma in situ (DCIS) and invasive ductal carcinoma of no special type (IDC‐NST). JPs harbored clonal somatic PIK3CA hotspot mutations in two cases. In the JP with coexisting DCIS and IDC‐NST, these lesions were clonally related to the associated JP, sharing a clonal PIK3CA E542K somatic hotspot mutation. JP showed a paucity of copy number alterations, whereas the associated DCIS and IDC‐NST showed concurrent 1q gains/16q losses, hallmarks of estrogen receptor (ER)‐positive breast cancers. We observed JP to harbor a dominant aging‐related mutational signature, whereas coexisting DCIS and IDC‐NST showed greater exposure to an APOBEC signature. Taken together, our findings suggest that, at least in a subset of cases, JP might constitute the substrate from which DCIS and invasive breast carcinomas develop.
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Affiliation(s)
- Timothy M D'Alfonso
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arnaud Da Cruz Paula
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mahsa Vahdatinia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrea Gazzo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lorenzo Ferrando
- Department of Internal Medicine, University of Genoa, Genoa, Italy
| | - Edaise M da Silva
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Esther Cheng
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lisa Sclafani
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarat Chandarlapaty
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hong Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Syed A Hoda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Hannah Y Wen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edi Brogi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, 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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Esai Selvan M, Zauderer MG, Rudin CM, Jones S, Mukherjee S, Offit K, Onel K, Rennert G, Velculescu VE, Lipkin SM, Klein RJ, Gümüş ZH. Inherited Rare, Deleterious Variants in ATM Increase Lung Adenocarcinoma Risk. J Thorac Oncol 2020; 15:1871-1879. [PMID: 32866655 PMCID: PMC8496202 DOI: 10.1016/j.jtho.2020.08.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 07/05/2020] [Accepted: 08/12/2020] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Lung cancer is the leading cause of cancer deaths in the world, and lung adenocarcinoma (LUAD) is its most prevalent subtype. Symptoms are often found in advanced disease in which treatment options are limited. Identifying genetic risk factors will enable better identification of high-risk individuals. METHODS To identify LUAD risk genes, we performed a case-control association study for gene-level burden of rare, deleterious variants (RDVs) in germline whole-exome sequencing data of 1083 patients with LUAD and 7650 controls, split into discovery and validation cohorts. Of these, we performed whole-exome sequencing on 97 patients and acquired the rest from multiple public databases. We annotated all rare variants for pathogenicity conservatively, using the guidelines of the American College of Medical Genetics and Genomics and ClinVar curation, and investigated gene-level RDV burden using penalized logistic regression. All statistical tests were two-sided. RESULTS We discovered and replicated the finding that the burden of germline ATM RDVs was significantly higher in patients with LUAD versus controls (combined cohort OR = 4.6; p = 1.7e-04; 95% confidence interval = 2.2-9.5; 1.21% of cases; 0.24% of controls). Germline ATM RDVs were also enriched in an independent clinical cohort of 1594 patients from the MSK-IMPACT study (0.63%). In addition, we observed that an Ashkenazi Jewish (AJ) founder ATM variant, rs56009889, was statistically significantly more frequent in AJ cases versus AJ controls in our cohort (combined AJ cohort OR = 2.7, p = 6.9e-03, 95% confidence interval = 1.3-5.3). CONCLUSIONS Our results indicate that ATM is a moderate-penetrance LUAD risk gene and that LUAD may be a part of the ATM-related cancer syndrome spectrum. Individuals with ATM RDVs are at an elevated LUAD risk and can benefit from increased surveillance (particularly computed tomography scanning), early detection, and chemoprevention programs, improving prognosis.
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Affiliation(s)
- Myvizhi Esai Selvan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Marjorie G Zauderer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Siân Jones
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Semanti Mukherjee
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kenan Onel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Gad Rennert
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Clalit National Israeli Cancer Control Center, Haifa, Israel
| | - Victor E Velculescu
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Steven M Lipkin
- Departments of Medicine and Genetic Medicine, Weill Cornell Medical College, New York, New York
| | - Robert J Klein
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York.
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55
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Nientiedt C, Duensing A, Zschäbitz S, Jäger D, Hohenfellner M, Stenzinger A, Duensing S. PARP inhibition in prostate cancer. Genes Chromosomes Cancer 2020; 60:344-351. [PMID: 33084183 DOI: 10.1002/gcc.22903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/05/2020] [Accepted: 10/05/2020] [Indexed: 12/11/2022] Open
Abstract
Defects in DNA damage repair genes are more common in prostate cancer than previously thought. These alterations provide an opportunity for precision oncology approaches and a number of studies have now shown that PARP inhibitors can have significant antitumor activity in men with DNA damage repair-deficient metastatic castration-resistant prostate cancer. This review summarizes the key clinical trials related to the use of PARP inhibitors in prostate cancer. Besides clinical outcomes, toxicity, and PARP inhibitor resistance, the role of different DNA repair genes in the response to PARP inhibition will be discussed.
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Affiliation(s)
- Cathleen Nientiedt
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, Heidelberg, Germany
| | - Anette Duensing
- Cancer Therapeutics Program, UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA.,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,Precision Oncology of Urological Malignancies, Department of Urology, University Hospital Heidelberg, Heidelberg, Germany.,Department of Urology, University Hospital Heidelberg, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Stefanie Zschäbitz
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, Heidelberg, Germany
| | - Dirk Jäger
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, Heidelberg, Germany
| | - Markus Hohenfellner
- Department of Urology, University Hospital Heidelberg, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | | | - Stefan Duensing
- Department of Urology, University Hospital Heidelberg, National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Molecular Urooncology, Department of Urology, University Hospital Heidelberg, Heidelberg, Germany
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The genomic landscape of metastatic histologic special types of invasive breast cancer. NPJ Breast Cancer 2020; 6:53. [PMID: 33083532 PMCID: PMC7560857 DOI: 10.1038/s41523-020-00195-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023] Open
Abstract
Histologic special types of breast cancer (BC) account for ~20% of BCs. Large sequencing studies of metastatic BC have focused on invasive ductal carcinomas of no special type (IDC-NSTs). We sought to define the repertoire of somatic genetic alterations of metastatic histologic special types of BC. We reanalyzed targeted capture sequencing data of 309 special types of BC, including metastatic and primary invasive lobular carcinomas (ILCs; n = 132 and n = 127, respectively), mixed mucinous (n = 5 metastatic and n = 14 primary), micropapillary (n = 12 metastatic and n = 8 primary), and metaplastic BCs (n = 6 metastatic and n = 5 primary), and compared metastatic histologic special types of BC to metastatic IDC-NSTs matched according to clinicopathologic characteristics and to primary special type BCs. The genomic profiles of metastatic and primary special types of BC were similar. Important differences, however, were noted: metastatic ILCs harbored a higher frequency of genetic alterations in TP53, ESR1, FAT1, RFWD2, and NF1 than primary ILCs, and in CDH1, PIK3CA, ERBB2, TBX3, NCOR1, and RFWD2 than metastatic IDC-NSTs. Metastatic ILCs displayed a higher mutational burden, and more frequently dominant APOBEC mutational signatures than primary ILCs and matched metastatic IDC-NSTs. ESR1 and NCOR mutations were frequently detected in metastatic mixed mucinous BCs, whereas PIK3CA and TP53 were the most frequently altered genes in metastatic micropapillary and metaplastic BCs, respectively. Taken together, primary and metastatic BCs histologic special types have remarkably similar repertoires of somatic genetic alterations. Metastatic ILCs more frequently harbor APOBEC mutational signatures than primary ILCs and metastatic IDC-NSTs.
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Völkel G, Laban S, Fürstberger A, Kühlwein SD, Ikonomi N, Hoffmann TK, Brunner C, Neuberg DS, Gaidzik V, Döhner H, Kraus JM, Kestler HA. Analysis, identification and visualization of subgroups in genomics. Brief Bioinform 2020; 22:5909009. [PMID: 32954413 PMCID: PMC8138884 DOI: 10.1093/bib/bbaa217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 12/22/2022] Open
Abstract
Motivation Cancer is a complex and heterogeneous disease involving multiple somatic mutations that accumulate during its progression. In the past years, the wide availability of genomic data from patients’ samples opened new perspectives in the analysis of gene mutations and alterations. Hence, visualizing and further identifying genes mutated in massive sets of patients are nowadays a critical task that sheds light on more personalized intervention approaches. Results Here, we extensively review existing tools for visualization and analysis of alteration data. We compare different approaches to study mutual exclusivity and sample coverage in large-scale omics data. We complement our review with the standalone software AVAtar (‘analysis and visualization of alteration data’) that integrates diverse aspects known from different tools into a comprehensive platform. AVAtar supplements customizable alteration plots by a multi-objective evolutionary algorithm for subset identification and provides an innovative and user-friendly interface for the evaluation of concurrent solutions. A use case from personalized medicine demonstrates its unique features showing an application on vaccination target selection. Availability AVAtar is available at: https://github.com/sysbio-bioinf/avatar Contact hans.kestler@uni-ulm.de, phone: +49 (0) 731 500 24 500, fax: +49 (0) 731 500 24 502
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Affiliation(s)
| | | | | | | | | | - Thomas K Hoffmann
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Germany
| | - Cornelia Brunner
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Germany
| | - Donna S Neuberg
- Department of Biostatistics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Verena Gaidzik
- Department of Internal Medicine III, Ulm University Medical Center, Germany
| | - Hartmut Döhner
- Department of Internal Medicine III, Ulm University Medical Center, Germany
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Stasenko M, Jayakumaran G, Cowan R, Broach V, Chi DS, Rossi A, Hollman TJ, Zehir A, Abu-Rustum NR, Leitao MM. Genomic Alterations as Potential Therapeutic Targets in Extramammary Paget's Disease of the Vulva. JCO Precis Oncol 2020; 4:PO.20.00073. [PMID: 33015527 PMCID: PMC7529529 DOI: 10.1200/po.20.00073] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2020] [Indexed: 12/12/2022] Open
Abstract
PURPOSE To identify genomic alterations as potential therapeutic targets in extramammary Paget disease (EMPD) of the vulva. METHODS We identified all patients with primary vulvar EMPD who were treated at our institution and underwent paired tumor-normal massively parallel sequencing of 410-468 cancer-related genes (MSK-IMPACT assay). EMPD of the vulva samples sequenced from 2014 to 2019 were reviewed and somatic mutations identified, with specific focus on mutations of potential therapeutic targets. Clinical data were abstracted from electronic medical records. Microsatellite instability (MSI) was assessed by MSIscore. RESULTS Tumors of 26 patients with EMPD underwent genomic sequencing. At diagnosis, all patients had noninvasive or microinvasive (< 1 mm) disease; invasive disease eventually developed in 2 patients. Primary treatment was surgery for 19 patients (73%) and imiquimod topical therapy for 7 (27%). Seven patients had ≥ 2 surgeries as part of clinical course (1 patient had 5 vulvar resections). Samples had a median of 2 coding mutations in the genes analyzed (range, 0-29). The most common mutations were in PIK3CA (n = 9; 35%), ERBB2 (4 mutations and 3 copy number alterations; 27%), and TP53 (n = 7; 27%). MSIscore was available for 23 samples; all were microsatellite stable. After tumor genomic profiling, a patient who was initially treated with multiple resections and imiquimod was found to have a PIK3CA p.E542K mutation. She underwent PI3K-inhibitor treatment for 18 months before disease progression. CONCLUSION EMPD of the vulva has a chronic and relapsing course, often requiring multiple surgical resections. Effective topical treatments are lacking. We identified targetable mutations (PIK3CA or ERBB2) in > 25% of a real-world clinical cohort. Additional prospective research implementing targetable therapies for EMPD treatment is warranted.
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Affiliation(s)
- Marina Stasenko
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gowtham Jayakumaran
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Renee Cowan
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Vance Broach
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Dennis S. Chi
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anthony Rossi
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Travis J. Hollman
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nadeem R. Abu-Rustum
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mario M. Leitao
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
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Da Cruz Paula A, da Silva EM, Segura SE, Pareja F, Bi R, Selenica P, Kim SH, Ferrando L, Vahdatinia M, Soslow RA, Vidal A, Gatius S, Przybycin CG, Abu-Rustum NR, Matias-Guiu X, Rubin BP, Reis-Filho JS, DeLair DF, Weigelt B. Genomic profiling of primary and recurrent adult granulosa cell tumors of the ovary. Mod Pathol 2020; 33:1606-1617. [PMID: 32203090 PMCID: PMC7390666 DOI: 10.1038/s41379-020-0514-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/23/2020] [Accepted: 02/24/2020] [Indexed: 02/06/2023]
Abstract
Adult-type granulosa cell tumor (aGCT) is a rare malignant ovarian sex cord-stromal tumor, harboring recurrent FOXL2 c.C402G/p.C134W hotspot mutations in 97% of cases. These tumors are considered to have a favorable prognosis, however aGCTs have a tendency for local spread and late recurrences, which are associated with poor survival rates. We sought to determine the genetic alterations associated with aGCT disease progression. We subjected primary non-recurrent aGCTs (n = 7), primary aGCTs that subsequently recurred (n = 9) and their matched recurrences (n = 9), and aGCT recurrences without matched primary tumors (n = 10) to targeted massively parallel sequencing of ≥410 cancer-related genes. In addition, three primary non-recurrent aGCTs and nine aGCT recurrences were subjected to FOXL2 and TERT promoter Sanger sequencing analysis. All aGCTs harbored the FOXL2 C134W hotspot mutation. TERT promoter mutations were found to be significantly more frequent in recurrent (18/28, 64%) than primary aGCTs (5/19, 26%, p = 0.017). In addition, mutations affecting TP53, MED12, and TET2 were restricted to aGCT recurrences. Pathway annotation of altered genes demonstrated that aGCT recurrences displayed an enrichment for genetic alterations affecting cell cycle pathway-related genes. Analysis of paired primary and recurrent aGCTs revealed that TERT promoter mutations were either present in both primary tumors and matched recurrences or were restricted to the recurrence and absent in the respective primary aGCT. Clonal composition analysis of these paired samples further revealed that aGCTs display intra-tumor genetic heterogeneity and harbor multiple clones at diagnosis and relapse. We observed that in a subset of cases, recurrences acquired additional genetic alterations not present in primary aGCTs, including TERT, MED12, and TP53 mutations and CDKN2A/B homozygous deletions. Albeit harboring relatively simple genomes, our data provide evidence to suggest that aGCTs are genetically heterogeneous tumors and that TERT promoter mutations and/or genetic alterations affecting other cell cycle-related genes may be associated with disease progression and recurrences.
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Affiliation(s)
- Arnaud Da Cruz Paula
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edaise M da Silva
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sheila E Segura
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Pathology and Laboratory Medicine, Indiana University, Indianapolis, IN, USA
| | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rui Bi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Fudan University Shanghai Cancer Center, Shanghai, PR China
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarah H Kim
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lorenzo Ferrando
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Internal Medicine, University of Genoa, Genova, Italy
| | - Mahsa Vahdatinia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert A Soslow
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - August Vidal
- Department of Pathology, Hospital Universitari de Bellvitge, IDIBELL, University of Barcelona, CIBERONC, Barcelona, Spain
| | - Sonia Gatius
- Department of Pathology, Hospital Universitari Arnau de Vilanova, IRBLLEIDA, University of Lleida, CIBERONC, Lleida, Spain
| | - Christopher G Przybycin
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Nadeem R Abu-Rustum
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xavier Matias-Guiu
- Department of Pathology, Hospital Universitari de Bellvitge, IDIBELL, University of Barcelona, CIBERONC, Barcelona, Spain
- Department of Pathology, Hospital Universitari Arnau de Vilanova, IRBLLEIDA, University of Lleida, CIBERONC, Lleida, Spain
| | - Brian P Rubin
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Deborah F DeLair
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Pathology, NYU Langone Health, New York, NY, USA.
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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60
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Tung NM, Boughey JC, Pierce LJ, Robson ME, Bedrosian I, Dietz JR, Dragun A, Gelpi JB, Hofstatter EW, Isaacs CJ, Jatoi I, Kennedy E, Litton JK, Mayr NA, Qamar RD, Trombetta MG, Harvey BE, Somerfield MR, Zakalik D. Management of Hereditary Breast Cancer: American Society of Clinical Oncology, American Society for Radiation Oncology, and Society of Surgical Oncology Guideline. J Clin Oncol 2020; 38:2080-2106. [PMID: 32243226 DOI: 10.1200/jco.20.00299] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
PURPOSE To develop recommendations for management of patients with breast cancer (BC) with germline mutations in BC susceptibility genes. METHODS The American Society of Clinical Oncology, American Society for Radiation Oncology, and Society of Surgical Oncology convened an Expert Panel to develop recommendations based on a systematic review of the literature and a formal consensus process. RESULTS Fifty-eight articles met eligibility criteria and formed the evidentiary basis for the local therapy recommendations; six randomized controlled trials of systemic therapy met eligibility criteria. RECOMMENDATIONS Patients with newly diagnosed BC and BRCA1/2 mutations may be considered for breast-conserving therapy (BCT), with local control of the index cancer similar to that of noncarriers. The significant risk of a contralateral BC (CBC), especially in young women, and the higher risk of new cancers in the ipsilateral breast warrant discussion of bilateral mastectomy. Patients with mutations in moderate-risk genes should be offered BCT. For women with mutations in BRCA1/2 or moderate-penetrance genes who are eligible for mastectomy, nipple-sparing mastectomy is a reasonable approach. There is no evidence of increased toxicity or CBC events from radiation exposure in BRCA1/2 carriers. Radiation therapy should not be withheld in ATM carriers. For patients with germline TP53 mutations, mastectomy is advised; radiation therapy is contraindicated except in those with significant risk of locoregional recurrence. Platinum agents are recommended versus taxanes to treat advanced BC in BRCA carriers. In the adjuvant/neoadjuvant setting, data do not support the routine addition of platinum to anthracycline- and taxane-based chemotherapy. Poly (ADP-ribose) polymerase (PARP) inhibitors (olaparib and talazoparib) are preferable to nonplatinum single-agent chemotherapy for treatment of advanced BC in BRCA1/2 carriers. Data are insufficient to recommend PARP inhibitor use in the early setting or in moderate-penetrance carriers. Additional information available at www.asco.org/breast-cancer-guidelines.
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Affiliation(s)
| | | | - Lori J Pierce
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI
| | - Mark E Robson
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Jill R Dietz
- Case Western Reserve University School of Medicine and University Hospitals, Cleveland, OH
| | | | | | | | | | - Ismail Jatoi
- University of Texas Health Science Center at San Antonio, San Antonio, TX
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61
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Liu YL, Selenica P, Zhou Q, Iasonos A, Callahan M, Feit NZ, Boland J, Vazquez-Garcia I, Mandelker D, Zehir A, Burger RA, Powell DJ, Friedman C, Cadoo K, Grisham R, Konner JA, O'Cearbhaill RE, Aghajanian C, Reis-Filho JS, Weigelt B, Zamarin D. BRCA Mutations, Homologous DNA Repair Deficiency, Tumor Mutational Burden, and Response to Immune Checkpoint Inhibition in Recurrent Ovarian Cancer. JCO Precis Oncol 2020; 4:2000069. [PMID: 32923884 DOI: 10.1200/po.20.00069] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2020] [Indexed: 12/21/2022] Open
Abstract
PURPOSE Homologous DNA repair-deficient (HRD) ovarian cancers (OCs), including those with BRCA1/2 mutations, have higher levels of genetic instability, potentially resulting in higher immunogenicity, and have been suggested to respond better to immune checkpoint inhibitors (ICIs) than homologous DNA repair-proficient OCs. However, clinical evidence is lacking. The study aimed to evaluate the associations between BRCA1/2 mutations, HRD, and other genomic parameters and response to ICIs and survival in OC. METHODS This is a single-institution retrospective analysis of women with recurrent OC treated with ICIs. BRCA1/2 mutation status and clinicopathologic variables were abstracted from the medical records. Targeted and whole-exome sequencing data available for a subset of patients were used to assess tumor mutational burden (TMB), HRD, and fraction of genome altered (FGA). ICI response was defined as lack of disease progression for ≥ 24 weeks. Associations of BRCA1/2 status and genomic alterations with progression-free survival (PFS) and overall survival (OS) were determined using Cox proportional hazards models. RESULTS Of the 143 women treated with ICIs, 134 had known BRCA1/2 mutation status. Deleterious germline or somatic BRCA1/2 mutations were present in 31 women (24%). There was no association between presence of BRCA1/2 mutations and response (P = .796) or survival. Genomic analysis in 73 women found no association between TMB (P = .344) or HRD (P = .222) and response, PFS, or OS. There were also no significant differences in somatic genetic alterations between responders and nonresponders. High FGA was associated with an improvement in PFS (P = .014) and OS (P = .01). CONCLUSION TMB, BRCA1/2 mutations, and HRD are not associated with response or survival, cautioning against their use as selection criteria for ICI in recurrent OC. FGA should be investigated further as a biomarker of response to immunotherapy in OC.
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Affiliation(s)
- Ying L Liu
- Department of Medicine, Gynecologic Medical Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Qin Zhou
- Department of Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alexia Iasonos
- Department of Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Margaret Callahan
- Department of Medicine, Gynecologic Medical Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY.,Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Noah Z Feit
- Department of Medicine, Gynecologic Medical Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Julia Boland
- Department of Medicine, Gynecologic Medical Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Diana Mandelker
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Robert A Burger
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA
| | - Daniel J Powell
- Department of Pathology, University of Pennsylvania, Philadelphia, PA
| | - Claire Friedman
- Department of Medicine, Gynecologic Medical Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Karen Cadoo
- Department of Medicine, Gynecologic Medical Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Rachel Grisham
- Department of Medicine, Gynecologic Medical Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Jason A Konner
- Department of Medicine, Gynecologic Medical Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Roisin E O'Cearbhaill
- Department of Medicine, Gynecologic Medical Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Carol Aghajanian
- Department of Medicine, Gynecologic Medical Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Dmitriy Zamarin
- Department of Medicine, Gynecologic Medical Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY.,Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY
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62
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Li N, McInerny S, Zethoven M, Cheasley D, Lim BWX, Rowley SM, Devereux L, Grewal N, Ahmadloo S, Byrne D, Lee JEA, Li J, Fox SB, John T, Antill Y, Gorringe KL, James PA, Campbell IG. Combined Tumor Sequencing and Case-Control Analyses of RAD51C in Breast Cancer. J Natl Cancer Inst 2020; 111:1332-1338. [PMID: 30949688 DOI: 10.1093/jnci/djz045] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/07/2019] [Accepted: 04/03/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Loss-of-function variants in RAD51C are associated with familial ovarian cancer, but its role in hereditary breast cancer remains unclear. The aim of this study was to couple breast tumor sequencing with case-control data to clarify the contribution of RAD51C to hereditary breast cancer. METHODS RAD51C was sequenced in 3080 breast cancer index cases that were negative in BRCA1/2 clinical tests and 4840 population-matched cancer-free controls. Pedigree and pathology data were analyzed. Nine breast cancers and one ovarian cancer from RAD51C variant carriers were sequenced to identify biallelic inactivation of RAD51C, copy number variation, mutational signatures, and the spectrum of somatic mutations in breast cancer driver genes. The promoter of RAD51C was analyzed for DNA methylation. RESULTS A statistically significant excess of loss-of-function variants was identified in 3080 cases (0.4%) compared with 2 among 4840 controls (0.04%; odds ratio = 8.67, 95% confidence interval = 1.89 to 80.52, P< .001), with more than half of the carriers having no personal or family history of ovarian cancer. In addition, the association was highly statistically significant among cases with estrogen-negative (P <. 001) or triple-negative cancer (P < .001), but not in estrogen-positive cases. Tumor sequencing from carriers confirmed bi-allelic inactivation in all the triple-negative cases and was associated with high homologous recombination deficiency scores and mutational signature 3 indicating homologous recombination repair deficiency. CONCLUSIONS This study provides evidence that germline loss-of-function variants of RAD51C are associated with hereditary breast cancer, particularly triple-negative type. RAD51C-null breast cancers possess similar genomic and clinical features to BRCA1-null cancers and may also be vulnerable to DNA double-strand break inducing chemotherapies and poly ADP-ribose polymerase inhibitors.
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63
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Armstrong SA, Schultz CW, Azimi-Sadjadi A, Brody JR, Pishvaian MJ. ATM Dysfunction in Pancreatic Adenocarcinoma and Associated Therapeutic Implications. Mol Cancer Ther 2020; 18:1899-1908. [PMID: 31676541 DOI: 10.1158/1535-7163.mct-19-0208] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 06/24/2019] [Accepted: 08/28/2019] [Indexed: 02/06/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal solid malignancies with very few therapeutic options to treat advanced or metastatic disease. The utilization of genomic sequencing has identified therapeutically relevant alterations in approximately 25% of PDAC patients, most notably in the DNA damage response and repair (DDR) genes, rendering cancer cells more sensitive to DNA-damaging agents and to DNA damage response inhibitors, such as PARP inhibitors. ATM is one of the most commonly mutated DDR genes, with somatic mutations identified in 2% to 18% of PDACs and germline mutations identified in 1% to 34% of PDACs. ATM plays a complex role as a cell-cycle checkpoint kinase, regulator of a wide array of downstream proteins, and responder to DNA damage for genome stability. The disruption of ATM signaling leads to downstream reliance on ATR and CHK1, among other DNA-repair mechanisms, which may enable exploiting the inhibition of downstream proteins as therapeutic targets in ATM-mutated PDACs. In this review, we detail the function of ATM, review the current data on ATM deficiency in PDAC, examine the therapeutic implications of ATM alterations, and explore the current clinical trials surrounding the ATM pathway.
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Affiliation(s)
- Samantha A Armstrong
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia
| | - Christopher W Schultz
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, and the Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Ariana Azimi-Sadjadi
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia
| | - Jonathan R Brody
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, and the Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
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64
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Stasenko M, Feit N, Lee SSK, Shepherd C, Soslow RA, Cadoo KA, Alektiar K, Da Silva EM, Martins Sebastião AP, Leitao MM, Gardner G, Selenica P, Abu-Rustum NR, Weigelt B, Mueller JJ. Clinical patterns and genomic profiling of recurrent 'ultra-low risk' endometrial cancer. Int J Gynecol Cancer 2020; 30:717-723. [PMID: 32376737 PMCID: PMC7295026 DOI: 10.1136/ijgc-2020-001241] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE Despite good prognosis for patients with low-risk endometrial cancer, a small subset of women with low-grade/low-stage endometrial cancer experience disease recurrence and death. The aim of this study was to characterize clinical features and mutational profiles of recurrent, low-grade, non-myoinvasive, 'ultra-low risk' endometrioid endometrial adenocarcinomas. METHODS We retrospectively identified patients with International Federation of Gynecology and Obstetrics (FIGO) stage IA endometrioid endometrial cancers who underwent primary surgery at our institution, between January 2009 and February 2017, with follow-up of ≥12 months. 'Ultra-low risk' was defined as FIGO tumor grade 1, non-myoinvasive, and lacking lymphovascular space invasion. Tumor-normal profiling using massively parallel sequencing targeting 468 genes was performed. Microsatellite instability was assessed using MSIsensor. DNA mismatch repair (MMR) protein proficiency was determined by immunohistochemistry. RESULTS A total of 486 patients with ultra-low risk endometrioid endometrial cancers were identified: 14 (2.9%) of 486 patients developed a recurrence. Median follow-up for non-recurrent endometrioid endometrial cancers: 34 (range 12-116) months; for recurrent endometrioid endometrial cancers: 50.5 (range 20-116) months. Patients with recurrent disease were older, had lower body mass index, and were most commonly non-White (p=0.025, p<0.001, and p<0.001, respectively). Other clinical characteristics did not differ. MMR immunohistochemistry was obtained for 211 (43%) tumors: 158 (75%) MMR-proficient and 53 (25%) MMR-deficient. Primary tumors of 9 recurrent and 27 non-recurrent endometrioid endometrial cancers underwent mutational profiling. Most were microsatellite stable (6/9, 67% recurrent; 25/27, 93% non-recurrent). Recurrent PTEN and PIK3CA mutations were present in both groups. Exon 3 CTNNB1 hotspot mutations were found in 4/9 (44%) recurrent and 8/27 (30%) non-recurrent (p=0.44). CONCLUSIONS Patients diagnosed with ultra-low risk endometrioid endometrial cancers have an overall excellent prognosis. However, in our study, 2.9% of patients with no identifiable clinical or pathologic risk factors developed recurrence. Further work is warranted to elucidate the mechanism for recurrence in this population.
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Affiliation(s)
- Marina Stasenko
- Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Noah Feit
- Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Simon S K Lee
- Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Cassandra Shepherd
- Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Robert A Soslow
- Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Karen A Cadoo
- Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Kaled Alektiar
- Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Edaise M Da Silva
- Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Mario M Leitao
- Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ginger Gardner
- Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Pier Selenica
- Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Britta Weigelt
- Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jennifer J Mueller
- Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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65
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Kutasovic JR, McCart Reed AE, Sokolova A, Lakhani SR, Simpson PT. Morphologic and Genomic Heterogeneity in the Evolution and Progression of Breast Cancer. Cancers (Basel) 2020; 12:E848. [PMID: 32244556 PMCID: PMC7226487 DOI: 10.3390/cancers12040848] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 12/13/2022] Open
Abstract
: Breast cancer is a remarkably complex and diverse disease. Subtyping based on morphology, genomics, biomarkers and/or clinical parameters seeks to stratify optimal approaches for management, but it is clear that every breast cancer is fundamentally unique. Intra-tumour heterogeneity adds further complexity and impacts a patient's response to neoadjuvant or adjuvant therapy. Here, we review some established and more recent evidence related to the complex nature of breast cancer evolution. We describe morphologic and genomic diversity as it arises spontaneously during the early stages of tumour evolution, and also in the context of treatment where the changing subclonal architecture of a tumour is driven by the inherent adaptability of tumour cells to evolve and resist the selective pressures of therapy.
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Affiliation(s)
- Jamie R. Kutasovic
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane 4029, Australia; (J.R.K.); (A.E.M.R.); (A.S.); (S.R.L.)
- QIMR Berghofer Medical Research Institute, Herston 4006, Australia
| | - Amy E. McCart Reed
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane 4029, Australia; (J.R.K.); (A.E.M.R.); (A.S.); (S.R.L.)
- QIMR Berghofer Medical Research Institute, Herston 4006, Australia
| | - Anna Sokolova
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane 4029, Australia; (J.R.K.); (A.E.M.R.); (A.S.); (S.R.L.)
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Herston, Brisbane 4029, Australia
| | - Sunil R. Lakhani
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane 4029, Australia; (J.R.K.); (A.E.M.R.); (A.S.); (S.R.L.)
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Herston, Brisbane 4029, Australia
| | - Peter T. Simpson
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane 4029, Australia; (J.R.K.); (A.E.M.R.); (A.S.); (S.R.L.)
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66
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Pareja F, Brown DN, Lee JY, Da Cruz Paula A, Selenica P, Bi R, Geyer FC, Gazzo A, da Silva EM, Vahdatinia M, Stylianou AA, Ferrando L, Wen HY, Hicks JB, Weigelt B, Reis-Filho JS. Whole-Exome Sequencing Analysis of the Progression from Non-Low-Grade Ductal Carcinoma In Situ to Invasive Ductal Carcinoma. Clin Cancer Res 2020; 26:3682-3693. [PMID: 32220886 DOI: 10.1158/1078-0432.ccr-19-2563] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 01/28/2020] [Accepted: 03/24/2020] [Indexed: 12/12/2022]
Abstract
PURPOSE Ductal carcinoma in situ (DCIS) is a nonobligate precursor of invasive breast cancer. Here, we sought to investigate the level of intralesion genetic heterogeneity in DCIS and the patterns of clonal architecture changes in the progression from DCIS to invasive disease. EXPERIMENTAL DESIGN Synchronous DCIS (n = 27) and invasive ductal carcinomas of no special type (IDC-NSTs; n = 26) from 25 patients, and pure DCIS (n = 7) from 7 patients were microdissected separately and subjected to high-depth whole-exome (n = 56) or massively parallel sequencing targeting ≥410 key cancer-related genes (n = 4). Somatic genetic alterations, mutational signatures, clonal composition, and phylogenetic analyses were defined using validated computational methods. RESULTS DCIS revealed genetic alterations similar to those of synchronously diagnosed IDC-NSTs and of non-related IDC-NSTs from The Cancer Genome Atlas (TCGA), whereas pure DCIS lacked PIK3CA mutations. Clonal decomposition and phylogenetic analyses based on somatic mutations and copy number alterations revealed that the mechanisms of progression of DCIS to invasive carcinoma are diverse, and that clonal selection might have constituted the mechanism of progression from DCIS to invasive disease in 28% (7/25) of patients. DCIS displaying a pattern of clonal selection in the progression to invasive cancer harbored higher levels of intralesion genetic heterogeneity than DCIS where no clonal selection was observed. CONCLUSIONS Intralesion genetic heterogeneity is a common feature in DCIS synchronously diagnosed with IDC-NST. DCIS is a nonobligate precursor of IDC-NST, whose mechanisms of progression to invasive breast cancer are diverse and vary from case to case.
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Affiliation(s)
- Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David N Brown
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ju Youn Lee
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Arnaud Da Cruz Paula
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rui Bi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Felipe C Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrea Gazzo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Edaise M da Silva
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mahsa Vahdatinia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anthe A Stylianou
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lorenzo Ferrando
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Internal Medicine, University of Genoa, Genova, Italy
| | - Hannah Y Wen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James B Hicks
- Department of Biological Sciences, University of Southern California, Los Angeles, California
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Jorge S Reis-Filho
- 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
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67
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Basturk O, Weigelt B, Adsay V, Benhamida JK, Askan G, Wang L, Arcila ME, Zamboni G, Fukushima N, Gularte-Mérida R, Da Cruz Paula A, Selenica P, Kumar R, Pareja F, Maher CA, Scholes J, Oda Y, Santini D, Doyle LA, Petersen I, Flucke U, Koelsche C, Reynolds SJ, Yavas A, von Deimling A, Reis-Filho JS, Klimstra DS. Sclerosing epithelioid mesenchymal neoplasm of the pancreas - a proposed new entity. Mod Pathol 2020; 33:456-467. [PMID: 31383964 PMCID: PMC7000300 DOI: 10.1038/s41379-019-0334-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 02/07/2023]
Abstract
We have encountered pancreatic tumors with unique histologic features, which do not conform to any of the known tumors of the pancreas or other anatomical sites. We aimed to define their clinicopathologic features and whether they are characterized by recurrent molecular signatures. Eight cases were identified; studied histologically and by immunohistochemistry. Selected cases were also subjected to whole-exome sequencing (WES; n = 4), RNA-sequencing (n = 6), Archer FusionPlex assay (n = 5), methylation profiling using the Illumina MethylationEPIC (850k) array platform (n = 6), and TERT promoter sequencing (n = 5). Six neoplasms occurred in females. The mean age was 43 years (range: 26-75). Five occurred in the head/neck of the pancreas. All patients were treated surgically; none received neoadjuvant/adjuvant therapy. All patients are free of disease after 53 months of median follow-up (range: 8-94). The tumors were well-circumscribed, and the median size was 1.8 cm (range: 1.3-5.8). Microscopically, the unencapsulated tumors had a geographic pattern of epithelioid cell nests alternating with spindle cell fascicles. Some areas showed dense fibrosis, in which enmeshed tumor cells imparted a slit-like pattern. The predominant epithelioid cells had scant cytoplasm and round-oval nuclei with open chromatin. The spindle cells displayed irregular, hyperchromatic nuclei. Mitoses were rare. No lymph node metastases were identified. All tumors were positive for vimentin, CD99 and cytokeratin (patchy), while negative for markers of solid pseudopapillary neoplasm, neuroendocrine, acinar, myogenic/rhabdoid, vascular, melanocytic, or lymphoid differentiation, gastrointestinal stromal tumor as well as MUC4. Whole-exome sequencing revealed no recurrent somatic mutations or amplifications/homozygous deletions in any known oncogenes or tumor suppressor genes. RNA-sequencing and the Archer FusionPlex assay did not detect any recurrent likely pathogenic gene fusions. Single sample gene set enrichment analysis revealed that these tumors display a likely mesenchymal transcriptomic program. Unsupervised analysis (t-SNE) of their methylation profiles against a set of different mesenchymal neoplasms demonstrated a distinct methylation pattern. Here, we describe pancreatic neoplasms with unique morphologic/immunophenotypic features and a distinct methylation pattern, along with a lack of abnormalities in any of key genetic drivers, supporting that these neoplasms represent a novel entity with an indolent clinical course. Given their mesenchymal transcriptomic features, we propose the designation of "sclerosing epithelioid mesenchymal neoplasm" of the pancreas.
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Affiliation(s)
- Olca Basturk
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
| | - Volkan Adsay
- Department of Pathology, Koç University, Istanbul,
Turkey
| | - Jamal K. Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
| | - Gokce Askan
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
| | - Lu Wang
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
| | - Maria E. Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
| | - Giuseppe Zamboni
- Department of Pathology, University of Verona and IRCCS
Sacro Cuore Don Calabria Hospital, Negrar, Verona, Italy
| | | | | | - Arnaud Da Cruz Paula
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
| | - Rahul Kumar
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
| | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
| | | | - John Scholes
- Department of Pathology, St. Francis Hospital and Medical
Center, Hartford, CT, USA
| | - Yoshinao Oda
- Department of Pathology, Kyushu University, Fukuoka,
Fukuoka Prefecture, Japan
| | - Donatella Santini
- Department of Pathology, Azienda Ospedaliera-Universitaria
di Bologna, Italy
| | - Leona A. Doyle
- Department of Pathology, Brigham and Women’s
Hospital, Boston, MA, USA
| | - Iver Petersen
- Department of Pathology, SRH Poliklinik Gera GmbH, Gera,
Germany
| | - Uta Flucke
- Department of Pathology, Radboud University Medical
Center, Nijmegen, The Netherlands
| | | | | | - Aslihan Yavas
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
| | - Andreas von Deimling
- Department of Pathology, University Hospital Heidelberg
and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jorge S. Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
| | - David S. Klimstra
- Department of Pathology, Memorial Sloan Kettering Cancer
Center, New York, NY, USA
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Abida W, Campbell D, Patnaik A, Shapiro JD, Sautois B, Vogelzang NJ, Voog EG, Bryce AH, McDermott R, Ricci F, Rowe J, Zhang J, Piulats JM, Fizazi K, Merseburger AS, Higano CS, Krieger LE, Ryan CJ, Feng FY, Simmons AD, Loehr A, Despain D, Dowson M, Green F, Watkins SP, Golsorkhi T, Chowdhury S. Non-BRCA DNA Damage Repair Gene Alterations and Response to the PARP Inhibitor Rucaparib in Metastatic Castration-Resistant Prostate Cancer: Analysis From the Phase II TRITON2 Study. Clin Cancer Res 2020; 26:2487-2496. [PMID: 32086346 DOI: 10.1158/1078-0432.ccr-20-0394] [Citation(s) in RCA: 274] [Impact Index Per Article: 68.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/12/2020] [Accepted: 02/18/2020] [Indexed: 02/07/2023]
Abstract
PURPOSE Genomic alterations in DNA damage repair (DDR) genes other than BRCA may confer synthetic lethality with PARP inhibition in metastatic castration-resistant prostate cancer (mCRPC). To test this hypothesis, the phase II TRITON2 study of rucaparib included patients with mCRPC and deleterious non-BRCA DDR gene alterations. PATIENTS AND METHODS TRITON2 enrolled patients who had progressed on one or two lines of next-generation androgen receptor-directed therapy and one taxane-based chemotherapy for mCRPC. Key endpoints were investigator-assessed radiographic response per modified RECIST/PCWG3 and PSA response (≥50% decrease from baseline). RESULTS TRITON2 enrolled 78 patients with a non-BRCA DDR gene alteration [ATM (n = 49), CDK12 (n = 15), CHEK2 (n = 12), and other DDR genes (n = 14)]. Among patients evaluable for each endpoint, radiographic and PSA responses were observed in a limited number of patients with an alteration in ATM [2/19 (10.5%) and 2/49 (4.1%), respectively], CDK12 [0/10 (0%) and 1/15 (6.7%), respectively], or CHEK2 [1/9 (11.1%) and 2/12 (16.7%), respectively], including no radiographic or PSA responses in 11 patients with confirmed biallelic ATM loss or 11 patients with ATM germline mutations. Responses were observed in patients with alterations in the DDR genes PALB2, FANCA, BRIP1, and RAD51B. CONCLUSIONS In this prospective, genomics-driven study of rucaparib in mCRPC, we found limited radiographic/PSA responses to PARP inhibition in men with alterations in ATM, CDK12, or CHEK2. However, patients with alterations in other DDR-associated genes (e.g., PALB2) may benefit from PARP inhibition.See related commentary by Sokolova et al., p. 2439.
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Affiliation(s)
- Wassim Abida
- Genitourinary Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - David Campbell
- Medical Oncology, Barwon Health, University Hospital Geelong, Geelong, Victoria, Australia
| | - Akash Patnaik
- Hematology and Oncology, University of Chicago Comprehensive Cancer Center, Chicago, Illinois
| | - Jeremy D Shapiro
- Medical Oncology, Cabrini Hospital, Malvern, Victoria, Australia
| | | | - Nicholas J Vogelzang
- Medical Oncology, Comprehensive Cancer Centers of Nevada and US Oncology Research, Las Vegas, Nevada
| | - Eric G Voog
- Medical Oncology, Clinique Victor Hugo Centre Jean Bernard, Le Mans, France
| | - Alan H Bryce
- Hematology/Oncology, Mayo Clinic, Phoenix, Arizona
| | - Ray McDermott
- Genito-Urinary Oncology, Adelaide and Meath Hospital (Incorporating the National Children's Hospital), Tallaght, Dublin, Ireland
| | - Francesco Ricci
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | - Julie Rowe
- Division of Oncology, Department of Internal Medicine, The University of Texas Health Science Center at Houston and Memorial Hermann Cancer Center, Houston, Texas
| | - Jingsong Zhang
- Genitourinary Oncology, H. Lee Moffitt Cancer Center, Tampa, Florida
| | - Josep Maria Piulats
- Medical Oncology, Institut Català d'Oncologia, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL); ONCOBELL; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC); Hospitalet de Llobregat, Barcelona, Spain
| | - Karim Fizazi
- Department of Cancer Medicine, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Axel S Merseburger
- Department of Urology, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Celestia S Higano
- Department of Medicine, Division of Oncology, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Laurence E Krieger
- Oncology, Northern Cancer Institute, St Leonards, New South Wales, Australia
| | - Charles J Ryan
- Department of Medicine, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Felix Y Feng
- Department of Radiation Oncology, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Andrew D Simmons
- Translational Medicine, Clovis Oncology, Inc., Boulder, Colorado
| | - Andrea Loehr
- Translational Medicine, Clovis Oncology, Inc., Boulder, Colorado
| | | | - Melanie Dowson
- Study Operations, Clovis Oncology UK, Ltd, Cambridge, United Kingdom
| | - Foad Green
- Translational Medicine, Clovis Oncology, Inc., Boulder, Colorado
| | - Simon P Watkins
- Clinical Science, Clovis Oncology UK, Ltd, Cambridge, United Kingdom
| | - Tony Golsorkhi
- Clinical Development, Clovis Oncology, Inc., Boulder, Colorado
| | - Simon Chowdhury
- Medical Oncology, Guy's Hospital and Sarah Cannon Research Institute, London, United Kingdom
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Xu P, Sun Y, Song Y, Jiao J, Shen B, Li W, Jiang C, Li Y, Zhang X, Yu J, Fu L, Guo X. ATM kinase regulates tumor immunoreactions in lymphocyte-predominant breast cancer through modulation of NKG2D ligand and TNF cytokines on tumor cells. Med Mol Morphol 2020; 53:210-220. [PMID: 32067111 DOI: 10.1007/s00795-020-00247-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 02/03/2020] [Indexed: 11/26/2022]
Abstract
To explore impact of Ataxia telangiectasia mutated (ATM) kinase on immunoreactions in lymphocyte-predominant breast cancer (LPBC), particularly its role in triple negative breast cancer (TNBC), 194 cases of LPBC were identified with pertinent clinical information retrieved. The expressions of ATM, activated ATM (P-ATM), Fas ligand (FASL), tumor necrosis factor-related apoptosis-induced ligand (TRAIL), major histocompatibility complex class I chain-related protein A (MICA), CD8, and Forkhead box P3 (FOXP3) were assessed by immunohistochemically. We found that ATM expressed on tumor cells was correlated with upregulated expression of P-ATM and MICA (P < 0.05), down-regulated expression of FASL and TRAIL (P < 0.01), and decreased Ki-67 tumor labeling (P < 0.05). However, within the TNBC group, only a negative correlation with FASL expression was found (P = 0.001). ATM and MICA expressions were significantly down -regulated in TNBC (P < 0.01) compared to non-TNBC, while TRAIL was significantly upregulated (P < 0.01). Tregs were increased in TNBC (P < 0.05), with CD8 + TILs decreased (P < 0.01). Ki-67 index was higher in TNBC than in non-TNBC (P < 0.01). ATM may play an important role in immunoreaction of LPBC, probably through upregulation of MICA and down-regulation of FASL and TRAIL. The down-regulated ATM expression in TNBC might be responsible for impaired tumor immunoactivity, rapid tumor growth, and aggressive clinical course.
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Affiliation(s)
- Peng Xu
- Department of Breast Pathology and Lab, Key Laboratory of Breast Cancer of Breast Cancer Prevention and Therapy, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, West Huanhu Road, Tianjin, 300060, China
| | - Yuanyuan Sun
- Department of Breast Pathology and Lab, Key Laboratory of Breast Cancer of Breast Cancer Prevention and Therapy, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, West Huanhu Road, Tianjin, 300060, China
| | - Yuanming Song
- Department of Breast Pathology and Lab, Key Laboratory of Breast Cancer of Breast Cancer Prevention and Therapy, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, West Huanhu Road, Tianjin, 300060, China
| | - Jiao Jiao
- Department of Breast Pathology and Lab, Key Laboratory of Breast Cancer of Breast Cancer Prevention and Therapy, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, West Huanhu Road, Tianjin, 300060, China
| | - Beibei Shen
- Department of Breast Pathology and Lab, Key Laboratory of Breast Cancer of Breast Cancer Prevention and Therapy, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, West Huanhu Road, Tianjin, 300060, China
| | - Weidong Li
- Department of Breast Pathology and Lab, Key Laboratory of Breast Cancer of Breast Cancer Prevention and Therapy, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, West Huanhu Road, Tianjin, 300060, China
| | - Chengying Jiang
- Department of Breast Pathology and Lab, Key Laboratory of Breast Cancer of Breast Cancer Prevention and Therapy, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, West Huanhu Road, Tianjin, 300060, China
| | - Yaqing Li
- Department of Breast Pathology and Lab, Key Laboratory of Breast Cancer of Breast Cancer Prevention and Therapy, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, West Huanhu Road, Tianjin, 300060, China
| | - Xinmin Zhang
- Department of Pathology, Cooper Medical School of Rowan University, Camden, NJ, USA
| | - Jinpu Yu
- Cancer Molecular Diagnostics Core, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Key Laboratory of Cancer Immunology and Biotherapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Li Fu
- Department of Breast Pathology and Lab, Key Laboratory of Breast Cancer of Breast Cancer Prevention and Therapy, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, West Huanhu Road, Tianjin, 300060, China
| | - Xiaojing Guo
- Department of Breast Pathology and Lab, Key Laboratory of Breast Cancer of Breast Cancer Prevention and Therapy, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, West Huanhu Road, Tianjin, 300060, China.
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70
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Olson N, Gularte-Mérida R, Selenica P, Da Cruz Paula A, Alemar B, Weigelt B, Lefferts J, Linos K. Molecular Characterization of a Rare Dedifferentiated Liposarcoma With Rhabdomyosarcomatous Differentiation in a 24 Year Old. Int J Surg Pathol 2019; 28:454-463. [PMID: 31801397 PMCID: PMC8302235 DOI: 10.1177/1066896919890401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Aims. The aim of this study was to identify potential driver genetic alterations in a dedifferentiated liposarcoma (DDLPS) with rhabdomyosarcomatous differentiation. Methods and Results. A 24-year-old female underwent resection of an abdominal mass, which on a previous biopsy demonstrated rhabdomyosarcomatous differentiation concerning for embryonal rhabdomyosarcoma. Histologically the resected tumor displayed a high-grade sarcoma with rhabdomyosarcomatous differentiation in the background of well-differentiated liposarcoma consistent with DDLPS. Fluorescence in situ hybridization confirmed MDM2 amplification, as did array-based copy number profiling. Whole-exome sequencing revealed a somatic FGFR1 hotspot mutation and RNA sequencing an LMNB2-MAP2K6 fusion only within the dedifferentiated component. Conclusions. This study represents an in-depth examination of a rare DDLPS with rhabdomyosarcomatous differentiation in a young individual. Additionally, it is also instructive of a potential pitfall when assessing for MDM2 amplification in small biopsies. Despite exhaustive analysis, mutation and gene copy number analysis did not identify any molecular events that would underlie the rhabdomyoblastic differentiation. Our understanding of what causes some tumors to dedifferentiate as well as undergo divergent differentiation is limited, and larger studies are needed.
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Affiliation(s)
- Nicholas Olson
- Dartmouth-Hitchcock Medical Center and Geisel School of Medicine, Lebanon, NH, USA
| | | | - Pier Selenica
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.,University of Maastricht, Maastricht, Netherlands
| | | | - Barbara Alemar
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joel Lefferts
- Dartmouth-Hitchcock Medical Center and Geisel School of Medicine, Lebanon, NH, USA
| | - Konstantinos Linos
- Dartmouth-Hitchcock Medical Center and Geisel School of Medicine, Lebanon, NH, USA
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71
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Póti Á, Gyergyák H, Németh E, Rusz O, Tóth S, Kovácsházi C, Chen D, Szikriszt B, Spisák S, Takeda S, Szakács G, Szallasi Z, Richardson AL, Szüts D. Correlation of homologous recombination deficiency induced mutational signatures with sensitivity to PARP inhibitors and cytotoxic agents. Genome Biol 2019; 20:240. [PMID: 31727117 PMCID: PMC6857305 DOI: 10.1186/s13059-019-1867-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 10/28/2019] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Homologous recombination (HR) repair deficiency arising from defects in BRCA1 or BRCA2 is associated with characteristic patterns of somatic mutations. In this genetic study, we ask whether inactivating mutations in further genes of the HR pathway or the DNA damage checkpoint also give rise to somatic mutation patterns that can be used for treatment prediction. RESULTS Using whole genome sequencing of an isogenic knockout cell line panel, we find a universal HR deficiency-specific base substitution signature that is similar to COSMIC signature 3. In contrast, we detect different deletion phenotypes corresponding to specific HR mutants. The inactivation of BRCA2 or PALB2 leads to larger deletions, typically with microhomology, when compared to the disruption of BRCA1, RAD51 paralogs, or RAD54. Comparison with the deletion spectrum of Cas9 cut sites suggests that most spontaneously arising genomic deletions are not the consequence of double-strand breaks. Surprisingly, the inactivation of checkpoint kinases ATM and CHK2 has no mutagenic consequences. Analysis of tumor exomes with biallelic inactivating mutations in the investigated genes confirms the validity of the cell line models. We present a comprehensive analysis of sensitivity of the investigated mutants to 13 therapeutic agents for the purpose of correlating genomic mutagenic phenotypes with drug sensitivity. CONCLUSION Our results suggest that no single genomic mutational class shows perfect correlation with sensitivity to common treatments, but the contribution of COSMIC signature 3 to base substitutions, or a combined measure of different features, may be reasonably good at predicting platinum and PARP inhibitor sensitivity.
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Affiliation(s)
- Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
| | - Hella Gyergyák
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
| | - Orsolya Rusz
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
- Department of Oncotherapy, University of Szeged, Szeged, Hungary
| | - Szilárd Tóth
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
| | - Csenger Kovácsházi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
| | - Dan Chen
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
| | - Bernadett Szikriszt
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
| | - Sándor Spisák
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Shunichi Takeda
- Department of Radiation Genetics, Kyoto University Medical School, Kyoto, 606-8501, Japan
| | - Gergely Szakács
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
- Institute of Cancer Research, Medical University Vienna, Vienna, Austria
| | - Zoltan Szallasi
- Computational Health Informatics Program (CHIP), Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Danish Cancer Society Research Center, Copenhagen, Denmark
- SE-NAP, Brain Metastasis Research Group, 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | | | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary.
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72
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Blom M, Schoenaker MHD, Hulst M, de Vries MC, Weemaes CMR, Willemsen MAAP, Henneman L, van der Burg M. Dilemma of Reporting Incidental Findings in Newborn Screening Programs for SCID: Parents' Perspective on Ataxia Telangiectasia. Front Immunol 2019; 10:2438. [PMID: 31781088 PMCID: PMC6851017 DOI: 10.3389/fimmu.2019.02438] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/30/2019] [Indexed: 12/20/2022] Open
Abstract
Background: Ataxia Telangiectasia (A-T) is a severe DNA repair disorder that leads to a broad range of symptoms including neurodegeneration and a variable immunodeficiency. A-T is one of the incidental findings that accompanies newborn screening (NBS) for severe combined immunodeficiency (SCID), leading to an early diagnosis of A-T at birth in a pre-symptomatic stage. While some countries embrace all incidental findings, the current policy in the Netherlands on reporting untreatable incidental findings is more conservative. We present parents' perspectives and considerations on the various advantages vs. disadvantages of early and late diagnosis of A-T. Methods: A questionnaire was developed and sent to 4,000 parents of healthy newborns who participated in the Dutch SONNET-study (implementation pilot for newborn screening for SCID). The questionnaire consisted of open-ended and scale questions on advantages and disadvantages of early and late diagnosis of A-T. To address potential bias, demographic characteristics of the study sample were compared to a reference population. Results: A total of 664 of 4,000 parents sent back the questionnaire (response rate 16.6%). The vast majority of parents (81.9%) favored early diagnosis of A-T over late diagnosis. Main arguments were to avoid a long period of uncertainty prior to diagnosis and to ensure the most optimal clinical care and guidance from the onset of symptoms. Parents who favored late diagnosis of A-T stated that early diagnosis would not lead to improved quality of life and preferred to enjoy the asymptomatic "golden years" with their child. The majority of parents (81.1%) stated that they would participate in newborn screening for A-T if a test was available. Conclusions: Reporting untreatable incidental findings remains a disputed topic worldwide. Although the current policy in the Netherlands is not to report untreatable incidental findings, unless the health advantage is clear, the majority of parents of healthy newborns are in favor of an early A-T diagnosis in the pre-symptomatic phase of the disorder. Our results as well as other studies that showed support for the screening of untreatable disorders may serve as valuable tools to inform policymakers in their considerations about NBS for untreatable disorders.
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Affiliation(s)
- Maartje Blom
- Department of Pediatrics, Leiden University Medical Centre, Leiden, Netherlands
| | - Michiel H. D. Schoenaker
- Department of Pediatric Neurology, Radboudumc Amalia Children's Hospital and Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Myrthe Hulst
- Department of Biologicals, Innovation and Screening, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Martine C. de Vries
- Department of Medical Ethics and Health Law, Leiden University Medical Center, Leiden, Netherlands
| | - Corry M. R. Weemaes
- Department of Pediatrics, Radboudumc Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, Netherlands
| | - Michèl A. A. P. Willemsen
- Department of Pediatric Neurology, Radboudumc Amalia Children's Hospital and Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Pediatrics, Radboudumc Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, Netherlands
| | - Lidewij Henneman
- Department of Clinical Genetics, Amsterdam Reproduction & Development Research Institute, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, Netherlands
| | - Mirjam van der Burg
- Department of Pediatrics, Leiden University Medical Centre, Leiden, Netherlands
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73
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Li A, Geyer FC, Blecua P, Lee JY, Selenica P, Brown DN, Pareja F, Lee SSK, Kumar R, Rivera B, Bi R, Piscuoglio S, Wen HY, Lozada JR, Gularte-Mérida R, Cavallone L, Rezoug Z, Nguyen-Dumont T, Peterlongo P, Tondini C, Terkelsen T, Rønlund K, Boonen SE, Mannerma A, Winqvist R, Janatova M, Rajadurai P, Xia B, Norton L, Robson ME, Ng PS, Looi LM, Southey MC, Weigelt B, Soo-Hwang T, Tischkowitz M, Foulkes WD, Reis-Filho JS. Homologous recombination DNA repair defects in PALB2-associated breast cancers. NPJ Breast Cancer 2019; 5:23. [PMID: 31428676 PMCID: PMC6687719 DOI: 10.1038/s41523-019-0115-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/04/2019] [Indexed: 01/02/2023] Open
Abstract
Mono-allelic germline pathogenic variants in the Partner And Localizer of BRCA2 (PALB2) gene predispose to a high-risk of breast cancer development, consistent with the role of PALB2 in homologous recombination (HR) DNA repair. Here, we sought to define the repertoire of somatic genetic alterations in PALB2-associated breast cancers (BCs), and whether PALB2-associated BCs display bi-allelic inactivation of PALB2 and/or genomic features of HR-deficiency (HRD). Twenty-four breast cancer patients with pathogenic PALB2 germline mutations were analyzed by whole-exome sequencing (WES, n = 16) or targeted capture massively parallel sequencing (410 cancer genes, n = 8). Somatic genetic alterations, loss of heterozygosity (LOH) of the PALB2 wild-type allele, large-scale state transitions (LSTs) and mutational signatures were defined. PALB2-associated BCs were found to be heterogeneous at the genetic level, with PIK3CA (29%), PALB2 (21%), TP53 (21%), and NOTCH3 (17%) being the genes most frequently affected by somatic mutations. Bi-allelic PALB2 inactivation was found in 16 of the 24 cases (67%), either through LOH (n = 11) or second somatic mutations (n = 5) of the wild-type allele. High LST scores were found in all 12 PALB2-associated BCs with bi-allelic PALB2 inactivation sequenced by WES, of which eight displayed the HRD-related mutational signature 3. In addition, bi-allelic inactivation of PALB2 was significantly associated with high LST scores. Our findings suggest that the identification of bi-allelic PALB2 inactivation in PALB2-associated BCs is required for the personalization of HR-directed therapies, such as platinum salts and/or PARP inhibitors, as the vast majority of PALB2-associated BCs without PALB2 bi-allelic inactivation lack genomic features of HRD.
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Affiliation(s)
- Anqi Li
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
- Department of Pathology, Fudan University Shanghai Cancer Center and Shanghai Medical College, Fudan University, Shanghai, P.R. China
| | - Felipe C. Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Pedro Blecua
- Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Ju Youn Lee
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - David N. Brown
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Simon S. K. Lee
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Rahul Kumar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Barbara Rivera
- Departments of Oncology and Human Genetics, McGill University, Montreal, Quebec Canada
- Cancer Axis, Lady Davis Institute, Jewish General Hospital, Montreal, Quebec Canada
| | - Rui Bi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
- Department of Pathology, Fudan University Shanghai Cancer Center and Shanghai Medical College, Fudan University, Shanghai, P.R. China
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Hannah Y. Wen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - John R. Lozada
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | | | - Luca Cavallone
- Departments of Oncology and Human Genetics, McGill University, Montreal, Quebec Canada
- Cancer Axis, Lady Davis Institute, Jewish General Hospital, Montreal, Quebec Canada
| | - Zoulikha Rezoug
- Cancer Prevention Center, Jewish General Hospital, Montreal, Quebec Canada
| | - Tu Nguyen-Dumont
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia
| | - Paolo Peterlongo
- IFOM, The Italian Foundation for Cancer Research Institute of Molecular Oncology, Milan, Italy
| | | | - Thorkild Terkelsen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Karina Rønlund
- Department of Clinical Genetics, Vejle Hospital, Vejle, Denmark
| | - Susanne E. Boonen
- Clinical Genetics Unit, Department of Pediatrics, Zealand University Hospital, Roskilde, Denmark
| | - Arto Mannerma
- Biocenter Kuopio and Cancer Center of Easter Finland, University of Eastern Finland, Kuopio, Finland
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Marketa Janatova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | | | - Bing Xia
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ USA
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Mark E. Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Pei-Sze Ng
- Cancer Research Malaysia, Subang Jaya, Malaysia
| | - Lai-Meng Looi
- Department of Pathology, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Melissa C. Southey
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Teo Soo-Hwang
- Cancer Research Malaysia, Subang Jaya, Malaysia
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Marc Tischkowitz
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - William D. Foulkes
- Cancer Axis, Lady Davis Institute, Jewish General Hospital, Montreal, Quebec Canada
- Cancer Prevention Center, Jewish General Hospital, Montreal, Quebec Canada
- Cancer Program, Research Institute McGill University Health Centre, Montreal, Quebec Canada
| | - Jorge S. Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
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74
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Cybulska P, Paula ADC, Tseng J, Leitao MM, Bashashati A, Huntsman DG, Nazeran TM, Aghajanian C, Abu-Rustum NR, DeLair DF, Shah SP, Weigelt B. Molecular profiling and molecular classification of endometrioid ovarian carcinomas. Gynecol Oncol 2019; 154:516-523. [PMID: 31340883 DOI: 10.1016/j.ygyno.2019.07.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Endometrioid ovarian carcinomas (EOCs) comprise 5-10% of all ovarian cancers and commonly co-occur with synchronous endometrioid endometrial cancer (EEC). We sought to examine the molecular characteristics of pure EOCs in patients without concomitant EEC. METHODS EOCs and matched normal samples were subjected to massively parallel sequencing targeting 341-468 cancer-related genes (n = 8) or whole-genome sequencing (n = 28). Mutational frequencies of EOCs were compared to those of high-grade serous ovarian cancers (HGSOCs; n = 224) and EECs (n = 186) from The Cancer Genome Atlas, and synchronous EOCs (n = 23). RESULTS EOCs were heterogeneous, frequently harboring KRAS, PIK3CA, PTEN, CTNNB1, ARID1A and TP53 mutations. EOCs were distinct from HGSOCs at the mutational level, less frequently harboring TP53 but more frequently displaying KRAS, PIK3CA, PIK3R1, PTEN and CTNNB1 mutations. Compared to synchronous EOCs and pure EECs, pure EOCs less frequently harbored PTEN, PIK3R1 and ARID1A mutations. Akin to EECs, EOCs could be stratified into the four molecular subtypes: 3% POLE (ultramutated), 19% MSI (hypermutated), 17% copy-number high (serous-like) and 61% copy-number low (endometrioid). In addition to microsatellite instability, a subset of EOCs harbored potentially targetable mutations, including AKT1 and ERBB2 hotspot mutations. EOCs of MSI (hypermutated) subtype uniformly displayed a good outcome. CONCLUSIONS EOCs are heterogeneous at the genomic level and harbor targetable genetic alterations. Despite the similarities in the repertoire of somatic mutations between pure EOCs, synchronous EOCs and EECs, the frequencies of mutations affecting known driver genes differ. Further studies are required to define the impact of the molecular subtypes on the outcome and treatment of EOC patients.
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Affiliation(s)
- Paulina Cybulska
- Department of Surgery, Gynecology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arnaud Da Cruz Paula
- Department of Surgery, Gynecology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jill Tseng
- Department of Surgery, Gynecology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mario M Leitao
- Department of Surgery, Gynecology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ali Bashashati
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - David G Huntsman
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Tayyebeh M Nazeran
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Carol Aghajanian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem R Abu-Rustum
- Department of Surgery, Gynecology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Deborah F DeLair
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sohrab P Shah
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada; Department of Epidemiology & Biostatistics, Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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75
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Selenica P, Raj N, Kumar R, Brown DN, Arqués O, Reidy D, Klimstra D, Snuderl M, Serrano J, Palmer HG, Weigelt B, Reis-Filho JS, Scaltriti M. Solid pseudopapillary neoplasms of the pancreas are dependent on the Wnt pathway. Mol Oncol 2019; 13:1684-1692. [PMID: 30972907 PMCID: PMC6670010 DOI: 10.1002/1878-0261.12490] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/07/2019] [Accepted: 04/08/2019] [Indexed: 12/14/2022] Open
Abstract
Solid pseudopapillary neoplasms (SPNs) are rare and relatively indolent tumors of the pancreas. While primary SPNs can be surgically resected, there are currently no therapies available for patients with advanced stage disease. Given that these tumors frequently carry CTNNB1 hotspot (recurrently mutated loci in a gene) mutations resulting in β‐catenin nuclear accumulation, it has been speculated that the Wnt pathway may be a driver in this disease. Here, we present a comprehensive “multi‐omics” study where the genome, transcriptome, and methylome of SPNs were analyzed. We found that SPNs are characterized by a low‐complexity genome where somatic mutations in CTNNB1, present in 100% of the cases, are the only actionable genomic lesions. Compared to more common subtypes of pancreatic tumors (adenocarcinomas and pancreatic neuroendocrine tumors), SPNs show high expression levels of genes belonging to the Wnt pathway. Their methylome was consistent with an epithelial cell origin and a general upregulation of Wnt pathway genes. Clinical studies to evaluate the exquisite sensitivity of SPNs to inhibitors of the Wnt pathway are warranted.
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Affiliation(s)
- Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nitya Raj
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rahul Kumar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David N Brown
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Oriol Arqués
- Department of Pathology, New York University Langone Medical Center and Medical School, NY, USA
| | - Diane Reidy
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David Klimstra
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matija Snuderl
- Department of Pathology, New York University Langone Medical Center and Medical School, NY, USA
| | - Jonathan Serrano
- Department of Pathology, New York University Langone Medical Center and Medical School, NY, USA
| | - Héctor G Palmer
- Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - Britta Weigelt
- Department of Pathology, 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.,Human Oncology & Pathogenesis Program (HOPP), Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maurizio Scaltriti
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Human Oncology & Pathogenesis Program (HOPP), Memorial Sloan Kettering Cancer Center, New York, NY, USA
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76
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Nones K, Johnson J, Newell F, Patch AM, Thorne H, Kazakoff SH, de Luca XM, Parsons MT, Ferguson K, Reid LE, McCart Reed AE, Srihari S, Lakis V, Davidson AL, Mukhopadhyay P, Holmes O, Xu Q, Wood S, Leonard C, Beesley J, Harris JM, Barnes D, Degasperi A, Ragan MA, Spurdle AB, Khanna KK, Lakhani SR, Pearson JV, Nik-Zainal S, Chenevix-Trench G, Waddell N, Simpson PT. Whole-genome sequencing reveals clinically relevant insights into the aetiology of familial breast cancers. Ann Oncol 2019; 30:1071-1079. [PMID: 31090900 PMCID: PMC6637375 DOI: 10.1093/annonc/mdz132] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Whole-genome sequencing (WGS) is a powerful method for revealing the diversity and complexity of the somatic mutation burden of tumours. Here, we investigated the utility of tumour and matched germline WGS for understanding aetiology and treatment opportunities for high-risk individuals with familial breast cancer. PATIENTS AND METHODS We carried out WGS on 78 paired germline and tumour DNA samples from individuals carrying pathogenic variants in BRCA1 (n = 26) or BRCA2 (n = 22) or from non-carriers (non-BRCA1/2; n = 30). RESULTS Matched germline/tumour WGS and somatic mutational signature analysis revealed patients with unreported, dual pathogenic germline variants in cancer risk genes (BRCA1/BRCA2; BRCA1/MUTYH). The strategy identified that 100% of tumours from BRCA1 carriers and 91% of tumours from BRCA2 carriers exhibited biallelic inactivation of the respective gene, together with somatic mutational signatures suggestive of a functional deficiency in homologous recombination. A set of non-BRCA1/2 tumours also had somatic signatures indicative of BRCA-deficiency, including tumours with BRCA1 promoter methylation, and tumours from carriers of a PALB2 pathogenic germline variant and a BRCA2 variant of uncertain significance. A subset of 13 non-BRCA1/2 tumours from early onset cases were BRCA-proficient, yet displayed complex clustered structural rearrangements associated with the amplification of oncogenes and pathogenic germline variants in TP53, ATM and CHEK2. CONCLUSIONS Our study highlights the role that WGS of matched germline/tumour DNA and the somatic mutational signatures can play in the discovery of pathogenic germline variants and for providing supporting evidence for variant pathogenicity. WGS-derived signatures were more robust than germline status and other genomic predictors of homologous recombination deficiency, thus impacting the selection of platinum-based or PARP inhibitor therapy. In this first examination of non-BRCA1/2 tumours by WGS, we illustrate the considerable heterogeneity of these tumour genomes and highlight that complex genomic rearrangements may drive tumourigenesis in a subset of cases.
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Affiliation(s)
- K Nones
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - J Johnson
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD
| | - F Newell
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - A M Patch
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - H Thorne
- kConFab Investigators, The Peter MacCallum Cancer Centre, Melbourne, VIC; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC
| | - S H Kazakoff
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - X M de Luca
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD
| | - M T Parsons
- Molecular Cancer Epidemiology Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - K Ferguson
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD
| | - L E Reid
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD
| | - A E McCart Reed
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD
| | - S Srihari
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD; Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD
| | - V Lakis
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - A L Davidson
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD; Faculty of Medicine, The University of Queensland, Brisbane, QLD
| | - P Mukhopadhyay
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - O Holmes
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - Q Xu
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - S Wood
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - C Leonard
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - J Beesley
- Cancer Genetics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - J M Harris
- Faculty of Health, School Biomedical Science - Queensland University of Technology, Brisbane, QLD, Australia
| | - D Barnes
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge
| | - A Degasperi
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge; Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge, UK
| | - M A Ragan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD
| | - A B Spurdle
- Molecular Cancer Epidemiology Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - K K Khanna
- Signal Transduction Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - S R Lakhani
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD; Royal Brisbane & Women's Hospital, Pathology Queensland, Brisbane, QLD, Australia
| | - J V Pearson
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - S Nik-Zainal
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge; Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge, UK
| | - G Chenevix-Trench
- Cancer Genetics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - N Waddell
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD.
| | - P T Simpson
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD.
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77
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DNA Repair Deficiency in Breast Cancer: Opportunities for Immunotherapy. JOURNAL OF ONCOLOGY 2019; 2019:4325105. [PMID: 31320901 PMCID: PMC6607732 DOI: 10.1155/2019/4325105] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/04/2019] [Accepted: 05/29/2019] [Indexed: 12/19/2022]
Abstract
Historically the development of anticancer treatments has been focused on their effect on tumor cells alone. However, newer treatments have shifted attention to targets on immune cells, resulting in dramatic responses. The effect of DNA repair deficiency on the microenvironment remains an area of key interest. Moreover, established therapies such as DNA damaging treatments such as chemotherapy and PARP inhibitors further modify the tumor microenvironment. Here we describe DNA repair pathways in breast cancer and activation of innate immune pathways in DNA repair deficiency, in particular, the STING (STimulator of INterferon Genes) pathway. Breast tumors with DNA repair deficiency are associated with upregulation of immune checkpoints including PD-L1 (Programmed Death Ligand-1) and may represent a target population for single agent or combination immunotherapy treatment.
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78
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Weigelt B, Vargas HA, Selenica P, Geyer FC, Mazaheri Y, Blecua P, Conlon N, Hoang LN, Jungbluth AA, Snyder A, Ng CKY, Papanastasiou AD, Sosa RE, Soslow RA, Chi DS, Gardner GJ, Shen R, Reis-Filho JS, Sala E. Radiogenomics Analysis of Intratumor Heterogeneity in a Patient With High-Grade Serous Ovarian Cancer. JCO Precis Oncol 2019; 3:1800410. [PMID: 32914032 DOI: 10.1200/po.18.00410] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2019] [Indexed: 12/21/2022] Open
Affiliation(s)
| | | | - Pier Selenica
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Pedro Blecua
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Niamh Conlon
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Lien N Hoang
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Charlotte K Y Ng
- Memorial Sloan Kettering Cancer Center, New York, NY.,University Hospital Basel, Basel, Switzerland
| | | | - Ramon E Sosa
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Dennis S Chi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ronglai Shen
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Evis Sala
- Memorial Sloan Kettering Cancer Center, New York, NY.,Cancer Research UK Cambridge Center, Cambridge, United Kingdom
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79
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Lozada JR, Geyer FC, Selenica P, Brown D, Alemar B, Merghoub T, Berger MF, Busam KJ, Halpern AC, Weigelt B, Reis-Filho JS, Hollmann TJ. Massively parallel sequencing analysis of benign melanocytic naevi. Histopathology 2019; 75:29-38. [PMID: 30791119 DOI: 10.1111/his.13843] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/16/2019] [Accepted: 02/18/2019] [Indexed: 12/18/2022]
Abstract
AIMS Melanocytic naevi are benign lesions of the skin or mucosa that may constitute non-obligate precursors of malignant melanoma, particularly when they show lentiginous and dysplastic features. The aim of this study was to investigate the repertoire of somatic genetic alterations in melanocytic naevi. METHODS AND RESULTS DNA extracted from 12 melanocytic naevi and DNA from matching normal tissue were separately microdissected and subjected to targeted massively parallel sequencing of ≥300 cancer genes. A median of 5.5 (range 1-12) non-synonymous somatic mutations were detected, with 10 cases harbouring mutually exclusive BRAF V600E (6/12) or NRAS (4/12) clonal hotspot mutations. One of the two cases lacking BRAF and NRAS mutations was a dysplastic naevus harbouring an HRAS Q61L hotspot mutation. Analysis of the laser-capture microdissected components of a naevus synchronously diagnosed with in-situ and invasive malignant melanoma revealed a truncal, clonal BRAF V600E mutation, and the acquisition of a CDKN2A homozygous deletion in the invasive component, in conjunction with additional clonal mutations affecting NF2, FAT4 and KDR in both in-situ and invasive malignant components. CONCLUSION Melanocytic naevi harbour recurrent BRAF V600E or NRAS hotspot mutations with low mutational burdens. Our findings also show that progression from naevi to malignant melanoma may be driven by the acquisition of additional genetic alterations, including CDKN2A homozygous deletions.
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Affiliation(s)
- John R Lozada
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Felipe C Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David Brown
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Barbara Alemar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Postgraduate Programme in Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Taha Merghoub
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Klaus J Busam
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Allan C Halpern
- Dermatology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, 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
| | - Travis J Hollmann
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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80
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Yadav S, Couch FJ. Germline Genetic Testing for Breast Cancer Risk: The Past, Present, and Future. Am Soc Clin Oncol Educ Book 2019; 39:61-74. [PMID: 31099663 DOI: 10.1200/edbk_238987] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The field of germline genetic testing for breast cancer (BC) risk has evolved substantially in the last decade. The introduction of multigene panel testing (MGPT) led to an urgent need to understand the cancer risk associated with several genes included in the panels. Although the research on understanding the cancer risk associated with mutations in several genes continues, there is also a need to understand the modifying effects of race and ethnicity, family history, and BC pathology on the prevalence of germline mutations and associated BC risk. Furthermore, polygenic risk scores (PRSs) to predict BC risk in patients with or without germline mutations in cancer-predisposition genes are now available for clinical use, although data on the clinical utility of PRSs are lacking. In patients with advanced BC associated with BRCA1/2 mutation, olaparib and talazoparib are now approved for treatment. In addition, molecular profiling studies are being used to clarify the BC tumor biology in mutation carriers to identify potential therapeutic options. In this article, we discuss these advances in the field of germline genetic testing and highlight current limitations and implications for clinical care.
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Affiliation(s)
| | - Fergus J Couch
- 2 Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
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81
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Mandelker D, Kumar R, Pei X, Selenica P, Setton J, Arunachalam S, Ceyhan-Birsoy O, Brown DN, Norton L, Robson ME, Wen HY, Powell S, Riaz N, Weigelt B, Reis-Filho JS. The Landscape of Somatic Genetic Alterations in Breast Cancers from CHEK2 Germline Mutation Carriers. JNCI Cancer Spectr 2019; 3:pkz027. [PMID: 31360903 PMCID: PMC6649818 DOI: 10.1093/jncics/pkz027] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 01/26/2019] [Accepted: 03/25/2019] [Indexed: 11/14/2022] Open
Abstract
Pathogenic germline variants in checkpoint kinase 2 (CHEK2), which plays pivotal roles in DNA damage response and cell cycle regulation, confer an increased breast cancer (BC) risk. Here, we investigated the phenotypic and genomic characteristics of 33 BCs from CHEK2 germline mutation carriers (16 high-risk variants and 17 low-risk p.Ile157Thr variants). CHEK2-associated BCs from patients with high-risk germline variants were largely hormone receptor-positive (87%, 13/15), and 81% (13/16) exhibited loss of heterozygosity (LOH) of the CHEK2 wild-type allele. Conversely, CHEK2-associated BCs from patients with the low-risk p.Ile157Thr variant displayed less-frequent loss of heterozygosity (5/17, 29%) and higher levels of CHEK2 protein expression than those with high-risk germline variants. CHEK2-associated BCs lacked a dominant mutational signature 3, a genomics feature of homologous recombination DNA repair deficiency (HRD). Our findings indicate that CHEK2-associated BCs are generally hormone receptor-positive and lack HRD-related mutational signatures, recapitulating the features of ATM-associated BCs. Specific CHEK2 germline variants may have a distinct impact on tumor biology.
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Affiliation(s)
- Diana Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rahul Kumar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Xin Pei
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jeremy Setton
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sasi Arunachalam
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ozge Ceyhan-Birsoy
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David N Brown
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark E Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hannah Y Wen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Simon Powell
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
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82
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Kraya AA, Maxwell KN, Wubbenhorst B, Wenz BM, Pluta J, Rech AJ, Dorfman LM, Lunceford N, Barrett A, Mitra N, Morrissette JJD, Feldman M, Nayak A, Domchek SM, Vonderheide RH, Nathanson KL. Genomic Signatures Predict the Immunogenicity of BRCA-Deficient Breast Cancer. Clin Cancer Res 2019; 25:4363-4374. [PMID: 30914433 DOI: 10.1158/1078-0432.ccr-18-0468] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 12/08/2018] [Accepted: 03/15/2019] [Indexed: 12/19/2022]
Abstract
PURPOSE Breast cancers with BRCA1/2 alterations have a relatively high mutational load, suggesting that immune checkpoint blockade may be a potential treatment option. However, the degree of immune cell infiltration varies widely, and molecular features contributing to this variability remain unknown. EXPERIMENTAL DESIGN We hypothesized that genomic signatures might predict immunogenicity in BRCA1/2 breast cancers. Using The Cancer Genome Atlas (TCGA) genomic data, we compared breast cancers with (89) and without (770) either germline or somatic BRCA1/2 alterations. We also studied 35 breast cancers with germline BRCA1/2 mutations from Penn using WES and IHC. RESULTS We found that homologous recombination deficiency (HRD) scores were negatively associated with expression-based immune indices [cytolytic index (P = 0.04), immune ESTIMATE (P = 0.002), type II IFN signaling (P = 0.002)] despite being associated with a higher mutational/neoantigen burden, in BRCA1/2 mutant breast cancers. Further, absence of allele-specific loss of heterozygosity (LOH negative; P = 0.01) or subclonality (P = 0.003) of germline and somatic BRCA1/2 mutations, respectively, predicted for heightened cytolytic activity. Gene set analysis found that multiple innate and adaptive immune pathways that converge on NF-κB may contribute to this heightened immunogenicity. IHC of Penn breast cancers demonstrated increased CD45+ (P = 0.039) and CD8+ infiltrates (P = 0.037) and increased PDL1 expression (P = 0.012) in HRD-low or LOH-negative cancers. Triple-negative cancers with low HRD had far greater CD8+ T cells (P = 0.0011) and Perforin 1 expression (P = 0.014) compared with hormone receptor-positive HRD-high cancers. CONCLUSIONS HRD scores and hormone receptor subtype are predictive of immunogenicity in BRCA1/2 breast cancers and may inform the design of optimal immune therapeutic strategies.
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Affiliation(s)
- Adam A Kraya
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kara N Maxwell
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Bradley Wubbenhorst
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Brandon M Wenz
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - John Pluta
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Andrew J Rech
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Liza M Dorfman
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Nicole Lunceford
- Division of Surgical Pathology, Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia Pennsylvania
| | - Amanda Barrett
- Division of Surgical Pathology, Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia Pennsylvania
| | - Nandita Mitra
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jennifer J D Morrissette
- Division of Precision and Computational Diagnostics, Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Michael Feldman
- Division of Surgical Pathology, Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia Pennsylvania.,Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Anupma Nayak
- Division of Surgical Pathology, Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia Pennsylvania
| | - Susan M Domchek
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Basser Center for BRCA, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Robert H Vonderheide
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Basser Center for BRCA, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Katherine L Nathanson
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania. .,Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Basser Center for BRCA, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
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83
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Marshall CH, Sokolova AO, McNatty AL, Cheng HH, Eisenberger MA, Bryce AH, Schweizer MT, Antonarakis ES. Differential Response to Olaparib Treatment Among Men with Metastatic Castration-resistant Prostate Cancer Harboring BRCA1 or BRCA2 Versus ATM Mutations. Eur Urol 2019; 76:452-458. [PMID: 30797618 DOI: 10.1016/j.eururo.2019.02.002] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/05/2019] [Indexed: 01/28/2023]
Abstract
BACKGROUND Poly ADP-ribose polymerase (PARP) inhibitors, such as olaparib, are being explored as a treatment option for metastatic castration-resistant prostate cancer (mCRPC) in men harboring mutations in homologous recombination DNA-repair genes. Whether responses to PARP inhibitors differ according to the affected gene is currently unknown. OBJECTIVE To determine whether responses to PARP inhibitors differ between men with BRCA1/2 and those with ATM mutations. DESIGN, SETTING, AND PARTICIPANTS This was a multicenter retrospective review of 23 consecutive men with mCRPC and pathogenic germline and/or somatic BRCA1/2 or ATM mutations treated with olaparib at three academic sites in the USA. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS The proportion of patients achieving a ≥50% decline in prostate-specific antigen (PSA50 response) was compared using Fisher's exact test. Clinical and radiographic progression-free survival (PFS) and overall survival were estimated using Kaplan-Meier analyses and compared using the log-rank test. RESULTS AND LIMITATIONS The study included two men with BRCA1 mutations, 15 with BRCA2 mutations, and six with ATM mutations. PSA50 responses to olaparib were achieved in 76% (13/17) of men with BRCA1/2 versus 0% (0/6) of men with ATM mutations (Fisher's exact test; p=0.002). Patients with BRCA1/2 mutations had median PFS of 12.3mo versus 2.4mo for those with ATM mutations (hazard ratio 0.17, 95% confidence interval 0.05-0.57; p=0.004). Limitations include the retrospective design and relatively small sample size. CONCLUSIONS Men with mCRPC harboring ATM mutations experienced inferior outcomes to PARP inhibitor therapy compared to those harboring BRCA1/2 mutations. Alternative therapies should be explored for patients with ATM mutations. PATIENT SUMMARY Mutations in BRCA1/2 and ATM genes are common in metastatic prostate cancer. In this study we compared outcomes for men with BRCA1/2 mutations to those for men with ATM mutations being treated with olaparib. We found that men with ATM mutations do not respond as well as men with BRCA1/2 mutations.
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Affiliation(s)
- Catherine H Marshall
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Alexandra O Sokolova
- Division of Medical Oncology, University of WashingtonUSA; Division of Clinical Research, Fred Hutch Cancer Research Center Seattle, Washington, USA
| | | | - Heather H Cheng
- Division of Medical Oncology, University of WashingtonUSA; Division of Clinical Research, Fred Hutch Cancer Research Center Seattle, Washington, USA
| | - Mario A Eisenberger
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Alan H Bryce
- Department of Oncology, Mayo Clinic, Scottsdale, AZ, USA
| | - Michael T Schweizer
- Division of Medical Oncology, University of WashingtonUSA; Division of Clinical Research, Fred Hutch Cancer Research Center Seattle, Washington, USA
| | - Emmanuel S Antonarakis
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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84
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Suwinski P, Ong C, Ling MHT, Poh YM, Khan AM, Ong HS. Advancing Personalized Medicine Through the Application of Whole Exome Sequencing and Big Data Analytics. Front Genet 2019; 10:49. [PMID: 30809243 PMCID: PMC6379253 DOI: 10.3389/fgene.2019.00049] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 01/21/2019] [Indexed: 12/11/2022] Open
Abstract
There is a growing attention toward personalized medicine. This is led by a fundamental shift from the ‘one size fits all’ paradigm for treatment of patients with conditions or predisposition to diseases, to one that embraces novel approaches, such as tailored target therapies, to achieve the best possible outcomes. Driven by these, several national and international genome projects have been initiated to reap the benefits of personalized medicine. Exome and targeted sequencing provide a balance between cost and benefit, in contrast to whole genome sequencing (WGS). Whole exome sequencing (WES) targets approximately 3% of the whole genome, which is the basis for protein-coding genes. Nonetheless, it has the characteristics of big data in large deployment. Herein, the application of WES and its relevance in advancing personalized medicine is reviewed. WES is mapped to Big Data “10 Vs” and the resulting challenges discussed. Application of existing biological databases and bioinformatics tools to address the bottleneck in data processing and analysis are presented, including the need for new generation big data analytics for the multi-omics challenges of personalized medicine. This includes the incorporation of artificial intelligence (AI) in the clinical utility landscape of genomic information, and future consideration to create a new frontier toward advancing the field of personalized medicine.
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Affiliation(s)
- Pawel Suwinski
- Malaysian Genomics Resource Centre Berhad, Kuala Lumpur, Malaysia
| | - ChuangKee Ong
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Serdang, Malaysia.,Centre of Genomics Research, Precision Medicine and Genomics, AstraZeneca UK Limited, London, United Kingdom
| | - Maurice H T Ling
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Serdang, Malaysia
| | - Yang Ming Poh
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Serdang, Malaysia
| | - Asif M Khan
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Serdang, Malaysia.,Graduate School of Medicine, Perdana University, Serdang, Malaysia
| | - Hui San Ong
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Serdang, Malaysia
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85
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Ashley CW, Da Cruz Paula A, Kumar R, Mandelker D, Pei X, Riaz N, Reis-Filho JS, Weigelt B. Analysis of mutational signatures in primary and metastatic endometrial cancer reveals distinct patterns of DNA repair defects and shifts during tumor progression. Gynecol Oncol 2018; 152:11-19. [PMID: 30415991 DOI: 10.1016/j.ygyno.2018.10.032] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/22/2018] [Accepted: 10/23/2018] [Indexed: 10/27/2022]
Abstract
OBJECTIVE Mutational signatures provide insights into the biological processes shaping tumor genomes and may inform patient therapy. We sought to define the mutational signatures of i) endometrioid and serous endometrial carcinomas (ECs), stratified into the four molecular subtypes, ii) uterine carcinosarcomas, and iii) matched primary and metastatic ECs. METHODS Whole-exome sequencing MC3 data from primary endometrioid and serous carcinomas (n = 232) and uterine carcinosarcomas (n = 57) from The Cancer Genome Atlas (TCGA), and matched primary and metastatic ECs (n = 61, 26 patients) were reanalyzed, subjected to mutational signature analysis using deconstructSigs, and correlated with clinicopathologic and genomic data. RESULTS POLE (ultramutated) and MSI (hypermutated) molecular subtypes displayed dominant mutational signatures associated with POLE mutations (15/17 cases) and microsatellite instability (55/65 cases), respectively. Most endometrioid and serous carcinomas of copy-number low (endometrioid) and copy-number high (serous-like) molecular subtypes, and carcinosarcomas displayed a dominant aging-associated signature 1. Only 15% (9/60) of copy-number high (serous-like) ECs had a dominant signature 3 (homologous recombination DNA repair deficiency (HRD)-related), a prevalence significantly lower than that found in high-grade serous ovarian carcinomas (54%, p < 0.001) or basal-like breast cancers (46%, p < 0.001). Shifts from aging- or POLE- to MSI-related mutational processes were observed in the progression from primary to metastatic ECs in a subset of cases. CONCLUSIONS The mutational processes underpinning ECs vary even among tumors of the same TCGA molecular subtype and in the progression from primary to metastatic ECs. Only a minority of copy-number high (serous-like) ECs display genomics features of HRD and would likely benefit from HRD-directed therapies.
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Affiliation(s)
- Charles W Ashley
- Department of Surgery, Gynecology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arnaud Da Cruz Paula
- Department of Surgery, Gynecology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rahul Kumar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Diana Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xin Pei
- Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem Riaz
- Radiation Oncology, 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
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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86
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Lee JY, Schizas M, Geyer FC, Selenica P, Piscuoglio S, Sakr RA, Ng CKY, Carniello JVS, Towers R, Giri DD, de Andrade VP, Papanastasiou AD, Viale A, Harris RS, Solit DB, Weigelt B, Reis-Filho JS, King TA. Lobular Carcinomas In Situ Display Intralesion Genetic Heterogeneity and Clonal Evolution in the Progression to Invasive Lobular Carcinoma. Clin Cancer Res 2018; 25:674-686. [PMID: 30185420 DOI: 10.1158/1078-0432.ccr-18-1103] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 07/26/2018] [Accepted: 08/31/2018] [Indexed: 11/16/2022]
Abstract
PURPOSE Lobular carcinoma in situ (LCIS) is a preinvasive lesion of the breast. We sought to define its genomic landscape, whether intralesion genetic heterogeneity is present in LCIS, and the clonal relatedness between LCIS and invasive breast cancers.Experimental Design: We reanalyzed whole-exome sequencing (WES) data and performed a targeted amplicon sequencing validation of mutations identified in 43 LCIS and 27 synchronous more clinically advanced lesions from 24 patients [9 ductal carcinomas in situ (DCIS), 13 invasive lobular carcinomas (ILC), and 5 invasive ductal carcinomas (IDC)]. Somatic genetic alterations, mutational signatures, clonal composition, and phylogenetic trees were defined using validated computational methods. RESULTS WES of 43 LCIS lesions revealed a genomic profile similar to that previously reported for ILCs, with CDH1 mutations present in 81% of the lesions. Forty-two percent (18/43) of LCIS were found to be clonally related to synchronous DCIS and/or ILCs, with clonal evolutionary patterns indicative of clonal selection and/or parallel/branched progression. Intralesion genetic heterogeneity was higher among LCIS clonally related to DCIS/ILC than in those nonclonally related to DCIS/ILC. A shift from aging to APOBEC-related mutational processes was observed in the progression from LCIS to DCIS and/or ILC in a subset of cases. CONCLUSIONS Our findings support the contention that LCIS has a repertoire of somatic genetic alterations similar to that of ILCs, and likely constitutes a nonobligate precursor of breast cancer. Intralesion genetic heterogeneity is observed in LCIS and should be considered in studies aiming to develop biomarkers of progression from LCIS to more advanced lesions.
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Affiliation(s)
- Ju Youn Lee
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michail Schizas
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Felipe C Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Institute of Pathology and Medical Genetics, University Hospital Basel, Basel, Switzerland
| | - Rita A Sakr
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Institute of Pathology and Medical Genetics, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | - Russell Towers
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dilip D Giri
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Victor P de Andrade
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Agnes Viale
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Reuben S Harris
- Howard Hughes Medical Institute, Masonic Cancer Center, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota
| | - David B Solit
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jorge S Reis-Filho
- 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
| | - Tari A King
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.
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87
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Sehdev A, Gbolahan O, Hancock BA, Stanley M, Shahda S, Wan J, Wu HH, Radovich M, O’Neil BH. Germline and Somatic DNA Damage Repair Gene Mutations and Overall Survival in Metastatic Pancreatic Adenocarcinoma Patients Treated with FOLFIRINOX. Clin Cancer Res 2018; 24:6204-6211. [DOI: 10.1158/1078-0432.ccr-18-1472] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/27/2018] [Accepted: 08/16/2018] [Indexed: 11/16/2022]
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