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Lu Q, Zhou H, Zhang J, Lee K, Chen L, Hong R, Jiang K, Xu F, Xia W, Cao B, Zhang J, Shao K, Sun P, Wang S. Clinicopathological characteristics and genomic profiling of pure mucinous breast cancer. Breast 2024; 76:103760. [PMID: 38896982 PMCID: PMC11231752 DOI: 10.1016/j.breast.2024.103760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 04/21/2024] [Accepted: 06/07/2024] [Indexed: 06/21/2024] Open
Abstract
PURPOSE Pure mucinous breast cancer (PMC) is a rare histological type with a favourable prognosis. However, cases with recurrence have been reported and diagnosed in clinical practice. The mechanisms underlying PMC recurrence remain unknown. In this study, we aimed to identify the prognostic factors associated with PMC. MATERIALS AND METHODS A total of 166 patients diagnosed with PMC were included. We compared the clinicopathological characteristics between patients with and without recurrence. The 21-gene assay was performed in 10 patients with recurrence and 20 TNM stage-matched patients without recurrence. Whole-exon sequencing was performed in 12 PMC primary tumours and four positive lymph nodes (LNs). RESULTS Tumour size, lymph node status and TNM staging differed significantly between recurrent group and non-recurrent group. And the 21-gene recurrence scores did not differ significantly between recurrent group and its TNM stage-matched non-recurrent group. The most frequently mutated genes in the primary tumours of regional LN-positive PMCs were ADCY10 (3/6) and SHANK3 (3/6), and they more recurrently harboured gains of 15q23, 17q23.2 and 20p11.21, and loss of 21p11.2. And these alterations were not detected in primary tumours of regional LN-negative PMCs. CONCLUSION TNM stage is an important prognostic factor in PMC. Although we revealed that regional LN-positive PMCs show increased occurrence of duplication variants at 15q23, 17q23.2 and 20p11.21, and deletion variants at 21p11.2. Further investigation, including multi-omics studies, are needed and may provide additional insights into the nature of PMC.
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Affiliation(s)
- Qianyi Lu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Hanxing Zhou
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Jianwei Zhang
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI-Shenzhen, Shenzhen 518083, PR China
| | - Kaping Lee
- First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510060, PR China
| | - Limin Chen
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Ruoxi Hong
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Kuikui Jiang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Fei Xu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Wen Xia
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Boyang Cao
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI-Shenzhen, Shenzhen 518083, PR China
| | - Jingmin Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China
| | - Kang Shao
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI-Shenzhen, Shenzhen 518083, PR China.
| | - Peng Sun
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China.
| | - Shusen Wang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, PR China.
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2
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Feinberg J, Da Cruz Paula A, da Silva EM, Pareja F, Patel J, Zhu Y, Selenica P, Leitao MM, Abu-Rustum NR, Reis-Filho JS, Joehlin-Price A, Weigelt B. Adenoid cystic carcinoma of the Bartholin's gland is underpinned by MYB- and MYBL1- rearrangements. Gynecol Oncol 2024; 185:58-67. [PMID: 38368814 PMCID: PMC11179993 DOI: 10.1016/j.ygyno.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 02/09/2024] [Indexed: 02/20/2024]
Abstract
OBJECTIVE Adenoid cystic carcinoma (AdCC) of the Bartholin's gland (AdCC-BG) is a very rare gynecologic vulvar malignancy. AdCC-BGs are slow-growing but locally aggressive and are associated with high recurrence rates. Here we sought to characterize the molecular underpinning of AdCC-BGs. METHODS AdCC-BGs (n = 6) were subjected to a combination of RNA-sequencing, targeted DNA-sequencing, reverse-transcription PCR, fluorescence in situ hybridization (FISH) and MYB immunohistochemistry (IHC). Clinicopathologic variables, somatic mutations, copy number alterations and chimeric transcripts were assessed. RESULTS All six AdCC-BGs were biphasic, composed of ductal and myoepithelial cells. Akin to salivary gland and breast AdCCs, three AdCC-BGs had the MYB::NFIB fusion gene with varying breakpoints, all of which were associated with MYB overexpression by IHC. Two AdCC-BGs were underpinned by MYBL1 fusion genes with different gene partners, including MYBL1::RAD51B and MYBL1::EWSR1 gene fusions, and showed MYB protein expression. Although the final AdCC-BG studied had MYB protein overexpression, no gene fusion was identified. AdCC-BGs harbored few additional somatic genetic alterations, and only few mutations in cancer-related genes were identified, including GNAQ, GNAS, KDM6A, AKT1 and BCL2, none of which were recurrent. Two AdCC-BGs, both with a MYB::NFIB fusion gene, developed metastatic disease. CONCLUSIONS AdCC-BGs constitute a convergent phenotype, whereby activation of MYB or MYBL1 can be driven by the MYB::NFIB fusion gene or MYBL1 rearrangements. Our observations further support the notion that AdCCs, irrespective of organ site, constitute a genotypic-phenotypic correlation. Assessment of MYB or MYBL1 rearrangements may be used as an ancillary marker for the diagnosis of AdCC-BGs.
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Affiliation(s)
- Jacqueline Feinberg
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arnaud Da Cruz Paula
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edaise M da Silva
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fresia Pareja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juber Patel
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yingjie Zhu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pier Selenica
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mario M Leitao
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem R Abu-Rustum
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amy Joehlin-Price
- Cleveland Clinic Pathology and Laboratory Medicine Institute, Cleveland, OH, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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3
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Blanco-Heredia J, Souza CA, Trincado JL, Gonzalez-Cao M, Gonçalves-Ribeiro S, Gil SR, Pravdyvets D, Cedeño S, Callari M, Marra A, Gazzo AM, Weigelt B, Pareja F, Vougiouklakis T, Jungbluth AA, Rosell R, Brander C, Tresserra F, Reis-Filho JS, Tiezzi DG, de la Iglesia N, Heyn H, De Mattos-Arruda L. Converging and evolving immuno-genomic routes toward immune escape in breast cancer. Nat Commun 2024; 15:1302. [PMID: 38383522 PMCID: PMC10882008 DOI: 10.1038/s41467-024-45292-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024] Open
Abstract
The interactions between tumor and immune cells along the course of breast cancer progression remain largely unknown. Here, we extensively characterize multiple sequential and parallel multiregion tumor and blood specimens of an index patient and a cohort of metastatic triple-negative breast cancers. We demonstrate that a continuous increase in tumor genomic heterogeneity and distinct molecular clocks correlated with resistance to treatment, eventually allowing tumors to escape from immune control. TCR repertoire loses diversity over time, leading to convergent evolution as breast cancer progresses. Although mixed populations of effector memory and cytotoxic single T cells coexist in the peripheral blood, defects in the antigen presentation machinery coupled with subdued T cell recruitment into metastases are observed, indicating a potent immune avoidance microenvironment not compatible with an effective antitumor response in lethal metastatic disease. Our results demonstrate that the immune responses against cancer are not static, but rather follow dynamic processes that match cancer genomic progression, illustrating the complex nature of tumor and immune cell interactions.
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Affiliation(s)
- Juan Blanco-Heredia
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Carla Anjos Souza
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Juan L Trincado
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
- Josep Carreras Leukemia Research Institute, Barcelona, Spain
| | | | | | - Sara Ruiz Gil
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | | | - Samandhy Cedeño
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain
| | - Maurizio Callari
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Antonio Marra
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrea M Gazzo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fresia Pareja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Theodore Vougiouklakis
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Achim A Jungbluth
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rafael Rosell
- Dexeus Institute of Oncology, Quironsalud Group, Barcelona, Spain
| | - Christian Brander
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain
- ICREA, Passeig de Lluís Companys, 23, Barcelona, Spain
- Universitat de Vic-Universitat Central de Catalunya, Catalunya, Spain
| | | | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Guimarães Tiezzi
- Department of Gynecology and Obstetrics - Breast Disease Division and Laboratory for Translational Data Science, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
- Advanced Research Center in Medicine (CEPAM), Union of the Colleges of the Great Lakes (UNILAGO), São José do Rio Preto, Brazil
| | | | - Holger Heyn
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
- Omniscope, Barcelona, Spain
| | - Leticia De Mattos-Arruda
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain.
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.
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4
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Derakhshan F, Da Cruz Paula A, Selenica P, da Silva EM, Grabenstetter A, Jalali S, Gazzo AM, Dopeso H, Marra A, Brown DN, Ross DS, Mandelker D, Razavi P, Chandarlapaty S, Wen HY, Brogi E, Zhang H, Weigelt B, Pareja F, Reis-Filho JS. Nonlobular Invasive Breast Carcinomas with Biallelic Pathogenic CDH1 Somatic Alterations: A Histologic, Immunophenotypic, and Genomic Characterization. Mod Pathol 2024; 37:100375. [PMID: 37925055 DOI: 10.1016/j.modpat.2023.100375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/25/2023] [Accepted: 10/30/2023] [Indexed: 11/06/2023]
Abstract
CDH1 encodes for E-cadherin, and its loss of function is the hallmark of invasive lobular carcinoma (ILC). Albeit vanishingly rare, biallelic CDH1 alterations may be found in nonlobular breast carcinomas (NL-BCs). We sought to determine the clinicopathologic characteristics and repertoire of genetic alterations of NL-BCs harboring CDH1 biallelic genetic alterations. Analysis of 5842 breast cancers (BCs) subjected to clinical tumor-normal sequencing with an FDA-cleared multigene panel was conducted to identify BCs with biallelic CDH1 pathogenic/likely pathogenic somatic mutations lacking lobular features. The genomic profiles of NL-BCs with CDH1 biallelic genetic alterations were compared with those of ILCs and invasive ductal carcinomas (IDCs), matched by clinicopathologic characteristics. Of the 896 CDH1-altered BCs, 889 samples were excluded based on the diagnosis of invasive mixed ductal/lobular carcinoma or ILC or the detection of monoallelic CDH1 alterations. Only 7 of the 5842 (0.11%) BCs harbored biallelic CDH1 alterations and lacked lobular features. Of these, 4/7 (57%) cases were ER-positive/HER2-negative, 1/7 (14%) was ER-positive/HER2-positive, and 2/7 (29%) were ER-negative/HER2-negative. In total, 5/7 (71%) were of Nottingham grade 2, and 2/7 (29%) were of grade 3. The NL-BCs with CDH1 biallelic genetic alterations included a mucinous carcinoma (n = 1), IDCs with focal nested growth (n = 2), IDC with solid papillary (n = 1) or apocrine (n = 2) features, and an IDC of no special type (NST; n = 1). E-cadherin expression, as detected by immunohistochemistry, was absent (3/5) or aberrant (discontinuous membranous/cytoplasmic/granular; 2/5). However, NL-BCs with CDH1 biallelic genetic alterations displayed recurrent genetic alterations, including TP53, PIK3CA (57%, 4/7; each), FGFR1, and NCOR1 (28%, 2/7, each) alterations. Compared with CDH1 wild-type IDC-NSTs, NL-BCs less frequently harbored GATA3 mutations (0% vs 47%, P = .03), but no significant differences were detected when compared with matched ILCs. Therefore, NL-BCs with CDH1 biallelic genetic alterations are vanishingly rare, predominantly comprise IDCs with special histologic features, and have genomic features akin to luminal B ER-positive BCs.
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Affiliation(s)
- Fatemeh Derakhshan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, 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 and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Edaise M da Silva
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anne Grabenstetter
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sahar Jalali
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrea M Gazzo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Higinio Dopeso
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Antonio Marra
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David N Brown
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dara S Ross
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Diana Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sarat Chandarlapaty
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hannah Y Wen
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Edi Brogi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hong Zhang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Fresia Pareja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; AstraZeneca, Gaithersburg, Maryland
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5
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Vahdatinia M, Derakhshan F, Da Cruz Paula A, Dopeso H, Marra A, Gazzo AM, Brown D, Selenica P, Ross DS, Razavi P, Zhang H, Weigelt B, Wen HY, Brogi E, Reis-Filho JS, Pareja F. KIT genetic alterations in breast cancer. J Clin Pathol 2023; 77:40-45. [PMID: 36323507 PMCID: PMC10151428 DOI: 10.1136/jcp-2022-208611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/12/2022] [Indexed: 01/19/2023]
Abstract
AIMS Activating somatic mutations or gene amplification of KIT result in constitutive activation of its receptor tyrosine kinase, which is targetable in various solid tumours. Here, we sought to investigate the presence of KIT genetic alterations in breast cancer (BC) and characterise the histological and genomic features of these tumours. METHODS A retrospective analysis of 5,575 BCs previously subjected to targeted sequencing using the FDA-authorised Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Targets (MSK-IMPACT) assay was performed to identify BCs with KIT alterations. A histological assessment of KIT-altered BCs was conducted, and their repertoire of genetic alterations was compared with that of BCs lacking KIT genetic alterations, matched for age, histological type, oestrogen receptor/HER2 status and sample type. RESULTS We identified 18 BCs (0.32%), including 9 primary and 9 metastatic BCs, with oncogenic/likely oncogenic genetic alterations affecting KIT, including activating somatic mutations (n=4) or gene amplification (n=14). All KIT-altered BCs were of high histological grade, although no distinctive histological features were observed. When compared with BCs lacking KIT genetic alterations, no distinctive genetic features were identified. In two metastatic KIT-altered BCs in which the matched primary BC had also been analysed by MSK-IMPACT, the KIT mutations were found to be restricted to the metastatic samples, suggesting that they were late events in the evolution of these cancers. CONCLUSIONS KIT genetic alterations are vanishingly rare in BC. KIT-altered BCs are of high grade but lack distinctive histological features. Genetic alterations in KIT might be late events in the evolution and/or progression of BC.
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Affiliation(s)
- Mahsa Vahdatinia
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Fatemeh Derakhshan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Arnaud Da Cruz Paula
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Higinio Dopeso
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Antonio Marra
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Andrea M Gazzo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David Brown
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Pier Selenica
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Dara S Ross
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hong Zhang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hannah Y Wen
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Edi Brogi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Fresia Pareja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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6
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Zhan H, Fineberg S, Podany P, Zeng J, Wang Y, Harigopal M, Singh K. Pathological response in mucinous carcinoma of breast after neoadjuvant therapy - a multi-institutional study. Hum Pathol 2023; 142:15-19. [PMID: 37972873 DOI: 10.1016/j.humpath.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/05/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023]
Abstract
Although mucinous carcinoma (MC) is considered a favorable histologic subtype of invasive breast cancer (BC), a subset of MC is managed with neoadjuvant therapy (NAT). The clinical and pathologic features of MC following NAT are not well characterized. The aim of this study is to characterize pathologic response in patients with MC treated with NAT, including neoadjuvant endocrine therapy (NET), neoadjuvant chemotherapy (NCT), and Herceptin-targeted NCT (H-NCT). We conducted a retrospective cohort study of 28 patients with MC who received preoperative adjuvant therapy followed by resection from three institutions between 2010 and 2020. Demographic and clinical information were retrieved from the medical records. Pathologic review of the post NAT resection specimens was performed including tumor grading, tumor size, staging, residual tumor cellularity, estrogen receptor (ER) and HER2 status. Nine (32 %) patients with ER+/HER2- MC received NET, 8 (29 %) ER+/HER2- MC were treated with NCT only and 11 (39 %) HER2+ MC received HER2-targeted NCT (H-NCT). The HER2+ MC patients were younger (45 vs. 64 years; p = 0.006). The HER2+ MC were of higher grade (p = 0.03) and more likely to be multifocal (p = 0.008). Only 2 of 28 (7 %) MC (both HER2+) showed complete pathologic response with residual acellular mucin pools. Persistent mass-forming mucin pools were present in 26 (93 %) cases. The residual tumor cellularity was markedly reduced (≤5 %) in H-NCT treated MC (11/11, 100 %), followed by NET group (6/9, 67 %) and NCT only group (4/8, 50 %) (p = 0.011). Similarly, a higher rate of pathologic response (pCR/RCB-I) was observed in H-NCT (7/11, 64 %), followed by NET group (5/9, 56 %), and NCT only group (1/7, 13 %) (p = 0.053). Post-therapy, all HER2+ MC were smaller than 2 cm and ypT size was significantly smaller in H-NCT group (11/11, 100 %) versus combined NET (5/9, 55 %) and NCT only groups (4/8, 50 %) (p = 0.029). We conclude that ER-/HER2+ and ER+/HER2-mucinous carcinomas of the breast show robust pathological response to neoadjuvant HER2 targeted and endocrine therapy, respectively. Our findings suggest that MC may show good response to endocrine therapy.
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Affiliation(s)
- Haiying Zhan
- Yale University School of Medicine, Department of Pathology, New Haven, CT, USA
| | - Susan Fineberg
- Montefiore Medical Center, Department of Pathology, New York, NY, USA
| | - Peter Podany
- Yale University School of Medicine, Department of Pathology, New Haven, CT, USA
| | - Jennifer Zeng
- Icahn School of Medicine at Mount Sinai, Department of Pathology, New York, NY, USA
| | - Yihong Wang
- Brown University Rhode Island Hospital, Department of Pathology, RI, USA
| | - Malini Harigopal
- Yale University School of Medicine, Department of Pathology, New Haven, CT, USA
| | - Kamaljeet Singh
- Brown University Women and Infants Hospital of Rhode Island, Department of Pathology, RI, USA.
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7
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Papanastasiou AD, De Filippo MR, Sirinian C, Selenica P, Repanti M, Reis-Filho JS, Weigelt B. Histologic and genomic characterization of a primary mucinous carcinoma of the skin. EJC SKIN CANCER 2023; 1:100011. [PMID: 38274496 PMCID: PMC10810048 DOI: 10.1016/j.ejcskn.2023.100011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Aims Primary skin mucinous carcinoma is a rare sweat gland neoplasm with a high local recurrence rate after conventional excision but a low distant-metastasis rate. The genetic underpinning of skin mucinous carcinoma is presently unknown. Here, we sought to define whether the repertoire of somatic mutations of a primary mucinous carcinoma of the skin would be similar to that of mucinous breast carcinomas, given the histologic similarities between these tumor types. Methods and results The tumor was situated in the dermis and partially involved the subcutaneous fat. Tumor cells were suspended in periodic acid-Schiff diastaseresistant- positive mucin lakes and expressed cytokeratin 7, synaptophysin and estrogen receptor. DNA samples extracted from microdissected tumor and matched normal tissue were subjected to massively parallel sequencing targeting 410 cancer-related genes. The skin mucinous tumor was found to have a low tumor mutation burden, but to harbor a clonal GATA3 frameshift mutation (p. T418Hfs*89) and amplification of FOXA1, genes not uncommonly altered in breast mucinous carcinomas. Conclusions In this primary skin mucinous carcinoma, GATA3 and FOXA1 driver genetic events were identified, consistent with a possible developmental relationship between skin and breast mucinous neoplasms.
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Affiliation(s)
| | - Maria R. De Filippo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chaido Sirinian
- Department of Biomedical Sciences, University of West Attica, Athens, Greece
| | - Pier Selenica
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Repanti
- Department of Pathology, Patras General Hospital, Patras, Greece
| | - Jorge S. Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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8
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Abstract
Breast carcinomas classified based on traditional morphologic assessment provide useful prognostic information. Although morphology is still the gold standard of classification, recent advances in molecular technologies have enabled the classification of these tumors into four distinct subtypes based on its intrinsic molecular profile that provide both predictive and prognostic information. This article describes the association between the different molecular subtypes with the histologic subtypes of breast cancer and illustrates how these subtypes may affect the appearance of tumors on imaging studies.
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Affiliation(s)
- Madhuchhanda Roy
- Department of Pathology and Laboratory Medicine, University of Wisconsin - Madison, B1761 WIMR, 1111 Highland Avenue, Madison, WI 53705, USA.
| | - Amy M Fowler
- Department of Radiology, Section of Breast Imaging and Intervention, University of Wisconsin - Madison, 600 Highland Avenue, Madison, WI 53792-3252, USA; Department of Medical Physics, University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, 600 Highland Avenue, Madison, WI 53792-3252, USA
| | - Gary A Ulaner
- Hoag Family Cancer Institute, 16105 Sand Canyon Avenue, Ste 215, Irvine, CA 92618, USA; Department of Radiology, Department of Translational Genomics, University of Southern California, Los Angeles, CA 90007, USA
| | - Aparna Mahajan
- Department of Pathology and Laboratory Medicine, University of Wisconsin - Madison, B1781 WIMR, 1111 Highland Avenue, Madison, WI 53705, USA
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9
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Thai JN, Lerwill MF, Chou SHS. Spectrum of Mucin-containing Lesions of the Breast: Multimodality Imaging Review with Pathologic Correlation. Radiographics 2023; 43:e230015. [PMID: 37792588 DOI: 10.1148/rg.230015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
Mucin-containing lesions of the breast encompass a wide range of benign and malignant processes. The spectrum of histologic findings includes incidental mucus-filled benign cysts or ducts, mucocele-like lesions (MLLs), mucin-producing ductal carcinoma in situ, and invasive mucinous carcinoma. MLL is characterized by the presence of mucin-containing cysts that are typically associated with extravasated stromal mucin. MLL is often benign but can be associated with epithelial atypia or malignancy. Mucinous carcinoma represents the malignant end of the spectrum of mucinous lesions of the breast. Evidence-based literature supports a conservative approach for benign MLLs without associated atypia or malignancy, reserving excision for those lesions exhibiting such pathologic features. The most common imaging finding for MLL is microcalcifications at mammography. No specific imaging feature is predictive of malignant outcome at surgical excision. Invasive mucinous carcinoma is a heterogeneous breast tumor subtype, as defined according to the World Health Organization criteria. Mucinous carcinomas are categorized into pure (>90% mucinous component) or mixed (10%-90% mucinous component) subtypes. Pure mucinous carcinomas are generally associated with excellent prognosis and survival, with a few exceptions. Mixed mucinous carcinomas do not have the same favorable prognosis and instead behave similarly to invasive breast carcinomas of no special type. Characteristic diagnostic imaging features can be identified for mucinous carcinoma based on its mucinous and nonmucinous contents. ©RSNA, 2023 Online supplemental material is available for this article. Quiz questions for this article are available through the Online Learning Center.
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Affiliation(s)
- Janice N Thai
- From the Department of Radiology, Division of Breast Imaging (J.N.T, S.H.S.C), and Department of Pathology (M.F.L.), Massachusetts General Hospital, Harvard Medical School, 55 Fruit St, Boston, MA 02114
| | - Melinda F Lerwill
- From the Department of Radiology, Division of Breast Imaging (J.N.T, S.H.S.C), and Department of Pathology (M.F.L.), Massachusetts General Hospital, Harvard Medical School, 55 Fruit St, Boston, MA 02114
| | - Shinn-Huey S Chou
- From the Department of Radiology, Division of Breast Imaging (J.N.T, S.H.S.C), and Department of Pathology (M.F.L.), Massachusetts General Hospital, Harvard Medical School, 55 Fruit St, Boston, MA 02114
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10
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Dabbs DJ, Huang RS, Ross JS. Novel markers in breast pathology. Histopathology 2023; 82:119-139. [PMID: 36468266 DOI: 10.1111/his.14770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/07/2022] [Accepted: 08/08/2022] [Indexed: 12/12/2022]
Abstract
Breast pathology is an ever-expanding database of information which includes markers, or biomarkers, that detect or help treat the disease as prognostic or predictive information. This review focuses on these aspects of biomarkers which are grounded in immunohistochemistry, liquid biopsies and next-generation sequencing.
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Affiliation(s)
- David J Dabbs
- PreludeDx, Laguna Hills, CA, USA.,Department of Pathology, University of Pittsburgh, Board Member, CASI (Consortium for Analytical Standardization in Immunohistochemistry), Pittsburgh, PA, USA
| | - Richard S Huang
- Clinical Development, Foundation Medicine, Cambridge, MA, USA
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11
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Silveira C, Sousa AC, Corredeira P, Martins M, Sousa AR, Da Cruz Paula A, Selenica P, Brown DN, Golkaram M, Kaplan S, Zhang S, Liu L, Weigelt B, Reis-Filho JS, Costa L, Carmo-Fonseca M. Comprehensive Genomic Profiling of Cell-Free Circulating Tumor DNA Detects Response to Ribociclib Plus Letrozole in a Patient with Metastatic Breast Cancer. Biomolecules 2022; 12:biom12121818. [PMID: 36551247 PMCID: PMC9775495 DOI: 10.3390/biom12121818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Analysis of cell-free circulating tumor DNA obtained by liquid biopsy is a non-invasive approach that may provide clinically actionable information when conventional tissue biopsy is inaccessible or infeasible. Here, we followed a patient with hormone receptor-positive and human epidermal growth factor receptor (HER) 2-negative breast cancer who developed bone metastases seven years after mastectomy. We analyzed circulating cell-free DNA (cfDNA) extracted from plasma using high-depth massively parallel sequencing targeting 468 cancer-associated genes, and we identified a clonal hotspot missense mutation in the PIK3CA gene (3:178952085, A > G, H1047R) and amplification of the CCND1 gene. Whole-exome sequencing revealed that both alterations were present in the primary tumor. After treatment with ribociclib plus letrozole, the genetic abnormalities were no longer detected in cfDNA. These results underscore the clinical utility of combining liquid biopsy and comprehensive genomic profiling to monitor treatment response in patients with metastasized breast cancer.
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Affiliation(s)
- Catarina Silveira
- GenoMed—Diagnósticos de Medicina Molecular, S.A., Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Ana Carla Sousa
- GenoMed—Diagnósticos de Medicina Molecular, S.A., Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Patrícia Corredeira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Marta Martins
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Ana Rita Sousa
- Serviço de Oncologia Médica, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Centro Académico de Medicina de Lisboa, Avenida Professor Egas Moniz, 1649-035 Lisboa, Portugal
| | - Arnaud Da Cruz Paula
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Pier Selenica
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - David N. Brown
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Mahdi Golkaram
- Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA
| | - Shannon Kaplan
- Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA
| | - Shile Zhang
- Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA
| | - Li Liu
- Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Jorge S. Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Luís Costa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
- Serviço de Oncologia Médica, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Centro Académico de Medicina de Lisboa, Avenida Professor Egas Moniz, 1649-035 Lisboa, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
- Correspondence:
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12
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Soong TR, Dillon DA, Rice-Stitt TL, Wieczorek TJ, Baker GM, Darvishian F, Collins LC, Lester SC, Schnitt SJ, Harrison BT. Invasive lobular carcinoma with extracellular mucin (ILCEM): clinicopathologic and molecular characterization of a rare entity. Mod Pathol 2022; 35:1370-1382. [PMID: 35477749 DOI: 10.1038/s41379-022-01084-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 02/07/2023]
Abstract
Invasive lobular carcinoma with extracellular mucin (ILCEM) is a rare histologic subtype of breast cancer. Little is known about the pathologic or genomic signatures that distinguish ILCEM from classic invasive lobular carcinoma (ILC) or mucinous carcinoma. We studied 17 breast cancers with lobular morphology and extracellular mucin. Thirteen tumors with sufficient tissue for DNA extraction were analyzed by a next generation sequencing (NGS) assay that interrogates 447 genes for mutations and copy number variations (CNVs). Median patient age was 66 yrs (range: 31-77 yrs). Sixteen patients presented with masses, 7 of which were >2 cm. Seven patients had lymph node metastases. The cases of ILCEM were moderately (n = 13) or poorly differentiated (n = 4), frequently exhibiting variant morphology that has not been previously described or emphasized, including grade 3 nuclei (n = 11), diffuse signet ring cells (n = 10), solid growth (n = 4), tumor necrosis (n = 3) or apocrine features (n = 2). All tumors showed absent or reduced membranous E-cadherin expression. Concurrent lobular carcinoma in situ (LCIS) was seen in 11/17 cases, 1 of which was a striking example of signet ring cell LCIS with extracellular mucin. Receptor profiles were ER+/HER2- (n = 15) and ER+/HER2+ (n = 2). With a median follow-up of 83.5 months (range: 3-171 months) in 12 patients with available information, 8 patients had recurrences resulting in 4 cancer-related deaths. The most common CNVs were 16q loss (n = 11) and 1q gain (n = 9). CDH1 gene-level alterations were detected in all but one case, including frameshift (n = 7), nonsense (n = 2), and donor splice site (n = 1) mutations and indels (n = 2). Recurrent mutations were also seen in PIK3CA (n = 3), POLQ (n = 3), TP53 (n = 3), ERBB3 (n = 3), ERBB2 (n = 2), and RUNX1 (n = 2). Genes with recurrent amplifications included GATA3 (n = 4), FOXA1 (n = 3), CCND1 (n = 2). Our data highlights ILCEM as a distinct variant of ILC that often presents with higher-grade and variant morphologic features and is associated with an aggressive clinical course. NGS data support an overall lobular-type molecular profile and reveal potentially targetable alterations in a subset of cases with recurrence.
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Affiliation(s)
- T Rinda Soong
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Deborah A Dillon
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | | | - Tad John Wieczorek
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.,Department of Pathology, Brigham and Women's Faulkner Hospital, Boston, MA, USA
| | - Gabrielle M Baker
- Harvard Medical School, Boston, MA, USA.,Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Farbod Darvishian
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA
| | - Laura C Collins
- Harvard Medical School, Boston, MA, USA.,Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Susan C Lester
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Stuart J Schnitt
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Beth T Harrison
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA. .,Harvard Medical School, Boston, MA, USA.
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13
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Jung M. Mucinous carcinoma of the breast: distinctive histopathologic and genetic characteristics. KOSIN MEDICAL JOURNAL 2022. [DOI: 10.7180/kmj.22.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Mucinous carcinoma is a rare histologic type of breast cancer that, when classified with favorable histology, can be treated with different therapeutic options. This study reviews the histologic findings of mucinous carcinoma that support or exclude favorable histology and emphasizes the necessity of an appropriate gross examination with radiologic findings for an accurate diagnosis. In addition, unusual findings such as micropapillary arrangements and lobular differentiation in mucinous carcinoma and their implications for prognosis and treatment are reviewed. Mucinous carcinoma involves upregulation of MUC2, a mucus-associated gene common in mucinous carcinoma of the breast as well as various other organs. In mucinous carcinoma, the fraction of genome altered and tumor mutation burden are lower than those of invasive carcinoma of no special type, the most common histology of breast cancer. In addition, the genetic alterations found in mucinous carcinoma are diverse, unlike the pathognomonic genetic alterations observed in other histologic types of breast cancer. These genetic features support the importance of conventional microscopic evaluations for the pathologic differential diagnosis of mucinous carcinoma of the breast in routine practice. A variety of breast lesions, including mucinous cystadenocarcinoma and mucocele-like lesions, as well as mucinous carcinoma from other organs, can mimic mucinous carcinoma of the breast. In order to obtain an accurate pathologic diagnosis, careful evaluation of the overall histopathologic characteristics and ancillary testing are required to provide information on appropriate treatment and prognosis.
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14
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Moukarzel LA, Ferrando L, Stylianou A, Lobaugh S, Wu M, Nobre SP, Iasonos A, Zoppoli G, Giri DD, Abu-Rustum NR, Broach VA, Iyengar NM, Weigelt B, Makker V. Impact of obesity and white adipose tissue inflammation on the omental microenvironment in endometrial cancer. Cancer 2022; 128:3297-3309. [PMID: 35793549 PMCID: PMC9976596 DOI: 10.1002/cncr.34356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/09/2022] [Accepted: 05/26/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND A complex relationship between adipose tissue and malignancy, involving an inflammatory response, has been reported. The goal of this work was to assess the prevalence of white adipose tissue (WAT) inflammation in patients with endometrial cancer (EC), and the association with circulating inflammation markers. Furthermore, the aim was to characterize the pathways activated in and the cell type composition of adipose tissue in patients with EC. METHODS Adipose tissue and blood samples were prospectively collected from 101 patients with EC at initial surgery. WAT inflammation was determined based on adipocytes surrounded by macrophages forming crown-like structures. Circulating levels of metabolic syndrome-associated and inflammatory markers were quantified. RNA-sequencing was performed on adipose samples (n = 55); differential gene expression, pathway, and cellular decomposition analyses were performed using state-of-the-art bioinformatics methods. RESULTS WAT inflammation was identified in 46 (45.5%) of 101 EC patients. Dyslipidemia, hypertension, and diabetes mellitus were significantly associated with WAT inflammation (p < .05). WAT inflammation was associated with greater body mass index (p < .001) and higher circulating levels of leptin, high-sensitivity C-reactive protein, and interleukin-6, as well as lower levels of adiponectin and sex hormone-binding globulin (p < .05). Transcriptomic analysis demonstrated increased levels of proinflammatory and pro-neoplastic-related gene expression in inflamed omental adipose tissue. CONCLUSIONS WAT inflammation is associated with metabolic syndrome, obesity, and inflammatory markers, as well as increased expression of proinflammatory and proneoplastic genes.
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Affiliation(s)
- Lea A. Moukarzel
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Lorenzo Ferrando
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Internal Medicine, University of Genoa, Genoa, Italy
| | - Anthe Stylianou
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Stephanie Lobaugh
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michelle Wu
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Silvana Pedra Nobre
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alexia Iasonos
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gabriele Zoppoli
- Department of Internal Medicine, University of Genoa, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Dilip D. Giri
- Department of Pathology, 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
- Department of OB/GYN, Weill Cornell Medical College, New York, NY
| | - Vance A. Broach
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of OB/GYN, Weill Cornell Medical College, New York, NY
| | - Neil M. Iyengar
- Breast Medicine Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Britta Weigelt
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Vicky Makker
- Department of Medicine, Weill Cornell Medical College, New York, NY
- Gynecologic Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
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15
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Kim SH, Basili T, Dopeso H, Cruz Paula AD, Bi R, Bhaloo SI, Pareja F, Li Q, da Silva EM, Zhu Y, Hoang T, Selenica P, Murali R, Chan E, Wu M, Derakhshan F, Maroldi A, Hanlon E, Ferreira CG, Lapa e Silva JR, Abu-Rustum NR, Zamarin D, Chandarlapaty S, Matrai C, Yoon JY, Reis-Filho JS, Park KJ, Weigelt B. Recurrent WWTR1 S89W mutations and Hippo pathway deregulation in clear cell carcinomas of the cervix. J Pathol 2022; 257:635-649. [PMID: 35411948 PMCID: PMC9881397 DOI: 10.1002/path.5910] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/12/2022] [Accepted: 04/06/2022] [Indexed: 01/31/2023]
Abstract
Clear cell carcinoma (CCC) of the cervix (cCCC) is a rare and aggressive type of human papillomavirus (HPV)-negative cervical cancer with limited effective treatment options for recurrent or metastatic disease. Historically, CCCs of the lower genital tract were associated with in utero diethylstilbestrol exposure; however, the genetic landscape of sporadic cCCCs remains unknown. Here we sought to define the molecular underpinning of cCCCs. Using a combination of whole-exome, targeted capture, and RNA-sequencing, we identified pathogenic genetic alterations in the Hippo signaling pathway in 50% (10/20) of cCCCs, including recurrent WWTR1 S89W somatic mutations in 40% (4/10) of the cases harboring mutations in the Hippo pathway. Irrespective of the presence or absence of Hippo pathway genetic alterations, however, all primary cCCCs analyzed in this study (n = 20) harbored features of Hippo pathway deregulation at the transcriptomic and protein levels. In vitro functional analysis revealed that expression of the WWTR1 S89W mutation leads to reduced binding of TAZ to 14-3-3, promoting constitutive nuclear translocation of TAZ and Hippo pathway repression. WWTR1 S89W expression was found to lead to acquisition of oncogenic behavior, including increased proliferation, migration, and colony formation in vitro as well as increased tumorigenesis in vivo, which could be reversed by targeted inhibition of the TAZ/YAP1 complex with verteporfin. Finally, xenografts expressing WWTR1 S89W displayed a shift in tumor phenotype, becoming more infiltrative as well as less differentiated, and were found to be composed of cells with conspicuous cytoplasmic clearing as compared to controls. Our results demonstrate that Hippo pathway alterations are likely drivers of cCCCs and likely contribute to the clear cell phenotype. Therapies targeting this pathway may constitute a new class of treatment for these rare, aggressive tumors. © 2022 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Sarah H. Kim
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Thais Basili
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Higinio Dopeso
- Department of Pathology and Laboratory Medicine, 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
| | - Rui Bi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, PR China
| | - Shirin Issa Bhaloo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fresia Pareja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Qing Li
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edaise M. da Silva
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yingjie Zhu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy Hoang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pier Selenica
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rajmohan Murali
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eric Chan
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michelle Wu
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fatemeh Derakhshan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ana Maroldi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Etta Hanlon
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Carlos Gil Ferreira
- Oncoclinicas Institute for Research and Education, Sao Paulo, Brazil,Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Nadeem R. Abu-Rustum
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dmitriy Zamarin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarat Chandarlapaty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cathleen Matrai
- Department of Pathology, Weill Cornell Medical Center, New York, NY, USA
| | - Ju-Yoon Yoon
- Department of Pathology, St Michael’s Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Jorge S. Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kay J. Park
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Correspondence to: KJ Park or B Weigelt, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA. or:
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Correspondence to: KJ Park or B Weigelt, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA. or:
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16
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Effect of postoperative radiotherapy in women with localized pure mucinous breast cancer after lumpectomy: a population-based study. Radiat Oncol 2022; 17:119. [PMID: 35799256 PMCID: PMC9264504 DOI: 10.1186/s13014-022-02082-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 06/13/2022] [Indexed: 12/03/2022] Open
Abstract
Purpose Pure mucinous breast cancer is a rare subtype of invasive breast cancer with favorable prognosis, in which the effect of postoperative radiotherapy remains unclear. We aimed to investigate the prognostic value of postoperative radiotherapy in women with localized pure mucinous breast cancer after lumpectomy.
Methods We conducted a retrospective cohort study to compare the effectiveness of postoperative radiotherapy (RT) and omitting postoperative radiotherapy (non-RT) in patients with first primary T1-2N0M0 (T ≤ 3 cm) pure mucinous breast cancer who underwent lumpectomy between 1998 and 2015 using the Surveillance, Epidemiology, and End Results (SEER) database. Breast cancer-specific survival (BCSS) was compared between RT and non-RT groups using Kaplan–Meier method and Cox proportional hazards regression model. Propensity score matching (PSM) was carried out to balance cohort baselines. In addition, an exploratory analysis was performed to verify the effectiveness of RT in subgroup patients. Results Of 7832 eligible patients, 5352 (68.3%) underwent lumpectomy with postoperative RT, 2480 (31.7%) received lumpectomy without postoperative RT. The median follow-up duration was 92 months. The median age was 66 years in the RT group and 76 years in the non-RT group.The 15-year BCSS was 94.39% (95% CI, 93.08% to 95.35%) in the RT group versus 91.45%(95% CI, 88.93% to 93.42%) in the non-RT group (P < 0.001). The adjusted hazard ratio for BCSS was 0.64 (95% CI, 0.49 to 0.83; P = 0.001) for RT group versus non-RT group. After propensity score matching, similar results were yielded. Adjuvant RT reduced the 15-year risk of breast cancer death from 7.92% to 6.15% (P = 0.039). The adjusted hazard ratio for BCSS were 0.66 (95%CI, 0.47 to 0.92; P = 0.014) for RT group versus non-RT group. The benefit of RT was well consistent across subgroup patients. Conclusion Among women with T1-2N0M0 (tumor size ≤ 3 cm) pure mucinous breast cancer, the addition of RT after lumpectomy was significantly associated with a reduced incidence of breast cancer death compared with non-RT, and the magnitude of benefit may be modest. This suggests that postoperative RT is recommended in the treatment of localized pure mucinous breast cancer.
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17
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Chevli N, Wang K, Haque W, Schwartz MR, Nangia J, Sasaki J, Farach AM, Hatch SS, Butler EB, Teh BS. Prognostic Impact of Radiation Therapy in Pure Mucinous Breast Carcinoma. Clin Breast Cancer 2022; 22:e807-e817. [DOI: 10.1016/j.clbc.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 06/23/2022] [Accepted: 06/29/2022] [Indexed: 11/03/2022]
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18
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Wu S, Gai JD, Yu XM, Mao X, Jin F. A novel nomogram and risk classification system for predicting lymph node metastasis of breast mucinous carcinoma: A SEER-based study. Cancer Med 2022; 11:4767-4783. [PMID: 35599552 PMCID: PMC9761057 DOI: 10.1002/cam4.4804] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 03/10/2022] [Accepted: 03/25/2022] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Mucinous breast cancer (MBC) is a rare disease, and patients with lymph node metastasis (LNM) have a poor prognosis. We aimed to explore the predictive factors of LNM and to construct a nomogram for predicting the risk of LNM and to identify the suitable axillary surgery for patients with diverse risks. PATIENTS AND METHODS Data were extracted from the Surveillance, Epidemiology, and End Results (SEER) database. Chi-square and rank-sum tests were used to analyze the differences between groups. Survival analysis was performed with Kaplan-Meier curves and log-rank tests. Independent factor identification and nomogram construction were performed with logistic regression analysis. The nomogram was qualified with a discrimination and calibration plot. Propensity score matching was performed to balance the disparities between groups. RESULTS Patients with metastatic lymph nodes have a worse prognosis. Univariate and multivariate analyses indicated that tumor size, grade, and age were independent risk factors for LNM. The nomogram constructed with these three factors can predict the risk of LNM with high accuracy (AUC: 0.767, 95% CI: 0.697-0.838) and good calibration. Based on the nomogram, a risk classification system satisfactorily stratified the patients into 3 groups with diverse risks of LNM. In the low-risk group, there were no significant differences between sentinel lymph node biopsy and no axillary surgery. In the middle- and high-risk groups, both SLNB and axillary lymph node dissection were superior to no axillary surgery, with similar survival benefits. CONCLUSIONS The nomogram based on tumor size, grade, and age could conveniently and accurately predict the risk of LNM in MBC and assist clinicians in optimizing surgical strategies.
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Affiliation(s)
- Shuang‐Ling Wu
- Department of Surgical Oncology and Breast Surgerythe First Affiliated Hospital of China Medical UniversityShenyangChina
| | - Jun Da Gai
- Department of Pathologythe First Affiliated Hospital of China Medical UniversityShenyangChina
| | - Xin Miao Yu
- Department of Surgical Oncology and Breast Surgerythe First Affiliated Hospital of China Medical UniversityShenyangChina
| | - Xiaoyun Mao
- Department of Surgical Oncology and Breast Surgerythe First Affiliated Hospital of China Medical UniversityShenyangChina
| | - Feng Jin
- Department of Surgical Oncology and Breast Surgerythe First Affiliated Hospital of China Medical UniversityShenyangChina
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19
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Kader T, Zethoven M, Gorringe KL. Evaluating statistical approaches to define clonal origin of tumours using bulk DNA sequencing: context is everything. Genome Biol 2022; 23:43. [PMID: 35109903 PMCID: PMC8809045 DOI: 10.1186/s13059-022-02600-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 01/03/2022] [Indexed: 12/19/2022] Open
Abstract
Clonal analysis of tumour sequencing data enables the evaluation of the relationship of histologically distinct synchronous lesions, such as co-existing benign areas, and temporally distinct tumours, such as primary-recurrence comparisons. In this review, we summarise statistical approaches that are commonly employed to define tumour clonal relatedness using data from bulk DNA technologies. We discuss approaches using total copy number, allele-specific copy number and mutation data, and the relative genomic resolution required for analysis and summarise some of the current tools for inferring clonal relationships. We argue that the impact of the biological context is critical in selecting any particular approach, such as the relative genomic complexity of the lesions being compared, and we recommend considering this context before employing any method to a new dataset.
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Affiliation(s)
- Tanjina Kader
- , Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, 3000, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3010, Australia
| | - Magnus Zethoven
- , Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, 3000, Australia
| | - Kylie L Gorringe
- , Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, 3000, Australia.
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3010, Australia.
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20
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Pareja F, Vahdatinia M, Marchio C, Lee SSK, Da Cruz Paula A, Derakhshan F, da Silva EM, Selenica P, Dopeso H, Chandarlapaty S, Wen HY, Vincent-Salomon A, Brogi E, Weigelt B, Reis-Filho JS. Neuroendocrine tumours of the breast: a genomic comparison with mucinous breast cancers and neuroendocrine tumours of other anatomic sites. J Clin Pathol 2022; 75:10-17. [PMID: 33148628 PMCID: PMC8260149 DOI: 10.1136/jclinpath-2020-207052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 01/03/2023]
Abstract
AIMS Breast neuroendocrine tumours (NETs) constitute a rare histologic subtype of oestrogen receptor (ER)-positive breast cancer, and their definition according to the WHO classification was revised in 2019. Breast NETs display histologic and transcriptomic similarities with mucinous breast carcinomas (MuBCs). Here, we sought to compare the repertoire of genetic alterations in breast NETs with MuBCs and NETs from other anatomic origins. METHODS On histologic review applying the new WHO criteria, 18 breast tumours with neuroendocrine differentiation were reclassified as breast NETs (n=10) or other breast cancers with neuroendocrine differentiation (n=8). We reanalysed targeted sequencing or whole-exome sequencing data of breast NETs (n=10), MuBCs type A (n=12) and type B (n=11). RESULTS Breast NETs and MuBCs were found to be genetically similar, harbouring a lower frequency of PIK3CA mutations, 1q gains and 16q losses than ER-positive/HER2-negative breast cancers. 3/10 breast NETs harboured the hallmark features of ER-positive disease (ie, PIK3CA mutations and concurrent 1q gains/16q losses). Breast NETs showed an enrichment of oncogenic/likely oncogenic mutations affecting transcription factors compared with common forms of ER-positive breast cancer and with pancreatic and pulmonary NETs. CONCLUSIONS Breast NETs are heterogeneous and are characterised by an enrichment of mutations in transcription factors and likely constitute a spectrum of entities histologically and genomically related to MuBCs. While most breast NETs are distinct from ER-positive/HER2-negative IDC-NSTs, a subset of breast NETs appears to be genetically similar to common forms of ER-positive breast cancer, suggesting that some breast cancers may acquire neuroendocrine differentiation later in tumour evolution.
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Affiliation(s)
- Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Mahsa Vahdatinia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Caterina Marchio
- Department of Medical Sciences, University of Turin, Turin, Italy,Unit of Pathology, Candiolo Cancer Institute, FPO IRCCS, Candiolo, Italy
| | - Simon S K Lee
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Arnaud Da Cruz Paula
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Fatemeh Derakhshan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Edaise M da Silva
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Higinio Dopeso
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Sarat Chandarlapaty
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Hannah Y Wen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Anne Vincent-Salomon
- Department de Medicine Diagnostique et Theranostique, Institut Curie, Paris, France
| | - Edi Brogi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
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21
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Thennavan A, Beca F, Xia Y, Recio SG, Allison K, Collins LC, Tse GM, Chen YY, Schnitt SJ, Hoadley KA, Beck A, Perou CM. Molecular analysis of TCGA breast cancer histologic types. CELL GENOMICS 2021; 1. [PMID: 35465400 DOI: 10.1016/j.xgen.2021.100067] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Breast cancer is classified into multiple distinct histologic types, and many of the rarer types have limited characterization. Here, we extend The Cancer Genome Atlas Breast Cancer (TCGA-BRCA) dataset with additional histologic type annotations, in a total of 1063 breast cancers. We analyze this extended dataset to define transcriptomic and genomic profiles of six rare special histologic types: cribriform, micropapillary, mucinous, papillary, metaplastic, and invasive carcinoma with medullary pattern. We show the broader applicability of our constructed special histologic type gene signatures in the TCGA Pan-Cancer Atlas dataset with a predictive model that detects mucinous histologic type across cancers of other organ systems. Using a normal mammary cell differentiation score analysis, we order histologic types into a continuum from stem cell-like to luminal progenitor-like to mature luminal-like. Finally, we classify TCGA-BRCA into 12 consensus groups based on integrated genomic and histological features. We present a rich openly accessible resource of histologic and genomic characterization of TCGA-BRCA to enable studies of the range of breast cancers.
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Affiliation(s)
- Aatish Thennavan
- Oral and Craniofacial Biomedicine Program, School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Francisco Beca
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Youli Xia
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Susana Garcia Recio
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kimberly Allison
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura C Collins
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Gary M Tse
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong
| | - Yunn-Yi Chen
- Department of Pathology and Laboratory Medicine, University of California, San Francisco, CA, 94143, USA
| | - Stuart J Schnitt
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School; Breast Oncology Program, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA 02115, USA
| | - Katherine A Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | | | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Department of Pathology & Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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22
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Schwartz CJ, da Silva EM, Marra A, Gazzo AM, Selenica P, Rai VK, Mandelker D, Pareja F, Misyura M, D'Alfonso TM, Brogi E, Drullinsky P, Razavi P, Robson ME, Drago JZ, Wen HY, Zhang L, Weigelt B, Shia J, Reis-Filho JS, Zhang H. Morphological and genomic characteristics of breast cancers occurring in individuals with Lynch Syndrome. Clin Cancer Res 2021; 28:404-413. [PMID: 34667028 DOI: 10.1158/1078-0432.ccr-21-2027] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/11/2021] [Accepted: 10/15/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Lynch syndrome (LS) is defined by germline pathogenic mutations involving DNA Mismatch Repair (MMR) genes and linked with the development of MMR-deficient (MMRd) colon and endometrial cancers. Whether breast cancers (BC) developing in context of LS are causally related to MMR deficiency (MMRd), remains controversial. Thus, we explored the morphological and genomic characteristics of BCs occurring in LS individuals. EXPERIMENTAL DESIGN A retrospective analysis of 20,110 cancer patients who underwent multigene panel genetic testing was performed to identify individuals with a likely pathogenic/pathogenic germline variant in MLH1, MSH2, MSH6 or PMS2 who developed BCs. The histological characteristics and immunohistochemical (IHC) assessment of BCs for MMR proteins and programmed death-ligand 1 (PD-L1) expression were assessed on cases with available materials. DNA samples from paired tumors and blood were sequenced with MSK-IMPACT ({greater than or equal to}468 key cancer genes). MSI status was assessed utilizing MSISensor. Mutational signatures were defined using SigMA. RESULTS 272 LS individuals were identified, 13 (5%) of whom had primary BCs. The majority of BCs (92%) were hormone receptor positive tumors. Five (42%) of 12 BCs displayed loss of MMR proteins by IHC. Four (36%) of 11 BCs subjected to tumor-normal sequencing showed dominant microsatellite instability mutational signatures, high tumor mutational burden and indeterminate (27%) or high MSISensor scores (9%). One patient with metastatic MMRd BC received anti-PD1 therapy and achieved a robust and durable response. CONCLUSIONS A subset of BCs developing in LS individuals are etiologically linked to MMRd and may benefit from anti-PD1/PD-L1 immunotherapy.
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Affiliation(s)
| | | | - Antonio Marra
- Division of Early Drug Development for Innovative Therapies, IEO, European Institute of Oncology IRCCS
| | - Andrea M Gazzo
- Department of Pathology, Memorial Sloan Kettering Cancer Center
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center
| | | | | | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center
| | | | | | - Edi Brogi
- Memorial Sloan Kettering Cancer Center
| | | | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center
| | - Mark E Robson
- Breast Medicine Service, Department of Medicine, Memorial Sloan Kettering Cancer Center
| | | | | | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center
| | | | - Hong Zhang
- Pathology, Memorial Sloan Kettering Cancer Center
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23
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Shakeel M, Khan SA, Mughal AJ, Irfan M, Hoessli DC, Choudhary MI, Aurongzeb M, Khan IA. Distinct genetic landscape and a low response to doxorubicin in a luminal-A breast cancer cell line of Pakistani origin. Mol Biol Rep 2021; 48:6821-6829. [PMID: 34495459 DOI: 10.1007/s11033-021-06681-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/23/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Breast cancers exhibit genetic heterogeneity which causes differential responses to various chemotherapy agents. Given the unique demographic and genomic background in South Asia, genetic architecture in breast cancers is not fully explored. METHODS AND RESULTS In this study, we determined the genetic landscape of our previously established luminal-A subtype breast cancer cell line (BC-PAK1), and compared it with a Caucasian origin MCF7 breast cancer cell line of the same molecular subtype. Deep whole-exome sequencing (100X) was performed from early passages of the primary cancer cells using the Illumina NextSeq500. Data analysis with in silico tools showed novel non-silent somatic mutations previously not described in breast cancers, including a frameshift insertion (p.Ala1591AlafsTer28) in CIC, and a frameshift deletion (p.Lys333LysfsTer21) in PABPC1. Five genes CDC27, PIK3CG, ARAP3, RAPGEF1, and EFNA3, related with cell cycle pathway (hsa04110), ErbB signaling pathway (hsa04012), Ras signaling pathway (hsa04014), and Rap1 signaling pathway (hsa04015) were found to have recurrent non-silent somatic mutations. Further, the major contribution of COSMIC signatures 3 (failure of DNA double-strand break repair by homologous recombination), and 12 (transcriptional strand-bias for T>C substitutions) was observed. Also, the somatic mutations landscape in BC-PAK1 was found to be different as compared to the MCF7 cell line. The unique genetic landscape of BC-PAK1 might be responsible for significantly reduced response to doxorubicin than the MCF7 cell line. CONCLUSION This study presents a distinct genetic architecture in luminal-A breast cancer potentially responsible for differential response to chemotherapy. Further studies on large cohorts of breast cancer patients are suggested for implementation in personalized medicine.
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Affiliation(s)
- Muhammad Shakeel
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, ICCBS, University of Karachi, Karachi, 75270, Pakistan.,Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Salman Ahmed Khan
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, ICCBS, University of Karachi, Karachi, 75270, Pakistan. .,Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan. .,Department of Molecular Medicine, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan.
| | - Anum Jabeen Mughal
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Irfan
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, ICCBS, University of Karachi, Karachi, 75270, Pakistan.,Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Daniel C Hoessli
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - M Iqbal Choudhary
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.,Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Muhammad Aurongzeb
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, ICCBS, University of Karachi, Karachi, 75270, Pakistan.,Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Ishtiaq Ahmad Khan
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, ICCBS, University of Karachi, Karachi, 75270, Pakistan. .,Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
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24
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da Silva EM, Fix DJ, Sebastiao APM, Selenica P, Ferrando L, Kim SH, Stylianou A, Da Cruz Paula A, Pareja F, Smith ES, Zehir A, Konner JA, Cadoo K, Reis-Filho JS, Abu-Rustum NR, Mueller JJ, Weigelt B, Park KJ. Mesonephric and mesonephric-like carcinomas of the female genital tract: molecular characterization including cases with mixed histology and matched metastases. Mod Pathol 2021; 34:1570-1587. [PMID: 33772212 PMCID: PMC8343944 DOI: 10.1038/s41379-021-00799-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/24/2021] [Accepted: 03/02/2021] [Indexed: 12/13/2022]
Abstract
Mesonephric carcinoma of the cervix is a rare tumor derived from Wolffian remnants. Mesonephric-like carcinomas of the ovary and endometrium, while morphologically similar, do not have obvious Wolffian derivation. Here, we sought to characterize the repertoire of genetic alterations in primary mesonephric and mesonephric-like carcinomas, in the distinct histologic components of mixed cases, as well as in matched primary tumors and metastases. DNA from microdissected tumor and normal tissue from mesonephric carcinomas (cervix, n = 8) and mesonephric-like carcinomas (ovarian n = 15, endometrial n = 13) were subjected to sequencing targeting 468 cancer-related genes. The histologically distinct components of four cases with mixed histology and four primary tumors and their matched metastases were microdissected and analyzed separately. Mesonephric-like carcinomas were underpinned by somatic KRAS mutations (25/28, 89%) akin to mesonephric carcinomas (8/8, 100%), but also harbored genetic alterations more frequently reported in Müllerian tumors. Mesonephric-like carcinomas that lacked KRAS mutations harbored NRAS (n = 2, ovary) or BRAF (n = 1, endometrium) hotspot mutations. PIK3CA mutations were identified in both mesonephric-like (8/28, 28%) and mesonephric carcinomas (2/8, 25%). Only mesonephric-like tumors harbored CTNNB1 hotspot (4/28, 14%) and PTEN (3/13, 23%) mutations. Copy number analysis revealed frequent gains of chromosomes 1q and 10 in both mesonephric (87% 1q; 50% chromosome 10) and mesonephric-like tumors (89% 1q; 43% chromosome 10). Chromosome 12 gains were more frequent in ovarian mesonephric-like carcinomas, and losses of chromosome 9 were more frequent in mesonephric than in mesonephric-like carcinomas (both p = 0.01, Fisher's exact test). The histologically distinct components of four mixed cases were molecularly related and shared similar patterns of genetic alterations. The progression from primary to metastatic lesions involved the acquisition of additional mutations, and/or shifts from subclonal to clonal mutations. Our findings suggest that mesonephric-like carcinomas are derived from a Müllerian substrate with differentiation along Wolffian/mesonephric lines.
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Affiliation(s)
- Edaise M da Silva
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel J Fix
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Hackensack University Medical Center, Hackensack, NJ, USA
| | - Ana Paula Martins Sebastiao
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medical Pathology, Federal University of Parana, Curitiba, PR, Brazil
| | - Pier Selenica
- Department of Pathology, 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, Genoa, Italy
| | - Sarah H Kim
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anthe Stylianou
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arnaud Da Cruz Paula
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Evan S Smith
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jason A Konner
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karen Cadoo
- Department of Medicine, 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
| | - Nadeem R Abu-Rustum
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jennifer J Mueller
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Kay J Park
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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25
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MEKK1-dependent activation of the CRL4 complex is important for DNA damage-induced degradation of p21 and DDB2 and cell survival. Mol Cell Biol 2021; 41:e0008121. [PMID: 34251884 PMCID: PMC8462458 DOI: 10.1128/mcb.00081-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cullin-4 ubiquitin ligase (CRL4) complexes are differentially composed and highly dynamic protein assemblies that control many biological processes including the global genome nucleotide excision repair (GG-NER) pathway. Here we identified the kinase mitogen-activated protein kinase kinase kinase 1 (MEKK1) as a novel constitutive interactor of a cytosolic CRL4 complex that disassembles after DNA damage due to the Caspase-mediated cleavage of MEKK1. The kinase activity of MEKK1 was important to trigger auto-ubiquitination of the CRL4 complex by K48- and K63-linked ubiquitin chains. MEKK1 knockdown prohibited DNA damage-induced degradation of the CRL4 component DNA-damage binding protein 2 (DDB2) and the CRL4 substrate p21 and also cell recovery and survival. A ubiquitin replacement strategy revealed a contribution of K63-branched ubiquitin chains for DNA damage-induced DDB2/p21 decay, cell cycle regulation and cell survival. These data might have also implications for cancer, as frequently occurring mutations of MEKK1 might have an impact on genome stability and the therapeutic efficacy of CRL4-dependent immunomodulatory drugs such as thalidomide-derivatives.
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26
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The genomic landscape of carcinomas with mucinous differentiation. Sci Rep 2021; 11:9478. [PMID: 33947930 PMCID: PMC8097060 DOI: 10.1038/s41598-021-89099-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 03/19/2021] [Indexed: 02/07/2023] Open
Abstract
Mucinous carcinomas can arise in any organ with epithelial cells that produce mucus. While mucinous tumors from different organs are histologically similar, it remains to be elucidated whether they share molecular alterations. Here we analyzed a total of 902 patients across six cancer types by comparing mucinous and non-mucinous samples, integrating text mining of pathology reports, gene expression, methylation, mutational and copy-number profiling. We found that, in addition to genes involved in mucin processing and secretion, MUC2 up-regulation is a multi-cancer biomarker of mucinous histology and is regulated by DNA methylation in colorectal, breast and stomach cancer. The majority of carcinomas with mucinous differentiation had fewer DNA copy-number alterations than non-mucinous tumors. The tumor mutational burden was lower in breast and lung with mucinous differentiation compared to their non-mucinous counterparts. We found several differences in the frequency of oncogenic gene and pathway alterations between mucinous and non-mucinous carcinomas, including a lower frequency of p53 pathway alterations in colorectal and lung cancer, and a lower frequency of PI-3-Kinase/Akt pathway alterations in breast and stomach cancer with mucinous differentiation. This study shows that carcinomas with mucinous differentiation originating from different organs share transcriptomic and genomic similarities. These results might pave the way for a more biologically relevant taxonomy for these rare cancers.
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27
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Ashley CW, Da Cruz Paula A, Ferrando L, Gularte-Mérida R, Sebastiao APM, Brown DN, Gazzo AM, Pareja F, Stylianou A, Abu-Rustum NR, Reis-Filho JS, Buehler D, Weisman P, Chiang S, Weigelt B. Genetic characterisation of adult primary pleomorphic uterine rhabdomyosarcoma and comparison with uterine carcinosarcoma. Histopathology 2021; 79:176-186. [PMID: 33527450 DOI: 10.1111/his.14346] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 01/27/2021] [Indexed: 11/28/2022]
Abstract
AIMS To characterise the genetic alterations in adult primary uterine rhabdomyosarcomas (uRMSs) and to investigate whether these tumours are genetically distinct from uterine carcinosarcomas (UCSs). METHODS AND RESULTS Three tumours originally diagnosed as primary adult pleomorphic uRMS were subjected to massively parallel sequencing targeting 468 cancer-related genes and RNA-sequencing. Mutational profiles were compared with those of UCSs (n = 57) obtained from The Cancer Genome Atlas. Sequencing data analyses were performed using validated bioinformatic approaches. Pathogenic TP53 mutations and high levels of genomic instability were detected in the three cases. uRMS1 harboured a likely pathogenic YTHDF2-FOXR1 fusion. uRMS2 harboured a PPP2R1A hotspot mutation and amplification of multiple genes, including WHSC1L1, FGFR1, MDM2, and CCNE1, whereas uRMS3 harboured an FBXW7 hotspot mutation and an ANKRD11 homozygous deletion. Hierarchical clustering of somatic mutations and copy number alterations revealed that these tumours initially diagnosed as pleomorphic uRMSs and UCSs were similar. Subsequent comprehensive pathological re-review of the three uRMSs revealed previously unidentified minute pan-cytokeratin-positive atypical glands in one case (uRMS3), favouring its reclassification as UCS with extensive rhabdomyosarcomatous overgrowth. CONCLUSIONS Adult pleomorphic uRMSs harbour TP53 mutations and high levels of copy number alterations. Our findings underscore the challenge in discriminating between uRMS and UCS with rhabdomyosarcomatous differentiation.
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Affiliation(s)
- Charles W Ashley
- Department of Surgery, 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
| | - Lorenzo Ferrando
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Internal Medicine, University of Genoa, Genoa, Italy
| | - Rodrigo Gularte-Mérida
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ana P M Sebastiao
- 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
| | - Andrea M Gazzo
- 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
| | - Anthe Stylianou
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem R Abu-Rustum
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Darya Buehler
- Department of Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Paul Weisman
- Department of Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Sarah Chiang
- 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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28
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da Silva EM, Selenica P, Vahdatinia M, Pareja F, Da Cruz Paula A, Ferrando L, Gazzo AM, Dopeso H, Ross DS, Bakhteri A, Riaz N, Chandarlapaty S, Razavi P, Norton L, Wen HY, Brogi E, Weigelt B, Zhang H, Reis-Filho JS. TERT promoter hotspot mutations and gene amplification in metaplastic breast cancer. NPJ Breast Cancer 2021; 7:43. [PMID: 33863915 PMCID: PMC8052452 DOI: 10.1038/s41523-021-00250-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/15/2021] [Indexed: 12/22/2022] Open
Abstract
Metaplastic breast cancers (MBCs) are characterized by complex genomes, which seem to vary according to their histologic subtype. TERT promoter hotspot mutations and gene amplification are rare in common forms of breast cancer, but present in a subset of phyllodes tumors. Here, we sought to determine the frequency of genetic alterations affecting TERT in a cohort of 60 MBCs with distinct predominant metaplastic components (squamous, 23%; spindle, 27%; osseous, 8%; chondroid, 42%), and to compare the repertoire of genetic alterations of MBCs according to the presence of TERT promoter hotspot mutations or gene amplification. Forty-four MBCs were subjected to: whole-exome sequencing (WES; n = 27) or targeted sequencing of 341-468 cancer-related genes (n = 17); 16 MBCs were subjected to Sanger sequencing of the TERT promoter, TP53 and selected exons of PIK3CA, HRAS, and BRAF. TERT promoter hotspot mutations (n = 9) and TERT gene amplification (n = 1) were found in 10 of the 60 MBCs analyzed, respectively. These TERT alterations were less frequently found in MBCs with predominant chondroid differentiation than in other MBC subtypes (p = 0.01, Fisher's exact test) and were mutually exclusive with TP53 mutations (p < 0.001, CoMEt). In addition, a comparative analysis of the MBCs subjected to WES or targeted cancer gene sequencing (n = 44) revealed that MBCs harboring TERT promoter hotspot mutations or gene amplification (n = 6) more frequently harbored PIK3CA than TERT wild-type MBCs (n = 38; p = 0.001; Fisher's exact test). In conclusion, TERT somatic genetic alterations are found in a subset of TP53 wild-type MBCs with squamous/spindle differentiation, highlighting the genetic diversity of these cancers.
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Affiliation(s)
- Edaise M da Silva
- 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
| | - Mahsa Vahdatinia
- 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
| | - Lorenzo Ferrando
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Internal Medicine, University of Genoa, Genova, Italy
| | - Andrea M Gazzo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Higinio Dopeso
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dara S Ross
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ariya Bakhteri
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarat Chandarlapaty
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 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
| | - Hong Zhang
- 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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29
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Schultheis AM, de Bruijn I, Selenica P, Macedo GS, da Silva EM, Piscuoglio S, Jungbluth AA, Park KJ, Klimstra DS, Wardelmann E, Hartmann W, Gerharz CD, von Petersdorff M, Buettner R, Reis-Filho JS, Weigelt B. Genomic characterization of small cell carcinomas of the uterine cervix. Mol Oncol 2021; 16:833-845. [PMID: 33830625 PMCID: PMC8847983 DOI: 10.1002/1878-0261.12962] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/06/2021] [Indexed: 12/19/2022] Open
Abstract
Small cell carcinoma (SCC) of the uterine cervix is a rare and aggressive form of neuroendocrine carcinoma, which resembles small cell lung cancer (SCLC) in its histology and poor survival rate. Here, we sought to define the genetic underpinning of SCCs of the uterine cervix and compare their mutational profiles with those of human papillomavirus (HPV)‐positive head and neck squamous cell carcinomas, HPV‐positive cervical carcinomas, and SCLCs using publicly available data. Using a combination of whole‐exome and targeted massively parallel sequencing, we found that the nine uterine cervix SCCs, which were HPV18‐positive (n = 8) or HPV16‐positive (n = 1), harbored a low mutation burden, few copy number alterations, and other than TP53 in two cases no recurrently mutated genes. The majority of mutations were likely passenger missense mutations, and only few affected previously described cancer‐related genes. Using RNA‐sequencing, we identified putative viral integration sites on 18q12.3 and on 8p22 in two SCCs of the uterine cervix. The overall nonsilent mutation rate of uterine cervix SCCs was significantly lower than that of SCLCs, HPV‐driven cervical adeno‐ and squamous cell carcinomas, or HPV‐positive head and neck squamous cell carcinomas. Unlike SCLCs, which are reported to harbor almost universal TP53 and RB1 mutations and a dominant tobacco smoke‐related signature 4, uterine cervix SCCs rarely harbored mutations affecting these genes (2/9, 22% TP53; 0% RB1) and displayed a dominant aging (67%) or APOBEC mutational signature (17%), akin to HPV‐driven cancers, including cervical adeno‐ and squamous cell carcinomas and head and neck squamous cell carcinomas. Taken together, in contrast to SCLCs, which are characterized by highly recurrent TP53 and RB1 alterations, uterine cervix SCCs were positive for HPV leading to inactivation of the suppressors p53 and RB, suggesting that these SCCs are convergent phenotypes.
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Affiliation(s)
- Anne M Schultheis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Pathology, University Hospital Cologne, Germany
| | - Ino de Bruijn
- 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
| | - Gabriel S Macedo
- Department of Pathology, 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
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Visceral Surgery Research Laboratory, Clarunis, Department of Biomedicine, University of Basel, Switzerland
| | - Achim A Jungbluth
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kay J Park
- 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
| | - Eva Wardelmann
- Department of Pathology, University Hospital Muenster, Germany
| | | | | | | | | | - 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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30
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Filippova OT, Selenica P, Pareja F, Vahdatinia M, Zhu Y, Pei X, Riaz N, Long Roche K, Chi DS, Abu-Rustum NR, Ellenson LH, Reis-Filho JS, Zamarin D, Weigelt B. Molecular characterization of high-grade serous ovarian cancers occurring in younger and older women. Gynecol Oncol 2021; 161:545-552. [PMID: 33674143 DOI: 10.1016/j.ygyno.2021.02.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/19/2021] [Indexed: 12/18/2022]
Abstract
OBJECTIVES To determine if the mutational landscapes and genomic features of homologous recombination DNA repair defects (HRD) vary between younger and older patients with high-grade serous ovarian cancer (HGSOC). METHODS Younger and older women were defined as bottom and top age quartiles, respectively. HGSOCs from 15 younger (median 49 years, range 35-53) and 15 older women (median 72 years, range 70-87) were subjected to whole-exome sequencing (WES). For validation, HGSOC WES data were obtained from The Cancer Genome Atlas (TCGA), including 38 younger (median 45 years, range 34-50) and 30 older women (median 74 years, range 68-84). Mutational profiles, BRCA1/2 status, genomic HRD features, and for TCGA cases RNA-sequencing-based HRD transcriptomic signatures were assessed. RESULTS In the institutional cohort, pathogenic germline BRCA1/2 mutations were more frequent in younger (5/15) than older women (0/15, p = 0.042). No somatic BRCA1/2 mutations were identified. HGSOCs from older patients preferentially displayed aging-related mutational signatures and, in contrast to younger patients, harbored CCNE1 amplifications (3/15, 20%). In the TCGA cohort, pathogenic germline BRCA1 (younger 8/38, older 0/30, p = 0.007) but not BRCA2 mutations (young 3/38, older 4/30, p = 0.691) were more frequent in younger patients. Again, no somatic BRCA1/2 mutations were identified. HGSOCs from younger women more frequently displayed genomic features of HRD (all, p < 0.05), a significant HRD gene-signature enrichment, but less frequently CCNE1 amplification (p = 0.05). Immunoreactive CLOVAR subtypes were more common in HGSOCs from younger women, and proliferative subtypes in HGSOCs from older women (p = 0.041). CONCLUSIONS HGSOC patients diagnosed at an older age less frequently harbor pathogenic BRCA1 germline mutations and genomic features of HRD than younger women. Individualized treatment options, particularly pertaining to use of PARP inhibitors, in older women may be warranted.
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Affiliation(s)
- Olga T Filippova
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pier Selenica
- 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
| | - Mahsa Vahdatinia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yingjie Zhu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xin Pei
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kara Long Roche
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dennis S Chi
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem R Abu-Rustum
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lora H Ellenson
- 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
| | - Dmitriy Zamarin
- 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.
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31
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Yim HE, Kim JH, Ahn MS, Jung Y, Roh J, Park SH, Kim TG, Choi JH, Kang SY. Clinicopathological and Molecular Analysis of 45 Cases of Pure Mucinous Breast Cancer. Front Oncol 2021; 10:558760. [PMID: 33732635 PMCID: PMC7956951 DOI: 10.3389/fonc.2020.558760] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 12/30/2020] [Indexed: 11/16/2022] Open
Abstract
Pure mucinous breast carcinoma (PMBC) is characterized by clusters of tumor cells floating in abundant extracellular mucin and can be classified into paucicellular (Type A) and hypercellular (Type B) subtypes. However, the clinicopathological and genomic differences between these two subtypes have not been well characterized. We retrospectively investigated the clinicopathologic features of 45 cases of surgically removed PMBC (31 Type A and 14 Type B). We also performed whole-exome sequencing (WES) in eight cases of PMBC. We found that Type B PMBC occurs at an older age and shows more aggressive clinical behavior than Type A. WES analysis revealed that HYDIN was the most frequently mutated gene in both types of PMBC. Although Type B PMBC showed a tendency toward more frequent genetic alterations, there were no statistically significant differences between the two subtypes in single nucleotide variants or insertions or deletions of bases associated with moderate or high effects. Our results provide additional evidence that PMBCs are clinicopathologically and genetically heterogeneous and lack pathognomonic genetic alterations. Further, Type B PMBC is more frequently associated with lymph node metastasis than Type A.
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Affiliation(s)
- Hyun Ee Yim
- Department of Pathology, Ajou University School of Medicine, Suwon, South Korea
| | - Jang-Hee Kim
- Department of Pathology, Ajou University School of Medicine, Suwon, South Korea
| | - Mi Sun Ahn
- Department of Hematology-Oncology, Ajou University School of Medicine, Suwon, South Korea
| | - Yongsik Jung
- Department of Surgery, Ajou University School of Medicine, Suwon, South Korea
| | - Jin Roh
- Department of Pathology, Ajou University School of Medicine, Suwon, South Korea
| | - So Hyun Park
- Department of Pathology, Ajou University School of Medicine, Suwon, South Korea
| | - Tae-Gyu Kim
- Department of Pathology, Ajou University School of Medicine, Suwon, South Korea
| | - Jin-Hyuk Choi
- Department of Hematology-Oncology, Ajou University School of Medicine, Suwon, South Korea
| | - Seok Yun Kang
- Department of Hematology-Oncology, Ajou University School of Medicine, Suwon, South Korea
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32
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Problematic breast tumors reassessed in light of novel molecular data. Mod Pathol 2021; 34:38-47. [PMID: 33024304 PMCID: PMC8260146 DOI: 10.1038/s41379-020-00693-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 09/17/2020] [Indexed: 02/07/2023]
Abstract
Breast cancer is a vastly heterogeneous disease encompassing a panoply of special histological subtypes. Although rare breast tumors have largely not been investigated systematically in large scale genomics series, recent studies have shed light on the genetic underpinnings of special histologic subtypes of breast cancer. Genomic analyses of estrogen receptor-positive special histologic types of breast cancer have not resulted in the identification of novel pathognomonic genetic alterations in addition to the confirmation of the presence of CDH1 loss-of-function mutations in invasive lobular carcinomas. By contrast, the analyses of triple-negative breast cancers have demonstrated that low-grade triple-negative breast cancers categorically differ from the common forms of high-grade triple-negative disease biologically and phenotypically and are underpinned by specific fusion genes or hotspot mutations. A subset of low-grade triple-negative disease has been shown to harbor highly recurrent if not pathognomonic genetic alterations, such as ETV6-NTRK3 fusion gene in secretory carcinomas, the MYB-NFIB fusion gene, MYBL1 rearrangements or MYB gene amplification in adenoid cystic carcinomas, and HRAS Q61 hotspot mutations coupled with mutations in PI3K pathway genes in estrogen receptor-negative adenomyoepitheliomas. A subset of these pathognomonic genetic alterations (e.g., NTRK1/2/3 fusion genes) now constitute an FDA approved indication for the use of TRK inhibitors in the advanced/metastatic setting. These studies have also corroborated that salivary gland-like tumors of the breast, other than acinic cell carcinomas, harbor the repertoire of somatic genetic alterations detected in their salivary gland counterparts. Reassuringly, the systematic study of special histologic types of breast cancer utilizing state-of-the-art sequencing approaches, rather than rendering pathology obsolete, has actually strengthened the importance of breast cancer histologic typing and is providing additional ancillary markers for the diagnosis of these rare but fascinating entities.
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33
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Chunn LM, Nefcy DC, Scouten RW, Tarpey RP, Chauhan G, Lim MS, Elenitoba-Johnson KSJ, Schwartz SA, Kiel MJ. Mastermind: A Comprehensive Genomic Association Search Engine for Empirical Evidence Curation and Genetic Variant Interpretation. Front Genet 2020; 11:577152. [PMID: 33281875 PMCID: PMC7691534 DOI: 10.3389/fgene.2020.577152] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 10/19/2020] [Indexed: 12/21/2022] Open
Abstract
Design and interpretation of genome sequencing assays in clinical diagnostics and research labs is complicated by an inability to identify information from the medical literature and related databases quickly, comprehensively and reproducibly. This challenge is compounded by the complexity and heterogeneity of nomenclatures used to describe diseases, genes and genetic variants. Mastermind is a widely-used bioinformatic platform of genomic associations that has indexed more than 7.5 M full-text articles and 2.5 M supplemental datasets. It has automatically identified, disambiguated and annotated >6.1 M genetic variants and identified >50 K disease-gene associations. Here, we describe how Mastermind improves the sensitivity and reproducibility of clinical variant interpretation and produces comprehensive genomic landscapes of genetic variants driving pharmaceutical research. We demonstrate an alarmingly high degree of heterogeneity across commercially available panels for hereditary cancer that is resolved by evidence from Mastermind. We further examined the sensitivity of Mastermind for variant interpretation by examining 108 clinically-encountered variants and comparing the results to alternate methods. Mastermind demonstrated a sensitivity of 98.4% compared to 4.4, 45.6, and 37.4% for alternatives PubMed, Google Scholar, and ClinVar, respectively, and a specificity of 98.5% compared to 45.1, 57.6, and 68.8% as well as an increase in content yield of 22.6-, 2.2-, and 2.6-fold. When curated for clinical significance, Mastermind identified more than 4.9-fold more pathogenic variants than ClinVar for representative genes. For structural variants, we compared Mastermind's ability to sensitively identify evidence for 10 representative disease-causing CNVs versus results identified in PubMed, as well as its ability to identify evidence for fusion events compared to COSMIC. Mastermind demonstrated a 4.0- to 43.9-fold increase in references for specific CNVs compared to PubMed, as well as 5.4-fold more fusion genes when compared with COSMIC's curated database. Additionally, Mastermind produced an 8.0-fold increase in reference citations for fusion events common to Mastermind and outside databases. Taken together, these results demonstrate the utility and superiority of Mastermind in terms of both sensitivity and specificity of automated results for clinical diagnostic variant interpretation for multiple genetic variant types and highlight the potential benefit in informing pharmaceutical research.
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Affiliation(s)
| | | | | | - Ryan P. Tarpey
- The Johns Hopkins Hospital, Department of Pharmacy, Baltimore, MD, United States
| | | | - Megan S. Lim
- Division of Hematopathology, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Kojo S. J. Elenitoba-Johnson
- Division of Precision and Computational Diagnostics, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, United States
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34
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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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35
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Dessources K, Da Cruz Paula A, Pareja F, Stylianou A, Cybulska P, Farmanbar A, Chandarlapaty S, Abu-Rustum NR, Reis-Filho JS, Weigelt B, Mueller JJ. Acquisition of APOBEC Mutagenesis and Microsatellite Instability Signatures in the Development of Brain Metastases in Low-Grade, Early-Stage Endometrioid Endometrial Carcinoma. JCO Precis Oncol 2020; 4:PO.20.00044. [PMID: 33163849 PMCID: PMC7608574 DOI: 10.1200/po.20.00044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2020] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anthe Stylianou
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Paulina Cybulska
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Amir Farmanbar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sarat Chandarlapaty
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 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
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36
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Mucinous carcinoma with micropapillary features is morphologically, clinically and genetically distinct from pure mucinous carcinoma of breast. Mod Pathol 2020; 33:1945-1960. [PMID: 32358590 DOI: 10.1038/s41379-020-0554-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/05/2020] [Accepted: 04/05/2020] [Indexed: 12/14/2022]
Abstract
Micropapillary features are seen in pure mucinous carcinoma of breast (PMC), which is termed mucinous carcinoma with micropapillary features (MPMC). However, whether MPMC can be identified as a morphologically, clinically or genetically distinct entity from PMC remains controversial. In this study, a retrospective review of 161 cases of breast mucinous carcinoma was conducted to assess the clinicopathologic features, prognostic implications, and genomic alterations of MPMC and PMC. MPMCs were identified in 32% of mucinous carcinomas showing an excellent interobserver agreement (ICC = 0.922). MPMCs occurred at a younger age and exhibited higher nuclear grade, more frequent lymph nodal metastasis, lymphovascular invasion, and HER2 amplification compared with PMCs. Survival analyses revealed that MPMCs show decreased progression-free survival compared with PMCs in both unmatched and matched cohorts. A similar outcome of distant disease-free survival was observed only in the unmatched cohort. However, no statistical difference in recurrence score was observed between MPMC and PMC using a 21-gene assay. Notably, both MPMCs and PMCs displayed low mutation burden, common mutations affecting TTN, GATA3, SF3B1, TP53, recurrent 6q14.1-q27 losses, and 8p11.21-q24.3 gains. GATA3, TP53, and SF3B1 were recurrently mutated in MPMCs, while PIK3CA mutations were exclusively detected in PMCs. Moreover, MPMCs harbored 17q and 20q gains as well as 17p losses, while PMCs displayed gains at 6p. PI3K-Akt, mTOR, ErbB, and focal adhesion pathways were more frequently deregulated in MPMCs than in PMCs, which may responsible for the aggressive tumor behavior of MPMCs. Our findings suggest that MPMC is morphologically, clinically, and genetically distinct from PMC.
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37
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Lu K, Wang X, Zhang W, Ye H, Lao L, Zhou X, Yao S, Lv F. Clinicopathological and genomic features of breast mucinous carcinoma. Breast 2020; 53:130-137. [PMID: 32781417 PMCID: PMC7419658 DOI: 10.1016/j.breast.2020.07.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/26/2020] [Accepted: 07/28/2020] [Indexed: 12/31/2022] Open
Abstract
Introduction Mucinous carcinoma (MC) of the breast is a special histological type of breast cancer. Clinicopathological characteristics and genomic features of MC is not fully understood. Materials and methods 186,497 primary breast cancer patients from SEER database diagnosed with invasive ductal carcinoma (IDC) or MC were included. 801 primary IDC or MC patients from TCGA cohort were included for transcriptomic and genomic analysis. Results MC patients were older, had lower tumor grade and T and N stage, higher hormone receptor positive proportions and lower HER2 positive proportions than IDC patients. Kaplan-Meier plots showed that the breast cancer-specific survival (BCSS) of MC patients was significantly better than IDC patients (P < 0.001). However, after adjusting for clinicopathological factors, survival advantage of MC disappeared. In terms of genomic features of MC, representative upregulated genes of MC in transcriptomic level were MUC2, TFF1 and CARTPT. Upregulated pathways of MC included neurotransmitter-related pathways. Moreover, MC was featured by the amplification of 6p25.2, 6q12 and 11q12.3. Conclusion MC is a distinct histological subtype compared with IDC in terms of clinicopathological characteristics and genomic features. Further investigation need to be conducted to explore the formation of this specific histological subtype. Mucinous breast carcinoma is a distinct histological subtype with better prognosis. The clinicopathological characteristics of mucinous breast carcinoma contributed to its good prognosis. Transcriptomic and genomic features of mucinous breast carcinoma contributed to its formation.
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Affiliation(s)
- Kebin Lu
- Department of General Surgery, Yuyao People's Hospital of Zhejiang Province, Yuyao, Zhejiang, 315400, PR China
| | - Xiao'e Wang
- Department of General Surgery, Yuyao People's Hospital of Zhejiang Province, Yuyao, Zhejiang, 315400, PR China
| | - Wenyuan Zhang
- Department of General Surgery, Yuyao People's Hospital of Zhejiang Province, Yuyao, Zhejiang, 315400, PR China
| | - Hui Ye
- Department of General Surgery, Yuyao People's Hospital of Zhejiang Province, Yuyao, Zhejiang, 315400, PR China
| | - Lingling Lao
- Department of General Surgery, Yuyao People's Hospital of Zhejiang Province, Yuyao, Zhejiang, 315400, PR China
| | - Xiaodong Zhou
- Department of General Surgery, Yuyao People's Hospital of Zhejiang Province, Yuyao, Zhejiang, 315400, PR China
| | - Sijie Yao
- Department of General Surgery, Yuyao People's Hospital of Zhejiang Province, Yuyao, Zhejiang, 315400, PR China
| | - Feng Lv
- Department of General Surgery, Yuyao People's Hospital of Zhejiang Province, Yuyao, Zhejiang, 315400, PR China.
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38
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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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39
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Weis-Banke SE, Lerdrup M, Kleine-Kohlbrecher D, Mohammad F, Sidoli S, Jensen ON, Yanase T, Nakamura T, Iwase A, Stylianou A, Abu-Rustum NR, Aghajanian C, Soslow R, Da Cruz Paula A, Koche RP, Weigelt B, Christensen J, Helin K, Cloos PAC. Mutant FOXL2 C134W Hijacks SMAD4 and SMAD2/3 to Drive Adult Granulosa Cell Tumors. Cancer Res 2020; 80:3466-3479. [PMID: 32641411 DOI: 10.1158/0008-5472.can-20-0259] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/26/2020] [Accepted: 06/30/2020] [Indexed: 12/11/2022]
Abstract
The mutant protein FOXL2C134W is expressed in at least 95% of adult-type ovarian granulosa cell tumors (AGCT) and is considered to be a driver of oncogenesis in this disease. However, the molecular mechanism by which FOXL2C134W contributes to tumorigenesis is not known. Here, we show that mutant FOXL2C134W acquires the ability to bind SMAD4, forming a FOXL2C134W/SMAD4/SMAD2/3 complex that binds a novel hybrid DNA motif AGHCAHAA, unique to the FOXL2C134W mutant. This binding induced an enhancer-like chromatin state, leading to transcription of nearby genes, many of which are characteristic of epithelial-to-mesenchymal transition. FOXL2C134W also bound hybrid loci in primary AGCT. Ablation of SMAD4 or SMAD2/3 resulted in strong reduction of FOXL2C134W binding at hybrid sites and decreased expression of associated genes. Accordingly, inhibition of TGFβ mitigated the transcriptional effect of FOXL2C134W. Our results provide mechanistic insight into AGCT pathogenesis, identifying FOXL2C134W and its interaction with SMAD4 as potential therapeutic targets to this condition. SIGNIFICANCE: FOXL2C134W hijacks SMAD4 and leads to the expression of genes involved in EMT, stemness, and oncogenesis in AGCT, making FOXL2C134W and the TGFβ pathway therapeutic targets in this condition. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/17/3466/F1.large.jpg.
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Affiliation(s)
- Stine E Weis-Banke
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen N, Denmark.,The Novo Nordisk Foundation Center for Stem Cell Research (DanStem), University of Copenhagen, Copenhagen N, Denmark
| | - Mads Lerdrup
- Center for Chromosome Stability, University of Copenhagen, Copenhagen N, Denmark
| | - Daniela Kleine-Kohlbrecher
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen N, Denmark.,The Novo Nordisk Foundation Center for Stem Cell Research (DanStem), University of Copenhagen, Copenhagen N, Denmark
| | - Faizaan Mohammad
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen N, Denmark.,The Novo Nordisk Foundation Center for Stem Cell Research (DanStem), University of Copenhagen, Copenhagen N, Denmark
| | - Simone Sidoli
- Department of Biochemistry and Molecular Biology, VILLUM Centre for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark.,Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, VILLUM Centre for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Toshihiko Yanase
- Seiwakai Muta Hospital, 3-9-1 Hoshikuma, Sawara-ku, Fukuoka, Japan
| | - Tomoko Nakamura
- Departments of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Akira Iwase
- Department of Obstetrics and Gynecology, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan
| | - Anthe Stylianou
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nadeem R Abu-Rustum
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Carol Aghajanian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Robert Soslow
- 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
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jesper Christensen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen N, Denmark.,The Novo Nordisk Foundation Center for Stem Cell Research (DanStem), University of Copenhagen, Copenhagen N, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen N, Denmark. .,The Novo Nordisk Foundation Center for Stem Cell Research (DanStem), University of Copenhagen, Copenhagen N, Denmark.,Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paul A C Cloos
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen N, Denmark. .,The Novo Nordisk Foundation Center for Stem Cell Research (DanStem), University of Copenhagen, Copenhagen N, Denmark
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40
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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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41
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Savage P, Pacis A, Kuasne H, Liu L, Lai D, Wan A, Dankner M, Martinez C, Muñoz-Ramos V, Pilon V, Monast A, Zhao H, Souleimanova M, Annis MG, Aguilar-Mahecha A, Lafleur J, Bertos NR, Asselah J, Bouganim N, Petrecca K, Siegel PM, Omeroglu A, Shah SP, Aparicio S, Basik M, Meterissian S, Park M. Chemogenomic profiling of breast cancer patient-derived xenografts reveals targetable vulnerabilities for difficult-to-treat tumors. Commun Biol 2020; 3:310. [PMID: 32546838 PMCID: PMC7298048 DOI: 10.1038/s42003-020-1042-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 05/26/2020] [Indexed: 02/08/2023] Open
Abstract
Subsets of breast tumors present major clinical challenges, including triple-negative, metastatic/recurrent disease and rare histologies. Here, we developed 37 patient-derived xenografts (PDX) from these difficult-to-treat cancers to interrogate their molecular composition and functional biology. Whole-genome and transcriptome sequencing and reverse-phase protein arrays revealed that PDXs conserve the molecular landscape of their corresponding patient tumors. Metastatic potential varied between PDXs, where low-penetrance lung micrometastases were most common, though a subset of models displayed high rates of dissemination in organotropic or diffuse patterns consistent with what was observed clinically. Chemosensitivity profiling was performed in vivo with standard-of-care agents, where multi-drug chemoresistance was retained upon xenotransplantation. Consolidating chemogenomic data identified actionable features in the majority of PDXs, and marked regressions were observed in a subset that was evaluated in vivo. Together, this clinically-annotated PDX library with comprehensive molecular and phenotypic profiling serves as a resource for preclinical studies on difficult-to-treat breast tumors.
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Affiliation(s)
- Paul Savage
- Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montréal, QC, H3A 1A3, Canada.,Department of Medicine, McGill University, Montréal, QC, H4A 3J1, Canada
| | - Alain Pacis
- Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montréal, QC, H3A 1A3, Canada.,Canadian Centre for Computational Genomics, McGill University and Genome Quebec Innovation Centre, Montréal, QC, H3A 0G1, Canada
| | - Hellen Kuasne
- Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montréal, QC, H3A 1A3, Canada
| | - Leah Liu
- Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montréal, QC, H3A 1A3, Canada
| | - Daniel Lai
- Department of Molecular Oncology, British Columbia Cancer Research Centre, University of British Columbia, Vancouver, BC, V5Z 1L3, Canada
| | - Adrian Wan
- Department of Molecular Oncology, British Columbia Cancer Research Centre, University of British Columbia, Vancouver, BC, V5Z 1L3, Canada
| | - Matthew Dankner
- Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montréal, QC, H3A 1A3, Canada.,Department of Medicine, McGill University, Montréal, QC, H4A 3J1, Canada
| | - Constanza Martinez
- Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montréal, QC, H3A 1A3, Canada.,Department of Pathology, McGill University, Montréal, QC, H4A 3J1, Canada
| | - Valentina Muñoz-Ramos
- Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montréal, QC, H3A 1A3, Canada
| | - Virginie Pilon
- Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montréal, QC, H3A 1A3, Canada
| | - Anie Monast
- Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montréal, QC, H3A 1A3, Canada
| | - Hong Zhao
- Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montréal, QC, H3A 1A3, Canada
| | - Margarita Souleimanova
- Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montréal, QC, H3A 1A3, Canada
| | - Matthew G Annis
- Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montréal, QC, H3A 1A3, Canada
| | | | - Josiane Lafleur
- Lady Davis Research Institute, Jewish General Hospital, Montréal, QC, H3T 1E2, Canada
| | - Nicholas R Bertos
- Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montréal, QC, H3A 1A3, Canada
| | - Jamil Asselah
- Department of Oncology, McGill University, Montréal, QC, H4A 3T2, Canada
| | - Nathaniel Bouganim
- Department of Oncology, McGill University, Montréal, QC, H4A 3T2, Canada
| | - Kevin Petrecca
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, H3A 2B4, Canada
| | - Peter M Siegel
- Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montréal, QC, H3A 1A3, Canada.,Department of Medicine, McGill University, Montréal, QC, H4A 3J1, Canada
| | - Atilla Omeroglu
- Department of Pathology, McGill University, Montréal, QC, H4A 3J1, Canada
| | - Sohrab P Shah
- Department of Molecular Oncology, British Columbia Cancer Research Centre, University of British Columbia, Vancouver, BC, V5Z 1L3, Canada.,Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Samuel Aparicio
- Department of Molecular Oncology, British Columbia Cancer Research Centre, University of British Columbia, Vancouver, BC, V5Z 1L3, Canada
| | - Mark Basik
- Lady Davis Research Institute, Jewish General Hospital, Montréal, QC, H3T 1E2, Canada.,Department of Surgery, Jewish General Hospital, Montréal, QC, H3T 1E2, Canada
| | - Sarkis Meterissian
- Department of Surgery, McGill University Health Centre, Montréal, QC, H4A 3J1, Canada
| | - Morag Park
- Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montréal, QC, H3A 1A3, Canada. .,Department of Medicine, McGill University, Montréal, QC, H4A 3J1, Canada. .,Department of Pathology, McGill University, Montréal, QC, H4A 3J1, Canada. .,Department of Biochemistry, McGill University, Montréal, QC, H3A 1A3, Canada.
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Pleomorphic adenomas and mucoepidermoid carcinomas of the breast are underpinned by fusion genes. NPJ Breast Cancer 2020; 6:20. [PMID: 32550265 PMCID: PMC7275089 DOI: 10.1038/s41523-020-0164-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/08/2020] [Indexed: 12/16/2022] Open
Abstract
Primary pleomorphic adenomas (PAs) and mucoepidermoid carcinomas (MECs) of the breast are vanishingly rare. Here we sought to determine whether breast PAs and MECs would be underpinned by the fusion genes reported to occur in their salivary gland counterparts. Our study included three breast PAs and one breast MEC, which were subjected to RNA sequencing (PAs, n = 2; MEC, n = 1) or to Archer FusionPlex sequencing (PA, n = 1). Our analyses revealed the presence of the HMGA2-WIF1 fusion gene in breast PA3, the CTNNB1-PLAG1 fusion gene in breast PA2, and the CRTC1-MAML2 fusion gene in the breast MEC analyzed (1/1). No oncogenic fusion genes were detected in breast PA1, and no additional oncogenic fusion genes were detected in the cases studied. The presence of the fusion genes identified was validated by fluorescence in situ hybridization (n = 1), reverse transcription-PCR (n = 1), or by both methods (n = 1). Taken together, our findings indicate that PAs and MECs arising in the breast resemble their salivary gland counterparts not only phenotypically but also at the genetic level. Furthermore, our data suggest that the molecular analysis of breast PAs and MECs might constitute a useful tool to aid in their differential diagnosis.
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Jiménez-Sánchez A, Cybulska P, Mager KL, Koplev S, Cast O, Couturier DL, Memon D, Selenica P, Nikolovski I, Mazaheri Y, Bykov Y, Geyer FC, Macintyre G, Gavarró LM, Drews RM, Gill MB, Papanastasiou AD, Sosa RE, Soslow RA, Walther T, Shen R, Chi DS, Park KJ, Hollmann T, Reis-Filho JS, Markowetz F, Beltrao P, Vargas HA, Zamarin D, Brenton JD, Snyder A, Weigelt B, Sala E, Miller ML. Unraveling tumor-immune heterogeneity in advanced ovarian cancer uncovers immunogenic effect of chemotherapy. Nat Genet 2020; 52:582-593. [PMID: 32483290 PMCID: PMC8353209 DOI: 10.1038/s41588-020-0630-5] [Citation(s) in RCA: 128] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 04/20/2020] [Indexed: 02/07/2023]
Abstract
In metastatic cancer, the degree of heterogeneity of the tumor microenvironment (TME) and its molecular underpinnings remain largely unstudied. To characterize the tumor-immune interface at baseline and during neoadjuvant chemotherapy (NACT) in high-grade serous ovarian cancer (HGSOC), we performed immunogenomic analysis of treatment-naive and paired samples from before and after treatment with chemotherapy. In treatment-naive HGSOC, we found that immune-cell-excluded and inflammatory microenvironments coexist within the same individuals and within the same tumor sites, indicating ubiquitous variability in immune cell infiltration. Analysis of TME cell composition, DNA copy number, mutations and gene expression showed that immune cell exclusion was associated with amplification of Myc target genes and increased expression of canonical Wnt signaling in treatment-naive HGSOC. Following NACT, increased natural killer (NK) cell infiltration and oligoclonal expansion of T cells were detected. We demonstrate that the tumor-immune microenvironment of advanced HGSOC is intrinsically heterogeneous and that chemotherapy induces local immune activation, suggesting that chemotherapy can potentiate the immunogenicity of immune-excluded HGSOC tumors.
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Affiliation(s)
- Alejandro Jiménez-Sánchez
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
- Department of Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paulina Cybulska
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Simon Koplev
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Oliver Cast
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | | | - Danish Memon
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ines Nikolovski
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yousef Mazaheri
- Department of Medical Physics and Radiology, Memorial Sloan Kettering Cancer Centre, New York, NY, USA
| | - Yonina Bykov
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Felipe C Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Geoff Macintyre
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
- Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Lena Morrill Gavarró
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Ruben M Drews
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Michael B Gill
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | | | - Ramon E Sosa
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert A Soslow
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tyler Walther
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ronglai Shen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dennis S Chi
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kay J Park
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Travis Hollmann
- 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
| | - Florian Markowetz
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Dmitriy Zamarin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Alexandra Snyder
- 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
| | - Evis Sala
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Radiology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Martin L Miller
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK.
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44
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Ginter PS, Tang X, Shin SJ. A review of mucinous lesions of the breast. Breast J 2020; 26:1168-1178. [PMID: 32419267 DOI: 10.1111/tbj.13878] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 11/28/2022]
Abstract
Mucinous lesions of the breast include a variety of benign and malignant epithelial processes that display intracytoplasmic or extracellular mucin, including mucocele-like lesions, mucinous carcinoma, solid papillary carcinoma, and other rare subtypes of mucin-producing carcinoma. The finding of free-floating or stromal mucin accumulations is a diagnostic challenge of which the significance depends on the clinical, radiologic, and pathologic context. This article emphasizes the differential diagnosis between benign and malignant mucin-producing lesions, with a brief consideration of potential mimics, such as biphasic and mesenchymal lesions with associated with mucinous, myxoid, or matrix material.
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Affiliation(s)
- Paula S Ginter
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Xiaoyu Tang
- Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, NY, USA
| | - Sandra J Shin
- Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, NY, USA
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45
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Muller KE, Marotti JD. Genotype-phenotype associations in breast pathology: Achievements of the past quarter century. Breast J 2020; 26:1123-1131. [PMID: 32367572 DOI: 10.1111/tbj.13861] [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: 09/11/2019] [Accepted: 09/18/2019] [Indexed: 12/27/2022]
Abstract
The first genotype-phenotype relationship in breast pathology developed in 1994 with the discovery of the CDH1 gene. This finding eventually provided biological insight into the characteristic morphology of invasive lobular carcinoma. Subsequent investigative efforts have uncovered additional molecular alterations largely responsible for the histology of several breast neoplasms including secretory carcinoma, adenoid cystic carcinoma, tall cell carcinoma with reversed polarity, fibroepithelial lesions, and most recently, adenomyoepithelioma. Evaluation of the genomic landscape of other special types of breast cancer with distinctive growth patterns, such as invasive mucinous carcinoma, have yet to uncover recurring cytogenetic and/or molecular alterations. Despite the lack of a hallmark alteration in mucinous carcinoma, it is important to note the relative decrease in PIK3CA mutations compared with invasive carcinoma of no special type. In this review, we describe the clinical and pathologic features of breast tumors with recognized genotype-phenotype correlations and summarize the molecular alterations of mucinous carcinoma.
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Affiliation(s)
- Kristen E Muller
- Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Jonathan D Marotti
- Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
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46
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Ban Y, Fischer JV, Maniar KP, Guo H, Zeng C, Li Y, Zhang Q, Wang X, Zhang W, Bulun SE, Wei JJ. Whole-Genome Sequencing and Target Validation Analysis of Müllerian Adenosarcoma: A Tumor With Complex but Specific Genetic Alterations. Front Oncol 2020; 10:538. [PMID: 32351899 PMCID: PMC7174971 DOI: 10.3389/fonc.2020.00538] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/25/2020] [Indexed: 12/16/2022] Open
Abstract
Mullerian adenosarcoma (MAS) is a biphasic tumor with malignant stroma. It is most commonly of endometrial origin but occasionally originates in the cervix, ovary, or other pelvic/peritoneal sites. The typical MAS is low grade with an indolent clinical course; however, tumors with sarcomatous overgrowth (SO) or a high-grade sarcoma tend to be aggressive. Tumor etiology is largely unknown. To better understand the global genome alterations and gene mutations in MAS, whole-genome sequencing (WGS) and target validation analysis were performed. MAS showed remarkable chromosome (chr) copy number variation (CNV), specifically, gains in chr 1q, 5p, 12p, 12q, and 17q and losses in chr 3p, 3q, 9p, and 11q. Gain of chr 12q13-15 was present in 50% of cases. The selected gene products in gain regions were upregulated as measured by immunohistochemistry. HMGA2 overexpression was significantly correlated with SO. While the structural variation (SV) rate was relatively low overall, a disproportionally high rate of break-ends at chr 7 was noted involving 6 in-frame rearrangement fusion genes. Among 40 frequently mutated genes detected by WGS and validated in 29 MAS by next generation sequencing (NGS), KMT2C, and BCOR were frequently seen in MAS both with and without SO, while MAGEC1 and KDM6B were strongly associated with SO. Overall, a higher rate of frequently mutated genes was found in MAS with SO (33%) than MAS without (11%). This study uncovers the complex and specific genetic alterations in this malignancy. The findings provide a tool for future investigation of these molecular changes in tumorigenesis and target therapies.
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Affiliation(s)
- Yanli Ban
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, Jinan, China
| | - Jean V. Fischer
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Kruti P. Maniar
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Haiyang Guo
- Department of Biology, Princess Margaret Cancer Centre, Ontario Cancer Institute, Toronto, ON, Canada
| | - Chang Zeng
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Yinuo Li
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Qing Zhang
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, Jinan, China
| | - Xinkun Wang
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Serdar E. Bulun
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Jian-Jun Wei
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
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47
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Rakha EA, Pareja FG. New Advances in Molecular Breast Cancer Pathology. Semin Cancer Biol 2020; 72:102-113. [PMID: 32259641 DOI: 10.1016/j.semcancer.2020.03.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 12/12/2022]
Abstract
Breast cancer (BC) comprises a diverse spectrum of diseases featuring distinct presentation, morphological, biological, and clinical phenotypes. BC behaviour and response to therapy also vary widely. Current evidence indicates that traditional prognostic and predictive classification systems are insufficient to reflect the biological and clinical heterogeneity of BC. Advancements in high-throughput molecular techniques and bioinformatics have contributed to the improved understanding of BC biology, refinement of molecular taxonomies and the development of novel prognostic and predictive molecular assays. Molecular testing has also become increasingly important in the diagnosis and treatment of BC in the era of precision medicine. Despite the enormous amount of research work to develop and refine BC molecular prognostic and predictive assays, it is still in evolution and proper incorporation of these molecular tests into clinical practice to guide patient's management remains a challenge. With the increasing use of more sophisticated high throughput molecular techniques, large amounts of data will continue to emerge, which could potentially lead to identification of novel therapeutic targets and allow more precise classification systems that can accurately predict outcome and response to therapy. In this review, we provide an update on the molecular classification of BC and molecular prognostic assays. Companion diagnostics, contribution of massive parallel sequencing and the use of liquid biopsy are also highlighted.
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Affiliation(s)
- Emad A Rakha
- Department of Histopathology, Division of Cancer and Stem Cells, School of Medicine, The University of Nottingham and Nottingham University Hospitals NHS Trust, Nottingham City Hospital, Nottingham, NG5 1PB, UK.
| | - Fresia G Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
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48
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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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49
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Testa U, Castelli G, Pelosi E. Breast Cancer: A Molecularly Heterogenous Disease Needing Subtype-Specific Treatments. Med Sci (Basel) 2020; 8:E18. [PMID: 32210163 PMCID: PMC7151639 DOI: 10.3390/medsci8010018] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/23/2020] [Accepted: 03/11/2020] [Indexed: 12/12/2022] Open
Abstract
Breast cancer is the most commonly occurring cancer in women. There were over two-million new cases in world in 2018. It is the second leading cause of death from cancer in western countries. At the molecular level, breast cancer is a heterogeneous disease, which is characterized by high genomic instability evidenced by somatic gene mutations, copy number alterations, and chromosome structural rearrangements. The genomic instability is caused by defects in DNA damage repair, transcription, DNA replication, telomere maintenance and mitotic chromosome segregation. According to molecular features, breast cancers are subdivided in subtypes, according to activation of hormone receptors (estrogen receptor and progesterone receptor), of human epidermal growth factors receptor 2 (HER2), and or BRCA mutations. In-depth analyses of the molecular features of primary and metastatic breast cancer have shown the great heterogeneity of genetic alterations and their clonal evolution during disease development. These studies have contributed to identify a repertoire of numerous disease-causing genes that are altered through different mutational processes. While early-stage breast cancer is a curable disease in about 70% of patients, advanced breast cancer is largely incurable. However, molecular studies have contributed to develop new therapeutic approaches targeting HER2, CDK4/6, PI3K, or involving poly(ADP-ribose) polymerase inhibitors for BRCA mutation carriers and immunotherapy.
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Affiliation(s)
- Ugo Testa
- Department of Oncology, Istituto Superiore di Sanità, Regina Elena 299, 00161 Rome, Italy; (G.C.); (E.P.)
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50
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Chen G, Cai Z, Dong X, Zhao J, Lin S, Hu X, Liu FE, Liu X, Zhang H. Genomic and Transcriptomic Landscape of Tumor Clonal Evolution in Cholangiocarcinoma. Front Genet 2020; 11:195. [PMID: 32231683 PMCID: PMC7083074 DOI: 10.3389/fgene.2020.00195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 02/19/2020] [Indexed: 12/15/2022] Open
Abstract
Cholangiocarcinoma remained a severe threat to human health. Deciphering the genomic and/or transcriptomic profiles of tumor has been proved to be a promising strategy for exploring the mechanism of tumorigenesis and development, which could also provide valuable insights into Cholangiocarcinoma. However, little knowledge has been obtained regarding to how the alteration among different omics levels is connected. Here, using whole exome sequencing and transcriptome sequencing, we performed a thorough evaluation for the landscape of genome and transcriptome in cholangiocarcinoma and illustrate the alteration of tumor on different biological levels. Meanwhile, we also identified the clonal structure of each included tumor sample and discovered different clonal evolution patterns related to patients’ survival. Furthermore, we extracted subnetworks that were greatly influenced by tumor clonal/subclonal mutations or transcriptome change. The topology relationship between genes affected by genomic/transcriptomic changes in biological interaction networks revealed that alteration of genome and transcriptome was highly correlated, and somatic mutations located on important genes might affect the expression of numerous genes in close range.
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Affiliation(s)
- Geng Chen
- School of Life Sciences and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Zhixiong Cai
- School of Life Sciences and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Xiuqing Dong
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
| | - Jing Zhao
- School of Life Sciences and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Song Lin
- School of Life Sciences and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Xi Hu
- School of Life Sciences and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Fang-E Liu
- Department of Nursing, School of Medicine, Xi'an Peihua University, Xi'an, China
| | - Xiaolong Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
| | - Huqing Zhang
- School of Life Sciences and Technology, Xi'an Jiaotong University, Xi'an, China
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