1
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Radner M, van Luttikhuizen JL, Bartels S, Bublitz J, Grote I, Rieger L, Christgen H, Stark H, Werlein C, Lafos M, Steinemann D, Lehmann U, Christgen M, Kreipe H. Chromosome 2q gain and epigenetic silencing of GATA3 in microglandular adenosis of the breast. J Pathol Clin Res 2021; 7:220-232. [PMID: 33382535 PMCID: PMC8073017 DOI: 10.1002/cjp2.195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/06/2020] [Accepted: 11/20/2020] [Indexed: 01/30/2023]
Abstract
Microglandular adenosis (MGA) represents a rare neoplasm of the mammary gland, which in a subset of cases may be associated with triple-negative breast cancer (BC). The biology of MGA is poorly understood. In this study, eight MGA cases (n = 4 with and n = 4 without associated BC) were subjected to a comprehensive characterization using immunohistochemistry, genome-wide DNA copy number (CN) profiling, fluorescence in situ hybridization (FISH), next-generation sequencing (NGS), and DNA methylation profiling using 850 K arrays and bisulfite pyrosequencing. Median patient age was 61 years (range 57-76 years). MGA lesions were estrogen receptor (ER)-negative, progesterone receptor-negative, HER2-negative, and S100-positive. DNA CN alterations (CNAs) were complex or limited to few gains and losses. CN gain on chromosome 2q was the most common CNA and was validated by FISH in five of eight cases. NGS demonstrated an average of two mutations per case (range 0-5) affecting 10 different genes (ARID1A, ATM, CTNNB1, FBXW7, FGFR2, MET, PIK3CA, PMS2, PTEN, and TP53). CNAs and mutations were similar in MGA and adjacent BC, indicating clonal relatedness. DNA methylation profiling identified aberrant hypermethylation of CpG sites within GATA3, a key transcription factor required for luminal differentiation. Immunohistochemistry showed regular GATA3 protein expression in the normal mammary epithelium and in ER-positive BC. Conversely, GATA3 was reduced or lost in all MGA cases tested (8/8). In conclusion, MGA is characterized by common CN gain on chromosome 2q and loss of GATA3. Epigenetic inactivation of GATA3 may provide a new clue to the peculiar biology of this rare neoplasia.
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Affiliation(s)
- Martin Radner
- Institute of PathologyHannover Medical SchoolHannoverGermany
| | | | - Stephan Bartels
- Institute of PathologyHannover Medical SchoolHannoverGermany
| | - Janin Bublitz
- Department of Human GeneticsHannover Medical SchoolHannoverGermany
| | - Isabel Grote
- Institute of PathologyHannover Medical SchoolHannoverGermany
| | - Luisa Rieger
- Institute of PathologyHannover Medical SchoolHannoverGermany
| | | | - Helge Stark
- Institute of PathologyHannover Medical SchoolHannoverGermany
| | | | - Marcel Lafos
- Institute of PathologyHannover Medical SchoolHannoverGermany
| | - Doris Steinemann
- Department of Human GeneticsHannover Medical SchoolHannoverGermany
| | - Ulrich Lehmann
- Institute of PathologyHannover Medical SchoolHannoverGermany
| | | | - Hans Kreipe
- Institute of PathologyHannover Medical SchoolHannoverGermany
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2
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Christgen M, Bartels S, van Luttikhuizen JL, Bublitz J, Rieger LU, Christgen H, Stark H, Sander B, Lehmann U, Steinemann D, Derksen PWB, Kreipe H. E-cadherin to P-cadherin switching in lobular breast cancer with tubular elements. Mod Pathol 2020; 33:2483-2498. [PMID: 32572153 PMCID: PMC7685979 DOI: 10.1038/s41379-020-0591-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 12/12/2022]
Abstract
Loss of E-cadherin expression due to mutation of the CDH1 gene is a characteristic feature of invasive lobular breast cancer (ILBC). Beta-catenin, which binds to the cytoplasmic domain of E-cadherin, is simultaneously downregulated, reflecting disassembly of adherens junctions (AJs) and loss of cell adhesion. E-cadherin to P-cadherin expression switching can rescue AJs and cell adhesion. However, P-cadherin has not been implicated in ILBC, so far. We aimed to characterize 13 ILBCs with exceptional histomorphology, which we termed ILBCs with tubular elements. The CDH1 mutational status was determined by next generation sequencing and whole-genome copy number (CN) profiling. Expression of cadherins was assessed by immunohistochemistry. ILBCs with tubular elements were ER-positive (13/13) and HER2-negative (13/13) and harbored deleterious CDH1 mutations (11/13) accompanied by loss of heterozygosity due to deletion of chromosome 16q22.1 (9/11). E-cadherin expression was lost or reduced in noncohesive tumor cells and in admixed tubular elements (13/13). Beta-catenin expression was lost in noncohesive tumor cells, but was retained in tubular elements (11/13), indicating focal rescue of AJ formation. N-cadherin and R-cadherin were always negative (0/13). Strikingly, P-cadherin was commonly positive (12/13) and immunoreactivity was accentuated in tubular elements. Adjacent lobular carcinoma in situ (LCIS) was always P-cadherin-negative (0/7). In a reference cohort of LCIS specimens, P-cadherin was constantly not expressed (0/25). In a reference cohort of invasive mammary carcinomas, P-cadherin-positive cases (36/268, 13%) were associated with triple-negative nonlobular breast cancer (P < 0.001). Compared with ILBCs from the reference cohort, P-cadherin expression was more common in ILBCs with tubular elements (12/13 versus 7/84, P < 0.001). In summary, E-cadherin to P-cadherin switching occurs in a subset of ILBCs. P-cadherin is the molecular determinant of a mixed-appearing histomorphology in ILBCs with tubular elements.
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Affiliation(s)
| | - Stephan Bartels
- grid.10423.340000 0000 9529 9877Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Jana L. van Luttikhuizen
- grid.10423.340000 0000 9529 9877Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Janin Bublitz
- grid.10423.340000 0000 9529 9877Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Luisa U. Rieger
- grid.10423.340000 0000 9529 9877Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Henriette Christgen
- grid.10423.340000 0000 9529 9877Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Helge Stark
- grid.10423.340000 0000 9529 9877Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Bjoern Sander
- grid.10423.340000 0000 9529 9877Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Ulrich Lehmann
- grid.10423.340000 0000 9529 9877Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Doris Steinemann
- grid.10423.340000 0000 9529 9877Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Patrick W. B. Derksen
- grid.7692.a0000000090126352Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hans Kreipe
- grid.10423.340000 0000 9529 9877Institute of Pathology, Hannover Medical School, Hannover, Germany
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3
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Kader T, Hill P, Zethoven M, Goode DL, Elder K, Thio N, Doyle M, Semple T, Sufyan W, Byrne DJ, Pang JMB, Murugasu A, Miligy IM, Green AR, Rakha EA, Fox SB, Mann GB, Campbell IG, Gorringe KL. Atypical ductal hyperplasia is a multipotent precursor of breast carcinoma. J Pathol 2019; 248:326-338. [PMID: 30843206 DOI: 10.1002/path.5262] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 02/28/2019] [Accepted: 03/04/2019] [Indexed: 12/18/2022]
Abstract
The current model for breast cancer progression proposes independent 'low grade (LG)-like' and 'high grade (HG)-like' pathways but lacks a known precursor to HG cancer. We applied low-coverage whole-genome sequencing to atypical ductal hyperplasia (ADH) with and without carcinoma to shed light on breast cancer progression. Fourteen out of twenty isolated ADH cases harboured at least one copy number alteration (CNA), but had fewer aberrations than LG or HG ductal carcinoma in situ (DCIS). ADH carried more HG-like CNA than LG DCIS (e.g. 8q gain). Correspondingly, 64% (7/11) of ADH cases with synchronous HG carcinoma were clonally related, similar to LG carcinoma (67%, 6/9). This study represents a significant shift in our understanding of breast cancer progression, with ADH as a common precursor lesion to the independent 'low grade-like' and 'high grade-like' pathways. These data suggest that ADH can be a precursor of HG breast cancer and that LG and HG carcinomas can evolve from a similar ancestor lesion. We propose that although LG DCIS may be committed to a LG molecular pathway, ADH may remain multipotent, progressing to either LG or HG carcinoma. This multipotent nature suggests that some ADH cases could be more clinically significant than LG DCIS, requiring biomarkers for personalising management. Copyright © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Tanjina Kader
- Peter MacCallum Cancer Centre, Melbourne, Australia.,The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia
| | - Prue Hill
- Department of Anatomical Pathology, St Vincent's Hospital, Fitzroy, Australia
| | | | - David L Goode
- Peter MacCallum Cancer Centre, Melbourne, Australia.,The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia
| | - Kenneth Elder
- The Breast Service, The Royal Women's Hospital, Melbourne, Australia
| | - Niko Thio
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Maria Doyle
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | - Wajiha Sufyan
- Territory Pathology, Royal Darwin Hospital, Darwin, Australia
| | | | | | - Anand Murugasu
- The Breast Service, The Royal Women's Hospital, Melbourne, Australia
| | - Islam M Miligy
- Division of Cancer and Stem Cells, Nottingham Breast Cancer Research Centre, School of Medicine, University of Nottingham, Nottingham, UK.,Department of Histopathology, Nottingham University Hospitals NHS Trust, City Hospital, Nottingham, UK
| | - Andrew R Green
- Division of Cancer and Stem Cells, Nottingham Breast Cancer Research Centre, School of Medicine, University of Nottingham, Nottingham, UK.,Department of Histopathology, Nottingham University Hospitals NHS Trust, City Hospital, Nottingham, UK
| | - Emad A Rakha
- Division of Cancer and Stem Cells, Nottingham Breast Cancer Research Centre, School of Medicine, University of Nottingham, Nottingham, UK.,Department of Histopathology, Nottingham University Hospitals NHS Trust, City Hospital, Nottingham, UK
| | | | - G Bruce Mann
- The Breast Service, The Royal Women's Hospital, Melbourne, Australia
| | - Ian G Campbell
- Peter MacCallum Cancer Centre, Melbourne, Australia.,The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia.,Department of Clinical Pathology, The University of Melbourne, Parkville, Australia
| | - Kylie L Gorringe
- Peter MacCallum Cancer Centre, Melbourne, Australia.,The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia.,Department of Clinical Pathology, The University of Melbourne, Parkville, Australia
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4
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Biermann J, Parris TZ, Nemes S, Danielsson A, Engqvist H, Werner Rönnerman E, Forssell-Aronsson E, Kovács A, Karlsson P, Helou K. Clonal relatedness in tumour pairs of breast cancer patients. Breast Cancer Res 2018; 20:96. [PMID: 30092821 PMCID: PMC6085699 DOI: 10.1186/s13058-018-1022-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 07/18/2018] [Indexed: 01/18/2023] Open
Abstract
Background Molecular classification of tumour clonality is currently not evaluated in multiple invasive breast carcinomas, despite evidence suggesting common clonal origins. There is no consensus about which type of data (e.g. copy number, mutation, histology) and especially which statistical method is most suitable to distinguish clonal recurrences from independent primary tumours. Methods Thirty-seven invasive breast tumour pairs were stratified according to laterality and time interval between the diagnoses of the two tumours. In a multi-omics approach, tumour clonality was analysed by integrating clinical characteristics (n = 37), DNA copy number (n = 37), DNA methylation (n = 8), gene expression microarray (n = 7), RNA sequencing (n = 3), and SNP genotyping data (n = 3). Different statistical methods, e.g. the diagnostic similarity index (SI), were used to classify the tumours as clonally related recurrences or independent primary tumours. Results The SI and hierarchical clustering showed similar tendencies and the highest concordance with the other methods. Concordant evidence for tumour clonality was found in 46% (17/37) of patients. Notably, no association was found between the current clinical guidelines and molecular tumour features. Conclusions A more accurate classification of clonal relatedness between multiple breast tumours may help to mitigate treatment failure and relapse by integrating tumour-associated molecular features, clinical parameters, and statistical methods. Guidelines need to be defined with exact thresholds to standardise clonality testing in a routine diagnostic setting. Electronic supplementary material The online version of this article (10.1186/s13058-018-1022-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jana Biermann
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, Box 425, SE-405 30, Gothenburg, Sweden.
| | - Toshima Z Parris
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, Box 425, SE-405 30, Gothenburg, Sweden
| | - Szilárd Nemes
- Swedish Hip Arthroplasty Register, 405 30, Gothenburg, Sweden
| | - Anna Danielsson
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, Box 425, SE-405 30, Gothenburg, Sweden
| | - Hanna Engqvist
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, Box 425, SE-405 30, Gothenburg, Sweden
| | - Elisabeth Werner Rönnerman
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, Box 425, SE-405 30, Gothenburg, Sweden.,Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Eva Forssell-Aronsson
- Department of Radiation Physics, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, 405 30, Gothenburg, Sweden
| | - Anikó Kovács
- Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Per Karlsson
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, Box 425, SE-405 30, Gothenburg, Sweden
| | - Khalil Helou
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, Sahlgrenska Academy at University of Gothenburg, Box 425, SE-405 30, Gothenburg, Sweden
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5
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Sun W, Feng L, Yang X, Li L, Liu Y, Lv N, Lin D. Clonality assessment of multifocal lung adenocarcinoma by pathology evaluation and molecular analysis. Hum Pathol 2018; 81:261-271. [PMID: 30420048 DOI: 10.1016/j.humpath.2018.01.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 12/25/2017] [Accepted: 01/02/2018] [Indexed: 12/25/2022]
Abstract
The aim of this study was to explore morphologic and molecular features distinguishing between multifocal lung adenocarcinoma (MLA) and intrapulmonary metastases (IMs). Sixteen patients with MLAs, a total of 34 tumors, were reviewed. Four approaches were used: (1) array-comparative genomic hybridization (CGH) as a standard clonality assessment; (2) EGFR and KRAS mutational profiles as a supplementary method; (3) comprehensive histologic assessment (CHA) was method I in pathology evaluation; and (4) CHA combined with lepidic component analysis was method II. The lepidic component was divided into low grade and high grade according to extent of atypia; tumors with low-grade lepidic component were defined as primary. Eight patients were found to have IMs and 8 to have multiple primaries (MPs) by array-CGH; 7 had MPs and 9 had IMs by method I; 5 had MPs and 11 had IMs by method II. Compared with array-CGH, method I had a lower coincidence rate (65%) than method II (85%). Univariate analysis revealed that patients with MP had a better clinical outcome than those with IM only if the MPs were diagnosed by array-CGH (P = .034) or method II (P = .027) but not EGFR/KRAS mutation (P = .843) or method I (P = .493). Our results suggest that a low-grade lepidic component is a sign of a primary tumor. CHA combined with a low-grade lepidic component (method II) is more accurate clinically and more cost-effective in distinguishing MLAs from IMs. Also, EGFR mutation is not an appropriate molecular marker for clonality assessment.
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Affiliation(s)
- Wei Sun
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, 100142 Beijing, China; Department of Pathology, Cancer Institute and Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, 100021 Beijing, China
| | - Lin Feng
- Department of Etiology and Carcinogenesis, Cancer Institute and Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, 100021 Beijing, China
| | - Xin Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, 100142 Beijing, China
| | - Lin Li
- Department of Pathology, Cancer Institute and Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, 100021 Beijing, China
| | - Yu Liu
- Department of Etiology and Carcinogenesis, Cancer Institute and Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, 100021 Beijing, China
| | - Ning Lv
- Department of Pathology, Cancer Institute and Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, 100021 Beijing, China.
| | - Dongmei Lin
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, 100142 Beijing, China.
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6
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Begg CB, Ostrovnaya I, Geyer FC, Papanastasiou AD, Ng CKY, Sakr R, Bernstein JL, Burke KA, King TA, Piscuoglio S, Mauguen A, Orlow I, Weigelt B, Seshan VE, Morrow M, Reis-Filho JS. Contralateral breast cancers: Independent cancers or metastases? Int J Cancer 2018; 142:347-356. [PMID: 28921573 PMCID: PMC5749409 DOI: 10.1002/ijc.31051] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/24/2017] [Accepted: 08/30/2017] [Indexed: 12/24/2022]
Abstract
A cancer in the contralateral breast in a woman with a previous or synchronous breast cancer is typically considered to be an independent primary tumor. Emerging evidence suggests that in a small subset of these cases the second tumor represents a metastasis. We sought to investigate the issue using massively parallel sequencing targeting 254 genes recurrently mutated in breast cancer. We examined the tumor archives at Memorial Sloan Kettering Cancer Center for the period 1995-2006 to identify cases of contralateral breast cancer where surgery for both tumors was performed at the Center. We report results from 49 patients successfully analyzed by a targeted massively parallel sequencing assay. Somatic mutations and copy number alterations were defined by state-of-the-art algorithms. Clonal relatedness was evaluated by statistical tests specifically designed for this purpose. We found evidence that the tumors in contralateral breasts were clonally related in three cases (6%) on the basis of matching mutations at codons where somatic mutations are rare. Clinical data and the presence of similar patterns of gene copy number alterations were consistent with metastasis for all three cases. In three additional cases, there was a solitary matching mutation at a common PIK3CA locus. The results suggest that a subset of contralateral breast cancers represent metastases rather than independent primary tumors. Massively parallel sequencing analysis can provide important evidence to clarify the diagnosis. However, given the inter-tumor mutational heterogeneity in breast cancer, sufficiently large gene panels need to be employed to define clonality convincingly in all cases.
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Affiliation(s)
- Colin B Begg
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Felipe C Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anastasios D Papanastasiou
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Metaxa Cancer Hospital/University of Patras, Patras, Greece
| | - Charlotte KY Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Institute of Pathology, University Hospital Basel, Switzerland
| | - Rita Sakr
- Breast Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonine L Bernstein
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kathleen A Burke
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- IBM Watson Health, Cambridge, MA USA
| | - Tari A King
- Dana-Farber Cancer Institute/Brigham and Women’s Hospital, Boston, MA USA
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Institute of Pathology, University Hospital Basel, Switzerland
| | - Audrey Mauguen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Venkatraman E Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Monica Morrow
- Breast Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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7
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Christgen M, Bartels S, van Luttikhuizen JL, Schieck M, Pertschy S, Kundu S, Lehmann U, Sander B, Pelz E, Länger F, Schlegelberger B, Steinemann D, Kreipe H. Subclonal analysis in a lobular breast cancer with classical and solid growth pattern mimicking a solid-papillary carcinoma. JOURNAL OF PATHOLOGY CLINICAL RESEARCH 2017; 3:191-202. [PMID: 28770103 PMCID: PMC5527319 DOI: 10.1002/cjp2.76] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 06/10/2017] [Indexed: 12/24/2022]
Abstract
Recently, a new variant of invasive lobular breast cancer (ILBC) with solid-papillary-like growth pattern has been described. We present a case of ILBC with solid-papillary-like growth pattern in the main tumour mass and classical invasive lobular growth pattern in adjacent satellite foci. The two tumour components were subjected to comprehensive molecular analyses. Both components were ER/PR-positive, HER2-negative, and showed a complete loss of E-cadherin and beta-catenin protein expression, as determined by immunohistochemistry. Gene expression profiling classified the main tumour and a satellite focus as luminal-B and luminal-A subtypes, respectively. Whole-genome copy number profiles were highly similar in both tumour components. Shared copy number alterations (CNAs) included gains of chromosome 1q21.1-q43 and losses of chromosome 16q11.2-q24.3, the locus of the CDH1/E-cadherin tumour suppressor gene. CNAs detected only in the main tumour included a gain of chromosome 20q12-q13.33 and a loss of chromosome 1p36.33-p34.3, which has recently been associated with the solid variant of ILBC. Next generation sequencing revealed an identical, truncating CDH1 mutation (p.G169fs*5) in both tumour components confirming a common clonal ancestry. In conclusion, we confirm the recently described variant of ILBC with solid-papillary-like growth pattern and provide evidence that it evolves from classical ILBC by subclonal evolution.
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Affiliation(s)
| | - Stephan Bartels
- Institute of Pathology, Hannover Medical SchoolHannoverGermany
| | | | | | - Stefanie Pertschy
- Department of Diagnostic RadiologyHannover Medical SchoolHannoverGermany
| | - Sudip Kundu
- Department of Obstetrics and GynecologyHannover Medical SchoolHannoverGermany
| | - Ulrich Lehmann
- Institute of Pathology, Hannover Medical SchoolHannoverGermany
| | - Bjoern Sander
- Institute of Pathology, Hannover Medical SchoolHannoverGermany
| | - Enrico Pelz
- Institute of Pathology ViersenViersenGermany
| | - Florian Länger
- Institute of Pathology, Hannover Medical SchoolHannoverGermany
| | | | - Doris Steinemann
- Department of Human GeneticsHannover Medical SchoolHannoverGermany
| | - Hans Kreipe
- Institute of Pathology, Hannover Medical SchoolHannoverGermany
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8
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Mauguen A, Seshan VE, Ostrovnaya I, Begg CB. Estimating the probability of clonal relatedness of pairs of tumors in cancer patients. Biometrics 2017; 74:321-330. [PMID: 28482133 DOI: 10.1111/biom.12710] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 03/01/2017] [Accepted: 03/01/2017] [Indexed: 12/31/2022]
Abstract
Next generation sequencing panels are being used increasingly in cancer research to study tumor evolution. A specific statistical challenge is to compare the mutational profiles in different tumors from a patient to determine the strength of evidence that the tumors are clonally related, that is, derived from a single, founder clonal cell. The presence of identical mutations in each tumor provides evidence of clonal relatedness, although the strength of evidence from a match is related to how commonly the mutation is seen in the tumor type under investigation. This evidence must be weighed against the evidence in favor of independent tumors from non-matching mutations. In this article, we frame this challenge in the context of diagnosis using a novel random effects model. In this way, by analyzing a set of tumor pairs, we can estimate the proportion of cases that are clonally related in the sample as well as the individual diagnostic probabilities for each case. The method is illustrated using data from a study to determine the clonal relationship of lobular carcinoma in situ with subsequent invasive breast cancers, where each tumor in the pair was subjected to whole exome sequencing. The statistical properties of the method are evaluated using simulations, demonstrating that the key model parameters are estimated with only modest bias in small samples in most configurations.
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Affiliation(s)
- Audrey Mauguen
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, 485 Lexington Avenue, 2nd Floor, New York, New York 10017, U.S.A
| | - Venkatraman E Seshan
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, 485 Lexington Avenue, 2nd Floor, New York, New York 10017, U.S.A
| | - Irina Ostrovnaya
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, 485 Lexington Avenue, 2nd Floor, New York, New York 10017, U.S.A
| | - Colin B Begg
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, 485 Lexington Avenue, 2nd Floor, New York, New York 10017, U.S.A
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9
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Walts AE, Mirocha JM, Leong T, Marchevsky AM. Pathologic Staging and Survival of Patients With Synchronous Bilateral Lung Carcinomas. Am J Clin Pathol 2016; 145:244-50. [PMID: 26796494 DOI: 10.1093/ajcp/aqv025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
OBJECTIVES To compare survival data in patients with resected bilateral synchronous pulmonary carcinomas with survival data from patients with lung cancer in pStages I through IV and to evaluate the usefulness of comprehensive histologic evaluation (CHE) of tumor histologic patterns to distinguish between synchronous primaries and intrapulmonary metastases. METHODS Ten-year overall survival (OS) data from 18 patients with 44 resected synchronous bilateral lung cancers, classified as "synchronous primaries" or "metastases" using CHE, were compared with survival data of 2,879 patients with lung cancer in pStages I through IV. RESULTS Forty and four tumors from 16 and two patients, respectively, were classified as synchronous primaries and metastases. There were no significant differences in survival between these 18 patients and pStage I controls or between the synchronous primaries and the metastases patient groups. However, there were significant differences in survival between the patients with resected synchronous bilateral tumors and each of the pStage II through IV control groups (P < .05). CONCLUSIONS Patients with resected synchronous bilateral lung cancers had similar 10-year OS to patients with stage I disease, regardless of CHE data. Most resected tumors were synchronous primaries by CHE.
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Affiliation(s)
- Ann E Walts
- From the Department of Pathology & Laboratory Medicine
| | | | - Trista Leong
- Cancer Registry, Cedars-Sinai Medical Center, Los Angeles, CA
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Bao L, Messer K, Schwab R, Harismendy O, Pu M, Crain B, Yost S, Frazer KA, Rana B, Hasteh F, Wallace A, Parker BA. Mutational Profiling Can Establish Clonal or Independent Origin in Synchronous Bilateral Breast and Other Tumors. PLoS One 2015; 10:e0142487. [PMID: 26554380 PMCID: PMC4640562 DOI: 10.1371/journal.pone.0142487] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 10/22/2015] [Indexed: 12/01/2022] Open
Abstract
Background Synchronous tumors can be independent primary tumors or a primary-metastatic (clonal) pair, which may have clinical implications. Mutational profiling of tumor DNA is increasingly common in the clinic. We investigated whether mutational profiling can distinguish independent from clonal tumors in breast and other cancers, using a carefully defined test based on the Clonal Likelihood Score (CLS = 100 x # shared high confidence (HC) mutations/ # total HC mutations). Methods Statistical properties of a formal test using the CLS were investigated. A high CLS is evidence in favor of clonality; the test is implemented as a one-sided binomial test of proportions. Test parameters were empirically determined using 16,422 independent breast tumor pairs and 15 primary-metastatic tumor pairs from 10 cancer types using The Cancer Genome Atlas. Results We validated performance of the test with its established parameters, using five published data sets comprising 15,758 known independent tumor pairs (maximum CLS = 4.1%, minimum p-value = 0.48) and 283 known tumor clonal pairs (minimum CLS 13%, maximum p-value <0.01), across renal cell, testicular, and colorectal cancer. The CLS test correctly classified all validation samples but one, which it appears may have been incorrectly classified in the published data. As proof-of-concept we then applied the CLS test to two new cases of invasive synchronous bilateral breast cancer at our institution, each with one hormone receptor positive (ER+/PR+/HER2-) lobular and one triple negative ductal carcinoma. High confidence mutations were identified by exome sequencing and results were validated using deep targeted sequencing. The first tumor pair had CLS of 81% (p-value < 10–15), supporting clonality. In the second pair, no common mutations of 184 variants were validated (p-value >0.99), supporting independence. A plausible molecular mechanism for the shift from hormone receptor positive to triple negative was identified in the clonal pair. Conclusion We have developed the statistical properties of a carefully defined Clonal Likelihood Score test from mutational profiling of tumor DNA. Under identified conditions, the test appears to reliably distinguish between synchronous tumors of clonal and of independent origin in several cancer types. This approach may have scientific and clinical utility.
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Affiliation(s)
- Lei Bao
- Moores Cancer Center, University of California San Diego, La Jolla, CA, United States of America
| | - Karen Messer
- Moores Cancer Center, University of California San Diego, La Jolla, CA, United States of America
- Division of Biostatistics, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, United States of America
- * E-mail:
| | - Richard Schwab
- Department of Medicine, University of California San Diego, La Jolla, CA, United States of America
| | - Olivier Harismendy
- Department of Pediatrics, University of California San Diego, La Jolla, CA, United States of America
| | - Minya Pu
- Moores Cancer Center, University of California San Diego, La Jolla, CA, United States of America
| | - Brian Crain
- Moores Cancer Center, University of California San Diego, La Jolla, CA, United States of America
| | - Shawn Yost
- Moores Cancer Center, University of California San Diego, La Jolla, CA, United States of America
| | - Kelly A. Frazer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, United States of America
| | - Brinda Rana
- Department of Psychiatry, University of California San Diego, La Jolla, CA, United States of America
| | - Farnaz Hasteh
- Department of Pathology, University of California San Diego, La Jolla, CA, United States of America
| | - Anne Wallace
- Department of Surgery, University of California San Diego, La Jolla, CA, United States of America
| | - Barbara A. Parker
- Department of Medicine, University of California San Diego, La Jolla, CA, United States of America
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Integrative genomics with mediation analysis in a survival context. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2013; 2013:413783. [PMID: 24454535 PMCID: PMC3878392 DOI: 10.1155/2013/413783] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 09/23/2013] [Indexed: 12/25/2022]
Abstract
DNA copy number aberrations (DCNA) and subsequent altered gene expression profiles may have a major impact on tumor initiation, on development, and eventually on recurrence and cancer-specific mortality. However, most methods employed in integrative genomic analysis of the two biological levels, DNA and RNA, do not consider survival time. In the present note, we propose the adoption of a survival analysis-based framework for the integrative analysis of DCNA and mRNA levels to reveal their implication on patient clinical outcome with the prerequisite that the effect of DCNA on survival is mediated by mRNA levels. The specific aim of the paper is to offer a feasible framework to test the DCNA-mRNA-survival pathway. We provide statistical inference algorithms for mediation based on asymptotic results. Furthermore, we illustrate the applicability of the method in an integrative genomic analysis setting by using a breast cancer data set consisting of 141 invasive breast tumors. In addition, we provide implementation in R.
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Nemes S, Danielsson A, Parris TZ, Jonasson JM, Bülow E, Karlsson P, Steineck G, Helou K. A diagnostic algorithm to identify paired tumors with clonal origin. Genes Chromosomes Cancer 2013; 52:1007-16. [DOI: 10.1002/gcc.22096] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 07/02/2013] [Indexed: 11/07/2022] Open
Affiliation(s)
- Szilárd Nemes
- Division of Clinical Cancer Epidemiology; Department of Oncology; Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg; Gothenburg Sweden
- Regional Cancer Centre (West); Western Sweden Health Care Region, Sahlgrenska University Hospital; Gothenburg Sweden
| | - Anna Danielsson
- Department of Oncology; Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg; Gothenburg Sweden
| | - Toshima Z. Parris
- Department of Oncology; Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg; Gothenburg Sweden
| | - Junmei Miao Jonasson
- Division of Clinical Cancer Epidemiology; Department of Oncology; Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg; Gothenburg Sweden
| | - Erik Bülow
- Regional Cancer Centre (West); Western Sweden Health Care Region, Sahlgrenska University Hospital; Gothenburg Sweden
| | - Per Karlsson
- Department of Oncology; Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg; Gothenburg Sweden
| | - Gunnar Steineck
- Division of Clinical Cancer Epidemiology; Department of Oncology; Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg; Gothenburg Sweden
- Division of Clinical Cancer Epidemiology; Department of Oncology and Pathology; Karolinska Institutet; Stockholm Sweden
| | - Khalil Helou
- Department of Oncology; Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg; Gothenburg Sweden
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Genomic aberrations in normal tissue adjacent to HER2-amplified breast cancers: field cancerization or contaminating tumor cells? Breast Cancer Res Treat 2012; 136:693-703. [PMID: 23104223 PMCID: PMC3511697 DOI: 10.1007/s10549-012-2290-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 10/04/2012] [Indexed: 10/27/2022]
Abstract
Field cancerization effects as well as isolated tumor cell foci extending well beyond the invasive tumor margin have been described previously to account for local recurrence rates following breast conserving surgery despite adequate surgical margins and breast radiotherapy. To look for evidence of possible tumor cell contamination or field cancerization by genetic effects, a pilot study (Study 1: 12 sample pairs) followed by a verification study (Study 2: 20 sample pairs) were performed on DNA extracted from HER2-positive breast tumors and matching normal adjacent mammary tissue samples excised 1-3 cm beyond the invasive tumor margin. High-resolution molecular inversion probe (MIP) arrays were used to compare genomic copy number variations, including increased HER2 gene copies, between the paired samples; as well, a detailed histologic and immunohistochemical (IHC) re-evaluation of all Study 2 samples was performed blinded to the genomic results to characterize the adjacent normal tissue composition bracketing the DNA-extracted samples. Overall, 14/32 (44 %) sample pairs from both studies produced genome-wide evidence of genetic aberrations including HER2 copy number gains within the adjacent normal tissue samples. The observed single-parental origin of monoallelic HER2 amplicon haplotypes shared by informative tumor-normal pairs, as well as commonly gained loci elsewhere on 17q, suggested the presence of contaminating tumor cells in the genomically aberrant normal samples. Histologic and IHC analyses identified occult 25-200 μm tumor cell clusters overexpressing HER2 scattered in more than half, but not all, of the genomically aberrant normal samples re-evaluated, but in none of the genomically normal samples. These genomic and microscopic findings support the conclusion that tumor cell contamination rather than genetic field cancerization represents the likeliest cause of local clinical recurrence rates following breast conserving surgery, and mandate caution in assuming the genomic normalcy of histologically benign appearing peritumor breast tissue.
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Ostrovnaya I, Seshan VE, Olshen AB, Begg CB. Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic profiles. Bioinformatics 2011; 27:1698-9. [PMID: 21546399 DOI: 10.1093/bioinformatics/btr267] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
SUMMARY If a cancer patient develops multiple tumors, it is sometimes impossible to determine whether these tumors are independent or clonal based solely on pathological characteristics. Investigators have studied how to improve this diagnostic challenge by comparing the presence of loss of heterozygosity (LOH) at selected genetic locations of tumor samples, or by comparing genomewide copy number array profiles. We have previously developed statistical methodology to compare such genomic profiles for an evidence of clonality. We assembled the software for these tests in a new R package called 'Clonality'. For LOH profiles, the package contains significance tests. The analysis of copy number profiles includes a likelihood ratio statistic and reference distribution, as well as an option to produce various plots that summarize the results. AVAILABILITY Bioconductor (http://bioconductor.org/packages/release/bioc/html/Clonality.html) and http://www.mskcc.org/mskcc/html/13287.cfm.
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Affiliation(s)
- Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
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