51
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Pladsen AV, Nilsen G, Rueda OM, Aure MR, Borgan Ø, Liestøl K, Vitelli V, Frigessi A, Langerød A, Mathelier A, Engebråten O, Kristensen V, Wedge DC, Van Loo P, Caldas C, Børresen-Dale AL, Russnes HG, Lingjærde OC. DNA copy number motifs are strong and independent predictors of survival in breast cancer. Commun Biol 2020; 3:153. [PMID: 32242091 PMCID: PMC7118095 DOI: 10.1038/s42003-020-0884-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 03/05/2020] [Indexed: 11/15/2022] Open
Abstract
Somatic copy number alterations are a frequent sign of genome instability in cancer. A precise characterization of the genome architecture would reveal underlying instability mechanisms and provide an instrument for outcome prediction and treatment guidance. Here we show that the local spatial behavior of copy number profiles conveys important information about this architecture. Six filters were defined to characterize regional traits in copy number profiles, and the resulting Copy Aberration Regional Mapping Analysis (CARMA) algorithm was applied to tumors in four breast cancer cohorts (n = 2919). The derived motifs represent a layer of information that complements established molecular classifications of breast cancer. A score reflecting presence or absence of motifs provided a highly significant independent prognostic predictor. Results were consistent between cohorts. The nonsite-specific occurrence of the detected patterns suggests that CARMA captures underlying replication and repair defects and could have a future potential in treatment stratification.
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Affiliation(s)
- Arne V Pladsen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Ullernchausseen 70 N-0310, Oslo, Norway
| | - Gro Nilsen
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Gaustadalléen 23 B N-0373, Oslo, Norway
| | - Oscar M Rueda
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Miriam R Aure
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Ullernchausseen 70 N-0310, Oslo, Norway
| | - Ørnulf Borgan
- Department of Mathematics, University of Oslo, Moltke Moes vei 35 N-0851, Oslo, Norway
| | - Knut Liestøl
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Gaustadalléen 23 B N-0373, Oslo, Norway
| | - Valeria Vitelli
- Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Domus Medica, Sognsvannsveien 9 N-0372, Oslo, Norway
| | - Arnoldo Frigessi
- Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Domus Medica, Sognsvannsveien 9 N-0372, Oslo, Norway
| | - Anita Langerød
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Ullernchausseen 70 N-0310, Oslo, Norway
| | - Anthony Mathelier
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Ullernchausseen 70 N-0310, Oslo, Norway
- Centre for Molecular Medicine Norway, University of Oslo, Forskningsparken, Gaustadalléen 21 N-0349, Oslo, Norway
| | - Olav Engebråten
- Institute for Clinical Medicine, University of Oslo, Kirkeveien 166 N-0450, Oslo, Norway
- Department of Oncology, Oslo University Hospital, POB 4953 Nydalen, N-0424, Oslo, Norway
| | - Vessela Kristensen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Ullernchausseen 70 N-0310, Oslo, Norway
| | - David C Wedge
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Old Road Campus, Headington, Oxford, OX3 7FZ, UK
- NIHR Biomedical Research Centre, Warneford Ln, Headington, Oxford, OX3 7JX, UK
| | - Peter Van Loo
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Carlos Caldas
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Anne-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Ullernchausseen 70 N-0310, Oslo, Norway
- Institute for Clinical Medicine, University of Oslo, Kirkeveien 166 N-0450, Oslo, Norway
| | - Hege G Russnes
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Ullernchausseen 70 N-0310, Oslo, Norway
- Department of Pathology, Oslo University Hospital, POB 4953 Nydalen N-0424, Oslo, Norway
| | - Ole Christian Lingjærde
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Ullernchausseen 70 N-0310, Oslo, Norway.
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Gaustadalléen 23 B N-0373, Oslo, Norway.
- KG Jebsen Centre for B-cell malignancies, Institute for Clinical Medicine, University of Oslo, Ullernchausseen 70 N-0372, Oslo, Norway.
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52
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Hobolth A, Guo Q, Kousholt A, Jensen JL. A Unifying Framework and Comparison of Algorithms for Non‐negative Matrix Factorisation. Int Stat Rev 2020. [DOI: 10.1111/insr.12331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Asger Hobolth
- Department of MathematicsAarhus University Aarhus Denmark
- Bioinformatics Research CenterAarhus University Aarhus Denmark
| | - Qianyun Guo
- Bioinformatics Research CenterAarhus University Aarhus Denmark
| | - Astrid Kousholt
- Bioinformatics Research CenterAarhus University Aarhus Denmark
| | - Jens Ledet Jensen
- Department of MathematicsAarhus University Aarhus Denmark
- Centre for Digitalisation, Big Data and Data AnalyticsAarhus University Aarhus Denmark
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53
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CANCERSIGN: a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes. Sci Rep 2020; 10:1286. [PMID: 31992766 PMCID: PMC6987109 DOI: 10.1038/s41598-020-58107-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 01/06/2020] [Indexed: 11/20/2022] Open
Abstract
Analysis of cancer mutational signatures have been instrumental in identification of responsible endogenous and exogenous molecular processes in cancer. The quantitative approach used to deconvolute mutational signatures is becoming an integral part of cancer research. Therefore, development of a stand-alone tool with a user-friendly interface for analysis of cancer mutational signatures is necessary. In this manuscript we introduce CANCERSIGN, which enables users to identify 3-mer and 5-mer mutational signatures within whole genome, whole exome or pooled samples. Additionally, this tool enables users to perform clustering on tumor samples based on the proportion of mutational signatures in each sample. Using CANCERSIGN, we analysed all the whole genome somatic mutation datasets profiled by the International Cancer Genome Consortium (ICGC) and identified a number of novel signatures. By examining signatures found in exonic and non-exonic regions of the genome using WGS and comparing this to signatures found in WES data we observe that WGS can identify additional non-exonic signatures that are enriched in the non-coding regions of the genome while the deeper sequencing of WES may help identify weak signatures that are otherwise missed in shallower WGS data.
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54
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Trevino V. HotSpotAnnotations-a database for hotspot mutations and annotations in cancer. Database (Oxford) 2020; 2020:baaa025. [PMID: 32386297 PMCID: PMC7211031 DOI: 10.1093/database/baaa025] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 02/20/2020] [Accepted: 03/11/2020] [Indexed: 12/21/2022]
Abstract
Hotspots, recurrently mutated DNA positions in cancer, are thought to be oncogenic drivers because random chance is unlikely and the knowledge of clear examples of oncogenic hotspots in genes like BRAF, IDH1, KRAS and NRAS among many other genes. Hotspots are attractive because provide opportunities for biomedical research and novel treatments. Nevertheless, recent evidence, such as DNA hairpins for APOBEC3A, suggests that a considerable fraction of hotspots seem to be passengers rather than drivers. To document hotspots, the database HotSpotsAnnotations is proposed. For this, a statistical model was implemented to detect putative hotspots, which was applied to TCGA cancer datasets covering 33 cancer types, 10 182 patients and 3 175 929 mutations. Then, genes and hotspots were annotated by two published methods (APOBEC3A hairpins and dN/dS ratio) that may inform and warn researchers about possible false functional hotspots. Moreover, manual annotation from users can be added and shared. From the 23 198 detected as possible hotspots, 4435 were selected after false discovery rate correction and minimum mutation count. From these, 305 were annotated as likely for APOBEC3A whereas 442 were annotated as unlikely. To date, this is the first database dedicated to annotating hotspots for possible false functional hotspots.
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Affiliation(s)
- Victor Trevino
- Tecnologico de Monterrey, Escuela de Medicina, Cátedra de Bioinformática, Morones Prieto No. 3000, Colonia Los Doctores, Monterrey, Nuevo León 64710, Mexico
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55
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Li J, Liu C, Chen Y, Gao C, Wang M, Ma X, Zhang W, Zhuang J, Yao Y, Sun C. Tumor Characterization in Breast Cancer Identifies Immune-Relevant Gene Signatures Associated With Prognosis. Front Genet 2019; 10:1119. [PMID: 31781173 PMCID: PMC6861325 DOI: 10.3389/fgene.2019.01119] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 10/16/2019] [Indexed: 12/12/2022] Open
Abstract
There has been increasing attention on immune-oncology for its impressive clinical benefits in many different malignancies. However, due to molecular and genetic heterogeneity of tumors, the activities of traditional clinical and pathological criteria are far from satisfactory. Immune-based strategies have re-ignited hopes for the treatment and prevention of breast cancer. Prognostic or predictive biomarkers, associated with tumor immune microenvironment, may have great prospects in guiding patient management, identifying new immune-related molecular markers, establishing personalized risk assessment of breast cancer. Therefore, in this study, weighted gene co-expression network analysis (WGCNA), single-sample gene set enrichment analysis (ssGSEA), multivariate COX analysis, least absolute shrinkage, and selection operator (LASSO), and support vector machine-recursive feature elimination (SVM-RFE) algorithm, along with a series of analyses were performed, and four immune-related genes (APOD, CXCL14, IL33, and LIFR) were identified as biomarkers correlated with breast cancer prognosis. The findings may provide different insights into prognostic monitoring of immune-related targets for breast cancer or can be served as reference for the further research and validation of biomarkers.
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Affiliation(s)
- Jie Li
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Cun Liu
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yi Chen
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Chundi Gao
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Miyuan Wang
- College of Management, Beijing University of Chinese Medicine, Beijing, China
| | - Xiaoran Ma
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Wenfeng Zhang
- Clinical Medical Colleges, Weifang Medical University, Weifang, China
| | - Jing Zhuang
- Department of Oncology, Weifang Traditional Chinese Medicine Hospital, Weifang, Shandong, China
| | - Yan Yao
- Clinical Medical Colleges, Weifang Medical University, Weifang, China
| | - Changgang Sun
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
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56
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Beca F, Lee SSK, Pareja F, Da Cruz Paula A, Selenica P, Ferrando L, Gularte-Mérida R, Wen HY, Zhang H, Guerini-Rocco E, Rakha EA, Weigelt B, Reis-Filho JS. Whole-exome sequencing and RNA sequencing analyses of acinic cell carcinomas of the breast. Histopathology 2019; 75:931-937. [PMID: 31361912 DOI: 10.1111/his.13962] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 07/27/2019] [Indexed: 12/13/2022]
Abstract
AIMS Acinic cell carcinoma (ACC) of the breast is a rare histological form of triple-negative breast cancer (TNBC). Despite its unique histology, targeted sequencing analysis has failed to identify recurrent genetic alterations other than those found in common forms of TNBC. Here we subjected three breast ACCs to whole-exome and RNA sequencing to determine whether they would harbour a pathognomonic genetic alteration. METHODS AND RESULTS DNA and RNA samples from three breast ACCs were subjected to whole-exome sequencing and RNA-sequencing, respectively. Somatic mutations, copy number alterations, mutational signatures and fusion genes were determined with state-of-the-art bioinformatics methods. Our analyses revealed TP53 hotspot mutations associated with loss of heterozygosity of the wild-type allele in two cases. Mutations affecting homologous recombination DNA repair-related genes were found in two cases, and an MLH1 pathogenic germline variant was found in one case. In addition, copy number analysis revealed the presence of a somatic BRCA1 homozygous deletion and focal amplification of 12q14.3-12q21.1, encompassing MDM2, HMGA2, FRS2, and PTPRB. No oncogenic in-frame fusion transcript was identified in the three breast ACCs analysed. CONCLUSIONS No pathognomonic genetic alterations were detected in the breast ACCs analysed. These tumours have somatic genetic alterations similar to those of common forms of TNBC, and may show homologous recombination deficiency or microsatellite instability. These findings provide further insights into why breast ACCs, which are usually clinically indolent, may evolve into or in parallel with high-grade TNBC.
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Affiliation(s)
- Francisco Beca
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA
| | - Simon S K Lee
- 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
| | - 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, Genova, Italy
| | - Rodrigo Gularte-Mérida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hannah Y Wen
- 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
| | - Elena Guerini-Rocco
- Unit of Histopathology and Molecular Diagnostics, Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Emad A Rakha
- Department of Pathology, University of Nottingham, Nottingham, UK
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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57
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Angus L, Smid M, Wilting SM, van Riet J, Van Hoeck A, Nguyen L, Nik-Zainal S, Steenbruggen TG, Tjan-Heijnen VCG, Labots M, van Riel JMGH, Bloemendal HJ, Steeghs N, Lolkema MP, Voest EE, van de Werken HJG, Jager A, Cuppen E, Sleijfer S, Martens JWM. The genomic landscape of metastatic breast cancer highlights changes in mutation and signature frequencies. Nat Genet 2019; 51:1450-1458. [PMID: 31570896 PMCID: PMC6858873 DOI: 10.1038/s41588-019-0507-7] [Citation(s) in RCA: 206] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 08/29/2019] [Indexed: 02/02/2023]
Abstract
The whole-genome sequencing of prospectively collected tissue biopsies from 442 patients with metastatic breast cancer reveals that, compared to primary breast cancer, tumor mutational burden doubles, the relative contributions of mutational signatures shift and the mutation frequency of six known driver genes increases in metastatic breast cancer. Significant associations with pretreatment are also observed. The contribution of mutational signature 17 is significantly enriched in patients pretreated with fluorouracil, taxanes, platinum and/or eribulin, whereas the de novo mutational signature I identified in this study is significantly associated with pretreatment containing platinum-based chemotherapy. Clinically relevant subgroups of tumors are identified, exhibiting either homologous recombination deficiency (13%), high tumor mutational burden (11%) or specific alterations (24%) linked to sensitivity to FDA-approved drugs. This study provides insights into the biology of metastatic breast cancer and identifies clinically useful genomic features for the future improvement of patient management.
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Affiliation(s)
- Lindsay Angus
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Saskia M Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Job van Riet
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Arne Van Hoeck
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Luan Nguyen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Serena Nik-Zainal
- Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge, UK
| | - Tessa G Steenbruggen
- Department of Medical Oncology, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Vivianne C G Tjan-Heijnen
- Department of Medical Oncology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Mariette Labots
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Johanna M G H van Riel
- Department of Internal Medicine, Elisabeth-TweeSteden Hospital, Tilburg, The Netherlands
| | - Haiko J Bloemendal
- Department of Medical Oncology, Meander Medical Center, Amersfoort, The Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
| | - Neeltje Steeghs
- Department of Medical Oncology, the Netherlands Cancer Institute, Amsterdam, The Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
| | - Martijn P Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
| | - Emile E Voest
- Department of Medical Oncology, the Netherlands Cancer Institute, Amsterdam, The Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
| | - Harmen J G van de Werken
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Agnes Jager
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
- Hartwig Medical Foundation, Amsterdam, The Netherlands
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands.
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58
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Moelans CB, de Ligt J, van der Groep P, Prins P, Besselink NJM, Hoogstraat M, Ter Hoeve ND, Lacle MM, Kornegoor R, van der Pol CC, de Leng WWJ, Barbé E, van der Vegt B, Martens J, Bult P, Smit VTHBM, Koudijs MJ, Nijman IJ, Voest EE, Selenica P, Weigelt B, Reis-Filho JS, van der Wall E, Cuppen E, van Diest PJ. The molecular genetic make-up of male breast cancer. Endocr Relat Cancer 2019; 26:779-794. [PMID: 31340200 PMCID: PMC6938562 DOI: 10.1530/erc-19-0278] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 07/23/2019] [Indexed: 12/17/2022]
Abstract
Male breast cancer (MBC) is extremely rare and accounts for less than 1% of all breast malignancies. Therefore, clinical management of MBC is currently guided by research on the disease in females. In this study, DNA obtained from 45 formalin-fixed paraffin-embedded (FFPE) MBCs with and 90 MBCs (52 FFPE and 38 fresh-frozen) without matched normal tissues was subjected to massively parallel sequencing targeting all exons of 1943 cancer-related genes. The landscape of mutations and copy number alterations was compared to that of publicly available estrogen receptor (ER)-positive female breast cancers (smFBCs) and correlated to prognosis. From the 135 MBCs, 90% showed ductal histology, 96% were ER-positive, 66% were progesterone receptor (PR)-positive, and 2% HER2-positive, resulting in 50, 46 and 4% luminal A-like, luminal B-like and basal-like cases, respectively. Five patients had Klinefelter syndrome (4%) and 11% of patients harbored pathogenic BRCA2 germline mutations. The genomic landscape of MBC to some extent recapitulated that of smFBC, with recurrent PIK3CA (36%) and GATA3 (15%) somatic mutations, and with 40% of the most frequently amplified genes overlapping between both sexes. TP53 (3%) somatic mutations were significantly less frequent in MBC compared to smFBC, whereas somatic mutations in genes regulating chromatin function and homologous recombination deficiency-related signatures were more prevalent. MDM2 amplifications were frequent (13%), correlated with protein overexpression (P = 0.001) and predicted poor outcome (P = 0.007). In conclusion, despite similarities in the genomic landscape between MBC and smFBC, MBC is a molecularly unique and heterogeneous disease requiring its own clinical trials and treatment guidelines.
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Affiliation(s)
- Cathy B Moelans
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Joep de Ligt
- Department of Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Petra van der Groep
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Internal Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Pjotr Prins
- Department of Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Nicolle J M Besselink
- Department of Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
| | - Marlous Hoogstraat
- Department of Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Natalie D Ter Hoeve
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Miangela M Lacle
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Robert Kornegoor
- Department of Pathology, Gelre Ziekenhuizen, Appeldoorn, The Netherlands
| | - Carmen C van der Pol
- Cancer Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Wendy W J de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Ellis Barbé
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Bert van der Vegt
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - John Martens
- Department of Medical Oncology, Daniel den Hoed Cancer Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Peter Bult
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Marco J Koudijs
- Department of Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
| | - Isaac J Nijman
- Department of Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
| | - Emile E Voest
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Elsken van der Wall
- Cancer Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Edwin Cuppen
- Department of Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Cancer Genomics.nl, Center for Molecular Medicine, UMC Utrecht, Utrecht, The Netherlands
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
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59
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Chen Z, Wen W, Beeghly-Fadiel A, Shu XO, Díez-Obrero V, Long J, Bao J, Wang J, Liu Q, Cai Q, Moreno V, Zheng W, Guo X. Identifying Putative Susceptibility Genes and Evaluating Their Associations with Somatic Mutations in Human Cancers. Am J Hum Genet 2019; 105:477-492. [PMID: 31402092 PMCID: PMC6731359 DOI: 10.1016/j.ajhg.2019.07.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 07/10/2019] [Indexed: 12/23/2022] Open
Abstract
Genome-wide association studies (GWASs) have identified hundreds of genetic risk variants for human cancers. However, target genes for the majority of risk loci remain largely unexplored. It is also unclear whether GWAS risk-loci-associated genes contribute to mutational signatures and tumor mutational burden (TMB) in cancer tissues. We systematically conducted cis-expression quantitative trait loci (cis-eQTL) analyses for 294 GWAS-identified variants for six major types of cancer-colorectal, lung, ovary, prostate, pancreas, and melanoma-by using transcriptome data from the Genotype-Tissue Expression (GTEx) Project, the Cancer Genome Atlas (TCGA), and other public data sources. By using integrative analysis strategies, we identified 270 candidate target genes, including 99 with previously unreported associations, for six cancer types. By analyzing functional genomic data, our results indicate that 180 genes (66.7% of 270) had evidence of cis-regulation by putative functional variants via proximal promoter or distal enhancer-promoter interactions. Together with our previously reported associations for breast cancer risk, our results show that 24 genes are shared by at least two cancer types, including four genes for both breast and ovarian cancer. By integrating mutation data from TCGA, we found that expression levels of 33 and 66 putative susceptibility genes were associated with specific mutational signatures and TMB of cancer-driver genes, respectively, at a Bonferroni-corrected p < 0.05. Together, these findings provide further insight into our understanding of how genetic risk variants might contribute to carcinogenesis through the regulation of susceptibility genes that are related to the biogenesis of somatic mutations.
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Affiliation(s)
- Zhishan Chen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Alicia Beeghly-Fadiel
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Virginia Díez-Obrero
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona 08908, Spain; Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona 08908, Spain; Consortium for Biomedical Research in Epidemiology and Public Health, Barcelona 08908, Spain; Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona 08908, Spain
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Jiandong Bao
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA; College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Jing Wang
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program, Catalan Institute of Oncology, Barcelona 08908, Spain; Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute, Barcelona 08908, Spain; Consortium for Biomedical Research in Epidemiology and Public Health, Barcelona 08908, Spain; Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona 08908, Spain
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA.
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Bhagwate AV, Liu Y, Winham SJ, McDonough SJ, Stallings-Mann ML, Heinzen EP, Davila JI, Vierkant RA, Hoskin TL, Frost M, Carter JM, Radisky DC, Cunningham JM, Degnim AC, Wang C. Bioinformatics and DNA-extraction strategies to reliably detect genetic variants from FFPE breast tissue samples. BMC Genomics 2019; 20:689. [PMID: 31477010 PMCID: PMC6720378 DOI: 10.1186/s12864-019-6056-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/22/2019] [Indexed: 01/20/2023] Open
Abstract
Background Archived formalin fixed paraffin embedded (FFPE) samples are valuable clinical resources to examine clinically relevant morphology features and also to study genetic changes. However, DNA quality and quantity of FFPE samples are often sub-optimal, and resulting NGS-based genetics variant detections are prone to false positives. Evaluations of wet-lab and bioinformatics approaches are needed to optimize variant detection from FFPE samples. Results As a pilot study, we designed within-subject triplicate samples of DNA derived from paired FFPE and fresh frozen breast tissues to highlight FFPE-specific artifacts. For FFPE samples, we tested two FFPE DNA extraction methods to determine impact of wet-lab procedures on variant calling: QIAGEN QIAamp DNA Mini Kit (“QA”), and QIAGEN GeneRead DNA FFPE Kit (“QGR”). We also used negative-control (NA12891) and positive control samples (Horizon Discovery Reference Standard FFPE). All DNA sample libraries were prepared for NGS according to the QIAseq Human Breast Cancer Targeted DNA Panel protocol and sequenced on the HiSeq 4000. Variant calling and filtering were performed using QIAGEN Gene Globe Data Portal. Detailed variant concordance comparisons and mutational signature analysis were performed to investigate effects of FFPE samples compared to paired fresh frozen samples, along with different DNA extraction methods. In this study, we found that five times or more variants were called with FFPE samples, compared to their paired fresh-frozen tissue samples even after applying molecular barcoding error-correction and default bioinformatics filtering recommended by the vendor. We also found that QGR as an optimized FFPE-DNA extraction approach leads to much fewer discordant variants between paired fresh frozen and FFPE samples. Approximately 92% of the uniquely called FFPE variants were of low allelic frequency range (< 5%), and collectively shared a “C > T|G > A” mutational signature known to be representative of FFPE artifacts resulting from cytosine deamination. Based on control samples and FFPE-frozen replicates, we derived an effective filtering strategy with associated empirical false-discovery estimates. Conclusions Through this study, we demonstrated feasibility of calling and filtering genetic variants from FFPE tissue samples using a combined strategy with molecular barcodes, optimized DNA extraction, and bioinformatics methods incorporating genomics context such as mutational signature and variant allelic frequency. Electronic supplementary material The online version of this article (10.1186/s12864-019-6056-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aditya Vijay Bhagwate
- Departments of Health Science Research, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Yuanhang Liu
- Departments of Health Science Research, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Stacey J Winham
- Departments of Health Science Research, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Samantha J McDonough
- Departments of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | | | - Ethan P Heinzen
- Departments of Health Science Research, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Jaime I Davila
- Departments of Health Science Research, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Robert A Vierkant
- Departments of Health Science Research, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Tanya L Hoskin
- Departments of Health Science Research, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Marlene Frost
- Departments of Medical Oncology, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Jodi M Carter
- Departments of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Derek C Radisky
- Departments of Cancer Biology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Julie M Cunningham
- Departments of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Amy C Degnim
- Departments of Surgery, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Chen Wang
- Departments of Health Science Research, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA.
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61
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Smith ES, Da Cruz Paula A, Cadoo KA, Abu-Rustum NR, Pei X, Brown DN, Ferrando L, Sebastiao APM, Riaz N, Robson ME, Soslow RA, Reis-Filho JS, Mandelker D, Weigelt B. Endometrial Cancers in BRCA1 or BRCA2 Germline Mutation Carriers: Assessment of Homologous Recombination DNA Repair Defects. JCO Precis Oncol 2019; 3:PO.19.00103. [PMID: 32914019 PMCID: PMC7446423 DOI: 10.1200/po.19.00103] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2019] [Indexed: 01/20/2023] Open
Abstract
PURPOSE Endometrial cancer (EC) is not considered a component of the hereditary breast and ovarian cancer syndrome but can arise in patients with germline BRCA1/2 (gBRCA1/2) mutations. Biallelic BRCA1/2 alterations are associated with genomic features of homologous recombination DNA repair deficiency (HRD) in cancer. We sought to determine if ECs in gBRCA1/2 mutation carriers harbor biallelic alterations and/or features of HRD. METHODS Of 769 patients with EC who underwent germline panel testing, 10 pathogenic gBRCA1/2 mutation carriers were identified, and their tumor- and normal-derived DNA was subjected to massively parallel sequencing targeting at least 410 cancer-related genes. Three gBRCA1/2-associated ECs were identified in 232 ECs subjected to whole-exome sequencing by The Cancer Genome Atlas. Somatic mutations, copy number alterations, loss of heterozygosity, microsatellite instability (MSI), and genomic HRD features were assessed. RESULTS Of the 13 patients included who had EC, eight harbored pathogenic gBRCA1 mutations and five harbored gBRCA2 mutations. Eight (100%) and two (40%) ECs harbored biallelic BRCA1 and BRCA2 alterations through loss of heterozygosity of the wild-type allele. All ECs harbored somatic TP53 mutations. One monoallelic/sporadic gBRCA2-associated EC had MLH1 promoter methylation and was MSI high. High large-scale state transition scores, a genomic feature of HRD, were found only in ECs with bi- but not monoallelic BRCA1/2 alterations. The Signature Multivariate Analysis HRD signature Sig3 was enriched in biallelic gBRCA1/2 ECs, and the three ECs from The Cancer Genome Atlas with BRCA1 biallelic alterations subjected to whole-exome sequencing displayed a dominant HRD-related mutational signature 3. CONCLUSION A subset of gBRCA1/2-associated ECs harbor biallelic BRCA1/2 alterations and genomic features of HRD, which may benefit from homologous recombination-directed treatment regimens. ECs in BRCA2 mutation carriers might be sporadic and even MSI high, and may potentially benefit from immune-checkpoint inhibition.
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Affiliation(s)
- Evan S. Smith
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Xin Pei
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Lorenzo Ferrando
- Memorial Sloan Kettering Cancer Center, New York, NY
- University of Genoa, Genoa, Italy
| | | | - Nadeem Riaz
- Memorial Sloan Kettering Cancer Center, New York, NY
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Integrated analyses of murine breast cancer models reveal critical parallels with human disease. Nat Commun 2019; 10:3261. [PMID: 31332182 PMCID: PMC6646342 DOI: 10.1038/s41467-019-11236-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/27/2019] [Indexed: 12/20/2022] Open
Abstract
Mouse models have an essential role in cancer research, yet little is known about how various models resemble human cancer at a genomic level. Here, we complete whole genome sequencing and transcriptome profiling of two widely used mouse models of breast cancer, MMTV-Neu and MMTV-PyMT. Through integrative in vitro and in vivo studies, we identify copy number alterations in key extracellular matrix proteins including collagen 1 type 1 alpha 1 (COL1A1) and chondroadherin (CHAD) that drive metastasis in these mouse models. In addition to copy number alterations, we observe a propensity of the tumors to modulate tyrosine kinase-mediated signaling through mutation of phosphatases such as PTPRH in the MMTV-PyMT mouse model. Mutation in PTPRH leads to increased phospho-EGFR levels and decreased latency. These findings underscore the importance of understanding the complete genomic landscape of a mouse model and illustrate the utility this has in understanding human cancers. Mouse models are an essential tool in breast cancer research. Here, the authors present the genomic and transcriptomic profiles of two widely used mouse models, revealing parallels with the human disease specifically with metastasis and treatment response.
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63
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Sun J, Wang C, Zhang Y, Xu L, Fang W, Zhu Y, Zheng Y, Chen X, Xie X, Hu X, Hu W, Zheng J, Li P, Yu J, Mei Z, Cai X, Wang B, Hu Z, Shu Y, Shen H, Gu Y. Genomic signatures reveal DNA damage response deficiency in colorectal cancer brain metastases. Nat Commun 2019; 10:3190. [PMID: 31320627 PMCID: PMC6639368 DOI: 10.1038/s41467-019-10987-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 06/06/2019] [Indexed: 12/12/2022] Open
Abstract
Brain metastases (BM) of colorectal cancer (CRC) are rare but lethal, and an understanding of their genomic landscape is lacking. We conduct an analysis of whole-exome sequencing (WES) and whole-genome sequencing (WGS) data on 19 trios of patient-matched BMs, primary CRC tumors, and adjacent normal tissue. Compared with primary CRC, BM exhibits elevated mutational signatures of homologous recombination deficiency (HRD) and mismatch repair deficiency (MMRD). Further analysis reveals two DNA damage response (DDR) signatures could emerge early and are enhanced in BM tissues but are eliminated eventually in matched primary CRC tissues. BM-specific mutations in DDR genes and elevated microsatellite instability (MSI) levels support the importance of DDR in the brain metastasis of CRC. We also identify BM-related genes (e.g., SCN7A, SCN5A, SCN2A, IKZF1, and PDZRN4) that carry frequent BM-specific mutations. These results provide a better understanding of the BM mutational landscape and insights into treatment.
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Affiliation(s)
- Jing Sun
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Cheng Wang
- Department of Epidemiology and Biostatistics, School of Public Health; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211116, China
- Department of Bioinformatics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211116, China
| | - Yi Zhang
- Department of General Surgery, The First Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China
| | - Lingyan Xu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Weijia Fang
- Cancer Biotherapy Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Yuping Zhu
- Department of Colorectal Surgery, The Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Yi Zheng
- Cancer Biotherapy Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Xiaofeng Chen
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Xiju Xie
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Xinhua Hu
- Department of neurosurgery, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Weidong Hu
- Department of Neurology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Jingyu Zheng
- Department of Pathology, The Affiliated Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008, China
| | - Ping Li
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Jian Yu
- Department of Pathology and Radiation Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Zhu Mei
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
- Department of Oncology, Sir Run Run Hospital, Nanjing Medical University, Nanjing, 211116, China
| | - Xiaomin Cai
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Biao Wang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, School of Public Health; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211116, China
| | - Yongqian Shu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, School of Public Health; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211116, China.
| | - Yanhong Gu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.
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64
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Mechanisms of Genomic Instability in Breast Cancer. Trends Mol Med 2019; 25:595-611. [DOI: 10.1016/j.molmed.2019.04.004] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/29/2019] [Accepted: 04/04/2019] [Indexed: 12/22/2022]
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Van Hoeck A, Tjoonk NH, van Boxtel R, Cuppen E. Portrait of a cancer: mutational signature analyses for cancer diagnostics. BMC Cancer 2019; 19:457. [PMID: 31092228 PMCID: PMC6521503 DOI: 10.1186/s12885-019-5677-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/03/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND In the past decade, systematic and comprehensive analyses of cancer genomes have identified cancer driver genes and revealed unprecedented insight into the molecular mechanisms underlying the initiation and progression of cancer. These studies illustrate that although every cancer has a unique genetic make-up, there are only a limited number of mechanisms that shape the mutational landscapes of cancer genomes, as reflected by characteristic computationally-derived mutational signatures. Importantly, the molecular mechanisms underlying specific signatures can now be dissected and coupled to treatment strategies. Systematic characterization of mutational signatures in a cancer patient's genome may thus be a promising new tool for molecular tumor diagnosis and classification. RESULTS In this review, we describe the status of mutational signature analysis in cancer genomes and discuss the opportunities and relevance, as well as future challenges, for further implementation of mutational signatures in clinical tumor diagnostics and therapy guidance. CONCLUSIONS Scientific studies have illustrated the potential of mutational signature analysis in cancer research. As such, we believe that the implementation of mutational signature analysis within the diagnostic workflow will improve cancer diagnosis in the future.
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Affiliation(s)
- Arne Van Hoeck
- Center for Molecular Medicine and Oncode Institute, University Medical Centre Utrecht, Heidelberglaan 100, 3584CX Utrecht, The Netherlands
| | - Niels H. Tjoonk
- Center for Molecular Medicine and Oncode Institute, University Medical Centre Utrecht, Heidelberglaan 100, 3584CX Utrecht, The Netherlands
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584CS Utrecht, The Netherlands
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584CS Utrecht, The Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Centre Utrecht, Heidelberglaan 100, 3584CX Utrecht, The Netherlands
- Hartwig Medical Foundation, Science Park 408, 1098XH Amsterdam, The Netherlands
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66
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Kucab JE, Zou X, Morganella S, Joel M, Nanda AS, Nagy E, Gomez C, Degasperi A, Harris R, Jackson SP, Arlt VM, Phillips DH, Nik-Zainal S. A Compendium of Mutational Signatures of Environmental Agents. Cell 2019; 177:821-836.e16. [PMID: 30982602 PMCID: PMC6506336 DOI: 10.1016/j.cell.2019.03.001] [Citation(s) in RCA: 349] [Impact Index Per Article: 69.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/21/2018] [Accepted: 02/28/2019] [Indexed: 12/21/2022]
Abstract
Whole-genome-sequencing (WGS) of human tumors has revealed distinct mutation patterns that hint at the causative origins of cancer. We examined mutational signatures in 324 WGS human-induced pluripotent stem cells exposed to 79 known or suspected environmental carcinogens. Forty-one yielded characteristic substitution mutational signatures. Some were similar to signatures found in human tumors. Additionally, six agents produced double-substitution signatures and eight produced indel signatures. Investigating mutation asymmetries across genome topography revealed fully functional mismatch and transcription-coupled repair pathways. DNA damage induced by environmental mutagens can be resolved by disparate repair and/or replicative pathways, resulting in an assortment of signature outcomes even for a single agent. This compendium of experimentally induced mutational signatures permits further exploration of roles of environmental agents in cancer etiology and underscores how human stem cell DNA is directly vulnerable to environmental agents. VIDEO ABSTRACT.
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Affiliation(s)
- Jill E Kucab
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, 150 Stamford Street, London SE1 9NH, UK
| | - Xueqing Zou
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK; MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | | | - Madeleine Joel
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, 150 Stamford Street, London SE1 9NH, UK
| | - A Scott Nanda
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK
| | - Eszter Nagy
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, 150 Stamford Street, London SE1 9NH, UK
| | - Celine Gomez
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Andrea Degasperi
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK; MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Rebecca Harris
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Stephen P Jackson
- The Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Volker M Arlt
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, 150 Stamford Street, London SE1 9NH, UK
| | - David H Phillips
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, 150 Stamford Street, London SE1 9NH, UK.
| | - Serena Nik-Zainal
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK; MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.
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67
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El Hachem G, Gombos A, Awada A. Recent advances in understanding breast cancer and emerging therapies with a focus on luminal and triple-negative breast cancer. F1000Res 2019; 8:F1000 Faculty Rev-591. [PMID: 31069063 PMCID: PMC6492227 DOI: 10.12688/f1000research.17542.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/17/2019] [Indexed: 12/26/2022] Open
Abstract
Breast cancer is a global health issue. For decades, breast cancer was classified into many histological subtypes on the basis of microscopic and immunohistochemical evaluation. The discovery of many key genomic driver events involved in breast cancer carcinogenesis resulted in a better understanding of the tumor biology, the disease heterogeneity and the prognosis leading to the discovery of new modalities of targeted therapies and opening horizons toward a more personalized medicine. In recent years, many therapeutic options emerged in the field of metastatic breast carcinoma, especially for the luminal subtypes. They were able to transform the course of the disease while maintaining quality of life. However, the options are still limited for triple-negative breast cancer, but the better knowledge of its complex biology and the discovery of molecular targets are promising for more efficient novel therapies.
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Affiliation(s)
- Georges El Hachem
- Department of Hematology and Medical Oncology, Saint George Hospital University Medical Center, University of Balamand, Beirut, Lebanon
| | - Andrea Gombos
- Oncology Medicine Department, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Ahmad Awada
- Oncology Medicine Department, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
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68
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Jiang YZ, Ma D, Suo C, Shi J, Xue M, Hu X, Xiao Y, Yu KD, Liu YR, Yu Y, Zheng Y, Li X, Zhang C, Hu P, Zhang J, Hua Q, Zhang J, Hou W, Ren L, Bao D, Li B, Yang J, Yao L, Zuo WJ, Zhao S, Gong Y, Ren YX, Zhao YX, Yang YS, Niu Z, Cao ZG, Stover DG, Verschraegen C, Kaklamani V, Daemen A, Benson JR, Takabe K, Bai F, Li DQ, Wang P, Shi L, Huang W, Shao ZM. Genomic and Transcriptomic Landscape of Triple-Negative Breast Cancers: Subtypes and Treatment Strategies. Cancer Cell 2019; 35:428-440.e5. [PMID: 30853353 DOI: 10.1016/j.ccell.2019.02.001] [Citation(s) in RCA: 487] [Impact Index Per Article: 97.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 01/16/2019] [Accepted: 02/04/2019] [Indexed: 01/23/2023]
Abstract
We comprehensively analyzed clinical, genomic, and transcriptomic data of a cohort of 465 primary triple-negative breast cancer (TNBC). PIK3CA mutations and copy-number gains of chromosome 22q11 were more frequent in our Chinese cohort than in The Cancer Genome Atlas. We classified TNBCs into four transcriptome-based subtypes: (1) luminal androgen receptor (LAR), (2) immunomodulatory, (3) basal-like immune-suppressed, and (4) mesenchymal-like. Putative therapeutic targets or biomarkers were identified among each subtype. Importantly, the LAR subtype showed more ERBB2 somatic mutations, infrequent mutational signature 3 and frequent CDKN2A loss. The comprehensive profile of TNBCs provided here will serve as a reference to further advance the understanding and precision treatment of TNBC.
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Affiliation(s)
- Yi-Zhou Jiang
- Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai 200032, P.R. China
| | - Ding Ma
- Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai 200032, P.R. China
| | - Chen Suo
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, 2005 Songhu Road, Shanghai 200438, P.R. China; Department of Epidemiology, School of Public Health, Fudan University, Shanghai 200032, P.R. China
| | - Jinxiu Shi
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai (CHGC) and Shanghai Industrial Technology Institute (SITI), 250 Bibo Road, Shanghai 201203, P.R. China
| | - Mengzhu Xue
- SARI Center for Stem Cell and Nanomedicine, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, P.R. China
| | - Xin Hu
- Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai 200032, P.R. China
| | - Yi Xiao
- Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai 200032, P.R. China
| | - Ke-Da Yu
- Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai 200032, P.R. China
| | - Yi-Rong Liu
- Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai 200032, P.R. China
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, 2005 Songhu Road, Shanghai 200438, P.R. China
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, 2005 Songhu Road, Shanghai 200438, P.R. China
| | - Xiangnan Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, 2005 Songhu Road, Shanghai 200438, P.R. China
| | - Chenhui Zhang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai (CHGC) and Shanghai Industrial Technology Institute (SITI), 250 Bibo Road, Shanghai 201203, P.R. China
| | - Pengchen Hu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai (CHGC) and Shanghai Industrial Technology Institute (SITI), 250 Bibo Road, Shanghai 201203, P.R. China
| | - Jing Zhang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai (CHGC) and Shanghai Industrial Technology Institute (SITI), 250 Bibo Road, Shanghai 201203, P.R. China
| | - Qi Hua
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai (CHGC) and Shanghai Industrial Technology Institute (SITI), 250 Bibo Road, Shanghai 201203, P.R. China
| | - Jiyang Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, 2005 Songhu Road, Shanghai 200438, P.R. China
| | - Wanwan Hou
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, 2005 Songhu Road, Shanghai 200438, P.R. China
| | - Luyao Ren
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, 2005 Songhu Road, Shanghai 200438, P.R. China
| | - Ding Bao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, 2005 Songhu Road, Shanghai 200438, P.R. China
| | - Bingying Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, 2005 Songhu Road, Shanghai 200438, P.R. China
| | - Jingcheng Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, 2005 Songhu Road, Shanghai 200438, P.R. China
| | - Ling Yao
- Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai 200032, P.R. China
| | - Wen-Jia Zuo
- Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai 200032, P.R. China
| | - Shen Zhao
- Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai 200032, P.R. China
| | - Yue Gong
- Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai 200032, P.R. China
| | - Yi-Xing Ren
- Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai 200032, P.R. China
| | - Ya-Xin Zhao
- Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai 200032, P.R. China
| | - Yun-Song Yang
- Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai 200032, P.R. China
| | - Zhenmin Niu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai (CHGC) and Shanghai Industrial Technology Institute (SITI), 250 Bibo Road, Shanghai 201203, P.R. China
| | - Zhi-Gang Cao
- Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai 200032, P.R. China
| | - Daniel G Stover
- The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Claire Verschraegen
- The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Virginia Kaklamani
- Division Hematology/Oncology, University of Texas Health Science Center San Antonio, San Antonio, TX 78284, USA
| | - Anneleen Daemen
- Department of Bioinformatics & Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - John R Benson
- Cambridge Breast Unit, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Kazuaki Takabe
- Division of Breast Surgery, Department of Surgical Oncology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Fan Bai
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, P.R. China
| | - Da-Qiang Li
- Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai 200032, P.R. China
| | - Peng Wang
- Bio-med Big Data Center, CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P.R. China.
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, 2005 Songhu Road, Shanghai 200438, P.R. China.
| | - Wei Huang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai (CHGC) and Shanghai Industrial Technology Institute (SITI), 250 Bibo Road, Shanghai 201203, P.R. China.
| | - Zhi-Ming Shao
- Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai 200032, P.R. China.
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Murphy C, Muscat A, Ashley D, Mukaro V, West L, Liao Y, Chisanga D, Shi W, Collins I, Baron-Hay S, Patil S, Lindeman G, Khasraw M. Tailored NEOadjuvant epirubicin, cyclophosphamide and Nanoparticle Albumin-Bound paclitaxel for breast cancer: The phase II NEONAB trial-Clinical outcomes and molecular determinants of response. PLoS One 2019; 14:e0210891. [PMID: 30763338 PMCID: PMC6375556 DOI: 10.1371/journal.pone.0210891] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 12/28/2018] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND This study evaluated the feasibility of achieving high response rates in stage II or III breast cancer by tailoring neoadjuvant therapy using clinical and histopathological features and the Oncotype DX Breast Recurrence Score. Genomic determinants of response and resistance were also explored. PATIENTS AND OUTCOME MEASURES Fifty-one patients were enrolled. The primary cohort comprised 40 patients: 15 human epidermal growth factor receptor type 2 (HER2)-amplified; 15 triple-negative (TNBC); and ten hormone receptor (HR)-positive, HER2-non-amplified tumours; with recurrence scores ≥25. Patients were treated with epirubicin and cyclophosphamide, followed by nab-paclitaxel, with the addition of trastuzumab if HER2-amplified. The primary endpoint was pathological complete response (pCR) in the breast. Pre- and post-treatment tumour samples underwent variant burden, gene and gene pathway, mutational signature profile and clonal evolution analyses. RESULTS The pCR rates were: overall 55% (n = 22), HER2-amplified 80% (n = 12), triple-negative 46% (n = 7) and HR-positive, HER2-non-amplified 30% (n = 3). Grade 3 or 4 adverse events included febrile neutropenia (8%), neutropenia (18%), sensory neuropathy (5%), deranged transaminases (5%), fatigue (2%), diarrhoea (2%), and pneumothorax (2%). Molecular analyses demonstrated strong similarities between residual disease and matched primary tumour. ATM signalling pathway alterations and the presence of a COSMIC Signature 3 implied the majority of tumours contained some form of homologous repair deficiency. ATM pathway alterations were identified in the subset of TNBC patients who did not achieve pCR; Signature 3 was present in both pCR and non-pCR subgroups. Clonal evolution analyses demonstrated both persistence and emergence of chemoresistant clones. CONCLUSIONS This treatment regime resulted in a high rate of pCR, demonstrating that tailored neoadjuvant therapy using a genomic recurrence score is feasible and warrants further investigation. Molecular analysis revealed few commonalities between patients. For TNBC future clinical gains will require precision medicine, potentially using DNA sequencing to identify specific targets for individuals with resistant disease. TRIAL REGISTRATION Clinicaltrials.gov NCT01830244.
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Affiliation(s)
- Caitlin Murphy
- University Hospital Geelong, Geelong, Victoria, Australia
- School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - Andrea Muscat
- School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - David Ashley
- University Hospital Geelong, Geelong, Victoria, Australia
- School of Medicine, Deakin University, Geelong, Victoria, Australia
- Preston Robert Tisch Brain Tumor Center, Duke University, Durham, North Carolina, United States of America
| | - Violet Mukaro
- University Hospital Geelong, Geelong, Victoria, Australia
- School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - Linda West
- University Hospital Geelong, Geelong, Victoria, Australia
- Lake Imaging, Geelong, Victoria, Australia
| | - Yang Liao
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - David Chisanga
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Wei Shi
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Ian Collins
- School of Medicine, Deakin University, Geelong, Victoria, Australia
- South West Health Care, Warrnambool, Victoria, Australia
| | - Sally Baron-Hay
- Royal North Shore Hospital, St Leonards, New South Wales, Australia
- North Shore Private Hospital, St Leonards, New South Wales, Australia
| | - Sujata Patil
- Memorial Sloan Kettering Cancer Center, New York, United States of America
| | - Geoffrey Lindeman
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Mustafa Khasraw
- University Hospital Geelong, Geelong, Victoria, Australia
- School of Medicine, Deakin University, Geelong, Victoria, Australia
- National Health and Medical Research Council Clinical Trials Centre, University of Sydney, New South Wales, Australia
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70
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Kalimutho M, Nones K, Srihari S, Duijf PHG, Waddell N, Khanna KK. Patterns of Genomic Instability in Breast Cancer. Trends Pharmacol Sci 2019; 40:198-211. [PMID: 30736983 DOI: 10.1016/j.tips.2019.01.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 12/14/2018] [Accepted: 01/08/2019] [Indexed: 01/02/2023]
Abstract
Breast cancer is one of the most common cancers affecting women. Despite significant improvements in overall survival, it remains a significant cause of death worldwide. Genomic instability (GI) is a hallmark of cancer and plays a pivotal role in breast cancer development and progression. In the past decade, high-throughput technologies have provided a wealth of information that has facilitated the identification of a diverse repertoire of mutated genes and mutational processes operative across cancers. Here, we review recent findings on genomic alterations and mutational processes in breast cancer pathogenesis. Most importantly, we summarize the clinical challenges and opportunities to utilize omics-based signatures for better management of breast cancer patients and treatment decision-making.
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Affiliation(s)
- Murugan Kalimutho
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006, Australia.
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006, Australia
| | - Sriganesh Srihari
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Pascal H G Duijf
- University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, 37 Kent Street, Brisbane, QLD 4102, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006, Australia
| | - Kum Kum Khanna
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD 4006, Australia.
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71
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Affiliation(s)
- Serena Nik-Zainal
- Department of Medical Genetics, Addenbrooke's Treatment Centre, The Clinical School, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK.
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Achrol AS, Rennert RC, Anders C, Soffietti R, Ahluwalia MS, Nayak L, Peters S, Arvold ND, Harsh GR, Steeg PS, Chang SD. Brain metastases. Nat Rev Dis Primers 2019; 5:5. [PMID: 30655533 DOI: 10.1038/s41572-018-0055-y] [Citation(s) in RCA: 541] [Impact Index Per Article: 108.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An estimated 20% of all patients with cancer will develop brain metastases, with the majority of brain metastases occurring in those with lung, breast and colorectal cancers, melanoma or renal cell carcinoma. Brain metastases are thought to occur via seeding of circulating tumour cells into the brain microvasculature; within this unique microenvironment, tumour growth is promoted and the penetration of systemic medical therapies is limited. Development of brain metastases remains a substantial contributor to overall cancer mortality in patients with advanced-stage cancer because prognosis remains poor despite multimodal treatments and advances in systemic therapies, which include a combination of surgery, radiotherapy, chemotherapy, immunotherapy and targeted therapies. Thus, interest abounds in understanding the mechanisms that drive brain metastases so that they can be targeted with preventive therapeutic strategies and in understanding the molecular characteristics of brain metastases relative to the primary tumour so that they can inform targeted therapy selection. Increased molecular understanding of the disease will also drive continued development of novel immunotherapies and targeted therapies that have higher bioavailability beyond the blood-tumour barrier and drive advances in radiotherapies and minimally invasive surgical techniques. As these discoveries and innovations move from the realm of basic science to preclinical and clinical applications, future outcomes for patients with brain metastases are almost certain to improve.
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Affiliation(s)
- Achal Singh Achrol
- Department of Neurosurgery and Neurosciences, John Wayne Cancer Institute and Pacific Neuroscience Institute, Santa Monica, CA, USA.
| | - Robert C Rennert
- Department of Neurosurgery, University of California-San Diego, San Diego, CA, USA.
| | - Carey Anders
- Division of Hematology/Oncology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | | | - Manmeet S Ahluwalia
- Burkhardt Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland, OH, USA
| | - Lakshmi Nayak
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Solange Peters
- Medical Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Nils D Arvold
- Department of Radiation Oncology, St. Luke's Cancer Center, Duluth, MN, USA
| | - Griffith R Harsh
- Department of Neurosurgery, University of California-Davis, School of Medicine, Sacramento, CA, USA
| | - Patricia S Steeg
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Center, Bethesda, MD, USA
| | - Steven D Chang
- Department of Neurosurgery, University of California-Davis, School of Medicine, Sacramento, CA, USA.
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Reilly NM, Yard BD, Pittman DL. Homologous Recombination-Mediated DNA Repair and Implications for Clinical Treatment of Repair Defective Cancers. Methods Mol Biol 2019; 1999:3-29. [PMID: 31127567 DOI: 10.1007/978-1-4939-9500-4_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Double-strand DNA breaks (DSBs) are generated by ionizing radiation and as intermediates during the processing of DNA, such as repair of interstrand cross-links and collapsed replication forks. These potentially deleterious DSBs are repaired primarily by the homologous recombination (HR) and nonhomologous end joining (NHEJ) DNA repair pathways. HR utilizes a homologous template to accurately restore damaged DNA, whereas NHEJ utilizes microhomology to join breaks in close proximity. The pathway available for DSB repair is dependent upon the cell cycle stage; for example, HR primarily functions during the S/G2 stages while NHEJ can repair DSBs at any cell cycle stage. Posttranslational modifications (PTMs) promote activity of specific pathways and subpathways through enzyme activation and precisely timed protein recruitment and degradation. This chapter provides an overview of PTMs occurring during DSB repair. In addition, clinical phenotypes associated with HR-defective cancers, such as mutational signatures used to predict response to poly(ADP-ribose) polymerase inhibitors, are discussed. Understanding these processes will provide insight into mechanisms of genome maintenance and likely identify targets and new avenues for therapeutic interventions.
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Affiliation(s)
- Nicole M Reilly
- Fondazione Piemontese per la Ricerca sul Cancro ONLUS, Candiolo, Italy
| | - Brian D Yard
- Department of Translational Hematology and Oncology Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Douglas L Pittman
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA.
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Kalinowski L, Saunus JM, McCart Reed AE, Lakhani SR. Breast Cancer Heterogeneity in Primary and Metastatic Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1152:75-104. [DOI: 10.1007/978-3-030-20301-6_6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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RAD-ical New Insights into RAD51 Regulation. Genes (Basel) 2018; 9:genes9120629. [PMID: 30551670 PMCID: PMC6316741 DOI: 10.3390/genes9120629] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/04/2018] [Accepted: 12/07/2018] [Indexed: 01/17/2023] Open
Abstract
The accurate repair of DNA is critical for genome stability and cancer prevention. DNA double-strand breaks are one of the most toxic lesions; however, they can be repaired using homologous recombination. Homologous recombination is a high-fidelity DNA repair pathway that uses a homologous template for repair. One central HR step is RAD51 nucleoprotein filament formation on the single-stranded DNA ends, which is a step required for the homology search and strand invasion steps of HR. RAD51 filament formation is tightly controlled by many positive and negative regulators, which are collectively termed the RAD51 mediators. The RAD51 mediators function to nucleate, elongate, stabilize, and disassemble RAD51 during repair. In model organisms, RAD51 paralogs are RAD51 mediator proteins that structurally resemble RAD51 and promote its HR activity. New functions for the RAD51 paralogs during replication and in RAD51 filament flexibility have recently been uncovered. Mutations in the human RAD51 paralogs (RAD51B, RAD51C, RAD51D, XRCC2, XRCC3, and SWSAP1) are found in a subset of breast and ovarian cancers. Despite their discovery three decades ago, few advances have been made in understanding the function of the human RAD51 paralogs. Here, we discuss the current perspective on the in vivo and in vitro function of the RAD51 paralogs, and their relationship with cancer in vertebrate models.
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Abstract
Somatic structural variants undoubtedly play important roles in driving tumourigenesis. This is evident despite the substantial technical challenges that remain in accurately detecting structural variants and their breakpoints in tumours and in spite of our incomplete understanding of the impact of structural variants on cellular function. Developments in these areas of research contribute to the ongoing discovery of structural variation with a clear impact on the evolution of the tumour and on the clinical importance to the patient. Recent large whole genome sequencing studies have reinforced our impression of each tumour as a unique combination of mutations but paradoxically have also discovered similar genome-wide patterns of single-nucleotide and structural variation between tumours. Statistical methods have been developed to deconvolute mutation patterns, or signatures, that recur across samples, providing information about the mutagens and repair processes that may be active in a given tumour. These signatures can guide treatment by, for example, highlighting vulnerabilities in a particular tumour to a particular chemotherapy. Thus, although the complete reconstruction of the full evolutionary trajectory of a tumour genome remains currently out of reach, valuable data are already emerging to improve the treatment of cancer.
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Affiliation(s)
- Ailith Ewing
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH42XU, UK
| | - Colin Semple
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH42XU, UK
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77
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Ashley CW, Da Cruz Paula A, Kumar R, Mandelker D, Pei X, Riaz N, Reis-Filho JS, Weigelt B. Analysis of mutational signatures in primary and metastatic endometrial cancer reveals distinct patterns of DNA repair defects and shifts during tumor progression. Gynecol Oncol 2018; 152:11-19. [PMID: 30415991 DOI: 10.1016/j.ygyno.2018.10.032] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/22/2018] [Accepted: 10/23/2018] [Indexed: 10/27/2022]
Abstract
OBJECTIVE Mutational signatures provide insights into the biological processes shaping tumor genomes and may inform patient therapy. We sought to define the mutational signatures of i) endometrioid and serous endometrial carcinomas (ECs), stratified into the four molecular subtypes, ii) uterine carcinosarcomas, and iii) matched primary and metastatic ECs. METHODS Whole-exome sequencing MC3 data from primary endometrioid and serous carcinomas (n = 232) and uterine carcinosarcomas (n = 57) from The Cancer Genome Atlas (TCGA), and matched primary and metastatic ECs (n = 61, 26 patients) were reanalyzed, subjected to mutational signature analysis using deconstructSigs, and correlated with clinicopathologic and genomic data. RESULTS POLE (ultramutated) and MSI (hypermutated) molecular subtypes displayed dominant mutational signatures associated with POLE mutations (15/17 cases) and microsatellite instability (55/65 cases), respectively. Most endometrioid and serous carcinomas of copy-number low (endometrioid) and copy-number high (serous-like) molecular subtypes, and carcinosarcomas displayed a dominant aging-associated signature 1. Only 15% (9/60) of copy-number high (serous-like) ECs had a dominant signature 3 (homologous recombination DNA repair deficiency (HRD)-related), a prevalence significantly lower than that found in high-grade serous ovarian carcinomas (54%, p < 0.001) or basal-like breast cancers (46%, p < 0.001). Shifts from aging- or POLE- to MSI-related mutational processes were observed in the progression from primary to metastatic ECs in a subset of cases. CONCLUSIONS The mutational processes underpinning ECs vary even among tumors of the same TCGA molecular subtype and in the progression from primary to metastatic ECs. Only a minority of copy-number high (serous-like) ECs display genomics features of HRD and would likely benefit from HRD-directed therapies.
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Affiliation(s)
- Charles W Ashley
- Department of Surgery, Gynecology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arnaud Da Cruz Paula
- Department of Surgery, Gynecology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rahul Kumar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Diana Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xin Pei
- Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem Riaz
- Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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78
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O'Leary B, Cutts RJ, Liu Y, Hrebien S, Huang X, Fenwick K, André F, Loibl S, Loi S, Garcia-Murillas I, Cristofanilli M, Huang Bartlett C, Turner NC. The Genetic Landscape and Clonal Evolution of Breast Cancer Resistance to Palbociclib plus Fulvestrant in the PALOMA-3 Trial. Cancer Discov 2018; 8:1390-1403. [PMID: 30206110 PMCID: PMC6368247 DOI: 10.1158/2159-8290.cd-18-0264] [Citation(s) in RCA: 376] [Impact Index Per Article: 62.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/09/2018] [Accepted: 09/06/2018] [Indexed: 12/20/2022]
Abstract
CDK4/6 inhibition with endocrine therapy is now a standard of care for advanced estrogen receptor-positive breast cancer. Mechanisms of CDK4/6 inhibitor resistance have been described preclinically, with limited evidence from clinical samples. We conducted paired baseline and end-of-treatment circulating tumor DNA sequencing from 195 patients in the PALOMA-3 randomized phase III trial of palbociclib plus fulvestrant versus placebo plus fulvestrant. We show that clonal evolution occurs frequently during treatment, reflecting substantial subclonal complexity in breast cancer that has progressed after prior endocrine therapy. RB1 mutations emerged only in the palbociclib plus fulvestrant arm and in a minority of patients (6/127, 4.7%, P = 0.041). New driver mutations emerged in PIK3CA (P = 0.00069) and ESR1 after treatment in both arms, in particular ESR1 Y537S (P = 0.0037). Evolution of driver gene mutations was uncommon in patients progressing early on palbociclib plus fulvestrant but common in patients progressing later on treatment. These findings inform future treatment strategies to address resistance to palbociclib plus fulvestrant.Significance: Acquired mutations from fulvestrant are a major driver of resistance to fulvestrant and palbociclib combination therapy. ESR1 Y537S mutation promotes resistance to fulvestrant. Clonal evolution results in frequent acquisition of driver mutations in patients progressing late on therapy, which suggests that early and late progression have distinct mechanisms of resistance. Cancer Discov; 8(11); 1390-403. ©2018 AACR. See related commentary by Schiff and Jeselsohn, p. 1352 This article is highlighted in the In This Issue feature, p. 1333.
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Affiliation(s)
- Ben O'Leary
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
- Breast Unit, Royal Marsden Hospital, London, United Kingdom
| | - Rosalind J Cutts
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | | | - Sarah Hrebien
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | | | - Kerry Fenwick
- Tumour Profiling Unit, The Institute of Cancer Research, London, United Kingdom
| | - Fabrice André
- Department of Medical Oncology, Institut Gustave Roussy, Villejuif, France
| | | | - Sherene Loi
- Division of Research and Cancer Medicine, University of Melbourne, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Isaac Garcia-Murillas
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Massimo Cristofanilli
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Chicago, Illinois
| | | | - Nicholas C Turner
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom.
- Breast Unit, Royal Marsden Hospital, London, United Kingdom
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The therapeutic significance of mutational signatures from DNA repair deficiency in cancer. Nat Commun 2018; 9:3292. [PMID: 30120226 PMCID: PMC6098043 DOI: 10.1038/s41467-018-05228-y] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 06/15/2018] [Indexed: 12/19/2022] Open
Abstract
Cancer is fundamentally a disease of the genome and inherited deficiencies in DNA repair pathways are well established to increase lifetime cancer risk. Computational analysis of pan-cancer data has identified signatures of mutational processes thought to be responsible for the pattern of mutations in any given cancer. These analyses identified altered DNA repair pathways in a much broader spectrum of cancers than previously appreciated with significant therapeutic implications. The development of DNA repair deficiency biomarkers is critical to the implementation of therapeutic targeting of repair-deficient tumors, using either DNA damaging agents or immunotherapy for the personalization of cancer therapy. Targeting DNA repair-deficient tumors is one of the most promising therapeutic strategies in cancer research; however, accurately predicting which tumors will respond can be a challenge. Here the authors present a review of the current state of knowledge in DNA repair deficiency across human cancers.
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80
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Kaiser VB, Semple CA. Chromatin loop anchors are associated with genome instability in cancer and recombination hotspots in the germline. Genome Biol 2018; 19:101. [PMID: 30060743 PMCID: PMC6066925 DOI: 10.1186/s13059-018-1483-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 07/13/2018] [Indexed: 01/07/2023] Open
Abstract
Background Chromatin loops form a basic unit of interphase nuclear organization, with chromatin loop anchor points providing contacts between regulatory regions and promoters. However, the mutational landscape at these anchor points remains under-studied. Here, we describe the unusual patterns of somatic mutations and germline variation associated with loop anchor points and explore the underlying features influencing these patterns. Results Analyses of whole genome sequencing datasets reveal that anchor points are strongly depleted for single nucleotide variants (SNVs) in tumours. Despite low SNV rates in their genomic neighbourhood, anchor points emerge as sites of evolutionary innovation, showing enrichment for structural variant (SV) breakpoints and a peak of SNVs at focal CTCF sites within the anchor points. Both CTCF-bound and non-CTCF anchor points harbour an excess of SV breakpoints in multiple tumour types and are prone to double-strand breaks in cell lines. Common fragile sites, which are hotspots for genome instability, also show elevated numbers of intersecting loop anchor points. Recurrently disrupted anchor points are enriched for genes with functions in cell cycle transitions and regions associated with predisposition to cancer. We also discover a novel class of CTCF-bound anchor points which overlap meiotic recombination hotspots and are enriched for the core PRDM9 binding motif, suggesting that the anchor points have been foci for diversity generated during recent human evolution. Conclusions We suggest that the unusual chromatin environment at loop anchor points underlies the elevated rates of variation observed, marking them as sites of regulatory importance but also genomic fragility. Electronic supplementary material The online version of this article (10.1186/s13059-018-1483-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vera B Kaiser
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.
| | - Colin A Semple
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
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81
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Shapiro M, Meier S, MacCarthy T. The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure. BMC Bioinformatics 2018; 19:163. [PMID: 29716522 PMCID: PMC5930495 DOI: 10.1186/s12859-018-2161-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 04/20/2018] [Indexed: 01/23/2023] Open
Abstract
Background Activation induced deaminase (AID) and apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3 (APOBEC3) are deaminases that mutate C to U on single-stranded DNA (ssDNA). AID is expressed primarily in germinal center B-cells, where it facilitates affinity maturation and class-switch recombination. APOBEC3 are a family of anti-viral proteins that act as part of the intrinsic immune response. In both cases, there are particular sequence motifs, also known as “mutation motifs”, to which these deaminases prefer to bind and mutate. Results We present a program, the cytidine deaminase under-representation reporter (CDUR) designed to statistically determine whether a given sequence has an under/over-representation of these mutation motifs. CDUR shows consitency with other studies of mutation motifs, as we show by analyzing sequences from the adeno-associated virus 2 (AAV2) and human papillomavirus (HPV). Conclusion Using various shuffling mechanisms to generate different null model distributions, we can tailor CDUR to correct for metrics such as GC-content, dinucleotide frequency, and codon bias.
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Affiliation(s)
- Maxwell Shapiro
- Department of Applied Mathematics and Statistics, Stony Brook University, 100 Nicolls Road, Stony Brook, NY, USA
| | - Stephen Meier
- Department of Applied Mathematics and Statistics, Stony Brook University, 100 Nicolls Road, Stony Brook, NY, USA
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, 100 Nicolls Road, Stony Brook, NY, USA. .,Laufer Center for Physical and Quantitative Biology, Stony Brook University, 100 Nicolls Road, Stony Brook, NY, USA.
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Jarvis MC, Ebrahimi D, Temiz NA, Harris RS. Mutation Signatures Including APOBEC in Cancer Cell Lines. JNCI Cancer Spectr 2018; 2. [PMID: 29888758 PMCID: PMC5993214 DOI: 10.1093/jncics/pky002] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Background: Multiple endogenous and exogenous sources of DNA damage contribute to the overall mutation burden in cancer, with distinct and overlapping combinations contributing to each cancer type. Many mutation sources result in characteristic mutation signatures, which can be deduced from tumor genomic DNA sequences. Examples include spontaneous hydrolytic deamination of methyl-cytosine bases in CG motifs (AGEING signature) and C-to-T and C-to-G mutations in 5'-TC(A/T) motifs (APOBEC signature). Methods: The deconstructSigs R package was used to analyze single-base substitution mutation signatures in more than 1000 cancer cell lines. Two additional approaches were used to analyze the APOBEC mutation signature. Results: Most cell lines show evidence for multiple mutation signatures. For instance, the AGEING signature, which is the largest source of mutation in most primary tumors, predominates in the majority of cancer cell lines. The APOBEC mutation signature is enriched in cancer cell lines from breast, lung, head/neck, bladder, and cervical cancers, where this signature also comprises a large fraction of all mutations. Conclusions: The single-base substitution mutation signatures of cancer cell lines often reflect those of the original tumors from which they are derived. Cancer cell lines with enrichments for distinct mutation signatures such as APOBEC have the potential to become model systems for fundamental research on the underlying mechanisms and for advancing clinical strategies to exploit these processes.
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Affiliation(s)
- Matthew C Jarvis
- Masonic Cancer Center (MCJ, DE, NAT, RSH), Center for Genome Engineering (MCJ, DE, RSH), Department of Biochemistry, Molecular Biology, and Biophysics (MCJ, DE, RSH), Institute for Molecular Virology (MCJ, DE, RSH), Institute for Health Informatics (NAT), Howard Hughes Medical Institute (RSH), University of Minnesota, Minneapolis, MN, USA
| | - Diako Ebrahimi
- Masonic Cancer Center (MCJ, DE, NAT, RSH), Center for Genome Engineering (MCJ, DE, RSH), Department of Biochemistry, Molecular Biology, and Biophysics (MCJ, DE, RSH), Institute for Molecular Virology (MCJ, DE, RSH), Institute for Health Informatics (NAT), Howard Hughes Medical Institute (RSH), University of Minnesota, Minneapolis, MN, USA
| | - Nuri A Temiz
- Masonic Cancer Center (MCJ, DE, NAT, RSH), Center for Genome Engineering (MCJ, DE, RSH), Department of Biochemistry, Molecular Biology, and Biophysics (MCJ, DE, RSH), Institute for Molecular Virology (MCJ, DE, RSH), Institute for Health Informatics (NAT), Howard Hughes Medical Institute (RSH), University of Minnesota, Minneapolis, MN, USA
| | - Reuben S Harris
- Masonic Cancer Center (MCJ, DE, NAT, RSH), Center for Genome Engineering (MCJ, DE, RSH), Department of Biochemistry, Molecular Biology, and Biophysics (MCJ, DE, RSH), Institute for Molecular Virology (MCJ, DE, RSH), Institute for Health Informatics (NAT), Howard Hughes Medical Institute (RSH), University of Minnesota, Minneapolis, MN, USA
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83
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Freedman RA, Partridge AH. Emerging Data and Current Challenges for Young, Old, Obese, or Male Patients with Breast Cancer. Clin Cancer Res 2018; 23:2647-2654. [PMID: 28572259 DOI: 10.1158/1078-0432.ccr-16-2552] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/20/2017] [Accepted: 04/04/2017] [Indexed: 11/16/2022]
Abstract
There are distinct subgroups of patients who have historically been underrepresented in most prospective clinical trials in breast cancer, including the youngest and oldest patients, male patients, and those struggling with obesity. Herein, we review current and future directions in research for each of these special populations with breast cancer, highlighting significant knowledge gaps and priorities in tumor biology and heterogeneity, therapeutic decision making promotion of adherence, supportive care, and psychosocial and functional well-being. In younger women, future study should focus on the biological underpinnings of aggressive disease and optimizing adherence and treatment decision making while addressing their unique survivorship needs. The latter includes generating a scientific basis for interruption of therapy for pregnancy. Among older patients, interventions should focus on increasing clinical trial accrual, predicting and mitigating toxicity so that functional status can be optimized, tailoring needs for dose modification, and anticipating life expectancy in the context of competing causes of death. For men with breast cancer, we need worldwide collaboration to answer even basic questions on optimal treatment, supportive care, and survivorship strategies. Finally, for those struggling with obesity, we need to better understand the biological associations with cancer incidence, prognosis and outcome, and how we can best intervene to assure weight loss at the "right time." It is only through highly collaborative, far-reaching, prospective, multidisciplinary, patient-centered, and patient-engaged efforts that we can optimize the physical and psychologic outcomes for all patients with breast cancer. Clin Cancer Res; 23(11); 2647-54. ©2017 AACRSee all articles in this CCR Focus section, "Breast Cancer Research: From Base Pairs to Populations."
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84
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Partridge AH, Carey LA. Unmet Needs in Clinical Research in Breast Cancer: Where Do We Need to Go? Clin Cancer Res 2018; 23:2611-2616. [PMID: 28572255 DOI: 10.1158/1078-0432.ccr-16-2633] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 04/10/2017] [Accepted: 04/10/2017] [Indexed: 12/20/2022]
Abstract
This CCR Focus highlights areas in breast cancer research with the greatest potential for clinical and therapeutic application. The articles in this CCR Focus address the state of the science in a broad range of areas with a focus on "hot" although sometimes controversial topics, unanswered questions, and unmet need. From mutational signatures, the cancer genomic revolution, and new inroads in immunotherapy for breast cancer to unique concerns of vulnerable populations as well as national and global health disparities, these works represent much of the promise of breast cancer research as well as the challenges in the coming years. Each review focuses not only on recent discoveries but also on putting the topic in context, including limitations to overcome. This overview is designed to further contextualize the highlighted issues within the broader research landscape. We also present new information from a poll of ALLIANCE for Clinical Trials in Oncology Breast Committee members regarding the most needed and viable potential future National Cancer Institute (NCI)-supported clinical trials in breast cancer. The great challenge is to translate the potential benefits of greater scientific knowledge reflected in this CCR Focus section into improvements in outcomes for individuals and populations with breast cancer. A unifying theme across the six articles contained in this CCR Focus is the increasingly recognized value and necessity of collaboration across disciplines from bench to bedside to populations. Only continued and iteratively amplified scientific, clinical, and governmental commitment to creating, testing, and implementing new knowledge will reduce the global morbidity and mortality of breast cancer. Clin Cancer Res; 23(11); 2611-6. ©2017 AACRSee all articles in this CCR Focus section, "Breast Cancer Research: From Base Pairs to Populations."
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Affiliation(s)
| | - Lisa A Carey
- Lineberger Cancer Center, University of North Carolina, Chapel Hill, North Carolina
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85
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Yates LR, Desmedt C. Translational Genomics: Practical Applications of the Genomic Revolution in Breast Cancer. Clin Cancer Res 2018; 23:2630-2639. [PMID: 28572257 DOI: 10.1158/1078-0432.ccr-16-2548] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/06/2017] [Accepted: 04/06/2017] [Indexed: 11/16/2022]
Abstract
The genomic revolution has fundamentally changed our perception of breast cancer. It is now apparent from DNA-based massively parallel sequencing data that at the genomic level, every breast cancer is unique and shaped by the mutational processes to which it was exposed during its lifetime. More than 90 breast cancer driver genes have been identified as recurrently mutated, and many occur at low frequency across the breast cancer population. Certain cancer genes are associated with traditionally defined histologic subtypes, but genomic intertumoral heterogeneity exists even between cancers that appear the same under the microscope. Most breast cancers contain subclonal populations, many of which harbor driver alterations, and subclonal structure is typically remodeled over time, across metastasis and as a consequence of treatment interventions. Genomics is deepening our understanding of breast cancer biology, contributing to an accelerated phase of targeted drug development and providing insights into resistance mechanisms. Genomics is also providing tools necessary to deliver personalized cancer medicine, but a number of challenges must still be addressed. Clin Cancer Res; 23(11); 2630-9. ©2017 AACRSee all articles in this CCR Focus section, "Breast Cancer Research: From Base Pairs to Populations."
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Affiliation(s)
- Lucy R Yates
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, United Kingdom.,Department of Clinical Oncology, Guys and St Thomas' NHS Trust, London, United Kingdom
| | - Christine Desmedt
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium.
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87
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Mutational and epigenetic signatures in cancer tissue linked to environmental exposures and lifestyle. Curr Opin Oncol 2018; 30:61-67. [DOI: 10.1097/cco.0000000000000418] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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88
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Monda V, Lupoli GA, Messina G, Peluso R, Panico A, Villano I, Salerno M, Sessa F, Marciello F, Moscatelli F, Valenzano A, Molino L, Lupoli R, Fonderico F, Tortora A, Pisano A, Ruberto M, Gabriella M, Cavaliere G, Trinchese G, Mollica MP, Cipolloni L, Cibelli G, Monda M, Lupoli G, Messina A. Improvement of Bone Physiology and Life Quality Due to Association of Risedronate and Anastrozole. Front Pharmacol 2017; 8:632. [PMID: 28955236 PMCID: PMC5601069 DOI: 10.3389/fphar.2017.00632] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 08/28/2017] [Indexed: 12/16/2022] Open
Abstract
The endocrine therapy is the new frontiers of many breast cancers hormone sensitive. Hormone therapy for treating women with hormone receptor-positive cancer suppresses breast cancer growth either by reducing estrogen synthesis or by interfering with the action of estrogen within tumor cells. In this prospective randomized observational study we investigate the effect of adjuvant anastrozole in monotherapy or associated with risedronate on bone physiology and quality of life in postmenopausal, hormone-sensitive early breast cancer women at mild to moderate risk of fragility fractures. Methods : 84 women were randomly assigned to receive anastrozole alone (group A) or anastrozole plus oral risedronate (group A+R). At baseline and after 24 months lumbar spine (LS) and femoral neck (FN) BMD were evaluated with dual-energy x-ray absorptiometry and health-related quality of life (HRQoL) was examined using the short-form healthy survey. Results : After 24 months, the group A+R has showed a significant increase in T-score for LS (p < 0.05) and for FN (p < 0.05) whereas women of group A had a statistically significant rate of bone loss both in LS T-score (p < 0.05) and in FN (p < 0.05). A significant change in T-score BMD was seen for group A+R compared with group A at the LS (p = 0.04) and at FN (p = 0.04). Finally, group A+R showed an overall significant improvement of health profile (SF-36) in group A (p = 0.03). Conclusion : Postmenopausal breast cancer women with osteopenia during treatment with anastrozole have considerable risk of developing osteoporosis during the first 2 years; preventive measures such as healthy lifestyle and daily supplements of calcium and vitamin D alone seem to be insufficient in holding their bones healthy. Our findings suggest the usefulness of addition of risedronate in order to prevent aromatase inhibitors-related bone loss, not only in case of high-risk of fractures, but also for women at mild-moderate risk. This determines a significant improvement in bone health and a positive impact on HRQoL.
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Affiliation(s)
- Vincenzo Monda
- Section of Human Physiology and Unit of Dietetic and Sport Medicine, Department of Experimental Medicine, University of Campania "L. Vanvitelli"Naples, Italy
| | - Gelsy A Lupoli
- Department of Clinical Medicine and Surgery, University of Naples Federico IINaples, Italy
| | - Giovanni Messina
- Department of Clinical and Experimental Medicine, University of FoggiaFoggia, Italy
| | - Rosario Peluso
- Section of Human Physiology and Unit of Dietetic and Sport Medicine, Department of Experimental Medicine, University of Campania "L. Vanvitelli"Naples, Italy.,Rheumatology Research Unit, University of Naples Federico IINaples, Italy
| | - Annalisa Panico
- Section of Human Physiology and Unit of Dietetic and Sport Medicine, Department of Experimental Medicine, University of Campania "L. Vanvitelli"Naples, Italy
| | - Ines Villano
- Department of Clinical Medicine and Surgery, University of Naples Federico IINaples, Italy
| | - Monica Salerno
- Department of Clinical and Experimental Medicine, University of FoggiaFoggia, Italy
| | - Francesco Sessa
- Department of Clinical and Experimental Medicine, University of FoggiaFoggia, Italy
| | - Francesca Marciello
- Section of Human Physiology and Unit of Dietetic and Sport Medicine, Department of Experimental Medicine, University of Campania "L. Vanvitelli"Naples, Italy
| | - Fiorenzo Moscatelli
- Department of Clinical and Experimental Medicine, University of FoggiaFoggia, Italy
| | - Anna Valenzano
- Department of Clinical and Experimental Medicine, University of FoggiaFoggia, Italy
| | - Leonardo Molino
- Rheumatology Research Unit, University of Naples Federico IINaples, Italy
| | - Roberta Lupoli
- Section of Human Physiology and Unit of Dietetic and Sport Medicine, Department of Experimental Medicine, University of Campania "L. Vanvitelli"Naples, Italy
| | - Francesco Fonderico
- Section of Human Physiology and Unit of Dietetic and Sport Medicine, Department of Experimental Medicine, University of Campania "L. Vanvitelli"Naples, Italy
| | - Anna Tortora
- Section of Human Physiology and Unit of Dietetic and Sport Medicine, Department of Experimental Medicine, University of Campania "L. Vanvitelli"Naples, Italy
| | - Agata Pisano
- Section of Human Physiology and Unit of Dietetic and Sport Medicine, Department of Experimental Medicine, University of Campania "L. Vanvitelli"Naples, Italy.,Department of Oncohematology, Santa Maria delle Grazie HospitalPozzuoli, Italy
| | - Maria Ruberto
- Department of Medical-Surgical and Dental Specialties, University of Campania "L.Vanvitelli"Naples, Italy
| | - Marsala Gabriella
- Struttura Complessa di Farmacia, Azienda Ospedaliero-Universitaria, Ospedali Riuniti di FoggiaFoggia, Italy
| | - Gina Cavaliere
- Department of Biology, University of Naples Federico IINaples, Italy
| | | | - Maria P Mollica
- Department of Biology, University of Naples Federico IINaples, Italy
| | | | - Giuseppe Cibelli
- Department of Clinical and Experimental Medicine, University of FoggiaFoggia, Italy
| | - Marcellino Monda
- Department of Clinical Medicine and Surgery, University of Naples Federico IINaples, Italy
| | - Giovanni Lupoli
- Section of Human Physiology and Unit of Dietetic and Sport Medicine, Department of Experimental Medicine, University of Campania "L. Vanvitelli"Naples, Italy
| | - Antonietta Messina
- Department of Clinical Medicine and Surgery, University of Naples Federico IINaples, Italy
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Vonderheide RH, Domchek SM, Clark AS. Immunotherapy for Breast Cancer: What Are We Missing? Clin Cancer Res 2017; 23:2640-2646. [PMID: 28572258 PMCID: PMC5480967 DOI: 10.1158/1078-0432.ccr-16-2569] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 02/15/2017] [Accepted: 04/05/2017] [Indexed: 02/07/2023]
Abstract
The recent demonstration of modest single-agent activity of programmed death-ligand 1 (PD-L1) and programmed death receptor-1 (PD-1) antibodies in patients with breast cancer has generated hope that breast cancer can be made amenable to immunotherapy. Depending on the subtype of breast cancer, it is now clear in both primary and metastatic disease that the extent of tumor-infiltrating T cells is not only prognostic for survival but predictive of response to nonimmune, standard therapies. Despite these findings, immune cytolytic activity in spontaneous breast tumors, the burden of nonsynonymous tumor mutations, and the predicted load of neoepitopes-factors linked to response to checkpoint blockade in other malignancies-are all relatively modest in breast cancer compared with melanoma or lung cancer. Thus, in breast cancer, combinations of immune agents with nonredundant mechanisms of action are high-priority strategies. For most breast cancers that exhibit relatively modest T-cell infiltration, major challenges include immune suppression in the tumor microenvironment as well as failed or suboptimal T-cell priming. Agents that trigger de novo T-cell responses may be critical for the successful development of cancer immunotherapy and immune prevention in breast cancer. Success may also require reaching beyond nonsynonymous mutations as the T-cell epitopes to target, especially as numerous unmutated proteins were validated as breast cancer-associated antigens in the pre-checkpoint era. A deeper understanding of the immunobiology of breast cancer will be critical for immunotherapy to become broadly relevant in this disease. Clin Cancer Res; 23(11); 2640-6. ©2017 AACRSee all articles in this CCR Focus section, "Breast Cancer Research: From Base Pairs to Populations."
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Affiliation(s)
- Robert H Vonderheide
- Abramson Cancer Center, Hematology-Oncology Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Susan M Domchek
- Abramson Cancer Center, Hematology-Oncology Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Amy S Clark
- Abramson Cancer Center, Hematology-Oncology Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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Reeder-Hayes KE, Anderson BO. Breast Cancer Disparities at Home and Abroad: A Review of the Challenges and Opportunities for System-Level Change. Clin Cancer Res 2017; 23:2655-2664. [PMID: 28572260 PMCID: PMC5499686 DOI: 10.1158/1078-0432.ccr-16-2630] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 03/03/2017] [Accepted: 04/06/2017] [Indexed: 01/06/2023]
Abstract
Sizeable disparities exist in breast cancer outcomes, both between Black and White patients in the United States, and between patients in the United States and other high-income countries compared with low- and middle-income countries (LMIC). In both settings, health system factors are key drivers of disparities. In the United States, Black women are more likely to die of breast cancer than Whites and have poorer outcomes, even among patients with similar stage and tumor subtype. Over-representation of higher risk "triple-negative" breast cancers contributes to breast cancer mortality in Black women; however, the greatest survival disparities occur within the good-prognosis hormone receptor-positive (HR+) subtypes. Disparities in access to treatment within the complex U.S. health system may be responsible for a substantial portion of these differences in survival. In LMICs, breast cancer mortality rates are substantially higher than in the United States, whereas incidence continues to rise. This mortality burden is largely attributable to health system factors, including late-stage presentation at diagnosis and lack of availability of systemic therapy. This article will review the existing evidence for how health system factors in the United States contribute to breast cancer disparities, discuss methods for studying the relationship of health system factors to racial disparities, and provide examples of health system interventions that show promise for mitigating breast cancer disparities. We will then review evidence of global breast cancer disparities in LMICs, the treatment factors that contribute to these disparities, and actions being taken to combat breast cancer disparities around the world. Clin Cancer Res; 23(11); 2655-64. ©2017 AACRSee all articles in this CCR Focus section, "Breast Cancer Research: From Base Pairs to Populations."
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Affiliation(s)
- Katherine E Reeder-Hayes
- Division of Hematology and Oncology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
- The University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina
| | - Benjamin O Anderson
- Departments of Surgery and Global Health Medicine, School of Medicine, University of Washington, Seattle, Washington
- Program in Epidemiology, Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
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