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Klocker EV, Hasenleithner S, Bartsch R, Gampenrieder SP, Egle D, Singer CF, Rinnerthaler G, Hubalek M, Schmitz K, Bago-Horvath Z, Petzer A, Heibl S, Heitzer E, Balic M, Gnant M. Clinical applications of next-generation sequencing-based ctDNA analyses in breast cancer: defining treatment targets and dynamic changes during disease progression. Mol Oncol 2024. [PMID: 38867388 DOI: 10.1002/1878-0261.13671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/03/2024] [Accepted: 05/17/2024] [Indexed: 06/14/2024] Open
Abstract
The advancements in the detection and characterization of circulating tumor DNA (ctDNA) have revolutionized precision medicine and are likely to transform standard clinical practice. The non-invasive nature of this approach allows for molecular profiling of the entire tumor entity, while also enabling real-time monitoring of the effectiveness of cancer therapies as well as the identification of resistance mechanisms to guide targeted therapy. Although the field of ctDNA studies offers a wide range of applications, including in early disease, in this review we mainly focus on the role of ctDNA in the dynamic molecular characterization of unresectable locally advanced and metastatic BC (mBC). Here, we provide clinical practice guidance for the rapidly evolving field of molecular profiling of mBC, outlining the current landscape of liquid biopsy applications and how to choose the right ctDNA assay. Additionally, we underline the importance of exploring the clinical relevance of novel molecular alterations that potentially represent therapeutic targets in mBC, along with mutations where targeted therapy is already approved. Finally, we present a potential roadmap for integrating ctDNA analysis into clinical practice.
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Affiliation(s)
- Eva Valentina Klocker
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Austria
| | - Samantha Hasenleithner
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Austria
| | - Rupert Bartsch
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Austria
| | - Simon P Gampenrieder
- Third Medical Department with Hematology and Medical Oncology, Hemostaseology, Rheumatology and Infectious Diseases, Oncologic Center, Paracelsus Medical University Salzburg, Austria
| | - Daniel Egle
- Department of Gynecology, Breast Cancer Center Tirol, Medical University of Innsbruck, Austria
| | - Christian F Singer
- Department of Gynecology, Breast Cancer Center Vienna, Medical University of Vienna, Austria
| | - Gabriel Rinnerthaler
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Austria
| | - Michael Hubalek
- Department of Gynecology, Breast Health Center Schwaz, Austria
| | - Katja Schmitz
- Institute of Pathology, University Medical Center Göttingen, Germany
- Tyrolpath Obrist Brunhuber GmbH and Krankenhaus St. Vinzenz, Zams, Austria
| | | | - Andreas Petzer
- Department of Internal Medicine I for Hematology with Stem Cell Transplantation, Hemostaseology and Medical Oncology, Barmherzige Schwestern, Elisabethinen, Ordensklinikum Linz GmbH, Austria
| | - Sonja Heibl
- Department of Internal Medicine IV, Klinikum Wels-Grieskirchen GmbH, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Christian Doppler Laboratory for Liquid Biopsies for early Detection of Cancer, Medical University of Graz, Austria
| | - Marija Balic
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Austria
- Division of Hematology and Medical Oncology, University of Pittsburgh School of Medicine, PA, USA
| | - Michael Gnant
- Comprehensive Cancer Center, Medical University of Vienna, Austria
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Almeida-Ferreira C, Marto CM, Carmo C, Almeida-Ferreira J, Frutuoso C, Carvalho MJ, Botelho MF, Laranjo M. Efficacy of Cold Atmospheric Plasma vs. Chemotherapy in Triple-Negative Breast Cancer: A Systematic Review. Int J Mol Sci 2024; 25:3254. [PMID: 38542225 PMCID: PMC10970295 DOI: 10.3390/ijms25063254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 04/09/2024] Open
Abstract
Breast cancer is a growing disease, with a high worldwide incidence and mortality rate among women. Among the various types, the treatment of triple-negative breast cancer (TNBC) remains a challenge. Considering the recent advances in cold atmospheric plasma (CAP) cancer research, our goal was to evaluate efficacy data from studies based on chemotherapy and CAP in TNBC cell lines and animal models. A search of the literature was carried out in the PubMed, Web of Science, Cochrane Library, and Embase databases. Of the 10,999 studies, there were fifty-four in vitro studies, three in vivo studies, and two in vitro and in vivo studies included. MDA-MB-231 cells were the most used. MTT, MTS, SRB, annexin-V/propidium iodide, trypan blue, and clonogenic assay were performed to assess efficacy in vitro, increasing the reliability and comprehensiveness of the data. There was found to be a decrease in cell proliferation after both chemotherapy and CAP; however, different protocol settings, including an extensive range of drug doses and CAP exposure times, were reported. For both therapies, a considerable reduction in tumor volume was observed in vivo compared with that of the untreated group. The treatment of TNBC cell lines with CAP proved successful, with apoptosis emerging as the predominant type of cellular death. This systematic review presents a comprehensive overview of the treatment landscape in chemotherapy and CAP regarding their efficacy in TNBC cell lines.
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Affiliation(s)
- Catarina Almeida-Ferreira
- Institute for Clinical and Biomedical Research (iCBR), Area of Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (C.A.-F.); (C.M.M.); (C.C.); (C.F.); (M.J.C.); (M.F.B.)
- Institute of Biophysics, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Carlos Miguel Marto
- Institute for Clinical and Biomedical Research (iCBR), Area of Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (C.A.-F.); (C.M.M.); (C.C.); (C.F.); (M.J.C.); (M.F.B.)
- Institute of Biophysics, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), University of Coimbra, 3000-354 Coimbra, Portugal
- Institute of Integrated Clinical Practice, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
- Laboratory for Evidence-Based Sciences and Precision Dentistry, Faculty of Medicine, University of Coimbra, 3000-075 Coimbra, Portugal
- Institute of Experimental Pathology, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Chrislaura Carmo
- Institute for Clinical and Biomedical Research (iCBR), Area of Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (C.A.-F.); (C.M.M.); (C.C.); (C.F.); (M.J.C.); (M.F.B.)
- Institute of Biophysics, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Coimbra Chemistry Center (CQC), Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
| | | | - Cristina Frutuoso
- Institute for Clinical and Biomedical Research (iCBR), Area of Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (C.A.-F.); (C.M.M.); (C.C.); (C.F.); (M.J.C.); (M.F.B.)
- Institute of Biophysics, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Gynecology Service, Coimbra Hospital and University Centre, Coimbra Health Local Unit, 3004-561 Coimbra, Portugal
| | - Maria João Carvalho
- Institute for Clinical and Biomedical Research (iCBR), Area of Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (C.A.-F.); (C.M.M.); (C.C.); (C.F.); (M.J.C.); (M.F.B.)
- Institute of Biophysics, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal
- Gynecology Service, Coimbra Hospital and University Centre, Coimbra Health Local Unit, 3004-561 Coimbra, Portugal
- Universitary Clinic of Gynecology, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Maria Filomena Botelho
- Institute for Clinical and Biomedical Research (iCBR), Area of Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (C.A.-F.); (C.M.M.); (C.C.); (C.F.); (M.J.C.); (M.F.B.)
- Institute of Biophysics, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), University of Coimbra, 3000-354 Coimbra, Portugal
| | - Mafalda Laranjo
- Institute for Clinical and Biomedical Research (iCBR), Area of Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (C.A.-F.); (C.M.M.); (C.C.); (C.F.); (M.J.C.); (M.F.B.)
- Institute of Biophysics, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), University of Coimbra, 3000-354 Coimbra, Portugal
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Yaghoubi Naei V, Bordhan P, Mirakhorli F, Khorrami M, Shrestha J, Nazari H, Kulasinghe A, Ebrahimi Warkiani M. Advances in novel strategies for isolation, characterization, and analysis of CTCs and ctDNA. Ther Adv Med Oncol 2023; 15:17588359231192401. [PMID: 37692363 PMCID: PMC10486235 DOI: 10.1177/17588359231192401] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 07/19/2023] [Indexed: 09/12/2023] Open
Abstract
Over the past decade, the detection and analysis of liquid biopsy biomarkers such as circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) have advanced significantly. They have received recognition for their clinical usefulness in detecting cancer at an early stage, monitoring disease, and evaluating treatment response. The emergence of liquid biopsy has been a helpful development, as it offers a minimally invasive, rapid, real-time monitoring, and possible alternative to traditional tissue biopsies. In resource-limited settings, the ideal platform for liquid biopsy should not only extract more CTCs or ctDNA from a minimal sample volume but also accurately represent the molecular heterogeneity of the patient's disease. This review covers novel strategies and advancements in CTC and ctDNA-based liquid biopsy platforms, including microfluidic applications and comprehensive analysis of molecular complexity. We discuss these systems' operational principles and performance efficiencies, as well as future opportunities and challenges for their implementation in clinical settings. In addition, we emphasize the importance of integrated platforms that incorporate machine learning and artificial intelligence in accurate liquid biopsy detection systems, which can greatly improve cancer management and enable precision diagnostics.
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Affiliation(s)
- Vahid Yaghoubi Naei
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
- Faculty of Medicine, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Pritam Bordhan
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
- Faculty of Science, Institute for Biomedical Materials & Devices, University of Technology Sydney, Australia
| | - Fatemeh Mirakhorli
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Motahare Khorrami
- Immunology Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jesus Shrestha
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Hojjatollah Nazari
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Arutha Kulasinghe
- Faculty of Medicine, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, 1, Broadway, Ultimo New South Wales 2007, Australia
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Telekes A, Horváth A. The Role of Cell-Free DNA in Cancer Treatment Decision Making. Cancers (Basel) 2022; 14:6115. [PMID: 36551600 PMCID: PMC9776613 DOI: 10.3390/cancers14246115] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
The aim of this review is to evaluate the present status of the use of cell-free DNA and its fraction of circulating tumor DNA (ctDNA) because this year July 2022, an ESMO guideline was published regarding the application of ctDNA in patient care. This review is for clinical oncologists to explain the concept, the terms used, the pros and cons of ctDNA; thus, the technical aspects of the different platforms are not reviewed in detail, but we try to help in navigating the current knowledge in liquid biopsy. Since the validated and adequately sensitive ctDNA assays have utility in identifying actionable mutations to direct targeted therapy, ctDNA may be used for this soon in routine clinical practice and in other different areas as well. The cfDNA fragments can be obtained by liquid biopsy and can be used for diagnosis, prognosis, and selecting among treatment options in cancer patients. A great proportion of cfDNA comes from normal cells of the body or from food uptake. Only a small part (<1%) of it is related to tumors, originating from primary tumors, metastatic sites, or circulating tumor cells (CTCs). Soon the data obtained from ctDNA may routinely be used for finding minimal residual disease, detecting relapse, and determining the sites of metastases. It might also be used for deciding appropriate therapy, and/or emerging resistance to the therapy and the data analysis of ctDNA may be combined with imaging or other markers. However, to achieve this goal, further clinical validations are inevitable. As a result, clinicians should be aware of the limitations of the assays. Of course, several open questions are still under research and because of it cfDNA and ctDNA testing are not part of routine care yet.
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Affiliation(s)
- András Telekes
- Omnimed-Etosz, Ltd., 81 Széher Rd., 1021 Budapest, Hungary
- Semmelweis University, 26. Üllői Rd., 1085 Budapest, Hungary
| | - Anna Horváth
- Department of Internal Medicine and Haematology, Semmelweis University, 46. Szentkirályi Rd., 1088 Budapest, Hungary
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Deng X, Zheng C, Tang F, Rosol TJ, Shao ZM. Editorial: Triple-negative breast cancer: Heterogeneity, tumor microenvironment and targeted therapy. Front Oncol 2022; 12:1026566. [PMID: 36483047 PMCID: PMC9725095 DOI: 10.3389/fonc.2022.1026566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/02/2022] [Indexed: 08/30/2023] Open
Affiliation(s)
- Xiyun Deng
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University School of Medicine, Changsha, Hunan, China
| | - Chanjuan Zheng
- Key Laboratory of Translational Cancer Stem Cell Research, Hunan Normal University School of Medicine, Changsha, Hunan, China
| | - Faqing Tang
- Clinical Laboratory of Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Key Laboratory of Oncotarget Gene, Changsha, Hunan, China
| | - Thomas J. Rosol
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, United States
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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Ohyama H, Hirotsu Y, Amemiya K, Amano H, Hirose S, Hosoda K, Oyama T, Iimuro Y, Kojima Y, Mikata R, Mochizuki H, Kato N, Omata M. Detection of actionable mutations in cytological specimens obtained by endoscopic ultrasound-guided fine needle aspiration with rapid onsite evaluation in pancreatic cancer. Ann Diagn Pathol 2022; 60:152008. [PMID: 35843025 DOI: 10.1016/j.anndiagpath.2022.152008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 07/07/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND It is not clear whether archived cytological specimens (ACSs) obtained with endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) with rapid onsite evaluation (ROSE) can be used for genomic profiling of tumors. We used ACSs to perform genomic analysis of specimens to identify oncogenic and druggable mutations. METHODS A panel of 60 significantly mutated genes specific to pancreatobiliary cancer was created and used for genomic analysis of 113 specimens of 44 formalin-fixed paraffin-embedded (FFPE) tissues and 69 ACSs obtained by EUS-FNA with ROSE were included. The quantity and quality of DNA extracted from FFPE tissues and ACSs were compared. We also compared DNA from spray and touch ACSs. Next, genomic profiles were compared. We also evaluated detection of target gene mutations in each specimen. RESULTS The amount of DNA in FFPE tissues was greater than in ACSs (P = 0.014), but the quality of DNA was comparable (P = 0.378). There was no quantitative or qualitative difference between spray and touch ACSs (P = 0.154 and P = 0.734, respectively). Oncogenic mutations were shared at 82 % in FFPE tissues and ACSs and 82 % in spray and touch ACSs. The sensitivity of genomic analysis in ACSs was 97 % (67 of 69), which was comparable to that of cytology (62 of 69, 90 %; P = 0.165), and was significantly higher than that of histology (32/44, 73 %; P < 0.001). Drug-matched mutations were identified in five of the 44 lesions (11 %). CONCLUSION Genomic analysis of ACSs is useful in the prognosis of pancreatic cancer because detection of driver mutations is similar to detection in FFPE tissues.
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Affiliation(s)
- Hiroshi Ohyama
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba City, Chiba 260-8677, Japan; Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan; Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan.
| | - Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan
| | - Kenji Amemiya
- Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan
| | - Hiroyuki Amano
- Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan
| | - Sumio Hirose
- Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan
| | - Kenji Hosoda
- Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan
| | - Toshio Oyama
- Department of Pathology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan
| | - Yuji Iimuro
- Department of Surgery, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan
| | - Yuichiro Kojima
- Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan
| | - Rintaro Mikata
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba City, Chiba 260-8677, Japan
| | - Hitoshi Mochizuki
- Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan; Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan
| | - Naoya Kato
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba City, Chiba 260-8677, Japan
| | - Masao Omata
- Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan; Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan; University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
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Image Genetic Analysis and Application Research Based on QRFPR and Other Neural Network-Related SNP Loci. BIOMED RESEARCH INTERNATIONAL 2022; 2022:5861928. [PMID: 36017394 PMCID: PMC9398771 DOI: 10.1155/2022/5861928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/13/2022] [Accepted: 07/20/2022] [Indexed: 11/18/2022]
Abstract
The development of neuroimaging technology and molecular genetics has produced a large amount of imaging genetics data, which has greatly promoted the study of complex mental diseases. However, because the feature dimension of the data is too high, the correlation measure assumes that the data obey Gaussian distribution, and traditional algorithms often cannot explain these two types of data well. This article mainly studies image genetics analysis and its application based on neural network. In this paper, based on the theory and application technology of neural network, the tree structure is established by prior knowledge, that is, each SNP site is used as a leaf node of the tree, and the LD block and genome formed by the linkage imbalance of multiple SNP sites are used as intermediate nodes. Then, the hierarchical relationship of features was introduced. On this basis, a sparse learning method based on tree structure guidance is used to select features from multiple features of multiple SNPs locus regression candidate brain regions. Finally, the identification of SNPs in feature selection is used to predict quantitative traits of brain regions. The distribution of the typical vector values obtained by the algorithm in the experimental data is basically consistent with the distribution of the median of the actual data, and the correlation coefficient obtained is closest to the actual correlation coefficient in the data set. The average correlation coefficient of the algorithm reaches 82.3%, which is about 4.2% higher than the control algorithm. Experimental results show that this method can not only significantly improve the regression performance but also detect the risk gene SNPs loci with spatial clustering features and functional interpretation significance. It is practical and effective to use it in clinical trials.
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Ohyama H, Mikata R, Hirotsu Y, Amemiya K, Miura Y, Hirose S, Oyama T, Takano A, Iimuro Y, Kojima Y, Mochizuki H, Ikeda J, Kato N, Omata M. Genomic profiling amplifies the utility of endoscopic ultrasound-guided fine needle biopsy by identifying clinically applicable druggable mutations in pancreatic cancer. Ann Diagn Pathol 2022; 60:152016. [PMID: 35905537 DOI: 10.1016/j.anndiagpath.2022.152016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 07/17/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND Genomic profiling of tumors is available, but whether the small fragment obtained via endoscopic ultrasound-guided fine needle biopsy (EUS-FNB) is sufficient for these examinations is unknown. Here we investigated whether EUS-FNB specimens are suitable for genomic profiling to identify oncogenic and drug-matched mutations. METHODS We constructed a pancreatobiliary cancer panel for targeted panel sequencing that covered 60 significantly mutated genes and compared the results with those of whole-exome sequencing (WES). In total, 20 and 53 formalin-fixed paraffin-embedded tissues obtained via surgery and EUS-FNB were analyzed, respectively. First, we examined the DNA quality and genomic profiles of 20 paired samples from 20 malignant lesions obtained via surgery and EUS-FNB. We then tested 33 samples obtained via EUS-FNB from 24 malignant and 9 benign lesions for the discrimination of malignancy. Finally, we explored drug-matched mutations from EUS-FNB specimens. RESULTS Although the DNA quantity obtained via surgery was higher than that obtained via EUS-FNB (P = 0.017), the DNA quality and mean depth were equivalent (P = 0.441 and P = 0.251). Panel sequencing of EUS-FNB specimens identified more oncogenic mutations than WES (90 % vs. 50 %). Furthermore, the number of oncogenic mutations did not differ between EUS-FNB and surgically resected specimens. Genomic profiling of EUS-FNB specimens enabled the discrimination of malignancy with 98 % accuracy. Of 44 malignant lesions, drug-matched alterations were identified in 14 % (6/44) of malignant lesions. CONCLUSION EUS-FNB specimens can be widely utilized for diagnostic purposes, discrimination of malignancy, and detection of drug-matched mutations for the treatment of pancreatic cancer.
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Affiliation(s)
- Hiroshi Ohyama
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba City, Chiba 260-8677, Japan; Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan; Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan.
| | - Rintaro Mikata
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba City, Chiba 260-8677, Japan
| | - Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan
| | - Kenji Amemiya
- Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan
| | - Yoshifumi Miura
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba City, Chiba 260-8677, Japan
| | - Sumio Hirose
- Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan
| | - Toshio Oyama
- Department of Pathology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan
| | - Atsushi Takano
- Department of Surgery, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan
| | - Yuji Iimuro
- Department of Surgery, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan
| | - Yuichiro Kojima
- Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan
| | - Hitoshi Mochizuki
- Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan; Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan
| | - Junichiro Ikeda
- Department of Molecular Pathology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba City, Chiba 260-8677, Japan
| | - Naoya Kato
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba City, Chiba 260-8677, Japan
| | - Masao Omata
- Genome Analysis Center, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan; Department of Gastroenterology, Yamanashi Central Hospital, 1-1-1 Fujimi, Kofu City, Yamanashi 400-8506, Japan; University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
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Abstract
Cancer cells shed naked DNA molecules into the circulation. This circulating tumor DNA (ctDNA) has become the predominant analyte for liquid biopsies to understand the mutational landscape of cancer. Coupled with next-generation sequencing, ctDNA can serve as an alternative substrate to tumor tissues for mutation detection and companion diagnostic purposes. In fact, recent advances in precision medicine have rapidly enabled the use of ctDNA to guide treatment decisions for predicting response and resistance to targeted therapies and immunotherapies. An advantage of using ctDNA over conventional tissue biopsies is the relatively noninvasive approach of obtaining peripheral blood, allowing for simple repeated and serial assessments. Most current clinical practice using ctDNA has endeavored to identify druggable and resistance mutations for guiding systemic therapy decisions, albeit mostly in metastatic disease. However, newer research is evaluating potential for ctDNA as a marker of minimal residual disease in the curative setting and as a useful screening tool to detect cancer in the general population. Here we review the history of ctDNA and liquid biopsies, technologies to detect ctDNA, and some of the current challenges and limitations in using ctDNA as a marker of minimal residual disease and as a general blood-based cancer screening tool. We also discuss the need to develop rigorous clinical studies to prove the clinical utility of ctDNA for future applications in oncology.
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10
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Liu MC, MacKay M, Kase M, Piwowarczyk A, Lo C, Schaeffer J, Finkle JD, Mason CE, Beaubier N, Blackwell KL, Park BH. Longitudinal Shifts of Solid Tumor and Liquid Biopsy Sequencing Concordance in Metastatic Breast Cancer. JCO Precis Oncol 2022; 6:e2100321. [PMID: 35721584 PMCID: PMC9200387 DOI: 10.1200/po.21.00321] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/17/2021] [Accepted: 03/24/2022] [Indexed: 11/21/2022] Open
Abstract
Tissue-based next-generation sequencing (NGS) in metastatic breast cancer (mBC) is limited by the inability to noninvasively track tumor evolution. Cell-free DNA (cfDNA) NGS has made sequential testing feasible; however, the relationship between cfDNA and tissue-based testing in mBC is not well understood. Here, we evaluate concordance between tissue and cfDNA NGS relative to cfDNA sampling frequency in a large, clinically annotated mBC data set. METHODS Tempus LENS was used to analyze deidentified records of mBC cases with Tempus xT (tissue) and xF (cfDNA) sequencing results. Then, various metrics of concordance were assessed within overlapping probe regions of the tissue and cfDNA assays (104 genes), focusing on pathogenic variants. Variant allele frequencies of discordant and concordant pathogenic variants were also compared. Analyses were stratified by mBC subtype and time between tests. RESULTS Records from 300 paired tissue and liquid biopsies were analyzed. Median time between tissue and blood collection was 78.5 days (standard deviation = 642.99). The median number of pathogenic variants/patient was one for cfDNA and two for tissue. Across the cohort, 77.8% of pathogenic tissue variants were found in cfDNA and 75.7% of pathogenic cfDNA variants were found in tissue when tests were ≤ 7 days apart, which decreased to 50.3% and 51.8%, respectively, for > 365 days. Furthermore, the median patient-level variant concordance was 67% when tests were ≤7 days apart and 30%-37% when > 30 days. The median variant allele frequencies of discordant variants were generally lower than those of concordant variants within the same time frame. CONCLUSION We observed high concordances between tissue and cfDNA results that generally decreased with longer durations between tests. Thus, cfDNA NGS reliably measures tissue genomics and is likely beneficial for longitudinal monitoring of molecular changes in mBC.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Ben Ho Park
- Vanderbilt University Medical Center, Nashville, TN
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11
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Hasenleithner SO, Speicher MR. A clinician’s handbook for using ctDNA throughout the patient journey. Mol Cancer 2022; 21:81. [PMID: 35307037 PMCID: PMC8935823 DOI: 10.1186/s12943-022-01551-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/24/2022] [Indexed: 12/15/2022] Open
Abstract
Abstract
Background
The promise of precision cancer medicine presently centers around the genomic sequence of a patient’s tumor being translated into timely, actionable information to inform clinical care. The analysis of cell-free DNA from liquid biopsy, which contains circulating tumor DNA (ctDNA) in patients with cancer, has proven to be amenable to various settings in oncology. However, open questions surrounding the clinical validity and utility of plasma-based analyses have hindered widespread clinical adoption.
Main body
Owing to the rapid evolution of the field, studies supporting the use of ctDNA as a biomarker throughout a patient’s journey with cancer have accumulated in the last few years, warranting a review of the latest status for clinicians who may employ ctDNA in their precision oncology programs. In this work, we take a step back from the intricate coverage of detection approaches described extensively elsewhere and cover basic concepts around the practical implementation of next generation sequencing (NGS)-guided liquid biopsy. We compare relevant targeted and untargeted approaches to plasma DNA analysis, describe the latest evidence for clinical validity and utility, and highlight the value of genome-wide ctDNA analysis, particularly as it relates to early detection strategies and discovery applications harnessing the non-coding genome.
Conclusions
The maturation of liquid biopsy for clinical application will require interdisciplinary efforts to address current challenges. However, patients and clinicians alike may greatly benefit in the future from its incorporation into routine oncology care.
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12
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Wang L, Zhai Q, Lu Q, Lee K, Zheng Q, Hong R, Wang S. Clinical genomic profiling to identify actionable alterations for very early relapsed triple-negative breast cancer patients in the Chinese population. Ann Med 2021; 53:1358-1369. [PMID: 34396843 PMCID: PMC8381897 DOI: 10.1080/07853890.2021.1966086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) represents about 19% of all breast cancer cases in the Chinese population. Lack of targeted therapy contributes to the poorer outcomes compared with other breast cancer subtypes. Comprehensive genomic profiling helps to explore the clinically relevant genomic alterations (CRGAs) and potential therapeutic targets in very-early-relapsed TNBC patients. METHODS Formalin-fixed paraffin-embedded (FFPE) tumour tissue specimens from 23 patients with very-early-relapsed TNBC and 13 patients with disease-free survival (DFS) more than 36 months were tested by FoundationOne CDx (F1CDx) in 324 genes and select gene rearrangements, along with genomic signatures including microsatellite instability (MSI) and tumour mutational burden (TMB). RESULTS In total, 137 CRGAs were detected in the 23 very-early-relapsed TNBC patients, averaging six alterations per sample. The mean TMB was 4 Muts/Mb, which was higher than that in non-recurrence patients, and is statistically significant. The top-ranked altered genes were TP53 (83%), PTEN (35%), RB1 (30%), PIK3CA (26%) and BRCA1 (22%). RB1 mutation carriers had shorter DFS. Notably, 100% of these patients had at least one CRGA, and 87% of patients had at least one actionable alteration. In pathway analysis, patients who carried a mutation in the cell cycle pathway were more likely to experience very early recurrence. Strikingly, we detected one patient with ERBB2 amplification and one patient with ERBB2 exon20 insertion, both of which were missed by immunohistochemistry (IHC). We also detected novel alterations of ROS1-EPHA7 fusion for the first time, which has not been reported in breast cancer before. CONCLUSIONS The comprehensive genomic profiling can identify novel treatment targets and address the limited options in TNBC patients. Therefore, incorporating F1CDx into TNBC may shed light on novel therapeutic opportunities for these very-early-relapsed TNBC patients.
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Affiliation(s)
- Liye Wang
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Qinglian Zhai
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Qianyi Lu
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Kaping Lee
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Qiufan Zheng
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Ruoxi Hong
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Shusen Wang
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
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13
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Peng Y, Mei W, Ma K, Zeng C. Circulating Tumor DNA and Minimal Residual Disease (MRD) in Solid Tumors: Current Horizons and Future Perspectives. Front Oncol 2021; 11:763790. [PMID: 34868984 PMCID: PMC8637327 DOI: 10.3389/fonc.2021.763790] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/03/2021] [Indexed: 12/12/2022] Open
Abstract
Circulating tumor DNA (ctDNA) is cell-free DNA (cfDNA) fragment in the bloodstream that originates from malignant tumors or circulating tumor cells. Recently, ctDNA has emerged as a promising non-invasive biomarker in clinical oncology. Analysis of ctDNA opens up new avenues for individualized cancer diagnosis and therapy in various types of tumors. Evidence suggests that minimum residual disease (MRD) is closely associated with disease recurrence, thus identifying specific genetic and molecular alterations as novel MRD detection targets using ctDNA has been a research focus. MRD is considered a promising prognostic marker to identify individuals at increased risk of recurrence and who may benefit from treatment. This review summarizes the current knowledge of ctDNA and MRD in solid tumors, focusing on the potential clinical applications and challenges. We describe the current state of ctDNA detection methods and the milestones of ctDNA development and discuss how ctDNA analysis may be an alternative for tissue biopsy. Additionally, we evaluate the clinical utility of ctDNA analysis in solid tumors, such as recurrence risk assessment, monitoring response, and resistance mechanism analysis. MRD detection aids in assessing treatment response, patient prognosis, and risk of recurrence. Moreover, this review highlights current advancements in utilizing ctDNA to monitor the MRD of solid tumors such as lung cancer, breast cancer, and colon cancer. Overall, the clinical application of ctDNA-based MRD detection can assist clinical decision-making and improve patient outcomes in malignant tumors.
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Affiliation(s)
- Yan Peng
- Department of Obstetrics, Longhua District Central Hospital, Shenzhen, China
| | - Wuxuan Mei
- Clinical Medical College, Hubei University of Science and Technology, Xianning, China
| | - Kaidong Ma
- Department of Obstetrics, Longhua District Central Hospital, Shenzhen, China
| | - Changchun Zeng
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Guangdong Medical University, Shenzhen, China
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14
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Bruzas S, Kuemmel S, Harrach H, Breit E, Ataseven B, Traut A, Rüland A, Kostara A, Chiari O, Dittmer-Grabowski C, Reinisch M. Next-Generation Sequencing-Directed Therapy in Patients with Metastatic Breast Cancer in Routine Clinical Practice. Cancers (Basel) 2021; 13:4564. [PMID: 34572791 PMCID: PMC8468801 DOI: 10.3390/cancers13184564] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 11/20/2022] Open
Abstract
Next-generation sequencing (NGS) followed by matched therapy has opened up new therapeutic options to patients with metastatic breast cancer (mBC). Here we report our experience with this approach in everyday clinical practice. This retrospective study included 95 patients with mBC who were genotyped with the FoundationOne® (CDx) assay in a commercial molecular pathology laboratory. Genetic alterations were identified in all tumor specimens, and 83 patients (87.4%) had a median of 2 (range, 1-6) potentially actionable alterations. A multidisciplinary tumor board recommended genomically guided therapy to 63 patients, 30 of whom received such treatment. Everolimus (n = 15) and anti-human epidermal growth factor receptor 2 (HER2) therapy (n = 6) were most frequently administered. The ratio of progression-free survival (PFS) under NGS-based therapy to PFS under the last line of standard therapy prior to NGS was >1.3 in 13 (43.3%) patients, indicative of a clinical benefit to NGS-directed therapy. One-year overall survival rates were 22.7% (95% CI, 6.5-44.4) in 65 patients allocated to the standard therapy versus 62.9% (95% CI, 41.6-78.2) in 30 patients receiving the matched therapy. In conclusion, NGS-matched treatment improved the clinical outcomes in a subgroup of mBC patients.
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Affiliation(s)
- Simona Bruzas
- Interdisciplinary Breast Unit, Kliniken Essen-Mitte, 45136 Essen, Germany; (S.B.); (S.K.); (H.H.); (E.B.); (A.R.); (A.K.); (O.C.); (C.D.-G.)
| | - Sherko Kuemmel
- Interdisciplinary Breast Unit, Kliniken Essen-Mitte, 45136 Essen, Germany; (S.B.); (S.K.); (H.H.); (E.B.); (A.R.); (A.K.); (O.C.); (C.D.-G.)
- Department of Gynecology with Breast Center, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Hakima Harrach
- Interdisciplinary Breast Unit, Kliniken Essen-Mitte, 45136 Essen, Germany; (S.B.); (S.K.); (H.H.); (E.B.); (A.R.); (A.K.); (O.C.); (C.D.-G.)
| | - Elisabeth Breit
- Interdisciplinary Breast Unit, Kliniken Essen-Mitte, 45136 Essen, Germany; (S.B.); (S.K.); (H.H.); (E.B.); (A.R.); (A.K.); (O.C.); (C.D.-G.)
| | - Beyhan Ataseven
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte, 45136 Essen, Germany; (B.A.); (A.T.)
- Department of Obstetrics and Gynecology, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Alexander Traut
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte, 45136 Essen, Germany; (B.A.); (A.T.)
| | - Anna Rüland
- Interdisciplinary Breast Unit, Kliniken Essen-Mitte, 45136 Essen, Germany; (S.B.); (S.K.); (H.H.); (E.B.); (A.R.); (A.K.); (O.C.); (C.D.-G.)
- Brustzentrum, St. Marienhospital, 52353 Düren, Germany
| | - Athina Kostara
- Interdisciplinary Breast Unit, Kliniken Essen-Mitte, 45136 Essen, Germany; (S.B.); (S.K.); (H.H.); (E.B.); (A.R.); (A.K.); (O.C.); (C.D.-G.)
| | - Ouafaa Chiari
- Interdisciplinary Breast Unit, Kliniken Essen-Mitte, 45136 Essen, Germany; (S.B.); (S.K.); (H.H.); (E.B.); (A.R.); (A.K.); (O.C.); (C.D.-G.)
| | - Christine Dittmer-Grabowski
- Interdisciplinary Breast Unit, Kliniken Essen-Mitte, 45136 Essen, Germany; (S.B.); (S.K.); (H.H.); (E.B.); (A.R.); (A.K.); (O.C.); (C.D.-G.)
| | - Mattea Reinisch
- Interdisciplinary Breast Unit, Kliniken Essen-Mitte, 45136 Essen, Germany; (S.B.); (S.K.); (H.H.); (E.B.); (A.R.); (A.K.); (O.C.); (C.D.-G.)
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15
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Tazzite A, Jouhadi H, Benider A, Nadifi S. BRCA Mutational Status is a Promising Predictive Biomarker for Platinum- based Chemotherapy in Triple-Negative Breast Cancer. Curr Drug Targets 2021; 21:962-973. [PMID: 32013831 DOI: 10.2174/1389450121666200203162541] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/21/2019] [Accepted: 12/18/2019] [Indexed: 01/18/2023]
Abstract
Triple-negative breast cancer (TNBC) can be distinguished from other breast malignancies by the lack of expression of estrogen receptors (ER), progesterone receptors (PR) as well as human epidermal growth factor receptor 2 (HER2). TNBC is associated with adverse clinical outcomes and high risk of metastasis. Currently, several clinical and translational reports are focusing on developing targeted therapies for this aggressive cancer. In addition to approved targeted drugs such as poly(ADP-ribose) polymerase inhibitors (PARPi) and immune-checkpoint inhibitors, platinum-based chemotherapy is still a cornerstone therapeutic option in TNBC. However, despite the observed improved outcomes with platinum- based chemotherapy in TNBC, there is still a large proportion of patients who do not respond to this treatment, hence, the need for predictive biomarkers to stratify TNBC patients and therefore, avoiding unwanted toxicities of these agents. With the emergence of genetic testing, several recent studies suggested mutations in breast cancer susceptibility gene (BRCA) in TNBC patients as important predictors of outcomes. These mutations alter the homologous recombination repair (HRR) mechanisms leading to genomic instability. Consequently, sensitivity to platinum-based treatments in this subpopulation of TNBC patients may be explained by cell death enhanced by deoxyribonucleic acid (DNA) damage induced by these potent anticancer drugs. Through this paper, we review several recent studies on this topic to better understand the mechanisms and discuss the potential of BRCA mutational status as a predictive biomarker of platinum-based chemotherapy in TNBC.
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Affiliation(s)
- Amal Tazzite
- Genetics and Molecular Pathology Laboratory, Medical school of Casablanca, Hassan II University, Casablanca, Morocco
| | - Hassan Jouhadi
- Mohammed VI Center for Cancer Treatment, Ibn Rochd University Hospital, Casablanca, Morocco
| | - Abdellatif Benider
- Mohammed VI Center for Cancer Treatment, Ibn Rochd University Hospital, Casablanca, Morocco
| | - Sellama Nadifi
- Genetics and Molecular Pathology Laboratory, Medical school of Casablanca, Hassan II University, Casablanca, Morocco
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16
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Cheng ML, Pectasides E, Hanna GJ, Parsons HA, Choudhury AD, Oxnard GR. Circulating tumor DNA in advanced solid tumors: Clinical relevance and future directions. CA Cancer J Clin 2021; 71:176-190. [PMID: 33165928 DOI: 10.3322/caac.21650] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/21/2020] [Accepted: 09/14/2020] [Indexed: 02/06/2023] Open
Abstract
The application of genomic profiling assays using plasma circulating tumor DNA (ctDNA) is rapidly evolving in the management of patients with advanced solid tumors. Diverse plasma ctDNA technologies in both commercial and academic laboratories are in routine or emerging use. The increasing integration of such testing to inform treatment decision making by oncology clinicians has complexities and challenges but holds significant potential to substantially improve patient outcomes. In this review, the authors discuss the current role of plasma ctDNA assays in oncology care and provide an overview of ongoing research that may inform real-world clinical applications in the near future.
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Affiliation(s)
- Michael L Cheng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Eirini Pectasides
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Glenn J Hanna
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Heather A Parsons
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Atish D Choudhury
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Geoffrey R Oxnard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
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17
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Rong G, Yi Z, Ma F, Guan Y, Xu Y, Li L, Xu B. DNA damage response as a prognostic indicator in metastatic breast cancer via mutational analysis. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:220. [PMID: 33708847 PMCID: PMC7940884 DOI: 10.21037/atm-20-2137] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Background High tumor heterogeneity contributes to breast cancer recurrence and metastasis. However, the lack of indicators to serve as precise and reliable means of predicting breast cancer prognosis has yet to be addressed. This study aims to reveal the prognostic relevance of mutations in metastatic breast cancer (MBC) by large-scale circulating tumor DNA (ctDNA) analysis in China. Methods We performed ctDNA panel-captured sequencing of 958 blood samples from MBC patients including 494 hormone receptor (HR)-positive cases, 130 human epidermal growth factor receptor 2-positive cases, and 177 triple-negative breast cancer (TNBC) cases. The somatic mutations and potential targets were assessed. Progression-free survival (PFS) was analyzed using the Kaplan-Meier method. Results In 801 of the 958 MBC blood samples, 663 mutated genes and 5,829 nonsynonymous alterations were identified. Mutated genes of the highest frequency were tumor protein p53 (TP53, 54%), phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha (PIK3CA, 41%), estrogen receptor 1 (ESR1, 12%), myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3, 11%), DNA (cytosine-5)-methyltransferase 3A (DNMT3A, 10%), erb-b2 receptor tyrosine kinase 2 (ERBB2, 10%), GATA binding protein 3 (GATA3, 8%), FAT atypical cadherin 1 (FAT1, 7%), phosphatase and tensin homolog (PTEN, 6%), and mitogen-activated protein kinase kinase kinase 1 (MAP3K1, 6%). Enriched mutations and driver genes in MBC varied across stages and in multiple subtypes. Moreover, TP53, ERBB2, or coexisting TP53/PIK3CA mutations in MBC were remarkably related with shorter PFS. Mutated DNA damage response (DDR) genes were significantly associated with tumor mutation burden and mutant-allele tumor heterogeneity score, as well as with worse clinical outcome. Conclusions Our findings indicate that the mutations of TP53, PIK3CA, ERBB2, and in particular, DDR genes, in MBC might be relevant indicators of unfavorable prognosis in MBC.
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Affiliation(s)
- Guohua Rong
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zongbi Yi
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanfang Guan
- Geneplus-Beijing, Beijing, China.,Geneplus-Beijing Institute, Beijing, China
| | - Yaping Xu
- Geneplus-Beijing, Beijing, China.,Geneplus-Beijing Institute, Beijing, China
| | - Lifeng Li
- Geneplus-Beijing, Beijing, China.,Geneplus-Beijing Institute, Beijing, China
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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18
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Abstract
Response evaluation for cancer treatment consists primarily of clinical and radiological assessments. In addition, a limited number of serum biomarkers that assess treatment response are available for a small subset of malignancies. Through recent technological innovations, new methods for measuring tumor burden and treatment response are becoming available. By utilization of highly sensitive techniques, tumor-specific mutations in circulating DNA can be detected and circulating tumor DNA (ctDNA) can be quantified. These so-called liquid biopsies provide both molecular information about the genomic composition of the tumor and opportunities to evaluate tumor response during therapy. Quantification of tumor-specific mutations in plasma correlates well with tumor burden. Moreover, with liquid biopsies, it is also possible to detect mutations causing secondary resistance during treatment. This review focuses on the clinical utility of ctDNA as a response and follow-up marker in patients with non-small cell lung cancer, melanoma, colorectal cancer, and breast cancer. Relevant studies were retrieved from a literature search using PubMed database. An overview of the available literature is provided and the relevance of ctDNA as a response marker in anti-cancer therapy for clinical practice is discussed. We conclude that the use of plasma-derived ctDNA is a promising tool for treatment decision-making based on predictive testing, detection of resistance mechanisms, and monitoring tumor response. Necessary steps for translation to daily practice and future perspectives are discussed.
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19
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Dupain C, Masliah‐Planchon J, Gu C, Girard E, Gestraud P, Du Rusquec P, Borcoman E, Bello D, Ricci F, Hescot S, Sablin M, Tresca P, de Moura A, Loirat D, Frelaut M, Vincent‐Salomon A, Lecerf C, Callens C, Antonio S, Franck C, Mariani O, Bièche I, Kamal M, Le Tourneau C, Servois V. Fine-needle aspiration as an alternative to core needle biopsy for tumour molecular profiling in precision oncology: prospective comparative study of next-generation sequencing in cancer patients included in the SHIVA02 trial. Mol Oncol 2021; 15:104-115. [PMID: 32750212 PMCID: PMC7782085 DOI: 10.1002/1878-0261.12776] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/07/2020] [Accepted: 07/30/2020] [Indexed: 12/15/2022] Open
Abstract
High-throughput molecular profiling of solid tumours using core needle biopsies (CNB) allows the identification of actionable molecular alterations, with around 70% success rate. Although several studies have demonstrated the utility of small biopsy specimens for molecular testing, there remains debate as to the sensitivity of the less invasive fine-needle aspiration (FNA) compared to CNB to detect molecular alterations. We aimed to prospectively evaluate the potential of FNA to detect such alterations in various tumour types as compared to CNB in cancer patients included in the SHIVA02 trial. An in-house amplicon-based targeted sequencing panel (Illumina TSCA 99.3 kb panel covering 87 genes) was used to identify pathogenic variants and gene copy number variations (CNV) in concomitant CNB and FNA samples obtained from 61 patients enrolled in the SHIVA02 trial (NCT03084757). The main tumour types analysed were breast (38%), colon (15%), pancreas (11%), followed by cervix and stomach (7% each). We report 123 molecular alterations (85 variants, 23 amplifications and 15 homozygous deletions) among which 98 (80%) were concordant between CNB and FNA. The remaining discordances were mainly related to deletions status, yet undetected alterations were not exclusively specific to FNA. Comparative analysis of molecular alterations in CNB and FNA showed high concordance in terms of variants as well as CNVs identified. We conclude FNA could therefore be used in routine diagnostics workflow and clinical trials for tumour molecular profiling with the advantages of being minimally invasive and preserve tissue material needed for diagnostic, prognostic or theranostic purposes.
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Affiliation(s)
- Célia Dupain
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
| | | | - Céline Gu
- Department of PathologyInstitut CuriePSL Research UniversityParisFrance
| | - Elodie Girard
- INSERM U900 Research UnitInstitut CurieSaint‐CloudFrance
| | | | - Pauline Du Rusquec
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
| | - Edith Borcoman
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
| | - Diana Bello
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
| | - Francesco Ricci
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
| | - Ségolène Hescot
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
| | - Marie‐Paule Sablin
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
| | - Patricia Tresca
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
| | - Alexandre de Moura
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
| | - Delphine Loirat
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
| | - Maxime Frelaut
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
| | | | - Charlotte Lecerf
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
| | - Céline Callens
- Department of GeneticsInstitut CuriePSL Research UniversityParisFrance
| | - Samantha Antonio
- Department of GeneticsInstitut CuriePSL Research UniversityParisFrance
| | - Coralie Franck
- Department of GeneticsInstitut CuriePSL Research UniversityParisFrance
| | - Odette Mariani
- Department of PathologyInstitut CuriePSL Research UniversityParisFrance
| | - Ivan Bièche
- Department of GeneticsInstitut CuriePSL Research UniversityParisFrance
- INSERM U1016Faculty of Pharmaceutical and Biological SciencesParis Descartes UniversityParisFrance
| | - Maud Kamal
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
| | - Christophe Le Tourneau
- Department of Drug Development and Innovation (D3i)Institut CurieParis & Saint‐CloudFrance
- INSERM U900 Research UnitInstitut CurieSaint‐CloudFrance
- Paris‐Saclay UniversityParisFrance
| | - Vincent Servois
- Department of RadiologyInstitut CuriePSL Research UniversityParis & Saint‐CloudFrance
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20
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Mo H, Wang X, Ma F, Qian Z, Sun X, Yi Z, Guan X, Li L, Liu B, Xu B. Genome-wide chromosomal instability by cell-free DNA sequencing predicts survival in patients with metastatic breast cancer. Breast 2020; 53:111-118. [PMID: 32738630 PMCID: PMC7503795 DOI: 10.1016/j.breast.2020.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/22/2020] [Accepted: 07/19/2020] [Indexed: 02/05/2023] Open
Abstract
Background Genome-wide chromosomal instability, instead of specific somatic mutations or copy-number alterations in selected genes, is a significant property of cancer and may suggest a new strategy for treatment. Here we utilized cell-free DNA (cfDNA) sequencing to display the whole picture of chromosomal instability in patients with metastatic breast cancer (MBC), and evaluate its predictive value for patient survival. Methods The clinical data of 65 patients who had frozen plasma and planned to change the therapeutic regimen were retrospectively enrolled. Low-coverage whole-genome sequencing of cfDNA was performed to generate the chromosomal instability represented by chromosomal instability (CIN) score. Results Tumors with diverse status of hormone receptor and HER2 represented diverse chromosomal instability across the whole genome. According to the receiver operating characteristic curve and the statistical distribution, CIN score exceed 3881 was defined as “High”. 32 (53.3%) patients with high CIN score had similar clinicopathologic characteristics compared with low CIN score patients. The median overall survival of patients with high CIN score was 21.2 months (95% CI 14.1–28.3), which was significantly inferior to those with low CIN score (not reached, P = 0.006). Regardless of various treatment regimens, the median progression free survival in patients with high CIN score was 7.3 months, which was significantly worse than those in the low CIN score population (11.0 months, P = 0.034). Multivariate analysis revealed that CIN score was an independent prognostic factor, with hazard ratio of 3.563 (P = 0.005). Conclusions To our knowledge, this is the first study illustrating the prognostic value of chromosomal instability derived from cfDNA in MBC. Novel UCAD pipeline to profile genome-wide chromosomal instability in cfDNA. Genome-wide chromosomal instability is a robust independent prognostic biomarker. HER2 amplification was successfully identified from cfDNA in our cohort.
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Affiliation(s)
- Hongnan Mo
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaobing Wang
- State Key Lab of Molecular Oncology, Laboratory of Cell and Molecular Biology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Ziliang Qian
- Prophet Genomics Inc, San Jose, USA; Suzhou Hongyuan Biotech Inc, Biobay, Suzhou, 215123, China
| | - Xiaoying Sun
- Department of Medical Oncology, Cancer Hospital of Huanxing, Beijing, China
| | - Zongbi Yi
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiuwen Guan
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lixi Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Binliang Liu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Hess J, Kohl T, Kotrová M, Rönsch K, Paprotka T, Mohr V, Hutzenlaub T, Brüggemann M, Zengerle R, Niemann S, Paust N. Library preparation for next generation sequencing: A review of automation strategies. Biotechnol Adv 2020; 41:107537. [DOI: 10.1016/j.biotechadv.2020.107537] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/27/2020] [Accepted: 03/16/2020] [Indexed: 01/08/2023]
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22
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Cocco S, Piezzo M, Calabrese A, Cianniello D, Caputo R, Di Lauro V, Fusco G, di Gioia G, Licenziato M, de Laurentiis M. Biomarkers in Triple-Negative Breast Cancer: State-of-the-Art and Future Perspectives. Int J Mol Sci 2020; 21:E4579. [PMID: 32605126 PMCID: PMC7369987 DOI: 10.3390/ijms21134579] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/23/2020] [Accepted: 06/25/2020] [Indexed: 12/12/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a heterogeneous group of tumors characterized by aggressive behavior, high risk of distant recurrence, and poor survival. Chemotherapy is still the main therapeutic approach for this subgroup of patients, therefore, progress in the treatment of TNBC remains an important challenge. Data derived from molecular technologies have identified TNBCs with different gene expression and mutation profiles that may help developing targeted therapies. So far, however, only a few of these have shown to improve the prognosis and outcomes of TNBC patients. Robust predictive biomarkers to accelerate clinical progress are needed. Herein, we review prognostic and predictive biomarkers in TNBC, discuss the current evidence supporting their use, and look at the future of this research field.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Michelino de Laurentiis
- Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, Via Mariano Semmola, 53, 80131 Napoli NA, Italy; (S.C.); (M.P.); (A.C.); (D.C.); (R.C.); (V.D.L.); (G.F.); (G.d.G.); (M.L.)
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Said R, Guibert N, Oxnard GR, Tsimberidou AM. Circulating tumor DNA analysis in the era of precision oncology. Oncotarget 2020; 11:188-211. [PMID: 32010431 PMCID: PMC6968778 DOI: 10.18632/oncotarget.27418] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 12/16/2019] [Indexed: 12/13/2022] Open
Abstract
The spatial and temporal genomic heterogeneity of various tumor types and advances in technology have stimulated the development of circulating tumor DNA (ctDNA) genotyping. ctDNA was developed as a non-invasive, cost-effective alternative to tumor biopsy when such biopsy is associated with significant risk, when tumor tissue is insufficient or inaccessible, and/or when repeated assessment of tumor molecular abnormalities is needed to optimize treatment. The role of ctDNA is now well established in the clinical decision in certain alterations and tumors, such as the epidermal growth factor receptor (EGFR) mutation in non-small cell lung cancer and the v-Ki-ras2 kirsten rat sarcoma viral oncogene homolog (KRAS) mutation in colorectal cancer. The role of ctDNA analysis in other tumor types remains to be validated. Evolving data indicate the association of ctDNA level with tumor burden, and the usefulness of ctDNA analysis in assessing minimal residual disease, in understanding mechanisms of resistance to treatment, and in dynamically guiding therapy. ctDNA analysis is increasingly used to select therapy. Carefully designed clinical trials that use ctDNA analysis will increase the rate of patients who receive targeted therapy, will elucidate our understanding of evolution of tumor biology and will accelerate drug development and implementation of precision medicine. In this article we provide a critical overview of clinical trials and evolving data of ctDNA analysis in specific tumors and across tumor types.
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Affiliation(s)
- Rabih Said
- Department of Investigational Cancer Therapeutics, Phase I Clinical Trials Program, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Oncology, St. George Hospital University Medical Center, University of Balamand, Beirut, Lebanon
- Co-authorship
| | - Nicolas Guibert
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Thoracic Oncology, Toulouse University Hospital, Toulouse, France
- Co-authorship
| | - Geoffrey R. Oxnard
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Apostolia M. Tsimberidou
- Department of Investigational Cancer Therapeutics, Phase I Clinical Trials Program, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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24
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Lee JS, Yost SE, Blanchard S, Schmolze D, Yin HH, Pillai R, Robinson K, Tang A, Martinez N, Portnow J, Wen W, Yim JH, Brauer HA, Ren Y, Luu T, Mortimer J, Yuan Y. Phase I clinical trial of the combination of eribulin and everolimus in patients with metastatic triple-negative breast cancer. Breast Cancer Res 2019; 21:119. [PMID: 31703728 PMCID: PMC6839083 DOI: 10.1186/s13058-019-1202-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/13/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Alteration of the PI3K/AKT/mTOR pathway is a common genomic abnormality detected in triple-negative breast cancer (TNBC). Everolimus acts synergistically with eribulin in TNBC cell lines and xenograft models. This phase I trial was designed to test the safety and tolerability of combining eribulin and everolimus in patients with metastatic TNBC. METHODS The primary objective of this study was to evaluate the safety and toxicities of the combination. Patients with metastatic TNBC who had up to four lines of prior chemotherapies were enrolled. The combination of eribulin and everolimus was tested using three dosing levels: A1 (everolimus 5 mg daily; eribulin 1.4 mg/m2 days 1 and 8 every 3 weeks), A2 (everolimus 7.5 mg daily; eribulin 1.4 mg/m2, days 1 and 8 every 3 weeks), and B1 (everolimus 5 mg daily; eribulin 1.1 mg/m2 days 1 and 8 every 3 weeks). RESULTS Twenty-seven patients with median age 55 years were enrolled. Among 8 evaluable patients who received dose level A1, 4 had dose-limiting toxicities (DLTs). Among 3 evaluable patients treated with dose level A2, 2 had DLTs. Among 12 evaluable patients who received dose level B1, 4 had DLTs. The DLTs were neutropenia, stomatitis, and hyperglycemia. Over the study period, 59% had a ≥ grade 3 toxicity, 44% had ≥ grade 3 hematologic toxicities, and 22% had grade 4 hematologic toxicities. The most common hematological toxicities were neutropenia, leukopenia, and lymphopenia. Thirty-three percent had grade 3 non-hematologic toxicities. The most common non-hematological toxicities were stomatitis, hyperglycemia, and fatigue. The median number of cycles completed was 4 (range 0-8). Among 25 eligible patients, 9 patients (36%) achieved the best response as partial response, 9 (36%) had stable disease, and 7 (28%) had progression. The median time to progression was 2.6 months (95% CI [2.1, 4.0]), and median overall survival (OS) was 8.3 months (95% CI [5.5, undefined]). CONCLUSION Eribulin 1.1 mg/m2 days 1 and 8 every 3 weeks with everolimus 5 mg daily was defined as the highest dose with acceptable toxicity (RP2D). The combination is safe, and efficacy is modest. A post hoc analysis showed that participants that used dexamethasone mouthwash stayed on treatment for one additional cycle. TRIAL REGISTRATION ClinicalTrials.gov, NCT02120469. Registered 18 April 2014.
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Affiliation(s)
- Jin Sun Lee
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center and Beckman Research Institute, 1500 E. Duarte Road, Duarte, CA, 91010, USA
| | - Susan E Yost
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center and Beckman Research Institute, 1500 E. Duarte Road, Duarte, CA, 91010, USA
| | - Suzette Blanchard
- Department of Biostatistics, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Daniel Schmolze
- Department of Pathology, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Hongwei Holly Yin
- Department of Pathology, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Raju Pillai
- Department of Pathology, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Kim Robinson
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center and Beckman Research Institute, 1500 E. Duarte Road, Duarte, CA, 91010, USA
| | - Aileen Tang
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center and Beckman Research Institute, 1500 E. Duarte Road, Duarte, CA, 91010, USA
| | - Norma Martinez
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center and Beckman Research Institute, 1500 E. Duarte Road, Duarte, CA, 91010, USA
| | - Jana Portnow
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center and Beckman Research Institute, 1500 E. Duarte Road, Duarte, CA, 91010, USA
| | - Wei Wen
- Department of Surgery, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - John H Yim
- Department of Surgery, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | | | - Yuqi Ren
- NanoString Technologies, Inc., Seattle, WA, USA
| | | | - Joanne Mortimer
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center and Beckman Research Institute, 1500 E. Duarte Road, Duarte, CA, 91010, USA.
| | - Yuan Yuan
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center and Beckman Research Institute, 1500 E. Duarte Road, Duarte, CA, 91010, USA.
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Snow A, Chen D, Lang JE. The current status of the clinical utility of liquid biopsies in cancer. Expert Rev Mol Diagn 2019; 19:1031-1041. [PMID: 31482746 DOI: 10.1080/14737159.2019.1664290] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Liquid biopsies have attracted considerable attention as potential diagnostic, prognostic, predictive, and screening assays in oncology. The term liquid biopsies include circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) in the blood. While many liquid biopsy technologies are under active investigation, relatively few liquid biopsy assays have been proven to serve as a diagnostic surrogate for biopsies of metastatic disease as predictive biomarkers to guide the selection of therapy in the clinic. Areas covered: The objective of this review is to highlight the status of liquid biopsies in solid tumors in the oncology literature with attention to proven utility as diagnostic surrogates for macrometastases. Expert opinion: Carefully designed clinical-translational studies are needed to establish the diagnostic accuracy and clinical utility of liquid biopsy biomarkers in oncology. Investigators must fully consider relevant pre-analytical variables, assay sensitivity, bioinformatics considerations as well as the clinical utility of rare event profiling in the context of the normal blood background. Future liquid biopsy research should address the concern that not all DNA mutations are expressed and should provide the means to discover potential therapeutic targets in metastatic patients via a minimally invasive blood draw.
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Affiliation(s)
- Anson Snow
- Department of Surgery, University of Southern California Norris Comprehensive Cancer Center , Los Angeles , CA , USA
| | - Denaly Chen
- Department of Medicine, University of Southern California Norris Comprehensive Cancer Center , Los Angeles , CA , USA
| | - Julie E Lang
- Department of Surgery, University of Southern California Norris Comprehensive Cancer Center , Los Angeles , CA , USA
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26
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Singh J, Asad S, Zhang Y, Nock W, Adams E, Damicis A, Ramaswamy B, Williams N, Parsons HA, Adalsteinsson VA, Winer EP, Lin NU, Partridge AH, Overmoyer B, Stover DG. Aggressive Subsets of Metastatic Triple Negative Breast Cancer. Clin Breast Cancer 2019; 20:e20-e26. [PMID: 31631016 DOI: 10.1016/j.clbc.2019.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/22/2019] [Accepted: 06/22/2019] [Indexed: 11/25/2022]
Abstract
BACKGROUND Relative to other metastatic breast cancer subtypes, metastatic triple-negative breast cancer (mTNBC) has a shorter duration of response to therapy and worse overall survival. Among patients with mTNBC, it is hypothesized that inflammatory breast cancer (IBC) and young women have particularly aggressive phenotypes. We investigated clinical and cell-free DNA (cfDNA) characteristics of inflammatory-mTNBC and young-mTNBC. PATIENTS AND METHODS We evaluated 158 patients with mTNBC who were stratified into 3 groups: (1) IBC; (2) patients aged 45 years or younger at primary diagnosis without IBC (non-IBC young); and (3) patients over age 45 at diagnosis without IBC. We evaluated clinicopathologic characteristics, sites of metastasis, survival outcomes, and the fraction of DNA in circulation derived from tumor (TFx). RESULTS Analysis of metastatic sites revealed that young patients without IBC had the most frequent lung metastases (P = .002). cfDNA analyses of first sample showed that TFx was highest in the non-IBC young group but not elevated in the IBC group (analysis of variance P = .056 for first TFx). Individually, median overall survival from metastatic diagnosis for the IBC group was 15.2 months; for the non-IBC young group, 21.2 months, and for the non-IBC over 45 group, 31.2 months. Patients with IBC and young patients without IBC had worse prognosis relative to patients over 45 without IBC (log-rank P = .023). CONCLUSIONS Among patients with mTNBC in this single-institution cohort, patients with IBC and young patients without IBC had significantly worse overall survival compared with patients over 45 without IBC. Young patients without IBC had significantly higher cfDNA TFx, whereas patients with IBC did not have elevated TFx despite a poor prognosis. These findings demonstrate that further analyses of mTNBC subsets are warranted.
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Affiliation(s)
- Jasneet Singh
- Department of Medicine, Ohio State University College of Medicine, Columbus, OH
| | - Sarah Asad
- Division of Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Yiqing Zhang
- Division of Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - William Nock
- Division of Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Elizabeth Adams
- Division of Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Adrienne Damicis
- College of Public Health, Division of Biostatistics, Ohio State University, Columbus, OH
| | - Bhuvaneswari Ramaswamy
- Department of Medicine, Ohio State University College of Medicine, Columbus, OH; Division of Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Nicole Williams
- Department of Medicine, Ohio State University College of Medicine, Columbus, OH; Division of Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Heather A Parsons
- Department of Medical Oncology, Susan F. Smith Center for Women's Cancers, Dana-Farber Cancer Institute, Boston, MA
| | | | - Eric P Winer
- Department of Medical Oncology, Susan F. Smith Center for Women's Cancers, Dana-Farber Cancer Institute, Boston, MA
| | - Nancy U Lin
- Department of Medical Oncology, Susan F. Smith Center for Women's Cancers, Dana-Farber Cancer Institute, Boston, MA
| | - Ann H Partridge
- Department of Medical Oncology, Susan F. Smith Center for Women's Cancers, Dana-Farber Cancer Institute, Boston, MA
| | - Beth Overmoyer
- Department of Medical Oncology, Susan F. Smith Center for Women's Cancers, Dana-Farber Cancer Institute, Boston, MA
| | - Daniel G Stover
- Department of Medicine, Ohio State University College of Medicine, Columbus, OH; Division of Medical Oncology, Ohio State University Comprehensive Cancer Center, Columbus, OH.
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Genomic testing, tumor microenvironment and targeted therapy of Hedgehog-related human cancers. Clin Sci (Lond) 2019; 133:953-970. [PMID: 31036756 DOI: 10.1042/cs20180845] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/24/2019] [Accepted: 04/11/2019] [Indexed: 12/12/2022]
Abstract
Hedgehog signals are transduced through Patched receptors to the Smoothened (SMO)-SUFU-GLI and SMO-Gi-RhoA signaling cascades. MTOR-S6K1 and MEK-ERK signals are also transduced to GLI activators through post-translational modifications. The GLI transcription network up-regulates target genes, such as BCL2, FOXA2, FOXE1, FOXF1, FOXL1, FOXM1, GLI1, HHIP, PTCH1 and WNT2B, in a cellular context-dependent manner. Aberrant Hedgehog signaling in tumor cells leads to self-renewal, survival, proliferation and invasion. Paracrine Hedgehog signaling in the tumor microenvironment (TME), which harbors cancer-associated fibroblasts, leads to angiogenesis, fibrosis, immune evasion and neuropathic pain. Hedgehog-related genetic alterations occur frequently in basal cell carcinoma (BCC) (85%) and Sonic Hedgehog (SHH)-subgroup medulloblastoma (87%) and less frequently in breast cancer, colorectal cancer, gastric cancer, pancreatic cancer, non-small-cell lung cancer (NSCLC) and ovarian cancer. Among investigational SMO inhibitors, vismodegib and sonidegib are approved for the treatment of patients with BCC, and glasdegib is approved for the treatment of patients with acute myeloid leukemia (AML). Resistance to SMO inhibitors is caused by acquired SMO mutations, SUFU deletions, GLI2 amplification, other by-passing mechanisms of GLI activation and WNT/β-catenin signaling activation. GLI-DNA-interaction inhibitors (glabrescione B and GANT61), GLI2 destabilizers (arsenic trioxide and pirfenidone) and a GLI-deacetylation inhibitor (4SC-202) were shown to block GLI-dependent transcription and tumorigenesis in preclinical studies. By contrast, SMO inhibitors can remodel the immunosuppressive TME that is dominated by M2-like tumor-associated macrophages (M2-TAMs), myeloid-derived suppressor cells and regulatory T cells, and thus, a Phase I/II clinical trial of the immune checkpoint inhibitor pembrolizumab with or without vismodegib in BCC patients is ongoing.
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28
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Button B, Croessmann S, Chu D, Rosen DM, Zabransky DJ, Dalton WB, Cravero K, Kyker-Snowman K, Waters I, Karthikeyan S, Christenson ES, Donaldson J, Hunter T, Dennison L, Ramin C, May B, Roden R, Petry D, Armstrong DK, Visvanathan K, Park BH. The estrogen receptor-alpha S118P variant does not affect breast cancer incidence or response to endocrine therapies. Breast Cancer Res Treat 2019; 174:401-412. [PMID: 30560461 PMCID: PMC6447053 DOI: 10.1007/s10549-018-05087-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 12/05/2018] [Indexed: 01/15/2023]
Abstract
PURPOSE Estrogen receptor-alpha (ER) is a therapeutic target of ER-positive (ER+) breast cancers. Although ER signaling is complex, many mediators of this pathway have been identified. Specifically, phosphorylation of ER at serine 118 affects responses to estrogen and therapeutic ligands and has been correlated with clinical outcomes in ER+ breast cancer patients. We hypothesized that a newly described germline variant (S118P) at this residue would drive cellular changes consistent with breast cancer development and/or hormone resistance. METHODS Isogenic human breast epithelial cell line models harboring ER S118P were developed via genome editing and characterized to determine the functional effects of this variant. We also examined the frequency of ER S118P in a case-control study (N = 536) of women with and without breast cancer with a familial risk. RESULTS In heterozygous knock-in models, the S118P variant demonstrated no significant change in proliferation, migration, MAP Kinase pathway signaling, or response to the endocrine therapies tamoxifen and fulvestrant. Further, there was no difference in the prevalence of S118P between women with and without cancer relative to population registry databases. CONCLUSIONS This study suggests that the ER S118P variant does not affect risk for breast cancer or hormone therapy resistance. Germline screening and modification of treatments for patients harboring this variant are likely not warranted.
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Affiliation(s)
- Berry Button
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sarah Croessmann
- Vanderbilt Ingram Cancer Center, Vanderbilt Universtiy Medical Center, 2220 Pierce Avenue, PRB 777, Nashville, TN, 37232, USA
| | - David Chu
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - D Marc Rosen
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel J Zabransky
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - W Brian Dalton
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Karen Cravero
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kelly Kyker-Snowman
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ian Waters
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Swathi Karthikeyan
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Eric S Christenson
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Josh Donaldson
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tasha Hunter
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lauren Dennison
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Cody Ramin
- The Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Betty May
- The Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Richard Roden
- The Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Dana Petry
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Deborah K Armstrong
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kala Visvanathan
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ben Ho Park
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Vanderbilt Ingram Cancer Center, Vanderbilt Universtiy Medical Center, 2220 Pierce Avenue, PRB 777, Nashville, TN, 37232, USA.
- Department of Chemical and Biomolecular Engineering, The Whiting School of Engineering, The Johns Hopkins University, Baltimore, MD, USA.
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29
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Huang M, Wei S. Overview of Molecular Testing of Cytology Specimens. Acta Cytol 2019; 64:136-146. [PMID: 30917368 DOI: 10.1159/000497187] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 01/23/2019] [Indexed: 12/15/2022]
Abstract
OBJECTIVE Utilizing cytology specimens for molecular testing has attracted increasing attention in the era of personalized medicine. Cytology specimens are clinically easier to access. The samples can be quickly and completely fixed in a very short time of fixation before tissue degradation occurs, compared to hours or days of fixation in surgical pathology specimens. In addition, cytology specimens can be fixed without formalin, which can significantly damage DNA and RNA. All these factors contribute to the superb quality of DNA and RNA in cytology specimens for molecular tests. STUDY DESIGN We summarize the most pertinent information in the literature regarding molecular testing in the field of cytopathology. RESULTS The first part focuses on the types of cytological specimens that can be used for molecular testing, including the advantages and limitations. The second section describes the common molecular tests and their clinical application. CONCLUSION Various types of cytology specimens are suitable for many molecular tests, which may require additional clinical laboratory validation.
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Affiliation(s)
- Min Huang
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Shuanzeng Wei
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA,
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Doll S, Gnad F, Mann M. The Case for Proteomics and Phospho-Proteomics in Personalized Cancer Medicine. Proteomics Clin Appl 2019; 13:e1800113. [PMID: 30790462 PMCID: PMC6519247 DOI: 10.1002/prca.201800113] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 02/01/2019] [Indexed: 02/06/2023]
Abstract
The concept of personalized medicine is predominantly been pursued through genomic and transcriptomic technologies, leading to the identification of multiple mutations in a large variety of cancers. However, it has proven challenging to distinguish driver and passenger mutations and to deal with tumor heterogeneity and resistant clonal populations. More generally, these heterogeneous mutation patterns do not in themselves predict the tumor phenotype. Analysis of the expressed proteins in a tumor and their modification states reveals if and how these mutations are translated to the functional level. It is already known that proteomic changes including posttranslational modifications are crucial drivers of oncogenesis, but proteomics technology has only recently become comparable in depth and accuracy to RNAseq. These advances also allow the rapid and highly sensitive analysis of formalin-fixed and paraffin-embedded biobank tissues, on both the proteome and phosphoproteome levels. In this perspective, pioneering mass spectrometry-based proteomic studies are highlighted that pave the way toward clinical implementation. It is argued that proteomics and phosphoproteomics could provide the missing link to make omics analysis actionable in the clinic.
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Affiliation(s)
- Sophia Doll
- Department of Proteomics and Signal TransductionMax Planck Institute of Biochemistry82152MartinsriedGermany
- NNF Center for Protein ResearchFaculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Florian Gnad
- Department of Bioinformatics and Computational BiologyCell Signaling Technology Inc01923DanversMAUSA
| | - Matthias Mann
- Department of Proteomics and Signal TransductionMax Planck Institute of Biochemistry82152MartinsriedGermany
- NNF Center for Protein ResearchFaculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
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Lee JH, Jeong H, Choi JW, Oh HE, Kim YS. Liquid biopsy prediction of axillary lymph node metastasis, cancer recurrence, and patient survival in breast cancer: A meta-analysis. Medicine (Baltimore) 2018; 97:e12862. [PMID: 30334995 PMCID: PMC6211877 DOI: 10.1097/md.0000000000012862] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Liquid biopsies using circulating tumor DNA (ctDNA) and cell-free DNA (cfDNA) have been developed for early cancer detection and patient monitoring. To investigate the clinical usefulness of ctDNA aberrations and cfDNA levels in patients with breast cancer (BC), we conducted a meta-analysis of 69 published studies on 5736 patients with BC. METHODS The relevant publications were identified by searching PubMed and Embase databases. The effect sizes of outcome parameters were pooled using a random-effects model. RESULTS The ctDNA mutation rates of TP53, PIK3CA, and ESR1 were approximately 38%, 27%, and 32%, respectively. High levels of cfDNA were associated with BCs rather than with healthy controls. However, these detection rates were not satisfactory for BC screening. Although the precise mechanisms have been unknown, high cfDNA levels were significantly associated with axillary lymph node metastasis (odds ratio [OR] = 2.148, P = .030). The ctDNA mutations were significantly associated with cancer recurrence (OR = 3.793, P < .001), short disease-free survival (univariate hazard ratio [HR] = 5.180, P = .026; multivariate HR = 3.605, P = .001), and progression-free survival (HR = 1.311, P = .013) rates, and poor overall survival outcomes (HR = 2.425, P = .007). CONCLUSION This meta-analysis demonstrates that ctDNA mutation status predicts disease recurrence and unfavorable survival outcomes, while cfDNA levels can be predictive of axillary lymph node metastasis in patients with BC.
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Kurnit KC, Dumbrava EEI, Litzenburger B, Khotskaya YB, Johnson AM, Yap TA, Rodon J, Zeng J, Shufean MA, Bailey AM, Sánchez NS, Holla V, Mendelsohn J, Shaw KM, Bernstam EV, Mills GB, Meric-Bernstam F. Precision Oncology Decision Support: Current Approaches and Strategies for the Future. Clin Cancer Res 2018; 24:2719-2731. [PMID: 29420224 PMCID: PMC6004235 DOI: 10.1158/1078-0432.ccr-17-2494] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/02/2017] [Accepted: 01/30/2018] [Indexed: 12/11/2022]
Abstract
With the increasing availability of genomics, routine analysis of advanced cancers is now feasible. Treatment selection is frequently guided by the molecular characteristics of a patient's tumor, and an increasing number of trials are genomically selected. Furthermore, multiple studies have demonstrated the benefit of therapies that are chosen based upon the molecular profile of a tumor. However, the rapid evolution of genomic testing platforms and emergence of new technologies make interpreting molecular testing reports more challenging. More sophisticated precision oncology decision support services are essential. This review outlines existing tools available for health care providers and precision oncology teams and highlights strategies for optimizing decision support. Specific attention is given to the assays currently available for molecular testing, as well as considerations for interpreting alteration information. This article also discusses strategies for identifying and matching patients to clinical trials, current challenges, and proposals for future development of precision oncology decision support. Clin Cancer Res; 24(12); 2719-31. ©2018 AACR.
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Affiliation(s)
- Katherine C Kurnit
- Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Beate Litzenburger
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Bioinformatics, Qiagen Inc., Redwood City, California
| | - Yekaterina B Khotskaya
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Amber M Johnson
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Timothy A Yap
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jordi Rodon
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jia Zeng
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Md Abu Shufean
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ann M Bailey
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Nora S Sánchez
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Vijaykumar Holla
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John Mendelsohn
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kenna Mills Shaw
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Elmer V Bernstam
- School of Biomedical Informatics and Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Gordon B Mills
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Funda Meric-Bernstam
- Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas.
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Zivanovic Bujak A, Dawson SJ. Circulating Tumor DNA Guides Prognosis in Metastatic Triple-Negative Breast Cancer. J Clin Oncol 2018; 36:523-524. [PMID: 29298118 DOI: 10.1200/jco.2017.76.5461] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- Andjelija Zivanovic Bujak
- Andjelija Zivanovic Bujak and Sarah-Jane Dawson, Peter MacCallum Cancer Centre and University of Melbourne, Melbourne, Victoria, Australia
| | - Sarah-Jane Dawson
- Andjelija Zivanovic Bujak and Sarah-Jane Dawson, Peter MacCallum Cancer Centre and University of Melbourne, Melbourne, Victoria, Australia
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Stover DG, Parsons HA, Ha G, Freeman SS, Barry WT, Guo H, Choudhury AD, Gydush G, Reed SC, Rhoades J, Rotem D, Hughes ME, Dillon DA, Partridge AH, Wagle N, Krop IE, Getz G, Golub TR, Love JC, Winer EP, Tolaney SM, Lin NU, Adalsteinsson VA. Association of Cell-Free DNA Tumor Fraction and Somatic Copy Number Alterations With Survival in Metastatic Triple-Negative Breast Cancer. J Clin Oncol 2018; 36:543-553. [PMID: 29298117 PMCID: PMC5815405 DOI: 10.1200/jco.2017.76.0033] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Purpose Cell-free DNA (cfDNA) offers the potential for minimally invasive genome-wide profiling of tumor alterations without tumor biopsy and may be associated with patient prognosis. Triple-negative breast cancer (TNBC) is characterized by few mutations but extensive somatic copy number alterations (SCNAs), yet little is known regarding SCNAs in metastatic TNBC. We sought to evaluate SCNAs in metastatic TNBC exclusively via cfDNA and determine if cfDNA tumor fraction is associated with overall survival in metastatic TNBC. Patients and Methods In this retrospective cohort study, we identified 164 patients with biopsy-proven metastatic TNBC at a single tertiary care institution who received prior chemotherapy in the (neo)adjuvant or metastatic setting. We performed low-coverage genome-wide sequencing of cfDNA from plasma. Results Without prior knowledge of tumor mutations, we determined tumor fraction of cfDNA for 96.3% of patients and SCNAs for 63.9% of patients. Copy number profiles and percent genome altered were remarkably similar between metastatic and primary TNBCs. Certain SCNAs were more frequent in metastatic TNBCs relative to paired primary tumors and primary TNBCs in publicly available data sets The Cancer Genome Atlas and METABRIC, including chromosomal gains in drivers NOTCH2, AKT2, and AKT3. Prespecified cfDNA tumor fraction threshold of ≥ 10% was associated with significantly worse metastatic survival (median, 6.4 v 15.9 months) and remained significant independent of clinicopathologic factors (hazard ratio, 2.14; 95% CI, 1.4 to 3.8; P < .001). Conclusion We present the largest genomic characterization of metastatic TNBC to our knowledge, exclusively from cfDNA. Evaluation of cfDNA tumor fraction was feasible for nearly all patients, and tumor fraction ≥ 10% is associated with significantly worse survival in this large metastatic TNBC cohort. Specific SCNAs are enriched and prognostic in metastatic TNBC, with implications for metastasis, resistance, and novel therapeutic approaches.
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Affiliation(s)
- Daniel G. Stover
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Heather A. Parsons
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Gavin Ha
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Samuel S. Freeman
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - William T. Barry
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Hao Guo
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Atish D. Choudhury
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Gregory Gydush
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Sarah C. Reed
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Justin Rhoades
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Denisse Rotem
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Melissa E. Hughes
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Deborah A. Dillon
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Ann H. Partridge
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Nikhil Wagle
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Ian E. Krop
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Gad Getz
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Todd R. Golub
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - J. Christopher Love
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Eric P. Winer
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Sara M. Tolaney
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Nancy U. Lin
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
| | - Viktor A. Adalsteinsson
- Daniel G. Stover, Ohio State University Comprehensive Cancer Center, Columbus, OH; Heather A. Parsons, Gavin Ha, William T. Barry, Hao Guo, Atish D. Choudhury, Melissa E. Hughes, Deborah A. Dillon, Ann H. Partridge, Nikhil Wagle, Ian E. Krop, Todd R. Golub, Eric P. Winer, Sara M. Tolaney, and Nancy U. Lin, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital, Boston; Gavin Ha, Samuel S. Freeman, Atish D. Choudhury, Gregory Gydush, Sarah C. Reed, Justin Rhoades, Denisse Rotem, Nikhil Wagle, Gad Getz, Todd R. Golub, and Viktor A. Adalsteinsson, Broad Institute of Harvard and Massachusetts Institute of Technology; and J. Christopher Love, Massachusetts Institute of Technology, Cambridge, MA
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Affiliation(s)
- Joshua Donaldson
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Ben Ho Park
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218
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Nagahashi M, Ling Y, Hayashida T, Kitagawa Y, Futamura M, Yoshida K, Kuwayama T, Nakamura S, Toshikawa C, Yamauchi H, Yamauchi T, Kaneko K, Kanbayashi C, Sato N, Miyoshi Y, Tsuchida J, Nakajima M, Shimada Y, Ichikawa H, Lyle S, Takabe K, Okuda S, Wakai T. Actionable gene alterations in an Asian population with triple-negative breast cancer. JCO Precis Oncol 2018; 2. [PMID: 32529167 DOI: 10.1200/po.17.00211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Purpose It has been suggested that the biological characteristics of breast cancer may differ among different geographic or ethnic populations. Indeed, triple-negative breast cancer (TNBC), the most lethal breast cancer subgroup, has been reported to show a higher incidence in Japan than in the US. However, most genomic studies of these tumors are from Western countries and the genomic landscape of TNBC in an Asian population has not been thoroughly investigated. Here, we sought to elucidate the geographic and ethnic diversity of breast cancer by examining actionable driver alterations in TNBC tumors from Japanese patients and comparing them with The Cancer Genome Atlas (TCGA) database, which gather data primarily from non-Asian patients. Materials and Methods We performed comprehensive genomic profiling, including an analysis of 435 known cancer genes on Japanese TNBC patients (N=53) and compared the results to independent data obtained from TCGA (N=123). Results Driver alterations were identified in 51 out of 53 Japanese patients (96%). Although the overall alteration spectrum of Japanese patients was similar to that of the TCGA, we found significant differences in the frequencies of alterations in MYC and PTK2. We identified three patients (5.7%) with a high tumor mutation burden, although no microsatellite instability was observed in any of the Japanese patients. Importantly, pathway analysis revealed that 66.0% (35/53) of Japanese patients, as well as 66.7% (82/123) of the TCGA cohort, had alterations in at least one actionable gene targetable by an FDA-approved drug. Conclusion Our study identified actionable driver alterations in Japanese patients with TNBC, revealing new opportunities for targeted therapies in Asian patients.
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Affiliation(s)
- Masayuki Nagahashi
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata City, Niigata 951-8510, Japan
| | - YiWei Ling
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata City, Niigata 951-8510, Japan
| | - Tetsu Hayashida
- Department of Surgery, Keio University School of Medicine, 35 Shinano-machi, Shinjyuku-ku, Tokyo, 160-8582, Japan
| | - Yuko Kitagawa
- Department of Surgery, Keio University School of Medicine, 35 Shinano-machi, Shinjyuku-ku, Tokyo, 160-8582, Japan
| | - Manabu Futamura
- Department of Surgical Oncology, Gifu University Graduate School of Medicine, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Kazuhiro Yoshida
- Department of Surgical Oncology, Gifu University Graduate School of Medicine, 1-1 Yanagido, Gifu 501-1194, Japan
| | - Takashi Kuwayama
- Division of Breast Surgical Oncology, Department of Surgery, Showa University School of Medicine, 1-5-8, Hatanodai, Shinagawa-ku, Tokyo 142-8666, Japan
| | - Seigo Nakamura
- Division of Breast Surgical Oncology, Department of Surgery, Showa University School of Medicine, 1-5-8, Hatanodai, Shinagawa-ku, Tokyo 142-8666, Japan
| | - Chie Toshikawa
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata City, Niigata 951-8510, Japan.,Department of Breast Surgical Oncology, Department of Internal Medicine, St. Luke's International Hospital, 9-1 Akashicho, Chuo, Tokyo 104-8560, Japan
| | - Hideko Yamauchi
- Department of Breast Surgical Oncology, Department of Internal Medicine, St. Luke's International Hospital, 9-1 Akashicho, Chuo, Tokyo 104-8560, Japan
| | - Teruo Yamauchi
- Division of Medical Oncology, Department of Internal Medicine, St. Luke's International Hospital, 9-1 Akashicho, Chuo, Tokyo 104-8560, Japan
| | - Koji Kaneko
- Department of Breast Oncology, Niigata Cancer Center Hospital, 15-3 Kawagishi-cho 2-Chome, Chuo-ku, Niigata City, Niigata 951-8566, Japan
| | - Chizuko Kanbayashi
- Department of Breast Oncology, Niigata Cancer Center Hospital, 15-3 Kawagishi-cho 2-Chome, Chuo-ku, Niigata City, Niigata 951-8566, Japan
| | - Nobuaki Sato
- Department of Breast Oncology, Niigata Cancer Center Hospital, 15-3 Kawagishi-cho 2-Chome, Chuo-ku, Niigata City, Niigata 951-8566, Japan
| | - Yasuo Miyoshi
- Department of Surgery, Division of Breast and Endocrine, Hyogo College of Medicine, 1-1 Mukogawa-cho, Nishinomiya, Hyogo, 663-8501, Japan
| | - Junko Tsuchida
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata City, Niigata 951-8510, Japan
| | - Masato Nakajima
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata City, Niigata 951-8510, Japan
| | - Yoshifumi Shimada
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata City, Niigata 951-8510, Japan
| | - Hiroshi Ichikawa
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata City, Niigata 951-8510, Japan
| | - Stephen Lyle
- University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, Massachusetts 01655, USA
| | - Kazuaki Takabe
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata City, Niigata 951-8510, Japan.,Breast Surgery, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, New York 14263, USA.,Department of Surgery, University at Buffalo Jacobs School of Medicine and Biosciences, the State University of New York, USA.,Department of Breast Surgery and Oncology, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan.,Department of Surgery, Yokohama City University, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Shujiro Okuda
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata City, Niigata 951-8510, Japan
| | - Toshifumi Wakai
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata City, Niigata 951-8510, Japan
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Henry NL, Bedard PL, DeMichele A. Standard and Genomic Tools for Decision Support in Breast Cancer Treatment. Am Soc Clin Oncol Educ Book 2017; 37:106-115. [PMID: 28561710 DOI: 10.1200/edbk_175617] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Over the past few decades, comprehensive characterization of the cancer genome has elucidated pathways that drive cancer and mechanisms of resistance to therapy and provided important insights for development of new therapies. These advances have resulted in the development of prognostic and predictive tools for use in clinical settings, which can assist clinicians and patients in making informed decisions about the benefits of established therapies. In early-stage breast cancer, multiparameter genomic assays are now available for decision making about the duration of adjuvant endocrine therapy and the use of adjuvant chemotherapy. Similarly, in metastatic disease, there are multiple commercially available next-generation sequencing options for identifying genetic alterations in tumors that may be targeted with a drug. Although these tools hold great promise for providing precision medicine, it can be difficult for the treating physician to evaluate their clinical utility and appropriately select tools for individual clinical situations. This review summarizes the currently available genomic tools in breast cancer, the data underlying their clinical validity and utility, and how they can be used in conjunction with standard clinicopathologic data for making adjuvant and metastatic treatment decisions.
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Affiliation(s)
- N Lynn Henry
- From the University of Utah, Salt Lake City, UT; Department of Medicine, Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Philippe L Bedard
- From the University of Utah, Salt Lake City, UT; Department of Medicine, Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Angela DeMichele
- From the University of Utah, Salt Lake City, UT; Department of Medicine, Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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38
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Chung JH, Pavlick D, Hartmaier R, Schrock AB, Young L, Forcier B, Ye P, Levin MK, Goldberg M, Burris H, Gay LM, Hoffman AD, Stephens PJ, Frampton GM, Lipson DM, Nguyen DM, Ganesan S, Park BH, Vahdat LT, Leyland-Jones B, Mughal TI, Pusztai L, O'Shaughnessy J, Miller VA, Ross JS, Ali SM. Hybrid capture-based genomic profiling of circulating tumor DNA from patients with estrogen receptor-positive metastatic breast cancer. Ann Oncol 2017; 28:2866-2873. [PMID: 28945887 PMCID: PMC5834148 DOI: 10.1093/annonc/mdx490] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Genomic changes that occur in breast cancer during the course of disease have been informed by sequencing of primary and metastatic tumor tissue. For patients with relapsed and metastatic disease, evolution of the breast cancer genome highlights the importance of using a recent sample for genomic profiling to guide clinical decision-making. Obtaining a metastatic tissue biopsy can be challenging, and analysis of circulating tumor DNA (ctDNA) from blood may provide a minimally invasive alternative. PATIENTS AND METHODS Hybrid capture-based genomic profiling was carried out on ctDNA from 254 female patients with estrogen receptor-positive breast cancer. Peripheral blood samples were submitted by clinicians in the course of routine clinical care between May 2016 and March 2017. Sequencing of 62 genes was carried out to a median unique coverage depth of 7503×. Genomic alterations (GAs) in ctDNA were evaluated and compared with matched tissue samples and genomic datasets of tissue from breast cancer. RESULTS At least 1 GA was reported in 78% of samples. Frequently altered genes were TP53 (38%), ESR1 (31%) and PIK3CA (31%). Temporally matched ctDNA and tissue samples were available for 14 patients; 89% of mutations detected in tissue were also detected in ctDNA. Diverse ESR1 GAs including mutation, rearrangement and amplification, were observed. Multiple concurrent ESR1 GAs were observed in 40% of ESR1-altered cases, suggesting polyclonal origin; ESR1 compound mutations were also observed in two cases. ESR1-altered cases harbored co-occurring GAs in PIK3CA (35%), FGFR1 (16%), ERBB2 (8%), BRCA1/2 (5%), and AKT1 (4%). CONCLUSIONS GAs relevant to relapsed/metastatic breast cancer management were identified, including diverse ESR1 GAs. Genomic profiling of ctDNA demonstrated sensitive detection of mutations found in tissue. Detection of amplifications was associated with ctDNA fraction. Genomic profiling of ctDNA may provide a complementary and possibly alternative approach to tissue-based genomic testing for patients with estrogen receptor-positive metastatic breast cancer.
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Affiliation(s)
- J H Chung
- Foundation Medicine, Inc., Cambridge.
| | - D Pavlick
- Foundation Medicine, Inc., Cambridge
| | | | | | - L Young
- Foundation Medicine, Inc., Cambridge
| | - B Forcier
- Foundation Medicine, Inc., Cambridge
| | - P Ye
- Avera Cancer Institute, Sioux Falls
| | - M K Levin
- Baylor University Medical Center, Texas Oncology, US Oncology, Dallas
| | | | - H Burris
- Sarah Cannon Research Institute, Nashville
| | - L M Gay
- Foundation Medicine, Inc., Cambridge
| | | | | | | | | | - D M Nguyen
- Sutter Medical Group of the Redwoods, Santa Rosa
| | - S Ganesan
- Division of Medical Oncology, Department of Medicine, Rutgers Cancer Institute of New Jersey, New Brunswick
| | - B H Park
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore
| | - L T Vahdat
- Weill Cornell Breast Center, Weill Cornell Medicine, New York
| | | | - T I Mughal
- Foundation Medicine, Inc., Cambridge; Tufts University Medical Center, Boston
| | - L Pusztai
- Department of Breast Medical Oncology, Yale University, Yale Cancer Center, New Haven
| | - J O'Shaughnessy
- Baylor University Medical Center, Texas Oncology, US Oncology, Dallas
| | | | - J S Ross
- Foundation Medicine, Inc., Cambridge; Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, USA. mailto:
| | - S M Ali
- Foundation Medicine, Inc., Cambridge
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Marotti JD, de Abreu FB, Wells WA, Tsongalis GJ. Triple-Negative Breast Cancer. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 187:2133-2138. [DOI: 10.1016/j.ajpath.2017.05.018] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 05/01/2017] [Accepted: 05/23/2017] [Indexed: 02/06/2023]
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40
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Christenson ES, Dalton WB, Chu D, Waters I, Cravero K, Zabransky DJ, DeZern AE, Park BH. Single-Nucleotide Polymorphism Leading to False Allelic Fraction by Droplet Digital PCR. Clin Chem 2017; 63:1370-1376. [PMID: 28615231 DOI: 10.1373/clinchem.2017.273177] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 04/24/2017] [Indexed: 12/25/2022]
Abstract
BACKGROUND Molecular-based diagnostics have great utility for cancer detection. We have used droplet digital PCR (ddPCR) as a platform for identifying mutations in circulating plasma tumor DNA (ptDNA). We present the unexpected finding of a spurious mutant allele fraction that was discovered to be artifactual because of the presence of a single-nucleotide polymorphism (SNP) in a patient sample. DESIGN AND METHODS Probe and primer combinations for the K700 and V701 loci of the SF3B1 spliceosome gene were designed for ddPCR to identify the percentage of mutant and wild-type alleles. Clinical samples from patients with cancer with known SF3B1 mutations were collected and tested to evaluate the assays' ability to detect SF3B1 mutations in ptDNA. RESULTS Patient samples showed SF3B1 K700E mutations within the ptDNA of 4 patients with acute leukemia and 3 with myelodysplastic syndrome who were known to harbor this mutation. A blood sample from a patient with lung cancer with a known SF3B1 V701F mutation was also analyzed and this mutation was successfully identified in ptDNA. However, 1 of the patients with a K700E mutation was found to have a mutational burden of 98%. After careful analysis of this locus by Sanger sequencing and ddPCR, this patient was found to have an SNP (R702R), which prevented binding of the ddPCR wild-type probe to its cognate allele. CONCLUSIONS These results further support that ddPCR-based assays may be valuable companion diagnostics for the identification and monitoring of patients with cancer, but the results also emphasize the need to identify SNPs at loci that are being analyzed.
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Affiliation(s)
- Eric S Christenson
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - W Brian Dalton
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - David Chu
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Ian Waters
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Karen Cravero
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Daniel J Zabransky
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Amy E DeZern
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Ben Ho Park
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD; .,The Whiting School of Engineering, Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD
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41
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Dalton WB, Forde PM, Kang H, Connolly RM, Stearns V, Gocke CD, Eshleman JR, Axilbund J, Petry D, Geoghegan C, Wolff AC, Loeb DM, Pratilas CA, Meyer CF, Christenson ES, Slater SA, Ensminger J, Parsons HA, Park BH, Lauring J. Personalized Medicine in the Oncology Clinic: Implementation and Outcomes of the Johns Hopkins Molecular Tumor Board. JCO Precis Oncol 2017; 2017. [PMID: 30003184 DOI: 10.1200/po.16.00046] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Purpose Tumor genomic profiling for personalized oncology therapy is being widely applied in clinical practice even as it is being evaluated more formally in clinical trials. Given the complexities of genomic data and its application to clinical use, molecular tumor boards with diverse expertise can provide guidance to oncologists and patients seeking to implement personalized genetically targeted therapy in practice. Methods A multidisciplinary molecular tumor board reviewed tumor molecular profiling reports from consecutive referrals at the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins over a 3-year period. The tumor board weighed evidence for actionability of genomic alterations identified by molecular profiling and provided recommendations including US Food and Drug Administration-approved drug therapy, clinical trials of matched targeted therapy, off-label use of such therapy, and additional tumor or germline genetic testing. Results One hundred fifty-five patients were reviewed. Actionable genomic alterations were identified in 132 patients (85%). Off-label therapies were recommended in 37 patients (24%). Eleven patients were treated off-label, and 13 patients were enrolled onto clinical trials of matched targeted therapies. Median progression-free survival of patients treated with matched therapies was 5 months (95% CI, 2.9 months to not reached), and the progression-free survival probability at 6 months was 43%(95% CI, 26% to 71%). Lack of locally available clinical trials was the major limitation on clinical actionability of tumor profiling reports. Conclusion The molecular tumor board recommended off-label targeted therapies for a quarter of all patients reviewed. Outcomes were heterogeneous, although 43% of patients receiving genomically matched therapy derived clinical benefit lasting at least 6 months. Until more data become available from precision oncology trials, molecular tumor boards can help guide appropriate use of tumor molecular testing to direct therapy.
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Affiliation(s)
- W Brian Dalton
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Patrick M Forde
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Hyunseok Kang
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Roisin M Connolly
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Vered Stearns
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Christopher D Gocke
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - James R Eshleman
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | | | - Dana Petry
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | | | - Antonio C Wolff
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - David M Loeb
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | | | - Christian F Meyer
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Eric S Christenson
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Shannon A Slater
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Jennifer Ensminger
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Heather A Parsons
- Susan F. Smith Center for Women's Cancers, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Ben H Park
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Josh Lauring
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
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Somatic Tumor Mutations Detected by Targeted Next Generation Sequencing in Minute Amounts of Serum-Derived Cell-Free DNA. Sci Rep 2017; 7:2136. [PMID: 28522829 PMCID: PMC5437051 DOI: 10.1038/s41598-017-02388-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 04/18/2017] [Indexed: 01/15/2023] Open
Abstract
The use of blood-circulating cell-free DNA (cfDNA) as 'liquid-biopsy' is explored worldwide, with hopes for its potential in providing prognostic or predictive information in cancer treatment. In exploring cfDNA, valuable repositories are biobanks containing material collected over time, however these retrospective cohorts have restrictive resources. In this study, we aimed to detect tumor-specific mutations in only minute amounts of serum-derived cfDNA by using a targeted next generation sequencing (NGS) approach. In a retrospective cohort of ten metastatic breast cancer patients, we profiled DNA from primary tumor tissue (frozen), tumor-adjacent normal tissue (formalin-fixed paraffin embedded), and three consecutive serum samples (frozen). Our presented workflow includes comparisons with matched normal DNA or in silico reference DNA to discriminate germline from somatic variants, validation of variants through the detection in at least two DNA samples of an individual, and the use of public databases on variants. By our workflow, we were able to detect a total of four variants traceable as circulating tumor DNA (ctDNA) in the sera of three of the ten patients.
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Maxwell KN, Soucier-Ernst D, Tahirovic E, Troxel AB, Clark C, Feldman M, Colameco C, Kakrecha B, Langer M, Lieberman D, Morrissette JJD, Paul MR, Pan TC, Yee S, Shih N, Carpenter E, Chodosh LA, DeMichele A. Comparative clinical utility of tumor genomic testing and cell-free DNA in metastatic breast cancer. Breast Cancer Res Treat 2017. [PMID: 28500398 DOI: 10.1007/s10549‐017‐4257‐x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
Abstract
PURPOSE Breast cancer metastases differ biologically from primary disease; therefore, metastatic biopsies may assist in treatment decision making. Commercial genomic testing of both tumor and circulating tumor DNA have become available clinically, but utility of these tests in breast cancer management remains unclear. METHODS Patients undergoing a clinically indicated metastatic tumor biopsy were consented to the ongoing METAMORPH registry. Tumor and blood were collected at the time of disease progression before subsequent therapy, and patients were followed for response on subsequent treatment. Tumor testing (n = 53) and concurrent cell-free DNA (n = 32) in a subset of patients was performed using CLIA-approved assays. RESULTS The proportion of patients with a genomic alteration was lower in tumor than in blood (69 vs. 91%; p = 0.06). After restricting analysis to alterations covered on both platforms, 83% of tumor alterations were detected in blood, while 90% of blood alterations were detected in tumor. Mutational load specific for the panel genes was calculated for both tumor and blood. Time to progression on subsequent treatment was significantly shorter for patients whose tumors had high panel-specific mutational load (HR 0.31, 95% CI 0.12-0.78) or a TP53 mutation (HR 0.35, 95% CI 0.20-0.79), after adjusting for stage at presentation, hormone receptor status, prior treatment type, and number of lines of metastatic treatment. CONCLUSIONS Treating oncologists must distinguish platform differences from true biological heterogeneity when comparing tumor and cfDNA genomic testing results. Tumor and concurrent cfDNA contribute unique genomic information in metastatic breast cancer patients, providing potentially useful biomarkers for aggressive metastatic disease.
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Affiliation(s)
- Kara N Maxwell
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Danielle Soucier-Ernst
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Emin Tahirovic
- Department of Biostatistics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Andrea B Troxel
- Department of Population Health, NYU School of Medicine, New York, NY, USA
| | - Candace Clark
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Michael Feldman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher Colameco
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Bijal Kakrecha
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Melissa Langer
- University of Maryland School of Medicine, Baltimore, MD, USA
| | - David Lieberman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer J D Morrissette
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Matt R Paul
- Department of Cancer Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Tien-Chi Pan
- Department of Cancer Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Stephanie Yee
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Natalie Shih
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Erica Carpenter
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.,Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Lewis A Chodosh
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.,Department of Cancer Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.,Department of Medicine, Division of Endocrinology, Diabetes and Metabolism at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Angela DeMichele
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Department of Biostatistics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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Comparative clinical utility of tumor genomic testing and cell-free DNA in metastatic breast cancer. Breast Cancer Res Treat 2017; 164:627-638. [PMID: 28500398 DOI: 10.1007/s10549-017-4257-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 04/17/2017] [Indexed: 01/24/2023]
Abstract
PURPOSE Breast cancer metastases differ biologically from primary disease; therefore, metastatic biopsies may assist in treatment decision making. Commercial genomic testing of both tumor and circulating tumor DNA have become available clinically, but utility of these tests in breast cancer management remains unclear. METHODS Patients undergoing a clinically indicated metastatic tumor biopsy were consented to the ongoing METAMORPH registry. Tumor and blood were collected at the time of disease progression before subsequent therapy, and patients were followed for response on subsequent treatment. Tumor testing (n = 53) and concurrent cell-free DNA (n = 32) in a subset of patients was performed using CLIA-approved assays. RESULTS The proportion of patients with a genomic alteration was lower in tumor than in blood (69 vs. 91%; p = 0.06). After restricting analysis to alterations covered on both platforms, 83% of tumor alterations were detected in blood, while 90% of blood alterations were detected in tumor. Mutational load specific for the panel genes was calculated for both tumor and blood. Time to progression on subsequent treatment was significantly shorter for patients whose tumors had high panel-specific mutational load (HR 0.31, 95% CI 0.12-0.78) or a TP53 mutation (HR 0.35, 95% CI 0.20-0.79), after adjusting for stage at presentation, hormone receptor status, prior treatment type, and number of lines of metastatic treatment. CONCLUSIONS Treating oncologists must distinguish platform differences from true biological heterogeneity when comparing tumor and cfDNA genomic testing results. Tumor and concurrent cfDNA contribute unique genomic information in metastatic breast cancer patients, providing potentially useful biomarkers for aggressive metastatic disease.
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