1
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Zhao Y, Zhang B, Ma Y, Guo M, Zhao F, Chen J, Wang B, Jin H, Zhou F, Guan J, Zhao Q, Liu Q, Wang H, Zhao F, Wang X. Distinct molecular profiles drive multifaceted characteristics of colorectal cancer metastatic seeds. J Exp Med 2024; 221:e20231359. [PMID: 38502057 PMCID: PMC10949939 DOI: 10.1084/jem.20231359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/10/2023] [Accepted: 02/08/2024] [Indexed: 03/20/2024] Open
Abstract
Metastasis of primary tumors remains a challenge for early diagnosis and prevention. The cellular properties and molecular drivers of metastatically competent clones within primary tumors remain unclear. Here, we generated 10-16 single cell-derived lines from each of three colorectal cancer (CRC) tumors to identify and characterize metastatic seeds. We found that intrinsic factors conferred clones with distinct metastatic potential and cellular communication capabilities, determining organ-specific metastasis. Poorly differentiated or highly metastatic clones, rather than drug-resistant clones, exhibited poor clinical prognostic impact. Personalized genetic alterations, instead of mutation burden, determined the occurrence of metastatic potential during clonal evolution. Additionally, we developed a gene signature for capturing metastatic potential of primary CRC tumors and demonstrated a strategy for identifying metastatic drivers using isogenic clones with distinct metastatic potential in primary tumors. This study provides insight into the origin and mechanisms of metastasis and will help develop potential anti-metastatic therapeutic targets for CRC patients.
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Affiliation(s)
- Yuanyuan Zhao
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
- Institute for Intelligent Healthcare, Tsinghua University, Beijing, China
| | - Bing Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yiming Ma
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mengmeng Guo
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Fuqiang Zhao
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianan Chen
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bingzhi Wang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hua Jin
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Fulai Zhou
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Jiawei Guan
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Qian Zhao
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Qian Liu
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hongying Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Xia Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
- Institute for Intelligent Healthcare, Tsinghua University, Beijing, China
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2
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Bezrookove V, Kianian S, McGeever L, Jones R, Caressi C, Nosrati M, Kim KB, Leong SP, Miller JR, Desprez PY, Kashani-Sabet M. The Molecular Evolution of Melanoma Distant Metastases. J Invest Dermatol 2024:S0022-202X(24)00271-9. [PMID: 38582370 DOI: 10.1016/j.jid.2024.03.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/26/2024] [Accepted: 03/14/2024] [Indexed: 04/08/2024]
Abstract
The evolution of primary melanoma to lymph node and distant metastasis is incompletely understood. We examined the genomic diversity in melanoma progression in matched primary melanomas and lymph node and distant metastases from 17 patients. FISH analysis revealed cancer cell fractions with monotonic copy number alterations, including PHIP gain and PTEN loss, in the metastatic cascade. By contrast, the cancer cell fraction with copy number alterations for BPTF and MITF was reduced in lymph node metastases but increased in distant metastases. Separately, the cancer cell fraction with NCOA3 copy number alteration was comparable between primary tumors and lymph node metastases yet increased in distant metastases. These results suggest enrichment of the phosphoinositide 3-kinase and MITF pathways in the transition through the metastatic cascade. By contrast, next-generation sequencing analysis did not identify a consistent pattern of changes in variant allele frequency while revealing several intriguing findings, including decreased variant allele frequency in distant metastases and distinct drivers in lymph node versus distant metastases. These results provide evidence that distant melanoma metastasis does not always emanate from lymph node metastasis. These results enhance our understanding of clonal patterns of melanoma metastasis, with possible implications for targeted therapy and metastasis competency.
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Affiliation(s)
- Vladimir Bezrookove
- Center for Melanoma Research and Treatment, California Pacific Medical Center, San Francisco, California, USA; California Pacific Medical Center Research Institute, San Francisco, California, USA
| | - Sara Kianian
- Center for Melanoma Research and Treatment, California Pacific Medical Center, San Francisco, California, USA; California Pacific Medical Center Research Institute, San Francisco, California, USA
| | - Lea McGeever
- California Pacific Medical Center Research Institute, San Francisco, California, USA
| | - Robyn Jones
- California Pacific Medical Center Research Institute, San Francisco, California, USA
| | - Chongshan Caressi
- Center for Melanoma Research and Treatment, California Pacific Medical Center, San Francisco, California, USA; California Pacific Medical Center Research Institute, San Francisco, California, USA
| | - Mehdi Nosrati
- Center for Melanoma Research and Treatment, California Pacific Medical Center, San Francisco, California, USA; California Pacific Medical Center Research Institute, San Francisco, California, USA
| | - Kevin B Kim
- Center for Melanoma Research and Treatment, California Pacific Medical Center, San Francisco, California, USA; California Pacific Medical Center Research Institute, San Francisco, California, USA
| | - Stanley P Leong
- Center for Melanoma Research and Treatment, California Pacific Medical Center, San Francisco, California, USA; California Pacific Medical Center Research Institute, San Francisco, California, USA
| | - James R Miller
- Center for Melanoma Research and Treatment, California Pacific Medical Center, San Francisco, California, USA; California Pacific Medical Center Research Institute, San Francisco, California, USA
| | - Pierre-Yves Desprez
- California Pacific Medical Center Research Institute, San Francisco, California, USA
| | - Mohammed Kashani-Sabet
- Center for Melanoma Research and Treatment, California Pacific Medical Center, San Francisco, California, USA; California Pacific Medical Center Research Institute, San Francisco, California, USA.
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3
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Hu Y, Cheng L, Du S, Wang K, Liu S. Antioxidant curcumin induces oxidative stress to kill tumor cells (Review). Oncol Lett 2024; 27:67. [PMID: 38192657 PMCID: PMC10773205 DOI: 10.3892/ol.2023.14200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 11/24/2023] [Indexed: 01/10/2024] Open
Abstract
Curcumin is a plant polyphenol in turmeric root and a potent antioxidant. It binds to antioxidant response elements for gene regulation by nuclear factor erythroid 2-related factor 2, thereby suppressing reactive oxygen species (ROS) and exerting anti-inflammatory, anti-infective and other pharmacological effects. Of note, curcumin induces oxidative stress in tumors. It binds to several enzymes in tumors, such as carbonyl reductases, glutathione S-transferase P1 and nicotinamide adenine dinucleotide phosphate to induce mitochondrial damage, increase ROS production and ultimately induce tumor cell death. However, the instability and poor pharmacokinetic profile of curcumin in vivo limit its clinical application. Therefore, the effects of curcumin in vivo may be enhanced through its combination with drugs, derivative development and nanocarriers. In the present review, the mechanisms of curcumin that induce tumor cell death through oxidative stress are discussed. In addition, the methods used to enhance the antitumor activity of curcumin are described. Finally, the existing knowledge on the functions of curcumin in tumors, particularly in terms of oxidative stress, are summarized to facilitate future curcumin research.
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Affiliation(s)
- Ye Hu
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning 116622, P.R. China
| | - Lei Cheng
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning 116622, P.R. China
| | - Shuguang Du
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning 116622, P.R. China
| | - Kesi Wang
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning 116622, P.R. China
| | - Shuangping Liu
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning 116622, P.R. China
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4
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Hong ES, Messersmith WA, Hammad H, Cornish TC, Aisner DL. Tissue Displacement Versus Two Primary Colorectal Carcinomas? A Case Report on the Utility of Comparative Sequencing. JCO Precis Oncol 2022; 6:e2200252. [PMID: 36240469 PMCID: PMC9616644 DOI: 10.1200/po.22.00252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/01/2022] [Accepted: 09/01/2022] [Indexed: 06/16/2023] Open
Affiliation(s)
- Ellie S. Hong
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO
| | - Wells A. Messersmith
- Division of Medical Oncology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO
| | - Hazem Hammad
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO
| | - Toby C. Cornish
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO
| | - Dara L. Aisner
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO
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Marquardt A, Kollmannsberger P, Krebs M, Argentiero A, Knott M, Solimando AG, Kerscher AG. Visual Clustering of Transcriptomic Data from Primary and Metastatic Tumors-Dependencies and Novel Pitfalls. Genes (Basel) 2022; 13:genes13081335. [PMID: 35893071 PMCID: PMC9394300 DOI: 10.3390/genes13081335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/20/2022] [Accepted: 07/23/2022] [Indexed: 02/06/2023] Open
Abstract
Personalized oncology is a rapidly evolving area and offers cancer patients therapy options that are more specific than ever. However, there is still a lack of understanding regarding transcriptomic similarities or differences of metastases and corresponding primary sites. Applying two unsupervised dimension reduction methods (t-Distributed Stochastic Neighbor Embedding (t-SNE) and Uniform Manifold Approximation and Projection (UMAP)) on three datasets of metastases (n = 682 samples) with three different data transformations (unprocessed, log10 as well as log10 + 1 transformed values), we visualized potential underlying clusters. Additionally, we analyzed two datasets (n = 616 samples) containing metastases and primary tumors of one entity, to point out potential familiarities. Using these methods, no tight link between the site of resection and cluster formation outcome could be demonstrated, or for datasets consisting of solely metastasis or mixed datasets. Instead, dimension reduction methods and data transformation significantly impacted visual clustering results. Our findings strongly suggest data transformation to be considered as another key element in the interpretation of visual clustering approaches along with initialization and different parameters. Furthermore, the results highlight the need for a more thorough examination of parameters used in the analysis of clusters.
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Affiliation(s)
- André Marquardt
- Institute of Pathology, Klinikum Stuttgart, 70174 Stuttgart, Germany
- Institute of Pathology, University of Würzburg, 97080 Würzburg, Germany
- Bavarian Center for Cancer Research (BZKF), 97080 Würzburg, Germany
- Correspondence: (A.M.); (A.G.K.)
| | - Philip Kollmannsberger
- Center for Computational and Theoretical Biology, University of Würzburg, 97074 Würzburg, Germany;
| | - Markus Krebs
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, 97080 Würzburg, Germany;
- Department of Urology and Pediatric Urology, University Hospital Würzburg, 97080 Würzburg, Germany
| | - Antonella Argentiero
- IRCCS Istituto Tumori “Giovanni Paolo II” of Bari, 70124 Bari, Italy; (A.A.); (A.G.S.)
| | - Markus Knott
- Department of Hematology, Oncology, Stem Cell Transplantation and Palliative Care, Klinikum Stuttgart, 70174 Stuttgart, Germany;
- Stuttgart Cancer Center–Tumor Unit Eva Mayr-Stihl, Klinikum Stuttgart, 70174 Stuttgart, Germany
| | - Antonio Giovanni Solimando
- IRCCS Istituto Tumori “Giovanni Paolo II” of Bari, 70124 Bari, Italy; (A.A.); (A.G.S.)
- Guido Baccelli Unit of Internal Medicine, Department of Biomedical Sciences and Human Oncology, School of Medicine, Aldo Moro University of Bari, 70124 Bari, Italy
| | - Alexander Georg Kerscher
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, 97080 Würzburg, Germany;
- Correspondence: (A.M.); (A.G.K.)
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Anticancer and Anti-Metastatic Role of Thymoquinone: Regulation of Oncogenic Signaling Cascades by Thymoquinone. Int J Mol Sci 2022; 23:ijms23116311. [PMID: 35682990 PMCID: PMC9181073 DOI: 10.3390/ijms23116311] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 05/29/2022] [Accepted: 05/30/2022] [Indexed: 12/04/2022] Open
Abstract
Cancer is a life-threatening and multifaceted disease. Pioneering research works in the past three decades have mechanistically disentangled intertwined signaling networks which play contributory roles in carcinogenesis and metastasis. Phenomenal strides have been made in leveraging our scientific knowledge altogether to a new level of maturity. Rapidly accumulating wealth of information has underlined a myriad of transduction cascades which can be pharmaceutically exploited for cancer prevention/inhibition. Natural products serve as a treasure trove and compel interdisciplinary researchers to study the cancer chemopreventive roles of wide-ranging natural products in cell culture and preclinical studies. Experimental research related to thymoquinone has gradually gained momentum because of the extra-ordinary cancer chemopreventive multifunctionalities of thymoquinone. In this mini-review, we provide an overview of different cell signaling cascades reported to be regulated by thymoquinone for cancer chemoprevention. Essentially, thymoquinone efficacy has also been notably studied in animal models, which advocates for a rationale-based transition of thymoquinone from the pre-clinical pipeline to clinical trials.
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7
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Actionable Mutation Profile of Sun-Protected Melanomas in South America. Am J Dermatopathol 2022; 44:741-747. [PMID: 35503891 DOI: 10.1097/dad.0000000000002213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
ABSTRACT Melanomas that arise in sun-protected sites, including acral and oral mucosal melanomas, are likely under the control of unique, specific mechanisms that lead to mutagenesis through various pathways. In this study, we examined somatic mutations in tumors by targeted sequencing using a custom Ion Ampliseq Panel, comprising hotspots of 14 genes that are frequently mutated in solid tumors. Tumor DNA was extracted from 9 formalin fixation, paraffin-embedded sun-protected melanomas (4 primary oral mucosal melanomas and 5 acral lentiginous melanomas), and we identified mutations in the NRAS, PIK3CA, EGFR, HRAS, ERBB2, and ROS1 genes. This study reveals new actionable mutations that are potential targets in the treatment of photo-protected melanomas. Additional studies on more of these melanoma subtypes could confirm our findings and identify new mutations.
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8
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TP53 mutation is enriched in colorectal cancer liver metastasis in the context of polyclonal seeding. Pathol Res Pract 2022; 236:153958. [DOI: 10.1016/j.prp.2022.153958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/20/2022] [Accepted: 05/25/2022] [Indexed: 11/22/2022]
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9
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Patel SB, Bookstein R, Farahani N, Chevarie-Davis M, Pao A, Aguiluz A, Riley C, Hodge JC, Alkan S, Liu Z, Deng N, Lopategui JR. Recommendations for Specimen and Therapy Selection in Colorectal Cancer. Oncol Ther 2021; 9:451-469. [PMID: 33895946 PMCID: PMC8593092 DOI: 10.1007/s40487-021-00151-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/31/2021] [Indexed: 11/21/2022] Open
Abstract
INTRODUCTION Next-generation sequencing has emerged as a clinical tool for the identification of actionable mutations to triage advanced colorectal cancer patients for targeted therapies. The literature is conflicted as to whether primaries or their metastases should be selected for sequencing. Some authors suggest that either site may be sequenced, whereas others recommend sequencing the primary, the metastasis, or even both tumors. Here, we address this issue head on with a meta-analysis and provide for the first time a set of sensible recommendations to make this determination. METHODS From our own series, we include 43 tumors from 13 patients including 14 primaries, 10 regional lymph node metastases, 17 distant metastases, and two anastomotic recurrences sequenced using the 50 gene Ion AmpliSeq cancer NGS panel v2. RESULTS Based on our new cohort and a meta-analysis, we found that ~ 77% of patient-matched primary-metastatic pairs have identical alterations in these 50 cancer-associated genes. CONCLUSIONS Low tumor cellularity, tumor heterogeneity, clonal evolution, treatment status, sample quality, and/or size of the sequencing panel accounted for a proportion of the differential detection of mutations at primary and metastatic sites. The therapeutic implications of the most frequently discordant alterations (TP53, APC, PIK3CA, and SMAD4) are discussed. Our meta-analysis indicates that a subset of patients who fail initial therapy may benefit from sequencing of additional sites to identify new actionable genomic abnormalities not present in the initial analysis. Evidence-based recommendations are proposed.
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Affiliation(s)
- Snehal B Patel
- Cedars-Sinai Medical Center, Division of Molecular Pathology and Cytogenetics, Department of Pathology and Laboratory Medicine, 8700 Beverly Blvd., SSB #362, Los Angeles, CA, 90048, USA
- HeloGenika LLC, Dexter, MI, 48130, USA
| | - Robert Bookstein
- Cedars-Sinai Medical Center, Division of Molecular Pathology and Cytogenetics, Department of Pathology and Laboratory Medicine, 8700 Beverly Blvd., SSB #362, Los Angeles, CA, 90048, USA
| | - Navid Farahani
- Cedars-Sinai Medical Center, Division of Molecular Pathology and Cytogenetics, Department of Pathology and Laboratory Medicine, 8700 Beverly Blvd., SSB #362, Los Angeles, CA, 90048, USA
| | - Myriam Chevarie-Davis
- Cedars-Sinai Medical Center, Division of Molecular Pathology and Cytogenetics, Department of Pathology and Laboratory Medicine, 8700 Beverly Blvd., SSB #362, Los Angeles, CA, 90048, USA
| | - Andy Pao
- Cedars-Sinai Medical Center, Division of Molecular Pathology and Cytogenetics, Department of Pathology and Laboratory Medicine, 8700 Beverly Blvd., SSB #362, Los Angeles, CA, 90048, USA
| | - Angela Aguiluz
- Cedars-Sinai Medical Center, Division of Molecular Pathology and Cytogenetics, Department of Pathology and Laboratory Medicine, 8700 Beverly Blvd., SSB #362, Los Angeles, CA, 90048, USA
| | - Christian Riley
- Cedars-Sinai Medical Center, Division of Molecular Pathology and Cytogenetics, Department of Pathology and Laboratory Medicine, 8700 Beverly Blvd., SSB #362, Los Angeles, CA, 90048, USA
| | - Jennelle C Hodge
- Cedars-Sinai Medical Center, Division of Molecular Pathology and Cytogenetics, Department of Pathology and Laboratory Medicine, 8700 Beverly Blvd., SSB #362, Los Angeles, CA, 90048, USA
| | - Serhan Alkan
- Cedars-Sinai Medical Center, Division of Molecular Pathology and Cytogenetics, Department of Pathology and Laboratory Medicine, 8700 Beverly Blvd., SSB #362, Los Angeles, CA, 90048, USA
| | - Zhenqui Liu
- Cedars-Sinai Medical Center, Biostatistics and Bioinformatics Research Center, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, USA
| | - Nan Deng
- Cedars-Sinai Medical Center, Biostatistics and Bioinformatics Research Center, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, USA
| | - Jean R Lopategui
- Cedars-Sinai Medical Center, Division of Molecular Pathology and Cytogenetics, Department of Pathology and Laboratory Medicine, 8700 Beverly Blvd., SSB #362, Los Angeles, CA, 90048, USA.
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10
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Rosic J, Dragicevic S, Miladinov M, Despotovic J, Bogdanovic A, Krivokapic Z, Nikolic A. SMAD7 and SMAD4 expression in colorectal cancer progression and therapy response. Exp Mol Pathol 2021; 123:104714. [PMID: 34717960 DOI: 10.1016/j.yexmp.2021.104714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 08/12/2021] [Accepted: 10/18/2021] [Indexed: 12/24/2022]
Abstract
Inhibitory SMAD7 and common mediator SMAD4 play crucial roles in SMAD-dependent TGF-β signaling that is often disrupted in colorectal cancer (CRC). This study aimed to profile the expression of SMAD7 and SMAD4 in primary and metastatic CRC and to evaluate their significance in disease progression and therapy response. The expression of SMAD7 and SMAD4 genes was analyzed by quantitative real-time PCR in tissues from 35 primary and metastatic CRC patients and in vitro in 7 human cell lines originating from colon tissue. Expression levels of SMAD7 and SMAD4, as well as their ratio, were determined and their association with tumor characteristics and response to therapy were evaluated. SMAD4 level was significantly lower in tumors compared to non-tumor tissues in both primary (p = 0.001) and metastatic (p = 0.001) CRC patients, while tumor expression of SMAD7 was significantly lower from non-tumor tissue only in metastatic patients (p = 0.017). SMAD7/SMAD4 ratio was elevated in CRC primary tumor tissues and cell lines compared to corresponding non-tumor tissues and cell line, respectively (p = 0.003). SMAD7 expression was significantly elevated in primary tumor tissues obtained from responders to neoadjuvant chemoradiotherapy (nCRT) compared to non-responders (p = 0.014). Alterations of expression and ratio of SMAD7 and SMAD4 in CRC cell lines, primary rectal cancer, and liver metastasis emphasize the importance of these genes in different stages of disease progression. Differential expression of SMAD7 in responders versus non-responders to nCRT should be further investigated for its potential predictive value.
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Affiliation(s)
- Jovana Rosic
- School of Medicine, University of Belgrade, 11 000 Belgrade, Serbia.
| | - Sandra Dragicevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11 000 Belgrade, Serbia
| | - Marko Miladinov
- Clinic for Digestive Surgery, University Clinical Center of Serbia, 11 000 Belgrade, Serbia
| | - Jovana Despotovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11 000 Belgrade, Serbia
| | - Aleksandar Bogdanovic
- School of Medicine, University of Belgrade, 11 000 Belgrade, Serbia; Clinic for Digestive Surgery, University Clinical Center of Serbia, 11 000 Belgrade, Serbia
| | - Zoran Krivokapic
- School of Medicine, University of Belgrade, 11 000 Belgrade, Serbia; Clinic for Digestive Surgery, University Clinical Center of Serbia, 11 000 Belgrade, Serbia; Serbian Academy of Sciences and Arts, 11 000 Belgrade, Serbia
| | - Aleksandra Nikolic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11 000 Belgrade, Serbia
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11
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González-Martínez S, Pizarro D, Pérez-Mies B, Caniego-Casas T, Curigliano G, Cortés J, Palacios J. Clinical, Pathological, and Molecular Features of Breast Carcinoma Cutaneous Metastasis. Cancers (Basel) 2021; 13:5416. [PMID: 34771579 PMCID: PMC8582578 DOI: 10.3390/cancers13215416] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 12/20/2022] Open
Abstract
Cutaneous metastases (CMs) account for 2% of all skin malignancies, and nearly 70% of CMs in women originate from breast cancer (BC). CMs are usually associated with poor prognosis, are difficult to treat, and can pose diagnostic problems, such as in histopathological diagnosis when occurring long after development of the primary tumor. In addition, the molecular differences between the primary tumors and their CMs, and between CMs and metastases in other organs, are not well defined. Here, we review the main clinical, pathological, and molecular characteristics of breast cancer CMs. Identifying molecular markers in primary BC that predict CM and can be used to determine the molecular differences between primary tumors and their metastases is of great interest for the design of new therapeutic approaches.
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Affiliation(s)
- Silvia González-Martínez
- Clinical Researcher, Hospital Ramón y Cajal, 28034 Madrid, Spain;
- Fundación Contigo contra el Cáncer de la Mujer, 28010 Madrid, Spain
| | - David Pizarro
- Department of Pathology, Hospital Ramón y Cajal, 28034 Madrid, Spain; (D.P.); (B.P.-M.); (T.C.-C.)
| | - Belén Pérez-Mies
- Department of Pathology, Hospital Ramón y Cajal, 28034 Madrid, Spain; (D.P.); (B.P.-M.); (T.C.-C.)
- Institute Ramón y Cajal for Health Research (IRYCIS), 28034 Madrid, Spain
- CIBER-ONC, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Faculty of Medicine, University of Alcalá de Henares, Alcalá de Henares, 28801 Madrid, Spain
| | - Tamara Caniego-Casas
- Department of Pathology, Hospital Ramón y Cajal, 28034 Madrid, Spain; (D.P.); (B.P.-M.); (T.C.-C.)
| | - Giuseppe Curigliano
- European Institute of Oncology, IRCCS, 20141 Milan, Italy;
- Departament of Oncology and Hematology, University of Milan, 20122 Milan, Italy
| | - Javier Cortés
- CIBER-ONC, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department of Medicine, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, 28670 Madrid, Spain
- International Breast Cancer Center (IBCC), Quironsalud Group, 08017 Barcelona, Spain
- Medica Scientia Innovation Research, 08007 Barcelona, Spain
- Medica Scientia Innovation Research, Ridgewood, NJ 07450, USA
- Vall d’Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - José Palacios
- Department of Pathology, Hospital Ramón y Cajal, 28034 Madrid, Spain; (D.P.); (B.P.-M.); (T.C.-C.)
- Institute Ramón y Cajal for Health Research (IRYCIS), 28034 Madrid, Spain
- CIBER-ONC, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Faculty of Medicine, University of Alcalá de Henares, Alcalá de Henares, 28801 Madrid, Spain
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Abstract
Colorectal cancer has served as a genetic and biological paradigm for the evolution of solid tumors, and these insights have illuminated early detection, risk stratification, prevention, and treatment principles. Employing the hallmarks of cancer framework, we provide a conceptual framework to understand how genetic alterations in colorectal cancer drive cancer cell biology properties and shape the heterotypic interactions across cells in the tumor microenvironment. This review details research advances pertaining to the genetics and biology of colorectal cancer, emerging concepts gleaned from immune and single-cell profiling, and critical advances and remaining knowledge gaps influencing the development of effective therapies for this cancer that remains a major public health burden.
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Affiliation(s)
- Jiexi Li
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Xingdi Ma
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Deepavali Chakravarti
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Shabnam Shalapour
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Ronald A DePinho
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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13
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Alos L, Fuster C, Castillo P, Jares P, Garcia-Herrera A, Marginet M, Agreda F, Arance A, Gonzalvo E, Garcia M, Puig S, Teixido C. TP53 mutation and tumoral PD-L1 expression are associated with depth of invasion in desmoplastic melanomas. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1218. [PMID: 33178750 PMCID: PMC7607103 DOI: 10.21037/atm-20-1846] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Background Desmoplastic melanoma (DM) is a rare subtype of spindle cell malignant melanoma characterized by frequent local recurrences and hematogenous spread, but without molecular classification. The aim of the study was to investigate in a DM series the incidence of relevant gene alterations in cancer, the programmed death-ligand 1 (PD-L1) expression status and the association with clinicopathological features and melanoma progression. Methods A total of 38 patients were included. Clinical follow-up and the histopathological features of all cases were retrospectively collected. PD-L1 expression by immunohistochemistry (IHC) and BRAF genomic alterations by real-time PCR were determined in 34 samples. Additionally, a molecular analysis by next-generation sequencing was performed in 25 DMs. Results Tumors occurred predominantly in men (76%) and in the head and neck region (50%). Most tumors were pure DMs (66%), containing less than 10% of conventional melanoma. Overall, 48% of our cohort harbored TP53 mutations, most of them showing a molecular signature associated with ultraviolet (UV)-oncogenesis, and 29%, BRAF mutations. A positive correlation between TP53 with depth of invasion (P=0.005) and presence of elastosis (P=0.002) was found. High-expression of PD-L1 in tumor cells was observed in 38% of cases and correlated with depth of tumoral infiltration (P=0.003), TP53 (P=0.016), PD-1 (P<0.001) and tumor-infiltrating lymphocytes (TILS) (P<0.001). PD-L1 expression in immune cells correlated with PD-1 (P=0.006), tumoral PD-L1 expression (P=0.029) and TP53 mutation (P=0.002). Survival correlated with depth of invasion (P=0.003), stage of tumors (P=0.015), positive sentinel lymph node (P=0.004), lymph node metastasis (P=0.024) and distant metastasis (P<0.001). Conclusions Our results suggest that progressed DMs with deep tumoral infiltration frequently harbor TP53 mutations, PD-L1 expression and present a high inflammatory response, probably related to adaptive immune resistance in this tumor-type.
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Affiliation(s)
- Llucia Alos
- Department of Pathology, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Carla Fuster
- Department of Pathology, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Paola Castillo
- Department of Pathology, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Pedro Jares
- Department of Pathology, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Adriana Garcia-Herrera
- Department of Pathology, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Marta Marginet
- Department of Pathology, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Fernando Agreda
- Department of Urological Surgery, Hospital Trias I Pujol, Carretera de Canyet, Badalona, Spain
| | - Ana Arance
- Department of Medical Oncology, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Elena Gonzalvo
- Department of Pathology, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Mireia Garcia
- Department of Pathology, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Susana Puig
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,Department of Dermatology, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Cristina Teixido
- Department of Pathology, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
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14
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Foster JM, Patel A, Zhang C, Shostrom V, Brown K, Cushman-Vokoun AM. Investigating the utility of extended mutation analysis in gastrointestinal peritoneal metastasis. J Surg Oncol 2020; 122:1106-1113. [PMID: 32662065 DOI: 10.1002/jso.26114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 06/28/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND AND OBJECTIVES Outcomes for gastrointestinal peritoneal metastases (GI-PM) are worse compared to systemic metastases, with a paucity of data exploring extended mutation profiling. An exploratory mutation analysis in GI-PMs was performed as a "proof of concept" of potential predictive values of profiling in GI-PM and rates of actionable mutations. METHODS The study included 40 GI-PM patients: 14 low-grade mucinous carcinoma peritonei and 26 HG-PM (12 colons, 10 appendix, 4 small bowels). Demographics, histologies, peritoneal cancer indexes, cytoreduction scores, and survival data were collected. NGS 50-gene mutation profiling was performed on 38 specimens. The association of mutations with survival was evaluated in high-grade PM. RESULTS KRAS, TP53, and SMAD4 mutations were observed in 61%, 29%, and 8% of cases across all tumor histologies. In 66% cases >1 mutations occurred, associated with decreased survival in HG-PM: 32 vs 73 months, P = .03. TP53 or SMAD4 mutations were associated with decreased survival in HG-PM: 22 vs 48 months, P = .02. Actionable mutations were detected in 70%. CONCLUSION Actionable mutations were detected at high rates. GI-PMs have similar mutational profiles and TP53, SMAD4, and/or >1 mutation were associate with decreased survival in HG-PM. This data supports the concept of the extended mutation profiling utility in GI-PM warranting further investigation.
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Affiliation(s)
- Jason M Foster
- Department of Surgery, Division of Surgical Oncology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Asish Patel
- Department of Surgery, Division of Surgical Oncology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Chunmeng Zhang
- Department of Surgery, Division of Surgical Oncology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Valerie Shostrom
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, Nebraska
| | - Krista Brown
- Department of Surgery, Division of Surgical Oncology, University of Nebraska Medical Center, Omaha, Nebraska
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15
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Loo K, Gauvin G, Soliman I, Renzetti M, Deng M, Ross E, Luo B, Wu H, Reddy S, Olszanski AJ, Farma JM. Primary tumor characteristics and next-generation sequencing mutations as biomarkers for melanoma immunotherapy response. Pigment Cell Melanoma Res 2020; 33:878-888. [PMID: 32564504 DOI: 10.1111/pcmr.12909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/28/2020] [Accepted: 06/16/2020] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Considerable advances in melanoma have been realized through immunotherapy. The principal aim was to determine whether primary tumor characteristics or next-generation sequencing (NGS) could serve as markers of immunotherapy response. METHODS AND RESULTS The study cohort consisted of 67 patients who received immunotherapy for recurrent or metastatic melanoma and for whom primary tumor biopsies and pathology reports were available. A subset of 59 patient tumors were profiled using an NGS panel of 50 cancer-related genes. Objective response rate to immunotherapy was assessed using RECIST v1.1 criteria. Progression-free survival (PFS) and overall survival (OS) were used as endpoints. Lymphovascular invasion (LVI) strongly correlated with an increased proportion of immunotherapy responders (p = .002). PFS interval (p = .003) and OS (p = .036) were significantly higher in patients with LVI. NRAS mutation was more strongly correlated with an increased proportion of immunotherapy responders (p =.050). PFS was significantly higher in patients with NRAS mutation (p = .042); no difference in OS (p = .111). DISCUSSION This analysis demonstrates an association between lymphovascular invasion and immunotherapy response. Additionally, NGS mutation analysis demonstrated a potential association between NRAS mutations and immunotherapy response.
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Affiliation(s)
- Kimberly Loo
- Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA.,Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Gabrielle Gauvin
- Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Iman Soliman
- Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Madelyn Renzetti
- Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA.,Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Mengying Deng
- Department of Statistics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Eric Ross
- Department of Statistics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Biao Luo
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Hong Wu
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Sanjay Reddy
- Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Anthony J Olszanski
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Jeffrey M Farma
- Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
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16
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Dang HX, Krasnick BA, White BS, Grossman JG, Strand MS, Zhang J, Cabanski CR, Miller CA, Fulton RS, Goedegebuure SP, Fronick CC, Griffith M, Larson DE, Goetz BD, Walker JR, Hawkins WG, Strasberg SM, Linehan DC, Lim KH, Lockhart AC, Mardis ER, Wilson RK, Ley TJ, Maher CA, Fields RC. The clonal evolution of metastatic colorectal cancer. SCIENCE ADVANCES 2020; 6:eaay9691. [PMID: 32577507 PMCID: PMC7286679 DOI: 10.1126/sciadv.aay9691] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 04/10/2020] [Indexed: 06/11/2023]
Abstract
Tumor heterogeneity and evolution drive treatment resistance in metastatic colorectal cancer (mCRC). Patient-derived xenografts (PDXs) can model mCRC biology; however, their ability to accurately mimic human tumor heterogeneity is unclear. Current genomic studies in mCRC have limited scope and lack matched PDXs. Therefore, the landscape of tumor heterogeneity and its impact on the evolution of metastasis and PDXs remain undefined. We performed whole-genome, deep exome, and targeted validation sequencing of multiple primary regions, matched distant metastases, and PDXs from 11 patients with mCRC. We observed intricate clonal heterogeneity and evolution affecting metastasis dissemination and PDX clonal selection. Metastasis formation followed both monoclonal and polyclonal seeding models. In four cases, metastasis-seeding clones were not identified in any primary region, consistent with a metastasis-seeding-metastasis model. PDXs underrepresented the subclonal heterogeneity of parental tumors. These suggest that single sample tumor sequencing and current PDX models may be insufficient to guide precision medicine.
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Affiliation(s)
- Ha X. Dang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
- The Alvin J. Siteman Comprehensive Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Bradley A. Krasnick
- The Alvin J. Siteman Comprehensive Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Surgery, Washington University in St. Louis, St. Louis, MO, USA
- Barnes-Jewish Hospital, St. Louis, MO, USA
| | | | - Julie G. Grossman
- The Alvin J. Siteman Comprehensive Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Surgery, Washington University in St. Louis, St. Louis, MO, USA
- Barnes-Jewish Hospital, St. Louis, MO, USA
| | - Matthew S. Strand
- The Alvin J. Siteman Comprehensive Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Surgery, Washington University in St. Louis, St. Louis, MO, USA
- Barnes-Jewish Hospital, St. Louis, MO, USA
| | - Jin Zhang
- Department of Radiation Oncology, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Christopher A. Miller
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Robert S. Fulton
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - S. Peter Goedegebuure
- The Alvin J. Siteman Comprehensive Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Surgery, Washington University in St. Louis, St. Louis, MO, USA
- Barnes-Jewish Hospital, St. Louis, MO, USA
| | - Catrina C. Fronick
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Malachi Griffith
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
| | - David E. Larson
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - Brian D. Goetz
- The Alvin J. Siteman Comprehensive Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Jason R. Walker
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | - William G. Hawkins
- The Alvin J. Siteman Comprehensive Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Surgery, Washington University in St. Louis, St. Louis, MO, USA
- Barnes-Jewish Hospital, St. Louis, MO, USA
| | - Steven M. Strasberg
- The Alvin J. Siteman Comprehensive Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Surgery, Washington University in St. Louis, St. Louis, MO, USA
- Barnes-Jewish Hospital, St. Louis, MO, USA
| | - David C. Linehan
- Department of Surgery and The Wilmot Cancer Institute, University of Rochester School of Medicine, Rochester, NY, USA
| | - Kian H. Lim
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - A. Craig Lockhart
- Division of Medical Oncology, Department of Medicine, The Sylvester Comprehensive Cancer Center, University of Miami School of Medicine, Miami, FL, USA
| | - Elaine R. Mardis
- Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Richard K. Wilson
- Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Timothy J. Ley
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
- The Alvin J. Siteman Comprehensive Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Christopher A. Maher
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
- The Alvin J. Siteman Comprehensive Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Ryan C. Fields
- The Alvin J. Siteman Comprehensive Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
- Department of Surgery, Washington University in St. Louis, St. Louis, MO, USA
- Barnes-Jewish Hospital, St. Louis, MO, USA
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17
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Masoodi T, Siraj AK, Siraj S, Azam S, Qadri Z, Albalawy WN, Parvathareddy SK, Al-Sobhi SS, Al-Dayel F, Alkuraya FS, Al-Kuraya KS. Whole-Exome Sequencing of Matched Primary and Metastatic Papillary Thyroid Cancer. Thyroid 2020; 30:42-56. [PMID: 31668133 PMCID: PMC6983753 DOI: 10.1089/thy.2019.0052] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Background: Distant metastasis is a rare occurrence in thyroid cancer, and it can be associated with poor prognosis. The genomic repertoires of various solid malignancies have previously been reported but remain underexplored in metastatic papillary thyroid cancer (PTC). Furthermore, whether distant metastases harbor distinct genetic alterations beyond those observed in primary tumors is unknown. Methods: We performed whole-exome sequencing on 14 matched distant metastases, primary PTC tumors, and normal tissues. Point mutations, copy number alterations, cancer cell fractions, and mutational signatures were defined using the state-of-the-art bioinformatics methods. All likely deleterious variants were validated by orthogonal methods. Results: Genomic differences were observed between primary and distant metastatic deposits, with a median of 62% (range 21-92%) of somatic mutations detected in metastatic tissues, but absent from the corresponding primary tumor sample. Mutations in known driver genes including BRAF, NRAS, and HRAS were shared and preferentially clonal in both sites. However, likely deleterious variants affecting DNA methylation and transcriptional repression signaling genes including SIN3A, RBBP1, and CHD4 were found to be restricted in the metastatic lesions. Moreover, a mutational signature shift was observed between the mutations that are specific or enriched in the metastatic and primary lesions. Conclusions: Primary PTC and distant metastases differ in their range of somatic alterations. Genomic analysis of distant metastases provides an opportunity to identify potentially clinically informative alterations not detected in primary tumors, which might influence decisions for personalized therapy in PTC patients with distant metastasis.
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Affiliation(s)
- Tariq Masoodi
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Abdul K. Siraj
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Sarah Siraj
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Saud Azam
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Zeeshan Qadri
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Wafaa N. Albalawy
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | | | - Saif S. Al-Sobhi
- Department of Surgery, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Fouad Al-Dayel
- Department of Pathology, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Fowzan S. Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Fowzan S. Alkuraya, MD, Department of Genetics, King Faisal Specialist Hospital and Research Centre, MBC-03, PO Box 3354, Riyadh 11211, Saudi Arabia
| | - Khawla S. Al-Kuraya
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- Address correspondence to: Khawla S. Al-Kuraya, MD, Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, MBC#98-16, PO Box 3354, Riyadh 11211, Saudi Arabia
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18
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Moreno F, Gayarre J, López-Tarruella S, del Monte-Millán M, Picornell AC, Álvarez E, García-Saenz JÁ, Jerez Y, Márquez-Rodas I, Echavarría I, Palomero M, Bueno C, Aragón Bodí AM, Muñoz MS, González del Val R, Bueno O, Cebollero-Presmanes M, Ocaña I, Arias A, Romero P, Massarrah T, Ramos-Medina R, Martín M. Concordance of Genomic Variants in Matched Primary Breast Cancer, Metastatic Tumor, and Circulating Tumor DNA: The MIRROR Study. JCO Precis Oncol 2019; 3:1-16. [DOI: 10.1200/po.18.00263] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
PURPOSE Genetic heterogeneity between primary tumors and their metastatic lesions has been documented in several breast cancer studies. However, the selection of therapy for patients with metastatic breast cancer and the search for biomarkers for targeted therapy are often based on findings from the primary tumor, mainly because of the difficulty of distant metastasis core biopsies. New methods for monitoring genomic changes in metastatic breast cancer are needed (ie, circulating tumor DNA [ctDNA] genomic analysis). The objectives of this study were to assess the concordance of genomic variants between primary and metastatic tumor tissues and the sensitivity of plasma ctDNA analysis to identify variants detected in tumor biopsies. PATIENTS AND METHODS Next-generation sequencing technology was used to assess the genomic mutation profile of a panel of 54 cancer genes in matched samples of primary tumor, metastatic tumor, and plasma from 40 patients with metastatic breast cancer. RESULTS Using Ion Torrent technology (ThermoFisher Scientific, Waltham, MA), we identified 110 variants that were common to the primary and metastatic tumors. ctDNA analysis had a sensitivity of 0.972 in detecting variants present in both primary and metastatic tissues. In addition, we identified 13 variants in metastatic tissue and ctDNA not present in primary tumor. CONCLUSION We identified genomic variants present in metastatic biopsies and plasma ctDNA that were not present in the primary tumor. Deep sequencing of plasma ctDNA detected most DNA variants previously identified in matched primary and metastatic tissues. ctDNA might aid in therapy selection and in the search for biomarkers for drug development in metastatic breast cancer.
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Affiliation(s)
- Fernando Moreno
- Centro de Investigación Biomédica en Red Cáncer, Madrid, Spain
| | - Javier Gayarre
- Centro de Investigación Biomédica en Red Cáncer, Madrid, Spain
| | - Sara López-Tarruella
- Centro de Investigación Biomédica en Red Cáncer, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Universidad Complutense, Madrid, Spain
| | | | | | - Enrique Álvarez
- Centro de Investigación Biomédica en Red Cáncer, Madrid, Spain
| | | | - Yolanda Jerez
- Centro de Investigación Biomédica en Red Cáncer, Madrid, Spain
| | | | | | | | | | | | | | | | - Oscar Bueno
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | | | | | - Ainhoa Arias
- Centro de Investigación Biomédica en Red Cáncer, Madrid, Spain
| | - Paula Romero
- Centro de Investigación Biomédica en Red Cáncer, Madrid, Spain
| | | | | | - Miguel Martín
- Centro de Investigación Biomédica en Red Cáncer, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Universidad Complutense, Madrid, Spain
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19
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Mejbel HA, Arudra SKC, Pradhan D, Torres-Cabala CA, Nagarajan P, Tetzlaff MT, Curry JL, Ivan D, Duose DY, Luthra R, Prieto VG, Ballester LY, Aung PP. Immunohistochemical and Molecular Features of Melanomas Exhibiting Intratumor and Intertumor Histomorphologic Heterogeneity. Cancers (Basel) 2019; 11:E1714. [PMID: 31684113 PMCID: PMC6896082 DOI: 10.3390/cancers11111714] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 12/11/2022] Open
Abstract
Melanoma is a heterogeneous neoplasm at the histomorphologic, immunophenotypic, and molecular levels. Melanoma with extreme histomorphologic heterogeneity can pose a diagnostic challenge in which the diagnosis may predominantly rely on its immunophenotypic profile. However, tumor survival and response to therapy are linked to tumor genetic heterogeneity rather than tumor morphology. Therefore, understating the molecular characteristics of such melanomas become indispensable. In this study, DNA was extracted from 11 morphologically distinct regions in eight formalin-fixed, paraffin-embedded melanomas. In each region, mutations in 50 cancer-related genes were tested using next-generation sequencing (NGS). A tumor was considered genetically heterogeneous if at least one non-overlapping mutation was identified either between the histologically distinct regions of the same tumor (intratumor heterogeneity) or among the histologically distinct regions of the paired primary and metastatic tumors within the same patient (intertumor heterogeneity). Our results revealed that genetic heterogeneity existed in all tumors as non-overlapping mutations were detected in every tested tumor (n = 5, 100%; intratumor: n = 2, 40%; intertumor: n = 3, 60%). Conversely, overlapping mutations were also detected in all the tested regions (n = 11, 100%). Melanomas exhibiting histomorphologic heterogeneity are often associated with genetic heterogeneity, which might contribute to tumor survival and poor response to therapy.
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Affiliation(s)
- Haider A Mejbel
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Sri Krishna C Arudra
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Dinesh Pradhan
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Carlos A Torres-Cabala
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Priyadharsini Nagarajan
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Michael T Tetzlaff
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Jonathan L Curry
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Doina Ivan
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Dzifa Y Duose
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Raja Luthra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Victor G Prieto
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Leomar Y Ballester
- Department of Pathology and Laboratory Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Phyu P Aung
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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20
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Qiu T, Li W, Zhang F, Wang B, Ying J. Major challenges in accurate mutation detection of multifocal lung adenocarcinoma by next-generation sequencing. Cancer Biol Ther 2019; 21:170-177. [PMID: 31651223 DOI: 10.1080/15384047.2019.1674070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background: Many patients with advanced non-small cell lung cancer manifested with metastasis, and molecular heterogeneity may exhibit between primary and metastatic tumors. We sought to investigate the clinical detection strategy of primary and metastatic tumors in Chinese patients with NSCLC.Methods: Here, 77 paired tumors of Chinese patients with lung adenocarcinoma were analyzed, and 1836 mutation in hotspot regions of 22 genes were identified by next-generation sequencing. The expression of ALK in these paired tumors was also detected by immunohistochemistry.Results: The results showed that the concordance rate in multiple pulmonary nodules, primary-LN metastasis pairs and primary-distant metastasis pairs was 67.7%, 94.1% and 86.7%, respectively. In multiple pulmonary nodules, the concordance rate was 100% when the pathologic diagnosis was intrapulmonary metastasis, whereas the concordance rate was 23.1% when the pathologic diagnosis was multiple primary tumors. TP53 and CTNNB1 mutations were detected as the recurrent alterations in LN metastasis. Moreover, the concordance of ALK status was observed in these pairs.Conclusions: Our data suggested that hotspot mutations and ALK status in the primary-metastasis pairs had a high concordance in lung adenocarcinoma. Clinical detection of one lesion may be enough to identify the key alterations except that patients are diagnosed with multiple primary tumors or have disease progression after benefiting from target therapy.
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Affiliation(s)
- Tian Qiu
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Weihua Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fanshuang Zhang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bingning Wang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianming Ying
- Department of Pathology, 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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21
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Teeuwssen M, Fodde R. Cell Heterogeneity and Phenotypic Plasticity in Metastasis Formation: The Case of Colon Cancer. Cancers (Basel) 2019; 11:cancers11091368. [PMID: 31540068 PMCID: PMC6770401 DOI: 10.3390/cancers11091368] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 12/12/2022] Open
Abstract
The adenoma-to-carcinoma progression in colon cancer is driven by a sequential accumulation of genetic alterations at specific tumor suppressors and oncogenes. In contrast, the multistage route from the primary site to metastasis formation is underlined by phenotypic plasticity, i.e., the capacity of disseminated tumor cells to undergo transiently and reversible transformations in order to adapt to the ever-changing environmental contexts. Notwithstanding the considerable body of evidence in support of the role played by epithelial-to-mesenchymal transition (EMT)/mesenchymal-to-epithelial transition (MET) in metastasis, its rate-limiting function, the detailed underlying cellular and molecular mechanisms, and the extension of the necessary morphologic and epigenetic changes are still a matter of debate. Rather than leading to a complete epithelial or mesenchymal state, the EMT/MET-program generates migrating cancer cells displaying intermediate phenotypes featuring both epithelial and mesenchymal characteristics. In this review, we will address the role of colon cancer heterogeneity and phenotypic plasticity in metastasis formation and the contribution of EMT to these processes. The alleged role of hybrid epithelial/mesenchymal (E/M) in collective and/or single-cell migration during local dissemination at the primary site and more systemic spreading will also be highlighted.
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Affiliation(s)
- Miriam Teeuwssen
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands.
| | - Riccardo Fodde
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands.
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22
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Sung JY, Shin HT, Sohn KA, Shin SY, Park WY, Joung JG. Assessment of intratumoral heterogeneity with mutations and gene expression profiles. PLoS One 2019; 14:e0219682. [PMID: 31310640 PMCID: PMC6634409 DOI: 10.1371/journal.pone.0219682] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 06/30/2019] [Indexed: 02/07/2023] Open
Abstract
Intratumoral heterogeneity (ITH) refers to the presence of distinct tumor cell populations. It provides vital information for the clinical prognosis, drug responsiveness, and personalized treatment of cancer patients. As genomic ITH in various cancers affects the expression patterns of genes, the expression profile could be utilized for determining ITH level. Herein, we present a novel approach to directly detect high ITH defined as a larger number of subclones from the gene expression pattern through machine learning approaches. We examined associations between gene expression profile and ITH of 12 cancer types from The Cancer Genome Atlas (TCGA) database. Using stomach adenocarcinoma (STAD) showing high association, we evaluated the performance of our method in predicting ITH by employing three machine learning algorithms using gene expression profile data. We classified tumors into high and low heterogeneity groups using the learning model through the selection of LASSO feature. The result showed that support vector machines (SVMs) outperformed other algorithms (AUC = 0.84 in SVMs and 0.82 in Naïve Bayes) and we were able to improve predictive power by using both combined data from mutation and expression. Furthermore, we evaluated the prediction ability of each model using simulation data generated by mixing cell lines of the Cancer Cell Line Encyclopedia (CCLE), and obtained consistent results with using real dataset. Our approach could be utilized for discriminating tumors with heterogeneous cell populations to characterize ITH.
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Affiliation(s)
- Ji-Yong Sung
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
- Department of Health Science and Technology, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, Korea
| | - Hyun-Tae Shin
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
- Department of Health Science and Technology, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, Korea
| | - Kyung-Ah Sohn
- Department of Software and Computer Engineering, Ajou University, Suwon, Korea
| | - Soo-Yong Shin
- Department of Digital Health, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, Korea
- Big Data Research Center, Samsung Medical Center, Seoul, Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
- Department of Health Science and Technology, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, Korea
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Je-Gun Joung
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
- * E-mail:
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23
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Antoniou P, Ziogas DE, Mitsis M, Roukos DH. Precision oncology in patients with nonmetastatic disease: emerging reality or illusion. Future Oncol 2019; 15:1805-1810. [PMID: 31170806 DOI: 10.2217/fon-2019-0132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Persefoni Antoniou
- Centre for Biosystems & Genome Network Medicine, Ioannina University, Ioannina, Greece.,Department of Surgery, Ioannina University Hospital, Ioannina, Greece
| | - Demosthenes E Ziogas
- Centre for Biosystems & Genome Network Medicine, Ioannina University, Ioannina, Greece.,Department of Surgery, 'G Hatzikosta' General Hospital, Ioannina, Greece
| | - Michail Mitsis
- Department of Surgery, Ioannina University Hospital, Ioannina, Greece.,Cancer Biobank Centre, University of Ioannina, Ioannina, Greece
| | - Dimitrios H Roukos
- Centre for Biosystems & Genome Network Medicine, Ioannina University, Ioannina, Greece.,Department of Surgery, Ioannina University Hospital, Ioannina, Greece.,Cancer Biobank Centre, University of Ioannina, Ioannina, Greece.,Department of Systems Biology, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
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24
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Tyran M, Carbuccia N, Garnier S, Guille A, Adelaïde J, Finetti P, Toulzian J, Viens P, Tallet A, Goncalves A, Metellus P, Birnbaum D, Chaffanet M, Bertucci F. A Comparison of DNA Mutation and Copy Number Profiles of Primary Breast Cancers and Paired Brain Metastases for Identifying Clinically Relevant Genetic Alterations in Brain Metastases. Cancers (Basel) 2019; 11:cancers11050665. [PMID: 31086113 PMCID: PMC6562582 DOI: 10.3390/cancers11050665] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/08/2019] [Accepted: 05/11/2019] [Indexed: 12/15/2022] Open
Abstract
Improving the systemic treatment of brain metastases (BM) in primary breast cancer (PBC) is impaired by the lack of genomic characterization of BM. To estimate the concordance of DNA copy-number-alterations (CNAs), mutations, and actionable genetic alterations (AGAs) between paired samples, we performed whole-genome array-comparative-genomic-hybridization, and targeted-next-generation-sequencing on 14 clinical PBC–BM pairs. We found more CNAs, more mutations, and higher tumor mutational burden, and more AGAs in BM than in PBC; 92% of the pairs harbored at least one AGA in the BM not observed in the paired PBC. This concerned various therapeutic classes, including tyrosine-kinase-receptor-inhibitors, phosphatidylinositol 3-kinase/AKT/ mammalian Target of Rapamycin (PI3K/AKT/MTOR)-inhibitors, poly ADP ribose polymerase (PARP)-inhibitors, or cyclin-dependent kinase (CDK)-inhibitors. With regards to the PARP-inhibitors, the homologous recombination defect score was positive in 79% of BM, compared to 43% of PBC, discordant in 7 out of 14 pairs, and positive in the BM in 5 out of 14 cases. CDK-inhibitors were associated with the largest percentage of discordant AGA appearing in the BM. When considering the AGA with the highest clinical-evidence level, for each sample, 50% of the pairs harbored an AGA in the BM not detected or not retained from the analysis of the paired PBC. Thus, the profiling of BM provided a more reliable opportunity, than that of PBC, for diagnostic decision-making based on genomic analysis. Patients with BM deserve an investigation of several targeted therapies.
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Affiliation(s)
- Marguerite Tyran
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Aix-Marseille Université, Institut Paoli-Calmettes, F-13009 Marseille, France.
- Département de Radiothérapie, Institut Paoli-Calmettes, 13009 Marseille, France.
| | - Nadine Carbuccia
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Aix-Marseille Université, Institut Paoli-Calmettes, F-13009 Marseille, France.
| | - Séverine Garnier
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Aix-Marseille Université, Institut Paoli-Calmettes, F-13009 Marseille, France.
| | - Arnaud Guille
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Aix-Marseille Université, Institut Paoli-Calmettes, F-13009 Marseille, France.
| | - José Adelaïde
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Aix-Marseille Université, Institut Paoli-Calmettes, F-13009 Marseille, France.
| | - Pascal Finetti
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Aix-Marseille Université, Institut Paoli-Calmettes, F-13009 Marseille, France.
| | - Julien Toulzian
- Département d'Anatomopathologie, Institut Paoli-Calmettes, 13009 Marseille, France.
| | - Patrice Viens
- Département d'Oncologie Médicale, Institut Paoli-Calmettes, 13009 Marseille, France.
- Faculté de Médecine, Aix-Marseille Université, 13005 Marseille, France.
| | - Agnès Tallet
- Département de Radiothérapie, Institut Paoli-Calmettes, 13009 Marseille, France.
| | - Anthony Goncalves
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Aix-Marseille Université, Institut Paoli-Calmettes, F-13009 Marseille, France.
- Département d'Oncologie Médicale, Institut Paoli-Calmettes, 13009 Marseille, France.
- Faculté de Médecine, Aix-Marseille Université, 13005 Marseille, France.
| | - Philippe Metellus
- Département de Neurochirurgie et de Neuro-oncologie, Hôpital Privé Clairval, Ramsay-Générale de Santé and Institut de Neurophysiopathologie Equipe 10, UMR0751, CNRS, 13009 Marseille, France.
| | - Daniel Birnbaum
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Aix-Marseille Université, Institut Paoli-Calmettes, F-13009 Marseille, France.
| | - Max Chaffanet
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Aix-Marseille Université, Institut Paoli-Calmettes, F-13009 Marseille, France.
| | - François Bertucci
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, CNRS UMR7258, Aix-Marseille Université, Institut Paoli-Calmettes, F-13009 Marseille, France.
- Département d'Oncologie Médicale, Institut Paoli-Calmettes, 13009 Marseille, France.
- Faculté de Médecine, Aix-Marseille Université, 13005 Marseille, France.
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25
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Oyanagi H, Shimada Y, Nagahashi M, Ichikawa H, Tajima Y, Abe K, Nakano M, Kameyama H, Takii Y, Kawasaki T, Homma KI, Ling Y, Okuda S, Takabe K, Wakai T. SMAD4 alteration associates with invasive-front pathological markers and poor prognosis in colorectal cancer. Histopathology 2019; 74:873-882. [PMID: 30636020 PMCID: PMC6849740 DOI: 10.1111/his.13805] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 12/08/2018] [Indexed: 12/18/2022]
Abstract
Aims SMAD4 acts as a tumour suppressor, and the loss of SMAD4 is associated with poor prognosis in colorectal cancer (CRC) patients. Although next‐generation sequencing (NGS) enabled us to detect numerous genetic alterations in a single assay, the clinical significance of SMAD4 alteration detected with NGS has not been fully investigated. The aim of this study was to evaluate the clinicopathological characteristics and clinical significance of SMAD4 alteration detected with NGS in CRC. Methods and results We retrospectively investigated 201 patients with stage I–IV CRC, by using a 415‐gene panel. To analyse the relationship between SMAD4 alteration and other clinicopathological characteristics, we evaluated clinicopathological variables, including invasive‐front pathological markers: tumour budding, poorly differentiated cluster, and Crohn‐like lymphoid reaction. Fifty‐six patients (28%) had SMAD4 alteration: 24 and 32 patients had SMAD4 mutation and deletion, respectively. SMAD4 alteration was significantly associated with T category (P = 0.027), N category (P = 0.037), M category (P = 0.028), and invasive‐front pathological markers, such as poorly differentiated cluster grade 3 (P = 0.020) and absence of Crohn‐like lymphoid reaction (P = 0.004). Immunohistochemistry revealed that SMAD4 alteration was significantly associated with loss of SMAD4 (P = 0.023). In 90 patients with stage I–III disease, SMAD4 alteration was significantly associated with poor prognosis for relapse‐free and overall survival (P = 0.047; P = 0.022, respectively). Conversely, in 111 patients with stage IV disease, SMAD4 alteration was not significantly associated with overall survival. Conclusion SMAD4 alteration is associated with invasive‐front pathological markers and poor prognosis in stage I–III CRC patients.
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Affiliation(s)
- Hidehito Oyanagi
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yoshifumi Shimada
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Masayuki Nagahashi
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hiroshi Ichikawa
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yosuke Tajima
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kaoru Abe
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Masato Nakano
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hitoshi Kameyama
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yasumasa Takii
- Department of Surgery, Niigata Cancer Center Hospital, Niigata, Japan
| | - Takashi Kawasaki
- Department of Pathology, Niigata Cancer Center Hospital, Niigata, Japan
| | - Kei-Ichi Homma
- Department of Pathology, Niigata Cancer Center Hospital, Niigata, Japan
| | - Yiwei Ling
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Shujiro Okuda
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kazuaki Takabe
- Division of Breast Surgery, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.,Department of Surgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, The State University of New York, Buffalo, NY, USA.,Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo, Japan.,Department of Surgery, Yokohama City University, Yokohama, Japan
| | - Toshifumi Wakai
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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26
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Liao X, Hao Y, Zhang X, Ward S, Houldsworth J, Polydorides AD, Harpaz N. Clinicopathological characterization of SMAD4-mutated intestinal adenocarcinomas: A case-control study. PLoS One 2019; 14:e0212142. [PMID: 30730996 PMCID: PMC6366887 DOI: 10.1371/journal.pone.0212142] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/28/2019] [Indexed: 02/06/2023] Open
Abstract
The SMAD4 tumor suppressor gene product inhibits transforming growth factor-β-mediated signaling and is mutated in ~10% of colorectal carcinomas. The prognostic significance of SMAD4 mutations has been controversial. We studied the pathological and clinical characteristics of SMAD4-mutated intestinal adenocarcinomas using a retrospective case-control study design. Cases and controls were identified among 443 primary adenocarcinomas that had undergone next generation DNA sequencing (NGS) with the Ion AmpliSeq Cancer Hotspot Panel v2, which evaluates 50 cancer-related genes. Twenty-eight SMAD4-mutated (SMAD4m) patients were matched 1:2 with 56 consecutive SMAD4 wild-type (SMAD4wt) control patients from the same analysis stream. Compared with the SMAD4wt controls, the SMAD4m tumors were of higher stage (P = 0.026) and were more likely to feature mucinous differentiation (P = 0.0000), to occur in the setting of Crohn’s disease (P = 0.0041), and to harbor concurrent RAS mutations (P = 0.0178). Tumor mucin content was significantly correlated with mutations involving the MH2 domain of the SMAD4 protein (P = 0.0338). Correspondence between mutation sites and morphology was demonstrated directly in a mixed adenocarcinoma and neuroendocrine tumor where SMAD4 mutations involving different protein domains were found in histologically disparate tumor regions despite both containing identical KRAS and TP53 mutations.
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Affiliation(s)
- Xiaoyan Liao
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, United States of America
- * E-mail:
| | - Yansheng Hao
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Xiaofei Zhang
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Stephen Ward
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Jane Houldsworth
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Alexandros D. Polydorides
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Noam Harpaz
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
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27
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Bhullar DS, Barriuso J, Mullamitha S, Saunders MP, O'Dwyer ST, Aziz O. Biomarker concordance between primary colorectal cancer and its metastases. EBioMedicine 2019; 40:363-374. [PMID: 30733075 PMCID: PMC6413540 DOI: 10.1016/j.ebiom.2019.01.050] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 01/13/2019] [Accepted: 01/24/2019] [Indexed: 12/17/2022] Open
Abstract
Background The use of biomarkers to target anti-EGFR treatments for metastatic colorectal cancer (CRC) is well-established, requiring molecular analysis of primary or metastatic biopsies. We aim to review concordance between primary CRC and its metastatic sites. Methods A systematic review and meta-analysis of all published studies (1991–2018) reporting on biomarker concordance between primary CRC and its metastatic site(s) was undertaken according to PRISMA guidelines using several medical databases. Studies without matched samples or using peripheral blood for biomarker analysis were excluded. Findings 61 studies including 3565 patient samples were included. Median biomarker concordance for KRAS (n = 50) was 93.7% [[67], [68], [69], [70], [71], [72], [73], [74], [75], [76], [77], [78], [79], [80], [81], [82], [83], [84], [85], [86], [87], [88], [89], [90], [91], [92], [93], [94], [95], [96], [97], [98], [99], [100]], NRAS (n = 11) was 100% [[90], [91], [92], [93], [94], [95], [96], [97], [98], [99], [100]], BRAF (n = 22) was 99.4% [[80], [81], [82], [83], [84], [85], [86], [87], [88], [89], [90], [91], [92], [93], [94], [95], [96], [97], [98], [99], [100]], and PIK3CA (n = 17) was 93% [[42], [43], [44], [45], [46], [47], [48], [49], [50], [51], [52], [53], [54], [55], [56], [57], [58], [59], [60], [61], [62], [63], [64], [65], [66], [67], [68], [69], [70], [71], [72], [73], [74], [75], [76], [77], [78], [79], [80], [81], [82], [83], [84], [85], [86], [87], [88], [89], [90], [91], [92], [93], [94], [95], [96], [97], [98], [99], [100]]. Meta-analytic pooled discordance was 8% for KRAS (95% CI = 5–10%), 8% for BRAF (95% CI = 5–10%), 7% for PIK3CA (95% CI = 2–13%), and 28% overall (95% CI = 14–44%). The liver was the most commonly biopsied metastatic site (n = 2276), followed by lung (n = 438), lymph nodes (n = 1123), and peritoneum (n = 132). Median absolute concordance in multiple biomarkers was 81% (5–95%). Interpretation Metastatic CRC demonstrates high concordance across multiple biomarkers, suggesting that molecular testing of either the primary or liver and lung metastasis is adequate. More research on colorectal peritoneal metastases is required.
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Affiliation(s)
- D S Bhullar
- Colorectal & Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, UK; Division of Cancer Sciences, School of Medical Science, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - J Barriuso
- Colorectal & Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, UK; Division of Cancer Sciences, School of Medical Science, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - S Mullamitha
- Colorectal & Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, UK; Division of Cancer Sciences, School of Medical Science, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - M P Saunders
- Colorectal & Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, UK; Division of Cancer Sciences, School of Medical Science, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - S T O'Dwyer
- Colorectal & Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, UK; Division of Cancer Sciences, School of Medical Science, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - O Aziz
- Colorectal & Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, UK; Division of Cancer Sciences, School of Medical Science, Faculty of Biology, Medicine and Health, University of Manchester, UK.
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28
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de Melo FHM, Oliveira JS, Sartorelli VOB, Montor WR. Cancer Chemoprevention: Classic and Epigenetic Mechanisms Inhibiting Tumorigenesis. What Have We Learned So Far? Front Oncol 2018; 8:644. [PMID: 30627525 PMCID: PMC6309127 DOI: 10.3389/fonc.2018.00644] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 12/07/2018] [Indexed: 12/21/2022] Open
Abstract
Cancers derive from step by step processes which are differentiated by the progressively accumulated mutations. For some tumors there is a clear progressive advancement from benign lesions to malignancy and for these, preventive screening programs exist. In such cases having those benign lesions are a clear indicator of predisposition while for some other cases, familial patterns of cancer incidence and the identification of mutations are the main indicators of higher risk for having the disease. For patients identified as having predisposition, chemoprevention is a goal and in some cases a possibility. Chemoprevention is the use of any compound, either natural or synthetic that abrogates carcinogenesis or tumor progression, through different mechanisms, some of which have already been described. For example, the classic mechanisms may involve activation of free radical scavenging enzymes, control of chronic inflammation, and downregulation of specific signaling pathways. More recently, epigenetics allowed further understanding of the chemopreventive potential of several agents, such as sulforaphane, green tea derived compounds, resveratrol, isoflavones, and others which we exploit in this review article. Throughout the text we discuss the properties compounds should have in order to be classified as chemopreventive ones and the challenges in translational research in this area, as lots of the success achieved in vitro cannot be translated into the clinical settings, due to several different drawbacks, which include toxicity, cost, dose definition, patient adherence, and regimen of use.
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Affiliation(s)
| | - Julia Salles Oliveira
- Department of Physiological Sciences, Santa Casa de São Paulo School of Medical Sciences (FCMSCSP), São Paulo, Brazil
| | | | - Wagner Ricardo Montor
- Department of Physiological Sciences, Santa Casa de São Paulo School of Medical Sciences (FCMSCSP), São Paulo, Brazil
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Appenzeller S, Gesierich A, Thiem A, Hufnagel A, Jessen C, Kneitz H, Regensburger M, Schmidt C, Zirkenbach V, Bischler T, Schilling B, Siedel C, Goebeler ME, Houben R, Schrama D, Gehrig A, Rost S, Maurus K, Bargou R, Rosenwald A, Schartl M, Goebeler M, Meierjohann S. The identification of patient-specific mutations reveals dual pathway activation in most patients with melanoma and activated receptor tyrosine kinases in BRAF/NRAS wild-type melanomas. Cancer 2018; 125:586-600. [PMID: 30561760 DOI: 10.1002/cncr.31843] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 09/23/2018] [Accepted: 10/02/2018] [Indexed: 11/07/2022]
Abstract
BACKGROUND Increasing knowledge of cancer genomes has triggered the development of specific targeted inhibitors, thus providing a valuable therapeutic pool. METHODS In this report, the authors analyze the presence of targetable alterations in 136 tumor samples from 92 patients with melanoma using a comprehensive approach based on targeted DNA sequencing and supported by RNA and protein analysis. Three topics of high clinical relevance are addressed: the identification of rare, activating alterations; the detection of patient-specific, co-occurring single nucleotide variants (SNVs) and copy number variations (CNVs) in parallel pathways; and the presence of cancer-relevant germline mutations. RESULTS The analysis of patient-matched blood and tumor samples was done with a custom-designed gene panel that was enriched for genes from clinically targetable pathways. To detect alterations with high therapeutic relevance for patients with unknown driver mutations, genes that are untypical for melanoma also were included. Among all patients, CNVs were identified in one-third of samples and contained amplifications of druggable kinases, such as CDK4, ERBB2, and KIT. Considering SNVs and CNVs, 60% of patients with metastases exhibited co-occurring activations of at least 2 pathways, thus providing a rationale for individualized combination therapies. Unexpectedly, 9% of patients carry potentially protumorigenic germline mutations frequently affecting receptor tyrosine kinases. Remarkably two-thirds of BRAF/NRAS wild-type melanomas harbor activating mutations or CNVs in receptor tyrosine kinases. CONCLUSIONS The results indicate that the integrated analysis of SNVs, CNVs, and germline mutations reveals new druggable targets for combination tumor therapy.
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Affiliation(s)
- Silke Appenzeller
- Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany
| | - Anja Gesierich
- Department of Dermatology, Venereology, and Allergology and Skin Cancer Center, University Hospital Würzburg, Würzburg, Germany
| | - Alexander Thiem
- Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany.,Department of Dermatology, Venereology, and Allergology and Skin Cancer Center, University Hospital Würzburg, Würzburg, Germany
| | - Anita Hufnagel
- Department of Physiological Chemistry, University of Würzburg, Würzburg, Germany
| | - Christina Jessen
- Department of Physiological Chemistry, University of Würzburg, Würzburg, Germany
| | - Hermann Kneitz
- Department of Dermatology, Venereology, and Allergology and Skin Cancer Center, University Hospital Würzburg, Würzburg, Germany
| | - Martina Regensburger
- Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany.,Department of Physiological Chemistry, University of Würzburg, Würzburg, Germany
| | - Cornelia Schmidt
- Department of Physiological Chemistry, University of Würzburg, Würzburg, Germany
| | - Vanessa Zirkenbach
- Department of Physiological Chemistry, University of Würzburg, Würzburg, Germany
| | - Thorsten Bischler
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | - Bastian Schilling
- Department of Dermatology, Venereology, and Allergology and Skin Cancer Center, University Hospital Würzburg, Würzburg, Germany
| | - Claudia Siedel
- Department of Dermatology, Venereology, and Allergology and Skin Cancer Center, University Hospital Würzburg, Würzburg, Germany
| | | | - Roland Houben
- Department of Dermatology, Venereology, and Allergology and Skin Cancer Center, University Hospital Würzburg, Würzburg, Germany
| | - David Schrama
- Department of Dermatology, Venereology, and Allergology and Skin Cancer Center, University Hospital Würzburg, Würzburg, Germany
| | - Andrea Gehrig
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Simone Rost
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Katja Maurus
- Institute of Pathology, University of Würzburg, Würzburg, Germany
| | - Ralf Bargou
- Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany
| | | | - Manfred Schartl
- Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany.,Department of Physiological Chemistry, University of Würzburg, Würzburg, Germany.,Texas A&M Institute for Advanced Studies and Department of Biology, Texas A&M University, College Station, Texas
| | - Matthias Goebeler
- Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany.,Department of Dermatology, Venereology, and Allergology and Skin Cancer Center, University Hospital Würzburg, Würzburg, Germany
| | - Svenja Meierjohann
- Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany.,Department of Physiological Chemistry, University of Würzburg, Würzburg, Germany
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30
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Ferguson SD, Zheng S, Xiu J, Zhou S, Khasraw M, Brastianos PK, Kesari S, Hu J, Rudnick J, Salacz ME, Piccioni D, Huang S, Davies MA, Glitza IC, Heymach JV, Zhang J, Ibrahim NK, DeGroot JF, McCarty J, O'Brien BJ, Sawaya R, Verhaak RG, Reddy SK, Priebe W, Gatalica Z, Spetzler D, Heimberger AB. Profiles of brain metastases: Prioritization of therapeutic targets. Int J Cancer 2018; 143:3019-3026. [PMID: 29923182 PMCID: PMC6235694 DOI: 10.1002/ijc.31624] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/28/2018] [Accepted: 04/17/2018] [Indexed: 12/12/2022]
Abstract
We sought to compare the tumor profiles of brain metastases from common cancers with those of primary tumors and extracranial metastases in order to identify potential targets and prioritize rational treatment strategies. Tumor samples were collected from both the primary and metastatic sites of nonsmall cell lung cancer, breast cancer and melanoma from patients in locations worldwide, and these were submitted to Caris Life Sciences for tumor multiplatform analysis, including gene sequencing (Sanger and next-generation sequencing with a targeted 47-gene panel), protein expression (assayed by immunohistochemistry) and gene amplification (assayed by in situ hybridization). The data analysis considered differential protein expression, gene amplification and mutations among brain metastases, extracranial metastases and primary tumors. The analyzed population included: 16,999 unmatched primary tumor and/or metastasis samples: 8,178 nonsmall cell lung cancers (5,098 primaries; 2,787 systemic metastases; 293 brain metastases), 7,064 breast cancers (3,496 primaries; 3,469 systemic metastases; 99 brain metastases) and 1,757 melanomas (660 primaries; 996 systemic metastases; 101 brain metastases). TOP2A expression was increased in brain metastases from all 3 cancers, and brain metastases overexpressed multiple proteins clustering around functions critical to DNA synthesis and repair and implicated in chemotherapy resistance, including RRM1, TS, ERCC1 and TOPO1. cMET was overexpressed in melanoma brain metastases relative to primary skin specimens. Brain metastasis patients may particularly benefit from therapeutic targeting of enzymes associated with DNA synthesis, replication and/or repair.
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Affiliation(s)
- Sherise D. Ferguson
- Departments of NeurosurgeryThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - Siyuan Zheng
- Departments of Genome MedicineThe University of Texas MD Anderson Cancer CenterHoustonTX
| | | | - Shouhao Zhou
- Departments of BiostatisticsThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - Mustafa Khasraw
- NHMRC Clinical Trials CentreUniversity of SydneySydneyAustralia
| | | | - Santosh Kesari
- Pacific Neuroscience Institute and John Wayne Cancer Institute at Providence Saint John's Health CenterSanta MonicaCA
| | | | | | | | - David Piccioni
- Department of NeurosciencesUniversity of California at San Diego Moores Cancer CenterLa JollaCA
| | - Suyun Huang
- Departments of NeurosurgeryThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - Michael A. Davies
- Departments of Melanoma Medical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - Isabella C. Glitza
- Departments of Melanoma Medical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - John V. Heymach
- Departments of Thoracic OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - Jianjun Zhang
- Departments of Thoracic OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - Nuhad K. Ibrahim
- Departments of Breast Medical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - John F. DeGroot
- Departments of Neuro‐OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - Joseph McCarty
- Departments of NeurosurgeryThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - Barbara J. O'Brien
- Departments of Neuro‐OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - Raymond Sawaya
- Departments of NeurosurgeryThe University of Texas MD Anderson Cancer CenterHoustonTX
| | - Roeland G.W. Verhaak
- Departments of Genome MedicineThe University of Texas MD Anderson Cancer CenterHoustonTX
| | | | - Waldemar Priebe
- Departments of Experimental TherapeuticsThe University of Texas MD Anderson Cancer CenterHoustonTX
| | | | | | - Amy B. Heimberger
- Departments of NeurosurgeryThe University of Texas MD Anderson Cancer CenterHoustonTX
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31
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Ziogas DE, Kyrochristos ID, Roukos DH. Discovering novel valid biomarkers and drugs in patient-centric genomic trials: the new epoch of precision surgical oncology. Drug Discov Today 2018; 23:1848-1872. [DOI: 10.1016/j.drudis.2018.07.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 07/10/2018] [Accepted: 07/26/2018] [Indexed: 12/16/2022]
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32
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The gene mutational discrepancies between primary and paired metastatic colorectal carcinoma detected by next-generation sequencing. J Cancer Res Clin Oncol 2018; 144:2149-2159. [DOI: 10.1007/s00432-018-2742-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/21/2018] [Indexed: 01/22/2023]
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33
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Schrijver WAME, Selenica P, Lee JY, Ng CKY, Burke KA, Piscuoglio S, Berman SH, Reis-Filho JS, Weigelt B, van Diest PJ, Moelans CB. Mutation Profiling of Key Cancer Genes in Primary Breast Cancers and Their Distant Metastases. Cancer Res 2018; 78:3112-3121. [PMID: 29615433 PMCID: PMC6355142 DOI: 10.1158/0008-5472.can-17-2310] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 01/28/2018] [Accepted: 03/30/2018] [Indexed: 02/07/2023]
Abstract
Although the repertoire of somatic genetic alterations of primary breast cancers has been extensively catalogued, the genetic differences between primary and metastatic tumors have been less studied. In this study, we compared somatic mutations and gene copy number alterations of primary breast cancers and their matched metastases from patients with estrogen receptor (ER)-negative disease. DNA samples obtained from formalin-fixed paraffin-embedded ER-negative/HER2-positive (n = 9) and ER-, progesterone receptor (PR-), HER2-negative (n = 8) primary breast cancers and from paired brain or skin metastases and normal tissue were subjected to a hybridization capture-based massively parallel sequencing assay, targeting 341 key cancer genes. A large subset of nonsynonymous somatic mutations (45%) and gene copy number alterations (55%) was shared between the primary tumors and paired metastases. However, mutations restricted to either a given primary tumor or its metastasis, the acquisition of loss of heterozygosity of the wild-type allele, and clonal shifts of genes affected by somatic mutations, such as TP53 and RB1, were observed in the progression from primary tumors to metastases. No metastasis location-specific alterations were identified, but synchronous metastases showed higher concordance with the paired primary tumor than metachronous metastases. Novel potentially targetable alterations were found in the metastases relative to their matched primary tumors. These data indicate that repertoires of somatic genetic alterations in ER-negative metastatic breast cancers may differ from those of their primary tumors, even by the presence of driver and targetable somatic genetic alterations.Significance: Somatic genetic alterations in ER-negative breast cancer metastases may be distinct from those of their primary tumors, suggesting that for treatment-decision making, genetic analyses of DNA obtained from the metastatic lesion rather than from the primary tumor should be considered. Cancer Res; 78(12); 3112-21. ©2018 AACR.
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Affiliation(s)
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ju Youn Lee
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kathleen A Burke
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Samuel H Berman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, the Netherlands.
| | - Cathy B Moelans
- Department of Pathology, University Medical Center Utrecht, the Netherlands
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34
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Weinberg BA, Xiu J, Hwang JJ, Shields AF, Salem ME, Marshall JL. Immuno-Oncology Biomarkers for Gastric and Gastroesophageal Junction Adenocarcinoma: Why PD-L1 Testing May Not Be Enough. Oncologist 2018; 23:1171-1177. [PMID: 29703766 DOI: 10.1634/theoncologist.2018-0034] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 03/06/2018] [Indexed: 12/26/2022] Open
Abstract
PURPOSE The treatment of patients with advanced gastric and gastroesophageal junction (G/GEJ) adenocarcinomas has been transformed by the U.S. Food and Drug Administration approval of pembrolizumab. Tumor and adjacent tissue must stain positively for the programmed cell death ligand 1 (PD-L1) protein by companion diagnostic testing. However, some patients with PD-L1-negative tumors also benefit from pembrolizumab. High microsatellite instability (MSI) and tumor mutational load (TML) are positive predictive biomarkers for immune checkpoint inhibition (ICI) in other tumors. We sought to identify more patients who could benefit from ICI using alternative PD-L1 thresholds, MSI, and TML. METHODS Tumor specimens underwent next-generation sequencing (NGS) and PD-L1 testing using immunohistochemistry. NGS was used to determine TML and MSI. RESULTS We profiled 581 G/GEJ adenocarcinoma specimens. PD-L1 staining was scored for intensity (0, none; 1+, weak; 2+, moderate; 3+, strong). Using 2+ staining at a 5% threshold, 9.3% of tumors were PD-L1 positive, and using 1+ staining at 1%, 16.2% were PD-L1 positive. 6.9% of tumors had high MSI. High TML (≥17 mutations per megabase) was seen in 6.9%, and medium TML (≥7) was seen in 56.5% of tumors. Thirty (5.2%) PD-L1-negative tumors at the 1+, 1% threshold had high TML or high MSI. Primary tumors had higher rates of high TML (8.8% vs. 3.9%; p = .0377) and high MSI (8.5% vs. 3.9%; p = .0471) than metastases. CONCLUSION PD-L1 testing alone fails to detect patients who may benefit from ICI. Lower PD-L1 thresholds and TML testing should be considered in future clinical trials. IMPLICATIONS FOR PRACTICE Pembrolizumab is approved by the U.S. Food and Drug Administration for patients with refractory gastric and gastroesophageal cancers if the tumor and adjacent tissue stain positively for the programmed cell death ligand 1 (PD-L1) protein by companion diagnostic testing. Tumor mutational load, microsatellite instability (MSI), and alternative PD-L1 testing thresholds may serve as predictive biomarkers for response to immune checkpoint inhibition, and standard PD-L1 testing will not identify all patients who may benefit from this therapy.
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Affiliation(s)
- Benjamin A Weinberg
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Joanne Xiu
- Caris Life Sciences, Phoenix, Arizona, USA
| | - Jimmy J Hwang
- Levine Cancer Institute, Carolinas HealthCare System, Charlotte, North Carolina, USA
| | - Anthony F Shields
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, Michigan, USA
| | - Mohamed E Salem
- Levine Cancer Institute, Carolinas HealthCare System, Charlotte, North Carolina, USA
| | - John L Marshall
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
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35
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De Mattos-Arruda L, Ng CKY, Piscuoglio S, Gonzalez-Cao M, Lim RS, De Filippo MR, Fusco N, Schultheis AM, Ortiz C, Viteri S, Arias A, Macedo GS, Oliveira M, Gomez P, Teixidó C, Nuciforo P, Peg V, Saura C, Ramon Y Cajal S, Casas FT, Weigelt B, Cortes J, Seoane J, Reis-Filho JS. Genetic heterogeneity and actionable mutations in HER2-positive primary breast cancers and their brain metastases. Oncotarget 2018; 9:20617-20630. [PMID: 29755676 PMCID: PMC5945519 DOI: 10.18632/oncotarget.25041] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/12/2018] [Indexed: 12/19/2022] Open
Abstract
Brain metastases constitute a challenge in the management of patients with HER2-positive breast cancer treated with anti-HER2 systemic therapies. Here we sought to define the repertoire of mutations private to or enriched for in HER2-positive brain metastases. Massively parallel sequencing targeting all exons of 254 genes frequently mutated in breast cancers and/or related to DNA repair was used to characterize the spatial and temporal heterogeneity of HER2-positive breast cancers and their brain metastases in six patients. Data were analyzed with state-of-the-art bioinformatics algorithms and selected mutations were validated with orthogonal methods. Spatial and temporal inter-lesion genetic heterogeneity was observed in the HER2-positive brain metastases from an index patient subjected to a rapid autopsy. Genetic alterations restricted to the brain metastases included mutations in cancer genes FGFR2, PIK3CA and ATR, homozygous deletion in CDKN2A and amplification in KRAS. Shifts in clonal composition and the acquisition of additional mutations in the progression from primary HER2-positive breast cancer to brain metastases following anti-HER2 therapy were investigated in additional five patients. Likely pathogenic mutations private to or enriched in the brain lesions affected cancer and clinically actionable genes, including ATR, BRAF, FGFR2, MAP2K4, PIK3CA, RAF1 and TP53. Changes in clonal composition and the acquisition of additional mutations in brain metastases may affect potentially actionable genes in HER2-positive breast cancers. Our observations have potential clinical implications, given that treatment decisions for patients with brain metastatic disease are still mainly based on biomarkers assessed in the primary tumor.
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Affiliation(s)
- Leticia De Mattos-Arruda
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain.,Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Institute of Pathology, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | | | - Raymond S Lim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria R De Filippo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicola Fusco
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anne M Schultheis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Carolina Ortiz
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain
| | | | - Alexandra Arias
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain
| | - Gabriel S Macedo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mafalda Oliveira
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain
| | - Patricia Gomez
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain
| | | | - Paolo Nuciforo
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain
| | - Vicente Peg
- Vall d'Hebron Institute of Research, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Cristina Saura
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain
| | - Santiago Ramon Y Cajal
- Vall d'Hebron Institute of Research, Vall d'Hebron University Hospital, Barcelona, Spain
| | | | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Javier Cortes
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain.,Universitat Autònoma de Barcelona, Barcelona, Spain.,Ramon y Cajal University Hospital, Madrid, Spain
| | - Joan Seoane
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain.,Universitat Autònoma de Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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36
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Baretti M, Personeni N, Destro A, Santoro A, Rimassa L. Emergence of KRAS-mutation in liver metastases after an anti-EGFR treatment in patient with colorectal cancer: Are we aware of the therapeutic impact of intratumor heterogeneity? Cancer Biol Ther 2018; 19:659-663. [PMID: 29580164 DOI: 10.1080/15384047.2018.1450117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Tumors represent a dynamic system where the genomic plasticity permits to adapt to the perturbation induced by environmental pressures, supporting the importance of longitudinal tumor sampling strategies to deciphering the temporal acquisition of driver event that could impact treatment outcome. We describe the case of a metastatic colorectal cancer (mCRC) patient, RAS wild-type, who responded to anti-EGFR therapy and underwent liver surgery, revealing a KRAS mutations in the metastatic lesion, not detectable prior to initiation of therapy in the colonic biopsy. After liver surgery, the patient received chemotherapy alone, then underwent left colectomy and the final pathological report confirmed the KRAS wild-type status. We can speculate the existence of two distinct populations of KRAS wild-type and mutant CRC cells sharing the same genetic origin. The anti-EGFR treatment represented a selective pressure which allowed the selection of KRAS mutant subclones. The prognostic and /or predictive role of intratumor heterogeneity has not been assessed prospectively. Our case report is of clinical relevance because patients with mCRC who respond to anti-EGFR antibodies often develop resistance within several months of initiating therapy, thus outlining the importance to better ascertain the molecular landscape of tumors to design better therapeutic strategies.
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Affiliation(s)
- M Baretti
- a Medical Oncology and Hematology Unit, Humanitas Cancer Center, Humanitas Clinical and Research Center , Rozzano (Milan) , Italy
| | - N Personeni
- a Medical Oncology and Hematology Unit, Humanitas Cancer Center, Humanitas Clinical and Research Center , Rozzano (Milan) , Italy.,b Department of Medical Biotechnology and Translational Medicine , University of Milan , Milan , Italy
| | - A Destro
- c Pathology Unit , Humanitas Clinical and Research Center , Rozzano (Milan) , Italy
| | - A Santoro
- a Medical Oncology and Hematology Unit, Humanitas Cancer Center, Humanitas Clinical and Research Center , Rozzano (Milan) , Italy.,d Humanitas University , Rozzano (Milan) , Italy
| | - L Rimassa
- a Medical Oncology and Hematology Unit, Humanitas Cancer Center, Humanitas Clinical and Research Center , Rozzano (Milan) , Italy
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Perry EB, Makohon-Moore A, Zheng C, Kaufman CK, Cai J, Iacobuzio-Donahue CA, White RM. Tumor diversity and evolution revealed through RADseq. Oncotarget 2018; 8:41792-41805. [PMID: 28611298 PMCID: PMC5522028 DOI: 10.18632/oncotarget.18355] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 05/12/2017] [Indexed: 12/30/2022] Open
Abstract
Cancer is an evolutionary disease, and there is increasing interest in applying tools from evolutionary biology to understand cancer progression. Restriction-site associated DNA sequencing (RADseq) was developed for the field of evolutionary genetics to study adaptation and identify evolutionary relationships among populations. Here we apply RADseq to study tumor evolution, which allows for unbiased sampling of any desired frequency of the genome, overcoming the selection bias and cost limitations inherent to exome or whole-genome sequencing. We apply RADseq to both human pancreatic cancer and zebrafish melanoma samples. Using either a low-frequency (SbfI, 0.4% of the genome) or high-frequency (NsiI, 6-9% of the genome) cutter, we successfully identify single nucleotide substitutions and copy number alterations in tumors, which can be augmented by performing RADseq on sublineages within the tumor. We are able to infer phylogenetic relationships between primary tumors and metastases. These same methods can be used to identify somatic mosaicism in seemingly normal, non-cancerous tissues. Evolutionary studies of cancer that focus on rates of tumor evolution and evolutionary relationships among tumor lineages will benefit from the flexibility and efficiency of restriction-site associated DNA sequencing.
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Affiliation(s)
- Elizabeth B Perry
- Cancer Biology & Genetics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Biostatistics, Yale University, New Haven, Connecticut, USA
| | - Alvin Makohon-Moore
- The David M. Rubenstein Center for Pancreatic Cancer Research, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Caihong Zheng
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | - Jun Cai
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Christine A Iacobuzio-Donahue
- The David M. Rubenstein Center for Pancreatic Cancer Research, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Richard M White
- Cancer Biology & Genetics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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Li W, Qiu T, Ling Y, Gao S, Ying J. Subjecting appropriate lung adenocarcinoma samples to next-generation sequencing-based molecular testing: challenges and possible solutions. Mol Oncol 2018. [PMID: 29518290 PMCID: PMC5928389 DOI: 10.1002/1878-0261.12190] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Next-generation sequencing (NGS) has recently been rapidly adopted in the molecular diagnosis of cancer, but it still faces some obstacles. In this study, 665 lung adenocarcinoma samples (558 TKI-naive and 107 TKI-relapsed samples) were interrogated using NGS, and the challenges and possible solutions of subjecting appropriate tissue samples to NGS testing were explored. The results showed that lower frequencies of HER2/BRAF/PIK3CA and acquired EGFR T790M mutations were observed in biopsy samples with <20% tumor cellularity than in those with ≥20%, but there were no significant differences in the frequencies of EGFR or KRAS mutations. Moreover, tumor heterogeneity was assessed by heterogeneity score (HS), which was calculated through multiplying by 2 the mutant allele frequency (MAF) of tumor cells. In TKI-naive samples, intratumor heterogeneity could occur in EGFR, KRAS, HER2, BRAF, and PIK3CA mutant tumors, but the degree was variable. Higher EGFR, but lower BRAF and PIK3CA HS values were observed compared with KRAS HS. In TKI-relapsed samples, analysis of concomitant sensitizing EGFR and T790M MAFs showed that intratumor heterogeneity was common in acquired EGFR T790M mutant tumors. The mutational status between primary and metastatic tumors was usually concordant, but KRAS, HER2, and PIK3CA HS were significantly higher in metastatic tumors than in primary tumors. Additionally, the discordance rate of mutational status in multifocal lung adenocarcinomas diagnosed as equivocal or multiple primary tumors was high. Together, our findings demonstrate that a comprehensive quality assessment is necessary during tissue process to mitigate the challenges of poor tumor cellularity, tumor heterogeneity, and multifocal clonally independent tumors.
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Affiliation(s)
- Weihua Li
- Department of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tian Qiu
- Department of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yun Ling
- Department of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shugeng Gao
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianming Ying
- Department of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Rizzolo P, Navazio AS, Silvestri V, Valentini V, Zelli V, Zanna I, Masala G, Bianchi S, Scarnò M, Tommasi S, Palli D, Ottini L. Somatic alterations of targetable oncogenes are frequently observed in BRCA1/2 mutation negative male breast cancers. Oncotarget 2018; 7:74097-74106. [PMID: 27765917 PMCID: PMC5342038 DOI: 10.18632/oncotarget.12272] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 09/16/2016] [Indexed: 12/14/2022] Open
Abstract
Male breast cancer (MBC) is a rare disease. Due to its rarity, MBC research and clinical approach are mostly based upon data derived from its largely known female counterpart. We aimed at investigating whether MBC cases harbor somatic alterations of genes known as prognostic biomarkers and molecular therapeutic targets in female breast cancer. We examined 103 MBC cases, all characterized for germ-line BRCA1/2 mutations, for somatic alterations in PIK3CA, EGFR, ESR1 and CCND1 genes. Pathogenic mutations of PIK3CA were detected in 2% of MBCs. No pathogenic mutations were identified in ESR1 and EGFR. Gene copy number variations (CNVs) analysis showed amplification of PIK3CA in 8.1%, EGFR in 6.8% and CCND1 in 16% of MBCs, whereas deletion of ESR1 was detected in 15% of MBCs. Somatic mutations and gene amplification were found only in BRCA1/2 mutation negative MBCs. Significant associations emerged between EGFR amplification and large tumor size (T4), ER-negative and HER2-positive status, between CCND1 amplification and HER2-positive and MIB1-positive status, and between ESR1 deletion and ER-negative status. Our results show that amplification of targetable oncogenes is frequent in BRCA1/2 mutation negative MBCs and may identify MBC subsets characterized by aggressive phenotype that may benefit from potential targeted therapeutic approaches.
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Affiliation(s)
- Piera Rizzolo
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Anna Sara Navazio
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | | | - Virginia Valentini
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Veronica Zelli
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Ines Zanna
- Molecular and Nutritional Epidemiology Unit, Cancer Research and Prevention Institute (ISPO), Florence, Italy
| | - Giovanna Masala
- Molecular and Nutritional Epidemiology Unit, Cancer Research and Prevention Institute (ISPO), Florence, Italy
| | - Simonetta Bianchi
- Division of Pathological Anatomy, Department of Medical and Surgical Critical Care, University of Florence, Florence, Italy
| | - Marco Scarnò
- CINECA (Inter University Consortium for Super Computing), Rome, Italy
| | - Stefania Tommasi
- Molecular Genetics Laboratory, Istituto Tumori "Giovanni Paolo II", Bari, Italy
| | - Domenico Palli
- Molecular and Nutritional Epidemiology Unit, Cancer Research and Prevention Institute (ISPO), Florence, Italy
| | - Laura Ottini
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
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Kjällquist U, Erlandsson R, Tobin NP, Alkodsi A, Ullah I, Stålhammar G, Karlsson E, Hatschek T, Hartman J, Linnarsson S, Bergh J. Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs). BMC Cancer 2018; 18:174. [PMID: 29433456 PMCID: PMC5810006 DOI: 10.1186/s12885-018-4021-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 01/22/2018] [Indexed: 11/10/2022] Open
Abstract
Background Tumor heterogeneity in breast cancer tumors is today widely recognized. Most of the available knowledge in genetic variation however, relates to the primary tumor while metastatic lesions are much less studied. Many studies have revealed marked alterations of standard prognostic and predictive factors during tumor progression. Characterization of paired primary- and metastatic tissues should therefore be fundamental in order to understand mechanisms of tumor progression, clonal relationship to tumor evolution as well as the therapeutic aspects of systemic disease. Methods We performed full exome sequencing of primary breast cancers and their metastases in a cohort of ten patients and further confirmed our findings in an additional cohort of 20 patients with paired primary and metastatic tumors. Furthermore, we used gene expression from the metastatic lesions and a primary breast cancer data set to study the gene expression of the AKAP gene family. Results We report that somatic mutations in A-kinase anchoring proteins are enriched in metastatic lesions. The frequency of mutation in the AKAP gene family was 10% in the primary tumors and 40% in metastatic lesions. Several copy number variations, including deletions in regions containing AKAP genes were detected and showed consistent patterns in both investigated cohorts. In a second cohort containing 20 patients with paired primary and metastatic lesions, AKAP mutations showed an increasing variant allele frequency after multiple relapses. Furthermore, gene expression profiles from the metastatic lesions (n = 120) revealed differential expression patterns of AKAPs relative to the tumor PAM50 intrinsic subtype, which were most apparent in the basal-like subtype. This pattern was confirmed in primary tumors from TCGA (n = 522) and in a third independent cohort (n = 182). Conclusion Several studies from primary cancers have reported individual AKAP genes to be associated with cancer risk and metastatic relapses as well as direct involvement in cellular invasion and migration processes. Our findings reveal an enrichment of mutations in AKAP genes in metastatic breast cancers and suggest the involvement of AKAPs in the metastatic process. In addition, we report an AKAP gene expression pattern that consistently follows the tumor intrinsic subtype, further suggesting AKAP family members as relevant players in breast cancer biology. Electronic supplementary material The online version of this article (10.1186/s12885-018-4021-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Una Kjällquist
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institute and University Hospital, Stockholm, Sweden. .,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
| | - Rikard Erlandsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Nicholas P Tobin
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institute and University Hospital, Stockholm, Sweden
| | - Amjad Alkodsi
- Research Programs Unit, Genome-Scale Biology and Medicum, University of Helsinki, Helsinki, Finland
| | - Ikram Ullah
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institute and University Hospital, Stockholm, Sweden
| | - Gustav Stålhammar
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institute and University Hospital, Stockholm, Sweden
| | - Eva Karlsson
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institute and University Hospital, Stockholm, Sweden
| | - Thomas Hatschek
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institute and University Hospital, Stockholm, Sweden
| | - Johan Hartman
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institute and University Hospital, Stockholm, Sweden
| | - Sten Linnarsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jonas Bergh
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institute and University Hospital, Stockholm, Sweden
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Furuki H, Yamada T, Takahashi G, Iwai T, Koizumi M, Shinji S, Yokoyama Y, Takeda K, Taniai N, Uchida E. Evaluation of liquid biopsies for detection of emerging mutated genes in metastatic colorectal cancer. Eur J Surg Oncol 2018; 44:975-982. [PMID: 29452859 DOI: 10.1016/j.ejso.2018.01.224] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/19/2018] [Accepted: 01/24/2018] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Detection of gene mutations is important for planning molecular targeted therapy. Although most gene mutations are concordant between primary colon cancers and their liver metastases, new mutations can emerge in metastases. The liquid biopsy is a newly developed, gene analytic method to detect mutations in metastatic tumors. In this prospective study, we evaluated the applicability of liquid biopsies in the detection of mutations in primary and metastatic tumors. METHODS We included 22 patients with liver metastases from colorectal cancer and extracted DNA from primary colorectal tumors, metastatic liver tumors, and peripheral blood (liquid biopsy). Next-generation sequencing (NGS) and digital PCR were performed to detect mutations in these three sample types. RESULTS We found a total of 36 different mutations in samples from primary tumors, liver metastases, and liquid biopsies using NGS. Twenty-eight of these mutations were found in all three types of samples, whereas liquid biopsy did not identify four mutations that had been found in both primary tumors and liver metastases, but did identify four mutations that were found in liver tumors but not in primary tumors. The sensitivity of liquid biopsies for detecting mutations in liver metastases was 64% (23/36) using NGS and 89% (32/36, P = 0.02) using dPCR. The specificities of NGS and dPCR were 100% (23/23) and 100% (32/32), respectively. CONCLUSIONS Emerging mutations, which are not found in primary tumors, can be detected in their metastases and liquid biopsies.
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Affiliation(s)
- Hiroyasu Furuki
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Japan
| | - Takeshi Yamada
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Japan.
| | - Goro Takahashi
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Japan
| | - Takuma Iwai
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Japan
| | - Michihiro Koizumi
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Japan
| | - Seiichi Shinji
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Japan
| | - Yasuyuki Yokoyama
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Japan
| | - Kohki Takeda
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Japan
| | - Nobuhiko Taniai
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Japan
| | - Eiji Uchida
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Japan
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Agarwal A, Kasinathan A, Ganesan R, Balasubramanian A, Bhaskaran J, Suresh S, Srinivasan R, Aravind KB, Sivalingam N. Curcumin induces apoptosis and cell cycle arrest via the activation of reactive oxygen species-independent mitochondrial apoptotic pathway in Smad4 and p53 mutated colon adenocarcinoma HT29 cells. Nutr Res 2018; 51:67-81. [PMID: 29673545 DOI: 10.1016/j.nutres.2017.12.011] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 12/31/2017] [Accepted: 12/31/2017] [Indexed: 11/25/2022]
Abstract
Curcumin is a natural dietary polyphenol compound that has various pharmacological activities such as antiproliferative and cancer-preventive activities on tumor cells. Indeed, the role reactive oxygen species (ROS) generated by curcumin on cell death and cell proliferation inhibition in colon cancer is poorly understood. In the present study, we hypothesized that curcumin-induced ROS may promote apoptosis and cell cycle arrest in colon cancer. To test this hypothesis, the apoptosis-inducing potential and cell cycle inhibition effect of ROS induced by curcumin was investigated in Smd4 and p53 mutated HT-29 colon adenocarcinoma cells. We found that curcumin treatment significantly increased the level of ROS in HT-29 cells in a dose- and time-dependent manner. Furthermore, curcumin treatment markedly decreased the cell viability and proliferation potential of HT-29 cells in a dose- and time-dependent manner. Conversely, generation of ROS and inhibitory effect of curcumin on HT-29 cells were abrogated by N-acetylcysteine treatment. In addition, curcumin treatment did not show any cytotoxic effects on HT-29 cells. Furthermore, curcumin-induced ROS generation caused the DNA fragmentation, chromatin condensation, and cell nuclear shrinkage and significantly increased apoptotic cells in a dose- and time-dependent manner in HT-29 cells. However, pretreatment of N-acetylcysteine inhibited the apoptosis-triggering effect of curcumin-induced ROS in HT-29 cells. In addition, curcumin-induced ROS effectively mediated cell cycle inhibition in HT-29 cells. In conclusion, our data provide the first evidence that curcumin induces ROS independent apoptosis and cell cycle arrest in colon cancer cells that carry mutation on Smad4 and p53.
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Affiliation(s)
- Ayushi Agarwal
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur-603203, Tamilnadu, India
| | - Akiladdevi Kasinathan
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur-603203, Tamilnadu, India
| | - Ramamoorthi Ganesan
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur-603203, Tamilnadu, India
| | - Akhila Balasubramanian
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur-603203, Tamilnadu, India
| | - Jahnavi Bhaskaran
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur-603203, Tamilnadu, India
| | - Samyuktha Suresh
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur-603203, Tamilnadu, India
| | - Revanth Srinivasan
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur-603203, Tamilnadu, India
| | - K B Aravind
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur-603203, Tamilnadu, India
| | - Nageswaran Sivalingam
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur-603203, Tamilnadu, India.
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Comparative genomic analysis of primary tumors and metastases in breast cancer. Oncotarget 2017; 7:27208-19. [PMID: 27028851 PMCID: PMC5053643 DOI: 10.18632/oncotarget.8349] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/14/2016] [Indexed: 12/20/2022] Open
Abstract
Personalized medicine uses genomic information for selecting therapy in patients with metastatic cancer. An issue is the optimal tissue source (primary tumor or metastasis) for testing. We compared the DNA copy number and mutational profiles of primary breast cancers and paired metastases from 23 patients using whole-genome array-comparative genomic hybridization and next-generation sequencing of 365 “cancer-associated” genes. Primary tumors and metastases harbored copy number alterations (CNAs) and mutations common in breast cancer and showed concordant profiles. The global concordance regarding CNAs was shown by clustering and correlation matrix, which showed that each metastasis correlated more strongly with its paired tumor than with other samples. Genes with recurrent amplifications in breast cancer showed 100% (ERBB2, FGFR1), 96% (CCND1), and 88% (MYC) concordance for the amplified/non-amplified status. Among all samples, 499 mutations were identified, including 39 recurrent (AKT1, ERBB2, PIK3CA, TP53) and 460 non-recurrent variants. The tumors/metastases concordance of variants was 75%, higher for recurrent (92%) than for non-recurrent (73%) variants. Further mutational discordance came from very different variant allele frequencies for some variants. We showed that the chosen targeted therapy in two clinical trials of personalized medicine would be concordant in all but one patient (96%) when based on the molecular profiling of tumor and paired metastasis. Our results suggest that the genotyping of primary tumor may be acceptable to guide systemic treatment if the metastatic sample is not obtainable. However, given the rare but potentially relevant divergences for some actionable driver genes, the profiling of metastatic sample is recommended.
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44
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Grzywa TM, Paskal W, Włodarski PK. Intratumor and Intertumor Heterogeneity in Melanoma. Transl Oncol 2017; 10:956-975. [PMID: 29078205 PMCID: PMC5671412 DOI: 10.1016/j.tranon.2017.09.007] [Citation(s) in RCA: 177] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/14/2017] [Accepted: 09/17/2017] [Indexed: 12/25/2022] Open
Abstract
Melanoma is a cancer that exhibits one of the most aggressive and heterogeneous features. The incidence rate escalates. A high number of clones harboring various mutations contribute to an exceptional level of intratumor heterogeneity of melanoma. It also refers to metastases which may originate from different subclones of primary lesion. Such component of the neoplasm biology is termed intertumor and intratumor heterogeneity. These levels of tumor heterogeneity hinder accurate diagnosis and effective treatment. The increasing number of research on the topic reflects the need for understanding limitation or failure of contemporary therapies. Majority of analyses concentrate on mutations in cancer-related genes. Novel high-throughput techniques reveal even higher degree of variations within a lesion. Consolidation of theories and researches indicates new routes for treatment options such as targets for immunotherapy. The demand for personalized approach in melanoma treatment requires extensive knowledge on intratumor and intertumor heterogeneity on the level of genome, transcriptome/proteome, and epigenome. Thus, achievements in exploration of melanoma variety are described in details. Particularly, the issue of tumor heterogeneity or homogeneity given BRAF mutations is discussed.
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Affiliation(s)
- Tomasz M Grzywa
- The Department of Histology and Embryology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Banacha 1b, 02-091 Warsaw, Poland
| | - Wiktor Paskal
- The Department of Histology and Embryology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Banacha 1b, 02-091 Warsaw, Poland
| | - Paweł K Włodarski
- The Department of Histology and Embryology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Banacha 1b, 02-091 Warsaw, Poland.
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Vakiani E. Molecular Testing of Colorectal Cancer in the Modern Era: What Are We Doing and Why? Surg Pathol Clin 2017; 10:1009-1020. [PMID: 29103530 DOI: 10.1016/j.path.2017.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A plethora of tests are routinely ordered and interpreted by pathologists to assist the management of colorectal cancer patients. Many of these tests are immunohistochemistry assays using antibodies against prognostically relevant proteins, some of which predict therapeutic response. This review focuses on tissue DNA-based tests. It presents novel methodologies for assessing well-established biomarkers, updates the expanding spectrum of genetic alterations that are associated with resistance to inhibition of epidermal growth factor receptor signaling, and briefly discusses emerging actionable alterations that may translate into new therapeutic options for colorectal cancer patients. The utility of next-generation sequencing is emphasized.
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Affiliation(s)
- Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
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Tang X, Shi L, Xie N, Liu Z, Qian M, Meng F, Xu Q, Zhou M, Cao X, Zhu WG, Liu B. SIRT7 antagonizes TGF-β signaling and inhibits breast cancer metastasis. Nat Commun 2017; 8:318. [PMID: 28827661 PMCID: PMC5566498 DOI: 10.1038/s41467-017-00396-9] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 06/27/2017] [Indexed: 12/15/2022] Open
Abstract
Distant metastasis is the main cause of breast cancer-related death; however, effective therapeutic strategies targeting metastasis are still scarce. This is largely attributable to the spatiotemporal intratumor heterogeneity during metastasis. Here we show that protein deacetylase SIRT7 is significantly downregulated in breast cancer lung metastases in human and mice, and predicts metastasis-free survival. SIRT7 deficiency promotes breast cancer cell metastasis, while temporal expression of Sirt7 inhibits metastasis in polyomavirus middle T antigen breast cancer model. Mechanistically, SIRT7 deacetylates and promotes SMAD4 degradation mediated by β-TrCP1, and SIRT7 deficiency activates transforming growth factor-β signaling and enhances epithelial-to-mesenchymal transition. Significantly, resveratrol activates SIRT7 deacetylase activity, inhibits breast cancer lung metastases, and increases survival. Our data highlight SIRT7 as a modulator of transforming growth factor-β signaling and suppressor of breast cancer metastasis, meanwhile providing an effective anti-metastatic therapeutic strategy.Metastatic disease is the major reason for breast cancer-related deaths; therefore, a better understanding of this process and its players is needed. Here the authors report the role of SIRT7 in inhibiting SMAD4-mediated breast cancer metastasis providing a possible therapeutic avenue.
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Affiliation(s)
- Xiaolong Tang
- Department of Biochemistry and Molecular Biology, Shenzhen University Health Science Center, Shenzhen, 518060, China
- Center for Anti-aging and Regenerative Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Lei Shi
- Department of Biochemistry and Molecular Biology, Shenzhen University Health Science Center, Shenzhen, 518060, China
- Center for Anti-aging and Regenerative Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Ni Xie
- Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
| | - Zuojun Liu
- Department of Biochemistry and Molecular Biology, Shenzhen University Health Science Center, Shenzhen, 518060, China
- Center for Anti-aging and Regenerative Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Minxian Qian
- Department of Biochemistry and Molecular Biology, Shenzhen University Health Science Center, Shenzhen, 518060, China
- Center for Anti-aging and Regenerative Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Fanbiao Meng
- Department of Biochemistry and Molecular Biology, Shenzhen University Health Science Center, Shenzhen, 518060, China
- Center for Anti-aging and Regenerative Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Qingyang Xu
- Department of Biochemistry and Molecular Biology, Shenzhen University Health Science Center, Shenzhen, 518060, China
- Center for Anti-aging and Regenerative Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Mingyan Zhou
- Department of Biochemistry and Molecular Biology, Shenzhen University Health Science Center, Shenzhen, 518060, China
- Center for Anti-aging and Regenerative Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Xinyue Cao
- Department of Biochemistry and Molecular Biology, Shenzhen University Health Science Center, Shenzhen, 518060, China
- Center for Anti-aging and Regenerative Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Wei-Guo Zhu
- Department of Biochemistry and Molecular Biology, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Baohua Liu
- Department of Biochemistry and Molecular Biology, Shenzhen University Health Science Center, Shenzhen, 518060, China.
- Center for Anti-aging and Regenerative Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China.
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Sanfrancesco JM, Eble JN, Grignon DJ, Wang M, Zhang S, Sundaram CP, Idrees MT, Pili R, Kouba E, Cheng L. Preservation of truncal genomic alterations in clear cell and papillary renal cell carcinomas with sarcomatoid features: An intra- and intertumoral, multifocal fluorescence in situ hybridization analysis reveals limited genetic heterogeneity. Mol Carcinog 2017; 56:2527-2537. [DOI: 10.1002/mc.22699] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 06/19/2017] [Accepted: 06/29/2017] [Indexed: 01/12/2023]
Affiliation(s)
- Joseph M. Sanfrancesco
- Departments of Pathology and Laboratory Medicine; Indiana University School of Medicine; Indianapolis Indiana
| | - John N. Eble
- Departments of Pathology and Laboratory Medicine; Indiana University School of Medicine; Indianapolis Indiana
| | - David J. Grignon
- Departments of Pathology and Laboratory Medicine; Indiana University School of Medicine; Indianapolis Indiana
| | - Mingsheng Wang
- Departments of Pathology and Laboratory Medicine; Indiana University School of Medicine; Indianapolis Indiana
| | - Shaobo Zhang
- Departments of Pathology and Laboratory Medicine; Indiana University School of Medicine; Indianapolis Indiana
| | - Chandru P. Sundaram
- Departments of Urology; Indiana University School of Medicine; Indianapolis Indiana
| | - Muhammad T. Idrees
- Departments of Pathology and Laboratory Medicine; Indiana University School of Medicine; Indianapolis Indiana
| | - Roberto Pili
- Departments of Medicine; Indiana University School of Medicine; Indianapolis Indiana
| | - Erik Kouba
- Departments of Pathology and Laboratory Medicine; Indiana University School of Medicine; Indianapolis Indiana
| | - Liang Cheng
- Departments of Pathology and Laboratory Medicine; Indiana University School of Medicine; Indianapolis Indiana
- Departments of Urology; Indiana University School of Medicine; Indianapolis Indiana
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Stefanovic S, Wirtz R, Deutsch TM, Hartkopf A, Sinn P, Varga Z, Sobottka B, Sotiris L, Taran FA, Domschke C, Hennigs A, Brucker SY, Sohn C, Schuetz F, Schneeweiss A, Wallwiener M. Tumor biomarker conversion between primary and metastatic breast cancer: mRNA assessment and its concordance with immunohistochemistry. Oncotarget 2017; 8:51416-51428. [PMID: 28881657 PMCID: PMC5584258 DOI: 10.18632/oncotarget.18006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/05/2017] [Indexed: 01/09/2023] Open
Abstract
Biomarker changes between primary (PT) and metastatic tumor (MT) site may be significant in individualizing treatment strategies and can result from actual clonal evolution, biomarker conversion, or technical limitations of diagnostic tests. This study explored biomarker conversion during breast cancer (BC) progression in 67 patients with different tumor subtypes and metastatic sites via mRNA quantification and subsequently analyzed the concordance between real-time qPCR and immunohistochemistry (IHC). Immunostaining for estrogen receptor (ER), progesterone receptor (PR), HER2, and Ki-67 was performed on formalin-fixed, paraffin-embedded PT and MT tissue sections. RT-qPCR was performed using a multiplex RT-qPCR kit for ESR1, PGR, ERBB2, and MKI67 and the reference genes B2M and CALM2. Subsequent measurement of tumor biomarker mRNA expression to detect conversion revealed significant decreases in ESR1 and PGR mRNA and MKI67 upregulation (all p < 0.001) in MT compared to PT of all tumor subtypes and ERBB2 upregulation in MT from triple-negative PT patients (p = 0.023). Furthermore, ERBB2 mRNA was upregulated in MT brain biopsies, particularly those from triple-negative PTs (p = 0.023). High concordance between RT-qPCR and IHC was observed for ER/ESR1 (81%(κ 0.51) in PT and 84%(κ 0.34) in MT, PR/PGR (70%(κ 0.10) in PT and 78% (κ -0.32) in MT), and for HER2/ERBB2 (100% in PT and 89% in MT). Discordance between mRNA biomarker assessments of PT and MT resulting from receptor conversion calls for dynamic monitoring of BC tumor biomarkers. Overall, RT-qPCR assessment of BC target genes and their mRNA expression is highly concordant with IHC protein analysis in both primary and metastatic tumor.
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Affiliation(s)
- Stefan Stefanovic
- Department of Gynecology and Obstetrics, Heidelberg University Hospital, 69120 Heidelberg, Germany
- National Center for Tumor Diseases (NCT) Heidelberg, 69120 Heidelberg, Germany
| | - Ralph Wirtz
- Stratifyer Molecular Pathology GmbH, 50935 Cologne, Germany
| | - Thomas M. Deutsch
- National Center for Tumor Diseases (NCT) Heidelberg, 69120 Heidelberg, Germany
| | - Andreas Hartkopf
- Department of Women's Health, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Peter Sinn
- Department of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Zsuzsanna Varga
- Institute of Surgical Pathology, Zurich University Hospital, 8091 Zurich, Switzerland
| | - Bettina Sobottka
- Institute of Surgical Pathology, Zurich University Hospital, 8091 Zurich, Switzerland
| | - Lakis Sotiris
- Stratifyer Molecular Pathology GmbH, 50935 Cologne, Germany
| | - Florin-Andrei Taran
- Department of Women's Health, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Christoph Domschke
- Department of Gynecology and Obstetrics, Heidelberg University Hospital, 69120 Heidelberg, Germany
- National Center for Tumor Diseases (NCT) Heidelberg, 69120 Heidelberg, Germany
| | - Andre Hennigs
- Department of Gynecology and Obstetrics, Heidelberg University Hospital, 69120 Heidelberg, Germany
- National Center for Tumor Diseases (NCT) Heidelberg, 69120 Heidelberg, Germany
| | - Sara Y. Brucker
- Research Institute for Women's Health, Tübingen University Hospital, 72076 Tübingen, Germany
| | - Christof Sohn
- Department of Gynecology and Obstetrics, Heidelberg University Hospital, 69120 Heidelberg, Germany
- National Center for Tumor Diseases (NCT) Heidelberg, 69120 Heidelberg, Germany
| | - Florian Schuetz
- Department of Gynecology and Obstetrics, Heidelberg University Hospital, 69120 Heidelberg, Germany
- National Center for Tumor Diseases (NCT) Heidelberg, 69120 Heidelberg, Germany
| | - Andreas Schneeweiss
- Department of Gynecology and Obstetrics, Heidelberg University Hospital, 69120 Heidelberg, Germany
- National Center for Tumor Diseases (NCT) Heidelberg, 69120 Heidelberg, Germany
| | - Markus Wallwiener
- Department of Gynecology and Obstetrics, Heidelberg University Hospital, 69120 Heidelberg, Germany
- National Center for Tumor Diseases (NCT) Heidelberg, 69120 Heidelberg, Germany
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Vakiani E, Shah RH, Berger MF, Makohon-Moore AP, Reiter JG, Ostrovnaya I, Attiyeh MA, Cercek A, Shia J, Iacobuzio-Donahue CA, Solit DB, Weiser MR. Local recurrences at the anastomotic area are clonally related to the primary tumor in sporadic colorectal carcinoma. Oncotarget 2017; 8:42487-42494. [PMID: 28476018 PMCID: PMC5522082 DOI: 10.18632/oncotarget.17200] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 04/07/2017] [Indexed: 12/20/2022] Open
Abstract
PURPOSE Anastomotic recurrences (AR) occur in 2-10% of colorectal carcinoma cases after resection of primary tumor (PT). Currently, there are no molecular data investigating their genetic profile and multiple theories exist about their pathogenesis. The aim of our study was to compare the genomic profile of AR to that of the patients' corresponding matched PT and, when available, to a distant metastasis (DM). EXPERIMENTAL DESIGN Thirty-six tumors from 14 patients were genotyped using a capture-based, next-generation assay to define the mutational status of 341 cancer-associated genes. All patients had R0 resection of their PT and AR occurred 1.1-7.0 years following PT resection. A DM or a second AR was analyzed in 8 patients. All tumors were microsatellite stable except in one patient with Lynch syndrome. RESULTS A total of 254 somatic mutations were detected including 138 mutations in the microsatellite stable (MSS) cases. The most commonly mutated genes were APC, KRAS, TP53, PIK3CA, ATM and PIK3R1. In all patients with MSS tumors the AR and PT shared between 50-100% of mutations, including mutations in key driver genes, consistent with these tumors being clonally related. Genetic events private to DM were not detected in AR and phylogenetic analysis showed that ARs were more closely related to PT than DM. In the Lynch syndrome patient the PT and AR showed distinct somatic mutations consistent with independent primaries. CONCLUSIONS ARs are clonally related to PT in sporadic colorectal carcinomas and do not appear to represent seeding of the anastomotic site by distant metastases.
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Affiliation(s)
- Efsevia Vakiani
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Ronak H. Shah
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Michael F. Berger
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Alvin P. Makohon-Moore
- The David Rubenstein Pancreatic Cancer Research Center, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Johannes G. Reiter
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA, 02138, USA
| | - Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Marc A. Attiyeh
- The David Rubenstein Pancreatic Cancer Research Center, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Andrea Cercek
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Jinru Shia
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Christine A. Iacobuzio-Donahue
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
- The David Rubenstein Pancreatic Cancer Research Center, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - David B. Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Martin R. Weiser
- Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
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50
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Appierto V, Di Cosimo S, Reduzzi C, Pala V, Cappelletti V, Daidone MG. How to study and overcome tumor heterogeneity with circulating biomarkers: The breast cancer case. Semin Cancer Biol 2017; 44:106-116. [PMID: 28442298 DOI: 10.1016/j.semcancer.2017.04.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/14/2017] [Accepted: 04/18/2017] [Indexed: 12/22/2022]
Abstract
Breast cancer ranks first among female cancer-related deaths in Western countries. As the primary tumor can often be controlled by surgical resection, the survival of women with breast cancer is closely linked to the incidence of distant metastases. Molecular screening by next generation sequencing highlighted the spatial and temporal heterogeneity of solid tumors as well as the clonal evolution of cancer cells during progression and under treatment pressure. Such findings question whether an optimal assessment of disease progression and a screening for druggable mutations should be based on molecular features of primary or recurrent/metastatic lesions and therefore represent a crucial element for failure or success of personalized medicine. In fact, new targeted therapies may induce only short-term benefit annulled by the emergence of resistant clones with new driver mutations which would need to be rapidly and reliably identified. Serial tissue sampling is therefore essential but, unfortunately, also represents a problem since biopsies from solid lesions, which are invasive and potentially painful and risky, cannot be easily repeatedly sampled, are inaccessible or may not fully reflect tumor heterogeneity. The need to early detect and strike this "moving target" is now directing the scientific community toward liquid biopsy-based biomarkers, which include circulating tumor cells (CTC) and cell-free circulating tumor DNA (ctDNA), can be repeatedly assessed through non-invasive and easy-to-perform procedures and may act as reliable read-outs of functional and molecular features of recurrent/metastatic lesions. In this review we summarize the outcome of CTCs and ctDNA in breast cancer, with special reference on their role on unveiling and overcoming tumor heterogeneity, on their potential relevance for tumor surveillance and monitoring, and for the selection of therapeutic options. Finally, we propose integration between blood-based molecular and clinical approaches for monitoring disease progression according to the specific pattern of recurrence of the most aggressive breast cancer molecular subtypes.
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Affiliation(s)
- Valentina Appierto
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Via G.A. Amadeo, 42, 20133 Milan, Italy.
| | - Serena Di Cosimo
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Via G.A. Amadeo, 42, 20133 Milan, Italy.
| | - Carolina Reduzzi
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Via G.A. Amadeo, 42, 20133 Milan, Italy.
| | - Valentina Pala
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Via G.A. Amadeo, 42, 20133 Milan, Italy.
| | - Vera Cappelletti
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Via G.A. Amadeo, 42, 20133 Milan, Italy.
| | - Maria Grazia Daidone
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Via G.A. Amadeo, 42, 20133 Milan, Italy.
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