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Shahrouzi P, Forouz F, Mathelier A, Kristensen VN, Duijf PHG. Copy number alterations: a catastrophic orchestration of the breast cancer genome. Trends Mol Med 2024:S1471-4914(24)00120-5. [PMID: 38772764 DOI: 10.1016/j.molmed.2024.04.017] [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: 02/26/2024] [Revised: 04/12/2024] [Accepted: 04/26/2024] [Indexed: 05/23/2024]
Abstract
Breast cancer (BCa) is a prevalent malignancy that predominantly affects women around the world. Somatic copy number alterations (CNAs) are tumor-specific amplifications or deletions of DNA segments that often drive BCa development and therapy resistance. Hence, the complex patterns of CNAs complement BCa classification systems. In addition, understanding the precise contributions of CNAs is essential for tailoring personalized treatment approaches. This review highlights how tumor evolution drives the acquisition of CNAs, which in turn shape the genomic landscapes of BCas. It also discusses advanced methodologies for identifying recurrent CNAs, studying CNAs in BCa and their clinical impact.
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Affiliation(s)
- Parastoo Shahrouzi
- Department of Medical Genetics, Institute of Basic Medical Science, Faculty of Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway.
| | - Farzaneh Forouz
- School of Pharmacy, University of Queensland, Woolloongabba, Brisbane, Australia
| | - Anthony Mathelier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway; Center for Bioinformatics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway; Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Vessela N Kristensen
- Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway; Division of Medicine, Department of Clinical Molecular Biology and Laboratory Science (EpiGen), Akershus University Hospital, Lørenskog, Norway; Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Pascal H G Duijf
- Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway; Centre for Cancer Biology, UniSA Clinical and Health Sciences, University of South Australia and SA Pathology, Adelaide, Australia.
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2
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Chen H, Fang X, Shao J, Zhang Q, Xu L, Chen J, Mei Y, Jiang M, Wang Y, Li Z, Chen Z, Chen Y, Yu C, Ma L, Zhang P, Zhang T, Liao Y, Lv Y, Wang X, Yang L, Fu Y, Chen D, Jiang L, Yan F, Lu W, Chen G, Shen H, Wang J, Wang C, Liang T, Han X, Wang Y, Guo G. Pan-Cancer Single-Nucleus Total RNA Sequencing Using snHH-Seq. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2304755. [PMID: 38010945 PMCID: PMC10837386 DOI: 10.1002/advs.202304755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/11/2023] [Indexed: 11/29/2023]
Abstract
Tumor heterogeneity and its drivers impair tumor progression and cancer therapy. Single-cell RNA sequencing is used to investigate the heterogeneity of tumor ecosystems. However, most methods of scRNA-seq amplify the termini of polyadenylated transcripts, making it challenging to perform total RNA analysis and somatic mutation analysis.Therefore, a high-throughput and high-sensitivity method called snHH-seq is developed, which combines random primers and a preindex strategy in the droplet microfluidic platform. This innovative method allows for the detection of total RNA in single nuclei from clinically frozen samples. A robust pipeline to facilitate the analysis of full-length RNA-seq data is also established. snHH-seq is applied to more than 730 000 single nuclei from 32 patients with various tumor types. The pan-cancer study enables it to comprehensively profile data on the tumor transcriptome, including expression levels, mutations, splicing patterns, clone dynamics, etc. New malignant cell subclusters and exploring their specific function across cancers are identified. Furthermore, the malignant status of epithelial cells is investigated among different cancer types with respect to mutation and splicing patterns. The ability to detect full-length RNA at the single-nucleus level provides a powerful tool for studying complex biological systems and has broad implications for understanding tumor pathology.
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Affiliation(s)
- Haide Chen
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
- M20 Genomics, Hangzhou, 311121, China
| | - Xiunan Fang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, 999077, China
| | - Jikai Shao
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
| | - Qi Zhang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, 310006, China
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, 310006, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Liwei Xu
- Department of Thoracic Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, China
| | | | - Yuqing Mei
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Mengmeng Jiang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
| | - Yuting Wang
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Zhouyang Li
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Zihang Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, 310009, China
| | - Yang Chen
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology, Hangzhou, 310022, China
- The Second Clinical Medical College of Zhejiang Chinese Medical University Hangzhou, Hangzhou, 310053, China
| | - Chengxuan Yu
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Zhejiang Provincial Clinical Research Center for Cancer, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Lifeng Ma
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Peijing Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, 310058, China
| | | | - Yuan Liao
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- M20 Genomics, Hangzhou, 311121, China
| | | | - Xueyi Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Lei Yang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yuting Fu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Daobao Chen
- Department of Breast Surgery, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Liming Jiang
- Department of Radiology, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Feng Yan
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, 310009, China
| | - Wei Lu
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Zhejiang Provincial Clinical Research Center for Cancer, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Gao Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, 310009, China
| | - Huahao Shen
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- State Key Laboratory of Respiratory Disease, Guangzhou, 510120, China
| | - Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
| | - Changchun Wang
- Department of Thoracic Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, China
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology, Hangzhou, 310022, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, 310006, China
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, 310006, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Xiaoping Han
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yongcheng Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, 310058, China
- Institute of Hematology, Zhejiang University, Hangzhou, 310006, China
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3
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Kim MH, Kim GM, Ahn JM, Ryu WJ, Kim SG, Kim JH, Kim TY, Han HJ, Kim JY, Park HS, Park S, Park BW, Kim SI, Jeong J, Lee J, Paik S, Kim S, Jung KH, Cho EH, Sohn J. Copy number aberrations in circulating tumor DNA enables prognosis prediction and molecular characterization of breast cancer. J Natl Cancer Inst 2023; 115:1036-1049. [PMID: 37166557 PMCID: PMC10483335 DOI: 10.1093/jnci/djad080] [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: 10/27/2022] [Revised: 02/28/2023] [Accepted: 04/28/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Low-pass whole-genome sequencing (LP-WGS)-based circulating tumor DNA (ctDNA) analysis is a versatile tool for somatic copy number aberration (CNA) detection, and this study aims to explore its clinical implication in breast cancer. METHODS We analyzed LP-WGS ctDNA data from 207 metastatic breast cancer (MBC) patients to explore prognostic value of ctDNA CNA burden and validated it in 465 stage II-III triple-negative breast cancer (TNBC) patients who received neoadjuvant chemotherapy in phase III PEARLY trial (NCT02441933). The clinical implication of locus level LP-WGS ctDNA profiling was further evaluated. RESULTS We found that a high baseline ctDNA CNA burden predicts poor overall survival and progression-free survival of MBC patients. The post hoc analysis of the PEARLY trial showed that a high baseline ctDNA CNA burden predicted poor disease-free survival independent from pathologic complete response (pCR), validating its robust prognostic significance. The 24-month disease-free survival rate was 96.9% and 55.9% in [pCR(+) and low I-score] and [non-pCR and high I-score] patients, respectively. The locus-level ctDNA CNA profile classified MBC patients into 5 molecular clusters and revealed targetable oncogenic CNAs. LP-WGS ctDNA and in vitro analysis identified the BCL6 amplification as a resistance factor for CDK4/6 inhibitors. We estimated ctDNA-based homologous recombination deficiency status of patients by shallowHRD algorithm, which was highest in the TNBC and correlated with platinum-based chemotherapy response. CONCLUSIONS These results demonstrate LP-WGS ctDNA CNA analysis as an essential tool for prognosis prediction and molecular profiling. Particularly, ctDNA CNA burden can serve as a useful determinant for escalating or de-escalating (neo)adjuvant strategy in TNBC patients.
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Affiliation(s)
- Min Hwan Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Gun Min Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jin Mo Ahn
- Green Cross Genome, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Won-Ji Ryu
- Avison Biomedical Research Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seul-Gi Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jee Hung Kim
- Division of Medical Oncology, Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Tae Yeong Kim
- Avison Biomedical Research Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyun Ju Han
- Avison Biomedical Research Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jee Ye Kim
- Division of Breast Surgery, Department of Surgery, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyung Seok Park
- Division of Breast Surgery, Department of Surgery, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seho Park
- Division of Breast Surgery, Department of Surgery, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Byeong Woo Park
- Division of Breast Surgery, Department of Surgery, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seung Il Kim
- Division of Breast Surgery, Department of Surgery, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Joon Jeong
- Division of Breast Surgery, Department of Surgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jieun Lee
- Division of Medical Oncology, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Soonmyung Paik
- Severance Biomedical Science Institute and Department of Medical Oncology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sangwoo Kim
- Department of Biomedical Systems Informatics, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Kyung Hae Jung
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Eun Hae Cho
- Green Cross Genome, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Joohyuk Sohn
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
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4
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Zeng S, Xu Z, Liang Q, Thakur A, Liu Y, Zhou S, Yan Y. The prognostic gene CRABP2 affects drug sensitivity by regulating docetaxel-induced apoptosis in breast invasive carcinoma: A pan-cancer analysis. Chem Biol Interact 2023; 373:110372. [PMID: 36736488 DOI: 10.1016/j.cbi.2023.110372] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 01/21/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Abstract
Cellular retinoic acid-binding protein 2 (CRABP2), a specific transporter of retinoic acid, has been shown to have an important biological role in human cancers. However, due to the substantial variability among different tumors, the role of CRABP2 remains uncertain and has not yet been subjected to systematic analysis. Utilizing The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), Clinical Proteomic Tumor Analysis Consortium (CPTAC), Human Protein Atlas (HPA), Gene Expression Profiling Interactive Analysis 2 (GEPIA2), Kaplan-Meier Plotter, Biomarker Exploration of Solid Tumors (BEST), Cancer Cell Line Encyclopedia (CCLE), Receiver Operating Characteristic plotter (ROC plotter), and other online public tools, expression levels of CRABP2 in breast invasive carcinoma (BRCA), lung adenocarcinoma (LUAD), and ovarian serous cystadenocarcinoma (OV) were found to be significantly greater than those in adjacent normal tissues, suggesting a correlation to poor prognosis. Among the three, CRABP2 expression in BRCA was most closely associated with clinical prognosis. In a study of docetaxel-treated BRCA patients, CRABP2 expression was significantly higher in the drug-resistant group. Colony formation and flow cytometry analysis were used to further investigate the relationship between CRABP2 and docetaxel sensitivity in BRCA cells MDA-MB-231and BT549. The knockdown of CRABP2 expression significantly reduced cell growth and increased sensitivity to the chemotherapeutic agent docetaxel in BRCA cells. Furthermore, CRABP2 knockdown augmented docetaxel-induced apoptosis. Molecular docking using SwissDock tool revealed that CRABP2 had a greater binding affinity to docetaxel than docetaxel-targeted proteins. This research provides an insight into the expression and prognostic potential of CRABP2 in cancers and suggests that CRABP2 may control docetaxel sensitivity in BRCA cells through apoptosis, warranting further investigation.
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Affiliation(s)
- Shuangshuang Zeng
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Zhijie Xu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China; Department of Pathology, Xiangya Changde Hospital, Changde, 415000, Hunan, China
| | - Qiuju Liang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Abhimanyu Thakur
- Ben May Department for Cancer Research, Pritzker School of Molecular Engineering, University of Chicago, Illinois, USA
| | - Yuanhong Liu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Shangjun Zhou
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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5
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Liao YY, Cao WM. The progress in our understanding of CIN in breast cancer research. Front Oncol 2023; 13:1067735. [PMID: 36874134 PMCID: PMC9978327 DOI: 10.3389/fonc.2023.1067735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/02/2023] [Indexed: 02/18/2023] Open
Abstract
Chromosomal instability (CIN) is an important marker of cancer, which is closely related to tumorigenesis, disease progression, treatment efficacy, and patient prognosis. However, due to the limitations of the currently available detection methods, its exact clinical significance remains unknown. Previous studies have demonstrated that 89% of invasive breast cancer cases possess CIN, suggesting that it has potential application in breast cancer diagnosis and treatment. In this review, we describe the two main types of CIN and discuss the associated detection methods. Subsequently, we highlight the impact of CIN in breast cancer development and progression and describe how it can influence treatment and prognosis. The goal of this review is to provide a reference on its mechanism for researchers and clinicians.
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Affiliation(s)
- Yu-Yang Liao
- Wenzhou Medical University, Wenzhou, China.,Department of Breast Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, China
| | - Wen-Ming Cao
- Department of Breast Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, China
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6
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Li J, Kang J, Liu W, Liu J, Pan G, Mao A, Zhang Q, Lu J, Ding J, Li H. Docetaxel-resistant triple-negative breast cancer cell-derived exosomal lncRNA LINC00667 reduces the chemosensitivity of breast cancer cells to docetaxel <em>via</em> targeting miR-200b-3p/Bcl-2 axis. Eur J Histochem 2022; 66. [DOI: 10.4081/ejh.2022.3529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 09/29/2022] [Indexed: 11/22/2022] Open
Abstract
Development of docetaxel (TXT) resistance is a major obstacle for triple-negative breast cancer (TNBC) treatment. Additionally, chemoresistant cell-derived exosomes were able to change the chemo-response of chemosensitive recipient cells via transportation of lncRNAs. It has been shown that lncRNA LINC00667 level was significantly elevated in breast cancer tissues. Therefore, we explored whether LINC00667 level is increased in TXT-resistant TNBC cell-derived exosomes. In addition, whether exosomal LINC00667 derived from TXT-resistant TNBC cell could affect TXT sensitivity in TXT-sensitive TNBC cells was investigated as well. In the present study, exosomes were isolated from the TXT-resistant TNBC cells and from TXT-sensitive TNBC cells. Next, the level of LINC00667 in the isolated exosomes was detected with RT-qPCR. We found that LINC00667 expression was obviously elevated in TXT-resistant TNBC cell-derived exosomes compared to that in TXT-sensitive TNBC cell-derived exosomes. In addition, LINC00667 could be transferred from TXT-resistant TNBC cells to TNBC cells via exosomes. Moreover, TXT-resistant TNBC cell secreted exosomal LINC00667 markedly reduced the sensitivity of TNBC cells to TXT via upregulation of Bcl-2. Meanwhile, downregulation of LINC00667 notably enhanced the sensitivity of TXT-resistant TNBC cells to TXT through downregulation of Bcl-2. Additionally, LINC00667 was considered to be a ceRNA to sponge miR-200b-3p, thereby elevating Bcl-2 expression. Collectively, TXT-resistant TNBC cell-derived exosomal LINC00667 could decrease the chemosensitivity of TNBC cells to TXT via regulating miR-200b-3p/Bcl-2 axis. These findings suggested that LINC00667 might serve as a promising target for enhancing sensitivity of TNBC cells to TXT therapy.
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7
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Yang L, Zhang W, Qiu Q, Su Z, Tang M, Bai P, Si W, Zhu Z, Liu Y, Yang J, Kuang S, Liu J, Yan W, Shi M, Ye H, Yang Z, Chen L. Discovery of a Series of Hydroxamic Acid-Based Microtubule Destabilizing Agents with Potent Antitumor Activity. J Med Chem 2021; 64:15379-15401. [PMID: 34648295 DOI: 10.1021/acs.jmedchem.1c01451] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Hydroxamic acid group is one of the characteristic pharmacophores of histone deacetylase (HDAC) inhibitors. But here, we discovered a series of hydroxamic acid-based microtubule destabilizing agents (MDAs), which were derived from shortening the length of the linker in HDAC6 inhibitor SKLB-23bb. Interestingly, the low nanomolar antiproliferative activity of these MDAs depended on the presence of hydroxamic acid groups, but their inhibitory effects on HDAC were lost. Among them, 12b showed favorable metabolism stability, high bioavailability, and potent antitumor activity in multidrug-resistant cell lines and A2780/T xenograft model. More importantly, in the patient-derived xenograft models of triple-negative breast cancer and osimertinib-resistant non-small-cell lung cancer, both 20 mg/kg oral and 10 mg/kg intravenous administration of 12b could induce more than 70% tumor inhibition without obvious toxicity. Overall, we discovered that 12b, as a novel MDA based on hydroxamic acid, could serve as a potential MDA for further investigation.
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Affiliation(s)
- Linyu Yang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, Sichuan, China
| | - Wanhua Zhang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, Sichuan, China.,Department of Hematology, West China Hospital of Sichuan University, Chengdu 610041, Sichuan, China
| | - Qiang Qiu
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, Sichuan, China
| | - Zhengying Su
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, Sichuan, China
| | - Minghai Tang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, Sichuan, China
| | - Peng Bai
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, Sichuan, China
| | - Wenting Si
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, Sichuan, China
| | - Zejiang Zhu
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, Sichuan, China
| | - Yan Liu
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, Sichuan, China
| | - Jianhong Yang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, Sichuan, China
| | - Shuang Kuang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, Sichuan, China
| | - Jiang Liu
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, Sichuan, China
| | - Wei Yan
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, Sichuan, China
| | - Mingsong Shi
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, Sichuan, China
| | - Haoyu Ye
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, Sichuan, China
| | - Zhuang Yang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, Sichuan, China
| | - Lijuan Chen
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, Sichuan, China
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Ibragimova MK, Tsyganov MM, Litviakov NV. Molecular-Genetic Portrait of Breast Cancer with Triple Negative Phenotype. Cancers (Basel) 2021; 13:cancers13215348. [PMID: 34771512 PMCID: PMC8582512 DOI: 10.3390/cancers13215348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 10/21/2021] [Indexed: 12/31/2022] Open
Abstract
Simple Summary Breast cancer is a genetically heterogeneous disease with different molecular biological and clinical characteristics. The available knowledge about the genetic heterogeneity of the most aggressive molecular subtype of breast cancer—triple-negative—has led to discoveries in drug treatment. Identification of the molecular-genetic phenotype of breast cancer is an important prognostic factor of the disease and allows personalization of the patient’s treatment. Abstract Understanding of the genetic mechanisms and identification of the biological markers of tumor progression that form the individual molecular phenotype of transformed cells can characterize the degree of tumor malignancy, the ability to metastasize, the hormonal sensitivity, and the effectiveness of chemotherapy, etc. Breast cancer (BC) is a genetically heterogeneous disease with different molecular biological and clinical characteristics. The available knowledge about the genetic heterogeneity of the most aggressive molecular subtype of breast cancer—triple-negative (TN)—has led to discoveries in drug treatment, including the use of DNA damaging agents (platinum and PARP inhibitors) for these tumors, as well as the use of immunotherapy. Most importantly, the ability to prescribe optimal drug treatment regimens for patients with TNBC based on knowledge of the molecular-genetic characteristics of this subtype of BC will allow the achievement of high rates of overall and disease-free survival. Thus, identification of the molecular-genetic phenotype of breast cancer is an important prognostic factor of the disease and allows personalization of the patient’s treatment.
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Affiliation(s)
- Marina K. Ibragimova
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia; (M.M.T.); (N.V.L.)
- National Research Tomsk State University, 634050 Tomsk, Russia
- Correspondence:
| | - Matvey M. Tsyganov
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia; (M.M.T.); (N.V.L.)
| | - Nikolai V. Litviakov
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia; (M.M.T.); (N.V.L.)
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Ippolito MR, Martis V, Martin S, Tijhuis AE, Hong C, Wardenaar R, Dumont M, Zerbib J, Spierings DCJ, Fachinetti D, Ben-David U, Foijer F, Santaguida S. Gene copy-number changes and chromosomal instability induced by aneuploidy confer resistance to chemotherapy. Dev Cell 2021; 56:2440-2454.e6. [PMID: 34352223 DOI: 10.1016/j.devcel.2021.07.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 05/09/2021] [Accepted: 07/09/2021] [Indexed: 12/30/2022]
Abstract
Mitotic errors lead to aneuploidy, a condition of karyotype imbalance, frequently found in cancer cells. Alterations in chromosome copy number induce a wide variety of cellular stresses, including genome instability. Here, we show that cancer cells might exploit aneuploidy-induced genome instability and the resulting gene copy-number changes to survive under conditions of selective pressure, such as chemotherapy. Resistance to chemotherapeutic drugs was dictated by the acquisition of recurrent karyotypes, indicating that gene dosage might play a role in driving chemoresistance. Thus, our study establishes a causal link between aneuploidy-driven changes in gene copy number and chemoresistance and might explain why some chemotherapies fail to succeed.
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Affiliation(s)
- Marica Rosaria Ippolito
- Department of Experimental Oncology at IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Valentino Martis
- Department of Experimental Oncology at IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Sara Martin
- Department of Experimental Oncology at IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Andréa E Tijhuis
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, the Netherlands
| | - Christy Hong
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, the Netherlands
| | - René Wardenaar
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, the Netherlands
| | - Marie Dumont
- Institut Curie, PSL Research University, CNRS, UMR144, Paris, France
| | - Johanna Zerbib
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Diana C J Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, the Netherlands
| | | | - Uri Ben-David
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, the Netherlands
| | - Stefano Santaguida
- Department of Experimental Oncology at IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9/1, 20122 Milan, Italy.
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10
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Pariyar M, Johns A, Thorne RF, Scott RJ, Avery-Kiejda KA. Copy number variation in triple negative breast cancer samples associated with lymph node metastasis. Neoplasia 2021; 23:743-753. [PMID: 34225099 PMCID: PMC8259224 DOI: 10.1016/j.neo.2021.05.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/31/2021] [Indexed: 12/24/2022] Open
Abstract
Triple negative breast cancer (TNBC) is a highly metastatic and aggressive subtype of breast cancer and cases presenting with lymph node involvement have worse outcomes. This study aimed to determine the regions of copy number variation (CNV) associated with lymph node metastasis in TNBC patients. CNV analyses were performed in a study cohort of 23 invasive ductal carcinomas (IDCs), 12 lymph node metastases (LNmets), and 7 normal adjacent tissues (NATs); as well as in an independent cohort containing 70 TNBC IDCs and the same 7 NATs. CNV-associated genes were analyzed using GO-enrichment and Pathway analysis. The prognostic role for genes showing CNV-based changes in messenger RNA expression was determined using the Kaplan-Meier plotter database. For the IDCs, there were a number of variations that were common in both the study and independent cohorts in the amplified regions of 1q, 8q, 19 (p and q), 2p, 5p and the deleted regions in 8p followed by 5q, and 19p. The most frequently amplified regions in the LNmets of the study cohort were 4q28.3, 2p, 3q24, 1q21.2, 10p, 12p11.1, 8q, 20p11.22-20p11.21, 21q22.13, 6p22.1 and the most frequently deleted regions were in 1p36.23, 4q21.1 and 5q. A total of 686 (441 amplified and 245 deleted) genes were associated with LNmets. The LNmet-associated genes were highly enriched for “regulation of complement activation,” “regulation of protein activation cascade,” “regulation of humoral immune response,” “oxytocin signalling pathway,” and “TRAIL binding” pathways. Moreover, 6/686 LNmet-associated genes showed CNV-based changes in their mRNA expression of which, high expression of ASPM and KIF14 was significantly associated with worse relapse-free survival. This study has identified several CNV regions in TNBC that could play a major role in metastasis to the lymph node.
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Affiliation(s)
- Mamta Pariyar
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia; Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Andrea Johns
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia; Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Rick F Thorne
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia; Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia; Hunter Medical Research Institute, New Lambton Heights, NSW, Australia; NSW Health Pathology, John Hunter Hospital, New Lambton Heights, NSW, Australia
| | - Kelly A Avery-Kiejda
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia; Hunter Medical Research Institute, New Lambton Heights, NSW, Australia.
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Li S, Wu H, Huang X, Jian Y, Kong L, Xu H, Ouyang Y, Chen X, Wu G, Yu L, Wang X. BOP1 confers chemoresistance of triple-negative breast cancer by promoting CBP-mediated β-catenin acetylation. J Pathol 2021; 254:265-278. [PMID: 33797754 DOI: 10.1002/path.5676] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/03/2021] [Accepted: 03/30/2021] [Indexed: 12/26/2022]
Abstract
Chemoresistance is a major obstacle to the treatment of triple-negative breast cancer (TNBC), which has a poor prognosis. Increasing evidence has demonstrated the essential role of cancer stem cells (CSCs) in the process of TNBC chemoresistance. However, the underlying mechanism remains unclear. In the present study, we report that block of proliferation 1 (BOP1) serves as a key regulator of chemoresistance in TNBC. BOP1 expression was significantly upregulated in chemoresistant TNBC tissues, and high expression of BOP1 correlated with shorter overall survival and relapse-free survival in patients with TNBC. BOP1 overexpression promoted, while BOP1 downregulation inhibited the drug resistance and CSC-like phenotype of TNBC cells in vitro and in vivo. Moreover, BOP1 activated Wnt/β-catenin signaling by increasing the recruitment of cyclic AMP response element-binding protein (CBP) to β-catenin, enhancing CBP-mediated acetylation of β-catenin, and increasing the transcription of downstream stemness-related genes CD133 and ALDH1A1. Notably, treating with the β-catenin/CBP inhibitor PRI-724 induced an enhancement of chemotherapeutic response of paclitaxel in BOP1-overexpressing TNBC cells. These findings indicate that BOP1 is involved in chemoresistance development and might serve as a prognostic marker and therapeutic target in TNBC. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Siqi Li
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Haoming Wu
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | | | - Yunting Jian
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Lingzhi Kong
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Hongyi Xu
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China.,Department of Breast Surgery, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Ying Ouyang
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Xiangfu Chen
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Geyan Wu
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China.,Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, PR China
| | - Liang Yu
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Xi Wang
- Department of Breast Surgery, Sun Yat-sen University Cancer Center, Guangzhou, PR China
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12
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Activity of docetaxel, carboplatin, and doxorubicin in patient-derived triple-negative breast cancer xenografts. Sci Rep 2021; 11:7064. [PMID: 33782404 PMCID: PMC8007714 DOI: 10.1038/s41598-021-85962-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/28/2021] [Indexed: 01/05/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is highly responsive to neoadjuvant polychemotherapy regimens including anthracyclines, taxanes, and, more recently, carboplatin. However, there is inadequate information on the individual contribution of each of these agents to the global activity of the combinations, and the use of combinations of up to four of these drugs is associated with relevant toxicity. Identifying single-drug activity in the clinical neoadjuvant setting is challenging. We developed patient-derived xenografts (PDXs) from several chemotherapy-naïve TNBC samples to assess the antitumor activity of single drugs and combinations of drugs. PDXs were established from chemotherapy-naïve TNBC samples. Nine TNBC PDX models (all of which corresponded to a basal-like phenotype according to the PAM50 classifier) were treated with carboplatin, docetaxel, and doxorubicin and the combination of docetaxel and carboplatin. Only one of nine PDX models showed sensitivity to doxorubicin, while eight of nine PDX models showed sensitivity to docetaxel and carboplatin as single agents. The 3 PDX models derived from patients with gBRCA-1 or gPALB2 mutations were very sensitive to carboplatin single agent. All 6 PDX models from patients without hereditary germ-line mutations showed increased sensitivity to the combination of docetaxel and carboplatin. In the present study, docetaxel and carboplatin single agents were active drugs against basal-like TNBC, while doxorubicin monotherapy showed low activity. The combination of docetaxel and carboplatin was more effective than the drugs used as single agents, except in the PDX from patients with gBRCA1/PALB2 mutations.
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Gómez-Miragaya J, Morán S, Calleja-Cervantes ME, Collado-Sole A, Paré L, Gómez A, Serra V, Dobrolecki LE, Lewis MT, Diaz-Lagares A, Eroles P, Prat A, Esteller M, González-Suárez E. The Altered Transcriptome and DNA Methylation Profiles of Docetaxel Resistance in Breast Cancer PDX Models. Mol Cancer Res 2019; 17:2063-2076. [PMID: 31320385 DOI: 10.1158/1541-7786.mcr-19-0040] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 06/05/2019] [Accepted: 07/10/2019] [Indexed: 11/16/2022]
Abstract
Taxanes are standard therapy in clinical practice for metastatic breast cancer; however, primary or acquired chemoresistance are a common cause of mortality. Breast cancer patient-derived xenografts (PDX) are powerful tools for the study of cancer biology and drug treatment response. Specific DNA methylation patterns have been associated to different breast cancer subtypes but its association with chemoresistance remains unstudied. Aiming to elucidate docetaxel resistance mechanisms, we performed genome-wide DNA methylation in breast cancer PDX models, including luminal and triple-negative breast cancer (TNBC) models sensitive to docetaxel, their matched models after emergence of chemoresistance and residual disease after short-term docetaxel treatment. We found that DNA methylation profiles from breast cancer PDX models maintain the subtype-specific methylation patterns of clinical samples. Two main DNA methylation clusters were found in TNBC PDX and remain stable during the emergence of docetaxel resistance; however, some genes/pathways were differentially methylated according to docetaxel response. A DNA methylation signature of resistance able to segregate TNBC based on chemotherapy response was identified. Transcriptomic profiling of selected sensitive/resistant pairs and integrative analysis with methylation data demonstrated correlation between some differentially methylated and expressed genes in docetaxel-resistant TNBC PDX models. Multiple gene expression changes were found after the emergence of docetaxel resistance in TNBC. DNA methylation and transcriptional changes identified between docetaxel-sensitive and -resistant TNBC PDX models or residual disease may have predictive value for chemotherapy response in TNBC. IMPLICATIONS: Subtype-specific DNA methylation patterns are maintained in breast cancer PDX models. While no global methylation changes were found, we uncovered differentially DNA methylated and expressed genes/pathways associated with the emergence of docetaxel resistance in TNBC.
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Affiliation(s)
- Jorge Gómez-Miragaya
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Sebastián Morán
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | | | - Alejandro Collado-Sole
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Laia Paré
- Translational Genomics and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Antonio Gómez
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Violeta Serra
- Preclinical Research Program, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Lacey E Dobrolecki
- Departments of Molecular and Cellular Biology and Radiology, The Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Michael T Lewis
- Departments of Molecular and Cellular Biology and Radiology, The Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Angel Diaz-Lagares
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain.,Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), CIBERONC, Santiago de Compostela, Spain
| | - Pilar Eroles
- Biomedical Research Institute (INCLIVA), Valencia, Spain. CIBERONC, Spain
| | - Aleix Prat
- Translational Genomics and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain.,Josep Carreras Leukaemia Research Institute, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Eva González-Suárez
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain.
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