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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; 30:750-764. [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] [MESH Headings] [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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Gupta V, Vashisht V, Vashisht A, Mondal AK, Alptekin A, Singh H, Kolhe R. Comprehensive Analysis of Clinically Relevant Copy Number Alterations (CNAs) Using a 523-Gene Next-Generation Sequencing Panel and NxClinical Software in Solid Tumors. Genes (Basel) 2024; 15:396. [PMID: 38674331 PMCID: PMC11049607 DOI: 10.3390/genes15040396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Copy number alterations (CNAs) are significant in tumor initiation and progression. Identifying these aberrations is crucial for targeted therapies and personalized cancer diagnostics. Next-generation sequencing (NGS) methods present advantages in scalability and cost-effectiveness, surpassing limitations associated with reference assemblies and probe capacities in traditional laboratory approaches. This retrospective study evaluated CNAs in 50 FFPE tumor samples (breast cancer, ovarian carcinoma, pancreatic cancer, melanoma, and prostate carcinoma) using Illumina's TruSight Oncology 500 (TSO500) and the Affymetrix Oncoscan Molecular Inversion Probe (OS-MIP) (ThermoFisher Scientific, Waltham, MA, USA). NGS analysis with the NxClinical 6.2 software demonstrated a high sensitivity and specificity (100%) for CNA detection, with a complete concordance rate as compared to the OS-MIP. All 54 known CNAs were identified by NGS, with gains being the most prevalent (63%). Notable CNAs were observed in MYC (18%), TP53 (12%), BRAF (8%), PIK3CA, EGFR, and FGFR1 (6%) genes. The diagnostic parameters exhibited high accuracy, including a positive predictive value, negative predictive value, and overall diagnostic accuracy. This study underscores NxClinical as a reliable software for identifying clinically relevant gene alterations using NGS TSO500, offering valuable insights for personalized cancer treatment strategies based on CNA analysis.
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Affiliation(s)
- Vivek Gupta
- Department of Pathology, Government Institute of Medical Sciences, Greater Noida 201310, India;
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
| | - Vishakha Vashisht
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
| | - Ashutosh Vashisht
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
| | - Ashis K. Mondal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
| | - Ahmet Alptekin
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
| | - Harmanpreet Singh
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
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Becchi T, Beltrame L, Mannarino L, Calura E, Marchini S, Romualdi C. A pan-cancer landscape of pathogenic somatic copy number variations. J Biomed Inform 2023; 147:104529. [PMID: 37858853 DOI: 10.1016/j.jbi.2023.104529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 09/13/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023]
Abstract
OBJECTIVE Copy number variations (CNVs) play crucial roles in physiological and pathological processes, including cancer. However, the functional implications of somatic CNVs in tumor progression and evolution remain unclear. This study focuses on identifying CNV alterations with high pathogenic potential that drive and sustain tumorigenesis, distinguishing them from passenger alterations that accumulate during tumor growth. Our goal is to explore the variability of CNVs across different tumor types and infer their impact on tumor cell functions. METHODS Starting from 7352 copy number profiles across 33 different cancer types, we infer the pathogenicity of each CNV and perform both intra- and inter-tumor analyses to predict the functional impact of different genomic patterns. We evaluate the actionability of genes belonging to altered regions and we correlate the presence of pathogenic regions with genome instability patterns and patients' survival. RESULTS Our analysis uncovered large heterogeneity among different tumors suggesting in many cases distinct genetic drivers of tumorigenesis. Recurrent genomic alterations frequently coincide with dysfunctional homologous recombination pathways and negative regulation of the immune system. In certain tumors, the number of pathogenic CNVs emerged as a prognostic biomarker, highlighting their significance in cancer progression. CONCLUSION This study contributes to elucidate the functional impact of pathogenic CNVs in tumor progression and sheds light on their potential as prognostic markers in specific cancer types.
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Affiliation(s)
- Tommaso Becchi
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Luca Beltrame
- Laboratory of Cancer Pharmacology, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano - Milan, Italy
| | - Laura Mannarino
- Laboratory of Cancer Pharmacology, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano - Milan, Italy; Department of Biomedical Sciences, Humanitas University, via Rita Levi Montalcini 4, 20072 Pieve Emanuele - Milan, Italy
| | - Enrica Calura
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Sergio Marchini
- Laboratory of Cancer Pharmacology, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano - Milan, Italy
| | - Chiara Romualdi
- Department of Biology, University of Padova, 35131 Padova, Italy.
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4
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Shao G, Fan X, Zhang P, Liu X, Huang L, Ji S. Circ_0004676 exacerbates triple-negative breast cancer progression through regulation of the miR-377-3p/E2F6/PNO1 axis. Cell Biol Toxicol 2023; 39:2183-2205. [PMID: 35870038 DOI: 10.1007/s10565-022-09704-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/23/2022] [Indexed: 12/09/2022]
Abstract
BACKGROUND The significant roles of circular RNAs (circRNAs) in different cancers and diseases have been reported. We now focused on the possible role of a newly recognized circRNA, circ_0004674 in triple-negative breast cancer (TNBC), and the related downstream mechanism. METHODS The expression of circ_0004674 in TNBC tissues and cells was determined followed by analysis of the correlation between circ_0004674 and TNBC patients' prognosis. The interaction between circ_0004674, miR-377-3p, E2F6, and PNO1 was then identified using bioinformatics analysis combined with FISH, RIP, RNA pull-down, RT-qPCR, and Western blot analysis. Using gain-of-function and loss-of-function methods, we analyzed the effect of circ_0004674, miR-377-3p, E2F6, and PNO1 on TNBC in vivo and in vitro. RESULTS Increased circ_0004674 and E2F6 but decreased miR-377-3p were observed in TNBC tissues and MDA-MB-231 TNBC cells, all of which findings were associated with poor prognosis in patients with TNBC. Silencing of circ_0004676 remarkably suppressed the proliferation, cell cycle progression, and migration of TNBC cells in vitro, as well as inhibiting tumorigenesis and metastasis in vivo. Additionally, circ_0004676 served as a sponge of miR-377-3p which bound to the transcription factor E2F6. In the presence of overexpression of circ_0004676, E2F6 expression and its target PNO1 expression were elevated, while miR-377-3p expression was decreased. Interestingly, overexpression of E2F6 could reverse the inhibitory effect on tumor growth caused by downregulation of circ_0004676. CONCLUSION Our study highlighted the carcinogenic effect of circ_0004676 on TNBC through regulation of the miR-377-3p/E2F6/PNO1 axis. 1. Circ_0004674 is highly expressed in TNBC tissues and cells. 2. Circ_0004674 upregulates the expression of E2F6 by sponging miR-377-3p. 3. E2F6 upregulates PNO1 by binding to the PNO1 promoter. 4. Circ_0004674 favors TNBC progression by regulating the miR-377-3p/E2F6/PNO1 axis. 5. This study provides a new target for the treatment of TNBC.
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Affiliation(s)
- Guoli Shao
- Special Medical Service Center, Zhujiang Hospital of Southern Medical University, No. 253, Middle Gongye Road, Haizhu District, Guangzhou, 510282, People's Republic of China
| | - Xulong Fan
- Department of Breast Surgery, Maternity and Children's Healthcare Hospital of Foshan, Foshan, 528000, People's Republic of China
| | - Pusheng Zhang
- Department of General Surgery, Zhujiang Hospital of Southern Medical University, Guangzhou, 510282, People's Republic of China
| | - Xuewen Liu
- Special Medical Service Center, Zhujiang Hospital of Southern Medical University, No. 253, Middle Gongye Road, Haizhu District, Guangzhou, 510282, People's Republic of China
| | - Lei Huang
- Department of General Surgery, Zhujiang Hospital of Southern Medical University, Guangzhou, 510282, People's Republic of China
| | - Shufeng Ji
- Special Medical Service Center, Zhujiang Hospital of Southern Medical University, No. 253, Middle Gongye Road, Haizhu District, Guangzhou, 510282, People's Republic of China.
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Nagahashi M, Ling Y, Toshikawa C, Hayashida T, Kitagawa Y, Futamura M, Kuwayama T, Nakamura S, Yamauchi H, Yamauchi T, Kaneko K, Kanbayashi C, Sato N, Tsuchida J, Moro K, Nakajima M, Shimada Y, Ichikawa H, Lyle S, Miyoshi Y, Takabe K, Okuda S, Wakai T. Copy number alteration is an independent prognostic biomarker in triple-negative breast cancer patients. Breast Cancer 2023; 30:584-595. [PMID: 36930419 DOI: 10.1007/s12282-023-01449-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 03/05/2023] [Indexed: 03/18/2023]
Abstract
BACKGROUND Next-generation sequencing (NGS) has enabled comprehensive genomic profiling to identify gene alterations that play important roles in cancer biology. However, the clinical significance of these genomic alterations in triple-negative breast cancer (TNBC) patients has not yet been fully elucidated. The aim of this study was to clarify the clinical significance of genomic profiling data, including copy number alterations (CNA) and tumor mutation burden (TMB), in TNBC patients. METHODS A total of 47 patients with Stage I-III TNBC with genomic profiling of 435 known cancer genes by NGS were enrolled in this study. Disease-free survival (DFS) and overall survival (OS) were evaluated for their association to gene profiling data. RESULTS CNA-high patients showed significantly worse DFS and OS than CNA-low patients (p = 0.0009, p = 0.0041, respectively). TMB was not associated with DFS or OS in TNBC patients. Patients with TP53 alterations showed a tendency of worse DFS (p = 0.0953) and significantly worse OS (p = 0.0338) compared with patients without TP53 alterations. Multivariable analysis including CNA and other clinicopathological parameters revealed that CNA was an independent prognostic factor for DFS (p = 0.0104) and OS (p = 0.0306). Finally, multivariable analysis also revealed the combination of CNA-high and TP53 alterations is an independent prognostic factor for DFS (p = 0.0005) and OS (p = 0.0023). CONCLUSIONS We revealed that CNA, but not TMB, is significantly associated with DFS and OS in TNBC patients. The combination of CNA-high and TP53 alterations may be a promising biomarker that can inform beyond standard clinicopathologic factors to identify a subgroup of TNBC patients with significantly worse prognosis.
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Affiliation(s)
- Masayuki Nagahashi
- Department of Surgery, Division of Breast and Endocrine Surgery, School of Medicine, Hyogo Medical University, 1-1 Mukogawa-Cho, Nishinomiya, Hyogo, 663-8501, Japan.
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan.
| | - YiWei Ling
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, 2-5274 Gakkocho-dori, Chuo-Ku, Niigata, 951-8514, Japan
- Medical AI Center, Niigata University School of Medicine, 2-5274 Gakkocho-dori, Chuo-Ku, Niigata, 951-8514, Japan
| | - Chie Toshikawa
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan
- Department of Breast Surgical Oncology, St. Luke's International Hospital, 9-1 Akashicho, Chuo-Ku, Tokyo, 104-8560, Japan
| | - Tetsu Hayashida
- Department of Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Yuko Kitagawa
- Department of Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Manabu Futamura
- Department of Breast Surgery, Gifu University Hospital, 1-1 Yanagido, Gifu, 501-1194, Japan
| | - Takashi Kuwayama
- Division of Breast Surgical Oncology, Department of Surgery, Showa University School of Medicine, 1-5-8, Hatanodai, Shinagawa-Ku, Tokyo, 142-8666, Japan
| | - Seigo Nakamura
- Division of Breast Surgical Oncology, Department of Surgery, Showa University School of Medicine, 1-5-8, Hatanodai, Shinagawa-Ku, Tokyo, 142-8666, Japan
| | - Hideko Yamauchi
- Department of Breast Surgical Oncology, St. Luke's International Hospital, 9-1 Akashicho, Chuo-Ku, Tokyo, 104-8560, Japan
| | - Teruo Yamauchi
- Division of Medical Oncology, Department of Internal Medicine, St. Luke's International Hospital, 9-1 Akashicho, Chuo-Ku, Tokyo, 104-8560, Japan
| | - Koji Kaneko
- Department of Breast Oncology, Niigata Cancer Center Hospital, 15-3 Kawagishi-Cho 2-Chome, Chuo-Ku, Niigata, 951-8566, Japan
| | - Chizuko Kanbayashi
- Department of Breast Oncology, Niigata Cancer Center Hospital, 15-3 Kawagishi-Cho 2-Chome, Chuo-Ku, Niigata, 951-8566, Japan
| | - Nobuaki Sato
- Department of Breast Oncology, Niigata Cancer Center Hospital, 15-3 Kawagishi-Cho 2-Chome, Chuo-Ku, Niigata, 951-8566, Japan
| | - Junko Tsuchida
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan
| | - Kazuki Moro
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan
| | - Masato Nakajima
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan
| | - Yoshifumi Shimada
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan
| | - Hiroshi Ichikawa
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan
| | - Stephen Lyle
- University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA
| | - Yasuo Miyoshi
- Department of Surgery, Division of Breast and Endocrine Surgery, School of Medicine, Hyogo Medical University, 1-1 Mukogawa-Cho, Nishinomiya, Hyogo, 663-8501, Japan
| | - Kazuaki Takabe
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan
- Breast Surgery, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA
- Department of Surgery, University at Buffalo Jacobs School of Medicine and Biosciences, The State University of New York, Buffalo, NY, 14203, USA
- Department of Breast Surgery and Oncology, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-Ku, Tokyo, 160-8402, Japan
- Department of Surgery, Yokohama City University, 3-9 Fukuura, Kanazawa-Ku, Yokohama, 236-0004, Japan
| | - Shujiro Okuda
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, 2-5274 Gakkocho-dori, Chuo-Ku, Niigata, 951-8514, Japan
- Medical AI Center, Niigata University School of Medicine, 2-5274 Gakkocho-dori, Chuo-Ku, Niigata, 951-8514, Japan
| | - Toshifumi Wakai
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan
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MicroRNA-135 inhibits initiation of epithelial-mesenchymal transition in breast cancer by targeting ZNF217 and promoting m6A modification of NANOG. Oncogene 2022; 41:1742-1751. [PMID: 35121826 DOI: 10.1038/s41388-022-02211-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 01/11/2022] [Accepted: 01/25/2022] [Indexed: 12/24/2022]
Abstract
MicroRNAs play significant roles in various malignancies, with breast cancer (BC) being no exception. Consequently, we explored the functional mechanism of miR-135 in the progression of BC. In total, 55 pairs of BC and matched adjacent normal tissues were clinically collected from patients, followed by quantification of miR-135 and zinc finger protein 217 (ZNF217) expression patterns in BC tissues and cells. Accordingly, high ZNF217 expression and low miR-135 expression levels were identified in BC tissues and cells. Subsequently, the expressions of miR-135 and ZNF217 were altered to evaluate their effects on BC cell migration, invasion and EMT initiation. It was found that when ZNF217 was silenced or miR-135 was elevated, BC cell malignant behaviors were significantly inhibited, which was reproduced in nude mice for in vivo evidence. Furthermore, dual-luciferase reporter gene assay revealed the presence of direct binding between miR-135 and ZNF217. Subsequent co-immunoprecipitation, methylated-RNA binding protein immunoprecipitation and photoactivatable ribonucleoside enhanced-crosslinking and immunoprecipitation assays further revealed that ZNF217 could upregulate NANOG by reducing N6-methyladenosine levels via methyltransferase-like 13 (METTL3). Collectively, our findings highlighted the role of the miR-135/ZNF217/METTL3/NANOG axis in the progression of BC, emphasizing potential therapeutic targets ZNF217 silencing and miR-135 upregulation in preventing or treating BC.
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Lei H, Gertz EM, Schäffer AA, Fu X, Tao Y, Heselmeyer-Haddad K, Torres I, Li G, Xu L, Hou Y, Wu K, Shi X, Dean M, Ried T, Schwartz R. Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data. Bioinformatics 2021; 37:4704-4711. [PMID: 34289030 PMCID: PMC8665747 DOI: 10.1093/bioinformatics/btab504] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 05/19/2021] [Accepted: 07/05/2021] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION Computational reconstruction of clonal evolution in cancers has become a crucial tool for understanding how tumors initiate and progress and how this process varies across patients. The field still struggles, however, with special challenges of applying phylogenetic methods to cancers, such as the prevalence and importance of copy number alteration (CNA) and structural variation (SV) events in tumor evolution, which are difficult to profile accurately by prevailing sequencing methods in such a way that subsequent reconstruction by phylogenetic inference algorithms is accurate. RESULTS In the present work, we develop computational methods to combine sequencing with multiplex interphase fluorescence in situ hybridization (miFISH) to exploit the complementary advantages of each technology in inferring accurate models of clonal CNA evolution accounting for both focal changes and aneuploidy at whole-genome scales. By integrating such information in an integer linear programming (ILP) framework, we demonstrate on simulated data that incorporation of FISH data substantially improves accurate inference of focal CNA and ploidy changes in clonal evolution from deconvolving bulk sequence data. Analysis of real glioblastoma data for which FISH, bulk sequence, and single cell sequence are all available confirms the power of FISH to enhance accurate reconstruction of clonal copy number evolution in conjunction with bulk and optionally single-cell sequence data. AVAILABILITY Source code is available on Github at https://github.com/CMUSchwartzLab/FISH_deconvolution.
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Affiliation(s)
- Haoyun Lei
- Computational Biology Dept, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - E Michael Gertz
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alejandro A Schäffer
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Xuecong Fu
- Shenzhen Luohu People's Hospital, Shenzhen, 518000, China
| | - Yifeng Tao
- Computational Biology Dept, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Kerstin Heselmeyer-Haddad
- Genetics Branch, Cancer Genomics Section, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Irianna Torres
- Genetics Branch, Cancer Genomics Section, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Guibo Li
- Department of Biology, University of Copenhagen, Copenhagen, 1599, Denmark
| | - Liqin Xu
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Soltofts Plads, 2800 Kongens Lyngby, Denmark
| | - Yong Hou
- Department of Biology, University of Copenhagen, Copenhagen, 1599, Denmark
| | - Kui Wu
- Department of Biology, University of Copenhagen, Copenhagen, 1599, Denmark
| | - Xulian Shi
- Shenzhen Luohu People's Hospital, Shenzhen, 518000, China
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology & Genetics, National Cancer Institute, U.S. National Institutes of Health, Gaithersburg, MD, 20814, USA
| | - Thomas Ried
- Genetics Branch, Cancer Genomics Section, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Russell Schwartz
- Computational Biology Dept, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Dept. of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
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8
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Li Y, Wu H, Wang Q, Xu S. ZNF217: the cerberus who fails to guard the gateway to lethal malignancy. Am J Cancer Res 2021; 11:3378-3405. [PMID: 34354851 PMCID: PMC8332857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 05/14/2021] [Indexed: 06/13/2023] Open
Abstract
The aberrant expression of the zinc finger protein 217 (ZNF217) promotes multiple malignant phenotypes, such as replicative immortality, maintenance of proliferation, malignant heterogeneity, metastasis, and cell death resistance, via diverse mechanisms, including transcriptional activation, mRNA N6-methyladenosine (m6A) regulation, and protein interactions. The induction of these cellular processes by ZNF217 leads to therapeutic resistance and patients' poor outcomes. However, few ZNF217 related clinical applications or trials, have been reported. Moreover, looming observations about ZNF217 roles in m6A regulation and cancer immune response triggered significant attention while lacking critical evidence. Thus, in this review, we revisit the literature about ZNF217 and emphasize its importance as a prognostic biomarker for early prevention and as a therapeutic target.
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Affiliation(s)
- Yingpu Li
- Department of Breast Surgery, Harbin Medical University Cancer HospitalHarbin, China
| | - Hao Wu
- Sino-Russian Medical Research Center, Harbin Medical University Cancer HospitalHarbin, China
- Heilongjiang Academy of Medical SciencesHarbin, China
| | - Qin Wang
- Department of Breast Surgery, Harbin Medical University Cancer HospitalHarbin, China
- Sino-Russian Medical Research Center, Harbin Medical University Cancer HospitalHarbin, China
- Heilongjiang Academy of Medical SciencesHarbin, China
| | - Shouping Xu
- Department of Breast Surgery, Harbin Medical University Cancer HospitalHarbin, China
- Sino-Russian Medical Research Center, Harbin Medical University Cancer HospitalHarbin, China
- Heilongjiang Academy of Medical SciencesHarbin, China
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9
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Liegmann AS, Heselmeyer-Haddad K, Lischka A, Hirsch D, Chen WD, Torres I, Gemoll T, Rody A, Thorns C, Gertz EM, Alkemade H, Hu Y, Habermann JK, Ried T. Single Cell Genetic Profiling of Tumors of Breast Cancer Patients Aged 50 Years and Older Reveals Enormous Intratumor Heterogeneity Independent of Individual Prognosis. Cancers (Basel) 2021; 13:3366. [PMID: 34282768 PMCID: PMC8267950 DOI: 10.3390/cancers13133366] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023] Open
Abstract
PURPOSE Older breast cancer patients are underrepresented in cancer research even though the majority (81.4%) of women dying of breast cancer are 55 years and older. Here we study a common phenomenon observed in breast cancer which is a large inter- and intratumor heterogeneity; this poses a tremendous clinical challenge, for example with respect to treatment stratification. To further elucidate genomic instability and tumor heterogeneity in older patients, we analyzed the genetic aberration profiles of 39 breast cancer patients aged 50 years and older (median 67 years) with either short (median 2.4 years) or long survival (median 19 years). The analysis was based on copy number enumeration of eight breast cancer-associated genes using multiplex interphase fluorescence in situ hybridization (miFISH) of single cells, and by targeted next-generation sequencing of 563 cancer-related genes. RESULTS We detected enormous inter- and intratumor heterogeneity, yet maintenance of common cancer gene mutations and breast cancer specific chromosomal gains and losses. The gain of COX2 was most common (72%), followed by MYC (69%); losses were most prevalent for CDH1 (74%) and TP53 (69%). The degree of intratumor heterogeneity did not correlate with disease outcome. Comparing the miFISH results of diploid with aneuploid tumor samples significant differences were found: aneuploid tumors showed significantly higher average signal numbers, copy number alterations (CNAs) and instability indices. Mutations in PIKC3A were mostly restricted to luminal A tumors. Furthermore, a significant co-occurrence of CNAs of DBC2/MYC, HER2/DBC2 and HER2/TP53 and mutual exclusivity of CNAs of HER2 and PIK3CA mutations and CNAs of CCND1 and PIK3CA mutations were revealed. CONCLUSION Our results provide a comprehensive picture of genome instability profiles with a large variety of inter- and intratumor heterogeneity in breast cancer patients aged 50 years and older. In most cases, the distribution of chromosomal aneuploidies was consistent with previous results; however, striking exceptions, such as tumors driven by exclusive loss of chromosomes, were identified.
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Affiliation(s)
- Anna-Sophie Liegmann
- Section of Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, 23562 Lübeck, Germany; (A.-S.L.); (A.L.); (T.G.); (H.A.)
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.H.-H.); (D.H.); (W.-D.C.); (I.T.); (Y.H.)
| | - Kerstin Heselmeyer-Haddad
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.H.-H.); (D.H.); (W.-D.C.); (I.T.); (Y.H.)
| | - Annette Lischka
- Section of Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, 23562 Lübeck, Germany; (A.-S.L.); (A.L.); (T.G.); (H.A.)
| | - Daniela Hirsch
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.H.-H.); (D.H.); (W.-D.C.); (I.T.); (Y.H.)
- Institute of Pathology, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Wei-Dong Chen
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.H.-H.); (D.H.); (W.-D.C.); (I.T.); (Y.H.)
| | - Irianna Torres
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.H.-H.); (D.H.); (W.-D.C.); (I.T.); (Y.H.)
| | - Timo Gemoll
- Section of Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, 23562 Lübeck, Germany; (A.-S.L.); (A.L.); (T.G.); (H.A.)
| | - Achim Rody
- Department of Gynecology and Obstetrics, Campus Lübeck, University Hospital of Schleswig-Holstein, 23562 Lübeck, Germany;
| | - Christoph Thorns
- Institute of Pathology, Marienkrankenhaus Hamburg, 22087 Hamburg, Germany;
- Institute of Pathology, University of Lübeck and University Medical Center Schleswig-Holstein, 23562 Lübeck, Germany
| | - Edward Michael Gertz
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Hendrik Alkemade
- Section of Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, 23562 Lübeck, Germany; (A.-S.L.); (A.L.); (T.G.); (H.A.)
| | - Yue Hu
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.H.-H.); (D.H.); (W.-D.C.); (I.T.); (Y.H.)
| | - Jens K. Habermann
- Section of Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, 23562 Lübeck, Germany; (A.-S.L.); (A.L.); (T.G.); (H.A.)
- Department of Oncology-Pathology, Cancer Center Karolinska, Karolinska Institute, 171 77 Stockholm, Sweden
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.H.-H.); (D.H.); (W.-D.C.); (I.T.); (Y.H.)
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Bai H, Yu J, Jia S, Liu X, Liang X, Li H. Prognostic Value of the TP53 Mutation Location in Metastatic Breast Cancer as Detected by Next-Generation Sequencing. Cancer Manag Res 2021; 13:3303-3316. [PMID: 33889023 PMCID: PMC8057094 DOI: 10.2147/cmar.s298729] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/19/2021] [Indexed: 11/23/2022] Open
Abstract
Purpose The status of TP53 mutations was measured in cell-free DNA from patients with metastatic breast cancer (MBC) to investigate disease characteristics and the prognostic role of different locations of the TP53 mutation site. Patients and Methods Blood samples were taken from a total of 187 patients diagnosed with MBC who were treated at the Department of Breast Oncology, Peking University Cancer Hospital between January 2013 and March 2020. Next-generation sequencing was used to investigate the TP53 mutation spectra of circulating free DNA in these blood samples. Results Among the 187 MBC patients, TP53-mutated patients had a significantly shorter median disease-free survival (DFS) and overall survival (OS) compared with TP53 wild-type patients (P=0.001 and P=0.006, respectively). Additionally, in hormone receptor positive/HER2 negative (HR+/HER2-) and triple negative (TNBC) cohorts, TP53-mutated patients had a significantly shorter median DFS than TP53 wild-type patients (P=0.038 and P=0.023, respectively). The 79 patients with TP53 mutations carried 87 somatic TP53 mutations, of which most (77.0%) mapped to the DNA-binding domain (DBD) of the protein encoded by TP53 exons 5–8. In patients with TP53 mutations, those occurring in the non-DBD had a significantly shorter median DFS and OS than TP53 wild type (P<0.001 and P=0.001, respectively). Additionally, patients with non-missense mutations in the DBD had a significantly shorter median DFS and OS than TP53 wild-type patients (P=0.001 and P<0.001, respectively). TP53-mutated patients had a significantly shorter DFS than TP53 wild-type patients in the adjuvant endocrine therapy sensitive group (P=0.008), but differences in the endocrine therapy resistant group were not significant. Conclusion TP53-mutated MBC patients had a significantly worse outcome than TP53 wild-type patients especially those in HR+/HER2– and TNBC cohorts. Of TP53-mutated patients, those with non-missense mutations in the DBD had worse breast cancer-related survival. TP53 mutations were also associated with endocrine resistance.
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Affiliation(s)
- Han Bai
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, People's Republic of China
| | - Jianjun Yu
- Huidu Shanghai Medical Sciences, Shanghai, 201499, People's Republic of China
| | - Shidong Jia
- Huidu Shanghai Medical Sciences, Shanghai, 201499, People's Republic of China
| | - Xiaoran Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, People's Republic of China
| | - Xu Liang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, People's Republic of China
| | - Huiping Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, People's Republic of China
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