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Laisné M, Rodgers B, Benlamara S, Wicinski J, Nicolas A, Djerroudi L, Gupta N, Ferry L, Kirsh O, Daher D, Philippe C, Okada Y, Charafe-Jauffret E, Cristofari G, Meseure D, Vincent-Salomon A, Ginestier C, Defossez PA. A novel bioinformatic approach reveals cooperation between Cancer/Testis genes in basal-like breast tumors. Oncogene 2024; 43:1369-1385. [PMID: 38467851 PMCID: PMC11065691 DOI: 10.1038/s41388-024-03002-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 03/13/2024]
Abstract
Breast cancer is the most prevalent type of cancer in women worldwide. Within breast tumors, the basal-like subtype has the worst prognosis, prompting the need for new tools to understand, detect, and treat these tumors. Certain germline-restricted genes show aberrant expression in tumors and are known as Cancer/Testis genes; their misexpression has diagnostic and therapeutic applications. Here we designed a new bioinformatic approach to examine Cancer/Testis gene misexpression in breast tumors. We identify several new markers in Luminal and HER-2 positive tumors, some of which predict response to chemotherapy. We then use machine learning to identify the two Cancer/Testis genes most associated with basal-like breast tumors: HORMAD1 and CT83. We show that these genes are expressed by tumor cells and not by the microenvironment, and that they are not expressed by normal breast progenitors; in other words, their activation occurs de novo. We find these genes are epigenetically repressed by DNA methylation, and that their activation upon DNA demethylation is irreversible, providing a memory of past epigenetic disturbances. Simultaneous expression of both genes in breast cells in vitro has a synergistic effect that increases stemness and activates a transcriptional profile also observed in double-positive tumors. Therefore, we reveal a functional cooperation between Cancer/Testis genes in basal breast tumors; these findings have consequences for the understanding, diagnosis, and therapy of the breast tumors with the worst outcomes.
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Affiliation(s)
- Marthe Laisné
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France
| | - Brianna Rodgers
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France
| | - Sarah Benlamara
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France
| | - Julien Wicinski
- CRCM, Inserm, CNRS, Institut Paoli-Calmettes, Aix-Marseille University, Epithelial Stem Cells and Cancer Laboratory, Equipe Labellisée LIGUE Contre le Cancer, Marseille, France
| | - André Nicolas
- Platform of Experimental Pathology, Department of Diagnostic and Theranostic Medicine, Institut Curie-Hospital, 75005, Paris, France
| | - Lounes Djerroudi
- Department of Pathology, Institut Curie, 26 Rue d'Ulm, 75005, Paris, France
| | - Nikhil Gupta
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France
| | - Laure Ferry
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France
| | - Olivier Kirsh
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France
| | - Diana Daher
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France
| | | | - Yuki Okada
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Emmanuelle Charafe-Jauffret
- CRCM, Inserm, CNRS, Institut Paoli-Calmettes, Aix-Marseille University, Epithelial Stem Cells and Cancer Laboratory, Equipe Labellisée LIGUE Contre le Cancer, Marseille, France
| | | | - Didier Meseure
- Platform of Experimental Pathology, Department of Diagnostic and Theranostic Medicine, Institut Curie-Hospital, 75005, Paris, France
| | | | - Christophe Ginestier
- CRCM, Inserm, CNRS, Institut Paoli-Calmettes, Aix-Marseille University, Epithelial Stem Cells and Cancer Laboratory, Equipe Labellisée LIGUE Contre le Cancer, Marseille, France
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2
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Naik A, Lattab B, Qasem H, Decock J. Cancer testis antigens: Emerging therapeutic targets leveraging genomic instability in cancer. MOLECULAR THERAPY. ONCOLOGY 2024; 32:200768. [PMID: 38596293 PMCID: PMC10876628 DOI: 10.1016/j.omton.2024.200768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Cancer care has witnessed remarkable progress in recent decades, with a wide array of targeted therapies and immune-based interventions being added to the traditional treatment options such as surgery, chemotherapy, and radiotherapy. However, despite these advancements, the challenge of achieving high tumor specificity while minimizing adverse side effects continues to dictate the benefit-risk balance of cancer therapy, guiding clinical decision making. As such, the targeting of cancer testis antigens (CTAs) offers exciting new opportunities for therapeutic intervention of cancer since they display highly tumor specific expression patterns, natural immunogenicity and play pivotal roles in various biological processes that are critical for tumor cellular fitness. In this review, we delve deeper into how CTAs contribute to the regulation and maintenance of genomic integrity in cancer, and how these mechanisms can be exploited to specifically target and eradicate tumor cells. We review the current clinical trials targeting aforementioned CTAs, highlight promising pre-clinical data and discuss current challenges and future perspectives for future development of CTA-based strategies that exploit tumor genomic instability.
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Affiliation(s)
- Adviti Naik
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Boucif Lattab
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Hanan Qasem
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
- College of Health and Life Sciences (CHLS), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Julie Decock
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
- College of Health and Life Sciences (CHLS), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Doha, Qatar
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3
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Gardi N, Chaubal R, Parab P, Pachakar S, Kulkarni S, Shet T, Joshi S, Kembhavi Y, Chandrani P, Quist J, Kowtal P, Grigoriadis A, Sarin R, Govindarajan R, Gupta S. Natural History of Germline BRCA1 Mutated and BRCA Wild-type Triple-negative Breast Cancer. CANCER RESEARCH COMMUNICATIONS 2024; 4:404-417. [PMID: 38315150 PMCID: PMC10865976 DOI: 10.1158/2767-9764.crc-23-0277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/09/2023] [Accepted: 01/26/2024] [Indexed: 02/07/2024]
Abstract
We report a deep next-generation sequencing analysis of 13 sequentially obtained tumor samples, eight sequentially obtained circulating tumor DNA (ctDNA) samples and three germline DNA samples over the life history of 3 patients with triple-negative breast cancer (TNBC), 2 of whom had germline pathogenic BRCA1 mutation, to unravel tumor evolution. Tumor tissue from all timepoints and germline DNA was subjected to whole-exome sequencing (WES), custom amplicon deep sequencing (30,000X) of a WES-derived somatic mutation panel, and SNP arrays for copy-number variation (CNV), while whole transcriptome sequencing (RNA-seq) was performed only on somatic tumor.There was enrichment of homologous recombination deficiency signature in all tumors and widespread CNV, which remained largely stable over time. Somatic tumor mutation numbers varied between patients and within each patient (range: 70-216, one outlier). There was minimal mutational overlap between patients with TP53 being the sole commonly mutated gene, but there was substantial overlap in sequential samples in each patient. Each patient's tumor contained a founding ("stem") clone at diagnosis, which persisted over time, from which all other clones ("subclone") were derived ("branching evolution"), which contained mutations in well-characterized cancer-related genes like PDGFRB, ARID2, TP53 (Patient_02), TP53, BRAF, BRIP1, CSF3R (Patient_04), and TP53, APC, EZH2 (Patient_07). Including stem and subclones, tumors from all patients were polyclonal at diagnosis and during disease progression. ctDNA recapitulated most tissue-derived stem clonal and subclonal mutations while detecting some additional subclonal mutations. RNA-seq revealed a stable basal-like pattern, with most highly expressed variants belonging to stem clone. SIGNIFICANCE In germline BRCA1 mutated and BRCA wild-type patients, TNBC shows a branching evolutionary pattern of mutations with a single founding clone, are polyclonal throughout their disease course, and have widespread copy-number aberrations. This evolutionary pattern may be associated with treatment resistance or sensitivity and could be therapeutically exploited.
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Affiliation(s)
- Nilesh Gardi
- Department of Medical Oncology, Tata Memorial Centre, Mumbai
- Clinician Scientist Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Mumbai
| | - Rohan Chaubal
- Clinician Scientist Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Mumbai
- Department of Surgical Oncology, Tata Memorial Centre, Mumbai
| | - Pallavi Parab
- Department of Medical Oncology, Tata Memorial Centre, Mumbai
- Homi Bhabha National Institute, Mumbai
| | - Sunil Pachakar
- Department of Medical Oncology, Tata Memorial Centre, Mumbai
- Clinician Scientist Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Mumbai
| | - Suyash Kulkarni
- Homi Bhabha National Institute, Mumbai
- Department of Radiodiagnosis, Tata Memorial Centre, Mumbai
| | - Tanuja Shet
- Homi Bhabha National Institute, Mumbai
- Department of Pathology, Tata Memorial Centre, Mumbai
| | - Shalaka Joshi
- Homi Bhabha National Institute, Mumbai
- Department of Surgical Oncology, Tata Memorial Centre, Mumbai
| | - Yogesh Kembhavi
- Department of Medical Oncology, Tata Memorial Centre, Mumbai
- Homi Bhabha National Institute, Mumbai
| | - Pratik Chandrani
- Department of Medical Oncology, Tata Memorial Centre, Mumbai
- Homi Bhabha National Institute, Mumbai
| | - Jelmar Quist
- Cancer Bioinformatics, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
- Breast Cancer Now Unit, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Pradnya Kowtal
- Homi Bhabha National Institute, Mumbai
- DNA sequencing Facility, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai
| | - Anita Grigoriadis
- Cancer Bioinformatics, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
- Breast Cancer Now Unit, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Rajiv Sarin
- Homi Bhabha National Institute, Mumbai
- Department of Radiation Oncology, Tata Memorial Centre, Mumbai
| | | | - Sudeep Gupta
- Department of Medical Oncology, Tata Memorial Centre, Mumbai
- Clinician Scientist Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Mumbai
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Wang H, Xie R, Niu F, Yang Q, An L, Wu C, Liu X, Yang X. Structural and biochemical insights into the interaction mechanism underlying HORMAD1 and its partner proteins. Structure 2023; 31:1578-1588.e3. [PMID: 37794593 DOI: 10.1016/j.str.2023.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/02/2023] [Accepted: 09/07/2023] [Indexed: 10/06/2023]
Abstract
The mammalian HORMA domain-containing protein 1 (HORMAD1) regulates DNA mismatch repair and homologous recombination (HR) repair in many cancers. Here, we show that the structure of human HORMAD1 adopts a self-closed conformation and displays an intra-molecular HORMA domain-closure motif interaction mode. Structural and biochemical data suggest that the interaction modes of the peptide motifs from HORMAD2 and MCM9 with HORMAD1 are highly similar to that of HORMAD1 own closure motif. The peptide motifs from diverse binding partners of HORMAD1 share a conserved Ser-Glu-Pro sequence. Additionally, structural comparison unveiled the HORMA-peptide motif interaction mode diversity among HORMA-containing proteins. Finally, cell-based assays revealed that this HORMA-closure motif interaction pattern contributes to DNA mismatch repair and is required for HORMAD1-dependent HR repair. Together, our results provide structural and biochemical insights into the common theme and functional plasticity of the HORMA domain-containing protein family, and also reveal a universal regulation mechanism for HORMAD1.
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Affiliation(s)
- Hong Wang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071002, China
| | - Rong Xie
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071002, China; Department of Biochemistry and Molecular Biology, School of Basic Medicine and Life Science, Hainan Medical College, Haikou, Hainan 571199, China
| | - Fumin Niu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071002, China
| | - Qian Yang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071002, China
| | - Lina An
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071002, China
| | - Chen Wu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071002, China.
| | - Xiuhua Liu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071002, China.
| | - Xiaoyun Yang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071002, China; Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
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5
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Herrera LR, Johnson RA, McGlynn K, Gibbs ZA, Davis AJ, Whitehurst AW. The cancer testes antigen, HORMAD1, limits genomic instability in cancer cells by protecting stalled replication forks. J Biol Chem 2023; 299:105348. [PMID: 37838177 PMCID: PMC10656231 DOI: 10.1016/j.jbc.2023.105348] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/18/2023] [Accepted: 10/01/2023] [Indexed: 10/16/2023] Open
Abstract
Tumors anomalously induce the expression of meiotic genes, which are otherwise restricted only to developing gametes. If and how these aberrantly expressed meiotic proteins influence DNA metabolism is not clear, but could have important implications for how tumors acquire and mitigate genomic instability. HORMAD1 is a highly conserved meiotic protein that is frequently expressed in lung adenocarincoma where its expression correlates with reduced patient survival and increased mutation burden. Here, we find that HORMAD1 associates with the replisome and is critical for protecting stalled DNA replication forks. Loss of HORMAD1 leads to nascent DNA strand degradation, an event which is mediated by the MRE11-DNA2-BLM pathway. We find that these phenotypes are due to limited RAD51 loading onto stalled replication forks in the absence of HORMAD1. Ultimately, loss of HORMAD1 leads to increased DNA breaks and chromosomal defects, which is exacerbated dramatically by induction of replication stress. Tumor cells proliferate despite encountering chronic replication stress, placing them on the precipice of catastrophic genomic damage. Our data support the hypothesis that the aberrant expression of HORMAD1 is engaged to attenuate the accumulation of excessive DNA damage due to chronic replication stress, which may otherwise lead to accumulation of toxic levels of genomic instability.
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Affiliation(s)
- Luis Reza Herrera
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Ronnesha A Johnson
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Kathleen McGlynn
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Zane A Gibbs
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Anthony J Davis
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, Texas, USA.
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6
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Dai LJ, Ma D, Xu YZ, Li M, Li YW, Xiao Y, Jin X, Wu SY, Zhao YX, Wang H, Yang WT, Jiang YZ, Shao ZM. Molecular features and clinical implications of the heterogeneity in Chinese patients with HER2-low breast cancer. Nat Commun 2023; 14:5112. [PMID: 37607916 PMCID: PMC10444861 DOI: 10.1038/s41467-023-40715-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 08/04/2023] [Indexed: 08/24/2023] Open
Abstract
The molecular heterogeneity and distinct features of HER2-low breast cancers, particularly in the Chinese population, are not well understood, limiting its precise management in the era of antibody‒drug conjugates. To address this issue, we established a cohort of 434 Chinese patients with HER2-low breast cancer (433 female and one male) and integrated genomic, transcriptomic, proteomic, and metabolomic profiling data. In this cohort, HER2-low tumors are more distinguished from HER2-0 tumors in the hormone receptor-negative subgroup. Within HER2-low tumors, significant interpatient heterogeneity also exists in the hormone receptor-negative subgroup: basal-like tumors resemble HER2-0 disease, and non-basal-like HER2-low tumors mimic HER2-positive disease. These non-basal-like HER2-low tumors are enriched in the HER2-enriched subtype and the luminal androgen receptor subtype and feature PIK3CA mutation, FGFR4/PTK6/ERBB4 overexpression and lipid metabolism activation. Among hormone receptor-positive tumors, HER2-low tumors show less loss/deletion in 17q peaks than HER2-0 tumors. In this work, we reveal the heterogeneity of HER2-low breast cancers and emphasize the need for more precise stratification regarding hormone receptor status and molecular subtype.
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Affiliation(s)
- Lei-Jie Dai
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Ding Ma
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Yu-Zheng Xu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Ming Li
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Yu-Wei Li
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yi Xiao
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xi Jin
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Song-Yang Wu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Ya-Xin Zhao
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Han Wang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Wen-Tao Yang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
| | - Yi-Zhou Jiang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Zhi-Ming Shao
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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7
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Llano E, Pendás AM. Synaptonemal Complex in Human Biology and Disease. Cells 2023; 12:1718. [PMID: 37443752 PMCID: PMC10341275 DOI: 10.3390/cells12131718] [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: 05/23/2023] [Revised: 06/16/2023] [Accepted: 06/18/2023] [Indexed: 07/15/2023] Open
Abstract
The synaptonemal complex (SC) is a meiosis-specific multiprotein complex that forms between homologous chromosomes during prophase of meiosis I. Upon assembly, the SC mediates the synapses of the homologous chromosomes, leading to the formation of bivalents, and physically supports the formation of programmed double-strand breaks (DSBs) and their subsequent repair and maturation into crossovers (COs), which are essential for genome haploidization. Defects in the assembly of the SC or in the function of the associated meiotic recombination machinery can lead to meiotic arrest and human infertility. The majority of proteins and complexes involved in these processes are exclusively expressed during meiosis or harbor meiosis-specific subunits, although some have dual functions in somatic DNA repair and meiosis. Consistent with their functions, aberrant expression and malfunctioning of these genes have been associated with cancer development. In this review, we focus on the significance of the SC and their meiotic-associated proteins in human fertility, as well as how human genetic variants encoding for these proteins affect the meiotic process and contribute to infertility and cancer development.
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Affiliation(s)
- Elena Llano
- Departamento Fisiología y Farmacología, Universidad de Salamanca, 37007 Salamanca, Spain
- Molecular Mechanisms Program, Centro de Investigación del Cáncer, Instituto de Biologıía Molecular y Celular del Cáncer, CSIC-Universidad de Salamanca, 37007 Salamanca, Spain;
| | - Alberto M. Pendás
- Molecular Mechanisms Program, Centro de Investigación del Cáncer, Instituto de Biologıía Molecular y Celular del Cáncer, CSIC-Universidad de Salamanca, 37007 Salamanca, Spain;
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8
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Gantchev J, Messina-Pacheco J, Martínez Villarreal A, Ramchatesingh B, Lefrançois P, Xie P, Amar L, Xu HH, Raveendra K, Sikorski D, Guerra Ordaz DJ, Gill RPK, Lambert M, Litvinov IV. Ectopically Expressed Meiosis-Specific Cancer Testis Antigen HORMAD1 Promotes Genomic Instability in Squamous Cell Carcinomas. Cells 2023; 12:1627. [PMID: 37371097 DOI: 10.3390/cells12121627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/29/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Genomic instability is a prominent hallmark of cancer, however the mechanisms that drive and sustain this process remain elusive. Research demonstrates that numerous cancers with increased levels of genomic instability ectopically express meiosis-specific genes and undergo meiomitosis, the clash of mitotic and meiotic processes. These meiotic genes may represent novel therapeutic targets for the treatment of cancer. We studied the relationship between the expression of the meiosis protein HORMAD1 and genomic instability in squamous cell carcinomas (SCCs). First, we assessed markers of DNA damage and genomic instability following knockdown and overexpression of HORMAD1 in different cell lines representing SCCs and epithelial cancers. shRNA-mediated depletion of HORMAD1 expression resulted in increased genomic instability, DNA damage, increased sensitivity to etoposide, and decreased expression of DNA damage response/repair genes. Conversely, overexpression of HORMAD1 exhibited protective effects leading to decreased DNA damage, enhanced survival and decreased sensitivity to etoposide. Furthermore, we identified a meiotic molecular pathway that regulates HORMAD1 expression by targeting the upstream meiosis transcription factor STRA8. Our results highlight a specific relationship between HORMAD1 and genomic instability in SCCs, suggesting that selectively inhibiting HORMAD1, possibly, through STRA8 signaling, may provide a new paradigm of treatment options for HORMAD1-expressing SCCs.
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Affiliation(s)
- Jennifer Gantchev
- Research Institute of McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Julia Messina-Pacheco
- Research Institute of McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Department of Pathology, McGill University, Montreal, QC H4A 3J1, Canada
| | | | | | - Philippe Lefrançois
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Pingxing Xie
- Division of Dermatology, Department of Medicine, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Laetitia Amar
- Faculty of Medicine, McGill University, Montreal, QC H3G 2M1, Canada
| | - Hong Hao Xu
- Faculty of Medicine, Laval University, Quebec City, QC G1V 0A6, Canada
| | | | - Daniel Sikorski
- Faculty of Medicine, McGill University, Montreal, QC H3G 2M1, Canada
| | | | | | - Marine Lambert
- Research Institute of McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Ivan V Litvinov
- Research Institute of McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Division of Dermatology, Department of Medicine, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
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9
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Zhu Y, Liu Z, Gui L, Yun W, Mao C, Deng R, Yao Y, Yu Q, Feng J, Ma H, Bao W. Inhibition of CXorf56 promotes PARP inhibitor-induced cytotoxicity in triple-negative breast cancer. NPJ Breast Cancer 2023; 9:34. [PMID: 37156759 PMCID: PMC10167262 DOI: 10.1038/s41523-023-00540-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 04/11/2023] [Indexed: 05/10/2023] Open
Abstract
Poly(ADP-ribose) polymerase inhibitors (PARPis) induce DNA lesions that preferentially kill homologous recombination (HR)-deficient breast cancers induced by BRCA mutations, which exhibit a low incidence in breast cancer, thereby limiting the benefits of PARPis. Additionally, breast cancer cells, particularly triple-negative breast cancer (TNBC) cells, exhibit HR and PARPi resistance. Therefore, targets must be identified for inducing HR deficiency and sensitizing cancer cells to PARPis. Here, we reveal that CXorf56 protein increased HR repair in TNBC cells by interacting with the Ku70 DNA-binding domain, reducing Ku70 recruitment and promoting RPA32, BRCA2, and RAD51 recruitment to sites of DNA damage. Knockdown of CXorf56 protein suppressed HR in TNBC cells, specifically during the S and G2 phases, and increased cell sensitivity to olaparib in vitro and in vivo. Clinically, CXorf56 protein was upregulated in TNBC tissues and associated with aggressive clinicopathological characteristics and poor survival. All these findings indicate that treatment designed to inhibit CXorf56 protein in TNBC combined with PARPis may overcome drug resistance and expand the application of PARPis to patients with non-BRCA mutantion.
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Affiliation(s)
- Ying Zhu
- Department of General Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Zhixian Liu
- Department of Pharmacy, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Liang Gui
- Department of General Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Wen Yun
- Department of General Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Changfei Mao
- Department of General Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Rong Deng
- Department of General Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Yufeng Yao
- Department of General Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Qiao Yu
- Department of General Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jifeng Feng
- Department of General Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China.
| | - Hongxia Ma
- Department of Epidemiology, Center for Global Health, School of Public Health, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.
| | - Wei Bao
- Department of Pathology, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China.
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10
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Nin DS, Deng LW. Biology of Cancer-Testis Antigens and Their Therapeutic Implications in Cancer. Cells 2023; 12:cells12060926. [PMID: 36980267 PMCID: PMC10047177 DOI: 10.3390/cells12060926] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Tumour-specific antigens have been an area of interest in cancer therapy since their discovery in the middle of the 20th century. In the era of immune-based cancer therapeutics, redirecting our immune cells to target these tumour-specific antigens has become even more relevant. Cancer-testis antigens (CTAs) are a class of antigens with an expression specific to the testis and cancer cells. CTAs have also been demonstrated to be expressed in a wide variety of cancers. Due to their frequency and specificity of expression in a multitude of cancers, CTAs have been particularly attractive as cancer-specific therapeutic targets. There is now a rapid expansion of CTAs being identified and many studies have been conducted to correlate CTA expression with cancer and therapy-resistant phenotypes. Furthermore, there is an increasing number of clinical trials involving using some of these CTAs as molecular targets in pharmacological and immune-targeted therapeutics for various cancers. This review will summarise the current knowledge of the biology of known CTAs in tumorigenesis and the regulation of CTA genes. CTAs as molecular targets and the therapeutic implications of these CTA-targeted anticancer strategies will also be discussed.
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Affiliation(s)
- Dawn Sijin Nin
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD 7, 8 Medical Drive, Singapore 117596, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
| | - Lih-Wen Deng
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD 7, 8 Medical Drive, Singapore 117596, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
- National University Cancer Institute, National University Health System, 5 Lower Kent Ridge Road, Singapore 119074, Singapore
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11
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Anand J, Chiou L, Sciandra C, Zhang X, Hong J, Wu D, Zhou P, Vaziri C. Roles of trans-lesion synthesis (TLS) DNA polymerases in tumorigenesis and cancer therapy. NAR Cancer 2023; 5:zcad005. [PMID: 36755961 PMCID: PMC9900426 DOI: 10.1093/narcan/zcad005] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/10/2022] [Accepted: 01/30/2023] [Indexed: 02/08/2023] Open
Abstract
DNA damage tolerance and mutagenesis are hallmarks and enabling characteristics of neoplastic cells that drive tumorigenesis and allow cancer cells to resist therapy. The 'Y-family' trans-lesion synthesis (TLS) DNA polymerases enable cells to replicate damaged genomes, thereby conferring DNA damage tolerance. Moreover, Y-family DNA polymerases are inherently error-prone and cause mutations. Therefore, TLS DNA polymerases are potential mediators of important tumorigenic phenotypes. The skin cancer-propensity syndrome xeroderma pigmentosum-variant (XPV) results from defects in the Y-family DNA Polymerase Pol eta (Polη) and compensatory deployment of alternative inappropriate DNA polymerases. However, the extent to which dysregulated TLS contributes to the underlying etiology of other human cancers is unclear. Here we consider the broad impact of TLS polymerases on tumorigenesis and cancer therapy. We survey the ways in which TLS DNA polymerases are pathologically altered in cancer. We summarize evidence that TLS polymerases shape cancer genomes, and review studies implicating dysregulated TLS as a driver of carcinogenesis. Because many cancer treatment regimens comprise DNA-damaging agents, pharmacological inhibition of TLS is an attractive strategy for sensitizing tumors to genotoxic therapies. Therefore, we discuss the pharmacological tractability of the TLS pathway and summarize recent progress on development of TLS inhibitors for therapeutic purposes.
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Affiliation(s)
- Jay Anand
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
| | - Lilly Chiou
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Carly Sciandra
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xingyuan Zhang
- Department of Biostatistics, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3101 McGavran-Greenberg Hall, Chapel Hill, NC 27599, USA
| | - Jiyong Hong
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Di Wu
- Department of Biostatistics, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3101 McGavran-Greenberg Hall, Chapel Hill, NC 27599, USA
| | - Pei Zhou
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
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12
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Herrera LR, McGlynn K, Gibbs ZA, Davis AJ, Whitehurst AW. The Cancer Testes Antigen, HORMAD1, is a Tumor-Specific Replication Fork Protection Factor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526348. [PMID: 36778501 PMCID: PMC9915569 DOI: 10.1101/2023.01.31.526348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Tumors frequently activate the expression of genes that are only otherwise required for meiosis. HORMAD1, which is essential for meiotic recombination in multiple species, is expressed in over 50% of human lung adenocarcinoma cells (LUAD). We previously found that HORMAD1 promotes DNA double strand break (DSB) repair in LUAD. Here, we report that HORMAD1 takes on an additional role in protecting genomic integrity. Specifically, we find HORMAD1 is critical for protecting stalled DNA replication forks in LUAD. Loss of HORMAD1 leads to nascent DNA degradation, an event which is mediated by the MRE11-DNA2-BLM pathway. Moreover, following exogenous induction of DNA replication stress, HORMAD1 deleted cells accumulate single stranded DNA (ssDNA). We find that these phenotypes are the result of a lack of RAD51 and BRCA2 loading onto stalled replication forks. Ultimately, loss of HORMAD1 leads to increased DSBs and chromosomal aberrations in response to replication stress. Collectively, our data support a model where HORMAD1 expression is selected to mitigate DNA replication stress, which would otherwise induce deleterious genomic instability.
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13
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Tarantino D, Walker C, Weekes D, Pemberton H, Davidson K, Torga G, Frankum J, Mendes-Pereira AM, Prince C, Ferro R, Brough R, Pettitt SJ, Lord CJ, Grigoriadis A, Nj Tutt A. Functional screening reveals HORMAD1-driven gene dependencies associated with translesion synthesis and replication stress tolerance. Oncogene 2022; 41:3969-3977. [PMID: 35768547 PMCID: PMC9355871 DOI: 10.1038/s41388-022-02369-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 05/21/2022] [Accepted: 05/30/2022] [Indexed: 11/09/2022]
Abstract
HORMAD1 expression is usually restricted to germline cells, but it becomes mis-expressed in epithelial cells in ~60% of triple-negative breast cancers (TNBCs), where it is associated with elevated genomic instability (1). HORMAD1 expression in TNBC is bimodal with HORMAD1-positive TNBC representing a biologically distinct disease group. Identification of HORMAD1-driven genetic dependencies may uncover novel therapies for this disease group. To study HORMAD1-driven genetic dependencies, we generated a SUM159 cell line model with doxycycline-inducible HORMAD1 that replicated genomic instability phenotypes seen in HORMAD1-positive TNBC (1). Using small interfering RNA screens, we identified candidate genes whose depletion selectively inhibited the cellular growth of HORMAD1-expressing cells. We validated five genes (ATR, BRIP1, POLH, TDP1 and XRCC1), depletion of which led to reduced cellular growth or clonogenic survival in cells expressing HORMAD1. In addition to the translesion synthesis (TLS) polymerase POLH, we identified a HORMAD1-driven dependency upon additional TLS polymerases, namely POLK, REV1, REV3L and REV7. Our data confirms that out-of-context somatic expression of HORMAD1 can lead to genomic instability and reveals that HORMAD1 expression induces dependencies upon replication stress tolerance pathways, such as translesion synthesis. Our data also suggest that HORMAD1 expression could be a patient selection biomarker for agents targeting replication stress.
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Affiliation(s)
- Dalia Tarantino
- Breast Cancer Now Research Unit, King's College London, London, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Callum Walker
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Daniel Weekes
- Breast Cancer Now Research Unit, King's College London, London, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Helen Pemberton
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Kathryn Davidson
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Gonzalo Torga
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Jessica Frankum
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Ana M Mendes-Pereira
- Breast Cancer Now Research Unit, King's College London, London, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Cynthia Prince
- Breast Cancer Now Research Unit, King's College London, London, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Riccardo Ferro
- Breast Cancer Now Research Unit, King's College London, London, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Rachel Brough
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Stephen J Pettitt
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Christopher J Lord
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Anita Grigoriadis
- Breast Cancer Now Research Unit, King's College London, London, UK
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Andrew Nj Tutt
- Breast Cancer Now Research Unit, King's College London, London, UK.
- School of Cancer and Pharmaceutical Sciences, King's Health Partners AHSC, Faculty of Life Sciences and Medicine, King's College London, London, UK.
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
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14
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Takiyama T, Sera T, Nakamura M, Hoshino M, Uesugi K, Horike SI, Meguro-Horike M, Bessho R, Takiyama Y, Kitsunai H, Takeda Y, Sawamoto K, Yagi N, Nishikawa Y, Takiyama Y. A maternal high-fat diet induces fetal origins of NASH-HCC in mice. Sci Rep 2022; 12:13136. [PMID: 35907977 PMCID: PMC9338981 DOI: 10.1038/s41598-022-17501-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 07/26/2022] [Indexed: 11/09/2022] Open
Abstract
Maternal overnutrition affects offspring susceptibility to nonalcoholic steatohepatitis (NASH). Male offspring from high-fat diet (HFD)-fed dams developed a severe form of NASH, leading to highly vascular tumor formation. The cancer/testis antigen HORMA domain containing protein 1 (HORMAD1), one of 146 upregulated differentially expressed genes in fetal livers from HFD-fed dams, was overexpressed with hypoxia-inducible factor 1 alpha (HIF-1alpha) in hepatoblasts and in NASH-based hepatocellular carcinoma (HCC) in offspring from HFD-fed dams at 15 weeks old. Hypoxia substantially increased Hormad1 expression in primary mouse hepatocytes. Despite the presence of three putative hypoxia response elements within the mouse Hormad1 gene, the Hif-1alpha siRNA only slightly decreased hypoxia-induced Hormad1 mRNA expression. In contrast, N-acetylcysteine, but not rotenone, inhibited hypoxia-induced Hormad1 expression, indicating its dependency on nonmitochondrial reactive oxygen species production. Synchrotron-based phase-contrast micro-CT of the fetuses from HFD-fed dams showed significant enlargement of the liver accompanied by a consistent size of the umbilical vein, which may cause hypoxia in the fetal liver. Based on these findings, a maternal HFD induces fetal origins of NASH/HCC via hypoxia, and HORMAD1 is a potential therapeutic target for NASH/HCC.
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Affiliation(s)
- Takao Takiyama
- Division of Diabetes, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Toshihiro Sera
- Department of Mechanical Engineering, Faculty of Engineering, Kyushu University, Fukuoka, Japan
| | - Masanori Nakamura
- Department of Electrical and Mechanical Engineering, Nagoya Institute of Technology, Nagoya, Japan
| | - Masato Hoshino
- Japan Synchrotron Radiation Research Institute, Sayo-cho, Japan
| | - Kentaro Uesugi
- Japan Synchrotron Radiation Research Institute, Sayo-cho, Japan
| | - Shin-Ichi Horike
- Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
| | | | - Ryoichi Bessho
- Division of Diabetes, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Yuri Takiyama
- Division of Diabetes, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Hiroya Kitsunai
- Division of Diabetes, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Yasutaka Takeda
- Division of Diabetes, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Kazuki Sawamoto
- Division of Diabetes, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Naoto Yagi
- Japan Synchrotron Radiation Research Institute, Sayo-cho, Japan
| | - Yuji Nishikawa
- Department of Pathology, Asahikawa Medical University, Asahikawa, Japan
| | - Yumi Takiyama
- Division of Diabetes, Department of Medicine, Asahikawa Medical University, Asahikawa, Japan.
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15
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Raina VB, Schoot Uiterkamp M, Vader G. Checkpoint control in meiotic prophase: Idiosyncratic demands require unique characteristics. Curr Top Dev Biol 2022; 151:281-315. [PMID: 36681474 DOI: 10.1016/bs.ctdb.2022.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Chromosomal transactions such as replication, recombination and segregation are monitored by cell cycle checkpoint cascades. These checkpoints ensure the proper execution of processes that are needed for faithful genome inheritance from one cell to the next, and across generations. In meiotic prophase, a specialized checkpoint monitors defining events of meiosis: programmed DNA break formation, followed by dedicated repair through recombination based on interhomolog (IH) crossovers. This checkpoint shares molecular characteristics with canonical DNA damage checkpoints active during somatic cell cycles. However, idiosyncratic requirements of meiotic prophase have introduced unique features in this signaling cascade. In this review, we discuss the unique features of the meiotic prophase checkpoint. While being related to canonical DNA damage checkpoint cascades, the meiotic prophase checkpoint also shows similarities with the spindle assembly checkpoint (SAC) that guards chromosome segregation. We highlight these emerging similarities in the signaling logic of the checkpoints that govern meiotic prophase and chromosome segregation, and how thinking of these similarities can help us better understand meiotic prophase control. We also discuss work showing that, when aberrantly expressed, components of the meiotic prophase checkpoint might alter DNA repair fidelity and chromosome segregation in cancer cells. Considering checkpoint function in light of demands imposed by the special characteristics of meiotic prophase helps us understand checkpoint integration into the meiotic cell cycle machinery.
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Affiliation(s)
- Vivek B Raina
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York City, NY, United States
| | - Maud Schoot Uiterkamp
- Center for Reproductive Medicine, Reproductive Biology Laboratory, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands; Section of Oncogenetics, Department of Human Genetics, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Gerben Vader
- Center for Reproductive Medicine, Reproductive Biology Laboratory, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands; Section of Oncogenetics, Department of Human Genetics, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands.
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16
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Wang Y, Duan M, Peng Z, Fan R, He Y, Zhang H, Xiong W, Jiang W. Advances of DNA Damage Repair-Related Drugs and Combination With Immunotherapy in Tumor Treatment. Front Immunol 2022; 13:854730. [PMID: 35281059 PMCID: PMC8904426 DOI: 10.3389/fimmu.2022.854730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 01/31/2022] [Indexed: 12/21/2022] Open
Abstract
Cancer therapy has been an important and popular area in cancer research. With medical technology developing, the appearance of various targeted drugs and immunotherapy offer more choices to cancer treatment. With the increase in drug use, people have found more and more cases in which tumors are resistant to DNA damage repair (DDR)-based drugs. Recently, the concept of combination therapy has been brought up in cancer research. It takes advantages of combining two or more therapies with different mechanisms, aiming to benefit from the synergistic effects and finally rescue patients irresponsive to single therapies. Combination therapy has the potential to improve current treatment of refractory and drug-resistant tumors. Among the methods used in combination therapy, DDR is one of the most popular methods. Recent studies have shown that combined application of DDR-related drugs and immunotherapies significantly improve the therapeutic outcomes of malignant tumors, especially solid tumors.
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Affiliation(s)
- Yumin Wang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
| | - Meihan Duan
- School of Medicine, Tsinghua University, Beijing, China
| | - Zhouying Peng
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
| | - Ruohao Fan
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Yuxiang He
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China.,Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - Hua Zhang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Wei Xiong
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Weihong Jiang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
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17
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Liu K, Cheng L, Zhu K, Wang J, Shu Q. The cancer/testis antigen HORMAD1 mediates epithelial-mesenchymal transition to promote tumor growth and metastasis by activating the Wnt/β-catenin signaling pathway in lung cancer. Cell Death Dis 2022; 8:136. [PMID: 35347116 PMCID: PMC8960869 DOI: 10.1038/s41420-022-00946-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/26/2022] [Accepted: 03/15/2022] [Indexed: 01/03/2023]
Abstract
The cancer/testis antigen HORMAD1 is a mechanical regulator that modulates DNA homologous recombination repair and mismatch repair in multiple cancers. However, the role and underlying regulatory mechanisms of HORMAD1 in lung cancer progression remain unknown. Here, we show that HORMAD1 is upregulated in lung adenocarcinoma tissues compared with adjacent normal tissues and that aberrant HORMAD1 expression predicts poor prognosis. We further demonstrate that HORMAD1 promotes the proliferation, migration and invasion of lung cancer cells both in vitro and in vivo by inducing epithelial-mesenchymal transition (EMT). Subsequent mechanistic investigations revealed that HORMAD1 activates the Wnt/β-catenin pathway by increasing the phosphorylation level of AKT at Ser473 and that of GSK-3β at Ser9 in lung cancer cells, which decreases the phosphorylation level of β-catenin at Ser33/37/Thr41, enhances the cytoplasmic and nuclear accumulation of β-catenin and its transcriptional activity, consequently promoting EMT and lung cancer growth and metastasis. Our results provide new insights into the functional role and regulatory mechanism of HORMAD1 in lung cancer progression and identify HORMAD1 as a promising prognostic biomarker and therapeutic target for lung cancer.
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Affiliation(s)
- Kang Liu
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, China
| | - Li Cheng
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, Zhejiang Chinese Medical University, Hangzhou, China
| | - Kun Zhu
- Department of Pathology, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jinhu Wang
- Department of Surgical Oncology, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Qiang Shu
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, China. .,Department of Pediatric Surgery, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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18
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Lingg L, Rottenberg S, Francica P. Meiotic Genes and DNA Double Strand Break Repair in Cancer. Front Genet 2022; 13:831620. [PMID: 35251135 PMCID: PMC8895043 DOI: 10.3389/fgene.2022.831620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/02/2022] [Indexed: 12/16/2022] Open
Abstract
Tumor cells show widespread genetic alterations that change the expression of genes driving tumor progression, including genes that maintain genomic integrity. In recent years, it has become clear that tumors frequently reactivate genes whose expression is typically restricted to germ cells. As germ cells have specialized pathways to facilitate the exchange of genetic information between homologous chromosomes, their aberrant regulation influences how cancer cells repair DNA double strand breaks (DSB). This drives genomic instability and affects the response of tumor cells to anticancer therapies. Since meiotic genes are usually transcriptionally repressed in somatic cells of healthy tissues, targeting aberrantly expressed meiotic genes may provide a unique opportunity to specifically kill cancer cells whilst sparing the non-transformed somatic cells. In this review, we highlight meiotic genes that have been reported to affect DSB repair in cancers derived from somatic cells. A better understanding of their mechanistic role in the context of homology-directed DNA repair in somatic cancers may provide useful insights to find novel vulnerabilities that can be targeted.
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Affiliation(s)
- Lea Lingg
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Cancer Therapy Resistance Cluster, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Sven Rottenberg
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Cancer Therapy Resistance Cluster, Department for BioMedical Research, University of Bern, Bern, Switzerland
- Bern Center for Precision Medicine, University of Bern, Bern, Switzerland
- *Correspondence: Sven Rottenberg, ; Paola Francica,
| | - Paola Francica
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Cancer Therapy Resistance Cluster, Department for BioMedical Research, University of Bern, Bern, Switzerland
- *Correspondence: Sven Rottenberg, ; Paola Francica,
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19
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Jensch A, Lopes MB, Vinga S, Radde N. ROSIE: RObust Sparse ensemble for outlIEr detection and gene selection in cancer omics data. Stat Methods Med Res 2022; 31:947-958. [PMID: 35072570 PMCID: PMC9014683 DOI: 10.1177/09622802211072456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The extraction of novel information from omics data is a challenging task, in
particular, since the number of features (e.g. genes) often far exceeds the
number of samples. In such a setting, conventional parameter estimation leads to
ill-posed optimization problems, and regularization may be required. In
addition, outliers can largely impact classification accuracy. Here we introduce ROSIE, an ensemble classification approach, which combines
three sparse and robust classification methods for outlier detection and feature
selection and further performs a bootstrap-based validity check. Outliers of
ROSIE are determined by the rank product test using outlier rankings of all
three methods, and important features are selected as features commonly selected
by all methods. We apply ROSIE to RNA-Seq data from The Cancer Genome Atlas (TCGA) to classify
observations into Triple-Negative Breast Cancer (TNBC) and non-TNBC tissue
samples. The pre-processed dataset consists of 16,600 genes and more than 1,000 samples. We demonstrate that ROSIE selects important features
and outliers in a robust way. Identified outliers are concordant with the
distribution of the commonly selected genes by the three methods, and results
are in line with other independent studies. Furthermore, we discuss the
association of some of the selected genes with the TNBC subtype in other
investigations. In summary, ROSIE constitutes a robust and sparse procedure to
identify outliers and important genes through binary classification. Our
approach is ad hoc applicable to other datasets, fulfilling the overall goal of
simultaneously identifying outliers and candidate disease biomarkers to the
targeted in therapy research and personalized medicine frameworks.
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Affiliation(s)
- Antje Jensch
- Institute for Systems Theory and Automatic Control, 9149University of Stuttgart, Germany
| | - Marta B Lopes
- Center for Mathematics and Applications (CMA), NOVA School of Science and Technology, Caparica, Portugal.,NOVA Laboratory for Computer Science and Informatics (NOVA LINCS), NOVA School of Science and Technology, Caparica, Portugal
| | - Susana Vinga
- INESC-ID, Instituto Superior Técnico, 72971Universidade de Lisboa, Portugal.,IDMEC, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Nicole Radde
- Institute for Systems Theory and Automatic Control, 9149University of Stuttgart, Germany
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20
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Gu Y, Desai A, Corbett KD. Evolutionary Dynamics and Molecular Mechanisms of HORMA Domain Protein Signaling. Annu Rev Biochem 2022; 91:541-569. [PMID: 35041460 DOI: 10.1146/annurev-biochem-090920-103246] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Controlled assembly and disassembly of multi-protein complexes is central to cellular signaling. Proteins of the widespread and functionally diverse HORMA family nucleate assembly of signaling complexes by binding short peptide motifs through a distinctive safety-belt mechanism. HORMA proteins are now understood as key signaling proteins across kingdoms, serving as infection sensors in a bacterial immune system and playing central roles in eukaryotic cell cycle, genome stability, sexual reproduction, and cellular homeostasis pathways. Here, we describe how HORMA proteins' unique ability to adopt multiple conformational states underlies their functions in these diverse contexts. We also outline how a dedicated AAA+ ATPase regulator, Pch2/TRIP13, manipulates HORMA proteins' conformational states to activate or inactivate signaling in different cellular contexts. The emergence of Pch2/TRIP13 as a lynchpin for HORMA protein action in multiple genome-maintenance pathways accounts for its frequent misregulation in human cancers and highlights TRIP13 as a novel therapeutic target. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Yajie Gu
- Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, California, USA;
| | - Arshad Desai
- Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, California, USA; .,Section of Cell & Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California, USA.,Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, California, USA
| | - Kevin D Corbett
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
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21
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Wu SC, Münger K. Role and Clinical Utility of Cancer/Testis Antigens in Head and Neck Squamous Cell Carcinoma. Cancers (Basel) 2021; 13:cancers13225690. [PMID: 34830845 PMCID: PMC8616139 DOI: 10.3390/cancers13225690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/03/2021] [Accepted: 11/11/2021] [Indexed: 12/15/2022] Open
Abstract
Cancer/testis (CT) antigens exhibit selective expression predominantly in immunoprivileged tissues in non-pathological contexts but are aberrantly expressed in diverse cancers. Due to their expression pattern, they have historically been attractive targets for immunotherapies. A growing number of studies implicate CT antigens in almost all hallmarks of cancer, suggesting that they may act as cancer drivers. CT antigens are expressed in head and neck squamous cell carcinomas. However, their role in the pathogenesis of these cancers remains poorly studied. Given that CT antigens hold intriguing potential as therapeutic targets and as biomarkers for prognosis and that they can provide novel insights into oncogenic mechanisms, their further study in the context of head and squamous cell carcinoma is warranted.
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Affiliation(s)
- Sharon Changshan Wu
- Molecular Microbiology Program, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA;
| | - Karl Münger
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
- Correspondence:
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22
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Ryu WJ, Sohn JH. Molecular Targets and Promising Therapeutics of Triple-Negative Breast Cancer. Pharmaceuticals (Basel) 2021; 14:ph14101008. [PMID: 34681231 PMCID: PMC8540846 DOI: 10.3390/ph14101008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 12/11/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is one of the most heterogeneous diseases in solid tumors and has limited therapeutic options. Due to the lack of appropriate targetable markers, the mainstay therapeutic strategy for patients with TNBC has been chemotherapy for the last several decades. Indeed, TNBC tumors have no expression of estrogen receptor, progesterone receptor, or human epidermal growth factor receptor 2 (HER2); therefore, they do not respond to hormone therapy and HER2-targeted therapy. In this review paper, the molecular heterogeneities, possible therapeutic targets, and recently approved and upcoming drugs for TNBC will be summarized.
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Affiliation(s)
- Won-Ji Ryu
- Avison Biomedical Research Center, Yonsei University College of Medicine, Seoul 03722, Korea;
| | - Joo Hyuk Sohn
- Division of Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Korea
- Correspondence: ; Tel.: +82-02-2228-8135
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23
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Jay A, Reitz D, Namekawa SH, Heyer WD. Cancer testis antigens and genomic instability: More than immunology. DNA Repair (Amst) 2021; 108:103214. [PMID: 34481156 PMCID: PMC9196322 DOI: 10.1016/j.dnarep.2021.103214] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/13/2021] [Accepted: 08/14/2021] [Indexed: 12/29/2022]
Abstract
Cancer testis antigens or genes (CTA, CTG) are predominantly expressed in adult testes while silenced in most or all somatic tissues with sporadic expression in many human cancers. Concerted misexpression of numerous CTA/CTGs is rarely observed. This finding argues against the germ cell theory of cancer. A surprising number of CTA/CTGs are involved in meiotic chromosome metabolism and specifically in meiotic recombination. Recent discoveries with a group of CTGs established that their misexpression in somatic cells results in genomic instability by interfering with homologous recombination (HR), a DNA repair pathway for complex DNA damage such as DNA double-stranded breaks, interstrand crosslinks, and single-stranded DNA gaps. HR-deficient tumors have specific vulnerabilities and show synthetic lethality with inhibition of polyADP-ribose polymerase, opening the possibility that expression of CTA/CTGs that result in an HR-defect could be used as an additional biomarker for HR status. Here, we review the repertoire of CTA/CTGs focusing on a cohort that functions in meiotic chromosome metabolism by interrogating relevant cancer databases and discussing recent discoveries.
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Affiliation(s)
- Ash Jay
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, 95616-8665, USA
| | - Diedre Reitz
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, 95616-8665, USA
| | - Satoshi H Namekawa
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, 95616-8665, USA
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, 95616-8665, USA; Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, 95616-8665, USA.
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24
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Zong B, Sun L, Peng Y, Wang Y, Yu Y, Lei J, Zhang Y, Guo S, Li K, Liu S. HORMAD1 promotes docetaxel resistance in triple negative breast cancer by enhancing DNA damage tolerance. Oncol Rep 2021; 46:138. [PMID: 34036395 PMCID: PMC8165579 DOI: 10.3892/or.2021.8089] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/28/2021] [Indexed: 12/13/2022] Open
Abstract
HORMA domain‑containing protein 1 (HORMAD1), is normally expressed only in the germline, but is frequently re‑activated in human triple‑negative breast cancer (TNBC); however, its function in TNBC is largely unknown. In the present study, the expression and biological significance of HORMAD1 in human TNBC was evaluated. Bioinformatics analysis and reverse transcription‑quantitative PCR were used to evaluate HORMAD1 expression in datasets and cell lines. HORMAD1 protein expression was detected in TNBC samples using immunohistochemical assays, and the effect of HORMAD1 on cell proliferation was determined using Cell Counting Kit‑8, plate colony formation and standard growth curve assays. Cell cycle, reactive oxygen species (ROS) and apoptosis analyses were conducted using flow cytometry. The activity of caspases was measured using caspase activity assay kit. The levels of key apoptosis regulators and autophagy markers were detected by western blot analysis. TNBC cell survival and apoptosis were not influenced by small interfering RNA targeting HORMAD1 alone; however, HORMAD1 knockdown enhanced autophagy and docetaxel (Doc)‑induced apoptosis, compared with the control group. Furthermore, higher ROS levels and caspase‑3, ‑8 and ‑9 activity were detected in MDA‑MB‑436 TNBC cells with HORMAD1 knockdown upon exposure to Doc. The levels of the induced DNA damage marker γH2AX were also higher, while those of the DNA repair protein RAD51 were lower in TNBC cells with HORMAD1 knockdown compared with the controls. Furthermore, the expression of the autophagy marker P62 was enhanced in MDA‑MB‑231 cells in response to HORMAD1 overexpression. Notably, Doc‑induced apoptosis was similarly increased by both HORMAD1 overexpression and treatment with the autophagy inhibitor, 3‑methyladenine (3MA); however, the Doc‑induced increase in autophagy was not inhibited by 3MA. The present data indicated that HORMAD1 was involved in autophagy and that the inhibition of autophagy can partially enhance the induction of apoptosis by Doc. The role of HORMAD1 in the DNA damage tolerance of tumor cells may be the main reason for Doc resistance; hence, HORMAD1 could be an important therapeutic target in TNBC.
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Affiliation(s)
- Beige Zong
- Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, P.R. China
- Chongqing City Key Lab of Translational Medical Research in Cognitive Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Lu Sun
- Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, P.R. China
| | - Yang Peng
- Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, P.R. China
- Chongqing City Key Lab of Translational Medical Research in Cognitive Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Yihua Wang
- Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, P.R. China
| | - Yu Yu
- Department of Pathology, Chongqing Medical University, Chongqing 400015, P.R. China
| | - Jinwei Lei
- Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, P.R. China
- Chongqing City Key Lab of Translational Medical Research in Cognitive Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Yingzi Zhang
- Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, P.R. China
- Chongqing City Key Lab of Translational Medical Research in Cognitive Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Shipeng Guo
- Chongqing City Key Lab of Translational Medical Research in Cognitive Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Kang Li
- Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, P.R. China
- Chongqing City Key Lab of Translational Medical Research in Cognitive Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Shengchun Liu
- Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, P.R. China
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25
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Chen C, Gao D, Huo J, Qu R, Guo Y, Hu X, Luo L. Multiomics analysis reveals CT83 is the most specific gene for triple negative breast cancer and its hypomethylation is oncogenic in breast cancer. Sci Rep 2021; 11:12172. [PMID: 34108519 PMCID: PMC8190062 DOI: 10.1038/s41598-021-91290-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 05/25/2021] [Indexed: 02/05/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is a highly aggressive breast cancer (BrC) subtype lacking effective therapeutic targets currently. The development of multi-omics databases facilities the identification of core genes for TNBC. Using TCGA-BRCA and METABRIC datasets, we identified CT83 as the most TNBC-specific gene. By further integrating FUSCC-TNBC, CCLE, TCGA pan-cancer, Expression Atlas, and Human Protein Atlas datasets, we found CT83 is frequently activated in TNBC and many other cancers, while it is always silenced in non-TNBC, 120 types of normal non-testis tissues, and 18 types of blood cells. Notably, according to the TCGA-BRCA methylation data, hypomethylation on chromosome X 116,463,019 to 116,463,039 is significantly correlated with the abnormal activation of CT83 in BrC. Using Kaplan-Meier Plotter, we demonstrated that activated CT83 is significantly associated with unfavorably overall survival in BrC and worse outcomes in some other cancers. Furthermore, GSEA suggested that the abnormal activation of CT83 in BrC is probably oncogenic by triggering the activation of cell cycle signaling. Meanwhile, we also noticed copy number variations and mutations of CT83 are quite rare in any cancer type, and its role in immune infiltration is not significant. In summary, we highlighted the significance of CT83 for TNBC and presented a comprehensive bioinformatics strategy for single-gene analysis in cancer.
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Affiliation(s)
- Chen Chen
- grid.452884.7Breast and Thyroid Center, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Fenghuang N Rd, Zunyi, 563000 Guizhou China
| | - Dan Gao
- grid.452884.7Breast and Thyroid Center, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Fenghuang N Rd, Zunyi, 563000 Guizhou China
| | - Jinlong Huo
- grid.452884.7Breast and Thyroid Center, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Fenghuang N Rd, Zunyi, 563000 Guizhou China
| | - Rui Qu
- grid.452884.7Breast and Thyroid Center, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Fenghuang N Rd, Zunyi, 563000 Guizhou China
| | - Youming Guo
- grid.452884.7Breast and Thyroid Center, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Fenghuang N Rd, Zunyi, 563000 Guizhou China
| | - Xiaochi Hu
- grid.452884.7Breast and Thyroid Center, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Fenghuang N Rd, Zunyi, 563000 Guizhou China
| | - Libo Luo
- grid.452884.7Breast and Thyroid Center, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Fenghuang N Rd, Zunyi, 563000 Guizhou China
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26
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A survey of cancer genome signatures identifies genes connected to distinct chromosomal instability phenotypes. THE PHARMACOGENOMICS JOURNAL 2021; 21:390-401. [PMID: 33731882 DOI: 10.1038/s41397-021-00217-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 01/16/2021] [Accepted: 01/27/2021] [Indexed: 01/31/2023]
Abstract
Certain breast and ovarian cancers are characterised by high levels of chromosomal instability. We established a suite of eleven SNP array-based signatures of various forms of chromosomal instability. To understand what biological mechanisms might underpin these signatures, we generated and assembled genetic-feature data including allele-specific expression, fusion genes, gene expression, methylation, somatic coding mutations and protein expression. For each signature, we extracted a compendium of significantly associated genetic features using machine learning. We established an association between subchromosomal allelic imbalance-based measures and DNA repair genes. Numerical chromosomal instability and chromothripsis were found to have distinct genetic associations but shared a relationship to mitotic processes, while whole-genome doubling was characterised by TP53 mutation, and high AURKA and GINS1 expression. Furthermore, we identified two genetically distinct forms of tandem duplicator phenotypes. These findings identify potentially novel genomic targets for validation and drug development for specific subsets of breast and ovarian cancer.
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27
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ZNF91 deletion in human embryonic stem cells leads to ectopic activation of SVA retrotransposons and up-regulation of KRAB zinc finger gene clusters. Genome Res 2021; 31:551-563. [PMID: 33722937 PMCID: PMC8015857 DOI: 10.1101/gr.265348.120] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 02/02/2021] [Indexed: 01/27/2023]
Abstract
Transposable element (TE) invasions have shaped vertebrate genomes over the course of evolution. They have contributed an extra layer of species-specific gene regulation by providing novel transcription factor binding sites. In humans, SINE-VNTR-Alu (SVA) elements are one of three still active TE families; approximately 2800 SVA insertions exist in the human genome, half of which are human-specific. TEs are often silenced by KRAB zinc finger (KZNF) proteins recruiting corepressor proteins that establish a repressive chromatin state. A number of KZNFs have been reported to bind SVAs, but their individual contribution to repressing SVAs and their roles in suppressing SVA-mediated gene-regulatory effects remains elusive. We analyzed the genome-wide binding profile for ZNF91 in human cells and found that ZNF91 interacts with the VNTR region of SVAs. Through CRISPR-Cas9-mediated deletion of ZNF91 in human embryonic stem cells, we established that loss of ZNF91 results in increased transcriptional activity of SVAs. In contrast, SVA activation was not observed upon genetic deletion of the ZNF611 gene encoding another strong SVA interactor. Epigenetic profiling confirmed the loss of SVA repression in the absence of ZNF91 and revealed that mainly evolutionary young SVAs gain gene activation-associated epigenetic modifications. Genes close to activated SVAs showed a mild up-regulation, indicating SVAs adopt properties of cis-regulatory elements in the absence of repression. Notably, genome-wide derepression of SVAs elicited the communal up-regulation of KZNFs that reside in KZNF clusters. This phenomenon may provide new insights into the potential mechanisms used by the host genome to sense and counteract TE invasions.
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28
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Liu CC, Veeraraghavan J, Tan Y, Kim JA, Wang X, Loo SK, Lee S, Hu Y, Wang XS. A Novel Neoplastic Fusion Transcript, RAD51AP1-DYRK4, Confers Sensitivity to the MEK Inhibitor Trametinib in Aggressive Breast Cancers. Clin Cancer Res 2021; 27:785-798. [PMID: 33172895 PMCID: PMC7934498 DOI: 10.1158/1078-0432.ccr-20-2769] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/18/2020] [Accepted: 11/04/2020] [Indexed: 01/19/2023]
Abstract
PURPOSE Luminal B breast tumors are more aggressive estrogen receptor-positive (ER+) breast cancers characterized by aggressive clinical behavior and a high risk of metastatic dissemination. The underlying pathologic molecular events remain poorly understood with a paucity of actionable genetic drivers, which hinders the development of new treatment strategies. EXPERIMENTAL DESIGN We performed large-scale RNA sequencing analysis to identify chimerical transcripts preferentially expressed in luminal B breast cancer. The lead candidate was validated by reverse transcription PCR in breast cancer tissues. The effects of inducible ectopic expression or genetic silencing were assessed by phenotypic assays such as MTS, transwell, and transendothelial migration assays, and by clonogenic assays to assess MEK inhibitor sensitivity. Subcellular fractionation, Western blots, and immunoprecipitation were performed to characterize the protein products and elucidate the engaged mechanisms. RESULTS Here we report a novel tumor-specific chimeric transcript RAD51AP1-DYRK4 preferentially expressed in luminal B tumors. Analysis of 200 ER+ breast tumors detected RAD51AP1-DYRK4 overexpression in 19 tumors (9.5%), which is markedly enriched in the luminal B tumors (17.5%). Ectopic expression of RAD51AP1-DYRK4, but not wild-type RAD51AP1, leads to marked activation of MEK/ERK signaling, and endows increased cell motility and transendothelial migration. More importantly, RAD51AP1-DYRK4 appears to endow increased sensitivity to the MEK inhibitor trametinib through attenuating compensatory activation of HER2/PI3K/AKT under MEK inhibition. CONCLUSIONS This discovery sheds light on a new area of molecular pathobiology of luminal B tumors and implies potential new therapeutic opportunities for more aggressive breast tumors overexpressing this fusion.
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Affiliation(s)
- Chia-Chia Liu
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jamunarani Veeraraghavan
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Ying Tan
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Jin-Ah Kim
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Xian Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Suet Kee Loo
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Sanghoon Lee
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Yiheng Hu
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Xiao-Song Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania.
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
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29
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Sipos O, Tovey H, Quist J, Haider S, Nowinski S, Gazinska P, Kernaghan S, Toms C, Maguire S, Orr N, Linn SC, Owen J, Gillett C, Pinder SE, Bliss JM, Tutt A, Cheang MCU, Grigoriadis A. Assessment of structural chromosomal instability phenotypes as biomarkers of carboplatin response in triple negative breast cancer: the TNT trial. Ann Oncol 2021; 32:58-65. [PMID: 33098992 PMCID: PMC7784666 DOI: 10.1016/j.annonc.2020.10.475] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 08/05/2020] [Accepted: 10/13/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND In the TNT trial of triple negative breast cancer (NCT00532727), germline BRCA1/2 mutations were present in 28% of carboplatin responders. We assessed quantitative measures of structural chromosomal instability (CIN) to identify a wider patient subgroup within TNT with preferential benefit from carboplatin over docetaxel. PATIENTS AND METHODS Copy number aberrations (CNAs) were established from 135 formalin-fixed paraffin-embedded primary carcinomas using Illumina OmniExpress SNP-arrays. Seven published [allelic imbalanced CNA (AiCNA); allelic balanced CNA (AbCNA); copy number neutral loss of heterozygosity (CnLOH); number of telomeric allelic imbalances (NtAI); BRCA1-like status; percentage of genome altered (PGA); homologous recombination deficiency (HRD) scores] and two novel [Shannon diversity index (SI); high-level amplifications (HLAMP)] CIN-measurements were derived. HLAMP was defined based on the presence of at least one of the top 5% amplified cytobands located on 1q, 8q and 10p. Continuous CIN-measurements were divided into tertiles. All nine CIN-measurements were used to analyse objective response rate (ORR) and progression-free survival (PFS). RESULTS Patients with tumours without HLAMP had a numerically higher ORR and significantly longer PFS in the carboplatin (C) than in the docetaxel (D) arm [56% (C) versus 29% (D), PHLAMP,quiet = 0.085; PFS 6.1 months (C) versus 4.1 months (D), Pinteraction/HLAMP = 0.047]. In the carboplatin arm, patients with tumours showing intermediate telomeric NtAI and AiCNA had higher ORR [54% (C) versus 20% (D), PNtAI,intermediate = 0.03; 62% (C) versus 33% (D), PAiCNA,intermediate = 0.076]. Patients with high AiCNA and PGA had shorter PFS in the carboplatin arm [3.4 months (high) versus 5.7 months (low/intermediate); and 3.8 months (high) versus 5.6 months (low/intermediate), respectively; Pinteraction/AiCNA = 0.027, Padj.interaction/AiCNA = 0.125 and Pinteraction/PGA = 0.053, Padj.interaction/PGA = 0.176], whilst no difference was observed in the docetaxel arm. CONCLUSIONS Patients with tumours lacking HLAMP and demonstrating intermediate CIN-measurements formed a subgroup benefitting from carboplatin relative to docetaxel treatment within the TNT trial. This suggests a complex and paradoxical relationship between the extent of genomic instability in primary tumours and treatment response in the metastatic setting.
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Affiliation(s)
- O Sipos
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - H Tovey
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - J Quist
- Breast Cancer Now Unit, King's College London Faculty of Life Sciences and Medicine, London, UK; School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, UK
| | - S Haider
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - S Nowinski
- School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, UK
| | - P Gazinska
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - S Kernaghan
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - C Toms
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - S Maguire
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - N Orr
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - S C Linn
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - J Owen
- King's Health Partners Cancer Biobank, London, UK
| | - C Gillett
- King's Health Partners Cancer Biobank, London, UK
| | - S E Pinder
- School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, UK
| | - J M Bliss
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - A Tutt
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK; Breast Cancer Now Unit, King's College London Faculty of Life Sciences and Medicine, London, UK; School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, UK
| | - M C U Cheang
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - A Grigoriadis
- Breast Cancer Now Unit, King's College London Faculty of Life Sciences and Medicine, London, UK; School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, UK.
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30
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Sun H, Cui Y, Wang H, Liu H, Wang T. Comparison of methods for the detection of outliers and associated biomarkers in mislabeled omics data. BMC Bioinformatics 2020; 21:357. [PMID: 32795265 PMCID: PMC7646480 DOI: 10.1186/s12859-020-03653-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 07/10/2020] [Indexed: 02/08/2023] Open
Abstract
Background Previous studies have reported that labeling errors are not uncommon in omics data. Potential outliers may severely undermine the correct classification of patients and the identification of reliable biomarkers for a particular disease. Three methods have been proposed to address the problem: sparse label-noise-robust logistic regression (Rlogreg), robust elastic net based on the least trimmed square (enetLTS), and Ensemble. Ensemble is an ensembled classification based on distinct feature selection and modeling strategies. The accuracy of biomarker selection and outlier detection of these methods needs to be evaluated and compared so that the appropriate method can be chosen. Results The accuracy of variable selection, outlier identification, and prediction of three methods (Ensemble, enetLTS, Rlogreg) were compared for simulated and an RNA-seq dataset. On simulated datasets, Ensemble had the highest variable selection accuracy, as measured by a comprehensive index, and lowest false discovery rate among the three methods. When the sample size was large and the proportion of outliers was ≤5%, the positive selection rate of Ensemble was similar to that of enetLTS. However, when the proportion of outliers was 10% or 15%, Ensemble missed some variables that affected the response variables. Overall, enetLTS had the best outlier detection accuracy with false positive rates < 0.05 and high sensitivity, and enetLTS still performed well when the proportion of outliers was relatively large. With 1% or 2% outliers, Ensemble showed high outlier detection accuracy, but with higher proportions of outliers Ensemble missed many mislabeled samples. Rlogreg and Ensemble were less accurate in identifying outliers than enetLTS. The prediction accuracy of enetLTS was better than that of Rlogreg. Running Ensemble on a subset of data after removing the outliers identified by enetLTS improved the variable selection accuracy of Ensemble. Conclusions When the proportion of outliers is ≤5%, Ensemble can be used for variable selection. When the proportion of outliers is > 5%, Ensemble can be used for variable selection on a subset after removing outliers identified by enetLTS. For outlier identification, enetLTS is the recommended method. In practice, the proportion of outliers can be estimated according to the inaccuracy of the diagnostic methods used.
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Affiliation(s)
- Hongwei Sun
- Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan City, 030001, Shanxi, China.,Department of Health Statistics, School of Public Health and Management, Binzhou Medical University, City, Yantai, 264003, Shandong, China
| | - Yuehua Cui
- Department of Statistics and Probability, Michigan State University, East Lansing, MI, 48824, USA
| | - Hui Wang
- Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan City, 030001, Shanxi, China
| | - Haixia Liu
- Department of Health Statistics, School of Public Health and Management, Binzhou Medical University, City, Yantai, 264003, Shandong, China
| | - Tong Wang
- Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan City, 030001, Shanxi, China.
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31
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Zhang YP, Bao ZW, Wu JB, Chen YH, Chen JR, Xie HY, Zhou L, Wu J, Zheng SS. Cancer-Testis Gene Expression in Hepatocellular Carcinoma: Identification of Prognostic Markers and Potential Targets for Immunotherapy. Technol Cancer Res Treat 2020; 19:1533033820944274. [PMID: 32715976 PMCID: PMC7453447 DOI: 10.1177/1533033820944274] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Cancer-testis genes can serve as prognostic biomarkers and valuable targets for immunotherapy in multiple tumors because of their restricted expression in testis and cancer. However, their expression pattern in hepatocellular carcinoma is still not well understood. The purpose is to comprehensively characterize the cancer-testis gene expression in hepatocellular carcinoma as well as identify prognostic markers and potential targets for immunotherapy. METHODS Cancer-testis database and publicly available data sets reporting new cancer-testis genes were integrated, and then restricted them in a testis and hepatocellular carcinoma expression pattern. Pathway enrichment analysis and survival analysis were conducted to evaluate the biological function and prognostic effect of cancer-testis genes. Clustering analysis and coexpression analysis were performed to illustrate cancer-testis gene expression patterns in hepatocellular carcinoma. The association of gene expression of each cancer-testis gene to the corresponding methylation status was detected. Finally, we explored the associations between cancer-testis genes and CD8+ T-cell infiltration in hepatocellular carcinoma by TISIDB, and then validated it in an independent hepatocellular carcinoma cohort with 72 patients. RESULTS A total of 59 testis-specific genes were identified highly expressed in hepatocellular carcinoma. Pathway enrichment analysis revealed that cancer-testis genes in hepatocellular carcinoma significantly involves in the process of cell cycle regulation. Most of the cancer-testis genes were coexpressed, and cluster analysis suggested that cancer-testis gene expressed in hepatocellular carcinoma is independent of sex, hepatitis status, and histology type. We also found that demethylation might be a regulatory mechanism of cancer-testis gene expression in hepatocellular carcinoma. Survival analysis indicated that cancer-testis genes could predict the prognosis of patients with hepatocellular carcinoma. Furthermore, BUB1B was identified contributing to the resistance of CD8+ T-cell infiltration in hepatocellular carcinoma and was an independent prognostic factor both for overall survival and disease-free survival. CONCLUSIONS Our analysis enables better understanding of cancer-testis genes in hepatocellular carcinoma and provides potential targets for hepatocellular carcinoma treatment. Experimental and clinical studies are needed for further validations.
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Affiliation(s)
- Yan-Peng Zhang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, China
| | - Zhi-Wei Bao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jing-Bang Wu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, China
| | - Yun-Hao Chen
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, China
| | - Jun-Ru Chen
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, China
| | - Hai-Yang Xie
- NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, China
| | - Lin Zhou
- NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, China
| | - Jian Wu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, China
| | - Shu-Sen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, China
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32
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Aberrantly expressed HORMAD1 disrupts nuclear localization of MCM8-MCM9 complex and compromises DNA mismatch repair in cancer cells. Cell Death Dis 2020; 11:519. [PMID: 32647118 PMCID: PMC7347845 DOI: 10.1038/s41419-020-2736-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/17/2020] [Accepted: 06/22/2020] [Indexed: 12/14/2022]
Abstract
HORMAD1 is a meiosis-specific protein that promotes synapsis and recombination of homologous chromosomes in meiotic prophase. Originally identified as a cancer/testis antigen, HORMAD1 is also aberrantly expressed in several cancers. However, the functions of HORMAD1 in cancer cells are still not clear. Here, we show that HORMAD1 is aberrantly expressed in a wide variety of cancers and compromises DNA mismatch repair in cancer cells. Mechanistically, HORMAD1 interacts with MCM8–MCM9 complex and prevents its efficient nuclear localization. As a consequence, HORMAD1-expressing cancer cells have reduced MLH1 chromatin binding and DNA mismatch repair defects. Consistently, HORMAD1 expression is associated with increased mutation load and genomic instability in many cancers. Taken together, our study provides mechanistic insights into HORMAD1’s functions in cancer cells, which can potentially be exploited for targeted therapy of HORMAD1-expressing cancers.
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33
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Sato K, Brandsma I, van Rossum-Fikkert SE, Verkaik N, Oostra AB, Dorsman JC, van Gent DC, Knipscheer P, Kanaar R, Zelensky AN. HSF2BP negatively regulates homologous recombination in DNA interstrand crosslink repair. Nucleic Acids Res 2020; 48:2442-2456. [PMID: 31960047 PMCID: PMC7049687 DOI: 10.1093/nar/gkz1219] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 02/06/2023] Open
Abstract
The tumor suppressor BRCA2 is essential for homologous recombination (HR), replication fork stability and DNA interstrand crosslink (ICL) repair in vertebrates. We show that ectopic production of HSF2BP, a BRCA2-interacting protein required for meiotic HR during mouse spermatogenesis, in non-germline human cells acutely sensitize them to ICL-inducing agents (mitomycin C and cisplatin) and PARP inhibitors, resulting in a phenotype characteristic of cells from Fanconi anemia (FA) patients. We biochemically recapitulate the suppression of ICL repair and establish that excess HSF2BP compromises HR by triggering the removal of BRCA2 from the ICL site and thereby preventing the loading of RAD51. This establishes ectopic expression of a wild-type meiotic protein in the absence of any other protein-coding mutations as a new mechanism that can lead to an FA-like cellular phenotype. Naturally occurring elevated production of HSF2BP in tumors may be a source of cancer-promoting genomic instability and also a targetable vulnerability.
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Affiliation(s)
- Koichi Sato
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Inger Brandsma
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Sari E van Rossum-Fikkert
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Nicole Verkaik
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Anneke B Oostra
- Department of Clinical Genetics, VU University Medical Center, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands
| | - Josephine C Dorsman
- Department of Clinical Genetics, VU University Medical Center, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands
| | - Dik C van Gent
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Puck Knipscheer
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Alex N Zelensky
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
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34
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Gantchev J, Martínez Villarreal A, Gunn S, Zetka M, Ødum N, Litvinov IV. The ectopic expression of meiCT genes promotes meiomitosis and may facilitate carcinogenesis. Cell Cycle 2020; 19:837-854. [PMID: 32223693 DOI: 10.1080/15384101.2020.1743902] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cancer meiomitosis is defined as the concurrent activation of both mitotic and meiotic machineries in neoplastic cells that confer a selective advantage together with increased genomic instability. MeiCT (meiosis-specific cancer/testis) genes that perform specialized functions in the germline events required for the first meiotic division are ectopically expressed in several cancers. Here we describe the expression profiles of meiCT genes and proteins across a number of cancers and review the proposed mechanisms that increase aneuploidy and elicit reduction division in polyploid cells. These mechanisms are centered on the overexpression and function of meiCT proteins in cancers under various conditions that includes a response to genotoxic stress. Since meiCT genes are transcriptionally repressed in somatic cells, their target offers a promising therapeutic approach with limited toxicity to healthy tissues. Throughout the review, we provide a detailed description of the roles for each gene in the context of meiosis and we discuss proposed functions and outcomes resulting from their ectopic reactivation in cancer.
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Affiliation(s)
- Jennifer Gantchev
- Division of Dermatology, Department of Medicine, McGill University Health Centre, Montreal, QC, Canada
| | | | - Scott Gunn
- Division of Dermatology, Department of Medicine, McGill University Health Centre, Montreal, QC, Canada
| | - Monique Zetka
- Department of Biology, McGill University, Montreal, QC, Canada
| | - Neils Ødum
- Department of Microbiology and Immunology, The University of Copenhagen, Copenhagen, Denmark
| | - Ivan V Litvinov
- Division of Dermatology, Department of Medicine, McGill University Health Centre, Montreal, QC, Canada
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35
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Meyer F, Becker S, Classen S, Parplys AC, Mansour WY, Riepen B, Timm S, Ruebe C, Jasin M, Wikman H, Petersen C, Rothkamm K, Borgmann K. Prevention of DNA Replication Stress by CHK1 Leads to Chemoresistance Despite a DNA Repair Defect in Homologous Recombination in Breast Cancer. Cells 2020; 9:cells9010238. [PMID: 31963582 PMCID: PMC7017274 DOI: 10.3390/cells9010238] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/03/2020] [Accepted: 01/14/2020] [Indexed: 01/20/2023] Open
Abstract
Chromosomal instability not only has a negative effect on survival in triple-negative breast cancer, but also on the well treatable subgroup of luminal A tumors. This suggests a general mechanism independent of subtypes. Increased chromosomal instability (CIN) in triple-negative breast cancer (TNBC) is attributed to a defect in the DNA repair pathway homologous recombination. Homologous recombination (HR) prevents genomic instability by repair and protection of replication. It is unclear whether genetic alterations actually lead to a repair defect or whether superior signaling pathways are of greater importance. Previous studies focused exclusively on the repair function of HR. Here, we show that the regulation of HR by the intra-S-phase damage response at the replication is of overriding importance. A damage response activated by Ataxia telangiectasia and Rad3 related-checkpoint kinase 1 (ATR-CHK1) can prevent replication stress and leads to resistance formation. CHK1 thus has a preferred role over HR in preventing replication stress in TNBC. The signaling cascade ATR-CHK1 can compensate for a double-strand break repair error and lead to resistance of HR-deficient tumors. Established methods for the identification of HR-deficient tumors for Poly(ADP-Ribose)-Polymerase 1 (PARP1) inhibitor therapies should be extended to include analysis of candidates for intra-S phase damage response.
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Affiliation(s)
- Felix Meyer
- Laboratory of Radiobiology and Experimental Radiooncology, Center of Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (F.M.); (S.B.); (S.C.); (A.C.P.); (W.Y.M.); (B.R.); (K.R.)
| | - Saskia Becker
- Laboratory of Radiobiology and Experimental Radiooncology, Center of Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (F.M.); (S.B.); (S.C.); (A.C.P.); (W.Y.M.); (B.R.); (K.R.)
| | - Sandra Classen
- Laboratory of Radiobiology and Experimental Radiooncology, Center of Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (F.M.); (S.B.); (S.C.); (A.C.P.); (W.Y.M.); (B.R.); (K.R.)
| | - Ann Christin Parplys
- Laboratory of Radiobiology and Experimental Radiooncology, Center of Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (F.M.); (S.B.); (S.C.); (A.C.P.); (W.Y.M.); (B.R.); (K.R.)
| | - Wael Yassin Mansour
- Laboratory of Radiobiology and Experimental Radiooncology, Center of Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (F.M.); (S.B.); (S.C.); (A.C.P.); (W.Y.M.); (B.R.); (K.R.)
- Tumor Biology Department, National Cancer Institute, Cairo University, Cairo 11796, Egypt
| | - Britta Riepen
- Laboratory of Radiobiology and Experimental Radiooncology, Center of Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (F.M.); (S.B.); (S.C.); (A.C.P.); (W.Y.M.); (B.R.); (K.R.)
| | - Sara Timm
- Department of Radiation Oncology, Saarland University, 66421 Hamburg/Saar, Germany; (S.T.); (C.R.)
| | - Claudia Ruebe
- Department of Radiation Oncology, Saarland University, 66421 Hamburg/Saar, Germany; (S.T.); (C.R.)
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Harriet Wikman
- Department of Tumor Biology, University Center Hamburg-Eppendorf, 20246 Hamburg, Germany;
| | - Cordula Petersen
- Department of Radiotherapy and Radiooncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany;
| | - Kai Rothkamm
- Laboratory of Radiobiology and Experimental Radiooncology, Center of Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (F.M.); (S.B.); (S.C.); (A.C.P.); (W.Y.M.); (B.R.); (K.R.)
| | - Kerstin Borgmann
- Laboratory of Radiobiology and Experimental Radiooncology, Center of Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (F.M.); (S.B.); (S.C.); (A.C.P.); (W.Y.M.); (B.R.); (K.R.)
- Correspondence: ; Tel.: +49-40-74105-3596
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36
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Li S, Li Q, Lü J, Zhao Q, Li D, Shen L, Wang Z, Liu J, Xie D, Cho WC, Xu S, Yu Z. Targeted Inhibition of miR-221/222 Promotes Cell Sensitivity to Cisplatin in Triple-Negative Breast Cancer MDA-MB-231 Cells. Front Genet 2020; 10:1278. [PMID: 32010177 PMCID: PMC6971202 DOI: 10.3389/fgene.2019.01278] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 11/20/2019] [Indexed: 12/14/2022] Open
Abstract
Cisplatin has been widely used in the treatment of a various types of cancers including triple-negative breast cancer (TNBC) by damaging DNA and inducing apoptosis. However, its anti-cancer effects are often limited due to chemo-resistance, which is one of the main reasons causing cancer relapse and metastasis. To overcome resistance, cisplatin is often used in combination with other drugs or molecules. Our study found that the targeted inhibition of miR-221/222 in MDA-MB-231 cells promoted cisplatin-induced cell apoptosis, and increased the cell sensitivity to cisplatin in vitro. Much higher expression levels of miR-221/222 were detected in the cisplatin-resistant MDA-MB-231 cells and in cisplatin-resistant breast cancer patients. The combination chemotherapy of cisplatin with anti-miR-221/222 showed much higher efficiency in suppressing tumor growth in the mice transplanted with MDA-MB-231 cells. In addition, anti-miR-221 and anti-miR-222 showed synergetic effects on improving sensitivity to cisplatin in MDA-MB-231 cells. Suppression of SOCS1-STAT3-Bcl-2 pathway and activation of p53-Pten signaling both contribute to anti-miR-221/222-induced sensitivity to cisplatin in MDA-MB-231 cells. These findings suggest the potential of a novel approach for the combination chemotherapy of cisplatin with small non-coding RNA in treatment of human TNBC.
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Affiliation(s)
- Shujun Li
- Research Center for Translational Medicine, Department of Medical Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Maternal and Children Health Management, The Third Hospital of BaoGang Group, Baotou, China
| | - Qun Li
- Research Center for Translational Medicine, Department of Medical Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jinhui Lü
- Research Center for Translational Medicine, Department of Medical Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qian Zhao
- Research Center for Translational Medicine, Department of Medical Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Danni Li
- Research Center for Translational Medicine, Department of Medical Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Pathological Physiology, Tongji University School of Medicine, Shanghai, China
| | - Lei Shen
- Research Center for Translational Medicine, Department of Medical Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhongrui Wang
- Research Center for Translational Medicine, Department of Medical Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Junjun Liu
- Research Center for Translational Medicine, Department of Medical Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Dongping Xie
- Department of Pathological Physiology, Tongji University School of Medicine, Shanghai, China
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - Shaohua Xu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Shanghai, China
| | - Zuoren Yu
- Research Center for Translational Medicine, Department of Medical Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Pathological Physiology, Tongji University School of Medicine, Shanghai, China
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37
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Zhong G, Lou W, Shen Q, Yu K, Zheng Y. Identification of key genes as potential biomarkers for triple‑negative breast cancer using integrating genomics analysis. Mol Med Rep 2019; 21:557-566. [PMID: 31974598 PMCID: PMC6947886 DOI: 10.3892/mmr.2019.10867] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 08/30/2019] [Indexed: 12/19/2022] Open
Abstract
Triple-negative breast cancer (TNBC) accounts for the worst prognosis of all types of breast cancers due to a high risk of recurrence and a lack of targeted therapeutic options. Extensive effort is required to identify novel targets for TNBC. In the present study, a robust rank aggregation (RRA) analysis based on genome-wide gene expression datasets involving TNBC patients from the Gene Expression Omnibus (GEO) database was performed to identify key genes associated with TNBC. A total of 194 highly ranked differentially expressed genes (DEGs) were identified in TNBC vs. non-TNBC. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analysis was utilized to explore the biological functions of the identified genes. These DEGs were mainly involved in the biological processes termed positive regulation of transcription from RNA polymerase II promoter, negative regulation of apoptotic process, response to drug, response to estradiol and negative regulation of cell growth. Genes were mainly involved in the KEGG pathway termed estrogen signaling pathway. The aberrant expression of several randomly selected DEGs were further validated in cell lines, clinical tissues and The Cancer Genome Atlas (TCGA) cohort. Furthermore, all the top-ranked DEGs underwent survival analysis using TCGA database, of which overexpression of 4 genes (FABP7, ART3, CT83, and TTYH1) were positively correlated to the life expectancy (P<0.05) of TNBC patients. In addition, a model consisting of two genes (FABP7 and CT83) was identified to be significantly associated with the overall survival (OS) of TNBC patients by means of Cox regression, Kaplan-Meier, and receiver operating characteristic (ROC) analyses. In conclusion, the present study identified a number of key genes as potential biomarkers involved in TNBC, which provide novel insights into the tumorigenesis of TNBC at the gene level and may serve as independent prognostic factors for TNBC prognosis.
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Affiliation(s)
- Guansheng Zhong
- Department of Thyroid and Breast Surgery, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P.R. China
| | - Weiyang Lou
- Program of Innovative Therapeutics, First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang 310014, P.R. China
| | - Qinyan Shen
- Department of Surgical Oncology, Dongyang People's Hospital of Zhejiang, Dongyang, Zhejiang 322100, P.R. China
| | - Kun Yu
- Department of Thyroid and Breast Surgery, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P.R. China
| | - Yajuan Zheng
- Department of Thyroid and Breast Surgery, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P.R. China
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38
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Wang Z, Tu K, Xia L, Luo K, Luo W, Tang J, Lu K, Hu X, He Y, Qiao W, Zhou Y, Zhang J, Cao F, Dai S, Tian P, Wang Y, Liu L, Che G, Zhou Q, Xie D, Li W. The Open Chromatin Landscape of Non-Small Cell Lung Carcinoma. Cancer Res 2019; 79:4840-4854. [PMID: 31209061 DOI: 10.1158/0008-5472.can-18-3663] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 04/12/2019] [Accepted: 06/10/2019] [Indexed: 02/05/2023]
Abstract
Non-small cell lung carcinoma (NSCLC) is a major cancer type whose epigenetic alteration remains unclear. We analyzed open chromatin data with matched whole-genome sequencing and RNA-seq data of 50 primary NSCLC cases. We observed high interpatient heterogeneity of open chromatin profiles and the degree of heterogeneity correlated to several clinical parameters. Lung adenocarcinoma and lung squamous cell carcinoma (LUSC) exhibited distinct open chromatin patterns. Beyond this, we uncovered that the broadest open chromatin peaks indicated key NSCLC genes and led to less stable expression. Furthermore, we found that the open chromatin peaks were gained or lost together with somatic copy number alterations and affected the expression of important NSCLC genes. In addition, we identified 21 joint-quantitative trait loci (joint-QTL) that correlated to both assay for transposase accessible chromatin sequencing peak intensity and gene expression levels. Finally, we identified 87 regulatory risk loci associated with lung cancer-related phenotypes by intersecting the QTLs with genome-wide association study significant loci. In summary, this compendium of multiomics data provides valuable insights and a resource to understand the landscape of open chromatin features and regulatory networks in NSCLC. SIGNIFICANCE: This study utilizes state of the art genomic methods to differentiate lung cancer subtypes.See related commentary by Bowcock, p. 4808.
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Affiliation(s)
- Zhoufeng Wang
- Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Kailing Tu
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lin Xia
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Kai Luo
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wenxin Luo
- Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jie Tang
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Keying Lu
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xinlei Hu
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yijing He
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wenliang Qiao
- Lung Cancer Center, West China Hospital Sichuan University, Chengdu, Sichuan, China
| | - Yongzhao Zhou
- Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jun Zhang
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Feng Cao
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Shuiping Dai
- Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Panwen Tian
- Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ye Wang
- Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lunxu Liu
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Guowei Che
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Qinghua Zhou
- Lung Cancer Center, West China Hospital Sichuan University, Chengdu, Sichuan, China
| | - Dan Xie
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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Feichtinger J, McFarlane RJ. Meiotic gene activation in somatic and germ cell tumours. Andrology 2019; 7:415-427. [PMID: 31102330 PMCID: PMC6766858 DOI: 10.1111/andr.12628] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 12/20/2022]
Abstract
Background Germ cell tumours are uniquely associated with the gametogenic tissues of males and females. A feature of these cancers is that they can express genes that are normally tightly restricted to meiotic cells. This aberrant gene expression has been used as an indicator that these cancer cells are attempting a programmed germ line event, meiotic entry. However, work in non‐germ cell cancers has also indicated that meiotic genes can become aberrantly activated in a wide range of cancer types and indeed provide functions that serve as oncogenic drivers. Here, we review the activation of meiotic factors in cancers and explore commonalities between meiotic gene activation in germ cell and non‐germ cell cancers. Objectives The objectives of this review are to highlight key questions relating to meiotic gene activation in germ cell tumours and to offer possible interpretations as to the biological relevance in this unique cancer type. Materials and Methods PubMed and the GEPIA database were searched for papers in English and for cancer gene expression data, respectively. Results We provide a brief overview of meiotic progression, with a focus on the unique mechanisms of reductional chromosome segregation in meiosis I. We then offer detailed insight into the role of meiotic chromosome regulators in non‐germ cell cancers and extend this to provide an overview of how this might relate to germ cell tumours. Conclusions We propose that meiotic gene activation in germ cell tumours might not indicate an unscheduled attempt to enter a full meiotic programme. Rather, it might simply reflect either aberrant activation of a subset of meiotic genes, with little or no biological relevance, or aberrant activation of a subset of meiotic genes as positive tumour evolutionary/oncogenic drivers. These postulates provide the provocation for further studies in this emerging field.
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Affiliation(s)
- J Feichtinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Graz, Austria.,OMICS Center Graz, BioTechMed Graz, Graz, Austria
| | - R J McFarlane
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, Bangor, Gwynedd, UK
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40
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Sharma P, Barlow WE, Godwin AK, Pathak H, Isakova K, Williams D, Timms KM, Hartman AR, Wenstrup RJ, Linden HM, Tripathy D, Hortobagyi GN, Hayes DF. Impact of homologous recombination deficiency biomarkers on outcomes in patients with triple-negative breast cancer treated with adjuvant doxorubicin and cyclophosphamide (SWOG S9313). Ann Oncol 2019; 29:654-660. [PMID: 29293876 DOI: 10.1093/annonc/mdx821] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background Homologous recombination deficiency (HRD)-causing alterations have been reported in triple-negative breast cancer (TNBC). We hypothesized that TNBCs with HRD alterations might be more sensitive to anthracycline plus cyclophosphamide-based chemotherapy and report on HRD status and BRCA1 promoter methylation (PM) as prognostic markers in TNBC patients treated with adjuvant doxorubicin (A) and cyclophosphamide (C) in SWOG9313. Patients and methods In total, 425 TNBC patients were identified from S9313. HRD score, tumor BRCA1/2 sequencing, and BRCA1 PM were carried out on DNA isolated from formalin-fixed paraffin-embedded tissue. Positive HRD status was defined as either a deleterious tumor BRCA1/2 (tBRCA) mutation or a pre-defined HRD score ≥42. Markers were tested for prognostic value on disease-free survival (DFS) and overall survival (OS) using Cox regression models adjusted for treatment assignment and nodal status. Results HRD status was determined in 89% (379/425) of cases. Of these, 67% were HRD positive (27% with tBRCA mutation, 40% tBRCA-negative but HRD score ≥42). HRD-positive status was associated with a better DFS [hazard ratio (HR) 0.72; 95% confidence interval (CI) 0.51-1.00; P = 0.049] and non-significant trend toward better OS (HR = 0.71; 95% CI 0.48-1.03; P = 0.073). High HRD score (≥42) in tBRCA-negative patients (n = 274) was also associated with better DFS (HR = 0.64; 95% CI 0.43-0.94; P = 0.023) and OS (HR = 0.65; 95% CI 0.42-1.00; P = 0.049). BRCA1 PM was evaluated successfully in 82% (348/425) and detected in 32% of cases. The DFS HR for BRCA1 PM was similar to that for HRD but did not reach statistical significance (HR = 0.79; 95% CI 0.54-1.17; P = 0.25). Conclusions HRD positivity was observed in two-thirds of TNBC patients receiving adjuvant AC and was associated with better DFS. HRD status may identify TNBC patients who receive greater benefit from AC-based chemotherapy and should be evaluated further in prospective studies. Clinical Trials Number Int0137 (The trial pre-dates Clinicaltrial.Gov website establishment).
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Affiliation(s)
- P Sharma
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, USA.
| | - W E Barlow
- SWOG Statistical Center, Seattle, USA; Cancer, Research and Biostatistics (CRAB), Seattle, USA
| | - A K Godwin
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, USA
| | - H Pathak
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, USA
| | - K Isakova
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, USA
| | - D Williams
- Myriad Genetics, Inc., Salt Lake City, USA
| | - K M Timms
- Myriad Genetics, Inc., Salt Lake City, USA
| | | | | | - H M Linden
- Department of Medicine, University of Washington, Seattle, USA; Seattle Cancer Care Alliance, Seattle, USA
| | - D Tripathy
- Department of Breast Medical Onocolgy, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - G N Hortobagyi
- Department of Breast Medical Onocolgy, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - D F Hayes
- Department of Internal Medicine, University of Michigan, Ann Arbor, USA
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Quist J, Mirza H, Cheang MCU, Telli ML, O'Shaughnessy JA, Lord CJ, Tutt ANJ, Grigoriadis A. A Four-gene Decision Tree Signature Classification of Triple-negative Breast Cancer: Implications for Targeted Therapeutics. Mol Cancer Ther 2019; 18:204-212. [PMID: 30305342 PMCID: PMC6330084 DOI: 10.1158/1535-7163.mct-18-0243] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 08/02/2018] [Accepted: 10/05/2018] [Indexed: 12/12/2022]
Abstract
The molecular complexity of triple-negative breast cancers (TNBCs) provides a challenge for patient management. We set out to characterize this heterogeneous disease by combining transcriptomics and genomics data, with the aim of revealing convergent pathway dependencies with the potential for treatment intervention. A Bayesian algorithm was used to integrate molecular profiles in two TNBC cohorts, followed by validation using five independent cohorts (n = 1,168), including three clinical trials. A four-gene decision tree signature was identified, which robustly classified TNBCs into six subtypes. All four genes in the signature (EXO1, TP53BP2, FOXM1, and RSU1) are associated with either genomic instability, malignant growth, or treatment response. One of the six subtypes, MC6, encompassed the largest proportion of tumors (∼50%) in early diagnosed TNBCs. In TNBC patients with metastatic disease, the MC6 proportion was reduced to 25%, and was independently associated with a higher response rate to platinum-based chemotherapy. In TNBC cell line data, platinum sensitivity was recapitulated, and a sensitivity to the inhibition of the phosphatase PPM1D was revealed. Molecularly, MC6-TNBCs displayed high levels of telomeric allelic imbalances, enrichment of CD4+ and CD8+ immune signatures, and reduced expression of genes negatively regulating the MAPK signaling pathway. These observations suggest that our integrative classification approach may identify TNBC patients with discernible and theoretically pharmacologically tractable features that merit further studies in prospective trials.
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Affiliation(s)
- Jelmar Quist
- Cancer Bioinformatics, Cancer Centre at Guy's Hospital, King's College London, London, United Kingdom
- Breast Cancer Now Research Unit, Cancer Centre at Guy's Hospital, King's College London, London, United Kingdom
- School of Cancer and Pharmaceutical Sciences, Cancer Research UK King's Health Partners Centre, King's College London, London, United Kingdom
| | - Hasan Mirza
- Cancer Bioinformatics, Cancer Centre at Guy's Hospital, King's College London, London, United Kingdom
- Breast Cancer Now Research Unit, Cancer Centre at Guy's Hospital, King's College London, London, United Kingdom
- School of Cancer and Pharmaceutical Sciences, Cancer Research UK King's Health Partners Centre, King's College London, London, United Kingdom
| | - Maggie C U Cheang
- Clinical Trials and Statistics Unit (ICR-CTSU), The Institute of Cancer Research, Surrey, United Kingdom
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Melinda L Telli
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | | | - Christopher J Lord
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Andrew N J Tutt
- Breast Cancer Now Research Unit, Cancer Centre at Guy's Hospital, King's College London, London, United Kingdom
- School of Cancer and Pharmaceutical Sciences, Cancer Research UK King's Health Partners Centre, King's College London, London, United Kingdom
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Anita Grigoriadis
- Cancer Bioinformatics, Cancer Centre at Guy's Hospital, King's College London, London, United Kingdom.
- Breast Cancer Now Research Unit, Cancer Centre at Guy's Hospital, King's College London, London, United Kingdom
- School of Cancer and Pharmaceutical Sciences, Cancer Research UK King's Health Partners Centre, King's College London, London, United Kingdom
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Chen B, Tang H, Chen X, Zhang G, Wang Y, Xie X, Liao N. Transcriptomic analyses identify key differentially expressed genes and clinical outcomes between triple-negative and non-triple-negative breast cancer. Cancer Manag Res 2018; 11:179-190. [PMID: 30613165 PMCID: PMC6306052 DOI: 10.2147/cmar.s187151] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Purpose There are significant differences in the biological behavior between triple-negative breast cancer (TNBC) and non-triple-negative breast cancer (non-TNBC). In the present study, we identify key differential genes and clinical outcomes between TNBC and non-TNBC. Materials and methods Transcriptomic analyses used GEO datasets (GSE76275), gene ontology, KEGG pathway analysis and cBioPortal. Quantitative RT-PCR analysis (qRT-PCR) was used to validate the differentially expressed genes. We used the KM Plotter Online Tool and 240 patients with TNBC tissue microarray to assay the prognostic value of HORMAD1. Results The upregulated differentially expressed genes were enriched in transcription factor activity, sequence-specific DNA binding and nucleic acid binding transcription factor activity. Only 16 genes were upregulated when further screened for fold change >4-fold change. HORMAD1 and SOX8 exhibited high frequencies of change of greater than 10% (HORMAD1 was close to 20%). qRT-PCR results indicated that HORMAD1 and SOX8 mRNA levels were significantly upregulated in TNBC samples. In KM Plotter Online Tool, high HORMAD1 was associated with worse outcome. In our tissue microarray (including 240 TNBC tissues), IHC analysis revealed that 29.7% (55/240) of the tumor samples exhibited high HORMAD1 expression and 70.3% (185/240) of the tumor samples exhibited low HORMAD1 expression levels. Meanwhile, high HORMAD1 group has a bad prognosis. Conclusion The status of transcriptional activation is an important difference between TNBC and non-TNBC. HORMAD1 is a key differential gene associated with poor outcome in TNBC. Epigenetic therapy and agents targeting cancer/testis antigens might potentially help to customize therapies of TNBC.
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Affiliation(s)
- Bo Chen
- Department of Breast Cancer, Cancer Center, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China,
| | - Hailin Tang
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China,
| | - Xi Chen
- Department of Anatomy, Hengyang Medical College, University of South China, Hengyang, China
| | - Guochun Zhang
- Department of Breast Cancer, Cancer Center, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China,
| | - Yulei Wang
- Department of Breast Cancer, Cancer Center, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China,
| | - Xiaoming Xie
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China,
| | - Ning Liao
- Department of Breast Cancer, Cancer Center, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China,
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Mio C, Gerratana L, Bolis M, Caponnetto F, Zanello A, Barbina M, Di Loreto C, Garattini E, Damante G, Puglisi F. BET proteins regulate homologous recombination-mediated DNA repair: BRCAness and implications for cancer therapy. Int J Cancer 2018; 144:755-766. [PMID: 30259975 DOI: 10.1002/ijc.31898] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 08/28/2018] [Accepted: 09/20/2018] [Indexed: 12/29/2022]
Abstract
Bromodomain and Extra-Terminal (BET) proteins are historically involved in regulating gene expression and BRD4 was recently found to be involved in DNA damage regulation. Aims of our study were to assess BRD4 regulation in homologous recombination-mediated DNA repair and to explore novel clinical strategies through the combinations of the pharmacological induction of epigenetic BRCAness in BRCA1 wild-type triple negative breast cancer (TNBC) cells by means of BET inhibitors and compounds already available in clinic. Performing a dual approach (chromatin immunoprecipitation and RNA interference), the direct relationship between BRD4 and BRCA1/RAD51 expression was confirmed in TNBC cells. Moreover, BRD4 pharmacological inhibition using two BET inhibitors (JQ1 and GSK525762A) induced a dose-dependent reduction in BRCA1 and RAD51 levels and is able to hinder homologous recombination-mediated DNA damage repair, generating a BRCAness phenotype in TNBC cells. Furthermore, BET inhibition impaired the ability of TNBC cells to overcome the increase in DNA damage after platinum salts (i.e., CDDP) exposure, leading to massive cell death, and triggered synthetic lethality when combined with PARP inhibitors (i.e., AZD2281). Altogether, the present study confirms that BET proteins directly regulate the homologous recombination pathway and their inhibition induced a BRCAness phenotype in BRCA1 wild-type TNBC cells. Noteworthy, being this strategy based on drugs already available for human use, it is rapidly transferable and could potentially enable clinicians to exploit platinum salts and PARP inhibitors-based treatments in a wider population of TNBC patients and not just in a specific subgroup, after validating clinical trials.
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Affiliation(s)
- Catia Mio
- Department of Medicine (DAME), University of Udine, Udine, Italy
| | | | - Marco Bolis
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | | | - Andrea Zanello
- Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Mattia Barbina
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Carla Di Loreto
- Department of Medicine (DAME), University of Udine, Udine, Italy.,Institute of Pathology, ASUIUD University Hospital of Udine, Udine, Italy
| | - Enrico Garattini
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Giuseppe Damante
- Department of Medicine (DAME), University of Udine, Udine, Italy.,Institute of Medical Genetics, ASUIUD University Hospital of Udine, Udine, Italy
| | - Fabio Puglisi
- Department of Medicine (DAME), University of Udine, Udine, Italy.,Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
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Chartron E, Theillet C, Guiu S, Jacot W. Targeting homologous repair deficiency in breast and ovarian cancers: Biological pathways, preclinical and clinical data. Crit Rev Oncol Hematol 2018; 133:58-73. [PMID: 30661659 DOI: 10.1016/j.critrevonc.2018.10.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 09/25/2018] [Accepted: 10/30/2018] [Indexed: 12/16/2022] Open
Abstract
Mutation or epigenetic silencing of homologous recombination (HR) repair genes is characteristic of a growing proportion of triple-negative breast cancers (TNBCs) and high-grade serous ovarian carcinomas. Defects in HR lead to genome instability, allowing cells to acquire the multiple genetic alterations essential for cancer development. However, this deficiency can also be exploited by using DNA damaging agents or by targeting compensatory repair pathways. A noteworthy example is treatment of TNBC and epithelial ovarian cancer harboring BRCA1/2 germline mutations using platinum salts and/or PARP inhibitors. Dramatic responses to PARP inhibitors may support a wider use in the HR-deficient population beyond those with mutated germline BRCA1 and 2. In this review, we discuss HR deficiency hallmarks as predictive biomarkers for platinum salt and PARP inhibitor sensitivity for selecting patients affected by TNBC or epithelial ovarian cancer who could benefit from these therapeutic options.
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Affiliation(s)
- Elodie Chartron
- Department of medical oncology, Montpellier Academic Hospital, Montpellier, France
| | - Charles Theillet
- IRCM, INSERM, Université de Montpellier, ICM, Montpellier, France
| | - Séverine Guiu
- Department of Medical Oncology, Institut du Cancer de Montpellier, Montpellier, France
| | - William Jacot
- IRCM, INSERM, Université de Montpellier, ICM, Montpellier, France; Department of Medical Oncology, Institut du Cancer de Montpellier, Montpellier, France.
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A cancer-testis non-coding RNA LIN28B-AS1 activates driver gene LIN28B by interacting with IGF2BP1 in lung adenocarcinoma. Oncogene 2018; 38:1611-1624. [DOI: 10.1038/s41388-018-0548-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 09/11/2018] [Accepted: 09/14/2018] [Indexed: 12/19/2022]
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46
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Gao Y, Kardos J, Yang Y, Tamir TY, Mutter-Rottmayer E, Weissman B, Major MB, Kim WY, Vaziri C. The Cancer/Testes (CT) Antigen HORMAD1 promotes Homologous Recombinational DNA Repair and Radioresistance in Lung adenocarcinoma cells. Sci Rep 2018; 8:15304. [PMID: 30333500 PMCID: PMC6192992 DOI: 10.1038/s41598-018-33601-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/01/2018] [Indexed: 12/24/2022] Open
Abstract
The Cancer/Testes (CT) Antigen HORMAD1 is germ cell-restricted and plays developmental roles in generation and processing of meiotic DNA Double Strand Breaks (DSB). Many tumors aberrantly overexpress HORMAD1 yet the potential impact of this CT antigen on cancer biology is unclear. We tested a potential role of HORMAD1 in genome maintenance in lung adenocarcinoma cells. We show that HORMAD1 re-distributes to nuclear foci and co-localizes with the DSB marker γH2AX in response to ionizing radiation (IR) and chemotherapeutic agents. The HORMA domain and C-term disordered oligomerization motif are necessary for localization of HORMAD1 to IR-induced foci (IRIF). HORMAD1-depleted cells are sensitive to IR and camptothecin. In reporter assays, Homologous Recombination (HR)-mediated repair of targeted ISce1-induced DSBs is attenuated in HORMAD1-depleted cells. In Non-Homologous End Joining (NHEJ) reporter assays, HORMAD1-depletion does not affect repair of ISce1-induced DSB. Early DSB signaling events (including ATM phosphorylation and formation of γH2AX, 53BP1 and NBS1 foci) are intact in HORMAD1-depleted cells. However, generation of RPA-ssDNA foci and redistribution of RAD51 to DSB are compromised in HORMAD1-depleted cells, suggesting that HORMAD1 promotes DSB resection. HORMAD1-mediated HR is a neomorphic activity that is independent of its meiotic partners (including HORMAD2 and CCDC36. Bioinformatic analysis of TCGA data show that similar to known HR pathway genes HORMAD1 is overexpressed in lung adenocarcinomas. Overexpression of HR genes is associated with specific mutational profiles (including copy number variation). Taken together, we identify HORMAD1-dependent DSB repair as a new mechanism of radioresistance and a probable determinant of mutability in lung adenocarcinoma.
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Affiliation(s)
- Yanzhe Gao
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC, 27599, USA
| | - Jordan Kardos
- Lineberger Comprehensive Cancer Center, Curriculum in Genetics and Molecular Biology, and Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Yang Yang
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC, 27599, USA
| | - Tigist Y Tamir
- Department of Cell Biology and Physiology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Elizabeth Mutter-Rottmayer
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC, 27599, USA
| | - Bernard Weissman
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC, 27599, USA.,Lineberger Comprehensive Cancer Center, Curriculum in Genetics and Molecular Biology, and Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Michael B Major
- Department of Cell Biology and Physiology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - William Y Kim
- Lineberger Comprehensive Cancer Center, Curriculum in Genetics and Molecular Biology, and Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC, 27599, USA. .,Lineberger Comprehensive Cancer Center, Curriculum in Genetics and Molecular Biology, and Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA.
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47
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Robert M, Patsouris A, Frenel JS, Gourmelon C, Augereau P, Campone M. Emerging PARP inhibitors for treating breast cancer. Expert Opin Emerg Drugs 2018; 23:211-221. [DOI: 10.1080/14728214.2018.1527900] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Marie Robert
- René Gauducheau, Institut de Cancérologie de l’Ouest, St Herblain, France
| | - Anne Patsouris
- Paul Papin, Institut de Cancérologie de l’Ouest, Angers, France
| | | | - Carole Gourmelon
- René Gauducheau, Institut de Cancérologie de l’Ouest, St Herblain, France
| | - Paule Augereau
- Paul Papin, Institut de Cancérologie de l’Ouest, Angers, France
| | - Mario Campone
- René Gauducheau, Institut de Cancérologie de l’Ouest, St Herblain, France
- Medical oncology, Centre de Recherche en Cancérologie Nantes-Angers (CRNA), Saint-Herblain, France
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48
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Gibbs ZA, Whitehurst AW. Emerging Contributions of Cancer/Testis Antigens to Neoplastic Behaviors. Trends Cancer 2018; 4:701-712. [PMID: 30292353 DOI: 10.1016/j.trecan.2018.08.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/24/2018] [Accepted: 08/27/2018] [Indexed: 02/07/2023]
Abstract
Tumors of nearly every origin activate the expression of genes normally restricted to gametogenic cells. These genes encode proteins termed cancer/testis (CT) antigens, since expression outside of their naturally immune-privileged site can evoke an immune response. Despite extensive efforts to exploit CT antigens as immunotherapeutic targets, investigation of whether these proteins participate in tumorigenic processes has lagged. Here, we discuss emerging evidence that demonstrates that CT antigens can confer a selective advantage to tumor cells by promoting oncogenic processes or permitting evasion of tumor-suppressive mechanisms. These advances indicate the inherent flexibility of tumor cell regulatory networks to engage aberrantly expressed proteins to promote neoplastic behaviors, which could ultimately present novel therapeutic entry points.
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Affiliation(s)
- Zane A Gibbs
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA; Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Angelique W Whitehurst
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA; Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA.
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49
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Nichols BA, Oswald NW, McMillan EA, McGlynn K, Yan J, Kim MS, Saha J, Mallipeddi PL, LaDuke SA, Villalobos PA, Rodriguez-Canales J, Wistuba II, Posner BA, Davis AJ, Minna JD, MacMillan JB, Whitehurst AW. HORMAD1 Is a Negative Prognostic Indicator in Lung Adenocarcinoma and Specifies Resistance to Oxidative and Genotoxic Stress. Cancer Res 2018; 78:6196-6208. [PMID: 30185546 DOI: 10.1158/0008-5472.can-18-1377] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 07/10/2018] [Accepted: 08/30/2018] [Indexed: 12/21/2022]
Abstract
Cancer testis antigens (CTA) are expressed in testis and placenta and anomalously activated in a variety of tumors. The mechanistic contribution of CTAs to neoplastic phenotypes remains largely unknown. Using a chemigenomics approach, we find that the CTA HORMAD1 correlates with resistance to the mitochondrial complex I inhibitor piericidin A in non-small cell lung cancer (NSCLC). Resistance was due to a reductive intracellular environment that attenuated the accumulation of free radicals. In human lung adenocarcinoma (LUAD) tumors, patients expressing high HORMAD1 exhibited elevated mutational burden and reduced survival. HORMAD1 tumors were enriched for genes essential for homologous recombination (HR), and HORMAD1 promoted RAD51-filament formation, but not DNA resection, during HR. Accordingly, HORMAD1 loss enhanced sensitivity to γ-irradiation and PARP inhibition, and HORMAD1 depletion significantly reduced tumor growth in vivo These results suggest that HORMAD1 expression specifies a novel subtype of LUAD, which has adapted to mitigate DNA damage. In this setting, HORMAD1 could represent a direct target for intervention to enhance sensitivity to DNA-damaging agents or as an immunotherapeutic target in patients.Significance: This study uses a chemigenomics approach to demonstrate that anomalous expression of the CTA HORMAD1 specifies resistance to oxidative stress and promotes HR to support tumor cell survival in NSCLC. Cancer Res; 78(21); 6196-208. ©2018 AACR.
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Affiliation(s)
- Brandt A Nichols
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas
| | - Nathaniel W Oswald
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas
| | | | - Kathleen McGlynn
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas
| | - Jingsheng Yan
- Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, Texas
| | - Min S Kim
- Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, Texas
| | - Janapriya Saha
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, Texas
| | - Prema L Mallipeddi
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas
| | - Sydnie A LaDuke
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas
| | - Pamela A Villalobos
- Department of Translational Molecular Pathology, M.D. Anderson Cancer Center, Houston, Texas
| | - Jaime Rodriguez-Canales
- Department of Translational Molecular Pathology, M.D. Anderson Cancer Center, Houston, Texas
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, M.D. Anderson Cancer Center, Houston, Texas
| | - Bruce A Posner
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas
| | - Anthony J Davis
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, Texas
| | - John D Minna
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas.,Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, Texas
| | - John B MacMillan
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California
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50
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Segaert P, Lopes MB, Casimiro S, Vinga S, Rousseeuw PJ. Robust identification of target genes and outliers in triple-negative breast cancer data. Stat Methods Med Res 2018; 28:3042-3056. [PMID: 30146936 PMCID: PMC6745616 DOI: 10.1177/0962280218794722] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Correct classification of breast cancer subtypes is of high importance as it directly affects the therapeutic options. We focus on triple-negative breast cancer which has the worst prognosis among breast cancer types. Using cutting edge methods from the field of robust statistics, we analyze Breast Invasive Carcinoma transcriptomic data publicly available from The Cancer Genome Atlas data portal. Our analysis identifies statistical outliers that may correspond to misdiagnosed patients. Furthermore, it is illustrated that classical statistical methods may fail to identify outliers due to their heavy influence, prompting the need for robust statistics. Using robust sparse logistic regression we obtain 36 relevant genes, of which ca. 60% have been previously reported as biologically relevant to triple-negative breast cancer, reinforcing the validity of the method. The remaining 14 genes identified are new potential biomarkers for triple-negative breast cancer. Out of these, JAM3, SFT2D2, and PAPSS1 were previously associated to breast tumors or other types of cancer. The relevance of these genes is confirmed by the new DetectDeviatingCells outlier detection technique. A comparison of gene networks on the selected genes showed significant differences between triple-negative breast cancer and non-triple-negative breast cancer data. The individual role of FOXA1 in triple-negative breast cancer and non-triple-negative breast cancer, and the strong FOXA1-AGR2 connection in triple-negative breast cancer stand out. The goal of our paper is to contribute to the breast cancer/triple-negative breast cancer understanding and management. At the same time it demonstrates that robust regression and outlier detection constitute key strategies to cope with high-dimensional clinical data such as omics data.
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Affiliation(s)
| | - Marta B Lopes
- IDMEC, Instituto de Engenharia Mecânica, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Sandra Casimiro
- Luís Costa Lab, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Susana Vinga
- IDMEC, Instituto de Engenharia Mecânica, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,INESC-ID, Instituto de Engenharia de Sistemas e Computadores, Investigação e Desenvolvimento, Lisboa, Portugal
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