1
|
Patel JA, Kim H. The TIMELESS effort for timely DNA replication and protection. Cell Mol Life Sci 2023; 80:84. [PMID: 36892674 PMCID: PMC9998586 DOI: 10.1007/s00018-023-04738-3] [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: 01/06/2023] [Revised: 02/16/2023] [Accepted: 02/24/2023] [Indexed: 03/10/2023]
Abstract
Accurate replication of the genome is fundamental to cellular survival and tumor prevention. The DNA replication fork is vulnerable to DNA lesions and damages that impair replisome progression, and improper control over DNA replication stress inevitably causes fork stalling and collapse, a major source of genome instability that fuels tumorigenesis. The integrity of the DNA replication fork is maintained by the fork protection complex (FPC), in which TIMELESS (TIM) constitutes a key scaffold that couples the CMG helicase and replicative polymerase activities, in conjunction with its interaction with other proteins associated with the replication machinery. Loss of TIM or the FPC in general results in impaired fork progression, elevated fork stalling and breakage, and a defect in replication checkpoint activation, thus underscoring its pivotal role in protecting the integrity of both active and stalled replication forks. TIM is upregulated in multiple cancers, which may represent a replication vulnerability of cancer cells that could be exploited for new therapies. Here, we discuss recent advances on our understanding of the multifaceted roles of TIM in DNA replication and stalled fork protection, and how its complex functions are engaged in collaboration with other genome surveillance and maintenance factors.
Collapse
Affiliation(s)
- Jinal A Patel
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Basic Sciences Tower 8-125, 101 Nicolls Rd, Stony Brook, NY, 11794, USA
| | - Hyungjin Kim
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Basic Sciences Tower 8-125, 101 Nicolls Rd, Stony Brook, NY, 11794, USA.
- Stony Brook Cancer Center and Renaissance School of Medicine, Stony Brook University, Basic Sciences Tower 8-125, 101 Nicolls Rd, Stony Brook, NY, 11794, USA.
| |
Collapse
|
2
|
Hosseini K, Beirami SM, Forouhandeh H, Vahed SZ, Eyvazi S, Ramazani F, Tarhriz V, Ardalan M. The role of circadian gene timeless in gastrointestinal cancers. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
|
3
|
Shi WW, Guan JZ, Long YP, Song Q, Xiong Q, Qin BY, Ma ZQ, Hu Y, Yang B. Integrative transcriptional characterization of cell cycle checkpoint genes promotes clinical management and precision medicine in bladder carcinoma. Front Oncol 2022; 12:915662. [PMID: 36033441 PMCID: PMC9404245 DOI: 10.3389/fonc.2022.915662] [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: 04/08/2022] [Accepted: 07/20/2022] [Indexed: 12/24/2022] Open
Abstract
Background The aberrant regulation of cell cycle is significantly correlated with cancer carcinogenesis and progression, in which cell cycle checkpoints control phase transitions, cell cycle entry, progression, and exit. However, the integrative role of cell cycle checkpoint-related genes (CRGs) in bladder carcinoma (BC) remains unknown. Methods The transcriptomic data and clinical features of BC patients were downloaded from The Cancer Genome Atlas (TCGA), used to identify CRGs correlated with overall survival (OS) by univariate Cox regression analysis. Then, the multivariate and least absolute shrinkage and selection operator (LASSO) Cox regression analyses further developed a prognostic CRG signature, which was validated in three external datasets retrieved from Gene Expression Omnibus (GEO). The receiver operating characteristic curve (ROC) analysis was conducted for evaluating the performance of the CRG signature in prognosis prediction. RNA sequencing (RNA-Seq) was performed to explore the expression difference in the identified CRGs between tumor and normal tissue samples from 11 BC patients in the local cohort. Ultimately, genomic profiles and tumor microenvironment (TME), and the Genomics of Drug Sensitivity in Cancer (GDSC) were investigated to guide precision treatment for BC patients with different CRG features. Results The novel constructed 23-CRG prognostic signature could stratify BC patients into high-risk and low-risk groups with significantly different outcomes (median OS: 13.64 vs. 104.65 months). Notably, 19 CRGs were the first to be identified as being associated with BC progression. In three additional validation datasets (GSE13507, GSE31684, and GSE32548), higher CRG scores all indicated inferior survival, demonstrating the robust ability of the CRG signature in prognosis prediction. Moreover, the CRG signature as an independent prognostic factor had a robust and stable risk stratification for BC patients with different histological or clinical features. Then, a CRG signature-based nomogram with a better performance in prognostic prediction [concordance index (C-index): 0.76] was established. Functional enrichment analysis revealed that collagen-containing extracellular matrix (ECM), and ECM-related and MAPK signaling pathways were significantly associated with the signature. Further analysis showed that low-risk patients were characterized by particularly distinctive prevalence of FGFR3 (17.03% vs. 6.67%, p < 0.01) and POLE alterations (7.97% vs. 2.50%, p < 0.05), and enrichment of immune infiltrated cells (including CD8+ T cells, CD4+ naïve T cells, follicular helper T cells, Tregs, and myeloid dendritic cells). RNA-seq data in our local cohort supported the findings in the differentially expressed genes (DEGs) between tumor and normal tissue samples, and the difference in TME between high-risk and low-risk groups. Additionally, CRG signature score plus FGFR3 status divided BC patients into four molecular subtypes, with distinct prognosis, TME, and transcriptomic profiling of immune checkpoint genes. Of note, CRG signature score plus FGFR3 status could successfully distinguish BC patients who have a higher possibility of response to immunotherapy or chemotherapy drugs. Conclusions The CRG signature is a potent prognostic model for BC patients, and in combination with FGFR3 alterations, it had more practical capacity in the prediction of chemotherapy and immunotherapy response, helping guide clinical decision-making.
Collapse
Affiliation(s)
- Wei-Wei Shi
- Department of Medical Oncology, Senior Department of Oncology, The Fifth Medical Center of People’s Liberation Army (PLA) General Hospital, Beijing, China
| | - Jing-Zhi Guan
- Department of Medical Oncology, Senior Department of Oncology, The Fifth Medical Center of People’s Liberation Army (PLA) General Hospital, Beijing, China
| | - Ya-Ping Long
- School of Medicine, Nankai University, Tianjin, China
| | - Qi Song
- Department of Medical Oncology, Senior Department of Oncology, The Fifth Medical Center of People’s Liberation Army (PLA) General Hospital, Beijing, China
| | - Qi Xiong
- Department of Medical Oncology, Senior Department of Oncology, The Fifth Medical Center of People’s Liberation Army (PLA) General Hospital, Beijing, China
| | - Bo-Yu Qin
- Department of Medical Oncology, Senior Department of Oncology, The Fifth Medical Center of People’s Liberation Army (PLA) General Hospital, Beijing, China
| | - Zhi-Qiang Ma
- Department of Medical Oncology, Senior Department of Oncology, The Fifth Medical Center of People’s Liberation Army (PLA) General Hospital, Beijing, China
| | - Yi Hu
- Department of Medical Oncology, Senior Department of Oncology, The Fifth Medical Center of People’s Liberation Army (PLA) General Hospital, Beijing, China
- *Correspondence: Yi Hu, ; Bo Yang,
| | - Bo Yang
- Department of Medical Oncology, Senior Department of Oncology, The Fifth Medical Center of People’s Liberation Army (PLA) General Hospital, Beijing, China
- *Correspondence: Yi Hu, ; Bo Yang,
| |
Collapse
|
4
|
Cao M, Wang Y, Xiao Y, Zheng D, Zhi C, Xia X, Yuan X. Activation of the clock gene TIMELESS by H3k27 acetylation promotes colorectal cancer tumorigenesis by binding to Myosin-9. J Exp Clin Cancer Res 2021; 40:162. [PMID: 33971927 PMCID: PMC8108341 DOI: 10.1186/s13046-021-01936-4] [Citation(s) in RCA: 13] [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: 10/19/2020] [Accepted: 04/03/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a common tumor characterized by its high mortality. However, the underlying molecular mechanisms that drive CRC tumorigenesis are unclear. Clock genes have important roles in tumor development. In the present study, the expression and functions of clock gene TIMELESS (encoding the Timeless protein) in CRC were investigated. METHODS Immunohistochemistry, cell proliferation, migration, invasion, EMT and xenograft tumor experiments were used to prove the function of Timeless in the tumorigenesis of CRC. Immunoprecipitation, mass spectrometry, Immunofluorescence and Chromatin immunoprecipitation (ChIP) were utilized to clarify the mechanism of Timeless in regulating CRC tumorigenesis. RESULTS We found that Timeless was upregulated in CRC tissues compared with corresponding normal tissues and its expression was closely associated with the TNM stages and overall survival of CRC patients. Functional studies demonstrated that Timeless promoted the proliferation, invasion, and EMT of CRC cells in vitro and in vivo. Mechanistic investigations showed that Timeless activated the β-catenin signal pathway by binding to Myosin-9, which binds to β-catenin to induce its nuclear translocation. The upregulation of Timeless was attributed to CREB-binding protein (CBP)/p300-mediated H3K27 acetylation of the promoter region of Timeless. CONCLUSION Timeless regulates the tumorigenesis of CRC by binding to and regulating myosin-9, suggesting Timeless might be a potential prognostic biomarker and therapeutic target for CRC.
Collapse
Affiliation(s)
- Meng Cao
- Department of General Surgery, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Yi Wang
- Department of Anatomy, Histology and Embryology, Nanjing Medical University, Xuehai Building, Rm D509, 101 Longmian Avenue, Jiangning District, Nanjing, 211166, China
| | - Yijing Xiao
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, 210029, China
| | - Dandan Zheng
- Department of Anatomy, Histology and Embryology, Nanjing Medical University, Xuehai Building, Rm D509, 101 Longmian Avenue, Jiangning District, Nanjing, 211166, China
| | - Chunchun Zhi
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210002, China
| | - Xin Xia
- Department of Anatomy, Histology and Embryology, Nanjing Medical University, Xuehai Building, Rm D509, 101 Longmian Avenue, Jiangning District, Nanjing, 211166, China
| | - Xiaoqin Yuan
- Department of Anatomy, Histology and Embryology, Nanjing Medical University, Xuehai Building, Rm D509, 101 Longmian Avenue, Jiangning District, Nanjing, 211166, China.
- Key Laboratory for Aging & Disease, Nanjing Medical University, Nanjing, 211166, China.
| |
Collapse
|
5
|
Lindskrog SV, Prip F, Lamy P, Taber A, Groeneveld CS, Birkenkamp-Demtröder K, Jensen JB, Strandgaard T, Nordentoft I, Christensen E, Sokac M, Birkbak NJ, Maretty L, Hermann GG, Petersen AC, Weyerer V, Grimm MO, Horstmann M, Sjödahl G, Höglund M, Steiniche T, Mogensen K, de Reyniès A, Nawroth R, Jordan B, Lin X, Dragicevic D, Ward DG, Goel A, Hurst CD, Raman JD, Warrick JI, Segersten U, Sikic D, van Kessel KEM, Maurer T, Meeks JJ, DeGraff DJ, Bryan RT, Knowles MA, Simic T, Hartmann A, Zwarthoff EC, Malmström PU, Malats N, Real FX, Dyrskjøt L. An integrated multi-omics analysis identifies prognostic molecular subtypes of non-muscle-invasive bladder cancer. Nat Commun 2021; 12:2301. [PMID: 33863885 PMCID: PMC8052448 DOI: 10.1038/s41467-021-22465-w] [Citation(s) in RCA: 137] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 03/09/2021] [Indexed: 12/13/2022] Open
Abstract
The molecular landscape in non-muscle-invasive bladder cancer (NMIBC) is characterized by large biological heterogeneity with variable clinical outcomes. Here, we perform an integrative multi-omics analysis of patients diagnosed with NMIBC (n = 834). Transcriptomic analysis identifies four classes (1, 2a, 2b and 3) reflecting tumor biology and disease aggressiveness. Both transcriptome-based subtyping and the level of chromosomal instability provide independent prognostic value beyond established prognostic clinicopathological parameters. High chromosomal instability, p53-pathway disruption and APOBEC-related mutations are significantly associated with transcriptomic class 2a and poor outcome. RNA-derived immune cell infiltration is associated with chromosomally unstable tumors and enriched in class 2b. Spatial proteomics analysis confirms the higher infiltration of class 2b tumors and demonstrates an association between higher immune cell infiltration and lower recurrence rates. Finally, the independent prognostic value of the transcriptomic classes is documented in 1228 validation samples using a single sample classification tool. The classifier provides a framework for biomarker discovery and for optimizing treatment and surveillance in next-generation clinical trials.
Collapse
Affiliation(s)
- Sia Viborg Lindskrog
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Frederik Prip
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Philippe Lamy
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
| | - Ann Taber
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Clarice S Groeneveld
- Cartes d'Identité des Tumeurs (CIT) Program, Ligue Nationale Contre le Cancer, Paris, France
- Oncologie Moleculaire, UMR144, Institut Curie, Paris, France
| | - Karin Birkenkamp-Demtröder
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Jørgen Bjerggaard Jensen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Urology, Aarhus University Hospital, Aarhus N, Denmark
| | - Trine Strandgaard
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
| | - Emil Christensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Mateo Sokac
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Nicolai J Birkbak
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Lasse Maretty
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Gregers G Hermann
- Department of Urology, Herlev hospital, Copenhagen University, Copenhagen, Denmark
| | - Astrid C Petersen
- Department of Pathology, Aalborg University Hospital, Aalborg, Denmark
| | - Veronika Weyerer
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | | | - Marcus Horstmann
- Department of Urology, Jena University Hospital, Jena, Germany
- Department of Urology, Malteser Hospital St. Josephshospital, Krefeld Uerdingen, Krefeld, Germany
| | - Gottfrid Sjödahl
- Division of Urological Research, Department of Translational Medicine, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Mattias Höglund
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Torben Steiniche
- Department of Pathology, Aarhus University Hospital, Aarhus N, Denmark
| | - Karin Mogensen
- Department of Urology, Herlev hospital, Copenhagen University, Copenhagen, Denmark
| | - Aurélien de Reyniès
- Cartes d'Identité des Tumeurs (CIT) Program, Ligue Nationale Contre le Cancer, Paris, France
| | - Roman Nawroth
- Department of Urology, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany
| | - Brian Jordan
- Departments of Pathology, Urology, Biochemistry and Molecular Genetics, Northwestern University School of Medicine, Chicago, IL, USA
| | - Xiaoqi Lin
- Departments of Pathology, Urology, Biochemistry and Molecular Genetics, Northwestern University School of Medicine, Chicago, IL, USA
| | - Dejan Dragicevic
- Clinic of Urology, Clinical Centre of Serbia, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Douglas G Ward
- Bladder Cancer Research Centre, Institute of Cancer and Genomic Sciences, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Anshita Goel
- Bladder Cancer Research Centre, Institute of Cancer and Genomic Sciences, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Carolyn D Hurst
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Jay D Raman
- Department of Surgery, Division of Urology, Pennsylvania State University, Hershey, PA, USA
| | - Joshua I Warrick
- Department of Pathology and Laboratory Medicine, Division of Urology, Department of Biochemistry and Molecular Biology, Pennsylvania State University, Hershey, PA, USA
| | - Ulrika Segersten
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Danijel Sikic
- Department of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Kim E M van Kessel
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tobias Maurer
- Department of Urology, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany
- Department of Urology and Martini-Clinic, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Joshua J Meeks
- Departments of Pathology, Urology, Biochemistry and Molecular Genetics, Northwestern University School of Medicine, Chicago, IL, USA
| | - David J DeGraff
- Department of Pathology and Laboratory Medicine, Division of Urology, Department of Biochemistry and Molecular Biology, Pennsylvania State University, Hershey, PA, USA
| | - Richard T Bryan
- Bladder Cancer Research Centre, Institute of Cancer and Genomic Sciences, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Margaret A Knowles
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Tatjana Simic
- Institute of Medical and Clinical Biochemistry, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Ellen C Zwarthoff
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Per-Uno Malmström
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Center (CNIO), CIBERONC, Madrid, Spain
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Center (CNIO), Madrid, Spain
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, CIBERONC, Barcelona, Spain
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark.
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
| |
Collapse
|
6
|
Strandgaard T, Nordentoft I, Lamy P, Christensen E, Thomsen MBH, Jensen JB, Dyrskjøt L. Mutational Analysis of Field Cancerization in Bladder Cancer. Bladder Cancer 2020. [DOI: 10.3233/blc-200282] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND: Morphologically normal tissue, adjacent to tumors, contains multiple molecular changes, the so-called field cancerization. The multifocal and recurrent nature of bladder cancer has been hypothesized to originate from this. However, further studies are required to explore the mutational composition of normal tissue adjacent to tumors. OBJECTIVE: To analyze field cancerization in bladder cancer patients using a non-tumor guided approach. METHODS: We investigated the mutational landscape of normal appearing urothelium and paired bladder tumors from four patients by applying deep-targeted sequencing. RESULTS: Sequencing of 509 cancer driver genes revealed the presence of 2– 13 mutations exclusively localized in normal tissue (average target read depth 634×). Furthermore, 6– 13 mutations were shared between tumor and normal samples and 8– 75 mutations were exclusively detected in tumor samples. More mutations were observed in normal samples from patients with multifocal disease compared to patients with unifocal disease. Mutations in normal samples had lower variant allele fractions (VAF) compared to tumor mutations (p < 2.2*10–16). Furthermore, significant differences in the type of nucleotide changes between tumor, normal and shared mutations (p = 2.2*10–5) were observed, and mutations in APOBEC context were observed primarily among tumor mutations (p = 0.02). No differences in functional impact between normal, shared and tumor mutations were observed (p = 0.61). CONCLUSION: Overall, these findings support the presence of more than one field in the bladder, and document non-tumor specific driver mutations to be present in normal appearing bladder tissue.
Collapse
Affiliation(s)
- Trine Strandgaard
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Health, Aarhus University, Aarhus C, Denmark
| | - Iver Nordentoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
| | - Philippe Lamy
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
| | - Emil Christensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Health, Aarhus University, Aarhus C, Denmark
| | | | - Jørgen Bjerggaard Jensen
- Department of Clinical Medicine, Health, Aarhus University, Aarhus C, Denmark
- Department of Urology, Aarhus University Hospital, Aarhus N, Denmark
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Health, Aarhus University, Aarhus C, Denmark
| |
Collapse
|
7
|
Chakraborty A, Aziz F, Roh E, Le LTM, Dey R, Zhang T, Rathore MG, Biswas AS, Bode AM, Dong Z. Knock-down of the TIM/TIPIN complex promotes apoptosis in melanoma cells. Oncotarget 2020; 11:1846-1861. [PMID: 32499870 PMCID: PMC7244016 DOI: 10.18632/oncotarget.27572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/10/2020] [Indexed: 11/25/2022] Open
Abstract
The Timeless (TIM) and it's interacting partner TIPIN protein complex is well known for its role in replication checkpoints and normal DNA replication processes. Recent studies revealed the involvement of TIM and TIPIN in human malignancies; however, no evidence is available regarding the expression of the TIM/TIPIN protein complex or its potential role in melanoma. Therefore, we investigated the role of this complex in melanoma. To assess the role of the TIM/TIPIN complex in melanoma, we analyzed TIM/TIPIN expression data from the publicly accessible TCGA online database, Western blot analysis, and RT-qPCR in a panel of melanoma cell lines. Lentivirus-mediated TIM/TIPIN knockdown in A375 melanoma cells was used to examine proliferation, colony formation, and apoptosis. A xenograft tumor formation assay was also performed. The TIM/TIPIN complex is frequently overexpressed in melanoma cells compared to normal melanocytes. We also discovered that the overexpression of TIM and TIPIN was significantly associated with poorer prognosis of melanoma patients. Furthermore, we observed that shRNA-mediated knockdown of TIM and TIPIN reduced cell viability and proliferation due to the induction of apoptosis and increased levels of γH2AX, a marker of DNA damage. In a xenograft tumor nude mouse model, shRNA-knockdown of TIM/TIPIN significantly reduced tumor growth. Our results suggest that the TIM/TIPIN complex plays an important role in tumorigenesis of melanoma, which might reveal novel approaches for the development of new melanoma therapies. Our studies also provide a beginning structural basis for understanding the assembly of the TIM/TIPIN complex. Further mechanistic investigations are needed to determine the complex’s potential as a biomarker of melanoma susceptibility. Targeting TIM/TIPIN might be a potential therapeutic strategy against melanoma.
Collapse
Affiliation(s)
- Abhijit Chakraborty
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA.,Immunology, Allergy and Rheumatology Section, Baylor College of Medicine, Houston, TX 77030, USA
| | - Faisal Aziz
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Eunmiri Roh
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Le Thi My Le
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Raja Dey
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Tianshun Zhang
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Moeez G Rathore
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Aalekhya Sharma Biswas
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA.,Pediatric Gastroenterology and Liver Center, Baylor College of Medicine, Houston, Texas, Houston, TX 77030, USA
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Zigang Dong
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA.,College of Medicine, Zhengzhou University, Zhengzhou, Henan Province 450052, China
| |
Collapse
|
8
|
Zhou J, Zhang Y, Zou X, Kuai L, Wang L, Wang J, Shen F, Hu J, Zhang X, Huang Y, Chen Y. Aberrantly Expressed Timeless Regulates Cell Proliferation and Cisplatin Efficacy in Cervical Cancer. Hum Gene Ther 2020; 31:385-395. [PMID: 31870179 DOI: 10.1089/hum.2019.080] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Timeless is a regulator of molecular clockwork in Drosophila and related to cancer development in mammals. This study aimed to investigate the effect of Timeless on cell proliferation and cisplatin sensitivity in cervical cancer. Timeless expression was determined by bioinformatics analysis, immunohistochemistry, and quantitative polymerase chain reaction (qPCR). Chromatin immunoprecipitation assays and reporter gene assays were applied to determine the transcriptional factor contributing to Timeless upregulation. The effects of Timeless depletion on cell proliferation and cisplatin sensitivity were determined through in vitro and in vivo experiments. Cell apoptosis and senescence were assessed by flow cytometry and β-galactosidase staining. DNA damage and DNA repair pathways were determined by comet assay, immunofluorescent staining, and Western blot analysis. Timeless is aberrantly expressed in ∼52.5% of cervical cancer tissues. E2F1 and E2F4 contribute to the transcriptional activation of Timeless. Timeless depletion inhibits cell proliferation and increases cisplatin sensitivity in vitro and in vivo. Knockdown of Timeless induces cell apoptosis and cell senescence. Mechanically, Timeless silencing leads to DNA damage and impairs the activation of the ATR/CHK1 pathway in response to cisplatin in cervical cancer. Timeless is overexpressed in cervical cancer and regulates cell proliferation and cisplatin sensitivity, presenting an attractive target for cisplatin sensitizer in cervical cancer.
Collapse
Affiliation(s)
- Jinhua Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China.,Clinical Research Center of Obstetrics and Gynecology, Jiangsu Key Laboratory of Clinical Immunology, Soochow University, Suzhou, China.,Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yinghui Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xinwei Zou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Lingling Kuai
- Department of Obstetrics and Gynecology, Nanjing Maternity and Child Health Hospital, Nanjing, China
| | - Li Wang
- Department of Gynecology and Obstetrics, Changzhou Maternal and Child Health Care Hospital Affiliated Nanjing Medical University, Changzhou, China
| | - Juan Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Fangrong Shen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jinghui Hu
- Department of Gynecology, The First Affiliated Hospital of Zhejiang University Medical College, Hangzhou, China
| | - Xia Zhang
- Department of Obstetrics and Gynecology, TuHa Petroleum Hospital, Xinjiang, China
| | - Yazhen Huang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Youguo Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China.,Clinical Research Center of Obstetrics and Gynecology, Jiangsu Key Laboratory of Clinical Immunology, Soochow University, Suzhou, China.,Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, China
| |
Collapse
|
9
|
Bianco JN, Bergoglio V, Lin YL, Pillaire MJ, Schmitz AL, Gilhodes J, Lusque A, Mazières J, Lacroix-Triki M, Roumeliotis TI, Choudhary J, Moreaux J, Hoffmann JS, Tourrière H, Pasero P. Overexpression of Claspin and Timeless protects cancer cells from replication stress in a checkpoint-independent manner. Nat Commun 2019; 10:910. [PMID: 30796221 PMCID: PMC6385232 DOI: 10.1038/s41467-019-08886-8] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/05/2019] [Indexed: 12/31/2022] Open
Abstract
Oncogene-induced replication stress (RS) promotes cancer development but also impedes tumor growth by activating anti-cancer barriers. To determine how cancer cells adapt to RS, we have monitored the expression of different components of the ATR-CHK1 pathway in primary tumor samples. We show that unlike upstream components of the pathway, the checkpoint mediators Claspin and Timeless are overexpressed in a coordinated manner. Remarkably, reducing the levels of Claspin and Timeless in HCT116 cells to pretumoral levels impeded fork progression without affecting checkpoint signaling. These data indicate that high level of Claspin and Timeless increase RS tolerance by protecting replication forks in cancer cells. Moreover, we report that primary fibroblasts adapt to oncogene-induced RS by spontaneously overexpressing Claspin and Timeless, independently of ATR signaling. Altogether, these data indicate that enhanced levels of Claspin and Timeless represent a gain of function that protects cancer cells from of oncogene-induced RS in a checkpoint-independent manner.
Collapse
Affiliation(s)
- Julien N Bianco
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, 34396, Montpellier, France.,Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Valérie Bergoglio
- Cancer Research Center of Toulouse, INSERM U1037, CNRS ERL5294, University of Toulouse 3, 31037, Toulouse, France
| | - Yea-Lih Lin
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, 34396, Montpellier, France
| | - Marie-Jeanne Pillaire
- Cancer Research Center of Toulouse, INSERM U1037, CNRS ERL5294, University of Toulouse 3, 31037, Toulouse, France
| | - Anne-Lyne Schmitz
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, 34396, Montpellier, France
| | - Julia Gilhodes
- Clinical trials Office - Biostatistics Unit, Institute Claudius Regaud, Institute Universitaire du Cancer Toulouse-Oncopole (IUCT-O), 31100, Toulouse, France
| | - Amelie Lusque
- Clinical trials Office - Biostatistics Unit, Institute Claudius Regaud, Institute Universitaire du Cancer Toulouse-Oncopole (IUCT-O), 31100, Toulouse, France
| | - Julien Mazières
- Thoracic Oncology Department, Toulouse University Hospital, University Paul Sabatier, 31062, Toulouse, France
| | | | | | | | - Jérôme Moreaux
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, 34396, Montpellier, France
| | - Jean-Sébastien Hoffmann
- Cancer Research Center of Toulouse, INSERM U1037, CNRS ERL5294, University of Toulouse 3, 31037, Toulouse, France
| | - Hélène Tourrière
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, 34396, Montpellier, France.
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, 34396, Montpellier, France.
| |
Collapse
|
10
|
Liao H, Xie X, Xu Y, Huang G. Identification of driver genes associated with chemotherapy resistance of Ewing's sarcoma. Onco Targets Ther 2018; 11:6947-6956. [PMID: 30410352 PMCID: PMC6199211 DOI: 10.2147/ott.s172190] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Background The aim of this study was to identify the driver genes associated with chemotherapy resistance of Ewing’s sarcoma and potential targets for Ewing’s sarcoma treatment. Methods Two mRNA microarray datasets, GSE12102 and GSE17679, were downloaded from the Gene Expression Omnibus database, which contain 94 human Ewing’s sarcoma samples, including 65 from those who experienced a relapse and 29 from those with no evidence of disease. The differen tially expressed genes (DEGs) were identified using LIMMA package R. Subsequently, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed for DEGs using Database for Annotation, Visualization and Integrated Analysis. The protein–protein interaction network was constructed using Cytoscape software, and module analysis was performed using Molecular Complex Detection. Results A total of 206 upregulated DEGs and 141 downregulated DEGs were identified. Upregulated DEGs were primarily enriched in DNA replication, nucleoplasm and protein kinase binding for biological processes, cellular component and molecular functions, respectively. Downregulated DEGs were predominantly involved in receptor clustering, membrane raft, and ligand-dependent nuclear receptor binding. The protein–protein interaction network of DEGs consisted of 150 nodes and 304 interactions. Thirteen hub genes were identified, and biological analysis revealed that these genes were primarily enriched in cell division, cell cycle, and mitosis. Furthermore, based on closeness centrality, betweenness centrality, and degree centrality, the three most significant genes were identified as GAPDH, AURKA, and EHMT2. Furthermore, the significant network module was composed of nine genes. These genes were primarily enriched in mitotic nuclear division, mitotic chromosome condensation, and nucleoplasm. Conclusion These hub genes, especially GAPDH, AURKA, and EHMT2, may be closely associated with the progression of Ewing’s sarcoma chemotherapy resistance, and further experiments are needed for confirmation.
Collapse
Affiliation(s)
- Hongyi Liao
- Department of Orthopedic Surgery, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, People's Republic of China
| | - Xianbiao Xie
- Department of Orthopedic Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China,
| | - Yuanyuan Xu
- Department of Pediatrics, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Gang Huang
- Department of Orthopedic Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China,
| |
Collapse
|
11
|
Jaguva Vasudevan AA, Kreimer U, Schulz WA, Krikoni A, Schumann GG, Häussinger D, Münk C, Goering W. APOBEC3B Activity Is Prevalent in Urothelial Carcinoma Cells and Only Slightly Affected by LINE-1 Expression. Front Microbiol 2018; 9:2088. [PMID: 30233553 PMCID: PMC6132077 DOI: 10.3389/fmicb.2018.02088] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 08/15/2018] [Indexed: 12/20/2022] Open
Abstract
The most common mutational signature in urothelial carcinoma (UC), the most common type of urinary bladder cancer is assumed to be caused by the misdirected activity of APOBEC3 (A3) cytidine deaminases, especially A3A or A3B, which are known to normally restrict the propagation of exogenous viruses and endogenous retroelements such as LINE-1 (L1). The involvement of A3 proteins in urothelial carcinogenesis is unexpected because, to date, UC is thought to be caused by chemical carcinogens rather than viral activity. Therefore, we explored the relationship between A3 expression and L1 activity, which is generally upregulated in UC. We found that UC cell lines highly express A3B and in some cases A3G, but not A3A, and exhibit corresponding cytidine deamination activity in vitro. While we observed evidence suggesting that L1 expression has a weak positive effect on A3B and A3G expression and A3B promoter activity, neither efficient siRNA-mediated knockdown nor overexpression of functional L1 elements affected catalytic activity of A3 proteins consistently. However, L1 knockdown diminished proliferation of a UC cell line exhibiting robust endogenous L1 expression, but had little impact on a cell line with low L1 expression levels. Our results indicate that UC cells express A3B at levels exceeding A3A levels by far, making A3B the prime candidate for causing genomic mutations. Our data provide evidence that L1 activation constitutes only a minor and negligible factor involved in induction or upregulation of endogenous A3 expression in UC.
Collapse
Affiliation(s)
- Ananda Ayyappan Jaguva Vasudevan
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ulrike Kreimer
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Wolfgang A Schulz
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Aikaterini Krikoni
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Gerald G Schumann
- Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, Germany
| | - Dieter Häussinger
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Carsten Münk
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Wolfgang Goering
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Institute of Pathology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| |
Collapse
|
12
|
Höhn A, Krüger K, Skowron MA, Bormann S, Schumacher L, Schulz WA, Hoffmann MJ, Niegisch G, Fritz G. Distinct mechanisms contribute to acquired cisplatin resistance of urothelial carcinoma cells. Oncotarget 2018; 7:41320-41335. [PMID: 27191498 PMCID: PMC5173062 DOI: 10.18632/oncotarget.9321] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 04/22/2016] [Indexed: 12/12/2022] Open
Abstract
Cisplatin (CisPt) is frequently used in the therapy of urothelial carcinoma (UC). Its therapeutic efficacy is limited by inherent or acquired drug resistance. Here, we comparatively investigated the CisPt-induced response of two different parental urothelial carcinoma cell lines (RT-112, J-82) with that of respective drug resistant variants (RT-112R, J-82R) obtained upon month-long CisPt selection. Parental RT-112 cells were ~2.5 fold more resistant to CisPt than J-82 cells and showed a different expression pattern of CisPt-related resistance factors. CisPt resistant RT-112R and J-82R variants revealed a 2–3-fold increased CisPt resistance as compared to their corresponding parental counterparts. Acquired CisPt resistance was accompanied by morphological alterations resembling epithelial mesenchymal transition (EMT). RT-112R cells revealed lower apoptotic frequency and more pronounced G2/M arrest following CisPt exposure than RT-112 cells, whereas no differences in death induction were observed between J-82 and J-82R cells. CisPt resistant J-82R cells however were characterized by a reduced formation of CisPt-induced DNA damage and related DNA damage response (DDR) as compared to J-82 cells. Such difference was not observed between RT-112R and RT-112 cells. J-82R cells showed an enhanced sensitivity to pharmacological inhibition of checkpoint kinase 1 (Chk1) and, moreover, could be re-sensitized to CisPt upon Chk1 inhibition. Based on the data we suggest that mechanisms of acquired CisPt resistance of individual UC cells are substantially different, with apoptosis- and DDR-related mechanisms being of particular relevance. Moreover, the findings indicate that targeting of Chk1 might be useful to overcome acquired CisPt resistance of certain subtypes of UC.
Collapse
Affiliation(s)
- Annika Höhn
- Institute of Toxicology, Medical Faculty, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Katharina Krüger
- Institute of Toxicology, Medical Faculty, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Margaretha A Skowron
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Stefanie Bormann
- Institute of Toxicology, Medical Faculty, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Lena Schumacher
- Institute of Toxicology, Medical Faculty, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Wolfgang A Schulz
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Michèle J Hoffmann
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Günter Niegisch
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Gerhard Fritz
- Institute of Toxicology, Medical Faculty, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| |
Collapse
|
13
|
Chi L, Zou Y, Qin L, Ma W, Hao Y, Tang Y, Luo R, Wu Z. TIMELESS contributes to the progression of breast cancer through activation of MYC. Breast Cancer Res 2017; 19:53. [PMID: 28464854 PMCID: PMC5414141 DOI: 10.1186/s13058-017-0838-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/18/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Breast cancer is the most common malignancy and the leading cause of cancer death among women. TIMELESS (TIM), a circadian rhythm regulator, has been recently implicated in the progression of human cancer. However, the role of TIM in the progression of breast cancer has not been well-characterized. METHODS Immunohistochemistry (IHC) staining was used to examine TIM levels in breast cancer specimens. Mammosphere formation analysis and side population analysis were used to examine the effect of TIM on the self-renewal of breast cancer stem cells. A wound healing assay and a Transwell assay were used to determine the role of TIM in breast cancer cell migration and invasion. A soft agar growth assay in vitro and tumorigenicity in vivo were used to determine the role of TIM in tumorigenicity. RESULTS TIM levels in both breast cancer cell lines and tissues were significantly upregulated. Patients with high TIM had poorer prognosis than patients with low TIM. Overexpression of TIM dramatically enhanced, while knockdown of TIM suppressed the self-renewal of cancer stem cells (CSCs), cell invasion and migration abilities of breast cancer cells in vitro. Moreover, overexpression of TIM significantly augmented, while knockdown of TIM reduced the tumorigenicity of breast cancer cells in vivo. Mechanism studies revealed that TIM upregulated the expression and the trans-activity of the well-known oncogene MYC. Inhibition of MYC significantly blocked the effects of TIM on CSC population, cell invasion and anchor-independent cell growth. CONCLUSION TIM plays an important role in promoting breast cancer progression and may represent a novel therapeutic target for breast cancer.
Collapse
Affiliation(s)
- Limin Chi
- Cancer Center, TCM-Integrated Hospital, Southern Medical University, Guangzhou, 510315, China
| | - Yujiao Zou
- Cancer Center, TCM-Integrated Hospital, Southern Medical University, Guangzhou, 510315, China
| | - Ling Qin
- Cancer Center, TCM-Integrated Hospital, Southern Medical University, Guangzhou, 510315, China
| | - Weifeng Ma
- Department of Microbiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Yanyan Hao
- Cancer Center, TCM-Integrated Hospital, Southern Medical University, Guangzhou, 510315, China
| | - Yao Tang
- Cancer Center, TCM-Integrated Hospital, Southern Medical University, Guangzhou, 510315, China
| | - Rongcheng Luo
- Cancer Center, TCM-Integrated Hospital, Southern Medical University, Guangzhou, 510315, China.
| | - Ziqing Wu
- Cancer Center, TCM-Integrated Hospital, Southern Medical University, Guangzhou, 510315, China. .,Key Laboratory of Molecular Tumor Pathology of Guangdong Province, Southern Medical University, Guangzhou, 510515, China. .,Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China.
| |
Collapse
|
14
|
A stemness-related ZEB1-MSRB3 axis governs cellular pliancy and breast cancer genome stability. Nat Med 2017; 23:568-578. [PMID: 28394329 DOI: 10.1038/nm.4323] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 03/13/2017] [Indexed: 12/30/2022]
Abstract
Chromosomal instability (CIN), a feature of most adult neoplasms from their early stages onward, is a driver of tumorigenesis. However, several malignancy subtypes, including some triple-negative breast cancers, display a paucity of genomic aberrations, thus suggesting that tumor development may occur in the absence of CIN. Here we show that the differentiation status of normal human mammary epithelial cells dictates cell behavior after an oncogenic event and predetermines the genetic routes toward malignancy. Whereas oncogene induction in differentiated cells induces massive DNA damage, mammary stem cells are resistant, owing to a preemptive program driven by the transcription factor ZEB1 and the methionine sulfoxide reductase MSRB3. The prevention of oncogene-induced DNA damage precludes induction of the oncosuppressive p53-dependent DNA-damage response, thereby increasing stem cells' intrinsic susceptibility to malignant transformation. In accord with this model, a subclass of breast neoplasms exhibit unique pathological features, including high ZEB1 expression, a low frequency of TP53 mutations and low CIN.
Collapse
|
15
|
Vincent M, Mundbjerg K, Skou Pedersen J, Liang G, Jones PA, Ørntoft TF, Dalsgaard Sørensen K, Wiuf C. epiG: statistical inference and profiling of DNA methylation from whole-genome bisulfite sequencing data. Genome Biol 2017; 18:38. [PMID: 28222791 PMCID: PMC5320668 DOI: 10.1186/s13059-017-1168-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 02/07/2017] [Indexed: 02/11/2023] Open
Abstract
The study of epigenetic heterogeneity at the level of individual cells and in whole populations is the key to understanding cellular differentiation, organismal development, and the evolution of cancer. We develop a statistical method, epiG, to infer and differentiate between different epi-allelic haplotypes, annotated with CpG methylation status and DNA polymorphisms, from whole-genome bisulfite sequencing data, and nucleosome occupancy from NOMe-seq data. We demonstrate the capabilities of the method by inferring allele-specific methylation and nucleosome occupancy in cell lines, and colon and tumor samples, and by benchmarking the method against independent experimental data.
Collapse
Affiliation(s)
- Martin Vincent
- Department of Mathematical Sciences, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Kamilla Mundbjerg
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, 90089-9176, CA, USA
| | - Jakob Skou Pedersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, 8200, Denmark
| | - Gangning Liang
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, 90089, CA, USA
| | - Peter A Jones
- Van Andel Research Institute, Grand Rapids, 49503, MI, USA
| | - Torben Falck Ørntoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, 8200, Denmark
| | | | - Carsten Wiuf
- Department of Mathematical Sciences, University of Copenhagen, Copenhagen, 2100, Denmark.
| |
Collapse
|
16
|
Christensen E, Birkenkamp-Demtröder K, Nordentoft I, Høyer S, van der Keur K, van Kessel K, Zwarthoff E, Agerbæk M, Ørntoft TF, Jensen JB, Dyrskjøt L. Liquid Biopsy Analysis of FGFR3 and PIK3CA Hotspot Mutations for Disease Surveillance in Bladder Cancer. Eur Urol 2017; 71:961-969. [PMID: 28069289 DOI: 10.1016/j.eururo.2016.12.016] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 12/15/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND Disease surveillance in patients with bladder cancer is important for early diagnosis of progression and metastasis and for optimised treatment. OBJECTIVE To develop urine and plasma assays for disease surveillance for patients with FGFR3 and PIK3CA tumour mutations. DESIGN, SETTING, AND PARTICIPANTS Droplet digital polymerase chain reaction (ddPCR) assays were developed and tumour DNA from two patient cohorts was screened for FGFR3 and PIK3CA hotspot mutations. One cohort included 363 patients with non-muscle-invasive bladder cancer (NMIBC). The other cohort included 468 patients with bladder cancer undergoing radical cystectomy (Cx). Urine supernatants (NMIBC n=216, Cx n=27) and plasma samples (NMIBC n=39, Cx n=27) from patients harbouring mutations were subsequently screened using ddPCR assays. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Progression-free survival, recurrence-free survival, and overall survival were measured. Fisher's exact test, the Wilcoxon rank-sum test and Cox regression analysis were applied. RESULTS AND LIMITATIONS In total, 36% of the NMIBC patients (129/363) and 11% of the Cx patients (44/403) harboured at least one FGFR3 or PIK3CA mutation. Screening of DNA from serial urine supernatants from the NMIBC cohort revealed that high levels of tumour DNA (tDNA) were associated with later disease progression in NMIBC (p=0.003). Furthermore, high levels of tDNA in plasma samples were associated with recurrence in the Cx cohort (p=0.016). A positive correlation between tDNA levels in urine and plasma was observed (correlation coefficient 0.6). The retrospective study design and low volumes of plasma available for analysis were limitations of the study. CONCLUSIONS Increased levels of FGFR3 and PIK3CA mutated DNA in urine and plasma are indicative of later progression and metastasis in bladder cancer. PATIENT SUMMARY Urine and plasma from patients with bladder cancer may be monitored for diagnosis of progression and metastasis using mutation assays.
Collapse
Affiliation(s)
- Emil Christensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | - Iver Nordentoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Søren Høyer
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Kirstin van der Keur
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Kim van Kessel
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Ellen Zwarthoff
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Mads Agerbæk
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | | | | | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.
| |
Collapse
|
17
|
Zhang W, He W, Shi Y, Zhao J, Liu S, Zhang F, Yang J, Xie C, Zhang Y. Aberrant TIMELESS expression is associated with poor clinical survival and lymph node metastasis in early-stage cervical carcinoma. Int J Oncol 2016; 50:173-184. [DOI: 10.3892/ijo.2016.3784] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 11/22/2016] [Indexed: 11/06/2022] Open
|
18
|
Mutant allele specific imbalance in oncogenes with copy number alterations: Occurrence, mechanisms, and potential clinical implications. Cancer Lett 2016; 384:86-93. [PMID: 27725226 DOI: 10.1016/j.canlet.2016.10.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/03/2016] [Accepted: 10/03/2016] [Indexed: 01/16/2023]
Abstract
Mutant allele specific imbalance (MASI) was initially coined to describe copy number alterations associated with the mutant allele of an oncogene. The copy number gain (CNG) specific to the mutant allele can be readily observed in electropherograms. With the development of genome-wide analyses at base-pair resolution with copy number counts, we can now further differentiate MASI into those with CNG, with copy neutral alteration (also termed acquired uniparental disomy; UPD), or with loss of heterozygosity (LOH) due to the loss of the wild-type (WT) allele. Here we summarize the occurrence of MASI with CNG, aUPD, or MASI with LOH in some major oncogenes (such as EGFR, KRAS, PIK3CA, and BRAF). We also discuss how these various classifications of MASI have been demonstrated to impact tumorigenesis, progression, metastasis, prognosis, and potentially therapeutic responses in cancer, notably in lung, colorectal, and pancreatic cancers.
Collapse
|
19
|
Clinicopathological and Prognostic Value of Ki-67 Expression in Bladder Cancer: A Systematic Review and Meta-Analysis. PLoS One 2016; 11:e0158891. [PMID: 27410033 PMCID: PMC4943634 DOI: 10.1371/journal.pone.0158891] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 06/23/2016] [Indexed: 01/11/2023] Open
Abstract
Background Ki-67 is an established marker of cell proliferation, and the Ki-67 index correlates with the clinical course of several cancer types, including bladder cancer (BC). However, the clinicopathological and prognostic significance of Ki-67 in bladder cancer remains unclear. Therefore, we performed a systematic review and meta-analysis to clarify this relationship. Methods A comprehensive literature search for relevant studies published up to February 1, 2016, was performed using PubMed, Cochrane Library, Embase and ISI Web of Knowledge. The effects of Ki-67 expression on survival outcome in patients with BC and BC subtypes were evaluated. Furthermore, the relationship between Ki-67 expression and the clinicopathological features of BC were assessed. Results Thirty-one studies with 5147 bladder cancer patients were selected for evaluation. Ki-67 expression was significantly associated with shorter recurrence-free (HR 1.69, 95% CI: 1.33–2.14), progression-free (HR 1.89, 95% CI: 1.43–2.51), overall (HR 2.03, 95% CI: 1.31–3.16), and cancer-specific (HR 1.69, 95% CI: 1.47–1.95) survival. Moreover, whereas high expression was more common in high tumor stage, recurrence status, tumor size, there was no correlation between high Ki-67 expression and age, gender, smoking habits, and tumor number. Importantly, analysis of the different subgroups of BC suggested that significant correlations between high Ki-67 expression and survival outcome (recurrence-free/progression-free/overall/cancer-specific survival) are present only in European-American patients. Conclusion The present results indicate that over-expression of Ki-67 is distinctly correlated with poor patient survival. Ki-67 may serve as a valuable biomarker for prognosis in BC patients, particularly in non-Asian BC patients. The results suggest no significant association between Ki-67 expression and BC prognosis in Asian patients. Further efforts are needed to fully clarify this relationship.
Collapse
|
20
|
Li K, Shen B, Cheng X, Ma D, Jing X, Liu X, Yang W, Peng C, Qiu W. Phenotypic and Signaling Consequences of a Novel Aberrantly Spliced Transcript FGF Receptor-3 in Hepatocellular Carcinoma. Cancer Res 2016; 76:4205-15. [PMID: 27267910 DOI: 10.1158/0008-5472.can-15-3385] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 04/07/2016] [Indexed: 11/16/2022]
Abstract
Fibroblast growth factor receptor 3 (FGFR3) plays important roles in cell proliferation, differentiation, and angiogenesis. FGFR3 is abnormally upregulated in hepatocellular carcinoma (HCC), where it correlates positively with clinicopathologic index, HCC differentiation, and advanced nuclear grade. In this study, we describe an aberrantly spliced transcript of FGFR3, termed FGFR3Δ7-9, was identified as a high frequency even in HCC. FGFR3Δ7-9 lacks exons encoding the immunoglobulin-like III domain and promoted the proliferation, migration, and metastasis of HCC cells both in vitro and in vivo Coimmunoprecipation and surface plasmon resonance assays demonstrated that the binding affinity of the aberrant FGFR3Δ7-9 receptor to FGFs was significantly higher than wild-type FGFR3IIIc Furthermore, FGFR3Δ7-9 could be self-activated by homodimerization and autophosphorylation even in the absence of ligand. Finally, FGFR3Δ7-9 more potently induced phosphorylation of the ERK and AKT kinases, leading to abnormal downstream signaling through the ERK and PI3K/AKT/mTOR pathways. FGFR3Δ7-9 also upregulated the metastasis-associated molecules Snail, MMP-9, and downregulated E-cadherin, which associated directly with FGFR3Δ7-9 Thus, as a ligand-dependent or -independent receptor, FGFR3Δ7-9 exerted multiple potent oncogenic functions in HCC cells, including proliferation, migration, and lung metastatic capacity. Overall, FGFR3 mRNA missplicing in HCC contributes significantly to its malignant character, with implications for therapeutic targeting. Cancer Res; 76(14); 4205-15. ©2016 AACR.
Collapse
Affiliation(s)
- Ke Li
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Baiyong Shen
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xi Cheng
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ding Ma
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoqian Jing
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinyu Liu
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weiping Yang
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chenghong Peng
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Weihua Qiu
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| |
Collapse
|
21
|
A Timeless Link Between Circadian Patterns and Disease. Trends Mol Med 2016; 22:68-81. [DOI: 10.1016/j.molmed.2015.11.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/16/2015] [Accepted: 11/18/2015] [Indexed: 02/06/2023]
|
22
|
Macheret M, Halazonetis TD. DNA replication stress as a hallmark of cancer. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2015; 10:425-48. [PMID: 25621662 DOI: 10.1146/annurev-pathol-012414-040424] [Citation(s) in RCA: 507] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human cancers share properties referred to as hallmarks, among which sustained proliferation, escape from apoptosis, and genomic instability are the most pervasive. The sustained proliferation hallmark can be explained by mutations in oncogenes and tumor suppressors that regulate cell growth, whereas the escape from apoptosis hallmark can be explained by mutations in the TP53, ATM, or MDM2 genes. A model to explain the presence of the three hallmarks listed above, as well as the patterns of genomic instability observed in human cancers, proposes that the genes driving cell proliferation induce DNA replication stress, which, in turn, generates genomic instability and selects for escape from apoptosis. Here, we review the data that support this model, as well as the mechanisms by which oncogenes induce replication stress. Further, we argue that DNA replication stress should be considered as a hallmark of cancer because it likely drives cancer development and is very prevalent.
Collapse
Affiliation(s)
- Morgane Macheret
- Department of Molecular Biology, University of Geneva, 1205 Geneva, Switzerland;
| | | |
Collapse
|
23
|
Baldeyron C, Brisson A, Tesson B, Némati F, Koundrioukoff S, Saliba E, De Koning L, Martel E, Ye M, Rigaill G, Meseure D, Nicolas A, Gentien D, Decaudin D, Debatisse M, Depil S, Cruzalegui F, Pierré A, Roman-Roman S, Tucker GC, Dubois T. TIPIN depletion leads to apoptosis in breast cancer cells. Mol Oncol 2015; 9:1580-98. [PMID: 26004086 DOI: 10.1016/j.molonc.2015.04.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 03/10/2015] [Accepted: 04/23/2015] [Indexed: 12/31/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is the breast cancer subgroup with the most aggressive clinical behavior. Alternatives to conventional chemotherapy are required to improve the survival of TNBC patients. Gene-expression analyses for different breast cancer subtypes revealed significant overexpression of the Timeless-interacting protein (TIPIN), which is involved in the stability of DNA replication forks, in the highly proliferative associated TNBC samples. Immunohistochemistry analysis showed higher expression of TIPIN in the most proliferative and aggressive breast cancer subtypes including TNBC, and no TIPIN expression in healthy breast tissues. The depletion of TIPIN by RNA interference impairs the proliferation of both human breast cancer and non-tumorigenic cell lines. However, this effect may be specifically associated with apoptosis in breast cancer cells. TIPIN silencing results in higher levels of single-stranded DNA (ssDNA), indicative of replicative stress (RS), in TNBC compared to non-tumorigenic cells. Upon TIPIN depletion, the speed of DNA replication fork was significantly decreased in all BC cells. However, TIPIN-depleted TNBC cells are unable to fire additional replication origins in response to RS and therefore undergo apoptosis. TIPIN knockdown in TNBC cells decreases tumorigenicity in vitro and delays tumor growth in vivo. Our findings suggest that TIPIN is important for the maintenance of DNA replication and represents a potential treatment target for the worst prognosis associated breast cancers, such as TNBC.
Collapse
Affiliation(s)
- Céline Baldeyron
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Breast Cancer Biology Group, Department of Translational Research, Paris, F-75248, France
| | - Amélie Brisson
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Breast Cancer Biology Group, Department of Translational Research, Paris, F-75248, France
| | - Bruno Tesson
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Breast Cancer Biology Group, Department of Translational Research, Paris, F-75248, France; INSERM, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Paris, F-75248, France; Mines ParisTech, Fontainebleau, F-77300, France
| | - Fariba Némati
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Laboratory of Preclinical Investigation, Department of Translational Research, Paris, F-75248, France
| | - Stéphane Koundrioukoff
- Institut Curie, Centre de Recherche, Paris, F-75248, France; CNRS, UMR 3244, Paris, F-75248, France; Université Pierre and Marie Curie Paris VI, Paris, F-75005, France
| | - Elie Saliba
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Breast Cancer Biology Group, Department of Translational Research, Paris, F-75248, France
| | - Leanne De Koning
- Institut Curie, Centre de Recherche, Paris, F-75248, France; RPPA Platform, Department of Translational Research, Paris, F-75248, France
| | - Elise Martel
- Institut Curie, Investigative Pathology Platform, Paris, F-75248, France
| | - Mengliang Ye
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Breast Cancer Biology Group, Department of Translational Research, Paris, F-75248, France
| | - Guillem Rigaill
- Unité de Recherche en Génomique Végétale, INRA-CNRS-Université d'Evry Val d'Essonne, Evry, F-91057, France
| | - Didier Meseure
- Institut Curie, Investigative Pathology Platform, Paris, F-75248, France
| | - André Nicolas
- Institut Curie, Investigative Pathology Platform, Paris, F-75248, France
| | - David Gentien
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Platform of Molecular Biology Facilities, Department of Translational Research, Paris, F-75248, France
| | - Didier Decaudin
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Laboratory of Preclinical Investigation, Department of Translational Research, Paris, F-75248, France
| | - Michelle Debatisse
- Institut Curie, Centre de Recherche, Paris, F-75248, France; CNRS, UMR 3244, Paris, F-75248, France; Université Pierre and Marie Curie Paris VI, Paris, F-75005, France
| | - Stéphane Depil
- Institut de Recherches SERVIER, Pôle Innovation Thérapeutique Oncologie, Croissy-sur-Seine, F-78290, France
| | - Francisco Cruzalegui
- Institut de Recherches SERVIER, Pôle Innovation Thérapeutique Oncologie, Croissy-sur-Seine, F-78290, France
| | - Alain Pierré
- Institut de Recherches SERVIER, Pôle Innovation Thérapeutique Oncologie, Croissy-sur-Seine, F-78290, France
| | - Sergio Roman-Roman
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Breast Cancer Biology Group, Department of Translational Research, Paris, F-75248, France
| | - Gordon C Tucker
- Institut de Recherches SERVIER, Pôle Innovation Thérapeutique Oncologie, Croissy-sur-Seine, F-78290, France
| | - Thierry Dubois
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Breast Cancer Biology Group, Department of Translational Research, Paris, F-75248, France.
| |
Collapse
|
24
|
Watkins JA, Irshad S, Grigoriadis A, Tutt ANJ. Genomic scars as biomarkers of homologous recombination deficiency and drug response in breast and ovarian cancers. Breast Cancer Res 2014; 16:211. [PMID: 25093514 PMCID: PMC4053155 DOI: 10.1186/bcr3670] [Citation(s) in RCA: 227] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Poly (ADP-ribose) polymerase (PARP) inhibitors and platinum-based chemotherapies have been found to be particularly effective in tumors that harbor deleterious germline or somatic mutations in the BRCA1 or BRCA2 genes, the products of which contribute to the conservative homologous recombination repair of DNA double-strand breaks. Nonetheless, several setbacks in clinical trial settings have highlighted some of the issues surrounding the investigation of PARP inhibitors, especially the identification of patients who stand to benefit from such drugs. One potential approach to finding this patient subpopulation is to examine the tumor DNA for evidence of a homologous recombination defect. However, although the genomes of many breast and ovarian cancers are replete with aberrations, the presence of numerous factors able to shape the genomic landscape means that only some of the observed DNA abnormalities are the outcome of a cancer cell’s inability to faithfully repair DNA double-strand breaks. Consequently, recently developed methods for comprehensively capturing the diverse ways in which homologous recombination deficiencies may arise beyond BRCA1/2 mutation have used DNA microarray and sequencing data to account for potentially confounding features in the genome. Scores capturing telomeric allelic imbalance, loss of heterozygosity (LOH) and large scale transition score, as well as the total number of coding mutations are measures that summarize the total burden of certain forms of genomic abnormality. By contrast, other studies have comprehensively catalogued different types of mutational pattern and their relative contributions to a given tumor sample. Although at least one study to explore the use of the LOH scar in a prospective clinical trial of a PARP inhibitor in ovarian cancer is under way, limitations that result in a relatively low positive predictive value for these biomarkers remain. Tumors whose genome has undergone one or more events that restore high-fidelity homologous recombination are likely to be misclassified as double-strand break repair-deficient and thereby sensitive to PARP inhibitors and DNA damaging chemotherapies as a result of prior repair deficiency and its genomic scarring. Therefore, we propose that integration of a genomic scar-based biomarker with a marker of resistance in a high genomic scarring burden context may improve the performance of any companion diagnostic for PARP inhibitors.
Collapse
|
25
|
Yoshida K, Sato M, Hase T, Elshazley M, Yamashita R, Usami N, Taniguchi T, Yokoi K, Nakamura S, Kondo M, Girard L, Minna JD, Hasegawa Y. TIMELESS is overexpressed in lung cancer and its expression correlates with poor patient survival. Cancer Sci 2013; 104:171-7. [PMID: 23173913 DOI: 10.1111/cas.12068] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 11/13/2012] [Accepted: 11/14/2012] [Indexed: 12/31/2022] Open
Abstract
TIMELESS (TIM) is a mammalian homolog of a Drosophila circadian rhythm gene, but its circadian properties in mammals have yet to be determined. TIM appears to be essential for replication protection and genomic stability. Recently, the involvement of TIM in human malignancies has been reported; therefore, we investigated the role of TIM in lung cancer. Microarray expression analysis of lung cancer cell lines showed that TIM expression was elevated 3.7-fold (P < 0.001) in non-small cell lung cancer cell lines (n = 116) compared to normal lung controls (n = 59). In addition, small cell lung cancer cell lines (n = 29) expressed TIM at levels 2.2-fold (P < 0.001) higher than non-small cell lung cancer. Western blot analysis of 22 lung cancer cell lines revealed that all of them expressed TIM protein and that 20 cell lines (91%) expressed TIM protein at higher levels than a normal control line. Remarkably, immunohistochemistry of 30 surgically resected lung cancer specimens showed that all lung cancer specimens but no matched normal lung tissues were positive for TIM expression. Moreover, immunohistochemistry of surgically resected specimens from 88 consecutive patients showed that high TIM protein levels correlated with poor overall survival (P = 0.013). Mutation analysis for TIM in 23 lung cancer cell lines revealed no mutation. TIM knockdown suppressed proliferation and clonogenic growth, and induced apoptosis in H157 and H460 cells. Taken together, our findings suggest that TIM could be useful as a diagnostic and prognostic marker for lung cancer and targeting it would be of high therapeutic value for this disease.
Collapse
Affiliation(s)
- Kenya Yoshida
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|