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Tsuji K, Kikuchi E, Takashima Y, Shoji T, Takahashi H, Ito S, Morinaga D, Kashima M, Maeda M, Kitai H, Kikuchi J, Sakakibara-Konishi J, Konno S. Inhibition of non-homologous end joining mitigates paclitaxel resistance resulting from mitotic slippage in non-small cell lung cancer. Cell Cycle 2023; 22:1854-1864. [PMID: 37592765 PMCID: PMC10599168 DOI: 10.1080/15384101.2023.2243761] [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: 03/06/2023] [Revised: 07/08/2023] [Accepted: 07/30/2023] [Indexed: 08/19/2023] Open
Abstract
Mitotic slippage, which enables cancer cells to bypass cell death by transitioning from mitosis to the G1 phase without undergoing normal cytokinesis, is one likely mechanism of paclitaxel (PTX) resistance. DNA double-strand breaks (DSBs) in the G1 phase are mainly repaired through non-homologous end joining (NHEJ). Therefore, inhibiting NHEJ could augment the PTX-induced cytotoxicity by impeding the repair of PTX-induced DSBs during the G1 phase following mitotic slippage. We aimed to evaluate the effects of NHEJ inhibition on mitotic slippage after PTX treatment in non-small cell lung cancer (NSCLC). H1299, A549, H1975, and H520 NSCLC cell lines were employed. In addition, A-196 and JQ1 were used as NHEJ inhibitors. H1299 cells were PTX-resistant and exhibited an increased frequency of mitotic slippage upon PTX treatment. NHEJ inhibitors significantly augmented the PTX-induced cytotoxicity, DSBs, and apoptosis in H1299 cells. The newly generated PTX-resistant cells were even more prone to mitotic slippage following PTX treatment and susceptible to the combined therapy. Docetaxel further demonstrated synergistic effects with the NHEJ inhibitor in PTX-resistant cells. NHEJ inhibition may overcome intrinsic or acquired PTX resistance resulting from mitotic slippage by synergistically increasing the cytotoxic effects of antimitotic drugs in NSCLC.
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Affiliation(s)
- Kosuke Tsuji
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Eiki Kikuchi
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Kikuchi Medical–Respiratory Clinic, Sapporo, Japan
| | - Yuta Takashima
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Tetsuaki Shoji
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Hirofumi Takahashi
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Shotaro Ito
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Daisuke Morinaga
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Masahiro Kashima
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Makie Maeda
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Hidenori Kitai
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Junko Kikuchi
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Kikuchi Medical–Respiratory Clinic, Sapporo, Japan
- Department of Clinical Cancer Genomics, Hokkaido University Hospital, Sapporo, Japan
| | - Jun Sakakibara-Konishi
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Satoshi Konno
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, Japan
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2
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Wörthmüller J, Disler S, Pradervand S, Richard F, Haerri L, Ruiz Buendía GA, Fournier N, Desmedt C, Rüegg C. MAGI1 Prevents Senescence and Promotes the DNA Damage Response in ER + Breast Cancer. Cells 2023; 12:1929. [PMID: 37566008 PMCID: PMC10417439 DOI: 10.3390/cells12151929] [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: 05/09/2023] [Revised: 06/30/2023] [Accepted: 07/18/2023] [Indexed: 08/12/2023] Open
Abstract
MAGI1 acts as a tumor suppressor in estrogen receptor-positive (ER+) breast cancer (BC), and its loss correlates with a more aggressive phenotype. To identify the pathways and events affected by MAGI1 loss, we deleted the MAGI1 gene in the ER+ MCF7 BC cell line and performed RNA sequencing and functional experiments in vitro. Transcriptome analyses revealed gene sets and biological processes related to estrogen signaling, the cell cycle, and DNA damage responses affected by MAGI1 loss. Upon exposure to TNF-α/IFN-γ, MCF7 MAGI1 KO cells entered a deeper level of quiescence/senescence compared with MCF7 control cells and activated the AKT and MAPK signaling pathways. MCF7 MAGI1 KO cells exposed to ionizing radiations or cisplatin had reduced expression of DNA repair proteins and showed increased sensitivity towards PARP1 inhibition using olaparib. Treatment with PI3K and AKT inhibitors (alpelisib and MK-2206) restored the expression of DNA repair proteins and sensitized cells to fulvestrant. An analysis of human BC patients' transcriptomic data revealed that patients with low MAGI1 levels had a higher tumor mutational burden and homologous recombination deficiency. Moreover, MAGI1 expression levels negatively correlated with PI3K/AKT and MAPK signaling, which confirmed our in vitro observations. Pharmacological and genomic evidence indicate HDACs as regulators of MAGI1 expression. Our findings provide a new view on MAGI1 function in cancer and identify potential treatment options to improve the management of ER+ BC patients with low MAGI1 levels.
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Affiliation(s)
- Janine Wörthmüller
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
| | - Simona Disler
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
| | - Sylvain Pradervand
- Lausanne Genomic Technologies Facility (LGTF), University of Lausanne, 1015 Lausanne, Switzerland
| | - François Richard
- Laboratory for Translational Breast Cancer Research, KU Leuven, 3000 Leuven, Belgium
| | - Lisa Haerri
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
| | - Gustavo A. Ruiz Buendía
- Translational Data Science-Facility, AGORA Cancer Research Center, Swiss Institute of Bioinformatics (SIB), Bugnon 25A, 1005 Lausanne, Switzerland
| | - Nadine Fournier
- Translational Data Science-Facility, AGORA Cancer Research Center, Swiss Institute of Bioinformatics (SIB), Bugnon 25A, 1005 Lausanne, Switzerland
| | - Christine Desmedt
- Laboratory for Translational Breast Cancer Research, KU Leuven, 3000 Leuven, Belgium
| | - Curzio Rüegg
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
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3
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Venugopala KN. Targeting the DNA Damage Response Machinery for Lung Cancer Treatment. Pharmaceuticals (Basel) 2022; 15:ph15121475. [PMID: 36558926 PMCID: PMC9781725 DOI: 10.3390/ph15121475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Lung cancer is considered the most commonly diagnosed cancer and one of the leading causes of death globally. Despite the responses from small-cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC) patients to conventional chemo- and radiotherapies, the current outcomes are not satisfactory. Recently, novel advances in DNA sequencing technologies have started to take off which have provided promising tools for studying different tumors for systematic mutation discovery. To date, a limited number of DDR inhibition trials have been conducted for the treatment of SCLC and NSCLC patients. However, strategies to test different DDR inhibitor combinations or to target multiple pathways are yet to be explored. With the various biomarkers that have either been recently discovered or are the subject of ongoing investigations, it is hoped that future trials would be designed to allow for studying targeted treatments in a biomarker-enriched population, which is defensible for the improvement of prognosis for SCLC and NSCLC patients. This review article sheds light on the different DNA repair pathways and some of the inhibitors targeting the proteins involved in the DNA damage response (DDR) machinery, such as ataxia telangiectasia and Rad3-related protein (ATR), DNA-dependent protein kinase (DNA-PK), and poly-ADP-ribose polymerase (PARP). In addition, the current status of DDR inhibitors in clinical settings and future perspectives are discussed.
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Affiliation(s)
- Katharigatta N. Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia;
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban 4000, South Africa
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4
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Marvaso G, Corrao G, Zaffaroni M, Pepa M, Augugliaro M, Volpe S, Musi G, Luzzago S, Mistretta FA, Verri E, Cossu Rocca M, Ferro M, Petralia G, Nolè F, De Cobelli O, Orecchia R, Jereczek-Fossa BA. Therapeutic Sequences in the Treatment of High-Risk Prostate Cancer: Paving the Way Towards Multimodal Tailored Approaches. Front Oncol 2021; 11:732766. [PMID: 34422672 PMCID: PMC8371196 DOI: 10.3389/fonc.2021.732766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/13/2021] [Indexed: 12/21/2022] Open
Abstract
Various definitions are currently in use to describe high-risk prostate cancer. This variety in definitions is important for patient counseling, since predicted outcomes depend on which classification is applied to identify patient’s prostate cancer risk category. Historically, strategies for the treatment of localized high-risk prostate cancer comprise local approaches such as surgery and radiotherapy, as well as systemic approaches such as hormonal therapy. Nevertheless, since high-risk prostate cancer patients remain the group with higher-risk of treatment failure and mortality rates, nowadays, novel treatment strategies, comprising hypofractionated-radiotherapy, second-generation antiandrogens, and hadrontherapy, are being explored in order to improve their long-term oncological outcomes. This narrative review aims to report the current management of high-risk prostate cancer and to explore the future perspectives in this clinical setting.
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Affiliation(s)
- Giulia Marvaso
- Division of Radiation Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Giulia Corrao
- Division of Radiation Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Mattia Zaffaroni
- Division of Radiation Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Matteo Pepa
- Division of Radiation Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Matteo Augugliaro
- Division of Radiation Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Stefania Volpe
- Division of Radiation Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Gennaro Musi
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.,Department of Urology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Stefano Luzzago
- Department of Urology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | | | - Elena Verri
- Department of Medical Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Maria Cossu Rocca
- Department of Medical Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Matteo Ferro
- Department of Urology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Giuseppe Petralia
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.,Precision Imaging and Research Unit, Department of Medical Imaging and Radiation Sciences, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Franco Nolè
- Medical Oncology Division of Urogenital & Head & Neck Tumors, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Ottavio De Cobelli
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.,Department of Urology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Roberto Orecchia
- Scientific Directorate, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Barbara Alicja Jereczek-Fossa
- Division of Radiation Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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5
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Beta-Genus Human Papillomavirus 8 E6 Destabilizes the Host Genome by Promoting p300 Degradation. Viruses 2021; 13:v13081662. [PMID: 34452526 PMCID: PMC8402844 DOI: 10.3390/v13081662] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 01/10/2023] Open
Abstract
The beta genus of human papillomaviruses infects cutaneous keratinocytes. Their replication depends on actively proliferating cells and, thus, they conflict with the cellular response to the DNA damage frequently encountered by these cells. This review focus on one of these viruses (HPV8) that counters the cellular response to damaged DNA and mitotic errors by expressing a protein (HPV8 E6) that destabilizes a histone acetyltransferase, p300. The loss of p300 results in broad dysregulation of cell signaling that decreases genome stability. In addition to discussing phenotypes caused by p300 destabilization, the review contains a discussion of the extent to which E6 from other β-HPVs destabilizes p300, and provides a discussion on dissecting HPV8 E6 biology using mutants.
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6
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Katerji M, Duerksen-Hughes PJ. DNA damage in cancer development: special implications in viral oncogenesis. Am J Cancer Res 2021; 11:3956-3979. [PMID: 34522461 PMCID: PMC8414375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/04/2021] [Indexed: 06/13/2023] Open
Abstract
DNA lesions arise from a combination of physiological/metabolic sources and exogenous environmental influences. When left unrepaired, these alterations accumulate in the cells and can give rise to mutations that change the function of important proteins (i.e. tumor suppressors, oncoproteins), or cause chromosomal rearrangements (i.e. gene fusions) that also result in the deregulation of key cellular molecules. Progressive acquisition of such genetic changes promotes uncontrolled cell proliferation and evasion of cell death, and hence plays a key role in carcinogenesis. Another less-studied consequence of DNA damage accumulating in the host genome is the integration of oncogenic DNA viruses such as Human papillomavirus, Merkel cell polyomavirus, and Hepatitis B virus. This critical step of viral-induced carcinogenesis is thought to be particularly facilitated by DNA breaks in both viral and host genomes. Therefore, the impact of DNA damage on carcinogenesis is magnified in the case of such oncoviruses via the additional effect of increasing integration frequency. In this review, we briefly present the various endogenous and exogenous factors that cause different types of DNA damage. Next, we discuss the contribution of these lesions in cancer development. Finally, we examine the amplified effect of DNA damage in viral-induced oncogenesis and summarize the limited data existing in the literature related to DNA damage-induced viral integration. To conclude, additional research is needed to assess the DNA damage pathways involved in the transition from viral infection to cancer. Discovering that a certain DNA damaging agent increases the likelihood of viral integration will enable the development of prophylactic and therapeutic strategies designed specifically to prevent such integration, with an ultimate goal of reducing or eliminating these viral-induced malignancies.
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Affiliation(s)
- Meghri Katerji
- Department of Basic Science, Loma Linda University School of Medicine Loma Linda, CA 92354, USA
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7
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Yusoh NA, Ahmad H, Gill MR. Combining PARP Inhibition with Platinum, Ruthenium or Gold Complexes for Cancer Therapy. ChemMedChem 2020; 15:2121-2135. [PMID: 32812709 PMCID: PMC7754470 DOI: 10.1002/cmdc.202000391] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Indexed: 12/24/2022]
Abstract
Platinum drugs are heavily used first-line chemotherapeutic agents for many solid tumours and have stimulated substantial interest in the biological activity of DNA-binding metal complexes. These complexes generate DNA lesions which trigger the activation of DNA damage response (DDR) pathways that are essential to maintain genomic integrity. Cancer cells exploit this intrinsic DNA repair network to counteract many types of chemotherapies. Now, advances in the molecular biology of cancer has paved the way for the combination of DDR inhibitors such as poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi) and agents that induce high levels of DNA replication stress or single-strand break damage for synergistic cancer cell killing. In this review, we summarise early-stage, preclinical and clinical findings exploring platinum and emerging ruthenium anti-cancer complexes alongside PARPi in combination therapy for cancer and also describe emerging work on the ability of ruthenium and gold complexes to directly inhibit PARP activity.
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Affiliation(s)
- Nur Aininie Yusoh
- Department of ChemistryFaculty of ScienceUniversiti Putra Malaysia43400 UPMSerdang, SelangorMalaysia
| | - Haslina Ahmad
- Department of ChemistryFaculty of ScienceUniversiti Putra Malaysia43400 UPMSerdang, SelangorMalaysia
- Integrated Chemical BiophysicsFaculty of ScienceUniversiti Putra Malaysia43400 UPMSerdang, SelangorMalaysia
| | - Martin R. Gill
- Department of ChemistrySwansea UniversitySwanseaWales (UK
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8
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Hays E, Nettleton E, Carter C, Morales M, Vo L, Passo M, Vélez-Cruz R. The SWI/SNF ATPase BRG1 stimulates DNA end resection and homologous recombination by reducing nucleosome density at DNA double strand breaks and by promoting the recruitment of the CtIP nuclease. Cell Cycle 2020; 19:3096-3114. [PMID: 33044911 PMCID: PMC7714457 DOI: 10.1080/15384101.2020.1831256] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
DNA double strand breaks (DSBs) are among the most toxic DNA lesions and can be repaired accurately through homologous recombination (HR). HR requires processing of the DNA ends by nucleases (DNA end resection) in order to generate the required single-stranded DNA (ssDNA) regions. The SWI/SNF chromatin remodelers are 10–15 subunit complexes that contain one ATPase (BRG1 or BRM). Multiple subunits of these complexes have recently been identified as a novel family of tumor suppressors. These complexes are capable of remodeling chromatin by pushing nucleosomes along the DNA. More recent studies have identified these chromatin remodelers as important factors in DNA repair. Using the DR-U2OS reporter system, we show that the down regulation of BRG1 significantly reduces HR efficiency, while BRM has a minor effect. Inactivation of BRG1 impairs DSB repair and results in a defect in DNA end resection, as measured by the amount of BrdU-containing ssDNA generated after DNA damage. Inactivation of BRG1 also impairs the activation of the ATR kinase, reduces the levels of chromatin-bound RPA, and reduces the number of RPA and RAD51 foci after DNA damage. This defect in DNA end resection is explained by the defective recruitment of GFP-CtIP to laser-induced DSBs in the absence of BRG1. Importantly, we show that BRG1 reduces nucleosome density at DSBs. Finally, inactivation of BRG1 renders cells sensitive to anti-cancer drugs that induce DSBs. This study identifies BRG1 as an important factor for HR, which suggests that BRG1-mutated cancers have a DNA repair vulnerability that can be exploited therapeutically.
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Affiliation(s)
- Emily Hays
- Department of Biochemistry and Molecular Genetics, Midwestern University , Downers Grove, IL, USA.,College of Graduate Studies, Midwestern University , Downers Grove, IL, USA
| | - Elizabeth Nettleton
- Chicago College of Osteopathic Medicine, Midwestern University , Downers Grove, IL, USA
| | - Caitlin Carter
- Chicago College of Osteopathic Medicine, Midwestern University , Downers Grove, IL, USA
| | - Mariangel Morales
- College of Graduate Studies, Midwestern University , Downers Grove, IL, USA.,Biomedical Sciences Program, Midwestern University , Downers Grove, IL, USA
| | - Lynn Vo
- Chicago College of Osteopathic Medicine, Midwestern University , Downers Grove, IL, USA
| | - Max Passo
- College of Graduate Studies, Midwestern University , Downers Grove, IL, USA.,Biomedical Sciences Program, Midwestern University , Downers Grove, IL, USA
| | - Renier Vélez-Cruz
- Department of Biochemistry and Molecular Genetics, Midwestern University , Downers Grove, IL, USA.,College of Graduate Studies, Midwestern University , Downers Grove, IL, USA.,Chicago College of Optometry, Midwestern University , Downers Grove, IL, USA
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9
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Tang L, Chen R, Xu X. Synthetic lethality: A promising therapeutic strategy for hepatocellular carcinoma. Cancer Lett 2020; 476:120-128. [PMID: 32070778 DOI: 10.1016/j.canlet.2020.02.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 12/24/2022]
Abstract
Hepatocellular carcinoma (HCC), the main cause of liver cancer-related death, is one of the main cancers in terms of incidence and mortality. However, HCC is difficult to target and develops strong drug resistance. Therefore, a new treatment strategy is urgently needed. The clinical application of the concept of synthetic lethality in recent years provides a new therapeutic direction for the accurate treatment of HCC. Here, we introduce the concept of synthetic lethality, the screening used to study synthetic lethality, and the identified and potential genetic interactions that induce synthetic lethality in HCC. In addition, we propose opportunities and challenges for translating synthetic lethal interactions to the clinical treatment of HCC.
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Affiliation(s)
- Linsong Tang
- Department of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China; NHFPC Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, 310003, China.
| | - Ronggao Chen
- Department of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China; NHFPC Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, 310003, China.
| | - Xiao Xu
- Department of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China; NHFPC Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, 310003, China.
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10
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Dünker N, Jendrossek V. Implementation of the Chick Chorioallantoic Membrane (CAM) Model in Radiation Biology and Experimental Radiation Oncology Research. Cancers (Basel) 2019; 11:cancers11101499. [PMID: 31591362 PMCID: PMC6826367 DOI: 10.3390/cancers11101499] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 09/19/2019] [Accepted: 09/20/2019] [Indexed: 02/07/2023] Open
Abstract
Radiotherapy (RT) is part of standard cancer treatment. Innovations in treatment planning and increased precision in dose delivery have significantly improved the therapeutic gain of radiotherapy but are reaching their limits due to biologic constraints. Thus, a better understanding of the complex local and systemic responses to RT and of the biological mechanisms causing treatment success or failure is required if we aim to define novel targets for biological therapy optimization. Moreover, optimal treatment schedules and prognostic biomarkers have to be defined for assigning patients to the best treatment option. The complexity of the tumor environment and of the radiation response requires extensive in vivo experiments for the validation of such treatments. So far in vivo investigations have mostly been performed in time- and cost-intensive murine models. Here we propose the implementation of the chick chorioallantoic membrane (CAM) model as a fast, cost-efficient model for semi high-throughput preclinical in vivo screening of the modulation of the radiation effects by molecularly targeted drugs. This review provides a comprehensive overview on the application spectrum, advantages and limitations of the CAM assay and summarizes current knowledge of its applicability for cancer research with special focus on research in radiation biology and experimental radiation oncology.
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Affiliation(s)
- Nicole Dünker
- Institute for Anatomy II, Department of Neuroanatomy, University of Duisburg-Essen, University Medicine Essen, 45122 Essen, Germany.
| | - Verena Jendrossek
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, University Medicine Essen, 45122 Essen, Germany.
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11
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Nickel Carcinogenesis Mechanism: DNA Damage. Int J Mol Sci 2019; 20:ijms20194690. [PMID: 31546657 PMCID: PMC6802009 DOI: 10.3390/ijms20194690] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/15/2019] [Accepted: 09/20/2019] [Indexed: 12/14/2022] Open
Abstract
Nickel (Ni) is known to be a major carcinogenic heavy metal. Occupational and environmental exposure to Ni has been implicated in human lung and nasal cancers. Currently, the molecular mechanisms of Ni carcinogenicity remain unclear, but studies have shown that Ni-caused DNA damage is an important carcinogenic mechanism. Therefore, we conducted a literature search of DNA damage associated with Ni exposure and summarized known Ni-caused DNA damage effects. In vitro and vivo studies demonstrated that Ni can induce DNA damage through direct DNA binding and reactive oxygen species (ROS) stimulation. Ni can also repress the DNA damage repair systems, including direct reversal, nucleotide repair (NER), base excision repair (BER), mismatch repair (MMR), homologous-recombination repair (HR), and nonhomologous end-joining (NHEJ) repair pathways. The repression of DNA repair is through direct enzyme inhibition and the downregulation of DNA repair molecule expression. Up to now, the exact mechanisms of DNA damage caused by Ni and Ni compounds remain unclear. Revealing the mechanisms of DNA damage from Ni exposure may contribute to the development of preventive strategies in Ni carcinogenicity.
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12
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Targeting DNA Replication Stress and DNA Double-Strand Break Repair for Optimizing SCLC Treatment. Cancers (Basel) 2019; 11:cancers11091289. [PMID: 31480716 PMCID: PMC6770306 DOI: 10.3390/cancers11091289] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 08/22/2019] [Accepted: 08/27/2019] [Indexed: 12/12/2022] Open
Abstract
Small cell lung cancer (SCLC), accounting for about 15% of all cases of lung cancer worldwide, is the most lethal form of lung cancer. Despite an initially high response rate of SCLC to standard treatment, almost all patients are invariably relapsed within one year. Effective therapeutic strategies are urgently needed to improve clinical outcomes. Replication stress is a hallmark of SCLC due to several intrinsic factors. As a consequence, constitutive activation of the replication stress response (RSR) pathway and DNA damage repair system is involved in counteracting this genotoxic stress. Therefore, therapeutic targeting of such RSR and DNA damage repair pathways will be likely to kill SCLC cells preferentially and may be exploited in improving chemotherapeutic efficiency through interfering with DNA replication to exert their functions. Here, we summarize potentially valuable targets involved in the RSR and DNA damage repair pathways, rationales for targeting them in SCLC treatment and ongoing clinical trials, as well as possible predictive biomarkers for patient selection in the management of SCLC.
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13
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Takashima Y, Kikuchi E, Kikuchi J, Suzuki M, Kikuchi H, Maeda M, Shoji T, Furuta M, Kinoshita I, Dosaka‐Akita H, Sakakibara‐Konishi J, Konno S. Bromodomain and extraterminal domain inhibition synergizes with WEE1‐inhibitor AZD1775 effect by impairing nonhomologous end joining and enhancing DNA damage in nonsmall cell lung cancer. Int J Cancer 2019; 146:1114-1124. [DOI: 10.1002/ijc.32515] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 04/26/2019] [Accepted: 06/03/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Yuta Takashima
- Department of Respiratory Medicine, Faculty of Medicine and Graduate School of MedicineHokkaido University Sapporo Japan
| | - Eiki Kikuchi
- Department of Respiratory Medicine, Faculty of Medicine and Graduate School of MedicineHokkaido University Sapporo Japan
| | - Junko Kikuchi
- Department of Respiratory Medicine, Faculty of Medicine and Graduate School of MedicineHokkaido University Sapporo Japan
| | - Motofumi Suzuki
- Laboratory for Bioanalysis and Molecular ImagingGraduate School of Pharmaceutical Sciences, Hokkaido University Sapporo Japan
| | - Hajime Kikuchi
- Department of Respiratory Medicine, Faculty of Medicine and Graduate School of MedicineHokkaido University Sapporo Japan
- First Department of MedicineJA Obihiro Kosei Hospital Obihiro Japan
| | - Makie Maeda
- Department of Respiratory Medicine, Faculty of Medicine and Graduate School of MedicineHokkaido University Sapporo Japan
| | - Tetsuaki Shoji
- Department of Respiratory Medicine, Faculty of Medicine and Graduate School of MedicineHokkaido University Sapporo Japan
| | - Megumi Furuta
- Department of Respiratory Medicine, Faculty of Medicine and Graduate School of MedicineHokkaido University Sapporo Japan
| | - Ichiro Kinoshita
- Department of Medical Oncology, Faculty of Medicine and Graduate School of MedicineHokkaido University Sapporo Japan
| | - Hirotoshi Dosaka‐Akita
- Department of Medical Oncology, Faculty of Medicine and Graduate School of MedicineHokkaido University Sapporo Japan
| | - Jun Sakakibara‐Konishi
- Department of Respiratory Medicine, Faculty of Medicine and Graduate School of MedicineHokkaido University Sapporo Japan
| | - Satoshi Konno
- Department of Respiratory Medicine, Faculty of Medicine and Graduate School of MedicineHokkaido University Sapporo Japan
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14
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Kim IE, Kim S, Srivastava A, Saraiya B, Mayer T, Kim WJ, Kim IY. Similar incidence of DNA damage response pathway alterations between clinically localized and metastatic prostate cancer. BMC Urol 2019; 19:33. [PMID: 31060606 PMCID: PMC6501301 DOI: 10.1186/s12894-019-0453-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/27/2019] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND In this era of precision medicine, the DNA damage response (DDR) pathway has been shown to be a viable target of intervention in metastatic castration-resistant prostate cancer (CRPC) as approximately one-third of CRPC patients harbor DDR pathway mutations. To determine whether DDR pathway is a potential therapeutic target in localized disease, we analyzed The Cancer Genome Atlas (TCGA) in the present study. METHODS TCGA is a publically available cancer genome database that is sponsored by the United States National Cancer Institute. Total of 455 cases were available in the database at the time of this analysis. RESULTS DDR pathway gene mutations or copy number alterations were present in 136 (29.9%) of the 455 cases. On a univariate analysis, DDR pathway status did not correlate with serum prostate specific antigen, tumor stage or grade. However, among patients with high-risk features post-operatively (pathologic stage ≥ T3, Gleason score ≥ 8, or PSA > 20 ng/ml), DDR pathway alteration was associated with a lower overall survival (p = 0.0291). CONCLUSIONS Collectively these results suggest that DDR pathway alterations may also be significant in localized prostate cancer and agents such as PARP inhibitors should be considered in patients with a high-risk disease.
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Affiliation(s)
- Isaac E. Kim
- The Warren Alpert Medical School of Brown University, Providence, RI USA
| | - Sinae Kim
- Department of Biostatistics, Rutgers School of Public Health, The State University of New Jersey, New Brunswick, NJ USA
| | - Arnav Srivastava
- Section of Urologic Oncology, Division of Urology, Rutgers Cancer Institute of New Jersey and Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, 195 Little Albany Street, #4565, New Brunswick, NJ 08903 USA
| | - Biren Saraiya
- Department of Internal Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ USA
| | - Tina Mayer
- Department of Internal Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ USA
| | - Wun-Jae Kim
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, South Korea
| | - Isaac Yi Kim
- Section of Urologic Oncology, Division of Urology, Rutgers Cancer Institute of New Jersey and Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, 195 Little Albany Street, #4565, New Brunswick, NJ 08903 USA
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15
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Gibbs DR, Kaur A, Megalathan A, Sapkota K, Dhakal S. Build Your Own Microscope: Step-By-Step Guide for Building a Prism-Based TIRF Microscope. Methods Protoc 2018; 1:mps1040040. [PMID: 31164580 PMCID: PMC6481079 DOI: 10.3390/mps1040040] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 10/31/2018] [Accepted: 10/31/2018] [Indexed: 01/09/2023] Open
Abstract
Prism-based total internal reflection fluorescence (pTIRF) microscopy is one of the most widely used techniques for the single molecule analysis of a vast range of samples including biomolecules, nanostructures, and cells, to name a few. It allows for excitation of surface bound molecules/particles/quantum dots via evanescent field of a confined region of space, which is beneficial not only for single molecule detection but also for analysis of single molecule dynamics and for acquiring kinetics data. However, there is neither a commercial microscope available for purchase nor a detailed guide dedicated for building this microscope. Thus far, pTIRF microscopes are custom-built with the use of a commercially available inverted microscope, which requires high level of expertise in selecting and handling sophisticated instrument-parts. To directly address this technology gap, here we describe a step-by-step guide on how to build and characterize a pTIRF microscope for in vitro single-molecule imaging, nanostructure analysis and other life sciences research.
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Affiliation(s)
- Dalton R Gibbs
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA.
| | - Anisa Kaur
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA.
| | - Anoja Megalathan
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA.
| | - Kumar Sapkota
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA.
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA.
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16
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Wang J, Wang Y, Shen F, Xu Y, Zhang Y, Zou X, Zhou J, Chen Y. Maternal embryonic leucine zipper kinase: A novel biomarker and a potential therapeutic target of cervical cancer. Cancer Med 2018; 7:5665-5678. [PMID: 30334367 PMCID: PMC6246930 DOI: 10.1002/cam4.1816] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/12/2018] [Accepted: 08/31/2018] [Indexed: 12/30/2022] Open
Abstract
Maternal embryo leucine zipper kinase (MELK) is highly expressed in a variety of malignant tumors and involved in cell cycle regulation, cell proliferation, apoptosis, tumor formation etc However, the biological effects of MELK in cervical cancer are still uninvestigated. This study aimed to explore the expression of MELK in cervical cancer, as well as its effects on the proliferation, apoptosis, DNA damage repair on cervical cancer cell line in vitro and to provide novel ideas for further improving the clinical efficacy of cervical cancer. Immunohistochemistry, Western blot, RT‐qPCR, CCK8, and immunofluorescence techniques were used to detect the expression of MELK in cervical cancer tissues, paracancerous tissues, and cervical cancer cell lines. Several cervical cancer cell lines were treated with MELK knockdown by siRNA and MELK selective inhibitor OTSSP167. The effects on proliferation, apoptosis, and colony formation capacity, and tumor cell DNA damage repair‐related factor were detected in cell lines. Our data showed that the high expression rate of MELK in cervical cancer patients was 56.92%. MELK expression in cervical cancer samples was significantly higher than that in paraneoplastic tissues. Highly expressed MELK correlated with the cervical histopathological grading and greatly increased with the cervical histopathological grading, from normal cervix and cervical intraepithelial neoplasia to cervical cancer. Moreover, the abnormal expression of MELK was related to cervical cancer metastasis at early stage. The knockdown of MELK with siRNA and OTSSP167 had strong inhibition effects on the proliferation, apoptosis, and colony formation of cervical cancer cells. MELK knockdown could also aggravate the DNA damage of cervical cancer cells possibly by homologous recombination repair pathway. Therefore, MELK may be a predicting marker of poor prognosis of cervical cancer and may also be a new therapeutic target for cervical cancer, providing ideas for improving the therapeutic effect of cervical cancer.
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Affiliation(s)
- Juan Wang
- Department of Obstetrics and Gynecology, The First Hospital Affiliated Soochow University, Suzhou, China
| | - Yamei Wang
- Department of Obstetrics and Gynecology, The First Hospital Affiliated Soochow University, Suzhou, China
| | - Fangrong Shen
- Department of Obstetrics and Gynecology, The First Hospital Affiliated Soochow University, Suzhou, China
| | - Yanting Xu
- Department of Obstetrics and Gynecology, The First Hospital Affiliated Soochow University, Suzhou, China
| | - Yinghui Zhang
- Department of Obstetrics and Gynecology, The First Hospital Affiliated Soochow University, Suzhou, China
| | - Xinwei Zou
- Department of Obstetrics and Gynecology, The First Hospital Affiliated Soochow University, Suzhou, China
| | - Jinhua Zhou
- Department of Obstetrics and Gynecology, The First Hospital Affiliated Soochow University, Suzhou, China
| | - Youguo Chen
- Department of Obstetrics and Gynecology, The First Hospital Affiliated Soochow University, Suzhou, China
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17
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Gibbs DR, Dhakal S. Single-Molecule Imaging Reveals Conformational Manipulation of Holliday Junction DNA by the Junction Processing Protein RuvA. Biochemistry 2018; 57:3616-3624. [PMID: 29767969 DOI: 10.1021/acs.biochem.8b00404] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Interactions between DNA and motor proteins regulate nearly all biological functions of DNA such as gene expression, DNA replication and repair, and transcription. During the late stages of homologous recombination (HR), the Escherichia coli recombination machinery, RuvABC, resolves the four-way DNA motifs called Holliday junctions (HJs) that are formed during exchange of nucleotide sequences between two homologous duplex DNA. Although the formation of the RuvA-HJ complex is known to be the first critical step in the RuvABC pathway, the mechanism for the binding interaction between RuvA and HJ has remained elusive. Here, using single-molecule fluorescence resonance energy transfer (smFRET) and ensemble analyses, we show that RuvA stably binds to the HJ, halting its conformational dynamics. Our FRET experiments in different ionic environments created by Mg2+ and Na+ ions suggest that RuvA binds to the HJ via electrostatic interaction. Further, while recent studies have indicated that the HR process can be modulated for therapeutic applications by selective targeting of the HJ by chemotherapeutic drugs, we investigated the effect of drug-modified HJ on binding. Using cisplatin as a proof-of-concept drug, we show that RuvA binds to the cisplatin-modified HJ as efficiently as to the unmodified HJ, demonstrating that RuvA accommodates for the cisplatin-introduced charges and/or topological changes on the HJ.
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Affiliation(s)
- Dalton R Gibbs
- Department of Chemistry , Virginia Commonwealth University , 1001 West Main Street , Richmond , Virginia 23284 , United States
| | - Soma Dhakal
- Department of Chemistry , Virginia Commonwealth University , 1001 West Main Street , Richmond , Virginia 23284 , United States
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18
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Sen T, Gay CM, Byers LA. Targeting DNA damage repair in small cell lung cancer and the biomarker landscape. Transl Lung Cancer Res 2018. [PMID: 29535912 DOI: 10.21037/tlcr.2018.02.03] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Small cell lung cancer (SCLC) is an aggressive malignancy that accounts for 14% of all lung cancer diagnoses. Despite decades of active research, treatment options for SCLC are limited and resistance to the few Food and Drug Administration (FDA) approved therapies develops rapidly. With no approved targeted agents to date, new therapeutic strategies are desperately needed. SCLC is characterized by high mutation burden, ubiquitous loss of TP53 and RB1, mutually exclusive amplification of MYC family members, thereby, high genomic instability. Studies in the past few years have demonstrated the potential of targeting the DNA damage response (DDR) pathway as a promising therapeutic strategy for SCLC. Inhibitors targeting DDR proteins have shown promise in preclinical models, and are under clinical investigation as single agents and in combination with cytotoxic therapies. Recent efforts to expand the therapeutic arsenal toward SCLC have focused in part on immune checkpoint inhibitors, such as agents targeting the receptor-ligand pair programmed cell death protein 1 (PD-1) and programmed death-ligand 1 (PD-L1). Clinical trials have confirmed activity of these agents in extensive stage (ES)-SCLC. However, while several patients had dramatic responses, overall response rates to immune checkpoint blockade (ICB) remain poor. As a result, there is an urgent need to develop rational combination therapies to enhance response rates to immunotherapy in SCLC. Identification of predictive biomarkers for patient stratification, identifying effective combinations to overcome adaptive resistance to DDR-targeted therapies and identifying strategies to enhance response to immunotherapy are areas of active investigation in SCLC.
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Affiliation(s)
- Triparna Sen
- Department of Thoracic and Head & Neck Medical Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Carl M Gay
- Department of Thoracic and Head & Neck Medical Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Lauren Averett Byers
- Department of Thoracic and Head & Neck Medical Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
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van Niekerk G, Nell T, Engelbrecht AM. Domesticating Cancer: An Evolutionary Strategy in the War on Cancer. Front Oncol 2017; 7:304. [PMID: 29270389 PMCID: PMC5725441 DOI: 10.3389/fonc.2017.00304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 11/24/2017] [Indexed: 12/14/2022] Open
Abstract
Since cancer shares the same molecular machinery as the host, most therapeutic interventions that aim to target cancer would inadvertently also adversely affect the host. In addition, cancer continuously evolves, streamlining its host-derived genome for a new single-celled existence. In particular, short-term clinical success observed with most antineoplastic therapies directly relate to the fact that cancer is constantly evolving. However, the clonal evolution of cancer occasionally also render cancer cells uniquely susceptible to therapeutic interventions, as is exemplified by the clinical relevance of synthetic lethality. Synthetic lethality describes a situation where the simultaneous loss of function in two genes results in lethality, but where a loss of function in either single gene is tolerated. This observation suggests that the evolution of cancer, usually seen as a major clinical challenge, may also afford a key opportunity in lowering on-target toxicities accosted with chemotherapy. As an example, by subjecting cancer to specific selection regimes, cancer can in effect be placed on evolutionary trajectories leading to the development of “targetable” phenotypes such as synthetic lethal interactions. However, such a selection regime would have to overcome a range of obstacles such as on-target toxicity and the selection of an evolvable trait. Since the majority of cancer evolution manifests as a loss of function, we suggest that the induction of auxotrophic phenotypes (i.e., where an organism lose the ability to synthesize specific organic compounds required for growth and thus become dependent on it from dietary sources) may represent an attractive therapeutic option. As an example, animals can obtain vitamin C either by de novo synthesis or from their diet. However, since the maintenance of synthetic pathways is costly, such pathways are often lost if no longer necessary, resulting in the organism being auxotrophic toward the dietary compound. Similarly, increasing the maintenance cost of a redundant pathway in cancer cells is likely to select for clones that have lost such a redundant pathway. Inhibition of a pathway, while supporting the activity of a compensating pathway, may thus induce auxotrophism in cancer cells but not in genomic stable host cells.
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Affiliation(s)
- Gustav van Niekerk
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Theo Nell
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Anna-Mart Engelbrecht
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, South Africa
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20
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Wang X, Wang SS, Zhou L, Yu L, Zhang LM. A network-pathway based module identification for predicting the prognosis of ovarian cancer patients. J Ovarian Res 2016; 9:73. [PMID: 27806724 PMCID: PMC5093979 DOI: 10.1186/s13048-016-0285-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 10/25/2016] [Indexed: 12/19/2022] Open
Abstract
Background This study aimed to screen multiple genes biomarkers based on gene expression data for predicting the survival of ovarian cancer patients. Methods Two microarray data of ovarian cancer samples were collected from The Cancer Genome Atlas (TCGA) database. The data in the training set were used to construct Reactome functional interactions network, which then underwent Markov clustering, supervised principal components, Cox proportional hazard model to screen significantly prognosis related modules. The distinguishing ability of each module for survival was further evaluated by the testing set. Gene Ontology (GO) functional and pathway annotations were performed to identify the roles of genes in each module for ovarian cancer. Results The network based approach identified two 7-gene functional interaction modules (31: DCLRE1A, EXO1, KIAA0101, KIN, PCNA, POLD3, POLD2; 35: DKK3, FABP3, IRF1, AIM2, GBP1, GBP2, IRF2) that are associated with prognosis of ovarian cancer patients. These network modules are related to DNA repair, replication, immune and cytokine mediated signaling pathways. Conclusions The two 7-gene expression signatures may be accurate predictors of clinical outcome in patients with ovarian cancer and has the potential to develop new therapeutic strategies for ovarian cancer patients.
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Affiliation(s)
- Xin Wang
- Department of Gynaecology and Obstetrics, The 306 Hospital of PLA, Beijing, 100037, China
| | - Shan-Shan Wang
- Outpatient Pharmacy, Outpatient Department, NO.16 Chengzhuang Fengtai Distinct, Beijing, 100071, China
| | - Lin Zhou
- Department of Gynaecology and Obstetrics, The 306 Hospital of PLA, Beijing, 100037, China
| | - Li Yu
- Department of Gynaecology and Obstetrics, The 306 Hospital of PLA, Beijing, 100037, China
| | - Lan-Mei Zhang
- Department of Gynaecology and Obstetrics, The 306 Hospital of PLA, Beijing, 100037, China.
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