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Yu L, Li J, Zhang M, Li Y, Bai J, Liu P, Yan J, Wang C. Identification of RFC4 as a potential biomarker for pan-cancer involving prognosis, tumour immune microenvironment and drugs. J Cell Mol Med 2024; 28:e18478. [PMID: 39031628 PMCID: PMC11190950 DOI: 10.1111/jcmm.18478] [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: 02/04/2024] [Revised: 05/20/2024] [Accepted: 05/26/2024] [Indexed: 07/22/2024] Open
Abstract
RFC4 is required for DNA polymerase δ and DNA polymerase ε to initiate DNA template expansion. Downregulated RFC4 inhibits tumour proliferation by causing S-phase arrest and inhibiting mitosis, resulting in the reduction of tumour cells. RFC4 has been implicated that it plays an important role in the initiation and progression of cancers, but a comprehensive analysis of the role of RFC4 in cancer has not been performed. We comprehensively analysed the expression, prognosis, methylation level, splicing level, relationship of RFC4 and immune infiltration, and pan-cancer immunotherapy response used various databases (including TCGA, GTEx, UALCAN, Oncosplicing, TIDE, TISCH, HPA and CAMOIP), and experimented its biological function in HCC. Through pan-cancer analysis, we found that RFC4 is significantly upregulated in most tumours. The tumour patients with high expression of RFC4 have poor prognosis. The methylation level and variable splicing level of RFC4 were abnormal in most tumours compared with the adjacent tissues. Furthermore, RFC4 was closely associated with immune cell infiltration in various cancers. RFC4 was significantly co-expressed with immune checkpoints and other immune-related genes. The expression of RFC4 could indicate the immunotherapy efficacy of some tumours. The RFC4 expression was associated with sensitivity to specific small molecule drugs. Cell experiments have shown that downregulated RFC4 can inhibit cell cycle and tumour cell proliferation. We conducted a systematic pan-cancer analysis of RFC4, and the results showed that RFC4 can serve as a biomarker for cancer diagnosis and prognosis. These findings open new perspectives for precision medicine.
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Affiliation(s)
- Lei Yu
- School of Life ScienceInner Mongolia UniversityHohhotChina
| | - Jing Li
- School of Life ScienceInner Mongolia UniversityHohhotChina
| | - Mingyang Zhang
- School of Life ScienceInner Mongolia UniversityHohhotChina
| | - Yu Li
- School of Life ScienceInner Mongolia UniversityHohhotChina
| | - Jing Bai
- School of Life ScienceInner Mongolia UniversityHohhotChina
| | - Pengxia Liu
- School of Life ScienceInner Mongolia UniversityHohhotChina
| | - Jia Yan
- School of Basic medicalInner Mongolia Medical UniversityHohhotInner MongoliaChina
| | - Changshan Wang
- School of Life ScienceInner Mongolia UniversityHohhotChina
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2
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Avs KR, Pandi C, Kannan B, Pandi A, Jayaseelan VP, Arumugam P. RFC3 serves as a novel prognostic biomarker and target for head and neck squamous cell carcinoma. Clin Oral Investig 2023; 27:6961-6969. [PMID: 37861747 DOI: 10.1007/s00784-023-05316-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 10/08/2023] [Indexed: 10/21/2023]
Abstract
OBJECTIVE Head and neck squamous cell carcinoma (HNSCC) is a prevalent cancer that originates from the squamous cells. The role of the replication factor C subunit 3 (RFC3) in HNSCC progression remains elusive. The aim of this study was to uncover RFC3 significance in HNSCC. METHODS The Cancer Genome Atlas (TCGA-HNSCC) dataset was initially used to assess RFC3 expression and its association with HNSCC clinical features. Subsequently, quantitative reverse transcription PCR (RT-qPCR) confirmed RFC3 mRNA expression in oral squamous cell carcinoma (OSCC), a primary HNSCC type. Survival rates were evaluated using the Kaplan-Meier plot, while the Tumor Immune Estimation Resource (TIMER) database probed RFC3-immune cell interaction. Additionally, in silico tools were used to examine the RFC3 protein network and engagement in HNSCC pathways. RESULTS RFC3 expression is significantly upregulated in HNSCC, including OSCC. Upregulated RFC3 expression was significantly correlated with the clinicopathological features of HNSCC, including tumor stage, grade, metastasis, and patient survival. RFC3 is also associated with immune cell infiltration. Functional analysis has highlighted its involvement in DNA replication, mismatch repair, and cell cycle pathways. Interestingly, RFC3 high expression is linked to well-known oncogenic signaling pathways, such as MYC/MYCN, HIPPO, and mTOR. CONCLUSIONS In conclusion, RFC3 can be considered a novel prognostic biomarker for HNSCC, and further studies on its functional mechanisms may help to use RFC3 as a therapeutic target for HNSCC. CLINICAL RELEVANCE The clinical relevance of this study lies in identifying RFC3 as a novel biomarker and prognostic indicator for HNSCC, offering insights that could impact future clinical approaches.
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Affiliation(s)
- Keerthana Reddy Avs
- Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India
| | - Chandra Pandi
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu, 60007, India
| | - Balachander Kannan
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu, 60007, India
| | - Anitha Pandi
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu, 60007, India
| | - Vijayashree Priyadharsini Jayaseelan
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu, 60007, India
| | - Paramasivam Arumugam
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu, 60007, India.
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3
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Zhang J, Meng S, Wang X, Wang J, Fan X, Sun H, Ning R, Xiao B, Li X, Jia Y, Kong D, Chen R, Wang C, Ma D, Li S. Sequential gene expression analysis of cervical malignant transformation identifies RFC4 as a novel diagnostic and prognostic biomarker. BMC Med 2022; 20:437. [PMID: 36352434 PMCID: PMC9648022 DOI: 10.1186/s12916-022-02630-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 10/24/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cervical squamous cell carcinoma (SCC) is known to arise through increasingly higher-grade squamous intraepithelial lesions (SILs) or cervical intraepithelial neoplasias (CINs). This study aimed to describe sequential molecular changes and identify biomarkers in cervical malignant transformation. METHODS Multidimensional data from five publicly available microarray and TCGA-CESC datasets were analyzed. Immunohistochemistry was carried out on 354 cervical tissues (42 normal, 62 CIN1, 26 CIN2, 47 CIN3, and 177 SCC) to determine the potential diagnostic and prognostic value of identified biomarkers. RESULTS We demonstrated that normal epithelium and SILs presented higher molecular homogeneity than SCC. Genes in the region (e.g., 3q, 12q13) with copy number alteration or HPV integration were more likely to lose or gain expression. The IL-17 signaling pathway was enriched throughout disease progression with downregulation of IL17C and decreased Th17 cells at late stage. Furthermore, we identified AURKA, TOP2A, RFC4, and CEP55 as potential causative genes gradually upregulated during the normal-SILs-SCC transition. For detecting high-grade SIL (HSIL), TOP2A and RFC4 showed balanced sensitivity (both 88.2%) and specificity (87.1 and 90.1%), with high AUC (0.88 and 0.89). They had equivalent diagnostic performance alone to the combination of p16INK4a and Ki-67. Meanwhile, increased expression of RFC4 significantly and independently predicted favorable outcomes in multi-institutional cohorts of SCC patients. CONCLUSIONS Our comprehensive study of gene expression profiling has identified dysregulated genes and biological processes during cervical carcinogenesis. RFC4 is proposed as a novel surrogate biomarker for determining HSIL and HSIL+, and an independent prognostic biomarker for SCC.
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Affiliation(s)
- Jianwei Zhang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Silu Meng
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Xiaoyan Wang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Jun Wang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Xinran Fan
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Haiying Sun
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Ruoqi Ning
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Bing Xiao
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Xiangqin Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Yao Jia
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Dongli Kong
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Ruqi Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Changyu Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China. .,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.
| | - Ding Ma
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China. .,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.
| | - Shuang Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China. .,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.
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4
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Alam MS, Rahaman MM, Sultana A, Wang G, Mollah MNH. Statistics and network-based approaches to identify molecular mechanisms that drive the progression of breast cancer. Comput Biol Med 2022; 145:105508. [PMID: 35447458 DOI: 10.1016/j.compbiomed.2022.105508] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 12/13/2022]
Abstract
Breast cancer (BC) is one of the most malignant tumors and the leading cause of cancer-related death in women worldwide. So, an in-depth investigation on the molecular mechanisms of BC progression is required for diagnosis, prognosis and therapies. In this study, we identified 127 common differentially expressed genes (cDEGs) between BC and control samples by analyzing five gene expression profiles with NCBI accession numbers GSE139038, GSE62931, GSE45827, GSE42568 and GSE54002, based-on two statistical methods LIMMA and SAM. Then we constructed protein-protein interaction (PPI) network of cDEGs through the STRING database and selected top-ranked 7 cDEGs (BUB1, ASPM, TTK, CCNA2, CENPF, RFC4, and CCNB1) as a set of key genes (KGs) by cytoHubba plugin in Cytoscape. Several BC-causing crucial biological processes, molecular functions, cellular components, and pathways were significantly enriched by the estimated cDEGs including at-least one KGs. The multivariate survival analysis showed that the proposed KGs have a strong prognosis power of BC. Moreover, we detected some transcriptional and post-transcriptional regulators of KGs by their regulatory network analysis. Finally, we suggested KGs-guided three repurposable candidate-drugs (Trametinib, selumetinib, and RDEA119) for BC treatment by using the GSCALite online web tool and validated them through molecular docking analysis, and found their strong binding affinities. Therefore, the findings of this study might be useful resources for BC diagnosis, prognosis and therapies.
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Affiliation(s)
- Md Shahin Alam
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, 199 Ren'ai Road, Suzhou, 215123, Jiangsu, China; Bioinformatics Lab. (Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Matiur Rahaman
- Department of Statistics, Faculty of Science, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh; Bioinformatics Lab. (Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Adiba Sultana
- Center for Systems Biology, Soochow University, Suzhou, 215006, China; Bioinformatics Lab. (Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Guanghui Wang
- Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, 199 Ren'ai Road, Suzhou, 215123, Jiangsu, China.
| | - Md Nurul Haque Mollah
- Bioinformatics Lab. (Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh.
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5
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Rashidieh B, Molakarimi M, Mohseni A, Tria SM, Truong H, Srihari S, Adams RC, Jones M, Duijf PHG, Kalimutho M, Khanna KK. Targeting BRF2 in Cancer Using Repurposed Drugs. Cancers (Basel) 2021; 13:cancers13153778. [PMID: 34359683 PMCID: PMC8345145 DOI: 10.3390/cancers13153778] [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: 05/31/2021] [Revised: 07/16/2021] [Accepted: 07/21/2021] [Indexed: 11/29/2022] Open
Abstract
Simple Summary BRF2, a subunit of the RNA polymerase III transcription complex, is upregulated in a wide variety of cancers and is a potential therapeutic target; however, no effective drugs are available to target BRF2. The upregulation of BRF2 in cancer cells confers survival via the prevention of oxidative stress-induced apoptosis. In this manuscript, we report the identification of potential BRF2 inhibitors through in silico drug repurposing screening. We further characterized bexarotene as a hit compound for the development of selective BRF2 inhibitors and provide experimental validation to support the repurposing of this FDA-approved drug as an agent to reduce the cellular levels of ROS and consequent BRF2 expression in cancers with elevated levels of oxidative stress. Abstract The overexpression of BRF2, a selective subunit of RNA polymerase III, has been shown to be crucial in the development of several types of cancers, including breast cancer and lung squamous cell carcinoma. Predominantly, BRF2 acts as a central redox-sensing transcription factor (TF) and is involved in rescuing oxidative stress (OS)-induced apoptosis. Here, we showed a novel link between BRF2 and the DNA damage response. Due to the lack of BRF2-specific inhibitors, through virtual screening and molecular dynamics simulation, we identified potential drug candidates that interfere with BRF2-TATA-binding Protein (TBP)-DNA complex interactions based on binding energy, intermolecular, and torsional energy parameters. We experimentally tested bexarotene as a potential BRF2 inhibitor. We found that bexarotene (Bex) treatment resulted in a dramatic decline in oxidative stress and Tert-butylhydroquinone (tBHQ)-induced levels of BRF2 and consequently led to a decrease in the cellular proliferation of cancer cells which may in part be due to the drug pretreatment-induced reduction of ROS generated by the oxidizing agent. Our data thus provide the first experimental evidence that BRF2 is a novel player in the DNA damage response pathway and that bexarotene can be used as a potential inhibitor to treat cancers with the specific elevation of oxidative stress.
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Affiliation(s)
- Behnam Rashidieh
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (S.M.T.); (H.T.); (S.S.); (R.C.A.); (M.K.)
- Correspondence: (B.R.); (K.K.K.)
| | - Maryam Molakarimi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University (TMU), Nasr Bridge, Tehran 14115-154, Iran; (M.M.); (A.M.)
| | - Ammar Mohseni
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University (TMU), Nasr Bridge, Tehran 14115-154, Iran; (M.M.); (A.M.)
| | - Simon Manuel Tria
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (S.M.T.); (H.T.); (S.S.); (R.C.A.); (M.K.)
- School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
| | - Hein Truong
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (S.M.T.); (H.T.); (S.S.); (R.C.A.); (M.K.)
| | - Sriganesh Srihari
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (S.M.T.); (H.T.); (S.S.); (R.C.A.); (M.K.)
| | - Rachael C. Adams
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (S.M.T.); (H.T.); (S.S.); (R.C.A.); (M.K.)
| | - Mathew Jones
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia;
| | - Pascal H. G. Duijf
- Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology (QUT), Brisbane, QLD 4000, Australia;
- Centre for Data Science, Queensland University of Technology (QUT), Brisbane, QLD 4000, Australia
| | - Murugan Kalimutho
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (S.M.T.); (H.T.); (S.S.); (R.C.A.); (M.K.)
| | - Kum Kum Khanna
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia; (S.M.T.); (H.T.); (S.S.); (R.C.A.); (M.K.)
- Correspondence: (B.R.); (K.K.K.)
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6
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Liu Y, Ye X, Zhan X, Yu CY, Zhang J, Huang K. TPQCI: A topology potential-based method to quantify functional influence of copy number variations. Methods 2021; 192:46-56. [PMID: 33894380 DOI: 10.1016/j.ymeth.2021.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 12/21/2022] Open
Abstract
Copy number variation (CNV) is a major type of chromosomal structural variation that play important roles in many diseases including cancers. Due to genome instability, a large number of CNV events can be detected in diseases such as cancer. Therefore, it is important to identify the functionally important CNVs in diseases, which currently still poses a challenge in genomics. One of the critical steps to solve the problem is to define the influence of CNV. In this paper, we provide a topology potential based method, TPQCI, to quantify this kind of influence by integrating statistics, gene regulatory associations, and biological function information. We used this metric to detect functionally enriched genes on genomic segments with CNV in breast cancer and multiple myeloma and discovered biological functions influenced by CNV. Our results demonstrate that, by using our proposed TPQCI metric, we can detect disease-specific genes that are influenced by CNVs. Source codes of TPQCI are provided in Github (https://github.com/usos/TPQCI).
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Affiliation(s)
- Yusong Liu
- Collage of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, Heilongjiang 150001, China; Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Xiufen Ye
- Collage of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, Heilongjiang 150001, China
| | - Xiaohui Zhan
- Indiana University School of Medicine, Indianapolis, IN 46202, USA; National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, Guangdong 518037, China; Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Christina Y Yu
- Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
| | - Jie Zhang
- Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Kun Huang
- Indiana University School of Medicine, Indianapolis, IN 46202, USA; Regenstrief Institute, Indianapolis, IN 46202, USA.
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7
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Privitera AP, Barresi V, Condorelli DF. Aberrations of Chromosomes 1 and 16 in Breast Cancer: A Framework for Cooperation of Transcriptionally Dysregulated Genes. Cancers (Basel) 2021; 13:1585. [PMID: 33808143 PMCID: PMC8037453 DOI: 10.3390/cancers13071585] [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: 02/17/2021] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
Derivative chromosome der(1;16), isochromosome 1q, and deleted 16q-producing arm-level 1q-gain and/or 16q-loss-are recurrent cytogenetic abnormalities in breast cancer, but their exact role in determining the malignant phenotype is still largely unknown. We exploited The Cancer Genome Atlas (TCGA) data to generate and analyze groups of breast invasive carcinomas, called 1,16-chromogroups, that are characterized by a pattern of arm-level somatic copy number aberrations congruent with known cytogenetic aberrations of chromosome 1 and 16. Substantial differences were found among 1,16-chromogroups in terms of other chromosomal aberrations, aneuploidy scores, transcriptomic data, single-point mutations, histotypes, and molecular subtypes. Breast cancers with a co-occurrence of 1q-gain and 16q-loss can be distinguished in a "low aneuploidy score" group, congruent to der(1;16), and a "high aneuploidy score" group, congruent to the co-occurrence of isochromosome 1q and deleted 16q. Another three groups are formed by cancers showing separately 1q-gain or 16q-loss or no aberrations of 1q and 16q. Transcriptome comparisons among the 1,16-chromogroups, integrated with functional pathway analysis, suggested the cooperation of overexpressed 1q genes and underexpressed 16q genes in the genesis of both ductal and lobular carcinomas, thus highlighting the putative role of genes encoding gamma-secretase subunits (APH1A, PSEN2, and NCSTN) and Wnt enhanceosome components (BCL9 and PYGO2) in 1q, and the glycoprotein E-cadherin (CDH1), the E3 ubiquitin-protein ligase WWP2, the deubiquitinating enzyme CYLD, and the transcription factor CBFB in 16q. The analysis of 1,16-chromogroups is a strategy with far-reaching implications for the selection of cancer cell models and novel experimental therapies.
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Affiliation(s)
| | - Vincenza Barresi
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Via S. Sofia 89-97, 95123 Catania, Italy;
| | - Daniele Filippo Condorelli
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Via S. Sofia 89-97, 95123 Catania, Italy;
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8
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Schneider L, Kehl T, Thedinga K, Grammes NL, Backes C, Mohr C, Schubert B, Lenhof K, Gerstner N, Hartkopf AD, Wallwiener M, Kohlbacher O, Keller A, Meese E, Graf N, Lenhof HP. ClinOmicsTrailbc: a visual analytics tool for breast cancer treatment stratification. Bioinformatics 2020; 35:5171-5181. [PMID: 31038669 PMCID: PMC6954665 DOI: 10.1093/bioinformatics/btz302] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/02/2019] [Accepted: 04/26/2019] [Indexed: 01/10/2023] Open
Abstract
Motivation Breast cancer is the second leading cause of cancer death among women. Tumors, even of the same histopathological subtype, exhibit a high genotypic diversity that impedes therapy stratification and that hence must be accounted for in the treatment decision-making process. Results Here, we present ClinOmicsTrailbc, a comprehensive visual analytics tool for breast cancer decision support that provides a holistic assessment of standard-of-care targeted drugs, candidates for drug repositioning and immunotherapeutic approaches. To this end, our tool analyzes and visualizes clinical markers and (epi-)genomics and transcriptomics datasets to identify and evaluate the tumor’s main driver mutations, the tumor mutational burden, activity patterns of core cancer-relevant pathways, drug-specific biomarkers, the status of molecular drug targets and pharmacogenomic influences. In order to demonstrate ClinOmicsTrailbc’s rich functionality, we present three case studies highlighting various ways in which ClinOmicsTrailbc can support breast cancer precision medicine. ClinOmicsTrailbc is a powerful integrated visual analytics tool for breast cancer research in general and for therapy stratification in particular, assisting oncologists to find the best possible treatment options for their breast cancer patients based on actionable, evidence-based results. Availability and implementation ClinOmicsTrailbc can be freely accessed at https://clinomicstrail.bioinf.uni-sb.de. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Lara Schneider
- Center for Bioinformatics, Saarbrücken, Germany.,Saarbrücken Graduate School of Computer Science, Saarbrücken, Germany
| | - Tim Kehl
- Center for Bioinformatics, Saarbrücken, Germany.,Saarbrücken Graduate School of Computer Science, Saarbrücken, Germany
| | | | | | - Christina Backes
- Center for Bioinformatics, Saarbrücken, Germany.,Chair for Clinical Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany
| | - Christopher Mohr
- Quantitative Biology Center (QBiC), Tübingen, Germany.,Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
| | - Benjamin Schubert
- Department of Systems Biology, Boston, MA, USA.,Department of Cell Biology, Harvard Medical School, Boston, MA, USA.,cBio Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kerstin Lenhof
- Center for Bioinformatics, Saarbrücken, Germany.,Saarbrücken Graduate School of Computer Science, Saarbrücken, Germany
| | - Nico Gerstner
- Center for Bioinformatics, Saarbrücken, Germany.,Saarbrücken Graduate School of Computer Science, Saarbrücken, Germany
| | | | - Markus Wallwiener
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany.,National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
| | - Oliver Kohlbacher
- Quantitative Biology Center (QBiC), Tübingen, Germany.,Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany.,Center for Bioinformatics, University of Tübingen, Tübingen, Germany.,Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany.,Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Andreas Keller
- Center for Bioinformatics, Saarbrücken, Germany.,Chair for Clinical Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany
| | - Eckart Meese
- Center for Bioinformatics, Saarbrücken, Germany.,Human Genetics, Saarland University, Homburg, Germany
| | - Norbert Graf
- Center for Bioinformatics, Saarbrücken, Germany.,Department of Pediatric Oncology and Hematology, Medical School, Saarland University, Homburg, Germany
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9
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Bian Y, Li Q, Li Q, Pan R. Silencing of BRF2 inhibits the growth and metastasis of lung cancer cells. Mol Med Rep 2020; 22:1767-1774. [PMID: 32705258 PMCID: PMC7411291 DOI: 10.3892/mmr.2020.11285] [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] [Received: 01/06/2020] [Accepted: 05/15/2020] [Indexed: 12/21/2022] Open
Abstract
Transcription factor II B (TFIIB)‑related factor 2 (BRF2) is involved in the development of cancer, but its role in lung cancer is underreported. The present study aimed to explore the role of BRF2 in the regulation of lung cancer cells. Immunofluorescence staining and immunohistochemistry were performed to detect BRF2 protein expression in human lung cancer cells and tissues. Following cell transfection with small interfering RNA for silencing BRF2, the cell proliferation was examined by Cell Counting Kit‑8 and MTT assays. Cell apoptosis, migration and invasion were determined by flow cytometry, wound‑healing and Transwell assay. The expression levels of Akt, phosphorylated (p)‑Akt, Bax, E‑cadherin, Bcl‑2, N‑cadherin, Snail and epidermal growth factor receptor (EGFR) in human lung cancer A549 cells were detected by western blotting. The results demonstrated that BRF2 expression was increased in human lung cancer cells and tissues, and that silencing of BRF2 promoted cell apoptosis but inhibited cell proliferation and migration. The protein expression levels of Akt, E‑cadherin, p‑Akt, Bcl‑2, N‑cadherin, Snail and EGFR in A549 cells were inhibited by silencing of BRF2, while expression levels of Bax and E‑cadherin were increased by silencing BRF2. In conclusion, BRF2 demonstrates high expression in lung cancer and silencing of BRF2 inhibits the growth and metastasis of lung cancer cells. The current findings provide a novel approach for the treatment of lung cancer.
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Affiliation(s)
- Yuan Bian
- Department of Respiratory Medicine, Zhuji Affiliated Hospital of Shaoxing University, Zhuji, Zhejiang 311800, P.R. China
| | - Qiu Li
- Department of Respiratory Medicine, Zhuji Affiliated Hospital of Shaoxing University, Zhuji, Zhejiang 311800, P.R. China
| | - Qiaolian Li
- Department of Respiratory Medicine, Zhuji Affiliated Hospital of Shaoxing University, Zhuji, Zhejiang 311800, P.R. China
| | - Ruigen Pan
- Department of Radiology, Zhuji Affiliated Hospital of Shaoxing University, Zhuji, Zhejiang 311800, P.R. China
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10
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Gong S, Qu X, Yang S, Zhou S, Li P, Zhang Q. RFC3 induces epithelial‑mesenchymal transition in lung adenocarcinoma cells through the Wnt/β‑catenin pathway and possesses prognostic value in lung adenocarcinoma. Int J Mol Med 2019; 44:2276-2288. [PMID: 31661124 PMCID: PMC6844605 DOI: 10.3892/ijmm.2019.4386] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 09/27/2019] [Indexed: 12/22/2022] Open
Abstract
Lung cancer is a malignant tumor responsible for the highest mortality rate in humans. The identification of novel functional genes is of great importance in the treatment of lung cancer. The reported roles of replication factor C subunit 3 (RFC3) in tumorigenesis are contradictory. The present study aimed to explore the role and mechanism of RFC3 in lung cancer cells. An immunohistochemical study of 165 lung cancer and adjacent tissues was conducted (123 lung adenocarcinoma tissues and 42 lung squamous cell carcinoma tissues). Kaplan-Meier analysis and Cox multivariate analysis were employed to explore the relationship between RFC3 and patient prognosis. In addition, the proliferation, cell cycle distribution and apoptosis of A549 and H1299 cells were determined by MTT assay and flow cytometry, respectively, following cell transfection to induce overexpression and knockdown of RFC3. A Boyden chamber assay and wound-healing assay were conducted to determine the invasive and migratory abilities of A549 and H1299 cells. Western blotting was used to analyze the effects of RFC3 overexpression and RFC3 small interfering RNA-induced knockdown, and to explore the potential mechanism and pathway underlying the effects of RFC3. Positive expression of RFC3 was detected in lung adenocarcinoma, and overexpression of RFC3 shortened the survival time of patients with lung adenocarcinoma. Furthermore, overexpression of RFC3 increased the invasion and migration of A549 cells, whereas knockdown of RFC3 significantly reduced the invasion and migration of H1299 cells. Ectopic expression of RFC3 induced epithelial-mesenchymal transition (EMT), as determined by downregulation of E-cadherin, and upregulation of N-cadherin, vimentin and Wnt signaling target genes, including c-MYC, Wnt1 and β-catenin, and the ratio of phosphorylated-glycogen synthase kinase 3 (GSK3)-β (Ser9)/GSK3-β. In conclusion, RFC3 may be considered a coactivator that promotes the Wnt/β-catenin signaling pathway, and induces EMT and metastasis in lung adenocarcinoma.
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Affiliation(s)
- Shulei Gong
- Department of Thoracic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Xiaohan Qu
- Department of Thoracic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Shize Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Siyu Zhou
- Department of Thoracic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Peiwen Li
- Department of Thoracic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Qigang Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
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11
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Kong J, Wang T, Zhang Z, Yang X, Shen S, Wang W. Five Core Genes Related to the Progression and Prognosis of Hepatocellular Carcinoma Identified by Analysis of a Coexpression Network. DNA Cell Biol 2019; 38:1564-1576. [PMID: 31633379 DOI: 10.1089/dna.2019.4932] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The molecular mechanism of tumorigenesis of the prevalent cancer hepatocellular carcinoma (HCC) is unclear. In this study, through weighted gene coexpression network analysis, a coexpression network was constructed by selecting the top 25% most variant genes in the dataset GSE62232. The average linkage hierarchical clustering identified 24 modules, and among them, the pink module associated with prognosis of HCC was screened. Five gene candidates (PCNA, RFC4, PTTG1, H2AFZ, and RRM1) with a common network in the module were screened after the protein-protein interaction network complex was combined with the coexpression network. After progression and survival analysis, all candidates were identified as real core genes. According to the Human Protein Atlas and the Oncomine database, these genes were dysregulated in HCC samples. The receiver operating characteristic curve proved that the expression levels of the core genes had high diagnostic efficacy. The results of gene set enrichment analysis and functional enrichment analysis demonstrated the importance of the cell cycle-related pathways in HCC progression and prognosis. In conclusion, the five real core genes and cell cycle-related pathways identified in this study could greatly improve the knowledge about HCC progression and contribute to HCC treatment.
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Affiliation(s)
- Junjie Kong
- Department of Liver Surgery, Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, P.R. China
| | - Tao Wang
- Department of Liver Surgery, Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, P.R. China
| | - Zifei Zhang
- Department of Liver Surgery, Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, P.R. China
| | - Xianwei Yang
- Department of Liver Surgery, Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, P.R. China
| | - Shu Shen
- Department of Liver Surgery, Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, P.R. China
| | - Wentao Wang
- Department of Liver Surgery, Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, P.R. China
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12
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Yang CW, Cao HH, Guo Y, Feng YM, Zhang N. Identification of Novel Breast Cancer Genes based on Gene Expression Profiles and PPI Data. CURR PROTEOMICS 2019. [DOI: 10.2174/1570164616666190126111354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:Breast cancer is one of the most common malignancies, and a threat to female health all over the world. However, the molecular mechanism of breast cancer has not been fully discovered yet.Objective:It is crucial to identify breast cancer-related genes, which could provide new biomarker for breast cancer diagnosis as well as potential treatment targets.Methods:Here we used the minimum redundancy-maximum relevance (mRMR) method to select significant genes, then mapped the transcripts of the genes on the Protein-Protein Interaction (PPI) network and traced the shortest path between each pair of two proteins.Results:As a result, we identified 24 breast cancer-related genes whose betweenness were over 700. The GO enrichment analysis indicated that the transcription and oxygen level are very important in breast cancer. And the pathway analysis indicated that most of these 24 genes are enriched in prostate cancer, endocrine resistance, and pathways in cancer.Conclusion:We hope these 24 genes might be useful for diagnosis, prognosis and treatment for breast cancer.
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Affiliation(s)
- Cheng-Wen Yang
- Tianjin Key Lab of BME Measurement, Department of Biomedical Engineering, Tianjin University, Tianjin, China
| | - Huan-Huan Cao
- Tianjin Key Lab of BME Measurement, Department of Biomedical Engineering, Tianjin University, Tianjin, China
| | - Yu Guo
- Tianjin Key Lab of BME Measurement, Department of Biomedical Engineering, Tianjin University, Tianjin, China
| | - Yuan-Ming Feng
- Tianjin Key Lab of BME Measurement, Department of Biomedical Engineering, Tianjin University, Tianjin, China
| | - Ning Zhang
- Tianjin Key Lab of BME Measurement, Department of Biomedical Engineering, Tianjin University, Tianjin, China
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13
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Kalimutho M, Sinha D, Mittal D, Srihari S, Nanayakkara D, Shafique S, Raninga P, Nag P, Parsons K, Khanna KK. Blockade of PDGFRβ circumvents resistance to MEK-JAK inhibition via intratumoral CD8 + T-cells infiltration in triple-negative breast cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:85. [PMID: 30777101 PMCID: PMC6379987 DOI: 10.1186/s13046-019-1075-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/30/2019] [Indexed: 12/26/2022]
Abstract
BACKGROUND Despite the increasing progress in targeted and immune based-directed therapies for other solid organ malignancies, currently there is no targeted therapy available for TNBCs. A number of mechanisms have been reported both in pre-clinical and clinical settings that involve inherent, acquired and adaptive resistance to small molecule inhibitors. Here, we demonstrated a novel resistance mechanism in TNBC cells mediated by PDGFRβ in response to JAK2 inhibition. METHODS Multiple in vitro (subG1, western blotting, immunofluorescence, RT-PCR, Immunoprecipitation), in vivo and publically available datasets were used. RESULTS We showed that TNBC cells exposed to MEK1/2-JAK2 inhibitors exhibit resistant colonies in anchorage-independent growth assays. Moreover, cells treated with various small molecule inhibitors including JAK2 promote PDGFRβ upregulation. Using publically available databases, we showed that patients expressing high PDGFRβ or its ligand PDGFB exhibit poor relapse-free survival upon chemotherapeutic treatment. Mechanistically we found that JAK2 expression controls steady state levels of PDGFRβ. Thus, co-blockade of PDGFRβ with JAK2 and MEK1/2 inhibitors completely eradicated resistant colonies in vitro. We found that triple-combined treatment had a significant impact on CD44+/CD24- stem-cell-like cells. Likewise, we found a significant tumor growth inhibition in vivo through intratumoral CD8+ T cells infiltration in a manner that is reversed by anti-CD8 antibody treatment. CONCLUSION These findings reveal a novel regulatory role of JAK2-mediated PDGFRβ proteolysis and provide an example of a PDGFRβ-mediated resistance mechanism upon specific target inhibition in TNBC.
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Affiliation(s)
- Murugan Kalimutho
- Signal Transduction laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia.
| | - Debottam Sinha
- Signal Transduction laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Deepak Mittal
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Sriganesh Srihari
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Devathri Nanayakkara
- Signal Transduction laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Shagufta Shafique
- Signal Transduction laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Prahlad Raninga
- Signal Transduction laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Purba Nag
- Signal Transduction laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia.,School of Environment and Science, Griffith University, Nathan, QLD, 4111, Australia
| | - Kate Parsons
- Signal Transduction laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Kum Kum Khanna
- Signal Transduction laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia.
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14
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Tang X, Xu Y, Lu L, Jiao Y, Liu J, Wang L, Zhao H. Identification of key candidate genes and small molecule drugs in cervical cancer by bioinformatics strategy. Cancer Manag Res 2018; 10:3533-3549. [PMID: 30271202 PMCID: PMC6145638 DOI: 10.2147/cmar.s171661] [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] [Indexed: 11/23/2022] Open
Abstract
Purpose Cervical cancer (CC) is one of the most common malignant tumors among women. The present study aimed at integrating two expression profile datasets to identify critical genes and potential drugs in CC. Materials and methods Expression profiles, GSE7803 and GSE9750, were integrated using bioinformatics methods, including differentially expressed genes analysis, Kyoto Encyclopedia of Genes and Genomes pathway analysis, and protein–protein interaction (PPI) network construction. Subsequently, survival analysis was performed among the key genes using Gene Expression Profiling Interactive Analysis websites. Connectivity Map (CMap) was used to query potential drugs for CC. Results A total of 145 upregulated genes and 135 downregulated genes in CC were identified. The functional changes of these differentially expressed genes related to CC were mainly associated with cell cycle, DNA replication, p53 signaling pathway, and oocyte meiosis. A PPI network was identified by STRING with 220 nodes and 2,111 edges. Thirteen key genes were identified as the intersecting genes of the enrichment pathways and the top 20 nodes in PPI network. Survival analysis revealed that high mRNA expression of MCM2, PCNA, and RFC4 was significantly associated with longer overall survival, and the survival was significantly better in the low-expression RRM2 group. Moreover, CMap predicted nine small molecules as possible adjuvant drugs to treat CC. Conclusion Our study found key dysregulated genes involved in CC and potential drugs to combat it, which might provide insights into CC pathogenesis and might shed light on potential CC treatments.
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Affiliation(s)
- Xin Tang
- School of Rehabilitation, Kunming Medical University, Kunming, China
| | - Yicong Xu
- Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, China, .,Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Kunming, China,
| | - Lin Lu
- Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, China, .,Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Kunming, China,
| | - Yang Jiao
- Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, China, .,Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Kunming, China,
| | - Jianjun Liu
- Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, China, .,Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Kunming, China,
| | - Linlin Wang
- Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, China, .,Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Kunming, China,
| | - Hongbo Zhao
- Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, China, .,Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Kunming, China,
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15
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Abstract
Breast cancer is known to be a heterogeneous disease driven by a large repertoire of molecular abnormalities, which contribute to its diverse clinical behaviour. Despite the success of targeted therapy approaches for breast cancer patient management, there is still a lack of the molecular understanding of aggressive forms of the disease and clinical management of these patients remains difficult. The advent of high-throughput sequencing technologies has paved the way for a more complete understanding of the molecular make-up of the breast cancer genome. As such, it is becoming apparent that disruption of canonical splicing within breast cancer governs its clinical progression. In this review, we discuss the role of dysregulation of spliceosomal component genes and associated factors in the progression of breast cancer, their role in therapy resistance and the use of quantitative isoform expression as potential prognostic and predictive biomarkers with a particular focus on oestrogen receptor-positive breast cancer.
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Affiliation(s)
- Abigail Read
- The Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer Research, London, UK
- Division of Molecular PathologyThe Institute of Cancer Research, London, UK
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer Research, London, UK
- Division of Molecular PathologyThe Institute of Cancer Research, London, UK
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16
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Wilke CM, Braselmann H, Hess J, Klymenko SV, Chumak VV, Zakhartseva LM, Bakhanova EV, Walch AK, Selmansberger M, Samaga D, Weber P, Schneider L, Fend F, Bösmüller HC, Zitzelsberger H, Unger K. A genomic copy number signature predicts radiation exposure in post-Chernobyl breast cancer. Int J Cancer 2018; 143:1505-1515. [PMID: 29663366 DOI: 10.1002/ijc.31533] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 01/18/2023]
Abstract
Breast cancer is the second leading cause of cancer death among women worldwide and besides life style, age and genetic risk factors, exposure to ionizing radiation is known to increase the risk for breast cancer. Further, DNA copy number alterations (CNAs), which can result from radiation-induced double-strand breaks, are frequently occurring in breast cancer cells. We set out to identify a signature of CNAs discriminating breast cancers from radiation-exposed and non-exposed female patients. We analyzed resected breast cancer tissues from 68 exposed female Chernobyl clean-up workers and evacuees and 68 matched non-exposed control patients for CNAs by array comparative genomic hybridization analysis (aCGH). Using a stepwise forward-backward selection approach a non-complex CNA signature, that is, less than ten features, was identified in the training data set, which could be subsequently validated in the validation data set (p value < 0.05). The signature consisted of nine copy number regions located on chromosomal bands 7q11.22-11.23, 7q21.3, 16q24.3, 17q21.31, 20p11.23-11.21, 1p21.1, 2q35, 2q35, 6p22.2. The signature was independent of any clinical characteristics of the patients. In all, we identified a CNA signature that has the potential to allow identification of radiation-associated breast cancer at the individual level.
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Affiliation(s)
- Christina M Wilke
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Herbert Braselmann
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group 'Personalized Radiotherapy of Head and Neck Cancer', Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, 85764, Germany
| | - Julia Hess
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group 'Personalized Radiotherapy of Head and Neck Cancer', Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, 85764, Germany
| | - Sergiy V Klymenko
- National Research Center for Radiation Medicine of National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | - Vadim V Chumak
- National Research Center for Radiation Medicine of National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | | | - Elena V Bakhanova
- National Research Center for Radiation Medicine of National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | - Axel K Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Martin Selmansberger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Daniel Samaga
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Peter Weber
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Ludmila Schneider
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group 'Personalized Radiotherapy of Head and Neck Cancer', Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, 85764, Germany
| | - Falko Fend
- Institute of Pathology and Neuropathology, Tübingen, Germany
| | | | - Horst Zitzelsberger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group 'Personalized Radiotherapy of Head and Neck Cancer', Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, 85764, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, München, Germany
| | - Kristian Unger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group 'Personalized Radiotherapy of Head and Neck Cancer', Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, 85764, Germany
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17
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RNF43 and ZNRF3 are commonly altered in serrated pathway colorectal tumorigenesis. Oncotarget 2018; 7:70589-70600. [PMID: 27661107 PMCID: PMC5342576 DOI: 10.18632/oncotarget.12130] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 09/02/2016] [Indexed: 12/20/2022] Open
Abstract
Serrated pathway colorectal cancers (CRCs) are characterised by a BRAF mutation and half display microsatellite instability (MSI). The Wnt pathway is commonly upregulated in conventional CRC through APC mutation. By contrast, serrated cancers do not mutate APC. We investigated mutation of the ubiquitin ligases RNF43 and ZNRF3 as alternate mechanism of altering the Wnt signal in serrated colorectal neoplasia. RNF43 was mutated in 47/54(87%) BRAF mutant/MSI and 8/33(24%) BRAF mutant/microsatellite stable cancers compared to only 3/79(4%) BRAF wildtype cancers (p<0.0001). ZNRF3 was mutated in 16/54(30%) BRAF mutant/MSI and 5/33(15%) BRAF mutant/microsatellite stable compared to 0/27 BRAF wild type cancers (p=0.004). An RNF43 frameshift mutation (X659fs) occurred in 80% BRAF mutant/MSI cancers. This high rate was verified in a second series of 25/35(71%) BRAF mutant/MSI cancers. RNF43 and ZNRF3 had lower transcript expression in BRAF mutant compared to BRAF wildtype cancers and less cytoplasmic protein expression in BRAF mutant/MSI compared to other subtypes. Treatment with a porcupine inhibitor reduced RNF43/ZNRF3 mutant colony growth by 50% and synergised with a MEK inhibitor to dramatically reduce growth. This study suggests inactivation of RNF43 and ZNRF3 is important in serrated tumorigenesis and has identified a potential therapeutic strategy for this cancer subtype.
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18
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Srihari S, Kwong R, Tran K, Simpson R, Tattam P, Smith E. Metabolic deregulation in prostate cancer. Mol Omics 2018; 14:320-329. [DOI: 10.1039/c8mo00170g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Using RNAseq data from prostate cancer tissues we identified up to six metabolic subtypes of prostate cancer that show distinct disease-free and/or metastasis-free survival.
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Affiliation(s)
| | - Ray Kwong
- MaxwellPlus+
- Fortitude Valley
- Australia
| | - Khoa Tran
- MaxwellPlus+
- Fortitude Valley
- Australia
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19
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An ensemble predictive modeling framework for breast cancer classification. Methods 2017; 131:128-134. [DOI: 10.1016/j.ymeth.2017.07.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 07/11/2017] [Accepted: 07/12/2017] [Indexed: 12/22/2022] Open
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20
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Choi JH, Kim MJ, Park YK, Im JY, Kwon SM, Kim HC, Woo HG, Wang HJ. Mutations acquired by hepatocellular carcinoma recurrence give rise to an aggressive phenotype. Oncotarget 2017; 8:22903-22916. [PMID: 28038442 PMCID: PMC5410272 DOI: 10.18632/oncotarget.14248] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 12/01/2016] [Indexed: 02/06/2023] Open
Abstract
Recurrence of hepatocellular carcinoma (HCC) even after curative resection causes dismal outcomes of patients. Here, to delineate the driver events of genomic and transcription alteration during HCC recurrence, we performed RNA-Seq profiling of the paired primary and recurrent tumors from two patients with intrahepatic HCC. By comparing the mutational and transcriptomic profiles, we identified somatic mutations acquired by HCC recurrence including novel mutants of GOLGB1 (E2721V) and SF3B3 (H804Y). By performing experimental evaluation using siRNA-mediated knockdown and overexpression constructs, we demonstrated that the mutants of GOLGB1 and SF3B3 can promote cell proliferation, colony formation, migration, and invasion of liver cancer cells. Transcriptome analysis also revealed that the recurrent HCCs reprogram their transcriptomes to acquire aggressive phenotypes. Network analysis revealed CXCL8 (IL-8) and SOX4 as common downstream targets of the mutants. In conclusion, we suggest that the mutations of GOLGB1 and SF3B3 are potential key drivers for the acquisition of an aggressive phenotype in recurrent HCC.
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Affiliation(s)
- Ji-Hye Choi
- Department of Physiology, Ajou University School of Medicine, Suwon, Korea.,Department of Biomedical Science, Graduate School, Ajou University, Suwon, Korea
| | - Min Jae Kim
- Department of Physiology, Ajou University School of Medicine, Suwon, Korea.,Department of Biomedical Science, Graduate School, Ajou University, Suwon, Korea
| | - Yong Keun Park
- Department of Surgery, Catholic Kwandong University International St. Mary's Hospital, Incheon, Korea
| | - Jong-Yeop Im
- Department of Physiology, Ajou University School of Medicine, Suwon, Korea.,Department of Biomedical Science, Graduate School, Ajou University, Suwon, Korea
| | - So Mee Kwon
- Department of Physiology, Ajou University School of Medicine, Suwon, Korea.,Department of Biomedical Science, Graduate School, Ajou University, Suwon, Korea
| | - Hyung Chul Kim
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Hyun Goo Woo
- Department of Physiology, Ajou University School of Medicine, Suwon, Korea.,Department of Biomedical Science, Graduate School, Ajou University, Suwon, Korea
| | - Hee-Jung Wang
- Department of Surgery, Ajou University School of Medicine, Suwon, Korea
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21
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Niu G, Wang D, Pei Y, Sun L. Systematic identification of key genes and pathways in the development of invasive cervical cancer. Gene 2017; 618:28-41. [DOI: 10.1016/j.gene.2017.03.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 02/13/2017] [Accepted: 03/16/2017] [Indexed: 11/30/2022]
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22
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Kalimutho M, Bain AL, Mukherjee B, Nag P, Nanayakkara DM, Harten SK, Harris JL, Subramanian GN, Sinha D, Shirasawa S, Srihari S, Burma S, Khanna KK. Enhanced dependency of KRAS-mutant colorectal cancer cells on RAD51-dependent homologous recombination repair identified from genetic interactions in Saccharomyces cerevisiae. Mol Oncol 2017; 11:470-490. [PMID: 28173629 PMCID: PMC5527460 DOI: 10.1002/1878-0261.12040] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 01/10/2017] [Accepted: 01/27/2017] [Indexed: 01/08/2023] Open
Abstract
Activating KRAS mutations drive colorectal cancer tumorigenesis and influence response to anti‐EGFR‐targeted therapy. Despite recent advances in understanding Ras signaling biology and the revolution in therapies for melanoma using BRAF inhibitors, no targeted agents have been effective in KRAS‐mutant cancers, mainly due to activation of compensatory pathways. Here, by leveraging the largest synthetic lethal genetic interactome in yeast, we identify that KRAS‐mutated colorectal cancer cells have augmented homologous recombination repair (HRR) signaling. We found that KRAS mutation resulted in slowing and stalling of the replication fork and accumulation of DNA damage. Moreover, we found that KRAS‐mutant HCT116 cells have an increase in MYC‐mediated RAD51 expression with a corresponding increase in RAD51 recruitment to irradiation‐induced DNA double‐strand breaks (DSBs) compared to genetically complemented isogenic cells. MYC depletion using RNA interference significantly reduced IR‐induced RAD51 foci formation and HRR. On the contrary, overexpression of either HA‐tagged wild‐type (WT) MYC or phospho‐mutant S62A increased RAD51 protein levels and hence IR‐induced RAD51 foci. Likewise, depletion of RAD51 selectively induced apoptosis in HCT116‐mutant cells by increasing DSBs. Pharmacological inhibition targeting HRR signaling combined with PARP inhibition selectivity killed KRAS‐mutant cells. Interestingly, these differences were not seen in a second isogenic pair of KRAS WT and mutant cells (DLD‐1), likely due to their nondependency on the KRAS mutation for survival. Our data thus highlight a possible mechanism by which KRAS‐mutant‐dependent cells drive HRR in vitro by upregulating MYC‐RAD51 expression. These data may offer a promising therapeutic vulnerability in colorectal cancer cells harboring otherwise nondruggable KRAS mutations, which warrants further investigation in vivo.
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Affiliation(s)
- Murugan Kalimutho
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia.,School of Natural Sciences, Griffith University, Nathan, Australia
| | - Amanda L Bain
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Bipasha Mukherjee
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Purba Nag
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia.,School of Natural Sciences, Griffith University, Nathan, Australia
| | - Devathri M Nanayakkara
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Sarah K Harten
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Janelle L Harris
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Goutham N Subramanian
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Debottam Sinha
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia.,School of Natural Sciences, Griffith University, Nathan, Australia
| | - Senji Shirasawa
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Japan
| | - Sriganesh Srihari
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
| | - Sandeep Burma
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kum Kum Khanna
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
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23
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Anderson AM, Kalimutho M, Harten S, Nanayakkara DM, Khanna KK, Ragan MA. The metastasis suppressor RARRES3 as an endogenous inhibitor of the immunoproteasome expression in breast cancer cells. Sci Rep 2017; 7:39873. [PMID: 28051153 PMCID: PMC5209724 DOI: 10.1038/srep39873] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 11/28/2016] [Indexed: 01/17/2023] Open
Abstract
In breast cancer metastasis, the dynamic continuum involving pro- and anti-inflammatory regulators can become compromised. Over 600 genes have been implicated in metastasis to bone, lung or brain but how these genes might contribute to perturbation of immune function is poorly understood. To gain insight, we adopted a gene co-expression network approach that draws on the functional parallels between naturally occurring bone marrow-derived mesenchymal stem cells (BM-MSCs) and cancer stem cells (CSCs). Our network analyses indicate a key role for metastasis suppressor RARRES3, including potential to regulate the immunoproteasome (IP), a specialized proteasome induced under inflammatory conditions. Knockdown of RARRES3 in near-normal mammary epithelial and breast cancer cell lines increases overall transcript and protein levels of the IP subunits, but not of their constitutively expressed counterparts. RARRES3 mRNA expression is controlled by interferon regulatory factor IRF1, an inducer of the IP, and is sensitive to depletion of the retinoid-related receptor RORA that regulates various physiological processes including immunity through modulation of gene expression. Collectively, these findings identify a novel regulatory role for RARRES3 as an endogenous inhibitor of IP expression, and contribute to our evolving understanding of potential pathways underlying breast cancer driven immune modulation.
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Affiliation(s)
- Alison M Anderson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane QLD 4072, Australia
| | - Murugan Kalimutho
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane QLD 4006, Australia
| | - Sarah Harten
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane QLD 4006, Australia
| | - Devathri M Nanayakkara
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane QLD 4006, Australia
| | - Kum Kum Khanna
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane QLD 4006, Australia
| | - Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane QLD 4072, Australia
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24
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An approach for deciphering patient-specific variations with application to breast cancer molecular expression profiles. J Biomed Inform 2016; 63:120-130. [DOI: 10.1016/j.jbi.2016.07.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 07/06/2016] [Accepted: 07/27/2016] [Indexed: 02/07/2023]
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