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Tomasoni D, Lombardo R, Lauria M. Strengths and limitations of non-disclosive data analysis: a comparison of breast cancer survival classifiers using VisualSHIELD. Front Genet 2024; 15:1270387. [PMID: 38348453 PMCID: PMC10859452 DOI: 10.3389/fgene.2024.1270387] [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: 07/31/2023] [Accepted: 01/08/2024] [Indexed: 02/15/2024] Open
Abstract
Preserving data privacy is an important concern in the research use of patient data. The DataSHIELD suite enables privacy-aware advanced statistical analysis in a federated setting. Despite its many applications, it has a few open practical issues: the complexity of hosting a federated infrastructure, the performance penalty imposed by the privacy-preserving constraints, and the ease of use by non-technical users. In this work, we describe a case study in which we review different breast cancer classifiers and report our findings about the limits and advantages of such non-disclosive suite of tools in a realistic setting. Five independent gene expression datasets of breast cancer survival were downloaded from Gene Expression Omnibus (GEO) and pooled together through the federated infrastructure. Three previously published and two newly proposed 5-year cancer-free survival risk score classifiers were trained in a federated environment, and an additional reference classifier was trained with unconstrained data access. The performance of these six classifiers was systematically evaluated, and the results show that i) the published classifiers do not generalize well when applied to patient cohorts that differ from those used to develop them; ii) among the methods we tried, the classification using logistic regression worked better on average, closely followed by random forest; iii) the unconstrained version of the logistic regression classifier outperformed the federated version by 4% on average. Reproducibility of our experiments is ensured through the use of VisualSHIELD, an open-source tool that augments DataSHIELD with new functions, a standardized deployment procedure, and a simple graphical user interface.
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Affiliation(s)
- Danilo Tomasoni
- Fondazione the Microsoft Research–University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, Italy
| | | | - Mario Lauria
- Fondazione the Microsoft Research–University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, Italy
- Department of Mathematics, University of Trento, Povo, Italy
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2
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Zhang Q, An ZY, Jiang W, Jin WL, He XY. Collagen code in tumor microenvironment: Functions, molecular mechanisms, and therapeutic implications. Biomed Pharmacother 2023; 166:115390. [PMID: 37660648 DOI: 10.1016/j.biopha.2023.115390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/25/2023] [Accepted: 08/26/2023] [Indexed: 09/05/2023] Open
Abstract
The tumor microenvironment (TME) is crucial in cancer progression, and the extracellular matrix (ECM) is an important TME component. Collagen is a major ECM component that contributes to tumor cell infiltration, expansion, and distant metastasis during cancer progression. Recent studies reported that collagen is deposited in the TME to form a collagen wall along which tumor cells can infiltrate and prevent drugs from working on the tumor cells. Collagen-tumor cell interaction is complex and requires the activation of multiple signaling pathways for biochemical and mechanical signaling interventions. In this review, we examine the effect of collagen deposition in the TME on tumor progression and discuss the interaction between collagen and tumor cells. This review aims to illustrate the functions and mechanisms of collagen in tumor progression in the TME and its role in tumor therapy. The findings indicated collagen in the TME appears to be a better target for cancer therapy.
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Affiliation(s)
- Qian Zhang
- Department of General Surgery, The Affiliated Provincial Hospital of Anhui Medical University, Hefei 230001, PR China
| | - Zi-Yi An
- The First Clinical Medical College of Lanzhou University, Lanzhou 730000, PR China; Institute of Cancer Neuroscience, Medical Frontier Innovation Research Center, The First Hospital of Lanzhou University, Lanzhou 730000, PR China
| | - Wen Jiang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230001, PR China; Anhui Public Health Clinical Center, Hefei 230001, PR China
| | - Wei-Lin Jin
- The First Clinical Medical College of Lanzhou University, Lanzhou 730000, PR China; Institute of Cancer Neuroscience, Medical Frontier Innovation Research Center, The First Hospital of Lanzhou University, Lanzhou 730000, PR China.
| | - Xin-Yang He
- Department of General Surgery, The Affiliated Provincial Hospital of Anhui Medical University, Hefei 230001, PR China; Department of General Surgery, The First Affiliated Hospital of University of Science and Technology of China (Anhui Provincial Hospital), Hefei 230001, PR China.
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3
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Liu Y, Yu K, Zhang K, Niu M, Chen Q, Liu Y, Wang L, Zhang N, Li W, Zhong X, Li G, Wu S, Zhang J, Liu Y. O-GlcNAcylation promotes topoisomerase IIα catalytic activity in breast cancer chemoresistance. EMBO Rep 2023; 24:e56458. [PMID: 37249035 PMCID: PMC10328065 DOI: 10.15252/embr.202256458] [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: 11/26/2022] [Revised: 05/06/2023] [Accepted: 05/12/2023] [Indexed: 05/31/2023] Open
Abstract
DNA topoisomerase IIα (TOP2A) plays a vital role in replication and cell division by catalytically altering DNA topology. It is a prominent target for anticancer drugs, but clinical efficacy is often compromised due to chemoresistance. In this study, we investigate the role of TOP2A O-GlcNAcylation in breast cancer cells and patient tumor tissues. Our results demonstrate that elevated TOP2A, especially its O-GlcNAcylation, promotes breast cancer malignant progression and resistance to adriamycin (Adm). O-GlcNAcylation at Ser1469 enhances TOP2A chromatin DNA binding and catalytic activity, leading to resistance to Adm in breast cancer cells and xenograft models. Mechanistically, O-GlcNAcylation-modulated interactions between TOP2A and cell cycle regulators influence downstream gene expression and contribute to breast cancer drug resistance. These results reveal a previously unrecognized mechanistic role for TOP2A O-GlcNAcylation in breast cancer chemotherapy resistance and provide support for targeting TOP2A O-GlcNAcylation in cancer therapy.
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Affiliation(s)
- Yangzhi Liu
- School of Life and Pharmaceutical SciencesDalian University of TechnologyPanjinChina
| | - Kairan Yu
- School of Life and Pharmaceutical SciencesDalian University of TechnologyPanjinChina
| | - Keren Zhang
- Department of ChemistryCollege of Science, Southern University of Science and TechnologyShenzhenChina
| | - Mingshan Niu
- Blood Diseases Institute, Xuzhou Medical UniversityXuzhouJiangsuChina
| | - Qiushi Chen
- Department of ChemistryThe University of Hong KongHong KongChina
- Laboratory for Synthetic Chemistry and Chemical Biology LimitedHong Kong Science ParkHong KongChina
| | - Yajie Liu
- School of Life and Pharmaceutical SciencesDalian University of TechnologyPanjinChina
| | - Lingyan Wang
- School of Life and Pharmaceutical SciencesDalian University of TechnologyPanjinChina
| | - Nana Zhang
- School of Life and Pharmaceutical SciencesDalian University of TechnologyPanjinChina
| | - Wenli Li
- School of Life and Pharmaceutical SciencesDalian University of TechnologyPanjinChina
| | - Xiaomin Zhong
- Department of OncologyThe Affiliated Huaian No. 1 People's Hospital of Nanjing Medical UniversityHuai'anChina
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalianChina
| | - Sijin Wu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalianChina
| | - Jianing Zhang
- School of Life and Pharmaceutical SciencesDalian University of TechnologyPanjinChina
| | - Yubo Liu
- School of Life and Pharmaceutical SciencesDalian University of TechnologyPanjinChina
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4
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Wang R, Xu K, Chen Q, Hu Q, Zhang J, Guan X. Cuproptosis engages in c-Myc-mediated breast cancer stemness. J Transl Med 2023; 21:409. [PMID: 37353799 PMCID: PMC10288777 DOI: 10.1186/s12967-023-04204-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 05/15/2023] [Indexed: 06/25/2023] Open
Abstract
BACKGROUND Intra-tumoral heterogeneity (ITH) is a distinguished hallmark of cancer, and cancer stem cells (CSCs) contribute to this malignant characteristic. Therefore, it is of great significance to investigate and even target the regulatory factors driving intra-tumoral stemness. c-Myc is a vital oncogene frequently overexpressed or amplified in various cancer types, including breast cancer. Our previous study indicated its potential association with breast cancer stem cell (BCSC) biomarkers. METHODS In this research, we performed immunohistochemical (IHC) staining on sixty breast cancer surgical specimens for c-Myc, CD44, CD24, CD133 and ALDH1A1. Then, we analyzed transcriptomic atlas of 1533 patients with breast cancer from public database. RESULTS IHC staining indicated the positive correlation between c-Myc and BCSC phenotype. Then, we used bioinformatic analysis to interrogate transcriptomics data of 1533 breast cancer specimens and identified an intriguing link among c-Myc, cancer stemness and copper-induced cell death (also known as "cuproptosis"). We screened out cuproptosis-related characteristics that predicts poor clinical outcomes and found that the pro-tumoral cuproptosis-based features were putatively enriched in MYC-targets and showed a significantly positive correlation with cancer stemness. CONCLUSION In addition to previous reports on its oncogenic roles, c-Myc showed significant correlation to stemness phenotype and copper-induced cell toxicity in breast cancer tissues. Moreover, transcriptomics data demonstrated that pro-tumoral cuproptosis biomarkers had putative positive association with cancer stemness. This research combined clinical samples with large-scale bioinformatic analysis, covered description and deduction, bridged classic oncogenic mechanisms to innovative opportunities, and inspired the development of copper-based nanomaterials in targeting highly heterogeneous tumors.
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Affiliation(s)
- Runtian Wang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Kun Xu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Qin Chen
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Qin Hu
- Department of Cardiothoracic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| | - Jian Zhang
- Phase I Clinical Trial Center, Fudan University Shanghai Cancer Center, Shanghai, China.
| | - Xiaoxiang Guan
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China.
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5
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Zhang D, Wang Y, Zhao F, Yang Q. Integrated multiomics analyses unveil the implication of a costimulatory molecule score on tumor aggressiveness and immune evasion in breast cancer: A large-scale study through over 8,000 patients. Comput Biol Med 2023; 159:106866. [PMID: 37068318 DOI: 10.1016/j.compbiomed.2023.106866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/05/2023] [Accepted: 03/30/2023] [Indexed: 04/08/2023]
Abstract
BACKGROUND Although immunotherapy has revolutionised cancer management, reliable genomic biomarkers for identifying eligible patient subpopulations are lacking. Costimulatory molecules play a crucial role in mounting anti-tumour responses, and clinical trials targeting these novel biomarkers are underway. However, whether these molecules can determine tumour aggressiveness and the risk of tumour evasion in breast cancer (BC) remains largely unknown. METHODS The whole-tissue transcriptomic data of 8236 patients with BC from 15 independent cohorts were extracted. An integrated scoring system named 'costimulatory molecule score' (CMS) was constructed and sufficient validated using least absolute shrinkage and selection operator regression (1000 iterations) and the random survival forest algorithm (1000 trees). The correlation among CMSs, cancer genotypes and clinicopathological characteristics was examined. Extensive multiomics and immunogenomic analyses were performed to investigate and verify the association among CMSs, enriched pathways, potential intrinsic and extrinsic immune escape mechanisms, immunotherapy response and therapeutic options. RESULTS The predictive role of CMS model that relies on expression pattern of merely 5 costimulatory genes for prognosis is almost universally applicable to BC patients in a platform-independent manner. Through internal and external in silico validation, high CMS was characterized by favorable genotypes but decreased tumor immunogenicity, activation of stroma, immune-suppressive states and potential immunotherapeutic resistance. Similar results were observed in a real-world immunotherapy cohort and Pan-Cancer analysis. CONCLUSION This comprehensive characterization indicates CMS model may be complemented for predicting tumor aggressiveness and immune evasion in BC patients, underlining the future clinical potential for further exploration of resistance mechanisms and optimization of immunotherapeutic strategies.
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Affiliation(s)
- Dong Zhang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, 250012, China; Department of Clinical Medicine, The First Clinical College, Shandong University, Jinan, 250012, China
| | - Yingnan Wang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, 250012, China; Department of Clinical Medicine, The First Clinical College, Shandong University, Jinan, 250012, China
| | - Faming Zhao
- Key Laboratory of Environmental Health, Ministry of Education & Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Qifeng Yang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, 250012, China; Pathology Tissue Bank, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China; Research Institute of Breast Cancer, Shandong University, Jinan, 250102, China.
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6
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Yang Y, Wang Z, He M, Diao L, Yu B, Li D. NAD+ biosynthesis metabolism predicts prognosis and indicates immune microenvironment for breast cancer. Pathol Oncol Res 2023; 29:1610956. [PMID: 37006438 PMCID: PMC10063816 DOI: 10.3389/pore.2023.1610956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023]
Abstract
The growing evidence implies that tumor cells need to increase NAD+ levels by upregulating NAD+ biosynthesis to satisfy their growth demand. NAD+ biosynthesis metabolism is implicated in tumor progression. Breast cancer (BC) is the most common malignant malignancy in the world. Nevertheless, the prognostic significance of NAD+ biosynthesis and its relationship with the tumor immune microenvironment in breast cancer still need further investigation. In this study, we obtained the mRNA expression data and clinical information of BC samples from public databases and calculated the level of NAD+ biosynthesis activity by single-sample gene set enrichment analysis (ssGSEA). We then explored the relationship between the NAD+ biosynthesis score, infiltrating immune cells, prognosis significance, immunogenicity and immune checkpoint molecules. The results demonstrated that patients with high NAD+ biosynthetic score displayed poor prognosis, high immune infiltration, high immunogenicity, elevated PD-L1 expression, and might more benefit from immunotherapy. Taken together, our studies not only deepened the understanding of NAD+ biosynthesis metabolism of breast cancer but also provided new insights into personalized treatment strategies and immunological therapies to improve the outcomes of breast cancer patients.
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Affiliation(s)
- Yuting Yang
- Department of Immunology, Medical College of Qingdao University, Qingdao, Shandong, China
| | - Ze Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing, China
| | - Mengqi He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing, China
| | - Lihong Diao
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Biyue Yu
- School of Life Sciences, Hebei University, Baoding, Hebei, China
| | - Dong Li
- Department of Immunology, Medical College of Qingdao University, Qingdao, Shandong, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing, China
- *Correspondence: Dong Li,
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7
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Sadeghi M, Gholizadeh M, Safataj N, Tahmasebivand M, Mohajeri G, Lotfi H, Bostanabad SY, Safar B, Salehi M. GLIS2 and CCND1 expression levels in breast cancer patients. Breast Dis 2023; 42:251-259. [PMID: 37574724 DOI: 10.3233/bd-220068] [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] [Indexed: 08/15/2023]
Abstract
BACKGROUND Breast cancer (BC) is the most prevalent cancer in women, with increasing incidence and death rates in recent years. Disruptions of different signaling pathways partially cause breast cancer. Hence, different genes through particular pathways are involved in BC tumorigenesis. METHODS In this study, we evaluated the expression level of GLIS2 and CCND1 genes in 50 patients. Also, in-silico analyses were used to enrich related signaling pathways involving the mentioned genes. RESULTS The results showed an increased expression level of Cyclin D1 and decreased expression level of GLIS2 in BC patients. Moreover, a relationship between aberrant expression levels of GLIS2 and CCND1 and BC development was determined. CONCLUSION These observations could help uncover new therapeutic targets for treating patients with BC in the progressive stage.
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Affiliation(s)
- Minoosh Sadeghi
- Department of Genetics, Faculty of Science, Shahrekord University, Shahrekord, Iran
| | - Majid Gholizadeh
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Neda Safataj
- Department of Genetics, Islamic Azad University, Shahrekord Branch, Shahrekord, Iran
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahsa Tahmasebivand
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Gholamreza Mohajeri
- Department of Surgery, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hajie Lotfi
- Cellular and Molecular Research Center, Research Institute for Prevention of Non-Communicable Disease, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Saber Yari Bostanabad
- Department of Pharmacology, Faculty of Pharmacy, Istanbul Health and Technology University, Istanbul, Turkey
| | - Behnaz Safar
- Department of Genetics, Faculty of Science, Shahrekord University, Shahrekord, Iran
| | - Mansoor Salehi
- Cellular, Molecular and Genetics Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
- Medical Genetics Research Center of Genome, Isfahan University of Medical Sciences, Isfahan, Iran
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Morelli MB, Nabissi M, Amantini C, Maggi F, Ricci-Vitiani L, Pallini R, Santoni G. TRPML2 Mucolipin Channels Drive the Response of Glioma Stem Cells to Temozolomide and Affect the Overall Survival in Glioblastoma Patients. Int J Mol Sci 2022; 23:ijms232315356. [PMID: 36499683 PMCID: PMC9738251 DOI: 10.3390/ijms232315356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/18/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The survival of patients with glioblastoma (GBM) is poor. The main cause is the presence of glioma stem cells (GSCs), exceptionally resistant to temozolomide (TMZ) treatment. This last may be related to the heterogeneous expression of ion channels, among them TRPML2. Its mRNA expression was evaluated in two different neural stem cell (NS/PC) lines and sixteen GBM stem-like cells by qRT-PCR. The response to TMZ was evaluated in undifferentiated or differentiated GSCs, and in TRPML2-induced or silenced GSCs. The relationship between TRPML2 expression and responsiveness to TMZ treatment was evaluated by MTT assay showing that increased TRPML2 mRNA levels are associated with resistance to TMZ. This research was deepened by qRT-PCR and western blot analysis. PI3K/AKT and JAK/STAT pathways as well as ABC and SLC drug transporters were involved. Finally, the relationship between TRPML2 expression and overall survival (OS) and progression-free survival (PFS) in patient-derived GSCs was evaluated by Kaplan-Meier analysis. The expression of TRPML2 mRNA correlates with worse OS and PFS in GBM patients. Thus, the expression of TRPML2 in GSCs influences the responsiveness to TMZ in vitro and affects OS and PFS in GBM patients.
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Affiliation(s)
- Maria Beatrice Morelli
- School of Pharmacy, University of Camerino, 62032 Camerino, Italy
- Correspondence: (M.B.M.); (G.S.); Tel.: +39-0737403312 (M.B.M.); +39-0737403319 (G.S.)
| | - Massimo Nabissi
- School of Pharmacy, University of Camerino, 62032 Camerino, Italy
| | - Consuelo Amantini
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy
| | - Federica Maggi
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy
| | - Lucia Ricci-Vitiani
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Roberto Pallini
- Institute of Neurosurgery, Gemelli University Polyclinic Foundation, Scientific Hospitalization and Care Institute (IRCCS), 00168 Rome, Italy
- Institute of Neurosurgery, School of Medicine, Catholic University, 00168 Rome, Italy
| | - Giorgio Santoni
- School of Pharmacy, University of Camerino, 62032 Camerino, Italy
- Correspondence: (M.B.M.); (G.S.); Tel.: +39-0737403312 (M.B.M.); +39-0737403319 (G.S.)
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9
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Coexpression of TRPML1 and TRPML2 Mucolipin Channels Affects the Survival of Glioblastoma Patients. Int J Mol Sci 2022; 23:ijms23147741. [PMID: 35887088 PMCID: PMC9321332 DOI: 10.3390/ijms23147741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/05/2022] [Accepted: 07/11/2022] [Indexed: 02/01/2023] Open
Abstract
Among brain cancers, glioblastoma (GBM) is the most malignant glioma with an extremely poor prognosis. It is characterized by high cell heterogeneity, which can be linked to its high malignancy. We have previously demonstrated that TRPML1 channels affect the OS of GBM patients. Herein, by RT-PCR, FACS and Western blot, we demonstrated that TRPML1 and TRPML2 channels are differently expressed in GBM patients and cell lines. Moreover, these channels partially colocalized in ER and lysosomal compartments in GBM cell lines, as evaluated by confocal analysis. Interestingly, the silencing of TRPML1 or TRPML2 by RNA interference results in the decrease in the other receptor at protein level. Moreover, the double knockdown of TRPML1 and TRPML2 leads to increased GBM cell survival with respect to single-channel-silenced cells, and improves migration and invasion ability of U251 cells. Finally, the Kaplan–Meier survival analysis demonstrated that patients with high TRPML2 expression in absence of TRPML1 expression strongly correlates with short OS, whereas high TRPML1 associated with low TRPML2 mRNA expression correlates with longer OS in GBM patients. The worst OS in GBM patients is associated with the loss of both TRPML1 and TRPML2 channels.
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10
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Shen MH, Huang CJ, Ho TF, Liu CY, Shih YY, Huang CS, Huang CC. Colorectal cancer concurrent gene signature based on coherent patterns between genomic and transcriptional alterations. BMC Cancer 2022; 22:590. [PMID: 35637462 PMCID: PMC9150289 DOI: 10.1186/s12885-022-09627-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 05/03/2022] [Indexed: 11/10/2022] Open
Abstract
Background The aim of the study was to enhance colorectal cancer prognostication by integrating single nucleotide polymorphism (SNP) and gene expression (GE) microarrays for genomic and transcriptional alteration detection; genes with concurrent gains and losses were used to develop a prognostic signature. Methods The discovery dataset comprised 32 Taiwanese colorectal cancer patients, of which 31 were assayed for GE and copy number variations (CNVs) with Illumina Human HT-12 BeadChip v4.0 and Omni 25 BeadChip v1.1. Concurrent gains and losses were declared if coherent manners were observed between GE and SNP arrays. Concurrent genes were also identified in The Cancer Genome Atlas Project (TCGA) as the secondary discovery dataset (n = 345). Results The “universal” concurrent genes, which were the combination of z-transformed correlation coefficients, contained 4022 genes. Candidate genes were evaluated within each of the 10 public domain microarray datasets, and 1655 (2000 probe sets) were prognostic in at least one study. Consensus across all datasets was used to build a risk predictive model, while distinct relapse-free/overall survival patterns between defined risk groups were observed among four out of five training datasets. The predictive accuracy of recurrence, metastasis, or death was between 61 and 86% (cross-validation area under the receiver operating characteristic (ROC) curve: 0.548-0.833) from five independent validation studies. Conclusion The colorectal cancer concurrent gene signature is prognostic in terms of recurrence, metastasis, or mortality among 1746 patients. Genes with coherent patterns between genomic and transcriptional contexts are more likely to provide prognostication for colorectal cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09627-9.
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Affiliation(s)
- Ming-Hung Shen
- Department of Surgery, Fu-Jen Catholic University Hospital, No. 69, Guizi Road, Taishan District, New Taipei City, 243, Taiwan.,Ph. D Program in Nutrition and Food Science, College of Human Ecology, Fu-Jen Catholic University, No. 510, Zhongzheng Rd., Xinzhuang Dist., New Taipei City, 242062, Taiwan.,School of Medicine, College of Medicine, Fu-Jen Catholic University, No. 510, Zhongzheng Rd., Xinzhuang Dist., New Taipei City, 242062, Taiwan
| | - Chi-Jung Huang
- Department of Biochemistry, National Defense Medical Center, No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City, 11490, Taiwan.,Department of Medical Research, Cathay General Hospital, No.280, Sec. 4, Renai Rd., Daan Dist., Taipei City, 106, Taiwan
| | - Thien-Fiew Ho
- Division of General Surgery, Cathay General Hospital Sijhih, No. 2, Ln. 59, Jiancheng Rd., Xizhi Dist., New Taipei City, 221, Taiwan
| | - Chih-Yi Liu
- Division of Pathology, Cathay General Hospital Sijhih, No. 2, Ln. 59, Jiancheng Rd., Xizhi Dist., New Taipei City, 221, Taiwan
| | - Ying-Yih Shih
- Division of Hematology and Oncology, Cathay General Hospital Sijhih, No. 2, Ln. 59, Jiancheng Rd., Xizhi Dist., New Taipei City, 221, Taiwan
| | - Ching-Shui Huang
- Department of Surgery, Cathay General Hospital, No.280, Sec. 4, Renai Rd., Daan Dist., Taipei City, 106, Taiwan. .,School of Medicine, College of Medicine, Taipei Medical University, 250 Wu-Hsing Street, Taipei City, 110, Taiwan.
| | - Chi-Cheng Huang
- Department of Surgery, Taipei Veterans General Hospital, No.201, Sec. 2, Shipai Rd., Beitou District, Taipei City, 11217, Taiwan. .,Comprehensive Breast Health Center, Taipei Veterans General Hospital, No.201, Sec. 2, Shipai Rd., Beitou District, Taipei City, Taiwan, 11217. .,Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, No.17, Xuzhou Rd., Taipei City, 100, Taiwan.
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11
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Biçer A, López-Henares P, Feu-Llauradó A, Sabariego M, Bayod S, Padilla L, Taco MR, Larriba Bartolomé S, Pérez-Riba M, Serrano-Candelas E. The PxIxIT motif of the RCAN3 Inhibits angiogenesis and tumor progression in Triple Negative Breast Cancer in Immunocompetent Mice. Carcinogenesis 2022; 43:808-812. [PMID: 35640493 DOI: 10.1093/carcin/bgac049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 04/10/2022] [Accepted: 05/29/2022] [Indexed: 11/14/2022] Open
Abstract
RCAN proteins are endogenous regulators of the calcineurin- cytosolic nuclear factor of activated T-cells (CN- NFATc) pathway that bind CN through similar conserved motifs PxIxIT and LxVP of the NFATc family. It has been reported that RCAN1 and RCAN3 protein levels correlate with overall survival of breast cancer patients. We have additionally provided supporting results about RCAN3 role on cancer showing that overexpression of the native PxIxIT sequence of RCAN3-derived R3 peptide (PSVVVH, EGFP-R3178-210) dramatically inhibits tumor growth and tumor angiogenesis in an orthotopic mouse model of Triple Negative breast cancer (TNBC). On the other hand, RCAN3 protein and its derived peptide EGFP-R3 178-210 bind to CN and inhibit NFAT-mediated cytokine gene expression without affecting CN phosphatase activity suggesting that RCAN3 and EGFP-R3 178-210 peptide have tumor suppressor and immunosuppressant activity. Due to the known relationship between tumor development and immune system, as well as the relevance of CN-NFATc in the regulation of the immune system, we decided to study the effect of EGFP-R3 178-210 peptide in a syngeneic TNBC model, in order to ensure that the role of RCAN3 as immunosuppressant do not override its tumor suppressor activity. Our results evidence that EGFP-R3 178-210 peptide displays an inhibitory potential on tumor growth and tumor angiogenesis similar to those obtained in the previous orthotopic TNBC model. These results highlight the importance of the RCAN3 peptide as a tumor suppressor protein and totally complement our previous results, indicating that this antitumor activity role is maintained in the presence of a complete functional immune system.
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Affiliation(s)
- Atilla Biçer
- Genes, Disease and Therapy Program, Human Molecular Genetics Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908 Hospitalet de Llobregat, Spain.,Centre for Genomic Regulation (CRG), Systems Biology Programme. Aiguader 88, Barcelona, 08003 Spain
| | | | - Andrea Feu-Llauradó
- Bellvitge University Hospital, Pathology Department. L'Hospitalet de Llobregat, Catalunya, ES
| | - Miguel Sabariego
- Genes, Disease and Therapy Program, Human Molecular Genetics Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908 Hospitalet de Llobregat, Spain.,Centre for Genomic Regulation (CRG), Systems Biology Programme. Aiguader 88, Barcelona, 08003 Spain
| | - Sergi Bayod
- Health & Biomedicine Department of LEITAT Technological Center, Parc Científic de Barcelona, Hèlix building. Baldiri Reixach 15-21, 08028 Barcelona, Spain
| | - Laura Padilla
- Health & Biomedicine Department of LEITAT Technological Center, Parc Científic de Barcelona, Hèlix building. Baldiri Reixach 15-21, 08028 Barcelona, Spain
| | - Mª Rosario Taco
- Bellvitge University Hospital, Pathology Department. L'Hospitalet de Llobregat, Catalunya, ES
| | - Sara Larriba Bartolomé
- Genes, Disease and Therapy Program, Human Molecular Genetics Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908 Hospitalet de Llobregat, Spain
| | - Mercè Pérez-Riba
- Genes, Disease and Therapy Program, Human Molecular Genetics Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908 Hospitalet de Llobregat, Spain
| | - Eva Serrano-Candelas
- Genes, Disease and Therapy Program, Human Molecular Genetics Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908 Hospitalet de Llobregat, Spain.,ProtoQSAR SL, Centro Europeo de Empresas Innovadoras (CEEI), Parque Tecnológico de Valencia, 46980 Paterna (Valencia), Spain
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12
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Reduced miR-371b-5p expression drives tumor progression via CSDE1/RAC1 regulation in triple-negative breast cancer. Oncogene 2022; 41:3151-3161. [PMID: 35490208 PMCID: PMC9135623 DOI: 10.1038/s41388-022-02326-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 04/11/2022] [Accepted: 04/14/2022] [Indexed: 11/25/2022]
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer; however, specific prognostic biomarkers have not yet been developed. In this study, we identified dysregulated microRNAs (miRNAs) in TNBC by profiling miRNA and mRNA expression. In patients with TNBC, miR-371b-5p expression was reduced, and miR-371b-5p overexpression significantly mitigated TNBC cell growth, migration, and invasion. In addition, we found that expression of cold shock domain-containing protein E1 (CSDE1), a direct target gene of miR-371b-5p, was upregulated in TNBC cells, and inhibition of CSDE1 expression alleviated TNBC cell growth by regulating RAC1 transcription. Mechanistically, CSDE1, phosphorylated C-terminal domain (p-CTD) of RNA polymerase II (RNAPII), and CDK7 form a complex, and downregulation of CSDE1 leads to weak interaction between RNAPII p-CTD and CDK7, resulting in a decrease in RNAPII p-CTD expression to reduce RAC1 transcript levels in CSDE1-deficient TNBC cells. Our data demonstrate that miR-371b-5p is a tumor-suppressive miRNA that regulates the CSDE1/Rac1 axis and could be a potential prognostic biomarker for TNBC.
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13
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Fuertes M, Elguero B, Gonilski-Pacin D, Herbstein F, Rosmino J, Ciancio del Giudice N, Fiz M, Falcucci L, Arzt E. Impact of RSUME Actions on Biomolecular Modifications in Physio-Pathological Processes. Front Endocrinol (Lausanne) 2022; 13:864780. [PMID: 35528020 PMCID: PMC9068994 DOI: 10.3389/fendo.2022.864780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/11/2022] [Indexed: 12/03/2022] Open
Abstract
The small RWD domain-containing protein called RSUME or RWDD3 was cloned from pituitary tumor cells with increasing tumorigenic and angiogenic proficiency. RSUME expression is induced under hypoxia or heat shock and is upregulated, at several pathophysiological stages, in tissues like pituitary, kidney, heart, pancreas, or adrenal gland. To date, several factors with essential roles in endocrine-related cancer appear to be modulated by RWDD3. RSUME regulates, through its post-translational (PTM) modification, pituitary tumor transforming gene (PTTG) protein stability in pituitary tumors. Interestingly, in these tumors, another PTM, the regulation of EGFR levels by USP8, plays a pathogenic role. Furthermore, RSUME suppresses ubiquitin conjugation to hypoxia-inducible factor (HIF) by blocking VHL E3-ubiquitin ligase activity, contributing to the development of von Hippel-Lindau disease. RSUME enhances protein SUMOylation of specific targets involved in inflammation such as IkB and the glucocorticoid receptor. For many of its actions, RSUME associates with regulatory proteins of ubiquitin and SUMO cascades, such as the E2-SUMO conjugase Ubc9 or the E3 ubiquitin ligase VHL. New evidence about RSUME involvement in inflammatory and hypoxic conditions, such as cardiac tissue response to ischemia and neuropathic pain, and its role in several developmental processes, is discussed as well. Given the modulation of PTMs by RSUME in neuroendocrine tumors, we focus on its interactors and its mode of action. Insights into functional implications and molecular mechanisms of RSUME action on biomolecular modifications of key factors of pituitary adenomas and renal cell carcinoma provide renewed information about new targets to treat these pathologies.
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Affiliation(s)
- Mariana Fuertes
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Belén Elguero
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - David Gonilski-Pacin
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Florencia Herbstein
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Josefina Rosmino
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Nicolas Ciancio del Giudice
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Manuel Fiz
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Lara Falcucci
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Eduardo Arzt
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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14
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Thorlacius-Ussing J, Jensen C, Madsen EA, Nissen NI, Manon-Jensen T, Chen IM, Johansen JS, Diab HMH, Jørgensen LN, Karsdal MA, Willumsen N. Type XX Collagen Is Elevated in Circulation of Patients with Solid Tumors. Int J Mol Sci 2022; 23:4144. [PMID: 35456962 PMCID: PMC9032593 DOI: 10.3390/ijms23084144] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 02/01/2023] Open
Abstract
In the tumor microenvironment, the extracellular matrix (ECM) has been recognized as an important part of cancer development. The dominant ECM proteins are the 28 types of collagens, each with a unique function in tissue architecture. Type XX collagen, however, is poorly characterized, and little is known about its involvement in cancer. We developed an ELISA quantifying type XX collagen, named PRO-C20, using a monoclonal antibody raised against the C-terminus. PRO-C20 and PRO-C1, an ELISA targeting the N-terminal pro-peptide of type I collagen, was measured in sera of 219 patients with various solid cancer types and compared to sera levels of 33 healthy controls. PRO-C20 was subsequently measured in a separate cohort comprising 36 patients with pancreatic ductal adenocarcinoma (PDAC) and compared to 20 healthy controls and 11 patients with chronic pancreatitis. PRO-C20 was significantly elevated in all cancers tested: bladder, breast, colorectal, head and neck, kidney, lung, melanoma, ovarian, pancreatic, prostate, and stomach cancer (p < 0.01−p < 0.0001). PRO-C1 was only elevated in patients with ovarian cancer. PRO-C20 could discriminate between patients and healthy controls with AUROC values ranging from 0.76 to 0.92. Elevated levels were confirmed in a separate cohort of patients with PDAC (p < 0.0001). High PRO-C20 levels (above 2.57 nM) were predictive of poor survival after adjusting for the presence of metastasis, age, and sex (HR: 4.25, 95% CI: 1.52−11.9, p-value: 0.006). Circulating type XX collagen is elevated in sera of patients with various types of cancer and has prognostic value in PDAC. If validated, PRO-C20 may be a novel biomarker for patients with solid tumors and can help understand the ECM biology of cancer.
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Affiliation(s)
- Jeppe Thorlacius-Ussing
- Biomarkers and Research, Nordic Bioscience A/S, 2730 Herlev, Denmark; (C.J.); (E.A.M.); (N.I.N.); (T.M.-J.); (M.A.K.); (N.W.)
- Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Christina Jensen
- Biomarkers and Research, Nordic Bioscience A/S, 2730 Herlev, Denmark; (C.J.); (E.A.M.); (N.I.N.); (T.M.-J.); (M.A.K.); (N.W.)
| | - Emilie A. Madsen
- Biomarkers and Research, Nordic Bioscience A/S, 2730 Herlev, Denmark; (C.J.); (E.A.M.); (N.I.N.); (T.M.-J.); (M.A.K.); (N.W.)
| | - Neel I. Nissen
- Biomarkers and Research, Nordic Bioscience A/S, 2730 Herlev, Denmark; (C.J.); (E.A.M.); (N.I.N.); (T.M.-J.); (M.A.K.); (N.W.)
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen (UCPH), 2200 Copenhagen, Denmark
| | - Tina Manon-Jensen
- Biomarkers and Research, Nordic Bioscience A/S, 2730 Herlev, Denmark; (C.J.); (E.A.M.); (N.I.N.); (T.M.-J.); (M.A.K.); (N.W.)
| | - Inna M. Chen
- Department of Oncology, Copenhagen University Hospital—Herlev and Gentofte, 2730 Herlev, Denmark; (I.M.C.); (J.S.J.)
| | - Julia S. Johansen
- Department of Oncology, Copenhagen University Hospital—Herlev and Gentofte, 2730 Herlev, Denmark; (I.M.C.); (J.S.J.)
- Department of Medicine, Copenhagen University Hospital—Herlev and Gentofte, 2730 Herlev, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark;
| | - Hadi M. H. Diab
- Digestive Disease Center, Bispebjerg Hospital, University of Copenhagen, 2400 Copenhagen, Denmark;
| | - Lars N. Jørgensen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark;
- Digestive Disease Center, Bispebjerg Hospital, University of Copenhagen, 2400 Copenhagen, Denmark;
| | - Morten A. Karsdal
- Biomarkers and Research, Nordic Bioscience A/S, 2730 Herlev, Denmark; (C.J.); (E.A.M.); (N.I.N.); (T.M.-J.); (M.A.K.); (N.W.)
| | - Nicholas Willumsen
- Biomarkers and Research, Nordic Bioscience A/S, 2730 Herlev, Denmark; (C.J.); (E.A.M.); (N.I.N.); (T.M.-J.); (M.A.K.); (N.W.)
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15
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Decision Theory versus Conventional Statistics for Personalized Therapy of Breast Cancer. J Pers Med 2022; 12:jpm12040570. [PMID: 35455687 PMCID: PMC9028435 DOI: 10.3390/jpm12040570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 11/17/2022] Open
Abstract
Estrogen and progesterone receptors being present or not represents one of the most important biomarkers for therapy selection in breast cancer patients. Conventional measurement by immunohistochemistry (IHC) involves errors, and numerous attempts have been made to increase precision by additional information from gene expression. This raises the question of how to fuse information, in particular, if there is disagreement. It is the primary domain of Dempster–Shafer decision theory (DST) to deal with contradicting evidence on the same item (here: receptor status), obtained through different techniques. DST is widely used in technical settings, such as self-driving cars and aviation, and is also promising to deliver significant advantages in medicine. Using data from breast cancer patients already presented in previous work, we focus on comparing DST with classical statistics in this work, to pave the way for its application in medicine. First, we explain how DST not only considers probabilities (a single number per sample), but also incorporates uncertainty in a concept of ‘evidence’ (two numbers per sample). This allows for very powerful displays of patient data in so-called ternary plots, a novel and crucial advantage for medical interpretation. Results are obtained according to conventional statistics (ODDS) and, in parallel, according to DST. Agreement and differences are evaluated, and the particular merits of DST discussed. The presented application demonstrates how decision theory introduces new levels of confidence in diagnoses derived from medical data.
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16
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Chen CC, Krogsaeter E, Kuo CY, Huang MC, Chang SY, Biel M. Endolysosomal cation channels point the way towards precision medicine of cancer and infectious diseases. Biomed Pharmacother 2022; 148:112751. [PMID: 35240524 DOI: 10.1016/j.biopha.2022.112751] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 11/02/2022] Open
Abstract
Infectious diseases and cancer are among the key medical challenges that humankind is facing today. A growing amount of evidence suggests that ion channels in the endolysosomal system play a crucial role in the pathology of both groups of diseases. The development of advanced patch-clamp technologies has allowed us to directly characterize ion fluxes through endolysosomal ion channels in their native environments. Endolysosomes are essential organelles for intracellular transport, digestion and metabolism, and maintenance of homeostasis. The endolysosomal ion channels regulate the function of the endolysosomal system through four basic mechanisms: calcium release, control of membrane potential, pH change, and osmolarity regulation. In this review, we put particular emphasis on the endolysosomal cation channels, including TPC2 and TRPML2, which are particularly important in monocyte function. We discuss existing endogenous and synthetic ligands of these channels and summarize current knowledge of their impact on channel activity and function in different cell types. Moreover, we summarize recent findings on the importance of TPC2 and TRPML2 channels as potential drug targets for the prevention and treatment of the emerging infectious diseases and cancer.
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Affiliation(s)
- Cheng-Chang Chen
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan.
| | | | - Ching-Ying Kuo
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Min-Chuan Huang
- Graduate Institute of Anatomy and Cell Biology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Sui-Yuan Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Martin Biel
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
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17
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Huang CS, Tsai ML, Lu TP, Tu CC, Liu CY, Huang CJ, Ho YS, Tu SH, Chuang EY, Tseng LM, Huang CC. The extended concurrent genes signature for disease-free survival in breast cancer. J Formos Med Assoc 2022; 121:1945-1955. [PMID: 35181201 DOI: 10.1016/j.jfma.2022.01.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/11/2021] [Accepted: 01/18/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND/PURPOSE Previously we had identified concurrent genes, which highlighted the interplay between copy number variation (CNV) and differential gene expression (GE) for Han Chinese breast cancers. The merit of the approach is to discovery biomarkers not identifiable by conventional GE only data, for which phenotype-correlation or gene variability is the criteria of gene selection. MATERIALS AND METHODS Thirty-one comparative genomic hybridization (CGH) and 83 GE microarrays were performed, with 29 breast cancers assayed from both platforms. Potential targets were revealed by Genomic Identification of Significant Targets in Cancer (GISTIC) from CGH arrays. Concurrent genes and genes with significant GISTIC scores were used to derive the extended concurrent genes signature, which was consensus from leading edge analysis across all studies and a supervised partial least square (PLS) regression predictive model of disease-free survival was constructed. RESULTS There were 1584 concurrent genes from 29 samples with both CGH and GE microarrays. Enriched concurrent genes sets for disease-free survival were identified independently from 83 GE arrays and another one with Han Chinese origin as well as three studies of Western origin. For five studies with disease-free survival follow up, prognostic discrepancy was observed between predicted high-risk and low-risk group patients. CONCLUSION We concluded that through parallel analyses of CGH and GE microarrays, the proposed extended concurrent gene expression signature can identify biomarkers with prognostic values.
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Affiliation(s)
- Ching-Shui Huang
- Division of General Surgery, Department of Surgery, Cathay General Hospital, Taipei, Taiwan; School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Ming-Lin Tsai
- Division of General Surgery, Department of Surgery, Cathay General Hospital, Taipei, Taiwan
| | - Tzu-Pin Lu
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Chao-Chiang Tu
- Department of Surgery, Fu-Jen Catholic University Hospital, New Taipei, Taiwan; School of Medicine, College of Medicine, Fu-Jen Catholic University, New Taipei, Taiwan
| | - Chih-Yi Liu
- Division of Pathology, Cathay General Hospital Sijhih, New Taipei, Taiwan
| | - Chi-Jung Huang
- Department of Medical Research, Cathay General Hospital, Taipei, Taiwan; Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan
| | - Yuan-Soon Ho
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan; Taipei Cancer Center, Taipei Medical University, Taipei, Taiwan; Department of Medical Laboratory, Taipei Medical University Hospital, Taipei, Taiwan; School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Shih-Hsin Tu
- School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Taipei Cancer Center, Taipei Medical University, Taipei, Taiwan; Division of Breast Surgery, Department of Surgery, Taipei Medical University Hospital, Taipei, Taiwan
| | - Eric Y Chuang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Ling-Ming Tseng
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei, Taiwan.
| | - Chi-Cheng Huang
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan; Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei, Taiwan.
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Santoni G, Amantini C, Nabissi M, Arcella A, Maggi F, Santoni M, Morelli MB. Functional In Vitro Assessment of VEGFA/NOTCH2 Signaling Pathway and pRB Proteasomal Degradation and the Clinical Relevance of Mucolipin TRPML2 Overexpression in Glioblastoma Patients. Int J Mol Sci 2022; 23:ijms23020688. [PMID: 35054871 PMCID: PMC8775570 DOI: 10.3390/ijms23020688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 12/30/2021] [Accepted: 01/06/2022] [Indexed: 12/28/2022] Open
Abstract
Glioblastoma (GBM) is the most malignant glioma with an extremely poor prognosis. It is characterized by high vascularization and its growth depends on the formation of new blood vessels. We have previously demonstrated that TRPML2 mucolipin channel expression increases with the glioma pathological grade. Herein by ddPCR and Western blot we found that the silencing of TRPML2 inhibits expression of the VEGFA/Notch2 angiogenic pathway. Moreover, the VEGFA/Notch2 expression increased in T98 and U251 cells stimulated with the TRPML2 agonist, ML2-SA1, or by enforced-TRPML2 levels. In addition, changes in TRPML2 expression or ML2-SA1-induced stimulation, affected Notch2 activation and VEGFA release. An increased invasion capability, associated with a reduced VEGF/VEGFR2 expression and increased vimentin and CD44 epithelial-mesenchymal transition markers in siTRPML2, but not in enforced-TRPML2 or ML2-SA1-stimulated glioma cells, was demonstrated. Furthermore, an increased sensitivity to Doxorubicin cytotoxicity was demonstrated in siTRPML2, whereas ML2-SA1-treated GBM cells were more resistant. The role of proteasome in Cathepsin B-dependent and -independent pRB degradation in siTRPML2 compared with siGLO cells was studied. Finally, through Kaplan-Meier analysis, we found that high TRPML2 mRNA expression strongly correlates with short survival in GBM patients, supporting TRPML2 as a negative prognostic factor in GBM patients.
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Affiliation(s)
- Giorgio Santoni
- School of Pharmacy, Section of Experimental Medicine, University of Camerino, 62032 Camerino, Italy;
- Correspondence: (G.S.); (M.B.M.); Tel.: +39-0737403319 (G.S.); +39-0737403312 (M.B.M.)
| | - Consuelo Amantini
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; (C.A.); (F.M.)
| | - Massimo Nabissi
- School of Pharmacy, Section of Experimental Medicine, University of Camerino, 62032 Camerino, Italy;
| | - Antonietta Arcella
- Neuropathology Laboratory, Istituto di Ricovero e Cura a Carattere Scientifico Neuromed, 86077 Pozzilli, Italy;
| | - Federica Maggi
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; (C.A.); (F.M.)
- Department of Molecular Medicine, Sapienza University, 00185 Rome, Italy
| | - Matteo Santoni
- Oncology Unit, Macerata Hospital, 62100 Macerata, Italy;
| | - Maria Beatrice Morelli
- School of Pharmacy, Section of Experimental Medicine, University of Camerino, 62032 Camerino, Italy;
- Correspondence: (G.S.); (M.B.M.); Tel.: +39-0737403319 (G.S.); +39-0737403312 (M.B.M.)
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19
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Vishwakarma GK, Kumari P, Bhattacharjee A. Thresholding of prominent biomarkers of breast cancer on overall survival using classification and regression tree. Cancer Biomark 2021; 34:319-328. [PMID: 35001879 DOI: 10.3233/cbm-210470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
BACKGROUND HER2, ER, PR, and ERBB2 play a vital role in treating breast cancer. These are significant predictive and prognosis biomarkers of breast cancer. OBJECTIVE We aim to obtain a unique biomarker-specific prediction on overall survival to know their survival and death risk. METHODS Survival analysis is performed on classified data using Classification and Regression Tree (CART) analysis. Hazard ratio and Confidence Interval are computed using MLE and the Bayesian approach with the CPH model for univariate and multivariable illustrations. Validation of CART is executed with the Brier score, and accuracy and sensitivity are obtained using the k-nn classifier. RESULTS Utilizing CART analysis, the cut-off value of continuous-valued biomarkers HER2, ER, PR, and ERBB2 are obtained as 14.707, 8.128, 13.153, and 6.884, respectively. Brier score of CART is 0.16 towards validation of methodology. Survival analysis gives a demonstration of the survival estimates with significant statistical strategies. CONCLUSIONS Patients with breast cancer are at low risk of death, whose HER2 value is below its cut-off value, and ER, PR, and ERBB2 values are greater than their cut-off values. This comparison is with the patient having the opposite side of these cut-off values for the same biomarkers.
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Affiliation(s)
- Gajendra K Vishwakarma
- Department of Mathematics & Computing, Indian Institute of Technology Dhanbad, Dhanbad-826004, India
| | - Pragya Kumari
- Department of Mathematics & Computing, Indian Institute of Technology Dhanbad, Dhanbad-826004, India
| | - Atanu Bhattacharjee
- Section of Biostatistics, Centre for Cancer Epidemiology, Tata Memorial Centre, Navi Mumbai, India.,Homi Bhabha National Institute, Mumbai, India
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Nwosu IO, Piccolo SR. A systematic review of datasets that can help elucidate relationships among gene expression, race, and immunohistochemistry-defined subtypes in breast cancer. Cancer Biol Ther 2021; 22:417-429. [PMID: 34412551 DOI: 10.1080/15384047.2021.1953902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Scholarly requirements have led to a massive increase of transcriptomic data in the public domain, with millions of samples available for secondary research. We identified gene-expression datasets representing 10,214 breast-cancer patients in public databases. We focused on datasets that included patient metadata on race and/or immunohistochemistry (IHC) profiling of the ER, PR, and HER-2 proteins. This review provides a summary of these datasets and describes findings from 32 research articles associated with the datasets. These studies have helped to elucidate relationships between IHC, race, and/or treatment options, as well as relationships between IHC status and the breast-cancer intrinsic subtypes. We have also identified broad themes across the analysis methodologies used in these studies, including breast cancer subtyping, deriving predictive biomarkers, identifying differentially expressed genes, and optimizing data processing. Finally, we discuss limitations of prior work and recommend future directions for reusing these datasets in secondary analyses.
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Affiliation(s)
| | - Stephen R Piccolo
- Department of Biology, Brigham Young University, Provo, Utah, United States
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21
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Molecular subtyping of breast cancer intrinsic taxonomy with oligonucleotide microarray and NanoString nCounter. Biosci Rep 2021; 41:229520. [PMID: 34387660 PMCID: PMC8385191 DOI: 10.1042/bsr20211428] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/12/2021] [Accepted: 08/12/2021] [Indexed: 11/17/2022] Open
Abstract
Breast cancer intrinsic subtypes have been identified based on the transcription of a predefined gene expression (GE) profiles and algorithm (PAM50). This study compared molecular subtyping with oligonucleotide microarray and NanoString nCounter assay. A total of 109 Taiwanese breast cancers (24 with adjacent normal breast tissues) were assayed with Affymetrix Human Genome U133 plus 2.0 microarrays and 144 were assayed with the NanoString nCounter while 64 patients were assayed for both platforms. Subtyping with the nearest centroid (single sample prediction) was performed, and 16 out of 24 (67%) matched normal breasts were categorized as the normal breast-like subtype. For 64 breast cancers assayed for both platforms, 41 (65%, one unclassified by microarray) were predicted with an identical subtype, resulting in a fair Kappa statistic of 0.60. Taking nCounter subtyping as the gold standard, prediction accuracy was 43% (3/7), 81% (13/16), 25% (5/20), and 100% (20/20) for basal-like, HER2-enriched, luminal A and luminal B subtype predicted from microarray GE profiles. Microarray identified more luminal B cases from luminal A subtype predicted by nCounter. It's not uncommon to use microarray for breast cancer molecular subtyping for research. Our study showed that fundamental discrepancy existed between distinct GE assays, and cross platform equivalence should be carefully appraised when molecular subtyping was conducted with oligonucleotide microarray.
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22
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Huang CS, Liu CY, Lu TP, Huang CJ, Chiu JH, Tseng LM, Huang CC. Targeted Sequencing of Taiwanese Breast Cancer with Risk Stratification by the Concurrent Genes Signature: A Feasibility Study. J Pers Med 2021; 11:jpm11070613. [PMID: 34203389 PMCID: PMC8306786 DOI: 10.3390/jpm11070613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/21/2021] [Accepted: 06/25/2021] [Indexed: 11/16/2022] Open
Abstract
Breast cancer is the most common female malignancy in Taiwan, while conventional clinical and pathological factors fail to provide full explanation for prognostic heterogeneity. The aim of the study was to evaluate the feasibility of targeted sequencing combined with concurrent genes signature to identify somatic mutations with clinical significance. The extended concurrent genes signature was based on the coherent patterns between genomic and transcriptional alterations. Targeted sequencing of 61 Taiwanese breast cancers revealed 1036 variants, including 76 pathogenic and 545 likely pathogenic variants based on the ACMG classification. The most frequently mutated genes were NOTCH, BRCA1, AR, ERBB2, FANCA, ATM, and BRCA2 and the most common pathogenic deletions were FGFR1, ATM, and WT1, while BRCA1 (rs1799965), FGFR2 (missense), and BRCA1 (rs1799949) were recurrent pathogenic SNPs. In addition, 38 breast cancers were predicted into 12 high-risk and 26 low-risk cases based on the extended concurrent genes signature, while the pathogenic PIK3CA variant (rs121913279) was significantly mutated between groups. Two deleterious SH3GLB2 mutations were further revealed by multivariate Cox’s regression (hazard ratios: 29.4 and 16.1). In addition, we identified several significantly mutated or pathogenic variants associated with differentially expressed signature genes. The feasibility of targeted sequencing in combination with concurrent genes risk stratification was ascertained. Future study to validate clinical applicability and evaluate potential actionability for Taiwanese breast cancers should be initiated.
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Affiliation(s)
- Ching-Shui Huang
- Division of General Surgery, Department of Surgery, Cathay General Hospital, Taipei 106, Taiwan;
- School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Chih-Yi Liu
- Department of Pathology, Cathay General Hospital Sijhih, New Taipei 221, Taiwan;
| | - Tzu-Pin Lu
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 110, Taiwan;
| | - Chi-Jung Huang
- Department of Medical Research, Cathay General Hospital, Taipei 106, Taiwan;
- National Defense Medical Center, Department of Biochemistry, Taipei 114, Taiwan
| | - Jen-Hwey Chiu
- Institute of Traditional Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11121, Taiwan;
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan;
| | - Ling-Ming Tseng
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan;
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 1121, Taiwan
| | - Chi-Cheng Huang
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 1121, Taiwan
- School of Public Health, College of Public Health, National Taiwan University, Taipei 100, Taiwan
- Correspondence:
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23
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Liu S, Wang L, Jiang D, Wei W, Nasir MF, Khan MS, Yousafi Q, Liu X, Fu X, Li X, Li J. Sumoylation as an Emerging Target in Therapeutics against Cancer. Curr Pharm Des 2021; 26:4764-4776. [PMID: 32568016 DOI: 10.2174/1381612826666200622124134] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/13/2020] [Indexed: 12/21/2022]
Abstract
Sumoylation is the Post-translational modification gaining most of the research interest recently. Sumoylation is involved in various crucial functions of the cell such as regulation of cell cycle, DNA damage repair, apoptosis, etc. Oncology is advancing in radiotherapy, targeted chemotherapy, various forms of immunotherapy and targeted gene therapy. Researches are being conducted to prove its connotation with a variety of cancers and inhibitors are being developed to obstruct the fatal effect caused by misbalance of the SUMO-catalytic cycle. It has been shown that up-regulation of certain enzymes of Sumoylation correlates with cancer incidence in most of the cases. However, in some cases, down-regulation also associates with cancer invasion such as underexpression of UBC9 in initial stage breast cancer. This can aid in future study, treatment, and diagnosis of a variety of cancers including breast cancer, prostate cancer, lung adenocarcinoma, melanoma, multiple myeloma, etc. Various mechanistic assays are being developed and used to identify potential inhibitors against the dysregulated proteins of Sumoylation. This review summarizes the normal roles of the enzymes involved in the SUMOcatalytic cycle, their misbalanced regulation leading to tumorigenesis and nearly all the potent inhibitors identified to date, while after detailed studied it was observed that ML-792 could be a promising inhibitor in treating cancers by inhibiting Sumoylation enzymes.
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Affiliation(s)
- Sitong Liu
- The Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, Jilin, China,College of Life Sciences, Jilin University, Changchun, 130012, China
| | - Lichun Wang
- The Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, Jilin, China
| | - Dongjun Jiang
- The Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, Jilin, China
| | - Wei Wei
- The Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, Jilin, China,Dental Hospital, Jilin University, Changchun 130021, China
| | - Mushyeda Fatima Nasir
- Department of Biosciences, Faculty of Sciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | - Muhammad Saad Khan
- Department of Biosciences, Faculty of Sciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | - Qudsia Yousafi
- Department of Biosciences, Faculty of Sciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | - Xintong Liu
- Dental Hospital, Jilin University, Changchun 130021, China
| | - Xueqi Fu
- College of Life Sciences, Jilin University, Changchun, 130012, China
| | - Xiaomeng Li
- The Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, Jilin, China
| | - Jiang Li
- Stomatological Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510150, China,Dental Hospital, Jilin University, Changchun 130021, China
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24
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Lin CC, Yang WH, Lin YT, Tang X, Chen PH, Ding CKC, Qu DC, Alvarez JV, Chi JT. DDR2 upregulation confers ferroptosis susceptibility of recurrent breast tumors through the Hippo pathway. Oncogene 2021; 40:2018-2034. [PMID: 33603168 PMCID: PMC7988308 DOI: 10.1038/s41388-021-01676-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 01/18/2021] [Accepted: 01/22/2021] [Indexed: 01/30/2023]
Abstract
Recurrent breast cancer presents significant challenges with aggressive phenotypes and treatment resistance. Therefore, novel therapeutics are urgently needed. Here, we report that murine recurrent breast tumor cells, when compared with primary tumor cells, are highly sensitive to ferroptosis. Discoidin Domain Receptor Tyrosine Kinase 2 (DDR2), the receptor for collagen I, is highly expressed in ferroptosis-sensitive recurrent tumor cells and human mesenchymal breast cancer cells. EMT regulators, TWIST and SNAIL, significantly induce DDR2 expression and sensitize ferroptosis in a DDR2-dependent manner. Erastin treatment induces DDR2 upregulation and phosphorylation, independent of collagen I. Furthermore, DDR2 knockdown in recurrent tumor cells reduces clonogenic proliferation. Importantly, both the ferroptosis protection and reduced clonogenic growth may be compatible with the compromised YAP/TAZ upon DDR2 inhibition. Collectively, these findings identify the important role of EMT-driven DDR2 upregulation in recurrent tumors in maintaining growth advantage but activating YAP/TAZ-mediated ferroptosis susceptibility, providing potential strategies to eradicate recurrent breast cancer cells with mesenchymal features.
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Affiliation(s)
- Chao-Chieh Lin
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA,Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Wen-Hsuan Yang
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA,Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yi-Tzu Lin
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA,Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaohu Tang
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA
| | - Po-Han Chen
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA,Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Chien-Kuang Cornelia Ding
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA,Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Dan Chen Qu
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA,Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - James V. Alvarez
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jen-Tsan Chi
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA,Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27710, USA;,Correspondence: Jen-Tsan Ashley Chi, Department of Molecular Genetics and Microbiology, Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27710, USA. TEL: (919) 668-4759,
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25
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Kenn M, Cacsire Castillo-Tong D, Singer CF, Karch R, Cibena M, Koelbl H, Schreiner W. Decision theory for precision therapy of breast cancer. Sci Rep 2021; 11:4233. [PMID: 33608588 PMCID: PMC7895957 DOI: 10.1038/s41598-021-82418-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 01/11/2021] [Indexed: 01/31/2023] Open
Abstract
Correctly estimating the hormone receptor status for estrogen (ER) and progesterone (PGR) is crucial for precision therapy of breast cancer. It is known that conventional diagnostics (immunohistochemistry, IHC) yields a significant rate of wrongly diagnosed receptor status. Here we demonstrate how Dempster Shafer decision Theory (DST) enhances diagnostic precision by adding information from gene expression. We downloaded data of 3753 breast cancer patients from Gene Expression Omnibus. Information from IHC and gene expression was fused according to DST, and the clinical criterion for receptor positivity was re-modelled along DST. Receptor status predicted according to DST was compared with conventional assessment via IHC and gene-expression, and deviations were flagged as questionable. The survival of questionable cases turned out significantly worse (Kaplan Meier p < 1%) than for patients with receptor status confirmed by DST, indicating a substantial enhancement of diagnostic precision via DST. This study is not only relevant for precision medicine but also paves the way for introducing decision theory into OMICS data science.
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Affiliation(s)
- Michael Kenn
- Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
| | - Dan Cacsire Castillo-Tong
- Translational Gynecology Group, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Christian F Singer
- Translational Gynecology Group, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Rudolf Karch
- Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
| | - Michael Cibena
- Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
| | - Heinz Koelbl
- Department of General Gynecology and Gynecologic Oncology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Wolfgang Schreiner
- Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria.
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26
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Residual risk stratification of Taiwanese breast cancers following curative therapies with the extended concurrent genes signature. Breast Cancer Res Treat 2021; 186:475-485. [PMID: 33392837 DOI: 10.1007/s10549-020-06058-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 12/11/2020] [Indexed: 10/22/2022]
Abstract
INTRODUCTION The aim of the study was to perform digital RNA counting to validate a gene expression signature for operable breast cancers initially treated with curative intention, and the risk of recurrence, distant metastasis, and mortality was predicted. METHODS Candidate genes were initially discovered from the coherent genomic and transcriptional alternations from microarrays, and the extended concurrent genes were used to build a risk stratification model from archived formalin-fixed paraffin-embedded (FFPE) tissues with the NanoString nCounter. RESULTS The extended concurrent genes signature was prognostic in 144 Taiwanese breast cancers (5-year relapse-free survival: 89.8 and 69.4% for low- and high-risk group, log-rank test: P = 0.004). Cross-platform comparability was evidenced from significant and positive correlations for most genes as well as equal covariance matrix across 64 patients assayed for both microarray and digital RNA counting. DISCUSSION Archived FFPE samples could be successfully assayed by the NanoString nCounter. The purposed signature was prognostic stratifying breast cancer patients into groups with distinct survival patterns, and clinical applicability of the residual risk model was proved.
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27
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Xie D, Luo X. Identification of four methylation-driven genes as candidate biomarkers for monitoring single-walled carbon nanotube-induced malignant transformation of the lung. Toxicol Appl Pharmacol 2020; 412:115391. [PMID: 33387576 DOI: 10.1016/j.taap.2020.115391] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 01/15/2023]
Abstract
Long-term exposure to carbon nanotubes (CNTs) has been reported to induce malignant transformation. This study aimed to screen candidate biomarkers for monitoring occupational workers to prevent the development of lung cancer. mRNA (GSE56104) and methylation (GSE153246) profiles of lung epithelial BEAS-2B cells exposed to malignant transformation dose of single-walled CNTs or control medium were downloaded from Gene Expression Omnibus database. A total of 1513 differentially expressed genes (DEGs) and 912 differentially methylated genes (DMGs) were identified using LIMMA method. The weighted correlation network analysis identified blue and turquoise modules were associated with malignant transformation of BEAS-2B cells, 124 DMGs of which were overlapped with DEGs. The mRNA and methylation levels of four methylation-driven DEGs were validated in both lung adenocarcinoma (LUAD) and squamous cell carcinomas (LUSC) of The Cancer Genome Atlas dataset and they were associated with overall survival of LUAD patients. Downregulation of PXMP4 and MCOLN2, while upregulation of MET was confirmed in both LUSC and LUAD via Human Protein Atlas analysis. PXMP4 and MET protein levels were also supported in the proteomic analysis of LUAD. Receiver operating characteristic (ROC) curve analysis showed the combination of four genes may be the optimal biomarker for predicting lung cancer, with the area under ROC curve >0.9. Function analysis revealed BARX2 may interact with CCND1 to regulate cell cycle; MET and PXMP4/MCOLN2 may positively correlate with CCR5/IL-6 or GATA3/HLA-DPB1/HLA-DPA1 to involve immune regulation. In conclusion, these four methylation-driven genes may be candidate prognostic and diagnostic biomarkers for single-walled CNT-related lung cancer.
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Affiliation(s)
- Dongli Xie
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai 201620, China
| | - Xiaogang Luo
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai 201620, China.
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28
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Germline Genetic Association between Stromal Interaction Molecule 1 (STIM1) and Clinical Outcomes in Breast Cancer Patients. J Pers Med 2020; 10:jpm10040287. [PMID: 33348924 PMCID: PMC7767290 DOI: 10.3390/jpm10040287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/09/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022] Open
Abstract
Among all cancers in women, breast cancer has the highest incidence. The mortality of breast cancer is highly associated with metastasis. Migration and malignant transformation of cancer cells have been reported to be modulated by store-operated calcium (SOC) channels, which control calcium signaling and cell proliferation pathways. Stromal interaction molecule 1 (STIM1) is a calcium sensor in the endoplasmic reticulum, triggering the activation of store-operated calcium signaling. However, the clinical relevance of STIM1 in breast cancer is still unclear. Here, we recruited 348 breast cancer patients and conducted a genetic association study to address this question. Four tagging germline single nucleotide variants (SNVs) in STIM1 were selected and RNA sequencing data of 525 breast cancer samples from The Cancer Genome Atlas (TCGA) database were evaluated. The results show that rs2304891 and rs3750996 were correlated with clinical stage of breast cancer. Expression quantitative trait loci (eQTL) analysis indicated that risk G allele of STIM1 contributed to the higher expression of STIM1. In addition, we found an increased risk of rs2304891 G allele and rs3750996 A allele in estrogen receptor (ER) positive and progesterone receptor (PR) positive patients. In conclusion, our results suggest that germline SNV, rs2304891 and rs3750996 as well as STIM1 expression are important biomarkers for the prediction of clinical outcomes in breast cancer patients.
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29
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Nguyen QH, Nguyen H, Nguyen T, Le DH. Multi-Omics Analysis Detects Novel Prognostic Subgroups of Breast Cancer. Front Genet 2020; 11:574661. [PMID: 33193681 PMCID: PMC7594512 DOI: 10.3389/fgene.2020.574661] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/23/2020] [Indexed: 12/02/2022] Open
Abstract
The unprecedented proliferation of recent large-scale and multi-omics databases of cancers has given us many new insights into genomic and epigenomic deregulation in cancer discovery in general. However, we wonder whether or not there exists a systematic connection between copy number aberrations (CNA) and methylation (MET)? If so, what is the role of this connection in breast cancer (BRCA) tumorigenesis and progression? At the same time, the PAM50 intrinsic subtypes of BRCA have gained the most attention from BRCA experts. However, this classification system manifests its weaknesses including low accuracy as well as a possible lack of association with biological phenotypes, and even further investigations on their clinical utility were still needed. In this study, we performed an integrative analysis of three-omics profiles, CNA, MET, and mRNA expression, in two BRCA patient cohorts (one for discovery and another for validation) – to elucidate those complicated relationships. To this purpose, we first established a set of CNAcor and METcor genes, which had CNA and MET levels significantly correlated (and anti-correlated) with their corresponding expression levels, respectively. Next, to revisit the current classification of BRCA, we performed single and integrated clustering analyses using our clustering method PINSPlus. We then discovered two biologically distinct subgroups that could be an improved and refined classification system for breast cancer patients, which can be validated by a third-party data. Further studies were then performed and realized each-subgroup-specific genes and different interactions between each of the two identified subgroups with the age factor. These findings can show promise as diagnostic and prognostic values in BRCA, and a potential alternative to the PAM50 intrinsic subtypes in the future.
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Affiliation(s)
- Quang-Huy Nguyen
- Department of Computational Biomedicine, Vingroup Big Data Institute, Hanoi, Vietnam.,Faculty of Pharmacy, Dainam University, Hanoi, Vietnam
| | - Hung Nguyen
- Department of Computer Science and Engineering, University of Nevada, Reno, Reno, NV, United States
| | - Tin Nguyen
- Department of Computer Science and Engineering, University of Nevada, Reno, Reno, NV, United States
| | - Duc-Hau Le
- Department of Computational Biomedicine, Vingroup Big Data Institute, Hanoi, Vietnam.,School of Computer Science and Engineering, Thuyloi University, Hanoi, Vietnam
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30
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Tsai HT, Huang CS, Tu CC, Liu CY, Huang CJ, Ho YS, Tu SH, Tseng LM, Huang CC. Multi-gene signature of microcalcification and risk prediction among Taiwanese breast cancer. Sci Rep 2020; 10:18276. [PMID: 33106505 PMCID: PMC7588423 DOI: 10.1038/s41598-020-74982-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 09/29/2020] [Indexed: 12/29/2022] Open
Abstract
Microcalcification is one of the most common radiological and pathological features of breast ductal carcinoma in situ (DCIS), and to a lesser extent, invasive ductal carcinoma. We evaluated messenger RNA (mRNA) transcriptional profiles associated with ectopic mammary mineralization. A total of 109 breast cancers were assayed with oligonucleotide microarrays. The associations of mRNA abundance with microcalcifications and relevant clinical features were evaluated. Microcalcifications were present in 86 (79%) patients by pathological examination, and 81 (94%) were with coexistent DCIS, while only 13 (57%) of 23 patients without microcalcification, the invasive diseases were accompanied with DCIS (χ2-test, P < 0.001). There were 69 genes with differential mRNA abundance between breast cancers with and without microcalcifications, and 11 were associated with high-grade (comedo) type DCIS. Enriched Gene Ontology categories included glycosaminoglycan and aminoglycan metabolic processes and protein ubiquitination, indicating an active secretory process. The intersection (18 genes) of microcalcificaion-associated and DCIS-associated genes provided the best predictive accuracy of 82% with Bayesian compound covariate predictor. Ten genes were further selected for prognostic index score construction, and five-year relapse free survival was 91% for low-risk and 83% for high-risk group (log-rank test, P = 0.10). Our study suggested that microcalcification is not only the earliest detectable radiological sign for mammography screening but the phenomenon itself may reflect the underling events during mammary carcinogenesis. Future studies to evaluate the prognostic significance of microcalcifications are warranted.
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Affiliation(s)
- Hsin-Tien Tsai
- Division of General Surgery, Department of Surgery, Cathay General Hospital, Taipei, Taiwan
| | - Ching-Shui Huang
- Division of General Surgery, Department of Surgery, Cathay General Hospital, Taipei, Taiwan.,Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chao-Chiang Tu
- Department of Surgery, Fu-Jen Catholic University Hospital, New Taipei, Taiwan.,School of Medicine, College of Medicine, Fu-Jen Catholic University, New Taipei, Taiwan
| | - Chih-Yi Liu
- Division of Pathology, Cathay General Hospital Sijhih, New Taipei, Taiwan
| | - Chi-Jung Huang
- Department of Medical Research, Cathay General Hospital, Taipei, Taiwan.,Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan
| | - Yuan-Soon Ho
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan.,Taipei Cancer Center, Taipei Medical University, Taipei, Taiwan.,Department of Medical Laboratory, Taipei Medical University Hospital, Taipei, Taiwan.,School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Shih-Hsin Tu
- Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Taipei Cancer Center, Taipei Medical University, Taipei, Taiwan.,Division of Breast Surgery, Department of Surgery, Taipei Medical University Hospital, Taipei, Taiwan
| | - Ling-Ming Tseng
- Comprehensive Breast Health Center, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd., Beitou District, Taipei City, 11217, Taiwan, ROC. .,School of Medicine, College of Medicine, National Yang-Ming University, Taipei, Taiwan.
| | - Chi-Cheng Huang
- Comprehensive Breast Health Center, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd., Beitou District, Taipei City, 11217, Taiwan, ROC.
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31
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Santoni G, Santoni M, Maggi F, Marinelli O, Morelli MB. Emerging Role of Mucolipins TRPML Channels in Cancer. Front Oncol 2020; 10:659. [PMID: 32411610 PMCID: PMC7198773 DOI: 10.3389/fonc.2020.00659] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/08/2020] [Indexed: 12/26/2022] Open
Affiliation(s)
- Giorgio Santoni
- Section of Immunopathology, School of Pharmacy, University of Camerino, Camerino, Italy
| | - Matteo Santoni
- Medical Oncology Unit, Hospital of Macerata, Macerata, Italy
| | - Federica Maggi
- Section of Immunopathology, School of Pharmacy, University of Camerino, Camerino, Italy.,Department of Molecular Medicine, University of Rome Sapienza, Rome, Italy
| | - Oliviero Marinelli
- Section of Immunopathology, School of Pharmacy, University of Camerino, Camerino, Italy.,School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
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Functional implications of miR-145/RCAN3 axis in the progression of cervical cancer. Reprod Biol 2020; 20:140-146. [PMID: 32345470 DOI: 10.1016/j.repbio.2020.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/09/2020] [Accepted: 04/02/2020] [Indexed: 12/24/2022]
Abstract
Cervical cancer, as the second leading cause of death in women malignant tumor, is not optimistic about survival rate and late recurrence rate. RCAN3 has been reported to function in a variety of diseases, but its relationship with cervical cancer has not been reported. This study aimed to investigate whether RCAN3 contributes to the development of cervical cancer and its mechanism. RCAN3 expression was analyzed in 306 cervical cancer tissues and 13 normal healthy tissues from TCGA and GTEX databases. Kaplan-Meier analysis and Cox regression analysis were carried out to assess the potential function of RCAN3. Subsequently, the upstream regulatory miRNA of RCAN3 was predicted by bioinformatics and confirmed using dual luciferase reporter assay. CCK-8, colony formation assay, transwell assay were used for functional analysis of miR-145/RCAN3 axis in vitro. The results showed that RCAN3 was highly expressed in cervical cancer tissues, leading to poor prognosis, and could be used as a prognostic factor for cervical cancer. MiR-145 directly targeted RCAN3, which was lowly expressed in cervical cancer tissues and cell lines, and the higher the miR-145 expression, the longer the survival time of patients. Finally, from the functional experiments results we can see that miR-145 can inhibit the proliferation, migration and invasion of cervical cancer cells, but overexpression of RCAN3 can reverse miR-145-mediated inhibition. To sum up, miR-145/RCAN3 axis may serve as a potential therapeutic target to regulate the progression of cervical cancer.
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Berthel E, Vincent A, Eberst L, Torres AG, Dacheux E, Rey C, Marcel V, Paraqindes H, Lachuer J, Catez F, de Pouplana LR, Treilleux I, Diaz JJ, Dalla Venezia N. Uncovering the Translational Regulatory Activity of the Tumor Suppressor BRCA1. Cells 2020; 9:cells9040941. [PMID: 32290274 PMCID: PMC7226996 DOI: 10.3390/cells9040941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/30/2020] [Accepted: 04/04/2020] [Indexed: 12/24/2022] Open
Abstract
BRCA1 inactivation is a hallmark of familial breast cancer, often associated with aggressive triple negative breast cancers. BRCA1 is a tumor suppressor with known functions in DNA repair, transcription regulation, cell cycle control, and apoptosis. In the present study, we demonstrate that BRCA1 is also a translational regulator. We previously showed that BRCA1 was implicated in translation regulation. Here, we asked whether translational control could be a novel function of BRCA1 that contributes to its tumor suppressive activity. A combination of RNA-binding protein immunoprecipitation, microarray analysis, and polysome profiling, was used to identify the mRNAs that were specifically deregulated under BRCA1 deficiency. Western blot analysis allowed us to confirm at the protein level the deregulated translation of a subset of mRNAs. A unique and dedicated cohort of patients with documented germ-line BRCA1 pathogenic variant statues was set up, and tissue microarrays with the biopsies of these patients were constructed and analyzed by immunohistochemistry for their content in each candidate protein. Here, we show that BRCA1 translationally regulates a subset of mRNAs with which it associates. These mRNAs code for proteins involved in major programs in cancer. Accordingly, the level of these key proteins is correlated with BRCA1 status in breast cancer cell lines and in patient breast tumors. ADAT2, one of these key proteins, is proposed as a predictive biomarker of efficacy of treatments recently recommended to patients with BRCA1 deficiency. This study proposes that translational control may represent a novel molecular mechanism with potential clinical impact through which BRCA1 is a tumor suppressor.
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Affiliation(s)
- Elise Berthel
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (E.B.) ; (A.V.) ; (E.D.) ; (V.M.) ; (H.P.) ; (F.C.) ; (J.-J.D.)
| | - Anne Vincent
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (E.B.) ; (A.V.) ; (E.D.) ; (V.M.) ; (H.P.) ; (F.C.) ; (J.-J.D.)
| | - Lauriane Eberst
- Centre Léon Bérard, Medical Oncology Department, Université de Lyon 1, F-69008 Lyon, France;
| | - Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain; (A.G.T.); (L.R.d.P.)
| | - Estelle Dacheux
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (E.B.) ; (A.V.) ; (E.D.) ; (V.M.) ; (H.P.) ; (F.C.) ; (J.-J.D.)
| | - Catherine Rey
- ProfileXpert, UNIV-US7 INSERM-UMS 3453 CNRS, F-69000 Lyon, France; (C.R.); (J.L.)
| | - Virginie Marcel
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (E.B.) ; (A.V.) ; (E.D.) ; (V.M.) ; (H.P.) ; (F.C.) ; (J.-J.D.)
| | - Hermes Paraqindes
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (E.B.) ; (A.V.) ; (E.D.) ; (V.M.) ; (H.P.) ; (F.C.) ; (J.-J.D.)
| | - Joël Lachuer
- ProfileXpert, UNIV-US7 INSERM-UMS 3453 CNRS, F-69000 Lyon, France; (C.R.); (J.L.)
| | - Frédéric Catez
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (E.B.) ; (A.V.) ; (E.D.) ; (V.M.) ; (H.P.) ; (F.C.) ; (J.-J.D.)
| | - Lluis Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain; (A.G.T.); (L.R.d.P.)
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Spain
| | - Isabelle Treilleux
- Department of Translational Research and Innovation, Centre Léon Bérard, F-69008 Lyon, France;
| | - Jean-Jacques Diaz
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (E.B.) ; (A.V.) ; (E.D.) ; (V.M.) ; (H.P.) ; (F.C.) ; (J.-J.D.)
| | - Nicole Dalla Venezia
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon 1, Centre Léon Bérard, F-69008 Lyon, France; (E.B.) ; (A.V.) ; (E.D.) ; (V.M.) ; (H.P.) ; (F.C.) ; (J.-J.D.)
- Correspondence: ; Tel.: +33-426-556-745
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Yan Z, Wang Q, Sun X, Ban B, Lu Z, Dang Y, Xie L, Zhang L, Li Y, Zhu W, Guo X. OSbrca: A Web Server for Breast Cancer Prognostic Biomarker Investigation With Massive Data From Tens of Cohorts. Front Oncol 2019; 9:1349. [PMID: 31921624 PMCID: PMC6932997 DOI: 10.3389/fonc.2019.01349] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 11/15/2019] [Indexed: 12/20/2022] Open
Abstract
Potential prognostic mRNA biomarkers are exploited to assist in the clinical management and treatment of breast cancer, which is the first life-threatening tumor in women worldwide. However, it is technically challenging for untrained researchers to process high dimensional profiling data to screen and validate the potential prognostic values of genes of interests in multiple cohorts. Our aim is to develop an easy-to-use web server to facilitate the screening, developing, and evaluating of prognostic biomarkers in breast cancers. Herein, we collected more than 7,400 cases of breast cancer with gene expression profiles and clinical follow-up information from The Cancer Genome Atlas and Gene Expression Omnibus data, and built an Online consensus Survival analysis web server for Breast Cancers, abbreviated OSbrca, to generate the Kaplan–Meier survival plot with a hazard ratio and log rank P-value for given genes in an interactive way. To examine the performance of OSbrca, the prognostic potency of 128 previously published biomarkers of breast cancer was reassessed in OSbrca. In conclusion, it is highly valuable for biologists and clinicians to perform the preliminary assessment and validation of novel or putative prognostic biomarkers for breast cancers. OSbrca could be accessed at http://bioinfo.henu.edu.cn/BRCA/BRCAList.jsp.
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Affiliation(s)
- Zhongyi Yan
- Cell Signal Transduction Laboratory, Department of Preventive Medicine, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Qiang Wang
- Cell Signal Transduction Laboratory, Department of Preventive Medicine, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Xiaoxiao Sun
- Cell Signal Transduction Laboratory, Department of Preventive Medicine, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Bingbing Ban
- Cell Signal Transduction Laboratory, Department of Preventive Medicine, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Zhendong Lu
- Cell Signal Transduction Laboratory, Department of Preventive Medicine, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Yifang Dang
- Cell Signal Transduction Laboratory, Department of Preventive Medicine, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Longxiang Xie
- Cell Signal Transduction Laboratory, Department of Preventive Medicine, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Lu Zhang
- Cell Signal Transduction Laboratory, Department of Preventive Medicine, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Yongqiang Li
- Cell Signal Transduction Laboratory, Department of Preventive Medicine, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Wan Zhu
- Department of Anesthesia, Stanford University, Stanford, CA, United States
| | - Xiangqian Guo
- Cell Signal Transduction Laboratory, Department of Preventive Medicine, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
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35
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Fallahi H, Godini R. System-level responses to cisplatin in pro-apoptotic stages of breast cancer MCF-7 cell line. Comput Biol Chem 2019; 83:107155. [PMID: 31706153 DOI: 10.1016/j.compbiolchem.2019.107155] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 07/09/2019] [Accepted: 10/23/2019] [Indexed: 01/21/2023]
Abstract
Cisplatin ceases cell division and induces apoptosis in cancer cell lines. It is well established that cisplatin alters the expression of many genes involved in several cellular processes and pathways including transcription, p53 signaling pathway, and apoptosis. However, system-wide responses to cisplatin in breast cancer cell lines have not been studied. Therefore, we have used a network analysis approach to unveil such responses at early stages of drug treatment. To do this, we have first identified those genes that are responding to cisplatin treatment in MCF-7 cell line. Network and gene ontology analyses were then employed to uncover the molecular pathways affected by cisplatin treatment. Then the results obtained from cisplatin-treated MCF7 cell line were compared to those obtained from other cancer cell lines at comparable time points. In conclusion, we found that ADCY9, GSK3B, MAPK14, NCK1, NCOA2, PIK3CA, PIK3CB, PTK2, RHOB act as hub genes in the cisplatin-responsive regulatory network at the pro-apoptotic stages. The results could be useful in finding new drugs to target these genes in order to obtain similar responses.
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Affiliation(s)
- Hossein Fallahi
- Department of Biology, Faculty of Science, Razi University, Kermanshah, 6714115111, Iran.
| | - Rasoul Godini
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, 3800, Australia
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36
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Edelmann D, Hummel M, Hielscher T, Saadati M, Benner A. Marginal variable screening for survival endpoints. Biom J 2019; 62:610-626. [DOI: 10.1002/bimj.201800269] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 05/23/2019] [Accepted: 06/04/2019] [Indexed: 01/31/2023]
Affiliation(s)
- Dominic Edelmann
- Division of Biostatistics German Cancer Research Center (DKFZ) Heidelberg Germany
| | - Manuela Hummel
- Division of Biostatistics German Cancer Research Center (DKFZ) Heidelberg Germany
| | - Thomas Hielscher
- Division of Biostatistics German Cancer Research Center (DKFZ) Heidelberg Germany
| | - Maral Saadati
- Division of Biostatistics German Cancer Research Center (DKFZ) Heidelberg Germany
| | - Axel Benner
- Division of Biostatistics German Cancer Research Center (DKFZ) Heidelberg Germany
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37
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Sangaralingam A, Dayem Ullah AZ, Marzec J, Gadaleta E, Nagano A, Ross-Adams H, Wang J, Lemoine NR, Chelala C. 'Multi-omic' data analysis using O-miner. Brief Bioinform 2019; 20:130-143. [PMID: 28981577 PMCID: PMC6357557 DOI: 10.1093/bib/bbx080] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Indexed: 12/19/2022] Open
Abstract
Innovations in -omics technologies have driven advances in biomedical research. However, integrating and analysing the large volumes of data generated from different high-throughput -omics technologies remain a significant challenge to basic and clinical scientists without bioinformatics skills or access to bioinformatics support. To address this demand, we have significantly updated our previous O-miner analytical suite, to incorporate several new features and data types to provide an efficient and easy-to-use Web tool for the automated analysis of data from '-omics' technologies. Created from a biologist's perspective, this tool allows for the automated analysis of large and complex transcriptomic, genomic and methylomic data sets, together with biological/clinical information, to identify significantly altered pathways and prioritize novel biomarkers/targets for biological validation. Our resource can be used to analyse both in-house data and the huge amount of publicly available information from array and sequencing platforms. Multiple data sets can be easily combined, allowing for meta-analyses. Here, we describe the analytical pipelines currently available in O-miner and present examples of use to demonstrate its utility and relevance in maximizing research output. O-miner Web server is free to use and is available at http://www.o-miner.org.
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Affiliation(s)
| | | | - Jacek Marzec
- Barts Cancer Institute, Queen Mary University of London
| | | | - Ai Nagano
- Barts Cancer Institute, Queen Mary University of London
| | | | - Jun Wang
- Barts Cancer Institute, Queen Mary University of London
| | | | - Claude Chelala
- Barts Cancer Institute, co-Lead of the Computational Biology Centre at the Life Science Initiative, Queen Mary University of London
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38
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Fuertes M, Sapochnik M, Tedesco L, Senin S, Attorresi A, Ajler P, Carrizo G, Cervio A, Sevlever G, Bonfiglio JJ, Stalla GK, Arzt E. Protein stabilization by RSUME accounts for PTTG pituitary tumor abundance and oncogenicity. Endocr Relat Cancer 2018; 25:665-676. [PMID: 29622689 DOI: 10.1530/erc-18-0028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 04/05/2018] [Indexed: 11/08/2022]
Abstract
Increased levels of the proto-oncogene pituitary tumor-transforming gene 1 (PTTG) have been repeatedly reported in several human solid tumors, especially in endocrine-related tumors such as pituitary adenomas. Securin PTTG has a critical role in pituitary tumorigenesis. However, the cause of upregulation has not been found yet, despite analyses made at the gene, promoter and mRNA level that show that no mutations, epigenetic modifications or other mechanisms that deregulate its expression may explain its overexpression and action as an oncogene. We describe that high PTTG protein levels are induced by the RWD-containing sumoylation enhancer (RWDD3 or RSUME), a protein originally identified in the same pituitary tumor cell line in which PTTG was also cloned. We demonstrate that PTTG and RSUME have a positive expression correlation in human pituitary adenomas. RSUME increases PTTG protein in pituitary tumor cell lines, prolongs the half-life of PTTG protein and regulates the PTTG induction by estradiol. As a consequence, RSUME enhances PTTG transcription factor and securin activities. PTTG hyperactivity on the cell cycle resulted in recurrent and unequal divisions without cytokinesis, and the consequential appearance of aneuploidies and multinucleated cells in the tumor. RSUME knockdown diminishes securin PTTG and reduces its tumorigenic potential in a xenograft mouse model. Taken together, our findings show that PTTG high protein steady state levels account for PTTG tumor abundance and demonstrate a critical role of RSUME in this process in pituitary tumor cells.
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Affiliation(s)
- M Fuertes
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck SocietyBuenos Aires, Argentina
| | - M Sapochnik
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck SocietyBuenos Aires, Argentina
| | - L Tedesco
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck SocietyBuenos Aires, Argentina
| | - S Senin
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck SocietyBuenos Aires, Argentina
| | - A Attorresi
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck SocietyBuenos Aires, Argentina
| | - P Ajler
- Servicio de NeurocirugíaHospital Italiano, Buenos Aires, Argentina
| | - G Carrizo
- Servicio de NeurocirugíaHospital Italiano, Buenos Aires, Argentina
| | - A Cervio
- Departamento de NeurocirugíaFundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Buenos Aires, Argentina
| | - G Sevlever
- Departamento de NeurocirugíaFundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Buenos Aires, Argentina
| | - J J Bonfiglio
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck SocietyBuenos Aires, Argentina
| | - G K Stalla
- Department of Clinical ResearchMax Planck Institute of Psychiatry, Munich, Germany
| | - E Arzt
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck SocietyBuenos Aires, Argentina
- Departamento de Fisiología y Biología Molecular y CelularFacultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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39
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Golightly NP, Bell A, Bischoff AI, Hollingsworth PD, Piccolo SR. Curated compendium of human transcriptional biomarker data. Sci Data 2018; 5:180066. [PMID: 29664470 PMCID: PMC5903354 DOI: 10.1038/sdata.2018.66] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 02/22/2018] [Indexed: 12/25/2022] Open
Abstract
One important use of genome-wide transcriptional profiles is to identify relationships between transcription levels and patient outcomes. These translational insights can guide the development of biomarkers for clinical application. Data from thousands of translational-biomarker studies have been deposited in public repositories, enabling reuse. However, data-reuse efforts require considerable time and expertise because transcriptional data are generated using heterogeneous profiling technologies, preprocessed using diverse normalization procedures, and annotated in non-standard ways. To address this problem, we curated 45 publicly available, translational-biomarker datasets from a variety of human diseases. To increase the data's utility, we reprocessed the raw expression data using a uniform computational pipeline, addressed quality-control problems, mapped the clinical annotations to a controlled vocabulary, and prepared consistently structured, analysis-ready data files. These data, along with scripts we used to prepare the data, are available in a public repository. We believe these data will be particularly useful to researchers seeking to perform benchmarking studies—for example, to compare and optimize machine-learning algorithms' ability to predict biomedical outcomes.
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Affiliation(s)
| | - Avery Bell
- Department of Biology, Brigham Young University, Provo, Utah 84602, USA
| | - Anna I Bischoff
- Department of Biology, Brigham Young University, Provo, Utah 84602, USA
| | - Parker D Hollingsworth
- Department of Biology, Brigham Young University, Provo, Utah 84602, USA.,Northeast Ohio Medical University, Rootstown, Ohio 44272, USA
| | - Stephen R Piccolo
- Department of Biology, Brigham Young University, Provo, Utah 84602, USA.,Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah 84602, USA
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40
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Wu Y, Tedesco L, Lucia K, Schlitter AM, Garcia JM, Esposito I, Auernhammer CJ, Theodoropoulou M, Arzt E, Renner U, Stalla GK. RSUME is implicated in tumorigenesis and metastasis of pancreatic neuroendocrine tumors. Oncotarget 2018; 7:57878-57893. [PMID: 27506944 PMCID: PMC5295397 DOI: 10.18632/oncotarget.11081] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 07/17/2016] [Indexed: 12/12/2022] Open
Abstract
The factors triggering pancreatic neuroendocrine tumor (PanNET) progression are largely unknown. Here we investigated the role and mechanisms of the sumoylation enhancing protein RSUME in PanNET tumorigenesis. Immunohistochemical studies showed that RSUME is strongly expressed in normal human pancreas, in particular in β-cells. RSUME expression is reduced in insulinomas and is nearly absent in other types of PanNETs suggesting a role in PanNET tumorigenesis. In human pancreatic neuroendocrine BON1 cells, RSUME stimulates hypoxia-inducible factor-1α (HIF-1α) and vascular endothelial growth factor-A (VEGF-A), which are key components of tumor neovascularisation. In contrast, RSUME suppresses nuclear factor-κB (NF-κB) and its target interleukin-8 (IL-8). Correspondingly, PanNET cells with RSUME knockdown showed decreased HIF-1α activity and increased NF-κB and IL-8 production leading to a moderate reduction of VEGF-A release as reduced HIF-1α/VEGF-A production is partly compensated by NF-κB/IL-8-induced VEGF-A. Notably, RSUME stabilizes the tumor suppressor PTEN, which is frequently lost in PanNETs and whose absence is associated with metastasis formation. In vivo orthotopic transplantation of PanNET cells with or without RSUME expression into nude mice showed that PanNETs without RSUME have reduced PTEN expression, grow faster and form multiple liver metastases. In sum, RSUME differentially regulates key components of PanNET formation suggesting that the observed loss of RSUME in advanced PanNETs is critically involved in PanNET tumorigenesis, particularly in metastasis formation.
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Affiliation(s)
- Yonghe Wu
- Department of Clinical Neuroendocrinology, Max Planck Institute of Psychiatry, Munich, Germany.,Current address: German Cancer Research Center, Heidelberg, Germany
| | - Lucas Tedesco
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Kristin Lucia
- Department of Clinical Neuroendocrinology, Max Planck Institute of Psychiatry, Munich, Germany
| | - Anna M Schlitter
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Jose Monteserin Garcia
- Department of Clinical Neuroendocrinology, Max Planck Institute of Psychiatry, Munich, Germany
| | - Irene Esposito
- Institute of Pathology, Technical University of Munich, Munich, Germany.,Current address: Institute of Pathology, University of Düsseldorf, Düsseldorf, Germany
| | - Christoph J Auernhammer
- Department of Internal Medicine II, University-Hospital Campus Grosshadern, Interdisciplinary Center of Neuroendocrine Tumours of the GastroEnteroPancreatic System (GEPNET-KUM), Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Marily Theodoropoulou
- Department of Clinical Neuroendocrinology, Max Planck Institute of Psychiatry, Munich, Germany
| | - Eduardo Arzt
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Buenos Aires, Argentina.,Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ulrich Renner
- Department of Clinical Neuroendocrinology, Max Planck Institute of Psychiatry, Munich, Germany
| | - Günter K Stalla
- Department of Clinical Neuroendocrinology, Max Planck Institute of Psychiatry, Munich, Germany
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Csde1 binds transcripts involved in protein homeostasis and controls their expression in an erythroid cell line. Sci Rep 2018; 8:2628. [PMID: 29422612 PMCID: PMC5805679 DOI: 10.1038/s41598-018-20518-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 01/18/2018] [Indexed: 01/12/2023] Open
Abstract
Expression of the RNA-binding protein Csde1 (Cold shock domain protein e1) is strongly upregulated during erythropoiesis compared to other hematopoietic lineages. Csde1 expression is impaired in the severe congenital anemia Diamond Blackfan Anemia (DBA), and reduced expression of Csde1 in healthy erythroblasts impaired their proliferation and differentiation. To investigate the cellular pathways controlled by Csde1 in erythropoiesis, we identified the transcripts that physically associate with Csde1 in erythroid cells. These mainly encoded proteins involved in ribogenesis, mRNA translation and protein degradation, but also proteins associated with the mitochondrial respiratory chain and mitosis. Crispr/Cas9-mediated deletion of the first cold shock domain of Csde1 affected RNA expression and/or protein expression of Csde1-bound transcripts. For instance, protein expression of Pabpc1 was enhanced while Pabpc1 mRNA expression was reduced indicating more efficient translation of Pabpc1 followed by negative feedback on mRNA stability. Overall, the effect of reduced Csde1 function on mRNA stability and translation of Csde1-bound transcripts was modest. Clones with complete loss of Csde1, however, could not be generated. We suggest that Csde1 is involved in feed-back control in protein homeostasis and that it dampens stochastic changes in mRNA expression.
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42
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High Expression of TET1 Predicts Poor Survival in Cytogenetically Normal Acute Myeloid Leukemia From Two Cohorts. EBioMedicine 2018; 28:90-96. [PMID: 29402726 PMCID: PMC5835576 DOI: 10.1016/j.ebiom.2018.01.031] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 01/23/2018] [Accepted: 01/23/2018] [Indexed: 12/15/2022] Open
Abstract
Ten-Eleven-Translocation 1 (TET1) plays a role in the DNA methylation process and gene activation. Recent reports suggest TET1 acts as an oncogene in leukemia development. However, the clinical relevance and biological insight of TET1 expression in cytogenetically normal acute myeloid leukemia (CN-AML) is unknown. In this study, quantification of TET1 transcript by real-time quantitative PCR in bone marrow blasts was performed in 360 CN-AML patients. As a result, high TET1 expression was more common in M0/M1 morphology and genes of NPM1 mutations, and underrepresented in CEBPA double allele mutations in our AML patients. In addition, we found overexpression of TET1 was associated with an inferior overall survival and event free survival in the two independent cohorts. Notably, mRNA and miRNA integrative analyses showed aberrant expression of several hub oncogenes appear to be regulated by some miRNAs like miR-127-5p, miR-494, miR-21 and miR-616 in high TET1 expressers. In conclusion, the TET1 gene expression might serve as a reliable predictor for patients survival in AML. High TET1 mRNA expression is associated with poor survival in cytogenetically normal acute myeloid leukemia. Several miRNAs and their targeting genes aberrantly expressed in high TET1 expressers. These signatures can help us to decipher the poor clinical outcome of AML patients with high TET1 expression.
Patients with acute myeloid leukemia had a poor survival. In this study, we found the TET1 expression can be served as a survival predictor. High expression of TET1 was associated with short survival time. A group of microRNAs and their targeting genes coexpressed in high TET1 expressers. These aberrant expressed signatures can help us to explain the poor survival of patients with high TET1 expression, and be used as the potential drug target in the future.
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Overexpression of transient receptor potential mucolipin-2 ion channels in gliomas: role in tumor growth and progression. Oncotarget 2017; 7:43654-43668. [PMID: 27248469 PMCID: PMC5190050 DOI: 10.18632/oncotarget.9661] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/01/2016] [Indexed: 11/25/2022] Open
Abstract
The Transient Receptor Potential (TRP) superfamily consists of cation-selective and non-selective ion channels playing an important role both in sensory physiology and in physiopathology in several complex diseases including cancers. Among TRP family, the mucolipin (TRPML1, −2, and −3) channels represent a distinct subfamily of endosome/lysosome Ca2+ channel proteins. Loss-of-function mutations in human TRPML-1 gene cause a neurodegenerative disease, Mucolipidosis Type IV, whereas at present no pathology has been associated to human TRPML-2 channels. Herein we found that human TRPML-2 is expressed both in normal astrocytes and neural stem/progenitor cells. By quantitative RT-PCR, western blot, cytofluorimetric and immunohistochemistry analysis we also demonstrated that TRPML-2 mRNA and protein are expressed at different levels in glioma tissues and high-grade glioma cell lines of astrocytic origin. TRPML-2 mRNA and protein levels increased with the pathological grade, starting from pylocitic astrocytoma (grade I) to glioblastoma (grade IV). Moreover, by RNA interference, we demonstrated a role played by TRPML-2 in survival and proliferation of glioma cell lines. In fact, knock-down of TRPML-2 inhibited the viability, altered the cell cycle, reduced the proliferation and induced apoptotic cell death in glioma cell lines. The DNA damage and apoptosis induced by TRPML-2 loss increased Ser139 H2AX phosphorylation and induced caspase-3 activation; furthermore, knock-down of TRPML-2 in T98 and U251 glioma cell lines completely abrogated Akt and Erk1/2 phosphorylation, as compared to untreated cells. Overall, the high TRPML-2 expression in glioma cells resulted in increased survival and proliferation signaling, suggesting a pro-tumorigenic role played by TRPML-2 in glioma progression.
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Chen P, Song W, Liu L. Genome-Wide Transcriptome Analysis of Estrogen Receptor-Positive and Human Epithelial Growth Factor Receptor 2-Positive Breast Cancers by Ribonucleic Acid Sequencing. Gynecol Obstet Invest 2017; 83:338-348. [PMID: 29241203 DOI: 10.1159/000484244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/13/2017] [Indexed: 11/19/2022]
Abstract
AIM The aim is to identify complex pathogenesis of breast cancer subtypes and disclose the whole landscape of altered transcriptional activities in these cancers. METHODS We downloaded raw expression data from public database, and performed transcriptome analysis of 8 estrogen receptor-positive (ER+) breast cancer tissue samples, 8 human epithelial growth factor receptor 2-positive (HER2+) breast cancer tissue samples, and 3 normal breast tissues by identification, functional annotation, and prediction of upstream regulators and cell-surface biomarkers of differentially expressed genes (DEGs). RESULTS We identified over 5,000 DEGs in each of ER+ and HER2+ breast cancers compared to normal tissues. Functional enrichment analysis of shared DEGs indicated significant changes in the regulation of immune -systems in the 2 subtypes. We further identified 1,871 DEGs between the 2 subtypes and disclosed great tumor heterogeneity. We identified 533 shared upregulated genes and predicted 17 upstream transcription factors, as well as identified differentially expressed cell-surface biomarkers for distinguishing our ER+ and HER2+ breast cancers. Further analysis also highlighted the limitation of the usage of HER2 alone in breast cancer classification. CONCLUSION Our findings in ER+ and HER2+ breast cancers provided novel insights into heterogeneous transcriptional activities underlying complex mechanisms of oncogenesis in breast cancers.
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Affiliation(s)
- Pengtao Chen
- Thyroid and Breast Surgery, Zhoukou Central Hospital of Henan Province, Zhoukou, China
| | - Wei Song
- School of Life Science, Shanghai University, Shanghai, China
| | - Liangli Liu
- Intensive Care Unit, Zhoukou Hospital of Traditional Chinese Medicine of Henan Province, Zhoukou, China
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Wang R, Li J, Zhao Y, Li Y, Yin L. Investigating the therapeutic potential and mechanism of curcumin in breast cancer based on RNA sequencing and bioinformatics analysis. Breast Cancer 2017; 25:206-212. [PMID: 29139094 DOI: 10.1007/s12282-017-0816-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/05/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND Breast cancer is a prevalent cancer in female. This study aims to investigate the therapeutic potential and mechanism of curcumin in breast cancer. METHODS After cultivation, human breast cancer cells (MCF-7 cells) were treated with 0.1% (v/v) 15 µmol/ml curcumin-dimethylsulfoxide solution and 0.1% (v/v) dimethylsulfoxide, respectively, at 37 °C and 5% CO2 for 48 h. Total RNA was extracted, cDNA library was constructed, and cDNAs were amplified and sequenced. After data preprocessing, the Cufflinks software was utilized to identify differentially expressed genes (DEGs, |log2 fold change| > 0.5 and p value < 0.05). Then, functional and pathway enrichment analyses were performed through DAVID (p value < 0.05) and WebGestalt [false discovery rate (FDR) < 0.05], respectively. Furthermore, drug and disease association analyses (FDR < 0.05) were conducted through WebGestalt and DAVID, respectively. STRING was employed to construct protein-protein interaction (PPI) network (combined score > 0.4). RESULTS After DEGs screening, 347 DEGs were identified. Up-regulated DEGs were enriched in 14 functions and 3 pathways, and associated with 12 drugs. Down-regulated DEGs were enriched in 14 functions and 9 pathways, and associated with 14 drugs. Moreover, 5 DEGs were associated with breast cancer, including PGAP3, MAP3K1, SERPINE1, PON2, and GSTO2. PPI network was constructed, and the top DEGs were FOS, VIM, FGF2, MAPK1, SPARC, TOMM7, PSMB10, TCEB2, SOCS1, COL4A1, UQCR11, SERPINE1, and ISG15. CONCLUSION Curcumin might have therapeutic potential in breast cancer through regulating breast cancer-related genes, including SERPINE1, PGAP3, MAP3K1, MAPK1, GSTO2, VIM, SPARC, and FGF2. However, validations are required.
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Affiliation(s)
- Rong Wang
- National Research Institute for Health and Family Planning, Beijing, 100081, China
| | - Jinbin Li
- Core Laboratory of Translational Medicine, Chinese PLA General Hospital, No. 28, Fuxing Road, Haidian District, Beijing, 100853, China
| | - Yulan Zhao
- The 88th Hospital of PLA, Tai'an, 271000, China
| | - Yapeng Li
- Core Laboratory of Translational Medicine, Chinese PLA General Hospital, No. 28, Fuxing Road, Haidian District, Beijing, 100853, China
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Ling Yin
- Core Laboratory of Translational Medicine, Chinese PLA General Hospital, No. 28, Fuxing Road, Haidian District, Beijing, 100853, China.
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Kenn M, Schlangen K, Castillo-Tong DC, Singer CF, Cibena M, Koelbl H, Schreiner W. Gene expression information improves reliability of receptor status in breast cancer patients. Oncotarget 2017; 8:77341-77359. [PMID: 29100391 PMCID: PMC5652334 DOI: 10.18632/oncotarget.20474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/06/2017] [Indexed: 12/28/2022] Open
Abstract
Immunohistochemical (IHC) determination of receptor status in breast cancer patients is frequently inaccurate. Since it directs the choice of systemic therapy, it is essential to increase its reliability. We increase the validity of IHC receptor expression by additionally considering gene expression (GE) measurements. Crisp therapeutic decisions are based on IHC estimates, even if they are borderline reliable. We further improve decision quality by a responsibility function, defining a critical domain for gene expression. Refined normalization is devised to file any newly diagnosed patient into existing data bases. Our approach renders receptor estimates more reliable by identifying patients with questionable receptor status. The approach is also more efficient since the rate of conclusive samples is increased. We have curated and evaluated gene expression data, together with clinical information, from 2880 breast cancer patients. Combining IHC with gene expression information yields a method more reliable and also more efficient as compared to common practice up to now. Several types of possibly suboptimal treatment allocations, based on IHC receptor status alone, are enumerated. A ‘therapy allocation check’ identifies patients possibly miss-classified. Estrogen: false negative 8%, false positive 6%. Progesterone: false negative 14%, false positive 11%. HER2: false negative 2%, false positive 50%. Possible implications are discussed. We propose an ‘expression look-up-plot’, allowing for a significant potential to improve the quality of precision medicine. Methods are developed and exemplified here for breast cancer patients, but they may readily be transferred to diagnostic data relevant for therapeutic decisions in other fields of oncology.
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Affiliation(s)
- Michael Kenn
- Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, A-1090 Vienna, Austria
| | - Karin Schlangen
- Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, A-1090 Vienna, Austria
| | - Dan Cacsire Castillo-Tong
- Translational Gynecology Group, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, A-1090 Vienna, Austria
| | - Christian F Singer
- Translational Gynecology Group, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, A-1090 Vienna, Austria
| | - Michael Cibena
- Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, A-1090 Vienna, Austria
| | - Heinz Koelbl
- Department of General Gynecology and Gynecologic Oncology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Wolfgang Schreiner
- Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, A-1090 Vienna, Austria
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D Antonio M, Weghorn D, D Antonio-Chronowska A, Coulet F, Olson KM, DeBoever C, Drees F, Arias A, Alakus H, Richardson AL, Schwab RB, Farley EK, Sunyaev SR, Frazer KA. Identifying DNase I hypersensitive sites as driver distal regulatory elements in breast cancer. Nat Commun 2017; 8:436. [PMID: 28874753 PMCID: PMC5585396 DOI: 10.1038/s41467-017-00100-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 06/01/2017] [Indexed: 12/03/2022] Open
Abstract
Efforts to identify driver mutations in cancer have largely focused on genes, whereas non-coding sequences remain relatively unexplored. Here we develop a statistical method based on characteristics known to influence local mutation rate and a series of enrichment filters in order to identify distal regulatory elements harboring putative driver mutations in breast cancer. We identify ten DNase I hypersensitive sites that are significantly mutated in breast cancers and associated with the aberrant expression of neighboring genes. A pan-cancer analysis shows that three of these elements are significantly mutated across multiple cancer types and have mutation densities similar to protein-coding driver genes. Functional characterization of the most highly mutated DNase I hypersensitive sites in breast cancer (using in silico and experimental approaches) confirms that they are regulatory elements and affect the expression of cancer genes. Our study suggests that mutations of regulatory elements in tumors likely play an important role in cancer development. Cancer driver mutations can occur within noncoding genomic sequences. Here, the authors develop a statistical approach to identify candidate noncoding driver mutations in DNase I hypersensitive sites in breast cancer and experimentally demonstrate they are regulatory elements of known cancer genes.
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Affiliation(s)
- Matteo D Antonio
- Moores Cancer Center, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Donate Weghorn
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | | | - Florence Coulet
- Department of Pediatrics, University of California, La Jolla, San Diego, CA, 92093, USA.,Department of Genetics, Pitie-Salpetriere Hospital, Pierre and Marie Curie University, Paris, 75013, France
| | - Katrina M Olson
- Department of Medicine, Division of Cardiology, University of California, La Jolla, San Diego, CA, 92093, USA.,Division of Biological Sciences, Section of Molecular Biology, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Christopher DeBoever
- Bioinformatics and Systems Biology, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Frauke Drees
- Department of Pediatrics, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Angelo Arias
- Department of Pediatrics, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Hakan Alakus
- Department of Pediatrics, University of California, La Jolla, San Diego, CA, 92093, USA.,Department of General, Visceral and Cancer Surgery, University of Cologne, Cologne, 50937, Germany
| | - Andrea L Richardson
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.,The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Richard B Schwab
- Moores Cancer Center, University of California, La Jolla, San Diego, CA, 92093, USA.,Department of Medicine, School of Medicine, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Emma K Farley
- Department of Medicine, Division of Cardiology, University of California, La Jolla, San Diego, CA, 92093, USA. .,Division of Biological Sciences, Section of Molecular Biology, University of California, La Jolla, San Diego, CA, 92093, USA.
| | - Shamil R Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
| | - Kelly A Frazer
- Moores Cancer Center, University of California, La Jolla, San Diego, CA, 92093, USA. .,Institute for Genomic Medicine, University of California, La Jolla, San Diego, CA, 92093, USA. .,Department of Pediatrics, University of California, La Jolla, San Diego, CA, 92093, USA.
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Klahan S, Wong HSC, Tu SH, Chou WH, Zhang YF, Ho TF, Liu CY, Yih SY, Lu HF, Chen SCC, Huang CC, Chang WC. Identification of genes and pathways related to lymphovascular invasion in breast cancer patients: A bioinformatics analysis of gene expression profiles. Tumour Biol 2017. [PMID: 28651487 DOI: 10.1177/1010428317705573] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Surgery is the most effective treatment for breast cancer patients. However, some patients developed recurrence and distant metastasis after surgery. Adjuvant therapy is considered for high-risk patients depending on several prognostic markers, and lymphovascular invasion has become one of such prognostic markers that help physicians to identify the risk for distant metastasis and recurrence. However, the mechanism of lymphovascular invasion in breast cancer remains unknown. This study aims to unveil the genes and pathways that may involve in lymphovascular invasion in breast cancer. In total, 108 breast cancer samples were collected during surgery and microarray analysis was performed. Significance analysis of the microarrays and limma package for R were used to examine differentially expressed genes between lymphovascular invasion-positive and lymphovascular invasion-negative cases. Network and pathway analyses were mapped using the Ingenuity Pathway Analysis and the Database for Annotation, Visualization and Integrated Discovery. In total, 86 differentially expressed genes, including 37 downregulated genes and 49 upregulated genes were identified in lymphovascular invasion-positive patients. Among these genes, TNFSF11, IL6ST, and EPAS1 play important roles in cytokine-receptor interaction, which is the most enriched pathway related to lymphovascular invasion. Moreover, the results also suggested that an imbalance between extracellular matrix components and tumor micro-environment could induce lymphovascular invasion. Our study evaluated the underlying mechanisms of lymphovascular invasion, which may further help to assess the risk of breast cancer progression and identify potential targets of adjuvant treatment.
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Affiliation(s)
- Sukhontip Klahan
- 1 Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University
| | - Henry Sung-Ching Wong
- 1 Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University.,2 Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Shih-Hsin Tu
- 3 Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,4 Taipei Cancer Center, Taipei Medical University, Taipei, Taiwan
| | - Wan-Hsuan Chou
- 2 Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Yan-Feng Zhang
- 5 HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Thien-Fiew Ho
- 6 Department of Surgery, Cathay General Hospital Sijhih, New Taipei City, Taiwan
| | - Chih-Yi Liu
- 7 Department of Pathology, Cathay General Hospital Sijhih, New Taipei City, Taiwan
| | - Shih-Ying Yih
- 8 Department of Hematology and Oncology, Cathay General Hospital Sijhih, New Taipei City, Taiwan
| | - Hsing Fang Lu
- 1 Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University
| | - Sean Chun-Chang Chen
- 9 Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University
| | - Chi-Cheng Huang
- 3 Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,10 Breast Center, Cathay General Hospital, Taipei, Taiwan.,11 School of Medicine, College of Medicine, Fu-Jen Catholic University, New Taipei, Taiwan
| | - Wei-Chiao Chang
- 1 Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University.,2 Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan.,12 Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,13 Department of Pharmacy, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.,14 Center for Biomarkers and Biotech Drugs, Kaohsiung Medical University, Kaohsiung, Taiwan
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Waldron L, Steimle JD, Greco TM, Gomez NC, Dorr KM, Kweon J, Temple B, Yang XH, Wilczewski CM, Davis IJ, Cristea IM, Moskowitz IP, Conlon FL. The Cardiac TBX5 Interactome Reveals a Chromatin Remodeling Network Essential for Cardiac Septation. Dev Cell 2016; 36:262-75. [PMID: 26859351 DOI: 10.1016/j.devcel.2016.01.009] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 11/21/2015] [Accepted: 01/08/2016] [Indexed: 12/15/2022]
Abstract
Human mutations in the cardiac transcription factor gene TBX5 cause congenital heart disease (CHD), although the underlying mechanism is unknown. We report characterization of the endogenous TBX5 cardiac interactome and demonstrate that TBX5, long considered a transcriptional activator, interacts biochemically and genetically with the nucleosome remodeling and deacetylase (NuRD) repressor complex. Incompatible gene programs are repressed by TBX5 in the developing heart. CHD mis-sense mutations that disrupt the TBX5-NuRD interaction cause depression of a subset of repressed genes. Furthermore, the TBX5-NuRD interaction is required for heart development. Phylogenetic analysis showed that the TBX5-NuRD interaction domain evolved during early diversification of vertebrates, simultaneous with the evolution of cardiac septation. Collectively, this work defines a TBX5-NuRD interaction essential to cardiac development and the evolution of the mammalian heart, and when altered may contribute to human CHD.
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Affiliation(s)
- Lauren Waldron
- University of North Carolina McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA; Integrative Program for Biological & Genome Sciences, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeffrey D Steimle
- Departments of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Todd M Greco
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Nicholas C Gomez
- Integrative Program for Biological & Genome Sciences, UNC-Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kerry M Dorr
- University of North Carolina McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA; Integrative Program for Biological & Genome Sciences, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Junghun Kweon
- Departments of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Brenda Temple
- R.L. Juliano Structural Bioinformatics Core, Department of Biochemistry and Biophysics, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xinan Holly Yang
- Departments of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Caralynn M Wilczewski
- University of North Carolina McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA; Integrative Program for Biological & Genome Sciences, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ian J Davis
- Department of Genetics, UNC-Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Ivan P Moskowitz
- Departments of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Frank L Conlon
- University of North Carolina McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA; Integrative Program for Biological & Genome Sciences, UNC-Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, UNC-Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, UNC-Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biology, UNC-Chapel Hill, Chapel Hill, NC 27599, USA.
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50
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Antico Arciuch VG, Tedesco L, Fuertes M, Arzt E. Role of RSUME in inflammation and cancer. FEBS Lett 2015; 589:3330-5. [PMID: 26297826 DOI: 10.1016/j.febslet.2015.07.048] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 07/28/2015] [Accepted: 07/29/2015] [Indexed: 01/06/2023]
Abstract
RSUME (for RWD-domain-containing sumoylation enhancer), RWDD3 gene, was identified from a pituitary tumor cell with increased tumorigenic and angiogenic potential, and has higher expression in cerebellum, pituitary, heart, kidney, liver, pancreas, adrenal gland and prostate. RSUME is induced by cellular stress like hypoxia and heat shock, and is increased in pituitary tumors, in gliomas and in VHL tumors. Seven splicing forms have been described. Two of them correspond to non-coding RNAs and the other five possess an RWD domain in the N-terminus and differ in their C-terminal end. RSUME enhances SUMO conjugation by interacting with the SUMO conjugase Ubc9, increases Ubc9 thioester formation and therefore favors sumoylation of specific targets. RSUME increases IκB levels and stabilizes HIF-1α during hypoxia, leading to inhibition of NF-κB and increased HIF-1 transcriptional activity. RSUME inhibits pVHL function, thus suppressing HIF-1 and 2α ubiquitination and degradation. Disruption of the RWD domain structure of RSUME indicated that this domain is critical for RSUME action. The findings point to an important role of RSUME in the regulation and stability of specific targets, which are key regulatory mediators in cancer and inflammation.
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Affiliation(s)
- Valeria G Antico Arciuch
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Lucas Tedesco
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Mariana Fuertes
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Eduardo Arzt
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Buenos Aires, Argentina; Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
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