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Wang G, Guo H, Ren Y, Chen W, Wang Y, Li J, Liu H, Xing J, Zhang Y, Li N. Triptolide enhances carboplatin-induced apoptosis by inhibiting nucleotide excision repair (NER) activity in melanoma. Front Pharmacol 2023; 14:1157433. [PMID: 37324464 PMCID: PMC10267402 DOI: 10.3389/fphar.2023.1157433] [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: 02/02/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Abstract
Introduction: Carboplatin (CBP) is a DNA damaging drug used to treat various cancers, including advanced melanoma. Yet we still face low response rates and short survival due to resistance. Triptolide (TPL) is considered to have multifunctional antitumor effects and has been confirmed to enhance the cytotoxic effects of chemotherapeutic drugs. Herein, we aimed to investigate the knowledge about the effects and mechanisms for the combined application of TPL and CBP against melanoma. Methods: Melanoma cell lines and xenograft mouse model were used to uncover the antitumor effects and the underlying molecular mechanisms of the alone or combined treatment of TPL and CBP in melanoma. Cell viability, migration, invasion, apoptosis, and DNA damage were detected by conventional methods. The rate-limiting proteins of the NER pathway were quantitated using PCR and Western blot. Fluorescent reporter plasmids were used to test the NER repair capacity. Results: Our results showed that the presence of TPL in CBP treatment could selectively inhibit NER pathway activity, and TPL exerts a synergistic effect with CBP to inhibit viability, migration, invasion, and induce apoptosis of A375 and B16 cells. Moreover, combined treatment with TPL and CBP significantly inhibited tumor progression in nude mice by suppressing cell proliferation and inducing apoptosis. Discussion: This study reveals the NER inhibitor TPL which has great potential in treating melanoma, either alone or in combination with CBP.
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Affiliation(s)
- Geng Wang
- Health Science Center, Ningbo University, Ningbo, China
| | - Hongmin Guo
- People’s Hospital of Changshou Chongqing, Chongqing, China
| | - Yan Ren
- Health Science Center, Ningbo University, Ningbo, China
| | - Weiyi Chen
- Health Science Center, Ningbo University, Ningbo, China
| | - Yixuan Wang
- Health Science Center, Ningbo University, Ningbo, China
| | - Jianing Li
- Health Science Center, Ningbo University, Ningbo, China
| | - Hua Liu
- Health Science Center, Ningbo University, Ningbo, China
| | - Jingjun Xing
- Health Science Center, Ningbo University, Ningbo, China
| | - Yanru Zhang
- Health Science Center, Ningbo University, Ningbo, China
| | - Na Li
- Health Science Center, Ningbo University, Ningbo, China
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Abd-Allah GM, Ismail A, El-Mahdy HA, Elsakka EG, El-Husseiny AA, Abdelmaksoud NM, Salman A, Elkhawaga SY, Doghish AS. miRNAs as potential game-changers in melanoma: A comprehensive review. Pathol Res Pract 2023; 244:154424. [PMID: 36989843 DOI: 10.1016/j.prp.2023.154424] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 03/28/2023]
Abstract
Melanoma is the sixth most frequent malignancy. It represents 1.7% of all cancer cases worldwide. Many risk factors are associated with melanoma including ultraviolet radiation skin phenotype, Pigmented Nevi, Pesticides, and genetic and epigenetic factors. Of the main epigenetic factors affecting melanoma are microribonucleic acids (miRNAs). They are short nucleic acid chains that have the potential to prevent the expression of a number of target genes. They could target a number of genes related to melanoma initiation, stemness, angiogenesis, apoptosis, proliferation, and potential resistance to treatment. Additionally, they can control several melanoma signaling pathways, including P53, WNT/-catenin, JAK/STAT, PI3K/AKT/mTOR axis, TGF- β, and EGFR. MiRNAs also play a role in the resistance of melanoma to essential treatment regimens. The stability and abundance of miRNAs might be important factors enhancing the use of miRNAs as markers of prognosis, diagnosis, stemness, survival, and metastasis in melanoma patients.
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Xu W, Yu H, Chen D, Pan W, Yang W, Miao J, Jia W, Zheng B, Liu Y, Chen X, Gao Y, Tian D. Identifying the potential transcriptional regulatory network in Hirschsprung disease by integrated analysis of microarray datasets. WORLD JOURNAL OF PEDIATRIC SURGERY 2023; 6:e000547. [PMID: 37082700 PMCID: PMC10111925 DOI: 10.1136/wjps-2022-000547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/13/2023] [Indexed: 04/22/2023] Open
Abstract
Objective Hirschsprung disease (HSCR) is one of the common neurocristopathies in children, which is associated with at least 20 genes and involves a complex regulatory mechanism. Transcriptional regulatory network (TRN) has been commonly reported in regulating gene expression and enteric nervous system development but remains to be investigated in HSCR. This study aimed to identify the potential TRN implicated in the pathogenesis and diagnosis of HSCR. Methods Based on three microarray datasets from the Gene Expression Omnibus database, the multiMiR package was used to investigate the microRNA (miRNA)-target interactions, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Then, we collected transcription factors (TFs) from the TransmiR database to construct the TF-miRNA-mRNA regulatory network and used cytoHubba to identify the key modules. Finally, the receiver operating characteristic (ROC) curve was determined and the integrated diagnostic models were established based on machine learning by the support vector machine method. Results We identified 58 hub differentially expressed microRNAs (DEMis) and 16 differentially expressed mRNAs (DEMs). The robust target genes of DEMis and DEMs mainly enriched in several GO/KEGG terms, including neurogenesis, cell-substrate adhesion, PI3K-Akt, Ras/mitogen-activated protein kinase and Rho/ROCK signaling. Moreover, 2 TFs (TP53 and TWIST1), 4 miRNAs (has-miR-107, has-miR-10b-5p, has-miR-659-3p, and has-miR-371a-5p), and 4 mRNAs (PIM3, CHUK, F2RL1, and CA1) were identified to construct the TF-miRNA-mRNA regulatory network. ROC analysis revealed a strong diagnostic value of the key TRN regulons (all area under the curve values were more than 0.8). Conclusion This study suggests a potential role of the TF-miRNA-mRNA network that can help enrich the connotation of HSCR pathogenesis and diagnosis and provide new horizons for treatment.
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Affiliation(s)
- Wenyao Xu
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
- Institute of Neurobiology, Environment and Genes Related to Diseases Key Laboratory of Chinese Ministry of Education, Xi'an Jiaotong University, Xi'an, China
| | - Hui Yu
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
- Institute of Neurobiology, Environment and Genes Related to Diseases Key Laboratory of Chinese Ministry of Education, Xi'an Jiaotong University, Xi'an, China
| | - Dian Chen
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Peking University, Beijing, China
| | - Weikang Pan
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Weili Yang
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Jing Miao
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Wanying Jia
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Baijun Zheng
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Yong Liu
- Institute of Neurobiology, Environment and Genes Related to Diseases Key Laboratory of Chinese Ministry of Education, Xi'an Jiaotong University, Xi'an, China
| | - Xinlin Chen
- Institute of Neurobiology, Environment and Genes Related to Diseases Key Laboratory of Chinese Ministry of Education, Xi'an Jiaotong University, Xi'an, China
| | - Ya Gao
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Donghao Tian
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
- Institute of Neurobiology, Environment and Genes Related to Diseases Key Laboratory of Chinese Ministry of Education, Xi'an Jiaotong University, Xi'an, China
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4
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Feng XE. miR-548b Suppresses Melanoma Cell Growth, Migration, and Invasion by Negatively Regulating Its Target Gene HMGB1. Cancer Biother Radiopharm 2021; 36:189-201. [PMID: 33750228 DOI: 10.1089/cbr.2019.3507] [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] [Indexed: 01/19/2023] Open
Abstract
Background: Melanoma is one of the most aggressive malignancies. Exploration of metastasis-related genes will improve the clinical outcomes of patients with melanoma. Recently, microRNAs (miRNAs) have been implicated in regulating the aggressiveness of melanoma. In the current study, the author demonstrated the expression of miR-548b and its functions in melanoma. Materials and Methods: The expression levels of miR-548b and high mobility group protein 1 (HMGB1) in melanoma specimens and adjacent normal tissues were examined using the quantitative real-time PCR method. The Cell Counting Kit-8 (CCK-8), wound healing test, and Transwell assays were conducted to examine the impact of miR-548b on aggressive phenotypes of melanoma cells. The protein expression of HMGB1 was detected by Western blot. The tumor growth of melanoma cells in vivo was analyzed using the transplanted tumor model. The expression of HMGB1 in vivo was assessed using immunohistochemistry assay. Results: miR-548b was significantly downregulated in the melanoma sample when compared with adjacent normal tissues. In addition, low levels of miR-548b were related to poor overall survival in patients with melanoma. As predicted, overexpression of miR-548b suppressed the growth and metastasis-associated traits of melanoma cells. Furthermore, the luciferase reporter gene assay and Western blotting revealed that HMGB1 was a target of miR-548b and its expression level was negatively modulated by miR-548b. Several rescue experiments indicated that reintroduction of HMGB1 abolished the inhibiting effects of miR-548b on melanoma cells. Finally, the author demonstrated that upregulation of miR-548b repressed melanoma cell growth in vivo. Conclusions: All these findings demonstrate that miR-548b serves as a cancer-suppressive miRNA in human melanoma by inhibiting HMGB1.
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Affiliation(s)
- Xi-En Feng
- Department of Dermatology, Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, China
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5
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Khoei SG, Sadeghi H, Samadi P, Najafi R, Saidijam M. Relationship between Sphk1/S1P and microRNAs in human cancers. Biotechnol Appl Biochem 2020; 68:279-287. [PMID: 32275078 DOI: 10.1002/bab.1922] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/04/2020] [Indexed: 12/12/2022]
Abstract
Sphingosine kinases type 1 (SphK1) is a key enzyme in the phosphorylation of sphingosine to sphingosine 1-phosphate (S1P). Different abnormalities in SphK1 functions may correspond with poor prognosis in various cancers. Additionally, upregulated SphK1/S1P could promote cancer cell proliferation, angiogenesis, mobility, invasion, and metastasis. MicroRNAs as conserved small noncoding RNAs play major roles in cancer initiation, progression, metastasis, etc. Their posttranscriptionally mechanisms could affect the development of cancer growth or tumorigenesis suppression. The growing number of studies has described that various microRNAs can be regulated by SphK1, and its expression level can also be regulated by microRNAs. In this review, the relationship of SphK1 and microRNA functions and their interaction in human malignancies have been discussed. Based on them novel treatment strategies can be introduced.
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Affiliation(s)
- Saeideh Gholamzadeh Khoei
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.,Student Research Committee, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Hamid Sadeghi
- Department of Microbiology and Virology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Pouria Samadi
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.,Student Research Committee, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Rezvan Najafi
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Massoud Saidijam
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
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6
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The miRNAs Role in Melanoma and in Its Resistance to Therapy. Int J Mol Sci 2020; 21:ijms21030878. [PMID: 32013263 PMCID: PMC7037367 DOI: 10.3390/ijms21030878] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/20/2020] [Accepted: 01/26/2020] [Indexed: 12/11/2022] Open
Abstract
Melanoma is the less common but the most malignant skin cancer. Since the survival rate of melanoma metastasis is about 10–15%, many different studies have been carried out in order to find a more effective treatment. Although the development of target-based therapies and immunotherapeutic strategies has improved chances for patient survival, melanoma treatment still remains a big challenge for oncologists. Here, we collect recent data about the emerging role of melanoma-associated microRNAs (miRNAs) currently available treatments, and their involvement in drug resistance. We also reviewed miRNAs as prognostic factors, because of their chemical stability and resistance to RNase activity, in melanoma progression. Moreover, despite miRNAs being considered small conserved regulators with the limitation of target specificity, we outline the dual role of melanoma-associated miRNAs, as oncogenic and/or tumor suppressive factors, compared to other tumors.
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7
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Khaire UM, Dhanalakshmi R. Stability of feature selection algorithm: A review. JOURNAL OF KING SAUD UNIVERSITY-COMPUTER AND INFORMATION SCIENCES 2019. [DOI: 10.1016/j.jksuci.2019.06.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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8
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Thyagarajan A, Shaban A, Sahu RP. MicroRNA-Directed Cancer Therapies: Implications in Melanoma Intervention. J Pharmacol Exp Ther 2018; 364:1-12. [PMID: 29054858 PMCID: PMC5733457 DOI: 10.1124/jpet.117.242636] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 08/22/2017] [Indexed: 12/15/2022] Open
Abstract
Acquired tumor resistance to cancer therapies poses major challenges in the treatment of cancers including melanoma. Among several signaling pathways or factors that affect neocarcinogenesis, cancer progression, and therapies, altered microRNAs (miRNAs) expression has been identified as a crucial player in modulating the key pathways governing these events. While studies in the miRNA field have grown exponentially in the last decade, much remains to be discovered, particularly with respect to their roles in cancer therapies. Since immune and nonimmune signaling cascades prevail in cancers, identification and evaluation of miRNAs, their molecular mechanisms and cellular targets involved in the underlying development of cancers, and acquired therapeutic resistance would help in devising new strategies for the prognosis, treatment, and an early detection of recurrence. Importantly, in-depth validation of miRNA-targeted molecular events could lead to the development of accurate progression-risk biomarkers, improved effectiveness, and improved patient responses to standard therapies. The current review focuses on the roles of miRNAs with recent updates on regulated cell cycle and proliferation, immune responses, oncogenic/epigenetic signaling pathways, invasion, metastasis, and apoptosis, with broader attention paid to melanomagenesis and melanoma therapies.
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Affiliation(s)
- Anita Thyagarajan
- Department of Pharmacology and Toxicology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio (A.T., R.P.S.); and Department of Pharmacology, Faculty of veterinary medicine, Zagazig University, Zagazig, Egypt (A.S.)
| | - Ahmed Shaban
- Department of Pharmacology and Toxicology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio (A.T., R.P.S.); and Department of Pharmacology, Faculty of veterinary medicine, Zagazig University, Zagazig, Egypt (A.S.)
| | - Ravi Prakash Sahu
- Department of Pharmacology and Toxicology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio (A.T., R.P.S.); and Department of Pharmacology, Faculty of veterinary medicine, Zagazig University, Zagazig, Egypt (A.S.)
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9
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Zang H, Peng J, Wang W, Fan S. Roles of microRNAs in the resistance to platinum based chemotherapy in the non-small cell lung cancer. J Cancer 2017; 8:3856-3861. [PMID: 29151973 PMCID: PMC5688939 DOI: 10.7150/jca.21267] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 07/24/2017] [Indexed: 12/29/2022] Open
Abstract
Platinum-based adjuvant chemotherapy improves survival among patients with lung tumors, in particular non-small cell lung cancer (NSCLC). But the predicament of drug resistance in NSCLC patients is frustrating us. The profiles of microRNAs are different between platinum chemotherapy resistant and sensitive NSCLC cells. Researches regarding microRNAs and their targets, in platinum drug resistant cases, illuminate novel ideals for platinum-based chemotherapy for NSCLC patients. Therefore, in this review we will focus on three aspects: Epithelial-mesenchymal transition (EMT), cell proliferation and apoptosis, and the roles of microRNAs in cisplatin (CDDP) and carboplatin (CBP) resistance.
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Affiliation(s)
- Hongjing Zang
- Department of Pathology, the Second Xiangya Hospital of Central South University, Changsha, Hunan, 410013, China
| | - Jianlun Peng
- Department of Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan, 410011, China
| | - Weiyuan Wang
- Department of Pathology, the Second Xiangya Hospital of Central South University, Changsha, Hunan, 410013, China
| | - Songqing Fan
- Department of Pathology, the Second Xiangya Hospital of Central South University, Changsha, Hunan, 410013, China
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10
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Improving the economics of NASH/NAFLD treatment through the use of systems biology. Drug Discov Today 2017; 22:1532-1538. [DOI: 10.1016/j.drudis.2017.07.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/27/2017] [Accepted: 07/12/2017] [Indexed: 12/13/2022]
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11
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Kwok GT, Zhao JT, Weiss J, Mugridge N, Brahmbhatt H, MacDiarmid JA, Robinson BG, Sidhu SB. Translational applications of microRNAs in cancer, and therapeutic implications. Noncoding RNA Res 2017; 2:143-150. [PMID: 30159433 PMCID: PMC6084838 DOI: 10.1016/j.ncrna.2017.12.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/11/2017] [Accepted: 12/11/2017] [Indexed: 12/19/2022] Open
Abstract
The search for targeted novel therapies for cancer is ongoing. MicroRNAs (miRNAs) display a number of characteristics making them an attractive and realisable option. In this review, we explore these applications, ranging from diagnostics, prognostics, disease surveillance, to being a primary therapy or a tool to sensitise patients to treatment modalities such as chemotherapy and radiotherapy. We take a particular perspective towards miRNAs and their impact on rare cancers. Advancement in the delivery of miRNAs, from viral vectors and liposomal delivery to nanoparticle based, has led to a number of pre-clinical and clinical applications for microRNA cancer therapeutics. This is promising, especially in the setting of rare cancers.
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Affiliation(s)
- Grace T. Kwok
- Cancer Genetics Laboratory, Kolling Institute of Medical Research, St Leonards, 2065 NSW, Australia
- Northern Clinical School, Royal North Shore Hospital and University of Sydney, St Leonards, 2065 Sydney, NSW, Australia
- University of Sydney Endocrine Surgery Unit, Royal North Shore Hospital, St Leonards, 2065 Sydney, NSW, Australia
| | - Jing Ting Zhao
- Cancer Genetics Laboratory, Kolling Institute of Medical Research, St Leonards, 2065 NSW, Australia
- Northern Clinical School, Royal North Shore Hospital and University of Sydney, St Leonards, 2065 Sydney, NSW, Australia
| | - Jocelyn Weiss
- EnGeneIC Pty Ltd, Lane Cove West, 2066 NSW, Australia
| | | | | | | | - Bruce G. Robinson
- Cancer Genetics Laboratory, Kolling Institute of Medical Research, St Leonards, 2065 NSW, Australia
- Northern Clinical School, Royal North Shore Hospital and University of Sydney, St Leonards, 2065 Sydney, NSW, Australia
| | - Stan B. Sidhu
- Cancer Genetics Laboratory, Kolling Institute of Medical Research, St Leonards, 2065 NSW, Australia
- Northern Clinical School, Royal North Shore Hospital and University of Sydney, St Leonards, 2065 Sydney, NSW, Australia
- University of Sydney Endocrine Surgery Unit, Royal North Shore Hospital, St Leonards, 2065 Sydney, NSW, Australia
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12
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Raghu VK, Ge X, Chrysanthis PK, Benos PV. Integrated Theory- and Data-driven Feature Selection in Gene Expression Data Analysis. PROCEEDINGS. INTERNATIONAL CONFERENCE ON DATA ENGINEERING 2017; 2017:1525-1532. [PMID: 29422764 PMCID: PMC5799807 DOI: 10.1109/icde.2017.223] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The exponential growth of high dimensional biological data has led to a rapid increase in demand for automated approaches for knowledge production. Existing methods rely on two general approaches to address this challenge: 1) the Theory-driven approach, which utilizes prior accumulated knowledge, and 2) the Data-driven approach, which solely utilizes the data to deduce scientific knowledge. Both of these approaches alone suffer from bias toward past/present knowledge, as they fail to incorporate all of the current knowledge that is available to make new discoveries. In this paper, we show how an integrated method can effectively address the high dimensionality of big biological data, which is a major problem for pure data-driven analysis approaches. We realize our approach in a novel two-step analytical workflow that incorporates a new feature selection paradigm as the first step to handling high-throughput gene expression data analysis and that utilizes graphical causal modeling as the second step to handle the automatic extraction of causal relationships. Our results, on real-world clinical datasets from The Cancer Genome Atlas (TCGA), demonstrate that our method is capable of intelligently selecting genes for learning effective causal networks.
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Affiliation(s)
- Vineet K Raghu
- Department of Computer Science, University of Pittsburgh
| | - Xiaoyu Ge
- Department of Computer Science, University of Pittsburgh
| | | | - Panayiotis V Benos
- Department of Computer Science, University of Pittsburgh
- Department of Computational and Systems Biology, University of Pittsburgh
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13
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Haga Y, Kanda T, Nakamura M, Nakamoto S, Sasaki R, Takahashi K, Wu S, Yokosuka O. Overexpression of c-Jun contributes to sorafenib resistance in human hepatoma cell lines. PLoS One 2017; 12:e0174153. [PMID: 28323861 PMCID: PMC5360329 DOI: 10.1371/journal.pone.0174153] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 03/03/2017] [Indexed: 02/07/2023] Open
Abstract
Background Despite recent advances in treatment strategies, it is still difficult to cure patients with hepatocellular carcinoma (HCC). Sorafenib is the only approved multiple kinase inhibitor for systemic chemotherapy in patients with advanced HCC. The majority of advanced HCC patients are resistant to sorafenib. The mechanisms of sorafenib resistance are still unknown. Methods The expression of molecules involved in the mitogen-activated protein kinase (MAPK) signaling pathway in human hepatoma cell lines was examined in the presence or absence of sorafenib. Apoptosis of human hepatoma cells treated with sorafenib was investigated, and the expression of Jun proto-oncogene (c-Jun) was measured. Results The expression and phosphorylation of c-Jun were enhanced in human hepatoma cell lines after treatment with sorafenib. Inhibiting c-Jun enhanced sorafenib-induced apoptosis. The overexpression of c-Jun impaired sorafenib-induced apoptosis. The expression of osteopontin, one of the established AP-1 target genes, was enhanced after treatment with sorafenib in human hepatoma cell lines. Conclusions The protein c-Jun plays a role in sorafenib resistance in human hepatoma cell lines. The modulation and phosphorylation of c-Jun could be a new therapeutic option for enhancing responsiveness to sorafenib. Modulating c-Jun may be useful for certain HCC patients with sorafenib resistance.
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Affiliation(s)
- Yuki Haga
- Department of Gastroenterology and Nephrology, Chiba University, Graduate School of Medicine, Chiba, Japan
| | - Tatsuo Kanda
- Department of Gastroenterology and Nephrology, Chiba University, Graduate School of Medicine, Chiba, Japan
- * E-mail:
| | - Masato Nakamura
- Department of Gastroenterology and Nephrology, Chiba University, Graduate School of Medicine, Chiba, Japan
| | - Shingo Nakamoto
- Department of Gastroenterology and Nephrology, Chiba University, Graduate School of Medicine, Chiba, Japan
- Department of Molecular Virology, Chiba University, Graduate School of Medicine, Chiba, Japan
| | - Reina Sasaki
- Department of Gastroenterology and Nephrology, Chiba University, Graduate School of Medicine, Chiba, Japan
| | - Koji Takahashi
- Department of Gastroenterology and Nephrology, Chiba University, Graduate School of Medicine, Chiba, Japan
| | - Shuang Wu
- Department of Gastroenterology and Nephrology, Chiba University, Graduate School of Medicine, Chiba, Japan
| | - Osamu Yokosuka
- Department of Gastroenterology and Nephrology, Chiba University, Graduate School of Medicine, Chiba, Japan
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14
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Cheerla N, Gevaert O. MicroRNA based Pan-Cancer Diagnosis and Treatment Recommendation. BMC Bioinformatics 2017; 18:32. [PMID: 28086747 PMCID: PMC5237282 DOI: 10.1186/s12859-016-1421-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 12/13/2016] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The current state-of-the-art in cancer diagnosis and treatment is not ideal; diagnostic tests are accurate but invasive, and treatments are "one-size fits-all" instead of being personalized. Recently, miRNA's have garnered significant attention as cancer biomarkers, owing to their ease of access (circulating miRNA in the blood) and stability. There have been many studies showing the effectiveness of miRNA data in diagnosing specific cancer types, but few studies explore the role of miRNA in predicting treatment outcome. METHODS Here we go a step further, using tissue miRNA and clinical data across 21 cancers from the 'The Cancer Genome Atlas' (TCGA) database. We use machine learning techniques to create an accurate pan-cancer diagnosis system, and a prediction model for treatment outcomes. Finally, using these models, we create a web-based tool that diagnoses cancer and recommends the best treatment options. RESULTS We achieved 97.2% accuracy for classification using a support vector machine classifier with radial basis. The accuracies improved to 99.9-100% when climbing up the embryonic tree and classifying cancers at different stages. We define the accuracy as the ratio of the total number of instances correctly classified to the total instances. The classifier also performed well, achieving greater than 80% sensitivity for many cancer types on independent validation datasets. Many miRNAs selected by our feature selection algorithm had strong previous associations to various cancers and tumor progression. Then, using miRNA, clinical and treatment data and encoding it in a machine-learning readable format, we built a prognosis predictor model to predict the outcome of treatment with 85% accuracy. We used this model to create a tool that recommends personalized treatment regimens. Both the diagnosis and prognosis model, incorporating semi-supervised learning techniques to improve their accuracies with repeated use, were uploaded online for easy access. CONCLUSION Our research is a step towards the final goal of diagnosing cancer and predicting treatment recommendations using non-invasive blood tests.
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Affiliation(s)
| | - Olivier Gevaert
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine, and Department of Biomedical Data Science, Stanford University, 1265 Welch Rd, Stanford, CA, USA
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Komina A, Palkina N, Aksenenko M, Tsyrenzhapova S, Ruksha T. Antiproliferative and Pro-Apoptotic Effects of MiR-4286 Inhibition in Melanoma Cells. PLoS One 2016; 11:e0168229. [PMID: 28005927 PMCID: PMC5179095 DOI: 10.1371/journal.pone.0168229] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 11/28/2016] [Indexed: 12/19/2022] Open
Abstract
INTRODUCTION MicroRNAs are essential regulators of gene expression at the post-transcriptional level. Their expression is altered in cancer tissues, and evaluation of these alterations is considered a promising tool used to diagnose and identify prognostic markers. MATERIALS AND METHODS The microRNA expression profiles of formalin-fixed, paraffin-embedded melanoma and melanocytic nevi samples were estimated with a microarray and subsequently validated by real-time PCR. Melanoma cells were transfected with miR-4286 inhibitor to evaluate the influence of this microRNA on the viability, proliferation, apoptosis, migration, and invasion of melanoma cells. RESULTS The microarray revealed that the expression of 1,171 microRNAs was altered in melanoma samples compared to melanocytic nevi. Real-time PCR validation experiments found the microRNA expression levels to correspond to the melanoma/melanocytic nevi microarray results. The pathway analysis identified 52 modulated pathways in melanoma. Moreover, the application of miR-4286 inhibitor to BRO melanoma cells resulted in a 2.6-fold increase in the apoptosis rate and a 1.7-fold decrease in the cell proliferation/viability but did not affect the invasiveness and migration of these cells. Furthermore, the use of miR-4286 inhibitor altered the mRNA expression of several miR-4286 gene targets: folylpolyglutamate synthase, RNA polymerase I-specific transcription initiation factor, apelin, G-protein-coupled receptor 55, and high-mobility group A1 protein, which have been implicated in cell proliferation/apoptosis regulation. Lastly, the transiently transfected SK-MEL-1 cells with miR-4286 inhibitor decreased proliferation rate and modulated folylpolyglutamate synthase rates of these cells. CONCLUSION Our results demonstrate that miR-4286 mediates proliferation and apoptosis in melanoma cells, these findings may represent a novel mechanism underlying these processes.
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Affiliation(s)
- Anna Komina
- Department of Pathophysiology, Krasnoyarsk State Medical University, Krasnoyarsk, Russian Federation
| | - Nadezhda Palkina
- Department of Pathophysiology, Krasnoyarsk State Medical University, Krasnoyarsk, Russian Federation
| | - Mariya Aksenenko
- Department of Pathophysiology, Krasnoyarsk State Medical University, Krasnoyarsk, Russian Federation
| | - Seseg Tsyrenzhapova
- Department of Pathophysiology, Krasnoyarsk State Medical University, Krasnoyarsk, Russian Federation
| | - Tatiana Ruksha
- Department of Pathophysiology, Krasnoyarsk State Medical University, Krasnoyarsk, Russian Federation
- * E-mail:
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Li S, Fang Y, Qin H, Fu W, Zhang X. miR-659-3p is involved in the regulation of the chemotherapy response of colorectal cancer via modulating the expression of SPHK1. Am J Cancer Res 2016; 6:1976-1985. [PMID: 27725903 PMCID: PMC5043107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 08/03/2016] [Indexed: 06/06/2023] Open
Abstract
Colorectal cancer (CRC) is one of most prevalent malignant diseases worldwide. Metastasis and chemo-resistance are the two prominent death-related factors of CRCs. Thus, it is urgent to understand the mechanism responsible for the chemo-resistant properties of CRC and develop new therapeutic methods. Here, we found that the expression of miR-659-3p was significantly reduced in cisplatin (CDDP)-resistant HT29 and LOVO colorectal cancer cells and in CDDP-resistant clinical colorectal cancer samples compared with respective CDDP-sensitive counterparts. Sphingosine kinase 1 (SPHK1) is a direct target of miR-659-3p in colorectal cancer cells, and it is negatively regulated by miR-659-3p. We found that anti-miR-659-3p could increase the IC50 of CDDP in parental HT29 and LOVO colorectal cancer cells; additionally, miR-659-3p mimics decreased the IC50 of CDDP in HT29/CDDP and LOVO/CDDP colorectal cancer cells. Furthermore, we showed that the miR-659-3p/SPHK1 pathway was involved in the regulation of chemotherapy responses of colorectal cancer cells in vivo. In all, our findings suggest a new mechanism involved in the regulation of the chemotherapy response of CRC and might provide new targets for CRC prevention and treatment.
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Affiliation(s)
- Shuyuan Li
- Department of Colorectal Surgery, Tianjin Union Medical CenterTianjin 300121, P. R. China
| | - Ying Fang
- Department of Pathology, The First Hospital of JiaxingZhejiang 314000, P. R. China
| | - Hai Qin
- Department of Colorectal Surgery, Tianjin Union Medical CenterTianjin 300121, P. R. China
| | - Wenzheng Fu
- Department of Colorectal Surgery, Tianjin Union Medical CenterTianjin 300121, P. R. China
| | - Xipeng Zhang
- Department of Colorectal Surgery, Tianjin Union Medical CenterTianjin 300121, P. R. China
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Caparello C, Meijer LL, Garajova I, Falcone A, Le Large TY, Funel N, Kazemier G, Peters GJ, Vasile E, Giovannetti E. FOLFIRINOX and translational studies: Towards personalized therapy in pancreatic cancer. World J Gastroenterol 2016; 22:6987-7005. [PMID: 27610011 PMCID: PMC4988311 DOI: 10.3748/wjg.v22.i31.6987] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/09/2016] [Accepted: 07/06/2016] [Indexed: 02/06/2023] Open
Abstract
Pancreatic cancer is an extremely aggressive disease; although progress has been made in the last few years, the prognosis of these patients remains dismal. FOLFIRINOX is now considered a standard treatment in first-line setting, since it demonstrated an improved overall and progression-free survival vs gemcitabine alone. However, the enthusiasm over the benefit of this three-drug regimen is tempered by the associated increased toxicity profile, and many efforts have been made to improve the feasibility of this schedule. After a more recent phase III trial showing an improved outcome over gemcitabine, the combination of gemcitabine/nab-paclitaxel emerged as another standard first-line treatment. However, this treatment is also associated with more side effects. In addition, despite initial promising data on the predictive role of SPARC levels, recent studies showed that these levels are not associated with nab-paclitaxel efficacy. The choice to use this treatment over FOLFIRINOX is therefore a topic of debate, also because no validated biomarkers to guide FOLFIRINOX treatment are available. In the era of actionable mutations and target agents it would be desirable to identify molecular factors or biomarkers to predict response to therapy in order to maximize the efficacy of treatment and avoid useless toxic effects for non-responding patients. However, until today the milestone of treatment for pancreatic cancer remains chemotherapy combinations, without predictive or monitoring tools existing to optimize therapy. This review analyzes the state-of-the-art treatments, promises and limitations of targeted therapies, ongoing trials and future perspectives, including potential role of microRNAs as predictive biomarkers.
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