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Meng X, Li Y, Wang F, Li T, Wang B, Wang Q, Long J, Xie H, Zhang Y, Li J. Quercetin attenuates inflammation in rosacea by directly targeting p65 and ICAM-1. Life Sci 2024; 347:122675. [PMID: 38688383 DOI: 10.1016/j.lfs.2024.122675] [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: 01/31/2024] [Revised: 04/08/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
AIMS Rosacea is an inflammatory skin disease with immune and vascular dysfunction. Although there are multiple treatment strategies for rosacea, the clinical outcomes are unsatisfactory. MAIN METHODS Combining transcriptome data and the Connectivity Map database quercetin was identified as a novel candidate for rosacea. Next, the therapeutic efficacy of quercetin was substantiated through proteomic analyses, in vivo experiments, and in vitro assays. Additionally, the utilization of DARTS, molecular docking and experimental verification revealed the therapeutic mechanisms of quercetin. KEY FINDINGS Treatment with quercetin resulted in the following effects: (i) it effectively ameliorated rosacea-like features by reducing immune infiltration and angiogenesis; (ii) it suppressed the expression of inflammatory mediators in HaCaT cells and HDMECs; (iii) it interacted with p65 and ICAM-1 directly, and this interaction resulted in the repression of NF-κB signal and ICAM-1 expression in rosacea. SIGNIFICANCE We show for the first time that quercetin interacted with p65 and ICAM-1 directly to alleviated inflammatory and vascular dysfunction, suggesting quercetin is a novel, promising therapeutic candidate for rosacea.
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Affiliation(s)
- Xin Meng
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China; Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
| | - Yangfan Li
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China; Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
| | - Fan Wang
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China; Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
| | - Tao Li
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China; Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
| | - Ben Wang
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China; Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Qian Wang
- Hunan Binsis Biotechnology Co., Ltd, Changsha, China
| | - Juan Long
- Department of Dermatology, Hunan Children's Hospital, Changsha, China
| | - Hongfu Xie
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China; Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
| | - Yiya Zhang
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China; Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.
| | - Ji Li
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China; Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.
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Wang L, Lu Y, Li D, Zhou Y, Yu L, Mesa Eguiagaray I, Campbell H, Li X, Theodoratou E. The landscape of the methodology in drug repurposing using human genomic data: a systematic review. Brief Bioinform 2024; 25:bbad527. [PMID: 38279645 PMCID: PMC10818097 DOI: 10.1093/bib/bbad527] [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: 07/17/2023] [Revised: 11/24/2023] [Accepted: 12/19/2023] [Indexed: 01/28/2024] Open
Abstract
The process of drug development is expensive and time-consuming. In contrast, drug repurposing can be introduced to clinical practice more quickly and at a reduced cost. Over the last decade, there has been a significant expansion of large biobanks that link genomic data to electronic health record data, public availability of various databases containing biological and clinical information and rapid development of novel methodologies and algorithms in integrating different sources of data. This review aims to provide a thorough summary of different strategies that utilize genomic data to seek drug-repositioning opportunities. We searched MEDLINE and EMBASE databases to identify eligible studies up until 1 May 2023, with a total of 102 studies finally included after two-step parallel screening. We summarized commonly used strategies for drug repurposing, including Mendelian randomization, multi-omic-based and network-based studies and illustrated each strategy with examples, as well as the data sources implemented. By leveraging existing knowledge and infrastructure to expedite the drug discovery process and reduce costs, drug repurposing potentially identifies new therapeutic uses for approved drugs in a more efficient and targeted manner. However, technical challenges when integrating different types of data and biased or incomplete understanding of drug interactions are important hindrances that cannot be disregarded in the pursuit of identifying novel therapeutic applications. This review offers an overview of drug repurposing methodologies, providing valuable insights and guiding future directions for advancing drug repurposing studies.
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Affiliation(s)
- Lijuan Wang
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Lu
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Doudou Li
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yajing Zhou
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lili Yu
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ines Mesa Eguiagaray
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Harry Campbell
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Xue Li
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Evropi Theodoratou
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, The University of Edinburgh MRC Institute of Genetics and Cancer, Edinburgh, UK
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Adikusuma W, Firdayani F, Irham LM, Darmawi D, Hamidy MY, Nopitasari BL, Soraya S, Azizah N. Integrated genomic network analysis revealed potential of a druggable target for hemorrhoid treatment. Saudi Pharm J 2023; 31:101831. [PMID: 37965490 PMCID: PMC10641558 DOI: 10.1016/j.jsps.2023.101831] [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: 08/19/2023] [Accepted: 10/14/2023] [Indexed: 11/16/2023] Open
Abstract
Hemorrhoids are a prevalent medical condition that necessitates effective treatment options. The current options for treatment consist of oral medications, topical applications, or surgery, yet a scarcity of highly effective drugs still exists. Genetic markers provide promising avenues for investigating the treatment of hemorrhoids, as they may reveal intricate biological mechanisms and targeted drug therapies, ultimately enhancing more precise treatment tailored to the patient. This study aims to identify new drug candidates for treating hemorrhoids through a meticulous bioinformatics approach and integrated with genomic network analysis. After extracting 21 druggable target genes using DrugBank from 293 genes connected to hemorrhoids, 87 possible drugs were selected. Three of these drugs (ketamine, methylene blue, and fulvestrant) hold potential in addressing issues associated with hemorrhoids and have been supported by clinical or preclinical studies. Eighty-four compounds present new therapeutic possibilities for managing hemorrhoids. We highlight that our findings indicate that NOX1 and NOS3 genes are promising biomarkers, with NOS3 gaining significance owing to its robust systemic functional annotations. Sapropterin, an existing drug, is closely associated with NOS3, providing a clear target for biomarker-driven interventions. This study illustrates the potential of combining genomic network analysis with bioinformatics to repurpose drugs for treating hemorrhoids. Subsequent research will explore the mechanisms for utilizing NOS3 targeting in the treatment of hemorrhoids.
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Affiliation(s)
- Wirawan Adikusuma
- Departement of Pharmacy, University of Muhammadiyah Mataram, Mataram, Indonesia
- Research Center for Vaccine and Drugs, National Research and Innovation Agency (BRIN), South Tangerang, Indonesia
| | - Firdayani Firdayani
- Research Center for Vaccine and Drugs, National Research and Innovation Agency (BRIN), South Tangerang, Indonesia
| | | | - Darmawi Darmawi
- Department of Histology, Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia
- Graduate School in Biomedical Sciences, Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia
| | - Muhammad Yulis Hamidy
- Department of Pharmacology, Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia
| | | | - Soraya Soraya
- Master Program in Biomedical Sciences, Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia
| | - Nurul Azizah
- Master Program in Biomedical Sciences, Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia
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Liao X, Ozcan M, Shi M, Kim W, Jin H, Li X, Turkez H, Achour A, Uhlén M, Mardinoglu A, Zhang C. Open MoA: revealing the mechanism of action (MoA) based on network topology and hierarchy. Bioinformatics 2023; 39:btad666. [PMID: 37930015 PMCID: PMC10637856 DOI: 10.1093/bioinformatics/btad666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/19/2023] [Accepted: 10/30/2023] [Indexed: 11/07/2023] Open
Abstract
MOTIVATION Many approaches in systems biology have been applied in drug repositioning due to the increased availability of the omics data and computational biology tools. Using a multi-omics integrated network, which contains information of various biological interactions, could offer a more comprehensive inspective and interpretation for the drug mechanism of action (MoA). RESULTS We developed a computational pipeline for dissecting the hidden MoAs of drugs (Open MoA). Our pipeline computes confidence scores to edges that represent connections between genes/proteins in the integrated network. The interactions showing the highest confidence score could indicate potential drug targets and infer the underlying molecular MoAs. Open MoA was also validated by testing some well-established targets. Additionally, we applied Open MoA to reveal the MoA of a repositioned drug (JNK-IN-5A) that modulates the PKLR expression in HepG2 cells and found STAT1 is the key transcription factor. Overall, Open MoA represents a first-generation tool that could be utilized for predicting the potential MoA of repurposed drugs and dissecting de novo targets for developing effective treatments. AVAILABILITY AND IMPLEMENTATION Source code is available at https://github.com/XinmengLiao/Open_MoA.
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Affiliation(s)
- Xinmeng Liao
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Mehmet Ozcan
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
- Department of Medical Biochemistry, Faculty of Medicine, Zonguldak Bulent Ecevit University, 67630 Zonguldak, Turkey
| | - Mengnan Shi
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Woonghee Kim
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Han Jin
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Xiangyu Li
- Guangzhou National Laboratory, Guangzhou, Guangdong Province 510005, China
| | - Hasan Turkez
- Department of Medical Biology, Faculty of Medicine, Atatürk University, Erzurum 25240, Turkey
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institute, 17176 Stockholm, Sweden
| | - Mathias Uhlén
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Adil Mardinoglu
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London SE1 9RT, United Kingdom
| | - Cheng Zhang
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
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Satria RD, Irham LM, Adikusuma W, Puspitaningrum AN, Afief AR, Khair RE, Septama AW. Identification of druggable genes for multiple myeloma based on genomic information. Genomics Inform 2023; 21:e31. [PMID: 37813627 PMCID: PMC10584652 DOI: 10.5808/gi.23011] [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: 02/09/2023] [Revised: 05/08/2023] [Accepted: 08/07/2023] [Indexed: 10/11/2023] Open
Abstract
Multiple myeloma (MM) is a hematological malignancy. It is widely believed that genetic factors play a significant role in the development of MM, as investigated in numerous studies. However, the application of genomic information for clinical purposes, including diagnostic and prognostic biomarkers, remains largely confined to research. In this study, we utilized genetic information from the Genomic-Driven Clinical Implementation for Multiple Myeloma database, which is dedicated to clinical trial studies on MM. This genetic information was sourced from the genome-wide association studies catalog database. We prioritized genes with the potential to cause MM based on established annotations, as well as biological risk genes for MM, as potential drug target candidates. The DrugBank database was employed to identify drug candidates targeting these genes. Our research led to the discovery of 14 MM biological risk genes and the identification of 10 drugs that target three of these genes. Notably, only one of these 10 drugs, panobinostat, has been approved for use in MM. The two most promising genes, calcium signal-modulating cyclophilin ligand (CAMLG) and histone deacetylase 2 (HDAC2), were targeted by four drugs (cyclosporine, belinostat, vorinostat, and romidepsin), all of which have clinical evidence supporting their use in the treatment of MM. Interestingly, five of the 10 drugs have been approved for other indications than MM, but they may also be effective in treating MM. Therefore, this study aimed to clarify the genomic variants involved in the pathogenesis of MM and highlight the potential benefits of these genomic variants in drug discovery.
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Affiliation(s)
- Rahmat Dani Satria
- Department of Clinical Pathology and Laboratory Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
- Clinical Laboratory Installation, Dr. Sardjito Central General Hospital, Yogyakarta 55281, Indonesia
| | - Lalu Muhammad Irham
- Faculty of Pharmacy, Universitas Ahmad Dahlan, Yogyakarta 55164, Indonesia
- Research Centre for Pharmaceutical Ingredients and Traditional Medicine, National Research and Innovation Agency (BRIN), South Tangerang 15314, Indonesia
| | - Wirawan Adikusuma
- Department of Pharmacy, University of Muhammadiyah Mataram, Mataram 83127, Indonesia
- Research Center for Vaccine and Drugs, National Research and Innovation Agency (BRIN), South Tangerang 15314, Indonesia
| | | | - Arief Rahman Afief
- Faculty of Pharmacy, Universitas Ahmad Dahlan, Yogyakarta 55164, Indonesia
| | - Riat El Khair
- Department of Clinical Pathology and Laboratory Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
- Clinical Laboratory Installation, Dr. Sardjito Central General Hospital, Yogyakarta 55281, Indonesia
| | - Abdi Wira Septama
- Research Center for Vaccine and Drugs, National Research and Innovation Agency (BRIN), South Tangerang 15314, Indonesia
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6
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Ahmed F, Samantasinghar A, Manzoor Soomro A, Kim S, Hyun Choi K. A systematic review of computational approaches to understand cancer biology for informed drug repurposing. J Biomed Inform 2023; 142:104373. [PMID: 37120047 DOI: 10.1016/j.jbi.2023.104373] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/25/2023] [Accepted: 04/23/2023] [Indexed: 05/01/2023]
Abstract
Cancer is the second leading cause of death globally, trailing only heart disease. In the United States alone, 1.9 million new cancer cases and 609,360 deaths were recorded for 2022. Unfortunately, the success rate for new cancer drug development remains less than 10%, making the disease particularly challenging. This low success rate is largely attributed to the complex and poorly understood nature of cancer etiology. Therefore, it is critical to find alternative approaches to understanding cancer biology and developing effective treatments. One such approach is drug repurposing, which offers a shorter drug development timeline and lower costs while increasing the likelihood of success. In this review, we provide a comprehensive analysis of computational approaches for understanding cancer biology, including systems biology, multi-omics, and pathway analysis. Additionally, we examine the use of these methods for drug repurposing in cancer, including the databases and tools that are used for cancer research. Finally, we present case studies of drug repurposing, discussing their limitations and offering recommendations for future research in this area.
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Affiliation(s)
- Faheem Ahmed
- Department of Mechatronics Engineering, Jeju National University, Republic of Korea
| | | | | | - Sejong Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea; Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea.
| | - Kyung Hyun Choi
- Department of Mechatronics Engineering, Jeju National University, Republic of Korea.
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7
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Optimal gene prioritization and disease prediction using knowledge based ontology structure. Biomed Signal Process Control 2023. [DOI: 10.1016/j.bspc.2022.104548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Irham LM, Adikusuma W, Lolita L, Puspitaningrum AN, Afief AR, Sarasmita MA, Dania H, Khairi S, Djalilah GN, Purwanto BD, Chong R. Investigation of susceptibility genes for chickenpox disease across multiple continents. Biochem Biophys Rep 2023; 33:101419. [PMID: 36620086 PMCID: PMC9816662 DOI: 10.1016/j.bbrep.2022.101419] [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: 10/04/2022] [Revised: 12/01/2022] [Accepted: 12/23/2022] [Indexed: 01/01/2023] Open
Abstract
Chickenpox (varicella) is caused by infection with the varicella-zoster virus (VZV), a neurotropic alpha herpes virus with a double-stranded DNA genome. Chickenpox can cause life-threatening complications, including subsequent bacterial infections, central nervous system symptoms, and even death without any risk factors. Few studies have been reported to investigate genetic susceptibility implicated in chickenpox. Herein, our study identified global genetic variants that potentially contributed to chickenpox susceptibility by utilizing the established bioinformatic-based approach. We integrated several databases, such as genome-wide association studies (GWAS) catalog, GTEx portal, HaploReg version 4.1, and Ensembl databases analyses to investigate susceptibility genes associated with chickenpox. Notably, increased expression of HLA-S, HCG4P5, and ABHD16A genes underlie enhanced chickenpox susceptibility in the European, American, and African populations. As compared to the Asian population, Europeans, Americans, and Africans have higher allele frequencies of the extant variants rs9266089, rs10947050, and rs79501286 from the susceptibility genes. Our study suggested that these susceptibility genes and associated genetic variants might play a critical role in chickenpox progression based on host genetics with clinical implications.
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Affiliation(s)
| | - Wirawan Adikusuma
- Department of Pharmacy, University of Muhammadiyah Mataram, Mataram, Indonesia
| | - Lolita Lolita
- Faculty of Pharmacy, Universitas Ahmad Dahlan, Yogyakarta, Indonesia
| | | | | | - Made Ary Sarasmita
- Pharmacy Study Program, Faculty of Science and Mathematics, Udayana University, Bali, Indonesia
| | - Haafizah Dania
- Faculty of Pharmacy, Universitas Ahmad Dahlan, Yogyakarta, Indonesia
| | - Sabiah Khairi
- School of Nursing, College of Nursing, Taipei Medical University, Taipei, 11031, Taiwan
| | | | - Barkah Djaka Purwanto
- Faculty of Medicine, University of Ahmad Dahlan, Yogyakarta, 55191, Indonesia
- PKU Muhammadiyah Bantul Hospital, Bantul, Yogyakarta, 55711, Indonesia
| | - Rockie Chong
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
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Identification of Potential Treatments for Acute Lymphoblastic Leukemia through Integrated Genomic Network Analysis. Pharmaceuticals (Basel) 2022; 15:ph15121562. [PMID: 36559013 PMCID: PMC9786277 DOI: 10.3390/ph15121562] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
The advancement of high-throughput sequencing and genomic analysis revealed that acute lymphoblastic leukemia (ALL) is a genetically heterogeneous disease. The abundance of such genetic data in ALL can also be utilized to identify potential targets for drug discovery and even drug repurposing. We aimed to determine potential genes for drug development and further guide the identification of candidate drugs repurposed for treating ALL through integrated genomic network analysis. Genetic variants associated with ALL were retrieved from the GWAS Catalog. We further applied a genomic-driven drug repurposing approach based on the six functional annotations to prioritize crucial biological ALL-related genes based on the scoring system. Lastly, we identified the potential drugs in which the mechanisms overlapped with the therapeutic targets and prioritized the candidate drugs using Connectivity Map (CMap) analysis. Forty-two genes were considered biological ALL-risk genes with ARID5B topping the list. Based on potentially druggable genes that we identified, palbociclib, sirolimus, and tacrolimus were under clinical trial for ALL. Additionally, chlorprothixene, sirolimus, dihydroergocristine, papaverine, and tamoxifen are the top five drug repositioning candidates for ALL according to the CMap score with dasatinib as a comparator. In conclusion, this study determines the practicability and the potential of integrated genomic network analysis in driving drug discovery in ALL.
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Mugiyanto E, Adikusuma W, Irham LM, Huang WC, Chang WC, Kuo CN. Integrated genomic analysis to identify druggable targets for pancreatic cancer. Front Oncol 2022; 12:989077. [PMID: 36531045 PMCID: PMC9752886 DOI: 10.3389/fonc.2022.989077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/19/2022] [Indexed: 03/31/2024] Open
Abstract
According to the National Comprehensive Cancer Network and the American Society of Clinical Oncology, the standard treatment for pancreatic cancer (PC) is gemcitabine and fluorouracil. Other chemotherapeutic agents have been widely combined. However, drug resistance remains a huge challenge, leading to the ineffectiveness of cancer therapy. Therefore, we are trying to discover new treatments for PC by utilizing genomic information to identify PC-associated genes as well as drug target genes for drug repurposing. Genomic information from a public database, the cBio Cancer Genomics Portal, was employed to retrieve the somatic mutation genes of PC. Five functional annotations were applied to prioritize the PC risk genes: Kyoto Encyclopedia of Genes and Genomes; biological process; knockout mouse; Gene List Automatically Derived For You; and Gene Expression Omnibus Dataset. DrugBank database was utilized to extract PC drug targets. To narrow down the most promising drugs for PC, CMap Touchstone analysis was applied. Finally, ClinicalTrials.gov and a literature review were used to screen the potential drugs under clinical and preclinical investigation. Here, we extracted 895 PC-associated genes according to the cBioPortal database and prioritized them by using five functional annotations; 318 genes were assigned as biological PC risk genes. Further, 216 genes were druggable according to the DrugBank database. CMap Touchstone analysis indicated 13 candidate drugs for PC. Among those 13 drugs, 8 drugs are in the clinical trials, 2 drugs were supported by the preclinical studies, and 3 drugs are with no evidence status for PC. Importantly, we found that midostaurin (targeted PRKA) and fulvestrant (targeted ESR1) are promising candidate drugs for PC treatment based on the genomic-driven drug repurposing pipelines. In short, integrated analysis using a genomic information database demonstrated the viability for drug repurposing. We proposed two drugs (midostaurin and fulvestrant) as promising drugs for PC.
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Affiliation(s)
- Eko Mugiyanto
- PhD Program in Clinical Drug Development of Herbal Medicine, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Department of Pharmacy, Faculty of Health Science, University of Muhammadiyah Pekajangan Pekalongan, Pekalongan, Indonesia
| | - Wirawan Adikusuma
- Department of Clinical Pharmacy, School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Department of Pharmacy, Faculty of Health Science, University of Muhammadiyah Mataram, Mataram, Indonesia
| | | | - Wan-Chen Huang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Wei-Chiao Chang
- PhD Program in Clinical Drug Development of Herbal Medicine, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Department of Clinical Pharmacy, School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Department of Pharmacy, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
- Integrative Research Center for Critical Care, Department of Pharmacy, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Chun-Nan Kuo
- Department of Clinical Pharmacy, School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Department of Pharmacy, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
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Genomic variants-driven drug repurposing for tuberculosis by utilizing the established bioinformatic-based approach. Biochem Biophys Rep 2022; 32:101334. [PMID: 36090591 PMCID: PMC9449755 DOI: 10.1016/j.bbrep.2022.101334] [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: 07/21/2022] [Revised: 08/08/2022] [Accepted: 08/22/2022] [Indexed: 11/21/2022] Open
Abstract
A major challenge in translating genomic variants of Tuberculosis (TB) into clinical implementation is to integrate the disease-associated variants and facilitate drug discovery through the concept of genomic-driven drug repurposing. Here, we utilized two established genomic databases, namely a Genome-Wide Association Study (GWAS) and a Phenome-Wide Association Study (PheWAS) to identify the genomic variants associated with TB disease and further utilize them for drug-targeted genes. We evaluated 3.425 genomic variants associated with TB disease which overlapped with 200 TB-associated genes. To prioritize the biological TB risk genes, we devised an in-silico pipeline and leveraged an established bioinformatics method based on six functional annotations (missense mutation, cis-eQTL, biological process, cellular component, molecular function, and KEGG molecular pathway analysis). Interestingly, based on the six functional annotations that we applied, we discovered that 14 biological TB risk genes are strongly linked to the deregulation of the biological TB risk genes. Hence, we demonstrated that 12 drug target genes overlapped with 40 drugs for other indications and further suggested that the drugs may be repurposed for the treatment of TB. We highlighted that CD44, CCR5, CXCR4, and C3 are highly promising proposed TB targets since they are connected to SELP and HLA-B, which are biological TB risk genes with high systemic scores on functional annotations. In sum, the current study shed light on the genomic variants involved in TB pathogenesis as the biological TB risk genes and provided empirical evidence that the genomics of TB may contribute to drug discovery. The feasibility of utilizing genomic variants to facilitate drug repurposing for Tuberculosis. Genomic information can be effectively used for drug discovery and treatment through genomic-based therapies. Findings from our research support the possibility of drug repurposing for Tuberculosis based on genomic variations.
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12
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Afief AR, Irham LM, Adikusuma W, Perwitasari DA, Brahmadhi A, Chong R. Integration of genomic variants and bioinformatic-based approach to drive drug repurposing for multiple sclerosis. Biochem Biophys Rep 2022; 32:101337. [PMID: 36105612 PMCID: PMC9464879 DOI: 10.1016/j.bbrep.2022.101337] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/25/2022] [Accepted: 08/25/2022] [Indexed: 01/04/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic autoimmune disease in the central nervous system (CNS) marked by inflammation, demyelination, and axonal loss. Currently available MS medication is limited, thereby calling for a strategy to accelerate new drug discovery. One of the strategies to discover new drugs is to utilize old drugs for new indications, an approach known as drug repurposing. Herein, we first identified 421 MS-associated SNPs from the Genome-Wide Association Study (GWAS) catalog (p-value < 5 × 10-8), and a total of 427 risk genes associated with MS using HaploReg version 4.1 under the criterion r 2 > 0.8. MS risk genes were then prioritized using bioinformatics analysis to identify biological MS risk genes. The prioritization was performed based on six defined categories of functional annotations, namely missense mutation, cis-expression quantitative trait locus (cis-eQTL), molecular pathway analysis, protein-protein interaction (PPI), genes overlap with knockout mouse phenotype, and primary immunodeficiency (PID). A total of 144 biological MS risk genes were found and mapped into 194 genes within an expanded PPI network. According to the DrugBank and the Therapeutic Target Database, 27 genes within the list targeted by 68 new candidate drugs were identified. Importantly, the power of our approach is confirmed with the identification of a known approved drug (dimethyl fumarate) for MS. Based on additional data from ClinicalTrials.gov, eight drugs targeting eight distinct genes are prioritized with clinical evidence for MS disease treatment. Notably, CD80 and CD86 pathways are promising targets for MS drug repurposing. Using in silico drug repurposing, we identified belatacept as a promising MS drug candidate. Overall, this study emphasized the integration of functional genomic variants and bioinformatic-based approach that reveal important biological insights for MS and drive drug repurposing efforts for the treatment of this devastating disease.
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Key Words
- ARE, Antioxidant Response Element
- ASN, Asian
- Autoimmune disease
- Bioinformatics
- CNS, Central Nervous System
- Drug repurposing
- FDA, Food and Drug Administration
- FDR, False Discovery Rate
- GO, Gene Ontology
- GWAS, Genome-Wide Association Study
- Genomic variants
- HLA, Human Leukocyte Antigen
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- MP, Mammalian Phenotype
- MS, Multiple Sclerosis
- Multiple sclerosis
- PID, Primary Immuno-deficiency
- PPI, Protein-Protein Interaction
- SNP, Single Nucleotide Polymorphism
- cis-eQTL, cis-expression Quantitative Trait Locus
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Affiliation(s)
| | | | - Wirawan Adikusuma
- Department of Pharmacy, University of Muhammadiyah Mataram, Mataram, Indonesia
| | | | - Ageng Brahmadhi
- Faculty of Medicine, Universitas Muhammadiyah Purwokerto, Purwokerto, Central Java, Indonesia
| | - Rockie Chong
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
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Gupta C, Xu J, Jin T, Khullar S, Liu X, Alatkar S, Cheng F, Wang D. Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer's disease. PLoS Comput Biol 2022; 18:e1010287. [PMID: 35849618 PMCID: PMC9333448 DOI: 10.1371/journal.pcbi.1010287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 07/28/2022] [Accepted: 06/07/2022] [Indexed: 12/03/2022] Open
Abstract
Dysregulation of gene expression in Alzheimer's disease (AD) remains elusive, especially at the cell type level. Gene regulatory network, a key molecular mechanism linking transcription factors (TFs) and regulatory elements to govern gene expression, can change across cell types in the human brain and thus serve as a model for studying gene dysregulation in AD. However, AD-induced regulatory changes across brain cell types remains uncharted. To address this, we integrated single-cell multi-omics datasets to predict the gene regulatory networks of four major cell types, excitatory and inhibitory neurons, microglia and oligodendrocytes, in control and AD brains. Importantly, we analyzed and compared the structural and topological features of networks across cell types and examined changes in AD. Our analysis shows that hub TFs are largely common across cell types and AD-related changes are relatively more prominent in some cell types (e.g., microglia). The regulatory logics of enriched network motifs (e.g., feed-forward loops) further uncover cell type-specific TF-TF cooperativities in gene regulation. The cell type networks are also highly modular and several network modules with cell-type-specific expression changes in AD pathology are enriched with AD-risk genes. The further disease-module-drug association analysis suggests cell-type candidate drugs and their potential target genes. Finally, our network-based machine learning analysis systematically prioritized cell type risk genes likely involved in AD. Our strategy is validated using an independent dataset which showed that top ranked genes can predict clinical phenotypes (e.g., cognitive impairment) of AD with reasonable accuracy. Overall, this single-cell network biology analysis provides a comprehensive map linking genes, regulatory networks, cell types and drug targets and reveals cell-type gene dysregulation in AD.
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Affiliation(s)
- Chirag Gupta
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jielin Xu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Ting Jin
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Saniya Khullar
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Xiaoyu Liu
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sayali Alatkar
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Daifeng Wang
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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14
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Kenneth K W To, Cho WCS. Drug repurposing for cancer therapy in the era of precision medicine. Curr Mol Pharmacol 2022; 15:895-903. [PMID: 35156588 DOI: 10.2174/1874467215666220214104530] [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: 08/26/2021] [Revised: 10/15/2021] [Accepted: 11/07/2021] [Indexed: 11/22/2022]
Abstract
Drug repurposing refers to the identification of clinically approved drugs, with the known safety profiles and defined pharmacokinetic properties, to new indications. Despite the advances in oncology research, cancers are still associated with the most unmet medical needs. Drug repurposing has emerged as a useful approach for the search for effective and durable cancer treatment. It may also represent a promising strategy to facilitate precision cancer treatment and to overcome drug resistance. The repurposing of non-cancer drugs for precision oncology effectively extends the inventory of actionable molecular targets and thus increases the number of patients who may benefit from precision cancer treatment. In cancer types where genetic heterogeneity is so high that it is not feasible to identify strong repurposed drug candidates for standard treatment, the precision oncology approach offers individual patients access to novel treatment options. For repurposed candidates with low potency, a combination of multiple repurposed drugs may produce a synergistic therapeutic effect. Precautions should be taken when combining repurposed drugs with anticancer agents to avoid detrimental drug-drug interactions and unwanted side effects. New multifactorial data analysis and artificial intelligence methods are needed to untangle the complex association of molecular signatures influencing specific cancer subtypes to facilitate drug repurposing in precision oncology.
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Affiliation(s)
- Kenneth K W To
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - William C S Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong SAR, China
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15
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Demirtas TY, Rahman MR, Yurtsever MC, Gov E. Forecasting Gastric Cancer Diagnosis, Prognosis, and Drug Repurposing with Novel Gene Expression Signatures. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:64-74. [PMID: 34910889 DOI: 10.1089/omi.2021.0195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Gastric cancer (GC) is a prevalent disease worldwide with high mortality and poor treatment success. Early diagnosis of GC and forecasting of its prognosis with the use of biomarkers are directly relevant to achieve both personalized/precision medicine and innovation in cancer therapeutics. Gene expression signatures offer one of the promising avenues of research in this regard, as well as guiding drug repurposing analyses in cancers. Using publicly accessible gene expression datasets from the Gene Expression Omnibus and The Cancer Genome Atlas (TCGA), we report here original findings on co-expressed gene modules that are differentially expressed between 133 GC samples and 46 normal tissues, and thus hold potential for novel diagnostic candidates for GC. Furthermore, we found two co-expressed gene modules were significantly associated with poor survival outcomes revealed by survival analysis of the RNA-Seq TCGA datasets. We identified STAT6 (signal transducer and activator of transcription 6) as a key regulator of the identified gene modules. Finally, potential therapeutic drugs that may target and reverse the expression of the identified altered gene modules examined for drug repurposing analyses and the unraveled compounds were further investigated in the literature by the text mining method. Accordingly, we found several repurposed drug candidates, including Trichostatin A, Vorinostat, Parthenolide, Panobinostat, Brefeldin A, Belinostat, and Danusertib. Through text mining analysis and literature search validation, Belinostat and Danusertib were suggested as possible novel drug candidates for GC treatment. These findings collectively inform multiple aspects of GC medical management, including its precision diagnosis, forecasting of possible outcomes, and drug repurposing for innovation in GC medicines in the future.
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Affiliation(s)
- Talip Yasir Demirtas
- Department of Bioengineering, Faculty of Engineering, Adana Alparslan Turkes Science and Technology University, Adana, Turkey
| | - Md Rezanur Rahman
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Merve Capkin Yurtsever
- Department of Bioengineering, Faculty of Engineering, Adana Alparslan Turkes Science and Technology University, Adana, Turkey
| | - Esra Gov
- Department of Bioengineering, Faculty of Engineering, Adana Alparslan Turkes Science and Technology University, Adana, Turkey
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16
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Liu T, Xia R, Li C, Chen X, Cai X, Li W. mRNA expression level of CDH2, LEP, POSTN, TIMP1 and VEGFC modulates 5-fluorouracil resistance in colon cancer cells. Exp Ther Med 2021; 22:1023. [PMID: 34373709 PMCID: PMC8343572 DOI: 10.3892/etm.2021.10455] [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: 08/18/2020] [Accepted: 04/22/2021] [Indexed: 11/30/2022] Open
Abstract
Drug resistance severely affects the clinical efficacy of therapeutic agents in patients with colon cancer. The aim of the present study was to identify genes involved in drug resistance in colon cancer using bioinformatics analysis and to identify the underlying mechanisms in vitro. Genes associated with cancer recurrence and chemotherapy resistance were identified using data mining. Immunohistochemistry was performed to analyze the protein expression level of genes of interest in human colon cancer tissues. Reverse transcription-quantitative PCR analysis was performed to analyze the gene expression level in patient samples and in colon cancer cell lines (HCT116 and LoVo). Cell viability was evaluated using the Cell Counting Kit-8 assay in the colon cancer cell lines. Apoptosis was measured using PI staining. The results from the present study revealed 602 genes using both ‘cancer recurrence’ and ‘chemoresistance’ terms on the GenCLiP3 website. Gene functional annotation was performed using the Database for Annotation, Visualization and Integrated Discovery then, the protein-protein interaction networks of the 602 genes were analyzed using STRING analysis. Further, in the GEPIA database, 14 genes (ATM, CDH2, CDKN2A, EPO, LEP, TGFB1, TIMP1, PGR, VEGFC, POSTN, BCL6, CYP19A1, NOTCH3 and XPA) were found to be upregulated in colon cancer tissue and were associated with poor prognosis in patients with colon cancer. Further analysis of 33 paired human colon cancer tissues revealed that 8 genes (ATM, CDH2, CDKN2A, LEP, PGR, TIMP1, POSTN and VEGFC) were significantly upregulated, which was consistent with the results obtained from the earlier analysis and 5 genes (CDH2, LEP, POSTN, TIMP1 and VEGFC) were associated with patient prognosis. Silencing of these 5 genes using small interfering RNAs significantly enhanced the sensitivity of colon cancer cells to the chemotherapeutic agent, 5-fluorouracil (5-FU). Taken together, the results suggested that CDH2, LEP, POSTN, TIMP1 and VEGFC might play a role in chemotherapeutic resistance in colon cancer and represent potential targets for overcoming 5-FU resistance in colon cancer.
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Affiliation(s)
- Tao Liu
- Department of Hepatobiliary Surgery, Xiang'an Hospital of Xiamen University, Xiamen, Fujian 361102, P.R. China
| | - Rongmu Xia
- School of Medicine, Xiamen University, Xiamen, Fujian 361102, P.R. China
| | - Chenmeng Li
- Department of Medical Oncology, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian 361003, P.R. China
| | - Xiaocong Chen
- School of Medicine, Xiamen University, Xiamen, Fujian 361102, P.R. China
| | - Xuemin Cai
- School of Medicine, Xiamen University, Xiamen, Fujian 361102, P.R. China
| | - Wengang Li
- Department of Hepatobiliary Surgery, Xiang'an Hospital of Xiamen University, Xiamen, Fujian 361102, P.R. China
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17
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Hernández-Lemus E, Martínez-García M. Pathway-Based Drug-Repurposing Schemes in Cancer: The Role of Translational Bioinformatics. Front Oncol 2021; 10:605680. [PMID: 33520715 PMCID: PMC7841291 DOI: 10.3389/fonc.2020.605680] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 11/24/2020] [Indexed: 12/11/2022] Open
Abstract
Cancer is a set of complex pathologies that has been recognized as a major public health problem worldwide for decades. A myriad of therapeutic strategies is indeed available. However, the wide variability in tumor physiology, response to therapy, added to multi-drug resistance poses enormous challenges in clinical oncology. The last years have witnessed a fast-paced development of novel experimental and translational approaches to therapeutics, that supplemented with computational and theoretical advances are opening promising avenues to cope with cancer defiances. At the core of these advances, there is a strong conceptual shift from gene-centric emphasis on driver mutations in specific oncogenes and tumor suppressors-let us call that the silver bullet approach to cancer therapeutics-to a systemic, semi-mechanistic approach based on pathway perturbations and global molecular and physiological regulatory patterns-we will call this the shrapnel approach. The silver bullet approach is still the best one to follow when clonal mutations in driver genes are present in the patient, and when there are targeted therapies to tackle those. Unfortunately, due to the heterogeneous nature of tumors this is not the common case. The wide molecular variability in the mutational level often is reduced to a much smaller set of pathway-based dysfunctions as evidenced by the well-known hallmarks of cancer. In such cases "shrapnel gunshots" may become more effective than "silver bullets". Here, we will briefly present both approaches and will abound on the discussion on the state of the art of pathway-based therapeutic designs from a translational bioinformatics and computational oncology perspective. Further development of these approaches depends on building collaborative, multidisciplinary teams to resort to the expertise of clinical oncologists, oncological surgeons, and molecular oncologists, but also of cancer cell biologists and pharmacologists, as well as bioinformaticians, computational biologists and data scientists. These teams will be capable of engaging on a cycle of analyzing high-throughput experiments, mining databases, researching on clinical data, validating the findings, and improving clinical outcomes for the benefits of the oncological patients.
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Affiliation(s)
- Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Mireya Martínez-García
- Sociomedical Research Unit, National Institute of Cardiology “Ignacio Chávez”, Mexico City, Mexico
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