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Benegas P, Ziegler B, Dieminger V, Bengió R, Zapata P, Larripa I, Ferri C. Expression of genes potentially involved in loss of response in patients with chronic myeloid leukemia. Gene 2024; 896:148047. [PMID: 38042214 DOI: 10.1016/j.gene.2023.148047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/28/2023] [Accepted: 11/28/2023] [Indexed: 12/04/2023]
Abstract
Chronic Myeloid Leukemia (CML) is a hematological malignancy characterized by the presence of the BCR::ABL1 fusion gene, which leads to uncontrolled cell growth and survival. Tyrosine kinase inhibitors (TKIs) have revolutionized the treatment of CML, but a significant proportion of patients develop resistance or lose response to these drugs. Understanding the molecular mechanisms underlying treatment response and resistance is crucial for improving patient outcomes. This study aimed to analyze the expression patterns of genes involved in treatment response and resistance in CML patients receiving TKI therapy. The expression levels of MET, FOXO3, p15, p16, HCK, and FYN genes were examined in CML patients and compared to healthy donors. Gene expression levels were compared between optimal responders (OR) and resistant patients (R) vs. healthy donors (HD). The MET and FOXO3 OR group showed significant differences compared with the HD, (p < 0.0001) and (p = 0.0003), respectively. p15 expression showed significant differences between OR and HD groups (p = 0.0078), while no significant differences were found in p16 expression between the HD groups. FYN showed a statistically significant difference between R vs. HD (p = 0.0157). The results of HCK expression analysis revealed significant differences between OR and HD (p = 0.0041) and between R and HD (p = 0.0026). When we analyzed OR patients with undetectable BCR::ABL1 transcripts, a greater expression of HCK was observed in the R group. These findings suggest that monitoring the expression levels of MET and FOXO3 genes could be valuable in predicting treatment response and relapse in CML patients. Our study provides important insights into the potential use of gene expression analysis as a tool for predicting treatment response and guiding treatment decisions in CML patients. This knowledge may ultimately contribute to the development of personalized treatment strategies to improve patient outcomes in CML.
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Affiliation(s)
- Paula Benegas
- Universidad Nacional de Misiones, Facultad de Ciencias Exactas Químicas y Naturales, Instituto de Biotecnología Misiones "Dra. María Ebe Reca" (INBIOMIS), Laboratorio de Biotecnología Molecular (BIOTECMOL), Misiones, Argentina; Consejo Nacional de Invetigaciones Cientìficas y Tècnicas (CONICET), Buenos Aires, Argentina
| | - Betiana Ziegler
- Universidad Nacional de Misiones, Facultad de Ciencias Exactas Químicas y Naturales, Instituto de Biotecnología Misiones "Dra. María Ebe Reca" (INBIOMIS), Laboratorio de Biotecnología Molecular (BIOTECMOL), Misiones, Argentina; Laboratorio de Genética Hematológica, IMEX, CONICET-Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Victoria Dieminger
- Universidad Nacional de Misiones, Facultad de Ciencias Exactas Químicas y Naturales, Instituto de Biotecnología Misiones "Dra. María Ebe Reca" (INBIOMIS), Laboratorio de Biotecnología Molecular (BIOTECMOL), Misiones, Argentina
| | - Raquel Bengió
- Departamento de Hemato-oncología, Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Pedro Zapata
- Universidad Nacional de Misiones, Facultad de Ciencias Exactas Químicas y Naturales, Instituto de Biotecnología Misiones "Dra. María Ebe Reca" (INBIOMIS), Laboratorio de Biotecnología Molecular (BIOTECMOL), Misiones, Argentina; Consejo Nacional de Invetigaciones Cientìficas y Tècnicas (CONICET), Buenos Aires, Argentina
| | - Irene Larripa
- Laboratorio de Genética Hematológica, IMEX, CONICET-Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Cristian Ferri
- Universidad Nacional de Misiones, Facultad de Ciencias Exactas Químicas y Naturales, Instituto de Biotecnología Misiones "Dra. María Ebe Reca" (INBIOMIS), Laboratorio de Biotecnología Molecular (BIOTECMOL), Misiones, Argentina.
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Padmanabhan R, Kheraldine H, Gupta I, Meskin N, Hamad A, Vranic S, Al Moustafa AE. Quantification of the growth suppression of HER2+ breast cancer colonies under the effect of trastuzumab and PD-1/PD-L1 inhibitor. Front Oncol 2022; 12:977664. [PMID: 36568154 PMCID: PMC9769711 DOI: 10.3389/fonc.2022.977664] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/26/2022] [Indexed: 12/12/2022] Open
Abstract
Introduction Immune checkpoint blockade (ICB)-based therapy is revolutionizing cancer treatment by fostering successful immune surveillance and effector cell responses against various types of cancers. However, patients with HER2+ cancers are yet to benefit from this therapeutic strategy. Precisely, several questions regarding the right combination of drugs, drug modality, and effective dose recommendations pertaining to the use of ICB-based therapy for HER2+ patients remain unanswered. Methods In this study, we use a mathematical modeling-based approach to quantify the growth inhibition of HER2+ breast cancer (BC) cell colonies (ZR75) when treated with anti-HER2; trastuzumab (TZ) and anti-PD-1/PD-L1 (BMS-202) agents. Results and discussion Our data show that a combination therapy of TZ and BMS-202 can significantly reduce the viability of ZR75 cells and trigger several morphological changes. The combination decreased the cell's invasiveness along with altering several key pathways, such as Akt/mTor and ErbB2 compared to monotherapy. In addition, BMS-202 causes dose-dependent growth inhibition of HER2+ BC cell colonies alone, while this effect is significantly improved when used in combination with TZ. Based on the in-vitro monoculture experiments conducted, we argue that BMS-202 can cause tumor growth suppression not only by mediating immune response but also by interfering with the growth signaling pathways of HER2+BC. Nevertheless, further studies are imperative to substantiate this argument and to uncover the potential crosstalk between PD-1/PD-L1 inhibitors and HER2 growth signaling pathways in breast cancer.
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Affiliation(s)
| | - Hadeel Kheraldine
- College of Medicine, Qatar University (QU) Health, Qatar University, Doha, Qatar,Biomedical Research Centre, Qatar University, Doha, Qatar
| | - Ishita Gupta
- College of Medicine, Qatar University (QU) Health, Qatar University, Doha, Qatar,Biomedical Research Centre, Qatar University, Doha, Qatar
| | - Nader Meskin
- Department of Electrical Engineering, Qatar University, Doha, Qatar,*Correspondence: Nader Meskin, ; Ala-Eddin Al Moustafa,
| | - Anas Hamad
- Pharmaceutical Department at Hamad Medical Corporation, Hamad Medical Corporation, Doha, Qatar
| | - Semir Vranic
- College of Medicine, Qatar University (QU) Health, Qatar University, Doha, Qatar
| | - Ala-Eddin Al Moustafa
- College of Medicine, Qatar University (QU) Health, Qatar University, Doha, Qatar,Biomedical Research Centre, Qatar University, Doha, Qatar,*Correspondence: Nader Meskin, ; Ala-Eddin Al Moustafa,
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Yin Z, Wong STC. Artificial intelligence unifies knowledge and actions in drug repositioning. Emerg Top Life Sci 2021; 5:803-813. [PMID: 34881780 PMCID: PMC8923082 DOI: 10.1042/etls20210223] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 11/17/2022]
Abstract
Drug repositioning aims to reuse existing drugs, shelved drugs, or drug candidates that failed clinical trials for other medical indications. Its attraction is sprung from the reduction in risk associated with safety testing of new medications and the time to get a known drug into the clinics. Artificial Intelligence (AI) has been recently pursued to speed up drug repositioning and discovery. The essence of AI in drug repositioning is to unify the knowledge and actions, i.e. incorporating real-world and experimental data to map out the best way forward to identify effective therapeutics against a disease. In this review, we share positive expectations for the evolution of AI and drug repositioning and summarize the role of AI in several methods of drug repositioning.
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Affiliation(s)
- Zheng Yin
- Department of Systems Medicine and Bioengineering, Houston Methodist Cancer Center and Ting Tsung & Wei Fong Chao Center for BRAIN, Houston Methodist Research Institute, Weill Cornell Medicine, Houston, TX 77030, U.S.A
| | - Stephen T C Wong
- Department of Systems Medicine and Bioengineering, Houston Methodist Cancer Center and Ting Tsung & Wei Fong Chao Center for BRAIN, Houston Methodist Research Institute, Weill Cornell Medicine, Houston, TX 77030, U.S.A
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Drug Repositioning and Subgroup Discovery for Precision Medicine Implementation in Triple Negative Breast Cancer. Cancers (Basel) 2021; 13:cancers13246278. [PMID: 34944904 PMCID: PMC8699385 DOI: 10.3390/cancers13246278] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 12/29/2022] Open
Abstract
Simple Summary The heterogeneity of complicated diseases like cancer negatively affects patients’ responses to treatment. Finding homogeneous subgroups of patients within the cancer population and finding the appropriate treatment for each subgroup will improve patients’ survival. In this study, we focus on triple-negative breast cancer (TNBC), where approximately 80% of patients do not entirely respond to chemotherapy. Our aim is to find subgroups of TNBC patients and identify drugs that have the potential to tailor treatments for each group through drug repositioning. After applying our method to TNBC, we found that different targeted mechanisms were suggested for different groups of patients. Our findings could help the research community to gain a better understanding of different subgroups within the TNBC population and can help the drugs to be repurposed with explainable results regarding the targeted mechanism. Abstract Breast cancer (BC) is the leading cause of death among female patients with cancer. Patients with triple-negative breast cancer (TNBC) have the lowest survival rate. TNBC has substantial heterogeneity within the BC population. This study utilized our novel patient stratification and drug repositioning method to find subgroups of BC patients that share common genetic profiles and that may respond similarly to the recommended drugs. After further examination of the discovered patient subgroups, we identified five homogeneous druggable TNBC subgroups. A drug repositioning algorithm was then applied to find the drugs with a high potential for each subgroup. Most of the top drugs for these subgroups were chemotherapy used for various types of cancer, including BC. After analyzing the biological mechanisms targeted by these drugs, ferroptosis was the common cell death mechanism induced by the top drugs in the subgroups with neoplasm subdivision and race as clinical variables. In contrast, the antioxidative effect on cancer cells was the common targeted mechanism in the subgroup of patients with an age less than 50. Literature reviews were used to validate our findings, which could provide invaluable insights to streamline the drug repositioning process and could be further studied in a wet lab setting and in clinical trials.
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Wang F, Ding Y, Lei X, Liao B, Wu FX. Human Protein Complex-Based Drug Signatures for Personalized Cancer Medicine. IEEE J Biomed Health Inform 2021; 25:4079-4088. [PMID: 34665747 DOI: 10.1109/jbhi.2021.3120933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Disease signature-based drug repositioning approaches typically first identify a disease signature from gene expression profiles of disease samples to represent a particular disease. Then such a disease signature is connected with the drug-induced gene expression profiles to find potential drugs for the particular disease. In order to obtain reliable disease signatures, the size of disease samples should be large enough, which is not always a single case in practice, especially for personalized medicine. On the other hand, the sample sizes of drug-induced gene expression profiles are generally large. In this study, we propose a new drug repositioning approach (HDgS), in which the drug signature is first identified from drug-induced gene expression profiles, and then connected to the gene expression profiles of disease samples to find the potential drugs for patients. In order to take the dependencies among genes into account, the human protein complexes (HPC) are used to define the drug signature. The proposed HDgS is applied to the drug-induced gene expression profiles in LINCS and several types of cancer samples. The results indicate that the HPC-based drug signature can effectively find drug candidates for patients and that the proposed HDgS can be applied for personalized medicine with even one patient sample.
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Li X, Wang L, Cykowski M, He T, Liu T, Chakranarayan J, Rivera A, Zhao H, Powell S, Xia W, Wong STC. OCIAD1 contributes to neurodegeneration in Alzheimer's disease by inducing mitochondria dysfunction, neuronal vulnerability and synaptic damages. EBioMedicine 2020; 51:102569. [PMID: 31931285 PMCID: PMC6957876 DOI: 10.1016/j.ebiom.2019.11.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/10/2019] [Accepted: 11/19/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Hyperamyloidosis in the brain is known as the earliest neuropathological change and a unique etiological factor in Alzheimer's disease (AD), while progressive neurodegeneration in certain vulnerable brain regions forms the basis of clinical syndromes. It is not clear how early hyperamyloidosis is implicated in progressive neurodegeneration and what factors contribute to the selective brain vulnerability in AD. METHODS Bioinformatics and experimental neurobiology methods were integrated to identify novel factors involved in the hyperamyloidosis-induced brain vulnerability in AD. We first examined neurodegeneration-specific gene signatures from sporadic AD patients and synaptic protein changes in young transgenic AD mice. Then, we systematically assessed the association of a top candidate gene with AD and investigated its mechanistic role in neurodegeneration. FINDINGS We identified the ovary-orientated protein OCIAD1 (Ovarian-Carcinoma-Immunoreactive-Antigen-Domain-Containing-1) as a neurodegeneration-associated factor for AD. Higher levels of OCIAD1, found in vulnerable brain areas and dystrophic neurites, were correlated with disease severity. Multiple early AD pathological events, particularly Aβ/GSK-3β signaling, elevate OCIAD1, which in turn interacts with BCL-2 to impair mitochondrial function and facilitates mitochondria-associated neuronal injury. Notably, elevated OCIAD1 by Aβ increases cell susceptibility to other AD pathological challenges. INTERPRETATION Our findings suggest that OCIAD1 contributes to neurodegeneration in AD by impairing mitochondria function, and subsequently leading to neuronal vulnerability, and synaptic damages. FUNDING Ting Tsung & Wei Fong Chao Foundation, John S Dunn Research Foundation, Cure Alzheimer's Fund, and NIH R01AG057635 to STCW.
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Affiliation(s)
- Xuping Li
- Ting Tsung & Wei Fong Chao Center for BRAIN, Weill Cornell Medicine, Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX 77030, USA.
| | - Lin Wang
- Department of Informatics Development, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Matthew Cykowski
- Departments of Pathology and Genome Medicine, Weill Cornell Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Tiancheng He
- Department of Informatics Development, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Timothy Liu
- Ting Tsung & Wei Fong Chao Center for BRAIN, Weill Cornell Medicine, Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX 77030, USA
| | - Joshua Chakranarayan
- Ting Tsung & Wei Fong Chao Center for BRAIN, Weill Cornell Medicine, Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX 77030, USA
| | - Andreana Rivera
- Departments of Pathology and Genome Medicine, Weill Cornell Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Hong Zhao
- Ting Tsung & Wei Fong Chao Center for BRAIN, Weill Cornell Medicine, Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX 77030, USA
| | - Suzanne Powell
- Departments of Pathology and Genome Medicine, Weill Cornell Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Weiming Xia
- Ting Tsung & Wei Fong Chao Center for BRAIN, Weill Cornell Medicine, Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX 77030, USA; Geriatric Research Education Clinical Center, Edith Nourse Rogers Memorial Veterans Hospital, Bedford, MA 01730, USA; Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Stephen T C Wong
- Ting Tsung & Wei Fong Chao Center for BRAIN, Weill Cornell Medicine, Houston Methodist Research Institute, 6670 Bertner Ave, Houston, TX 77030, USA; Department of Informatics Development, Houston Methodist Hospital, Houston, TX 77030, USA; Departments of Pathology and Genome Medicine, Weill Cornell Medicine, Houston Methodist Hospital, Houston, TX 77030, USA; Departments of Radiology, Weill Cornell Medicine, Houston Methodist Hospital, Houston, TX 77030, USA.
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Imatinib revives the therapeutic potential of metformin on ewing sarcoma by attenuating tumor hypoxic response and inhibiting convergent signaling pathways. Cancer Lett 2019; 469:195-206. [PMID: 31672491 DOI: 10.1016/j.canlet.2019.10.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/30/2019] [Accepted: 10/21/2019] [Indexed: 02/06/2023]
Abstract
Ewing sarcoma (EwS) is an aggressive pediatric tumor treated with intensive cytotoxic chemotherapies. Overall survival for metastatic or relapsed disease is only 20-30%. Metformin has long been an attractive therapeutic option for EwS, but hypoxia limits its efficacy. Through a systematic integration of drug combination screening, bioinformatics analyses, functional and in vivo studies, and correlation with clinical outcome, we identified another known drug, imatinib that could augment the in vivo anti-tumor capacity of metformin by attenuating tumor hypoxic response. This drug combination regimen widely suppressed multiple dominant mechanisms in EwS genesis, growth, and metastasis, including key EWS-FLI1 downstream targets that converge into the PI3K/AKT/mTOR signaling pathway. In addition, the combination significantly enhanced inhibition on tumor cell proliferation by standard EwS chemotherapy drugs, including cyclophosphamide and ifosfamide. This suggests a potential clinical benefit of the metformin/imatinib combination by allowing the reduction in dose intensity of standard chemotherapy without compromising survival outcome and represents a potential faster track application for EwS patients.
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Zhang SY, Zhang SW, Fan XN, Zhang T, Meng J, Huang Y. FunDMDeep-m6A: identification and prioritization of functional differential m6A methylation genes. Bioinformatics 2019; 35:i90-i98. [PMID: 31510685 PMCID: PMC6612877 DOI: 10.1093/bioinformatics/btz316] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
MOTIVATION As the most abundant mammalian mRNA methylation, N6-methyladenosine (m6A) exists in >25% of human mRNAs and is involved in regulating many different aspects of mRNA metabolism, stem cell differentiation and diseases like cancer. However, our current knowledge about dynamic changes of m6A levels and how the change of m6A levels for a specific gene can play a role in certain biological processes like stem cell differentiation and diseases like cancer is largely elusive. RESULTS To address this, we propose in this paper FunDMDeep-m6A a novel pipeline for identifying context-specific (e.g. disease versus normal, differentiated cells versus stem cells or gene knockdown cells versus wild-type cells) m6A-mediated functional genes. FunDMDeep-m6A includes, at the first step, DMDeep-m6A a novel method based on a deep learning model and a statistical test for identifying differential m6A methylation (DmM) sites from MeRIP-Seq data at a single-base resolution. FunDMDeep-m6A then identifies and prioritizes functional DmM genes (FDmMGenes) by combing the DmM genes (DmMGenes) with differential expression analysis using a network-based method. This proposed network method includes a novel m6A-signaling bridge (MSB) score to quantify the functional significance of DmMGenes by assessing functional interaction of DmMGenes with their signaling pathways using a heat diffusion process in protein-protein interaction (PPI) networks. The test results on 4 context-specific MeRIP-Seq datasets showed that FunDMDeep-m6A can identify more context-specific and functionally significant FDmMGenes than m6A-Driver. The functional enrichment analysis of these genes revealed that m6A targets key genes of many important context-related biological processes including embryonic development, stem cell differentiation, transcription, translation, cell death, cell proliferation and cancer-related pathways. These results demonstrate the power of FunDMDeep-m6A for elucidating m6A regulatory functions and its roles in biological processes and diseases. AVAILABILITY AND IMPLEMENTATION The R-package for DMDeep-m6A is freely available from https://github.com/NWPU-903PR/DMDeepm6A1.0. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Song-Yao Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, Department of intelligent science and technology, School of Automation, Northwestern Polytechnical University, Xían, China
| | - Shao-Wu Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, Department of intelligent science and technology, School of Automation, Northwestern Polytechnical University, Xían, China
| | - Xiao-Nan Fan
- Key Laboratory of Information Fusion Technology of Ministry of Education, Department of intelligent science and technology, School of Automation, Northwestern Polytechnical University, Xían, China
| | - Teng Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, Department of intelligent science and technology, School of Automation, Northwestern Polytechnical University, Xían, China
| | - Jia Meng
- Department of Biological Sciences, HRINU, SUERI, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - Yufei Huang
- Department of Electrical and Computer Engineering, The University of Texas at San Antonio, San Antonio, TX, USA
- Department of Epidemiology and Biostatistics, University of Texas Health San Antonio, San Antonio, TX, USA
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Jordan EJ, Patil K, Suresh K, Park JH, Mosse YP, Lemmon MA, Radhakrishnan R. Computational algorithms for in silico profiling of activating mutations in cancer. Cell Mol Life Sci 2019; 76:2663-2679. [PMID: 30982079 PMCID: PMC6589134 DOI: 10.1007/s00018-019-03097-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/01/2019] [Accepted: 04/08/2019] [Indexed: 12/17/2022]
Abstract
Methods to catalog and computationally assess the mutational landscape of proteins in human cancers are desirable. One approach is to adapt evolutionary or data-driven methods developed for predicting whether a single-nucleotide polymorphism (SNP) is deleterious to protein structure and function. In cases where understanding the mechanism of protein activation and regulation is desired, an alternative approach is to employ structure-based computational approaches to predict the effects of point mutations. Through a case study of mutations in kinase domains of three proteins, namely, the anaplastic lymphoma kinase (ALK) in pediatric neuroblastoma patients, serine/threonine-protein kinase B-Raf (BRAF) in melanoma patients, and erythroblastic oncogene B 2 (ErbB2 or HER2) in breast cancer patients, we compare the two approaches above. We find that the structure-based method is most appropriate for developing a binary classification of several different mutations, especially infrequently occurring ones, concerning the activation status of the given target protein. This approach is especially useful if the effects of mutations on the interactions of inhibitors with the target proteins are being sought. However, many patients will present with mutations spread across different target proteins, making structure-based models computationally demanding to implement and execute. In this situation, data-driven methods-including those based on machine learning techniques and evolutionary methods-are most appropriate for recognizing and illuminate mutational patterns. We show, however, that, in the present status of the field, the two methods have very different accuracies and confidence values, and hence, the optimal choice of their deployment is context-dependent.
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Affiliation(s)
- E Joseph Jordan
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Keshav Patil
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Krishna Suresh
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Jin H Park
- Department of Pharmacology, Yale University, New Haven, CT, USA
- Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Yael P Mosse
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Mark A Lemmon
- Department of Pharmacology, Yale University, New Haven, CT, USA
- Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Ravi Radhakrishnan
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
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Kim SH, Redvers RP, Chi LH, Ling X, Lucke AJ, Reid RC, Fairlie DP, Martin ACBM, Anderson RL, Denoyer D, Pouliot N. Identification of brain metastasis genes and therapeutic evaluation of histone deacetylase inhibitors in a clinically relevant model of breast cancer brain metastasis. Dis Model Mech 2018; 11:dmm.034850. [PMID: 29784888 PMCID: PMC6078399 DOI: 10.1242/dmm.034850] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 05/15/2018] [Indexed: 12/31/2022] Open
Abstract
Breast cancer brain metastases remain largely incurable. Although several mouse models have been developed to investigate the genes and mechanisms regulating breast cancer brain metastasis, these models often lack clinical relevance since they require the use of immunocompromised mice and/or are poorly metastatic to brain from the mammary gland. We describe the development and characterisation of an aggressive brain metastatic variant of the 4T1 syngeneic model (4T1Br4) that spontaneously metastasises to multiple organs, but is selectively more metastatic to the brain from the mammary gland than parental 4T1 tumours. As seen by immunohistochemistry, 4T1Br4 tumours and brain metastases display a triple-negative phenotype, consistent with the high propensity of this breast cancer subtype to spread to brain. In vitro assays indicate that 4T1Br4 cells have an enhanced ability to adhere to or migrate across a brain-derived endothelial monolayer and greater invasive response to brain-derived soluble factors compared to 4T1 cells. These properties are likely to contribute to the brain selectivity of 4T1Br4 tumours. Expression profiling and gene set enrichment analyses demonstrate the clinical relevance of the 4T1Br4 model at the transcriptomic level. Pathway analyses implicate tumour-intrinsic immune regulation and vascular interactions in successful brain colonisation, revealing potential therapeutic targets. Evaluation of two histone deacetylase inhibitors, SB939 and 1179.4b, shows partial efficacy against 4T1Br4 metastasis to brain and other sites in vivo, and potent radio-sensitising properties in vitro. The 4T1Br4 model provides a clinically relevant tool for mechanistic studies and to evaluate novel therapies against brain metastasis. This article has an associated First Person interview with Soo-Hyun Kim, joint first author of the paper. Summary: The authors introduce a new syngeneic mouse model of spontaneous breast cancer brain metastasis, demonstrate its phenotypic, functional and transcriptomic relevance to human TNBC brain metastasis, and test novel therapies.
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Affiliation(s)
- Soo-Hyun Kim
- Metastasis Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Richard P Redvers
- Metastasis Research Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia.,School of Cancer Medicine, La Trobe University Bundoora, VIC, 3086, Australia
| | - Lap Hing Chi
- Metastasis Research Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia.,School of Cancer Medicine, La Trobe University Bundoora, VIC, 3086, Australia
| | - Xiawei Ling
- Metastasis Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Andrew J Lucke
- Division of Chemistry and Structural Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Qld, 4072, Australia
| | - Robert C Reid
- Division of Chemistry and Structural Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Qld, 4072, Australia
| | - David P Fairlie
- Division of Chemistry and Structural Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Qld, 4072, Australia
| | | | - Robin L Anderson
- Metastasis Research Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia.,School of Cancer Medicine, La Trobe University Bundoora, VIC, 3086, Australia.,Department of Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Delphine Denoyer
- Matrix Microenvironment & Metastasis Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia
| | - Normand Pouliot
- School of Cancer Medicine, La Trobe University Bundoora, VIC, 3086, Australia .,Department of Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia.,Matrix Microenvironment & Metastasis Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia
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Cheng F, Hong H, Yang S, Wei Y. Individualized network-based drug repositioning infrastructure for precision oncology in the panomics era. Brief Bioinform 2017; 18:682-697. [PMID: 27296652 DOI: 10.1093/bib/bbw051] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Indexed: 12/12/2022] Open
Abstract
Advances in next-generation sequencing technologies have generated the data supporting a large volume of somatic alterations in several national and international cancer genome projects, such as The Cancer Genome Atlas and the International Cancer Genome Consortium. These cancer genomics data have facilitated the revolution of a novel oncology drug discovery paradigm from candidate target or gene studies toward targeting clinically relevant driver mutations or molecular features for precision cancer therapy. This focuses on identifying the most appropriately targeted therapy to an individual patient harboring a particularly genetic profile or molecular feature. However, traditional experimental approaches that are used to develop new chemical entities for targeting the clinically relevant driver mutations are costly and high-risk. Drug repositioning, also known as drug repurposing, re-tasking or re-profiling, has been demonstrated as a promising strategy for drug discovery and development. Recently, computational techniques and methods have been proposed for oncology drug repositioning and identifying pharmacogenomics biomarkers, but overall progress remains to be seen. In this review, we focus on introducing new developments and advances of the individualized network-based drug repositioning approaches by targeting the clinically relevant driver events or molecular features derived from cancer panomics data for the development of precision oncology drug therapies (e.g. one-person trials) to fully realize the promise of precision medicine. We discuss several potential challenges (e.g. tumor heterogeneity and cancer subclones) for precision oncology. Finally, we highlight several new directions for the precision oncology drug discovery via biotherapies (e.g. gene therapy and immunotherapy) that target the 'undruggable' cancer genome in the functional genomics era.
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12
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Lee YH, Choi H, Park S, Lee B, Yi GS. Drug repositioning for enzyme modulator based on human metabolite-likeness. BMC Bioinformatics 2017; 18:226. [PMID: 28617219 PMCID: PMC5471945 DOI: 10.1186/s12859-017-1637-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Recently, the metabolite-likeness of the drug space has emerged and has opened a new possibility for exploring human metabolite-like candidates in drug discovery. However, the applicability of metabolite-likeness in drug discovery has been largely unexplored. Moreover, there are no reports on its applications for the repositioning of drugs to possible enzyme modulators, although enzyme-drug relations could be directly inferred from the similarity relationships between enzyme's metabolites and drugs. METHODS We constructed a drug-metabolite structural similarity matrix, which contains 1,861 FDA-approved drugs and 1,110 human intermediary metabolites scored with the Tanimoto similarity. To verify the metabolite-likeness measure for drug repositioning, we analyzed 17 known antimetabolite drugs that resemble the innate metabolites of their eleven target enzymes as the gold standard positives. Highly scored drugs were selected as possible modulators of enzymes for their corresponding metabolites. Then, we assessed the performance of metabolite-likeness with a receiver operating characteristic analysis and compared it with other drug-target prediction methods. We set the similarity threshold for drug repositioning candidates of new enzyme modulators based on maximization of the Youden's index. We also carried out literature surveys for supporting the drug repositioning results based on the metabolite-likeness. RESULTS In this paper, we applied metabolite-likeness to repurpose FDA-approved drugs to disease-associated enzyme modulators that resemble human innate metabolites. All antimetabolite drugs were mapped with their known 11 target enzymes with statistically significant similarity values to the corresponding metabolites. The comparison with other drug-target prediction methods showed the higher performance of metabolite-likeness for predicting enzyme modulators. After that, the drugs scored higher than similarity score of 0.654 were selected as possible modulators of enzymes for their corresponding metabolites. In addition, we showed that drug repositioning results of 10 enzymes were concordant with the literature evidence. CONCLUSIONS This study introduced a method to predict the repositioning of known drugs to possible modulators of disease associated enzymes using human metabolite-likeness. We demonstrated that this approach works correctly with known antimetabolite drugs and showed that the proposed method has better performance compared to other drug target prediction methods in terms of enzyme modulators prediction. This study as a proof-of-concept showed how to apply metabolite-likeness to drug repositioning as well as potential in further expansion as we acquire more disease associated metabolite-target protein relations.
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Affiliation(s)
- Yoon Hyeok Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, South Korea
| | - Hojae Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, South Korea
| | - Seongyong Park
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, South Korea
| | - Boah Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, South Korea
| | - Gwan-Su Yi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, South Korea.
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Drug repositioning based on triangularly balanced structure for tissue-specific diseases in incomplete interactome. Artif Intell Med 2017; 77:53-63. [DOI: 10.1016/j.artmed.2017.03.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 01/06/2017] [Accepted: 03/17/2017] [Indexed: 01/16/2023]
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14
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Liu Z, Fang H, Slikker W, Tong W. Potential Reuse of Oncology Drugs in the Treatment of Rare Diseases. Trends Pharmacol Sci 2016; 37:843-857. [DOI: 10.1016/j.tips.2016.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/27/2016] [Accepted: 06/30/2016] [Indexed: 12/23/2022]
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15
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Epithelial derived CTGF promotes breast tumor progression via inducing EMT and collagen I fibers deposition. Oncotarget 2016; 6:25320-38. [PMID: 26318291 PMCID: PMC4694834 DOI: 10.18632/oncotarget.4659] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/17/2015] [Indexed: 12/21/2022] Open
Abstract
Interactions among tumor cells, stromal cells, and extracellular matrix compositions are mediated through cytokines during tumor progression. Our analysis of 132 known cytokines and growth factors in published clinical breast cohorts and our 84 patient-derived xenograft models revealed that the elevated connective tissue growth factor (CTGF) in tumor epithelial cells significantly correlated with poor clinical prognosis and outcomes. CTGF was able to induce tumor cell epithelial-mesenchymal transition (EMT), and promote stroma deposition of collagen I fibers to stimulate tumor growth and metastasis. This process was mediated through CTGF-tumor necrosis factor receptor I (TNFR1)-IκB autocrine signaling. Drug treatments targeting CTGF, TNFR1, and IκB signaling each prohibited the EMT and tumor progression.
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16
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Yeu Y, Yoon Y, Park S. Protein localization vector propagation: a method for improving the accuracy of drug repositioning. MOLECULAR BIOSYSTEMS 2016; 11:2096-102. [PMID: 25998487 DOI: 10.1039/c5mb00306g] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Identifying alternative indications for known drugs is important for the pharmaceutical industry. Many computational methods have been proposed for predicting unknown associations between drugs and target proteins associated with diseases. To produce better prediction, researchers should not only develop accurate algorithms but identify good features that reflect intracellular systems. In this paper, we proposed a novel method for exploiting protein localization. We generated localization vectors (LVs) from protein localization and propagated LVs through a protein interaction network to increase the coverage of the localization information. The LVs showed distinct patterns among targets of known drugs as well as independent characteristics compared to existing features. Based on the experimental results, we determined that including LVs improves cross-validation accuracy and, produces better novel predictions with real and independent clinical trial data. Moreover, the propagation of LVs showed a positive result that it can help in increasing the coverage of the prediction results.
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Affiliation(s)
- Yunku Yeu
- Department of Computer Science, Yonsei Univertity, 50 Yonsei-Ro, SeoDaeMun-Gu, Seoul 120-749, Republic of Korea.
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17
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Choi DS, Blanco E, Kim YS, Rodriguez AA, Zhao H, Huang THM, Chen CL, Jin G, Landis MD, Burey LA, Qian W, Granados SM, Dave B, Wong HH, Ferrari M, Wong STC, Chang JC. Chloroquine eliminates cancer stem cells through deregulation of Jak2 and DNMT1. Stem Cells 2015; 32:2309-23. [PMID: 24809620 DOI: 10.1002/stem.1746] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 03/01/2014] [Accepted: 03/30/2014] [Indexed: 12/31/2022]
Abstract
Triple negative breast cancer (TNBC) is known to contain a high percentage of CD44(+) /CD24(-/low) cancer stem cells (CSCs), corresponding with a poor prognosis despite systemic chemotherapy. Chloroquine (CQ), an antimalarial drug, is a lysotropic reagent which inhibits autophagy. CQ was identified as a potential CSC inhibitor through in silico gene expression signature analysis of the CD44(+) /CD24(-/low) CSC population. Autophagy plays a critical role in adaptation to stress conditions in cancer cells, and is related with drug resistance and CSC maintenance. Thus, the objectives of this study were to examine the potential enhanced efficacy arising from addition of CQ to standard chemotherapy (paclitaxel) in TNBC and to identify the mechanism by which CQ eliminates CSCs in TNBCs. Herein, we report that CQ sensitizes TNBC cells to paclitaxel through inhibition of autophagy and reduces the CD44(+) /CD24(-/low) CSC population in both preclinical and clinical settings. Also, we are the first to report a mechanism by which CQ regulates the CSCs in TNBC through inhibition of the Janus-activated kinase 2 (Jak2)-signal transducer and activator of transcription 3 signaling pathway by reducing the expression of Jak2 and DNA methyltransferase 1.
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Affiliation(s)
- Dong Soon Choi
- Methodist Cancer Center, Houston Methodist Hospital, Houston, Texas, USA
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Ung MH, Varn FS, Cheng C. IDEA: Integrated Drug Expression Analysis-Integration of Gene Expression and Clinical Data for the Identification of Therapeutic Candidates. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2015; 4:415-25. [PMID: 26312165 PMCID: PMC4544055 DOI: 10.1002/psp4.51] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/30/2015] [Indexed: 12/14/2022]
Abstract
Cancer drug discovery is an involved process spanning efforts from several fields of study and typically requires years of research and development. However, the advent of high-throughput genomic technologies has allowed for the use of in silico, genomics-based methods to screen drug libraries and accelerate drug discovery. Here we present a novel approach to computationally identify drug candidates for the treatment of breast cancer. In particular, we developed a Drug Regulatory Score similarity metric to evaluate gene expression profile similarity, in the context of drug treatment, and incorporated time-to-event patient survival information to develop an integrated analysis pipeline: Integrated Drug Expression Analysis (IDEA). We were able to predict drug candidates that have been known and those that have not been known in the literature to exhibit anticancer effects. Overall, our method enables quick preclinical screening of drug candidates for breast cancer and other diseases by using the most important indicator of drug efficacy: survival.
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Affiliation(s)
- M H Ung
- Department of Genetics, Geisel School of Medicine at Dartmouth Hanover, New Hampshire, USA
| | - F S Varn
- Department of Genetics, Geisel School of Medicine at Dartmouth Hanover, New Hampshire, USA
| | - C Cheng
- Department of Genetics, Geisel School of Medicine at Dartmouth Hanover, New Hampshire, USA ; Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth Lebanon, New Hampshire, USA ; Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth Lebanon, New Hampshire, USA
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Repurposing medicinal compounds for blood cancer treatment. Ann Hematol 2015; 94:1267-76. [PMID: 26048243 PMCID: PMC4488459 DOI: 10.1007/s00277-015-2412-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 05/28/2015] [Indexed: 01/14/2023]
Abstract
Drug development is being continuously scrutinised for its lack of productivity. Novel drug development is associated with high costs, high failure rates and lengthy development process. These downfalls combined with a huge demand in blood cancer for new therapeutic treatments have led many to consider the method of drug repurposing. Finding new therapeutic indications for already established drug substances is known as redirecting, repositioning, reprofiling, or repurposing of drugs. Off-patent and on-patent drugs can be screened for additional targets and new indications thus bringing them to clinical trials at a faster pace. This approach offers smaller research groups, such as those that are academic based, into the drug development industry. Drug repurposing can make use of previously published data concerning dosage, toxicology and mechanism of activity.
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Abstract
Multicolored proteins have allowed the color-coding of cancer cells growing in vivo and enabled the distinction of host from tumor with single-cell resolution. Non-invasive imaging with fluorescent proteins enabled the dynamics of metastatic cancer to be followed in real time in individual animals. Non-invasive imaging of cancer cells expressing fluorescent proteins has allowed the real-time determination of efficacy of candidate antitumor and antimetastatic agents in mouse models. The use of fluorescent proteins to differentially label cancer cells in the nucleus and cytoplasm can visualize the nuclear-cytoplasmic dynamics of cancer cells in vivo including: mitosis, apoptosis, cell-cycle position, and differential behavior of nucleus and cytoplasm that occurs during cancer-cell deformation and extravasation. Recent applications of the technology described here include linking fluorescent proteins with cell-cycle-specific proteins such that the cells change color from red to green as they transit from G1 to S phases. With the macro- and micro-imaging technologies described here, essentially any in vivo process can be imaged, giving rise to the new field of in vivo cell biology using fluorescent proteins.
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Affiliation(s)
- Robert M. Hoffman
- AntiCancer, Inc., Dept. of Surgery, University of California San Diego
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Zhong R, Allen JD, Xiao G, Xie Y. Ensemble-based network aggregation improves the accuracy of gene network reconstruction. PLoS One 2014; 9:e106319. [PMID: 25390635 PMCID: PMC4229114 DOI: 10.1371/journal.pone.0106319] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Accepted: 08/01/2014] [Indexed: 11/19/2022] Open
Abstract
Reverse engineering approaches to constructing gene regulatory networks (GRNs) based on genome-wide mRNA expression data have led to significant biological findings, such as the discovery of novel drug targets. However, the reliability of the reconstructed GRNs needs to be improved. Here, we propose an ensemble-based network aggregation approach to improving the accuracy of network topologies constructed from mRNA expression data. To evaluate the performances of different approaches, we created dozens of simulated networks from combinations of gene-set sizes and sample sizes and also tested our methods on three Escherichia coli datasets. We demonstrate that the ensemble-based network aggregation approach can be used to effectively integrate GRNs constructed from different studies – producing more accurate networks. We also apply this approach to building a network from epithelial mesenchymal transition (EMT) signature microarray data and identify hub genes that might be potential drug targets. The R code used to perform all of the analyses is available in an R package entitled “ENA”, accessible on CRAN (http://cran.r-project.org/web/packages/ENA/).
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Affiliation(s)
- Rui Zhong
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Jeffrey D. Allen
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- * E-mail:
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Toward better drug repositioning: prioritizing and integrating existing methods into efficient pipelines. Drug Discov Today 2013; 19:637-44. [PMID: 24239728 DOI: 10.1016/j.drudis.2013.11.005] [Citation(s) in RCA: 248] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/07/2013] [Accepted: 11/06/2013] [Indexed: 01/04/2023]
Abstract
Recycling old drugs, rescuing shelved drugs and extending patents' lives make drug repositioning an attractive form of drug discovery. Drug repositioning accounts for approximately 30% of the newly US Food and Drug Administration (FDA)-approved drugs and vaccines in recent years. The prevalence of drug-repositioning studies has resulted in a variety of innovative computational methods for the identification of new opportunities for the use of old drugs. Questions often arise from customizing or optimizing these methods into efficient drug-repositioning pipelines for alternative applications. It requires a comprehensive understanding of the available methods gained by evaluating both biological and pharmaceutical knowledge and the elucidated mechanism-of-action of drugs. Here, we provide guidance for prioritizing and integrating drug-repositioning methods for specific drug-repositioning pipelines.
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