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2023 Beijing Health Data Science Summit. HEALTH DATA SCIENCE 2024; 4:0112. [PMID: 38854991 PMCID: PMC11157085 DOI: 10.34133/hds.0112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/05/2023] [Indexed: 06/11/2024]
Abstract
The 5th annual Beijing Health Data Science Summit, organized by the National Institute of Health Data Science at Peking University, recently concluded with resounding success. This year, the summit aimed to foster collaboration among researchers, practitioners, and stakeholders in the field of health data science to advance the use of data for better health outcomes. One significant highlight of this year's summit was the introduction of the Abstract Competition, organized by Health Data Science, a Science Partner Journal, which focused on the use of cutting-edge data science methodologies, particularly the application of artificial intelligence in the healthcare scenarios. The competition provided a platform for researchers to showcase their groundbreaking work and innovations. In total, the summit received 61 abstract submissions. Following a rigorous evaluation process by the Abstract Review Committee, eight exceptional abstracts were selected to compete in the final round and give presentations in the Abstract Competition. The winners of the Abstract Competition are as follows:•First Prize: "Interpretable Machine Learning for Predicting Outcomes of Childhood Kawasaki Disease: Electronic Health Record Analysis" presented by researchers from the Chinese Academy of Medical Sciences, Peking Union Medical College, and Chongqing Medical University (presenter Yifan Duan).•Second Prize: "Survival Disparities among Mobility Patterns of Patients with Cancer: A Population-Based Study" presented by a team from Peking University (presenter Fengyu Wen).•Third Prize: "Deep Learning-Based Real-Time Predictive Model for the Development of Acute Stroke" presented by researchers from Beijing Tiantan Hospital (presenter Lan Lan). We extend our heartfelt gratitude to the esteemed panel of judges whose expertise and dedication ensured the fairness and quality of the competition. The judging panel included Jiebo Luo from the University of Rochester (chair), Shenda Hong from Peking University, Xiaozhong Liu from Worcester Polytechnic Institute, Liu Yang from Hong Kong Baptist University, Ma Jianzhu from Tsinghua University, Ting Ma from Harbin Institute of Technology, and Jian Tang from Mila-Quebec Artificial Intelligence Institute. We wish to convey our deep appreciation to Zixuan He and Haoyang Hong for their invaluable assistance in the meticulous planning and execution of the event. As the 2023 Beijing Health Data Science Summit comes to a close, we look forward to welcoming all participants to join us in 2024. Together, we will continue to advance the frontiers of health data science and work toward a healthier future for all.
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Kim Y, Han Y, Hopper C, Lee J, Joo JI, Gong JR, Lee CK, Jang SH, Kang J, Kim T, Cho KH. A gray box framework that optimizes a white box logical model using a black box optimizer for simulating cellular responses to perturbations. CELL REPORTS METHODS 2024; 4:100773. [PMID: 38744288 PMCID: PMC11133856 DOI: 10.1016/j.crmeth.2024.100773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 03/19/2024] [Accepted: 04/19/2024] [Indexed: 05/16/2024]
Abstract
Predicting cellular responses to perturbations requires interpretable insights into molecular regulatory dynamics to perform reliable cell fate control, despite the confounding non-linearity of the underlying interactions. There is a growing interest in developing machine learning-based perturbation response prediction models to handle the non-linearity of perturbation data, but their interpretation in terms of molecular regulatory dynamics remains a challenge. Alternatively, for meaningful biological interpretation, logical network models such as Boolean networks are widely used in systems biology to represent intracellular molecular regulation. However, determining the appropriate regulatory logic of large-scale networks remains an obstacle due to the high-dimensional and discontinuous search space. To tackle these challenges, we present a scalable derivative-free optimizer trained by meta-reinforcement learning for Boolean network models. The logical network model optimized by the trained optimizer successfully predicts anti-cancer drug responses of cancer cell lines, while simultaneously providing insight into their underlying molecular regulatory mechanisms.
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Affiliation(s)
- Yunseong Kim
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Younghyun Han
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Corbin Hopper
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jonghoon Lee
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jae Il Joo
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jeong-Ryeol Gong
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Chun-Kyung Lee
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Seong-Hoon Jang
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Junsoo Kang
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Taeyoung Kim
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Kwang-Hyun Cho
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
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Caba K, Tran-Nguyen VK, Rahman T, Ballester PJ. Comprehensive machine learning boosts structure-based virtual screening for PARP1 inhibitors. J Cheminform 2024; 16:40. [PMID: 38582911 PMCID: PMC10999096 DOI: 10.1186/s13321-024-00832-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/23/2024] [Indexed: 04/08/2024] Open
Abstract
Poly ADP-ribose polymerase 1 (PARP1) is an attractive therapeutic target for cancer treatment. Machine-learning scoring functions constitute a promising approach to discovering novel PARP1 inhibitors. Cutting-edge PARP1-specific machine-learning scoring functions were investigated using semi-synthetic training data from docking activity-labelled molecules: known PARP1 inhibitors, hard-to-discriminate decoys property-matched to them with generative graph neural networks and confirmed inactives. We further made test sets harder by including only molecules dissimilar to those in the training set. Comprehensive analysis of these datasets using five supervised learning algorithms, and protein-ligand fingerprints extracted from docking poses and ligand only features revealed one highly predictive scoring function. This is the PARP1-specific support vector machine-based regressor, when employing PLEC fingerprints, which achieved a high Normalized Enrichment Factor at the top 1% on the hardest test set (NEF1% = 0.588, median of 10 repetitions), and was more predictive than any other investigated scoring function, especially the classical scoring function employed as baseline.
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Affiliation(s)
- Klaudia Caba
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Viet-Khoa Tran-Nguyen
- Unité de Biologie Fonctionnelle et Adaptative (BFA), UFR Sciences du Vivant, Université Paris Cité, 75013, Paris, France
| | - Taufiq Rahman
- Department of Pharmacology, University of Cambridge, Cambridge, CB2 1PD, UK
| | - Pedro J Ballester
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
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Vasanthakumari P, Zhu Y, Brettin T, Partin A, Shukla M, Xia F, Narykov O, Weil MR, Stevens RL. A Comprehensive Investigation of Active Learning Strategies for Conducting Anti-Cancer Drug Screening. Cancers (Basel) 2024; 16:530. [PMID: 38339281 PMCID: PMC10854925 DOI: 10.3390/cancers16030530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/12/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
It is well-known that cancers of the same histology type can respond differently to a treatment. Thus, computational drug response prediction is of paramount importance for both preclinical drug screening studies and clinical treatment design. To build drug response prediction models, treatment response data need to be generated through screening experiments and used as input to train the prediction models. In this study, we investigate various active learning strategies of selecting experiments to generate response data for the purposes of (1) improving the performance of drug response prediction models built on the data and (2) identifying effective treatments. Here, we focus on constructing drug-specific response prediction models for cancer cell lines. Various approaches have been designed and applied to select cell lines for screening, including a random, greedy, uncertainty, diversity, combination of greedy and uncertainty, sampling-based hybrid, and iteration-based hybrid approach. All of these approaches are evaluated and compared using two criteria: (1) the number of identified hits that are selected experiments validated to be responsive, and (2) the performance of the response prediction model trained on the data of selected experiments. The analysis was conducted for 57 drugs and the results show a significant improvement on identifying hits using active learning approaches compared with the random and greedy sampling method. Active learning approaches also show an improvement on response prediction performance for some of the drugs and analysis runs compared with the greedy sampling method.
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Affiliation(s)
- Priyanka Vasanthakumari
- Division of Data Science and Learning, Argonne National Laboratory, Lemont, IL 60439, USA; (Y.Z.); (A.P.); (M.S.); (F.X.); (O.N.)
| | - Yitan Zhu
- Division of Data Science and Learning, Argonne National Laboratory, Lemont, IL 60439, USA; (Y.Z.); (A.P.); (M.S.); (F.X.); (O.N.)
| | - Thomas Brettin
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, IL 60439, USA; (T.B.); (R.L.S.)
| | - Alexander Partin
- Division of Data Science and Learning, Argonne National Laboratory, Lemont, IL 60439, USA; (Y.Z.); (A.P.); (M.S.); (F.X.); (O.N.)
| | - Maulik Shukla
- Division of Data Science and Learning, Argonne National Laboratory, Lemont, IL 60439, USA; (Y.Z.); (A.P.); (M.S.); (F.X.); (O.N.)
| | - Fangfang Xia
- Division of Data Science and Learning, Argonne National Laboratory, Lemont, IL 60439, USA; (Y.Z.); (A.P.); (M.S.); (F.X.); (O.N.)
| | - Oleksandr Narykov
- Division of Data Science and Learning, Argonne National Laboratory, Lemont, IL 60439, USA; (Y.Z.); (A.P.); (M.S.); (F.X.); (O.N.)
| | - Michael Ryan Weil
- Cancer Research Technology Program, Cancer Data Science Initiatives, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA;
| | - Rick L. Stevens
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, IL 60439, USA; (T.B.); (R.L.S.)
- Department of Computer Science, The University of Chicago, Chicago, IL 60637, USA
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Ogunleye A, Piyawajanusorn C, Ghislat G, Ballester PJ. Large-Scale Machine Learning Analysis Reveals DNA Methylation and Gene Expression Response Signatures for Gemcitabine-Treated Pancreatic Cancer. HEALTH DATA SCIENCE 2024; 4:0108. [PMID: 38486621 PMCID: PMC10904073 DOI: 10.34133/hds.0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 12/08/2023] [Indexed: 03/17/2024]
Abstract
Background: Gemcitabine is a first-line chemotherapy for pancreatic adenocarcinoma (PAAD), but many PAAD patients do not respond to gemcitabine-containing treatments. Being able to predict such nonresponders would hence permit the undelayed administration of more promising treatments while sparing gemcitabine life-threatening side effects for those patients. Unfortunately, the few predictors of PAAD patient response to this drug are weak, none of them exploiting yet the power of machine learning (ML). Methods: Here, we applied ML to predict the response of PAAD patients to gemcitabine from the molecular profiles of their tumors. More concretely, we collected diverse molecular profiles of PAAD patient tumors along with the corresponding clinical data (gemcitabine responses and clinical features) from the Genomic Data Commons resource. From systematically combining 8 tumor profiles with 16 classification algorithms, each of the resulting 128 ML models was evaluated by multiple 10-fold cross-validations. Results: Only 7 of these 128 models were predictive, which underlines the importance of carrying out such a large-scale analysis to avoid missing the most predictive models. These were here random forest using 4 selected mRNAs [0.44 Matthews correlation coefficient (MCC), 0.785 receiver operating characteristic-area under the curve (ROC-AUC)] and XGBoost combining 12 DNA methylation probes (0.32 MCC, 0.697 ROC-AUC). By contrast, the hENT1 marker obtained much worse random-level performance (practically 0 MCC, 0.5 ROC-AUC). Despite not being trained to predict prognosis (overall and progression-free survival), these ML models were also able to anticipate this patient outcome. Conclusions: We release these promising ML models so that they can be evaluated prospectively on other gemcitabine-treated PAAD patients.
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Affiliation(s)
- Adeolu Ogunleye
- Department of Organismal Biology,
Uppsala University, Uppsala, Sweden
| | | | - Ghita Ghislat
- Department of Life Sciences,
Imperial College London, London, UK
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Park A, Lee Y, Nam S. A performance evaluation of drug response prediction models for individual drugs. Sci Rep 2023; 13:11911. [PMID: 37488424 PMCID: PMC10366128 DOI: 10.1038/s41598-023-39179-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 07/20/2023] [Indexed: 07/26/2023] Open
Abstract
Drug response prediction is important to establish personalized medicine for cancer therapy. Model construction for predicting drug response (i.e., cell viability half-maximal inhibitory concentration [IC50]) of an individual drug by inputting pharmacogenomics in disease models remains critical. Machine learning (ML) has been predominantly applied for prediction, despite the advent of deep learning (DL). Moreover, whether DL or traditional ML models are superior for predicting cell viability IC50s has to be established. Herein, we constructed ML and DL drug response prediction models for 24 individual drugs and compared the performance of the models by employing gene expression and mutation profiles of cancer cell lines as input. We observed no significant difference in drug response prediction performance between DL and ML models for 24 drugs [root mean squared error (RMSE) ranging from 0.284 to 3.563 for DL and from 0.274 to 2.697 for ML; R2 ranging from -7.405 to 0.331 for DL and from -8.113 to 0.470 for ML]. Among the 24 individual drugs, the ridge model of panobinostat exhibited the best performance (R2 0.470 and RMSE 0.623). Thus, we selected the ridge model of panobinostat for further application of explainable artificial intelligence (XAI). Using XAI, we further identified important genomic features for panobinostat response prediction in the ridge model, suggesting the genomic features of 22 genes. Based on our findings, results for an individual drug employing both DL and ML models were comparable. Our study confirms the applicability of drug response prediction models for individual drugs.
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Affiliation(s)
- Aron Park
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Gachon University, Incheon, 21999, Republic of Korea
| | - Yeeun Lee
- Department of Genome Medicine and Science, AI Convergence Center for Medical Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon, 21565, Republic of Korea
| | - Seungyoon Nam
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Gachon University, Incheon, 21999, Republic of Korea.
- Department of Genome Medicine and Science, AI Convergence Center for Medical Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon, 21565, Republic of Korea.
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Johnson KB, Sharma A, Henry NL, Wei M, Bie B, Hershberger CE, Rhoades EE, Sen A, Johnson RE, Steenblik J, Hockings J, Budd GT, Eng C, Foss J, Rotroff DM. Genetic variations that influence paclitaxel pharmacokinetics and intracellular effects that may contribute to chemotherapy-induced neuropathy: A narrative review. FRONTIERS IN PAIN RESEARCH 2023; 4:1139883. [PMID: 37251592 PMCID: PMC10214418 DOI: 10.3389/fpain.2023.1139883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 04/05/2023] [Indexed: 05/31/2023] Open
Abstract
Taxanes, particularly paclitaxel and docetaxel, are chemotherapeutic agents commonly used to treat breast cancers. A frequent side effect is chemotherapy-induced peripheral neuropathy (CIPN) that occurs in up to 70% of all treated patients and impacts the quality of life during and after treatment. CIPN presents as glove and stocking sensory deficits and diminished motor and autonomic function. Nerves with longer axons are at higher risk of developing CIPN. The causes of CIPN are multifactorial and poorly understood, limiting treatment options. Pathophysiologic mechanisms can include: (i) disruptions of mitochondrial and intracellular microtubule functions, (ii) disruption of axon morphology, and (iii) activation of microglial and other immune cell responses, among others. Recent work has explored the contribution of genetic variation and selected epigenetic changes in response to taxanes for any insights into their relation to pathophysiologic mechanisms of CIPN20, with the hope of identifying predictive and targetable biomarkers. Although promising, many genetic studies of CIPN are inconsistent making it difficult to develop reliable biomarkers of CIPN. The aims of this narrative review are to benchmark available evidence and identify gaps in the understanding of the role genetic variation has in influencing paclitaxel's pharmacokinetics and cellular membrane transport potentially related to the development of CIPN.
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Affiliation(s)
- Ken B. Johnson
- Department of Anesthesiology, University of Utah, Salt Lake City, UT, United States
| | - Anukriti Sharma
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - N. Lynn Henry
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Mei Wei
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, United States
| | - Bihua Bie
- Department of Anesthesiology, Cleveland Clinic, Cleveland, OH, United States
| | - Courtney E. Hershberger
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Emily E. Rhoades
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Alper Sen
- Department of Anesthesiology, University of Utah, Salt Lake City, UT, United States
| | - Ryan E. Johnson
- Department of Anesthesiology, University of Utah, Salt Lake City, UT, United States
| | - Jacob Steenblik
- Department of Anesthesiology, University of Utah, Salt Lake City, UT, United States
| | - Jennifer Hockings
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
- Department of Pharmacy, Cleveland Clinic, Cleveland, OH, United States
| | - G. Thomas Budd
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Joseph Foss
- Department of Anesthesiology, Cleveland Clinic, Cleveland, OH, United States
| | - Daniel M. Rotroff
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
- Endocrinology and Metabolism Institute, Cleveland Clinic, Cleveland, OH, United States
- Center for Quantitative Metabolic Research, Cleveland Clinic, Cleveland, OH, United States
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Smith DA, Sadler MC, Altman RB. Promises and challenges in pharmacoepigenetics. CAMBRIDGE PRISMS. PRECISION MEDICINE 2023; 1:e18. [PMID: 37560024 PMCID: PMC10406571 DOI: 10.1017/pcm.2023.6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 08/11/2023]
Abstract
Pharmacogenetics, the study of how interindividual genetic differences affect drug response, does not explain all observed heritable variance in drug response. Epigenetic mechanisms, such as DNA methylation, and histone acetylation may account for some of the unexplained variances. Epigenetic mechanisms modulate gene expression and can be suitable drug targets and can impact the action of nonepigenetic drugs. Pharmacoepigenetics is the field that studies the relationship between epigenetic variability and drug response. Much of this research focuses on compounds targeting epigenetic mechanisms, called epigenetic drugs, which are used to treat cancers, immune disorders, and other diseases. Several studies also suggest an epigenetic role in classical drug response; however, we know little about this area. The amount of information correlating epigenetic biomarkers to molecular datasets has recently expanded due to technological advances, and novel computational approaches have emerged to better identify and predict epigenetic interactions. We propose that the relationship between epigenetics and classical drug response may be examined using data already available by (1) finding regions of epigenetic variance, (2) pinpointing key epigenetic biomarkers within these regions, and (3) mapping these biomarkers to a drug-response phenotype. This approach expands on existing knowledge to generate putative pharmacoepigenetic relationships, which can be tested experimentally. Epigenetic modifications are involved in disease and drug response. Therefore, understanding how epigenetic drivers impact the response to classical drugs is important for improving drug design and administration to better treat disease.
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Affiliation(s)
- Delaney A Smith
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Marie C Sadler
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- University Center for Primary Care and Public Health, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Russ B Altman
- Department of Bioengineering, Stanford University, Stanford, CA, USA
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Shin SY, Centenera MM, Hodgson JT, Nguyen EV, Butler LM, Daly RJ, Nguyen LK. A Boolean-based machine learning framework identifies predictive biomarkers of HSP90-targeted therapy response in prostate cancer. Front Mol Biosci 2023; 10:1094321. [PMID: 36743211 PMCID: PMC9892654 DOI: 10.3389/fmolb.2023.1094321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/06/2023] [Indexed: 01/20/2023] Open
Abstract
Precision medicine has emerged as an important paradigm in oncology, driven by the significant heterogeneity of individual patients' tumour. A key prerequisite for effective implementation of precision oncology is the development of companion biomarkers that can predict response to anti-cancer therapies and guide patient selection for clinical trials and/or treatment. However, reliable predictive biomarkers are currently lacking for many anti-cancer therapies, hampering their clinical application. Here, we developed a novel machine learning-based framework to derive predictive multi-gene biomarker panels and associated expression signatures that accurately predict cancer drug sensitivity. We demonstrated the power of the approach by applying it to identify response biomarker panels for an Hsp90-based therapy in prostate cancer, using proteomic data profiled from prostate cancer patient-derived explants. Our approach employs a rational feature section strategy to maximise model performance, and innovatively utilizes Boolean algebra methods to derive specific expression signatures of the marker proteins. Given suitable data for model training, the approach is also applicable to other cancer drug agents in different tumour settings.
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Affiliation(s)
- Sung-Young Shin
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia,Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia,*Correspondence: Sung-Young Shin, ; Lan K. Nguyen,
| | - Margaret M. Centenera
- South Australian Immunogenomics Cancer Institute and Freemasons Foundation Centre for Men’s Health, University of Adelaide, Adelaide, SA, Australia,South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Joshua T. Hodgson
- South Australian Immunogenomics Cancer Institute and Freemasons Foundation Centre for Men’s Health, University of Adelaide, Adelaide, SA, Australia,South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Elizabeth V. Nguyen
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia,Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Lisa M. Butler
- South Australian Immunogenomics Cancer Institute and Freemasons Foundation Centre for Men’s Health, University of Adelaide, Adelaide, SA, Australia,South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Roger J. Daly
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia,Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Lan K. Nguyen
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia,Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia,*Correspondence: Sung-Young Shin, ; Lan K. Nguyen,
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Du J, Huang M, Liu L. AI-Aided Disease Prediction in Visualized Medicine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1199:107-126. [PMID: 37460729 DOI: 10.1007/978-981-32-9902-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Artificial intelligence (AI) is playing a vitally important role in promoting the revolution of future technology. Healthcare is one of the promising applications in AI, which covers medical imaging, diagnosis, robotics, disease prediction, pharmacy, health management, and hospital management. Numbers of achievements that made in these fields overturn every aspect in traditional healthcare system. Therefore, to understand the state-of-art AI in healthcare, as well as the chances and obstacles in its development, the applications of AI in disease detection and outlook and the future trends of AI-aided disease prediction were discussed in this chapter.
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Affiliation(s)
- Juan Du
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China.
| | - Mengen Huang
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Lin Liu
- Tianjin Key Laboratory of Retinal Functions and Diseases, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
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Systematic Analysis of Genetic and Pathway Determinants of Eribulin Sensitivity across 100 Human Cancer Cell Lines from the Cancer Cell Line Encyclopedia (CCLE). Cancers (Basel) 2022; 14:cancers14184532. [PMID: 36139690 PMCID: PMC9496846 DOI: 10.3390/cancers14184532] [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: 08/12/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
Eribulin, a natural product-based microtubule targeting agent with cytotoxic and noncytotoxic mechanisms, is FDA approved for certain patients with advanced breast cancer and liposarcoma. To investigate the feasibility of developing drug-specific predictive biomarkers, we quantified antiproliferative activities of eribulin versus paclitaxel and vinorelbine against 100 human cancer cell lines from the Cancer Cell Line Encyclopedia, and correlated results with publicly available databases to identify genes and pathways associated with eribulin response, either uniquely or shared with paclitaxel or vinorelbine. Mean expression ratios of 11,985 genes between the most and least sensitive cell line quartiles were sorted by p-values and drug overlaps, yielding 52, 29 and 80 genes uniquely associated with eribulin, paclitaxel and vinorelbine, respectively. Further restriction to minimum 2-fold ratios followed by reintroducing data from the middle two quartiles identified 9 and 13 drug-specific unique fingerprint genes for eribulin and vinorelbine, respectively; surprisingly, no gene met all criteria for paclitaxel. Interactome and Reactome pathway analyses showed that unique fingerprint genes of both drugs were primarily associated with cellular signaling, not microtubule-related pathways, although considerable differences existed in individual pathways identified. Finally, four-gene (C5ORF38, DAAM1, IRX2, CD70) and five-gene (EPHA2, NGEF, SEPTIN10, TRIP10, VSIG10) multivariate regression models for eribulin and vinorelbine showed high statistical correlation with drug-specific responses across the 100 cell lines and accurately calculated predicted mean IC50s for the most and least sensitive cell line quartiles as surrogates for responders and nonresponders, respectively. Collectively, these results provide a foundation for developing drug-specific predictive biomarkers for eribulin and vinorelbine.
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Ogunleye AZ, Piyawajanusorn C, Gonçalves A, Ghislat G, Ballester PJ. Interpretable Machine Learning Models to Predict the Resistance of Breast Cancer Patients to Doxorubicin from Their microRNA Profiles. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2201501. [PMID: 35785523 PMCID: PMC9403644 DOI: 10.1002/advs.202201501] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/02/2022] [Indexed: 05/05/2023]
Abstract
Doxorubicin is a common treatment for breast cancer. However, not all patients respond to this drug, which sometimes causes life-threatening side effects. Accurately anticipating doxorubicin-resistant patients would therefore permit to spare them this risk while considering alternative treatments without delay. Stratifying patients based on molecular markers in their pretreatment tumors is a promising approach to advance toward this ambitious goal, but single-gene gene markers such as HER2 expression have not shown to be sufficiently predictive. The recent availability of matched doxorubicin-response and diverse molecular profiles across breast cancer patients permits now analysis at a much larger scale. 16 machine learning algorithms and 8 molecular profiles are systematically evaluated on the same cohort of patients. Only 2 of the 128 resulting models are substantially predictive, showing that they can be easily missed by a standard-scale analysis. The best model is classification and regression tree (CART) nonlinearly combining 4 selected miRNA isoforms to predict doxorubicin response (median Matthew correlation coefficient (MCC) and area under the curve (AUC) of 0.56 and 0.80, respectively). By contrast, HER2 expression is significantly less predictive (median MCC and AUC of 0.14 and 0.57, respectively). As the predictive accuracy of this CART model increases with larger training sets, its update with future data should result in even better accuracy.
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Affiliation(s)
- Adeolu Z. Ogunleye
- Cancer Research Center of Marseille (CRCM)INSERM U1068MarseilleF‐13009France
- Cancer Research Center of Marseille (CRCM)Institut Paoli‐CalmettesMarseilleF‐13009France
- Cancer Research Center of Marseille (CRCM)Aix‐Marseille UniversitéMarseilleF‐13284France
- Cancer Research Center of Marseille (CRCM)CNRS UMR7258MarseilleF‐13009France
| | - Chayanit Piyawajanusorn
- Cancer Research Center of Marseille (CRCM)INSERM U1068MarseilleF‐13009France
- Cancer Research Center of Marseille (CRCM)Institut Paoli‐CalmettesMarseilleF‐13009France
- Cancer Research Center of Marseille (CRCM)Aix‐Marseille UniversitéMarseilleF‐13284France
- Cancer Research Center of Marseille (CRCM)CNRS UMR7258MarseilleF‐13009France
| | - Anthony Gonçalves
- Cancer Research Center of Marseille (CRCM)INSERM U1068MarseilleF‐13009France
- Cancer Research Center of Marseille (CRCM)Institut Paoli‐CalmettesMarseilleF‐13009France
- Cancer Research Center of Marseille (CRCM)Aix‐Marseille UniversitéMarseilleF‐13284France
- Cancer Research Center of Marseille (CRCM)CNRS UMR7258MarseilleF‐13009France
| | - Ghita Ghislat
- Cancer Research Center of Marseille (CRCM)INSERM U1068MarseilleF‐13009France
- Cancer Research Center of Marseille (CRCM)Institut Paoli‐CalmettesMarseilleF‐13009France
- Cancer Research Center of Marseille (CRCM)Aix‐Marseille UniversitéMarseilleF‐13284France
- Cancer Research Center of Marseille (CRCM)CNRS UMR7258MarseilleF‐13009France
| | - Pedro J. Ballester
- Cancer Research Center of Marseille (CRCM)INSERM U1068MarseilleF‐13009France
- Cancer Research Center of Marseille (CRCM)Institut Paoli‐CalmettesMarseilleF‐13009France
- Cancer Research Center of Marseille (CRCM)Aix‐Marseille UniversitéMarseilleF‐13284France
- Cancer Research Center of Marseille (CRCM)CNRS UMR7258MarseilleF‐13009France
- Department of BioengineeringImperial College LondonLondonSW7 2AZUK
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13
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Rodrigues-Ferreira S, Nahmias C. Predictive biomarkers for personalized medicine in breast cancer. Cancer Lett 2022; 545:215828. [PMID: 35853538 DOI: 10.1016/j.canlet.2022.215828] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 07/04/2022] [Accepted: 07/10/2022] [Indexed: 12/14/2022]
Abstract
Breast cancer is one of the most frequent malignancies among women worldwide. Based on clinical and molecular features of breast tumors, patients are treated with chemotherapy, hormonal therapy and/or radiotherapy and more recently with immunotherapy or targeted therapy. These different therapeutic options have markedly improved patient outcomes. However, further improvement is needed to fight against resistance to treatment. In the rapidly growing area of research for personalized medicine, predictive biomarkers - which predict patient response to therapy - are essential tools to select the patients who are most likely to benefit from the treatment, with the aim to give the right therapy to the right patient and avoid unnecessary overtreatment. The search for predictive biomarkers is an active field of research that includes genomic, proteomic and/or machine learning approaches. In this review, we describe current strategies and innovative tools to identify, evaluate and validate new biomarkers. We also summarize current predictive biomarkers in breast cancer and discuss companion biomarkers of targeted therapy in the context of precision medicine.
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Affiliation(s)
- Sylvie Rodrigues-Ferreira
- Gustave Roussy Institute, INSERM U981, Prédicteurs moléculaires et nouvelles cibles en oncologie, Villejuif, France; LabEx LERMIT, Université Paris-Saclay, 92296 Châtenay-Malabry, France; Inovarion, 75005, Paris, France
| | - Clara Nahmias
- Gustave Roussy Institute, INSERM U981, Prédicteurs moléculaires et nouvelles cibles en oncologie, Villejuif, France; LabEx LERMIT, Université Paris-Saclay, 92296 Châtenay-Malabry, France.
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14
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Park A, Joo M, Kim K, Son WJ, Lim G, Lee J, Kim JH, Lee DH, Nam S. A comprehensive evaluation of regression-based drug responsiveness prediction models, using cell viability inhibitory concentrations (IC50 values). Bioinformatics 2022; 38:2810-2817. [PMID: 35561188 DOI: 10.1093/bioinformatics/btac177] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 03/06/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Predicting drug response is critical for precision medicine. Diverse methods have predicted drug responsiveness, as measured by the half-maximal drug inhibitory concentration (IC50), in cultured cells. Although IC50s are continuous, traditional prediction models have dealt mainly with binary classification of responsiveness. However, since there are few regression-based IC50 predictions, comprehensive evaluations of regression-based IC50 prediction models, including machine learning (ML) and deep learning (DL), for diverse data types and dataset sizes, have not been addressed. RESULTS Here, we constructed 11 input data settings, including multi-omics settings, with varying dataset sizes, then evaluated the performance of regression-based ML and DL models to predict IC50s. DL models considered two convolutional neural network architectures: CDRScan and residual neural network (ResNet). ResNet was introduced in regression-based DL models for predicting drug response for the first time. As a result, DL models performed better than ML models in all the settings. Also, ResNet performed better than or comparable to CDRScan and ML models in all settings. AVAILABILITY AND IMPLEMENTATION The data underlying this article are available in GitHub at https://github.com/labnams/IC50evaluation. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Aron Park
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Gachon University, Incheon 21999, Korea
| | - Minjae Joo
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Gachon University, Incheon 21999, Korea
| | | | - Won-Joon Son
- Samsung Advanced Institute of Technology, Samsung Electronics, Suwon, Gyeonggi-do 16678, Korea
| | - GyuTae Lim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Jinhyuk Lee
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Bioinformatics, University of Sciences and Technology, Daejeon 34113, Korea
| | - Jung Ho Kim
- Department of Internal Medicine, Gachon University Gil Medical Center, Gachon University School of Medicine, Incheon 21565, Korea
| | - Dae Ho Lee
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Gachon University, Incheon 21999, Korea
- Department of Internal Medicine, Gachon University Gil Medical Center, Gachon University School of Medicine, Incheon 21565, Korea
| | - Seungyoon Nam
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Gachon University, Incheon 21999, Korea
- AI Convergence Center for Medical Science, Department of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Korea
- Department of Life Sciences, Gachon University, Seongnam, Gyeonggi-do 13120, Korea
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15
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Cho H, Tong F, You S, Jung S, Kim WH, Kim J. Prediction of the Immune Phenotypes of Bladder Cancer Patients for Precision Oncology. IEEE OPEN JOURNAL OF ENGINEERING IN MEDICINE AND BIOLOGY 2022; 3:47-57. [PMID: 35519421 PMCID: PMC9060513 DOI: 10.1109/ojemb.2022.3163533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/27/2022] [Accepted: 03/19/2022] [Indexed: 11/11/2022] Open
Abstract
Bladder cancer (BC) is the most common urinary malignancy; however accurate diagnosis and prediction of recurrence after therapies remain elusive. This study aimed to develop a biosignature of immunotherapy-based responses using gene expression data. Publicly available BC datasets were collected, and machine learning (ML) approaches were applied to identify a novel biosignature to differentiate patient subgroups. Immune phenotyping of BC in the IMvigor210 dataset included three subtypes: inflamed, excluded, and desert immune. Immune phenotypes were analyzed with gene expressions using traditional but powerful classification methods such as random forests, Deep Neural Networks (DNN), Support Vector Machines (SVM) together with boosting and feature selection methods. Specifically, DNN yielded the highest area under the curve (AUC) with precision and recall (PR) curves and receiver operating characteristic (ROC) curves for each phenotype ([Formula: see text] and [Formula: see text], respectively) resulting in the identification of gene expression features useful for immune phenotype classification. Our results suggest significant potential to further develop and utilize machine learning algorithms for analysis of BC and its precaution. In conclusion, the findings from this study present a novel gene expression assay that can accurately discriminate BC patients from controls. Upon further validation in independent cohorts, this gene signature could be developed into a predictive test that can support clinical evaluation and patient care.
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Affiliation(s)
- Hyuna Cho
- Graduate School of Artificial Intelligence (GSAI)Pohang University of Science and TechnologyPohang37673South Korea
| | - Feng Tong
- Department of Computer Science and EngineeringUniversity of Texas at ArlingtonArlingtonTX76019USA
| | - Sungyong You
- Department of Surgery and Biomedical SciencesCedars-Sinai Medical CenterLos AngelesCA90048USA
| | - Sungyoung Jung
- Department of Electrical EngineeringUniversity of Texas at ArlingtonArlingtonTX76019USA
| | - Won Hwa Kim
- Graduate School of Artificial Intelligence (GSAI)Pohang University of Science and TechnologyPohang37673South Korea
- Department of Computer Science and EngineeringUniversity of Texas at ArlingtonArlingtonTX76019USA
- Department of Computer Science and EngineeringPohang University of Science and TechnologyPohang37673South Korea
| | - Jayoung Kim
- Department of Surgery and Biomedical SciencesCedars-Sinai Medical CenterLos AngelesCA90048USA
- Department of MedicineUniversity of California Los AngelesLos AngelesCA90095USA
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16
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Xia F, Allen J, Balaprakash P, Brettin T, Garcia-Cardona C, Clyde A, Cohn J, Doroshow J, Duan X, Dubinkina V, Evrard Y, Fan YJ, Gans J, He S, Lu P, Maslov S, Partin A, Shukla M, Stahlberg E, Wozniak JM, Yoo H, Zaki G, Zhu Y, Stevens R. A cross-study analysis of drug response prediction in cancer cell lines. Brief Bioinform 2022; 23:bbab356. [PMID: 34524425 PMCID: PMC8769697 DOI: 10.1093/bib/bbab356] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/26/2021] [Accepted: 08/11/2021] [Indexed: 11/28/2022] Open
Abstract
To enable personalized cancer treatment, machine learning models have been developed to predict drug response as a function of tumor and drug features. However, most algorithm development efforts have relied on cross-validation within a single study to assess model accuracy. While an essential first step, cross-validation within a biological data set typically provides an overly optimistic estimate of the prediction performance on independent test sets. To provide a more rigorous assessment of model generalizability between different studies, we use machine learning to analyze five publicly available cell line-based data sets: National Cancer Institute 60, ancer Therapeutics Response Portal (CTRP), Genomics of Drug Sensitivity in Cancer, Cancer Cell Line Encyclopedia and Genentech Cell Line Screening Initiative (gCSI). Based on observed experimental variability across studies, we explore estimates of prediction upper bounds. We report performance results of a variety of machine learning models, with a multitasking deep neural network achieving the best cross-study generalizability. By multiple measures, models trained on CTRP yield the most accurate predictions on the remaining testing data, and gCSI is the most predictable among the cell line data sets included in this study. With these experiments and further simulations on partial data, two lessons emerge: (1) differences in viability assays can limit model generalizability across studies and (2) drug diversity, more than tumor diversity, is crucial for raising model generalizability in preclinical screening.
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Affiliation(s)
| | | | | | | | | | - Austin Clyde
- Argonne National Laboratory
- University of Chicago
| | | | | | | | | | | | - Ya Ju Fan
- Lawrence Livermore National Laboratory
| | | | | | - Pinyi Lu
- Frederick National Laboratory for Cancer Research
| | | | | | | | | | | | | | - George Zaki
- Frederick National Laboratory for Cancer Research
| | | | - Rick Stevens
- Argonne National Laboratory
- University of Chicago
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17
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Bacolod MD, Fisher PB, Barany F. Multi-CpG linear regression models to accurately predict paclitaxel and docetaxel activity in cancer cell lines. Adv Cancer Res 2022; 158:233-292. [PMID: 36990534 DOI: 10.1016/bs.acr.2022.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The microtubule-targeting paclitaxel (PTX) and docetaxel (DTX) are widely used chemotherapeutic agents. However, the dysregulation of apoptotic processes, microtubule-binding proteins, and multi-drug resistance efflux and influx proteins can alter the efficacy of taxane drugs. In this review, we have created multi-CpG linear regression models to predict the activities of PTX and DTX drugs through the integration of publicly available pharmacological and genome-wide molecular profiling datasets generated using hundreds of cancer cell lines of diverse tissue of origin. Our findings indicate that linear regression models based on CpG methylation levels can predict PTX and DTX activities (log-fold change in viability relative to DMSO) with high precision. For example, a 287-CpG model predicts PTX activity at R2 of 0.985 among 399 cell lines. Just as precise (R2=0.996) is a 342-CpG model for predicting DTX activity in 390 cell lines. However, our predictive models, which employ a combination of mRNA expression and mutation as input variables, are less accurate compared to the CpG-based models. While a 290 mRNA/mutation model was able to predict PTX activity with R2 of 0.830 (for 546 cell lines), a 236 mRNA/mutation model could calculate DTX activity at R2 of 0.751 (for 531 cell lines). The CpG-based models restricted to lung cancer cell lines were also highly predictive (R2≥0.980) for PTX (74 CpGs, 88 cell lines) and DTX (58 CpGs, 83 cell lines). The underlying molecular biology behind taxane activity/resistance is evident in these models. Indeed, many of the genes represented in PTX or DTX CpG-based models have functionalities related to apoptosis (e.g., ACIN1, TP73, TNFRSF10B, DNASE1, DFFB, CREB1, BNIP3), and mitosis/microtubules (e.g., MAD1L1, ANAPC2, EML4, PARP3, CCT6A, JAKMIP1). Also represented are genes involved in epigenetic regulation (HDAC4, DNMT3B, and histone demethylases KDM4B, KDM4C, KDM2B, and KDM7A), and those that have never been previously linked to taxane activity (DIP2C, PTPRN2, TTC23, SHANK2). In summary, it is possible to accurately predict taxane activity in cell lines based entirely on methylation at multiple CpG sites.
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18
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Deep Learning for Human Disease Detection, Subtype Classification, and Treatment Response Prediction Using Epigenomic Data. Biomedicines 2021; 9:biomedicines9111733. [PMID: 34829962 PMCID: PMC8615388 DOI: 10.3390/biomedicines9111733] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/26/2021] [Accepted: 11/17/2021] [Indexed: 12/25/2022] Open
Abstract
Deep learning (DL) is a distinct class of machine learning that has achieved first-class performance in many fields of study. For epigenomics, the application of DL to assist physicians and scientists in human disease-relevant prediction tasks has been relatively unexplored until very recently. In this article, we critically review published studies that employed DL models to predict disease detection, subtype classification, and treatment responses, using epigenomic data. A comprehensive search on PubMed, Scopus, Web of Science, Google Scholar, and arXiv.org was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Among 1140 initially identified publications, we included 22 articles in our review. DNA methylation and RNA-sequencing data are most frequently used to train the predictive models. The reviewed models achieved a high accuracy ranged from 88.3% to 100.0% for disease detection tasks, from 69.5% to 97.8% for subtype classification tasks, and from 80.0% to 93.0% for treatment response prediction tasks. We generated a workflow to develop a predictive model that encompasses all steps from first defining human disease-related tasks to finally evaluating model performance. DL holds promise for transforming epigenomic big data into valuable knowledge that will enhance the development of translational epigenomics.
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19
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Artificial intelligence for the next generation of precision oncology. NPJ Precis Oncol 2021; 5:79. [PMID: 34408248 PMCID: PMC8373978 DOI: 10.1038/s41698-021-00216-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/21/2021] [Indexed: 12/14/2022] Open
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20
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Piyawajanusorn C, Nguyen LC, Ghislat G, Ballester PJ. A gentle introduction to understanding preclinical data for cancer pharmaco-omic modeling. Brief Bioinform 2021; 22:6343527. [PMID: 34368843 DOI: 10.1093/bib/bbab312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/25/2021] [Accepted: 07/20/2021] [Indexed: 12/16/2022] Open
Abstract
A central goal of precision oncology is to administer an optimal drug treatment to each cancer patient. A common preclinical approach to tackle this problem has been to characterize the tumors of patients at the molecular and drug response levels, and employ the resulting datasets for predictive in silico modeling (mostly using machine learning). Understanding how and why the different variants of these datasets are generated is an important component of this process. This review focuses on providing such introduction aimed at scientists with little previous exposure to this research area.
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Affiliation(s)
- Chayanit Piyawajanusorn
- Cancer Research Center of Marseille, INSERM U1068, F-13009 Marseille, France.,Institut Paoli-Calmettes, F-13009 Marseille, France.,Aix-Marseille Université, F-13284 Marseille, France.,CNRS UMR7258, F-13009 Marseille, France.,Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Linh C Nguyen
- Cancer Research Center of Marseille, INSERM U1068, F-13009 Marseille, France.,Institut Paoli-Calmettes, F-13009 Marseille, France.,Aix-Marseille Université, F-13284 Marseille, France.,CNRS UMR7258, F-13009 Marseille, France.,Department of Life Sciences, University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ghita Ghislat
- U1104, CNRS UMR7280, Centre d'Immunologie de Marseille-Luminy, Inserm, Marseille, France
| | - Pedro J Ballester
- Cancer Research Center of Marseille, INSERM U1068, F-13009 Marseille, France.,Institut Paoli-Calmettes, F-13009 Marseille, France.,Aix-Marseille Université, F-13284 Marseille, France.,CNRS UMR7258, F-13009 Marseille, France
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21
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Škubník J, Pavlíčková V, Ruml T, Rimpelová S. Current Perspectives on Taxanes: Focus on Their Bioactivity, Delivery and Combination Therapy. PLANTS (BASEL, SWITZERLAND) 2021; 10:569. [PMID: 33802861 PMCID: PMC8002726 DOI: 10.3390/plants10030569] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/09/2021] [Accepted: 03/15/2021] [Indexed: 12/14/2022]
Abstract
Taxanes, mainly paclitaxel and docetaxel, the microtubule stabilizers, have been well known for being the first-line therapy for breast cancer for more than the last thirty years. Moreover, they have been also used for the treatment of ovarian, hormone-refractory prostate, head and neck, and non-small cell lung carcinomas. Even though paclitaxel and docetaxel significantly enhance the overall survival rate of cancer patients, there are some limitations of their use, such as very poor water solubility and the occurrence of severe side effects. However, this is what pushes the research on these microtubule-stabilizing agents further and yields novel taxane derivatives with significantly improved properties. Therefore, this review article brings recent advances reported in taxane research mainly in the last two years. We focused especially on recent methods of taxane isolation, their mechanism of action, development of their novel derivatives, formulations, and improved tumor-targeted drug delivery. Since cancer cell chemoresistance can be an unsurpassable hurdle in taxane administration, a significant part of this review article has been also devoted to combination therapy of taxanes in cancer treatment. Last but not least, we summarize ongoing clinical trials on these compounds and bring a perspective of advancements in this field.
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Affiliation(s)
| | | | | | - Silvie Rimpelová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 3, 166 28 Prague 6, Czech Republic; (J.Š.); (V.P.); (T.R.)
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22
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A Compressive Review about Taxol ®: History and Future Challenges. Molecules 2020; 25:molecules25245986. [PMID: 33348838 PMCID: PMC7767101 DOI: 10.3390/molecules25245986] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/17/2022] Open
Abstract
Taxol®, which is also known as paclitaxel, is a chemotherapeutic agent widely used to treat different cancers. Since the discovery of its antitumoral activity, Taxol® has been used to treat over one million patients, making it one of the most widely employed antitumoral drugs. Taxol® was the first microtubule targeting agent described in the literature, with its main mechanism of action consisting of the disruption of microtubule dynamics, thus inducing mitotic arrest and cell death. However, secondary mechanisms for achieving apoptosis have also been demonstrated. Despite its wide use, Taxol® has certain disadvantages. The main challenges facing Taxol® are the need to find an environmentally sustainable production method based on the use of microorganisms, increase its bioavailability without exerting adverse effects on the health of patients and minimize the resistance presented by a high percentage of cells treated with paclitaxel. This review details, in a succinct manner, the main aspects of this important drug, from its discovery to the present day. We highlight the main challenges that must be faced in the coming years, in order to increase the effectiveness of Taxol® as an anticancer agent.
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23
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Rodrigues-Ferreira S, Moindjie H, Haykal MM, Nahmias C. Predicting and Overcoming Taxane Chemoresistance. Trends Mol Med 2020; 27:138-151. [PMID: 33046406 DOI: 10.1016/j.molmed.2020.09.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 01/01/2023]
Abstract
Taxanes are microtubule-targeting drugs used as cytotoxic chemotherapy to treat most solid tumors. The development of resistance to taxanes is a major cause of therapeutic failure and overcoming chemoresistance remains an important challenge to improve patient's outcome. Extensive efforts have been made recently to identify predictive biomarkers to select populations of patients who will benefit from taxane-based chemotherapy and avoid inefficient treatment of patients with innate resistance. This, together with the discovery of new mechanisms of resistance that include metabolic reprogramming and dialogue between tumor and its microenvironment, pave the way to a new era of personalized medicine. In this review, we recapitulate recent insights into taxane resistance and present promising emerging strategies to overcome chemoresistance in the future.
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Affiliation(s)
- Sylvie Rodrigues-Ferreira
- Université Paris-Saclay, Institut Gustave Roussy, Inserm U981, Biomarqueurs prédictifs et nouvelles stratégies thérapeutiques en oncologie, 94800, Villejuif, France; LabEx LERMIT, Université Paris Saclay, 92296 Châtenay-Malabry, France; Inovarion, 75005 Paris, France.
| | - Hadia Moindjie
- Université Paris-Saclay, Institut Gustave Roussy, Inserm U981, Biomarqueurs prédictifs et nouvelles stratégies thérapeutiques en oncologie, 94800, Villejuif, France; LabEx LERMIT, Université Paris Saclay, 92296 Châtenay-Malabry, France
| | - Maria M Haykal
- Université Paris-Saclay, Institut Gustave Roussy, Inserm U981, Biomarqueurs prédictifs et nouvelles stratégies thérapeutiques en oncologie, 94800, Villejuif, France; LabEx LERMIT, Université Paris Saclay, 92296 Châtenay-Malabry, France
| | - Clara Nahmias
- Université Paris-Saclay, Institut Gustave Roussy, Inserm U981, Biomarqueurs prédictifs et nouvelles stratégies thérapeutiques en oncologie, 94800, Villejuif, France; LabEx LERMIT, Université Paris Saclay, 92296 Châtenay-Malabry, France.
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24
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Misra R, Patra B, Varadharaj S, Verma RS. Establishing the promising role of novel combination of triple therapeutics delivery using polymeric nanoparticles for Triple negative breast cancer therapy. ACTA ACUST UNITED AC 2020; 11:199-207. [PMID: 34336608 PMCID: PMC8314031 DOI: 10.34172/bi.2021.27] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 06/23/2020] [Accepted: 07/04/2020] [Indexed: 12/23/2022]
Abstract
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Introduction: Triple-negative breast cancer (TNBC) is a lethal tumor with an advanced degree of metastasis and poor survivability as compared to other subtypes of breast cancer. TNBC which consists of 15 % of all types of breast cancer is categorized by the absence of expression of estrogen receptors (ER), progesterone receptors (PR) and human epidermal growth factor receptor-2 (HER2). This is the main reason for the failure of current hormonal receptor-based therapies against TNBCs, thus leading to poor patient outcomes. Therefore, there is a necessity to develop novel therapies targeting this devastating disease. Methods: In this study, we have targeted TNBC by simultaneous activation of apoptosis through DNA damage via cytotoxic agent such as paclitaxel (PAC), inhibition of PARP activity via PARP inhibitor, olaparib (OLA) and inhibiting the activity of FOXM1 proto-oncogenic transcription factor by using RNA interference technology (FOXM1-siRNA) in nanoformulations. Experiments conducted in this investigation include cellular uptake, cytotoxicity and apoptosis study using MDA-MB-231 cells. Results: The present study validates that co-delivery of two drugs (PAC and OLA) along with FOXM1-siRNA by cationic NPs, enhances the therapeutic outcome leading to greater cytotoxicity in TNBC cells. Conclusion: The current investigation focuses on designing a multifunctional drug delivery platform for concurrent delivery of either PAC or PARP inhibitor (olaparib) and FOXM1 siRNA in chitosan-coated poly(D, L-lactide-co-glycolide) (PLGA) nanoparticles (NPs) with the ability to emerge as a front runner therapeutic for TNBC therapy.
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Affiliation(s)
- Ranjita Misra
- Sathyabama Institute of Science and Technology, Centre for Nanoscience and Nanotechnology, Chennai, India
| | - Bamadeb Patra
- Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
| | - Sudha Varadharaj
- Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
| | - Rama Shanker Verma
- Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
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Poojan S, Bae SH, Min JW, Lee EY, Song Y, Kim HY, Sim HW, Kang EK, Kim YH, Lee HO, Hong Y, Park WY, Jang H, Hong KM. Cancer cells undergoing epigenetic transition show short-term resistance and are transformed into cells with medium-term resistance by drug treatment. Exp Mol Med 2020; 52:1102-1115. [PMID: 32661348 PMCID: PMC8080688 DOI: 10.1038/s12276-020-0464-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/06/2020] [Accepted: 05/12/2020] [Indexed: 01/08/2023] Open
Abstract
To elucidate the epigenetic mechanisms of drug resistance, epigenetically reprogrammed H460 cancer cells (R-H460) were established by the transient introduction of reprogramming factors. Then, the R-H460 cells were induced to differentiate by the withdrawal of stem cell media for various durations, which resulted in differentiated R-H460 cells (dR-H460). Notably, dR-H460 cells differentiated for 13 days (13dR-H460 cells) formed a significantly greater number of colonies showing drug resistance to both cisplatin and paclitaxel, whereas the dR-H460 cells differentiated for 40 days (40dR-H460 cells) lost drug resistance; this suggests that 13dR-cancer cells present short-term resistance (less than a month). Similarly, increased drug resistance to both cisplatin and paclitaxel was observed in another R-cancer cell model prepared from N87 cells. The resistant phenotype of the cisplatin-resistant (CR) colonies obtained through cisplatin treatment was maintained for 2–3 months after drug treatment, suggesting that drug treatment transforms cells with short-term resistance into cells with medium-term resistance. In single-cell analyses, heterogeneity was not found to increase in 13dR-H460 cells, suggesting that cancer cells with short-term resistance, rather than heterogeneous cells, may confer epigenetically driven drug resistance in our reprogrammed cancer model. The epigenetically driven short-term and medium-term drug resistance mechanisms could provide new cancer-fighting strategies involving the control of cancer cells during epigenetic transition. Cancer cells that are transiently resistant to drug therapies owing to changes in their gene expression patterns can become resistant for longer durations if exposed to the drug treatments. A team led by Kyeong-Man Hong and Hyonchol Jang from the National Cancer Center in Goyang, South Korea, used cellular reprogramming technologies to induce changes in the DNA markers that regulate gene expression. Working with lung and gastric cancer cell lines, the researchers found that such epigenetic alterations caused many cells to become resistant to the chemotherapy drugs cisplatin and paclitaxel. In the absence of treatment, the cells soon lost their drug resistance. In the presence of the chemotherapeutics, however, the resistance trait lasted longer, a finding that could inform best practice for how to administer cancer-fighting agents in the face of epigenetic-driven drug resistance.
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Affiliation(s)
- Shiv Poojan
- Research Institute, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Seung-Hyun Bae
- Research Institute, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do, Republic of Korea.,Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, 10408, Korea
| | - Jae-Woong Min
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Korea
| | - Eun Young Lee
- Research Institute, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Yura Song
- Research Institute, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Hee Yeon Kim
- Research Institute, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Hye Won Sim
- Research Institute, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Eun-Kyung Kang
- Research Institute, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Young-Ho Kim
- Research Institute, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Hae-Ock Lee
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Korea
| | - Yourae Hong
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Korea
| | - Hyonchol Jang
- Research Institute, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do, Republic of Korea. .,Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, 10408, Korea.
| | - Kyeong-Man Hong
- Research Institute, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do, Republic of Korea.
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Naulaerts S, Menden MP, Ballester PJ. Concise Polygenic Models for Cancer-Specific Identification of Drug-Sensitive Tumors from Their Multi-Omics Profiles. Biomolecules 2020; 10:E963. [PMID: 32604779 PMCID: PMC7356608 DOI: 10.3390/biom10060963] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/20/2020] [Accepted: 06/22/2020] [Indexed: 12/15/2022] Open
Abstract
In silico models to predict which tumors will respond to a given drug are necessary for Precision Oncology. However, predictive models are only available for a handful of cases (each case being a given drug acting on tumors of a specific cancer type). A way to generate predictive models for the remaining cases is with suitable machine learning algorithms that are yet to be applied to existing in vitro pharmacogenomics datasets. Here, we apply XGBoost integrated with a stringent feature selection approach, which is an algorithm that is advantageous for these high-dimensional problems. Thus, we identified and validated 118 predictive models for 62 drugs across five cancer types by exploiting four molecular profiles (sequence mutations, copy-number alterations, gene expression, and DNA methylation). Predictive models were found in each cancer type and with every molecular profile. On average, no omics profile or cancer type obtained models with higher predictive accuracy than the rest. However, within a given cancer type, some molecular profiles were overrepresented among predictive models. For instance, CNA profiles were predictive in breast invasive carcinoma (BRCA) cell lines, but not in small cell lung cancer (SCLC) cell lines where gene expression (GEX) and DNA methylation profiles were the most predictive. Lastly, we identified the best XGBoost model per cancer type and analyzed their selected features. For each model, some of the genes in the selected list had already been found to be individually linked to the response to that drug, providing additional evidence of the usefulness of these models and the merits of the feature selection scheme.
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Affiliation(s)
- Stefan Naulaerts
- Cancer Research Center of Marseille, INSERM U1068, F-13009 Marseille, France;
- Institut Paoli-Calmettes, F-13009 Marseille, France
- Aix-Marseille Université, F-13284 Marseille, France
- CNRS UMR7258, F-13009 Marseille, France
- Ludwig Institute for Cancer Research, de Duve Institute, Université catholique de Louvain, 1200 Brussels, Belgium
| | - Michael P. Menden
- Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany;
- Department of Biology, Ludwig-Maximilians University Munich, 82152 Planegg-Martinsried, Germany
- German Centre for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany
| | - Pedro J. Ballester
- Cancer Research Center of Marseille, INSERM U1068, F-13009 Marseille, France;
- Institut Paoli-Calmettes, F-13009 Marseille, France
- Aix-Marseille Université, F-13284 Marseille, France
- CNRS UMR7258, F-13009 Marseille, France
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Li H, Sze K, Lu G, Ballester PJ. Machine‐learning scoring functions for structure‐based virtual screening. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1478] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Hongjian Li
- Cancer Research Center of Marseille (INSERM U1068, Institut Paoli‐Calmettes, Aix‐Marseille Université UM105, CNRS UMR7258) Marseille France
- CUHK‐SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences Chinese University of Hong Kong Shatin Hong Kong
| | - Kam‐Heung Sze
- CUHK‐SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences Chinese University of Hong Kong Shatin Hong Kong
| | - Gang Lu
- CUHK‐SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences Chinese University of Hong Kong Shatin Hong Kong
| | - Pedro J. Ballester
- Cancer Research Center of Marseille (INSERM U1068, Institut Paoli‐Calmettes, Aix‐Marseille Université UM105, CNRS UMR7258) Marseille France
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Huang S, Yang J, Fong S, Zhao Q. Artificial intelligence in cancer diagnosis and prognosis: Opportunities and challenges. Cancer Lett 2019; 471:61-71. [PMID: 31830558 DOI: 10.1016/j.canlet.2019.12.007] [Citation(s) in RCA: 198] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/04/2019] [Accepted: 12/06/2019] [Indexed: 02/06/2023]
Abstract
Cancer is an aggressive disease with a low median survival rate. Ironically, the treatment process is long and very costly due to its high recurrence and mortality rates. Accurate early diagnosis and prognosis prediction of cancer are essential to enhance the patient's survival rate. Developments in statistics and computer engineering over the years have encouraged many scientists to apply computational methods such as multivariate statistical analysis to analyze the prognosis of the disease, and the accuracy of such analyses is significantly higher than that of empirical predictions. Furthermore, as artificial intelligence (AI), especially machine learning and deep learning, has found popular applications in clinical cancer research in recent years, cancer prediction performance has reached new heights. This article reviews the literature on the application of AI to cancer diagnosis and prognosis, and summarizes its advantages. We explore how AI assists cancer diagnosis and prognosis, specifically with regard to its unprecedented accuracy, which is even higher than that of general statistical applications in oncology. We also demonstrate ways in which these methods are advancing the field. Finally, opportunities and challenges in the clinical implementation of AI are discussed. Hence, this article provides a new perspective on how AI technology can help improve cancer diagnosis and prognosis, and continue improving human health in the future.
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Affiliation(s)
- Shigao Huang
- Cancer Center, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macao, China
| | - Jie Yang
- Department of Computer and Information Science, University of Macau, Taipa, Macau, China; Chongqing Industry&Trade Polytechnic, Chongqing, China
| | - Simon Fong
- Department of Computer and Information Science, University of Macau, Taipa, Macau, China; Zhuhai Institute of Advanced Technology Chinese Academy of Sciences, Zhuhai, China.
| | - Qi Zhao
- Cancer Center, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macao, China.
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