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Chi J, Shu J, Li M, Mudappathi R, Jin Y, Lewis F, Boon A, Qin X, Liu L, Gu H. Artificial Intelligence in Metabolomics: A Current Review. Trends Analyt Chem 2024; 178:117852. [PMID: 39071116 PMCID: PMC11271759 DOI: 10.1016/j.trac.2024.117852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Metabolomics and artificial intelligence (AI) form a synergistic partnership. Metabolomics generates large datasets comprising hundreds to thousands of metabolites with complex relationships. AI, aiming to mimic human intelligence through computational modeling, possesses extraordinary capabilities for big data analysis. In this review, we provide a recent overview of the methodologies and applications of AI in metabolomics studies in the context of systems biology and human health. We first introduce the AI concept, history, and key algorithms for machine learning and deep learning, summarizing their strengths and weaknesses. We then discuss studies that have successfully used AI across different aspects of metabolomic analysis, including analytical detection, data preprocessing, biomarker discovery, predictive modeling, and multi-omics data integration. Lastly, we discuss the existing challenges and future perspectives in this rapidly evolving field. Despite limitations and challenges, the combination of metabolomics and AI holds great promises for revolutionary advancements in enhancing human health.
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Affiliation(s)
- Jinhua Chi
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Jingmin Shu
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Ming Li
- Phoenix VA Health Care System, Phoenix, AZ 85012, USA
- University of Arizona College of Medicine, Phoenix, AZ 85004, USA
| | - Rekha Mudappathi
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Yan Jin
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Freeman Lewis
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Alexandria Boon
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
| | - Xiaoyan Qin
- College of Liberal Arts and Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Li Liu
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Haiwei Gu
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA
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Fierro-Monti I. RBPs: an RNA editor's choice. Front Mol Biosci 2024; 11:1454241. [PMID: 39165644 PMCID: PMC11333368 DOI: 10.3389/fmolb.2024.1454241] [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: 06/25/2024] [Accepted: 07/25/2024] [Indexed: 08/22/2024] Open
Abstract
RNA-binding proteins (RBPs) play a key role in gene expression and post-transcriptional RNA regulation. As integral components of ribonucleoprotein complexes, RBPs are susceptible to genomic and RNA Editing derived amino acid substitutions, impacting functional interactions. This article explores the prevalent RNA Editing of RBPs, unravelling the complex interplay between RBPs and RNA Editing events. Emphasis is placed on their influence on single amino acid variants (SAAVs) and implications for disease development. The role of Proteogenomics in identifying SAAVs is briefly discussed, offering insights into the RBP landscape. RNA Editing within RBPs emerges as a promising target for precision medicine, reshaping our understanding of genetic and epigenetic variations in health and disease.
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Nussinov R, Yavuz BR, Demirel HC, Arici MK, Jang H, Tuncbag N. Review: Cancer and neurodevelopmental disorders: multi-scale reasoning and computational guide. Front Cell Dev Biol 2024; 12:1376639. [PMID: 39015651 PMCID: PMC11249571 DOI: 10.3389/fcell.2024.1376639] [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: 01/25/2024] [Accepted: 06/10/2024] [Indexed: 07/18/2024] Open
Abstract
The connection and causality between cancer and neurodevelopmental disorders have been puzzling. How can the same cellular pathways, proteins, and mutations lead to pathologies with vastly different clinical presentations? And why do individuals with neurodevelopmental disorders, such as autism and schizophrenia, face higher chances of cancer emerging throughout their lifetime? Our broad review emphasizes the multi-scale aspect of this type of reasoning. As these examples demonstrate, rather than focusing on a specific organ system or disease, we aim at the new understanding that can be gained. Within this framework, our review calls attention to computational strategies which can be powerful in discovering connections, causalities, predicting clinical outcomes, and are vital for drug discovery. Thus, rather than centering on the clinical features, we draw on the rapidly increasing data on the molecular level, including mutations, isoforms, three-dimensional structures, and expression levels of the respective disease-associated genes. Their integrated analysis, together with chromatin states, can delineate how, despite being connected, neurodevelopmental disorders and cancer differ, and how the same mutations can lead to different clinical symptoms. Here, we seek to uncover the emerging connection between cancer, including pediatric tumors, and neurodevelopmental disorders, and the tantalizing questions that this connection raises.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, United States
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Bengi Ruken Yavuz
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, United States
| | | | - M. Kaan Arici
- Graduate School of Informatics, Middle East Technical University, Ankara, Türkiye
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, United States
| | - Nurcan Tuncbag
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Türkiye
- School of Medicine, Koc University, Istanbul, Türkiye
- Koc University Research Center for Translational Medicine (KUTTAM), Istanbul, Türkiye
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4
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Wang Z, Fan H, Wu J. Food-Derived Up-Regulators and Activators of Angiotensin Converting Enzyme 2: A Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12896-12914. [PMID: 38810024 PMCID: PMC11181331 DOI: 10.1021/acs.jafc.4c01594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/13/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024]
Abstract
Angiotensin-converting enzyme 2 (ACE2) is a key enzyme in the renin-angiotensin system (RAS), also serving as an amino acid transporter and a receptor for certain coronaviruses. Its primary role is to protect the cardiovascular system via the ACE2/Ang (1-7)/MasR cascade. Given the critical roles of ACE2 in regulating numerous physiological functions, molecules that can upregulate or activate ACE2 show vast therapeutic value. There are only a few ACE2 activators that have been reported, a wide range of molecules, including food-derived compounds, have been reported as ACE2 up-regulators. Effective doses of bioactive peptides range from 10 to 50 mg/kg body weight (BW)/day when orally administered for 1 to 7 weeks. Protein hydrolysates require higher doses at 1000 mg/kg BW/day for 20 days. Phytochemicals and vitamins are effective at doses typically ranging from 10 to 200 mg/kg BW/day for 3 days to 6 months, while Traditional Chinese Medicine requires doses of 1.25 to 12.96 g/kg BW/day for 4 to 8 weeks. ACE2 activation is linked to its hinge-bending region, while upregulation involves various signaling pathways, transcription factors, and epigenetic modulators. Future studies are expected to explore novel roles of ACE2 activators or up-regulators in disease treatments and translate the discovery to bedside applications.
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Affiliation(s)
- Zihan Wang
- Department
of Agricultural, Food and Nutritional Science, 4-10 Ag/For Building, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
- Cardiovascular
Research Centre, University of Alberta, Edmonton, Alberta T6G 2R7, Canada
| | - Hongbing Fan
- Department
of Animal and Food Sciences, University
of Kentucky, Lexington, Kentucky 40546, United States
| | - Jianping Wu
- Department
of Agricultural, Food and Nutritional Science, 4-10 Ag/For Building, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
- Cardiovascular
Research Centre, University of Alberta, Edmonton, Alberta T6G 2R7, Canada
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5
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Chakraborty S, Sharma G, Karmakar S, Banerjee S. Multi-OMICS approaches in cancer biology: New era in cancer therapy. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167120. [PMID: 38484941 DOI: 10.1016/j.bbadis.2024.167120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 04/01/2024]
Abstract
Innovative multi-omics frameworks integrate diverse datasets from the same patients to enhance our understanding of the molecular and clinical aspects of cancers. Advanced omics and multi-view clustering algorithms present unprecedented opportunities for classifying cancers into subtypes, refining survival predictions and treatment outcomes, and unravelling key pathophysiological processes across various molecular layers. However, with the increasing availability of cost-effective high-throughput technologies (HTT) that generate vast amounts of data, analyzing single layers often falls short of establishing causal relations. Integrating multi-omics data spanning genomes, epigenomes, transcriptomes, proteomes, metabolomes, and microbiomes offers unique prospects to comprehend the underlying biology of complex diseases like cancer. This discussion explores algorithmic frameworks designed to uncover cancer subtypes, disease mechanisms, and methods for identifying pivotal genomic alterations. It also underscores the significance of multi-omics in tumor classifications, diagnostics, and prognostications. Despite its unparalleled advantages, the integration of multi-omics data has been slow to find its way into everyday clinics. A major hurdle is the uneven maturity of different omics approaches and the widening gap between the generation of large datasets and the capacity to process this data. Initiatives promoting the standardization of sample processing and analytical pipelines, as well as multidisciplinary training for experts in data analysis and interpretation, are crucial for translating theoretical findings into practical applications.
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Affiliation(s)
- Sohini Chakraborty
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Gaurav Sharma
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Sricheta Karmakar
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Satarupa Banerjee
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India.
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Bahl A, Halappanavar S, Wohlleben W, Nymark P, Kohonen P, Wallin H, Vogel U, Haase A. Bioinformatics and machine learning to support nanomaterial grouping. Nanotoxicology 2024; 18:373-400. [PMID: 38949108 DOI: 10.1080/17435390.2024.2368005] [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: 12/28/2023] [Revised: 05/22/2024] [Accepted: 06/11/2024] [Indexed: 07/02/2024]
Abstract
Nanomaterials (NMs) offer plenty of novel functionalities. Moreover, their physicochemical properties can be fine-tuned to meet the needs of specific applications, leading to virtually unlimited numbers of NM variants. Hence, efficient hazard and risk assessment strategies building on New Approach Methodologies (NAMs) become indispensable. Indeed, the design, the development and implementation of NAMs has been a major topic in a substantial number of research projects. One of the promising strategies that can help to deal with the high number of NMs variants is grouping and read-across. Based on demonstrated structural and physicochemical similarity, NMs can be grouped and assessed together. Within an established NM group, read-across may be performed to fill in data gaps for data-poor variants using existing data for NMs within the group. Establishing a group requires a sound justification, usually based on a grouping hypothesis that links specific physicochemical properties to well-defined hazard endpoints. However, for NMs these interrelationships are only beginning to be understood. The aim of this review is to demonstrate the power of bioinformatics with a specific focus on Machine Learning (ML) approaches to unravel the NM Modes-of-Action (MoA) and identify the properties that are relevant to specific hazards, in support of grouping strategies. This review emphasizes the following messages: 1) ML supports identification of the most relevant properties contributing to specific hazards; 2) ML supports analysis of large omics datasets and identification of MoA patterns in support of hypothesis formulation in grouping approaches; 3) omics approaches are useful for shifting away from consideration of single endpoints towards a more mechanistic understanding across multiple endpoints gained from one experiment; and 4) approaches from other fields of Artificial Intelligence (AI) like Natural Language Processing or image analysis may support automated extraction and interlinkage of information related to NM toxicity. Here, existing ML models for predicting NM toxicity and for analyzing omics data in support of NM grouping are reviewed. Various challenges related to building robust models in the field of nanotoxicology exist and are also discussed.
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Affiliation(s)
- Aileen Bahl
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
- Freie Universität Berlin, Institute of Pharmacy, Berlin, Germany
| | - Sabina Halappanavar
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
| | - Wendel Wohlleben
- BASF SE, Department Analytical and Material Science and Department Experimental Toxicology and Ecology, Ludwigshafen, Germany
| | - Penny Nymark
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Pekka Kohonen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Håkan Wallin
- Department of Chemical and Biological Risk Factors, National Institute of Occupational Health, Oslo, Norway
- Department of Public Health, Copenhagen University, Copenhagen, Denmark
| | - Ulla Vogel
- National Research Centre for the Working Environment, Copenhagen, Denmark
| | - Andrea Haase
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
- Freie Universität Berlin, Institute of Pharmacy, Berlin, Germany
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Goldstein Y, Cohen OT, Wald O, Bavli D, Kaplan T, Benny O. Particle uptake in cancer cells can predict malignancy and drug resistance using machine learning. SCIENCE ADVANCES 2024; 10:eadj4370. [PMID: 38809990 PMCID: PMC11314625 DOI: 10.1126/sciadv.adj4370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 04/23/2024] [Indexed: 05/31/2024]
Abstract
Tumor heterogeneity is a primary factor that contributes to treatment failure. Predictive tools, capable of classifying cancer cells based on their functions, may substantially enhance therapy and extend patient life span. The connection between cell biomechanics and cancer cell functions is used here to classify cells through mechanical measurements, via particle uptake. Machine learning (ML) was used to classify cells based on single-cell patterns of uptake of particles with diverse sizes. Three pairs of human cancer cell subpopulations, varied in their level of drug resistance or malignancy, were studied. Cells were allowed to interact with fluorescently labeled polystyrene particles ranging in size from 0.04 to 3.36 μm and analyzed for their uptake patterns using flow cytometry. ML algorithms accurately classified cancer cell subtypes with accuracy rates exceeding 95%. The uptake data were especially advantageous for morphologically similar cell subpopulations. Moreover, the uptake data were found to serve as a form of "normalization" that could reduce variation in repeated experiments.
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Affiliation(s)
- Yoel Goldstein
- Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Ora T. Cohen
- Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Ori Wald
- Department of Cardiothoracic Surgery, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Danny Bavli
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Ofra Benny
- Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
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8
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Demircan Çeker D, Baysungur V, Evman S, Kolbaş İ, Gördebil A, Nalbantoğlu SM, Tambağ Y, Kaçar Ö, Midi A, Aslanoğlu H, Kara N, Algan N, Boyacioğlu A, Karademir Yilmaz B, Şahin A, Ülbeği Polat H, Şehitoğullari A, Çibikdiken AO, Büyükyilmaz M, Aydilek İB, Eneş A, Küçüker S, Karakaya F, Boyaci İ, Gümüş M, Şenol O, Öztuğ M, Saban E, Soysal Ö, Büyükpinarbaşili N, Turna A, Günlüoğlu MZ, Çakir A, Tekin Ş, Tazebay U, Karadağ A. LUNGBANK: a novel biorepository strategy tailored for comprehensive multiomics analysis and P-medicine applications in lung cancer. Turk J Biol 2024; 48:203-217. [PMID: 39050710 PMCID: PMC11265891 DOI: 10.55730/1300-0152.2696] [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: 05/17/2024] [Revised: 06/26/2024] [Accepted: 05/28/2024] [Indexed: 07/27/2024] Open
Abstract
Background/aim LUNGBANK was established as part of Project LUNGMARK, pioneering a biorepository dedicated exclusively to lung cancer research. It employs cutting-edge technologies to streamline the handling of biospecimens, ensuring the acquisition of high-quality samples. This infrastructure is fortified with robust data management capabilities, enabling seamless integration of diverse datasets. LUNGBANK functions not merely as a repository but as a sophisticated platform crucial for advancing lung cancer research, poised to facilitate significant discoveries. Materials and methods LUNGBANK was meticulously designed to optimize every stage of biospecimen handling, from collection and storage to processing. Rigorous standard operating procedures and stringent quality control measures guarantee the integrity of collected biospecimens. Advanced data management protocols facilitate the efficient integration and analysis of various datasets, enhancing the depth and breadth of research possibilities in lung cancer. Results LUNGBANK has amassed a comprehensive collection of biospecimens essential for unraveling the intricate molecular mechanisms of lung cancer. The integration of state-of-the-art technologies ensures the acquisition of top-tier data, fostering breakthroughs in translational and histological research. Moreover, the establishment of patient-derived systems by LUNGBANK underscores its pivotal role in personalized medicine approaches. Conclusion The establishment of LUNGBANK marks a significant milestone in addressing the critical challenges of lung cancer research. By providing researchers with high-quality biospecimens and advanced research tools, LUNGBANK not only supports Project LUNGMARK's objectives but also contributes extensively to the broader landscape of personalized medicine. It promises to enhance our understanding of lung cancer initiation, progression, and therapeutic interventions tailored to individual patient needs, thereby advancing the field towards more effective diagnostic and therapeutic strategies.
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Affiliation(s)
- Dilek Demircan Çeker
- Molecular Oncology Laboratory, Medical Biotechnology Research Group, VPLS, TÜBİTAK Marmara Research Center, Kocaeli, Turkiye
- Department of Molecular Biology and Genetics, Gebze Technical University, Kocaeli, Turkiye
| | - Volkan Baysungur
- Department of Thoracic Surgery, Faculty of Medicine, University of Health Sciences, İstanbul, Turkiye
- Department of Thoracic Surgery, Süreyyapaşa Training and Research Hospital, İstanbul, Turkiye
| | - Serdar Evman
- Department of Thoracic Surgery, Süreyyapaşa Training and Research Hospital, İstanbul, Turkiye
| | - İlker Kolbaş
- Department of Thoracic Surgery, Süreyyapaşa Training and Research Hospital, İstanbul, Turkiye
| | - Abdurrahim Gördebil
- Department of Thoracic Surgery, Süreyyapaşa Training and Research Hospital, İstanbul, Turkiye
| | - Sinem M Nalbantoğlu
- Molecular Oncology Laboratory, Medical Biotechnology Research Group, VPLS, TÜBİTAK Marmara Research Center, Kocaeli, Turkiye
| | - Yusuf Tambağ
- Software Technologies Research Institute, TÜBİTAK Informatics and Information Security Research Center, Ankara, Turkiye
| | - Ömer Kaçar
- Molecular Oncology Laboratory, Medical Biotechnology Research Group, VPLS, TÜBİTAK Marmara Research Center, Kocaeli, Turkiye
| | - Ahmet Midi
- Department of Pathology, Faculty of Medicine, Bahçeşehir University, İstanbul, Turkiye
| | - Hatice Aslanoğlu
- Department of Thoracic Surgery, Süreyyapaşa Training and Research Hospital, İstanbul, Turkiye
| | - Nülüfer Kara
- Department of Thoracic Surgery, Süreyyapaşa Training and Research Hospital, İstanbul, Turkiye
| | - Nilgün Algan
- Department of Thoracic Surgery, Süreyyapaşa Training and Research Hospital, İstanbul, Turkiye
| | - Ayberk Boyacioğlu
- Department of Thoracic Surgery, Süreyyapaşa Training and Research Hospital, İstanbul, Turkiye
| | - Betül Karademir Yilmaz
- Division of Biochemistry, Department of Basic Medical Sciences, Faculty of Medicine, Marmara University, İstanbul, Turkiye
- Genetic and Metabolic Diseases Research and Investigation Center (GEMHAM), Marmara University, İstanbul, Turkiye
| | - Ali Şahin
- Division of Biochemistry, Department of Basic Medical Sciences, Faculty of Medicine, Marmara University, İstanbul, Turkiye
- Genetic and Metabolic Diseases Research and Investigation Center (GEMHAM), Marmara University, İstanbul, Turkiye
| | - Hivda Ülbeği Polat
- Molecular Oncology Laboratory, Medical Biotechnology Research Group, VPLS, TÜBİTAK Marmara Research Center, Kocaeli, Turkiye
| | - Abidin Şehitoğullari
- Department of Thoracic Surgery, Faculty of Medicine, Sakarya University, Sakarya, Turkiye
| | - Ali Osman Çibikdiken
- Department of Computer Sciences and Engineering, KTO Karatay University, Konya, Turkiye
| | | | - İbrahim Berkan Aydilek
- Department of Computer Engineering, Faculty of Engineering, Harran University, Şanlıurfa, Turkiye
| | - Abdulkerim Eneş
- Department of Computer Engineering, Faculty of Engineering, Harran University, Şanlıurfa, Turkiye
| | - Sevde Küçüker
- Molecular Oncology Laboratory, Medical Biotechnology Research Group, VPLS, TÜBİTAK Marmara Research Center, Kocaeli, Turkiye
| | - Fatih Karakaya
- Molecular Oncology Laboratory, Medical Biotechnology Research Group, VPLS, TÜBİTAK Marmara Research Center, Kocaeli, Turkiye
| | - İhsan Boyaci
- Department of Internal Medicine, Faculty of Medicine, İstanbul Medipol University, İstanbul, Turkiye
| | - Mahmut Gümüş
- Department of Internal Medicine, Faculty of Medicine, İstanbul Medeniyet University, İstanbul, Turkiye
| | - Onur Şenol
- Department of Analytical Chemistry, Faculty of Pharmacy, Atatürk University, Erzurum, Turkiye
| | - Merve Öztuğ
- TÜBİTAK National Metrology Institute, Kocaeli, Turkiye
| | - Evren Saban
- TÜBİTAK National Metrology Institute, Kocaeli, Turkiye
| | - Ömer Soysal
- Department of Thoracic Surgery, Faculty of Medicine, Bezmialem Vakıf University, İstanbul, Turkiye
| | - Nur Büyükpinarbaşili
- Department of Pathology, Faculty of Medicine, Bezmialem Vakıf University, İstanbul, Turkiye
| | - Akif Turna
- Department of Thoracic Surgery, Faculty of Medicine, İstanbul University-Cerrahpaşa, İstanbul, Turkiye
| | - Mehmet Zeki Günlüoğlu
- Department of Thoracic Surgery, Faculty of Medicine, İstanbul Medipol University, İstanbul, Turkiye
| | - Aslı Çakir
- Department of Pathology, Faculty of Medicine, İstanbul Medipol University, İstanbul, Turkiye
| | - Şaban Tekin
- Division of Medical Biology, Department of Basic Medical Sciences, Faculty of Medicine, University of Health Sciences, İstanbul, Turkiye
| | - Uygar Tazebay
- Department of Molecular Biology and Genetics, Gebze Technical University, Kocaeli, Turkiye
| | - Abdullah Karadağ
- Molecular Oncology Laboratory, Medical Biotechnology Research Group, VPLS, TÜBİTAK Marmara Research Center, Kocaeli, Turkiye
- Institute of Biotechnology, Gebze Technical University, Kocaeli, Turkiye
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9
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Abdollahi H, Yousefirizi F, Shiri I, Brosch-Lenz J, Mollaheydar E, Fele-Paranj A, Shi K, Zaidi H, Alberts I, Soltani M, Uribe C, Saboury B, Rahmim A. Theranostic digital twins: Concept, framework and roadmap towards personalized radiopharmaceutical therapies. Theranostics 2024; 14:3404-3422. [PMID: 38948052 PMCID: PMC11209714 DOI: 10.7150/thno.93973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 04/22/2024] [Indexed: 07/02/2024] Open
Abstract
Radiopharmaceutical therapy (RPT) is a rapidly developing field of nuclear medicine, with several RPTs already well established in the treatment of several different types of cancers. However, the current approaches to RPTs often follow a somewhat inflexible "one size fits all" paradigm, where patients are administered the same amount of radioactivity per cycle regardless of their individual characteristics and features. This approach fails to consider inter-patient variations in radiopharmacokinetics, radiation biology, and immunological factors, which can significantly impact treatment outcomes. To address this limitation, we propose the development of theranostic digital twins (TDTs) to personalize RPTs based on actual patient data. Our proposed roadmap outlines the steps needed to create and refine TDTs that can optimize radiation dose to tumors while minimizing toxicity to organs at risk. The TDT models incorporate physiologically-based radiopharmacokinetic (PBRPK) models, which are additionally linked to a radiobiological optimizer and an immunological modulator, taking into account factors that influence RPT response. By using TDT models, we envisage the ability to perform virtual clinical trials, selecting therapies towards improved treatment outcomes while minimizing risks associated with secondary effects. This framework could empower practitioners to ultimately develop tailored RPT solutions for subgroups and individual patients, thus improving the precision, accuracy, and efficacy of treatments while minimizing risks to patients. By incorporating TDT models into RPTs, we can pave the way for a new era of precision medicine in cancer treatment.
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Affiliation(s)
- Hamid Abdollahi
- Department of Radiology, University of British Columbia, Vancouver, Canada
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, Canada
| | | | - Isaac Shiri
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
- Department of Cardiology, University Hospital Bern, Switzerland
| | - Julia Brosch-Lenz
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, Canada
- Department of Nuclear Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Elahe Mollaheydar
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, Canada
- Department of Biomedical Engineering, University of British Columbia, Vancouver, Canada
| | - Ali Fele-Paranj
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, Canada
- Department of Biomedical Engineering, University of British Columbia, Vancouver, Canada
- Department of Mathematics, University of British Columbia, Vancouver, Canada
| | - Kuangyu Shi
- Department of Nuclear Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department of Informatics, Technical University of Munich, Munich, Germany
| | - Habib Zaidi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
- Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Nuclear Medicine, University of Southern Denmark, Odense, Denmark
- University Research and Innovation Center, Óbuda University, Budapest, Hungary
| | - Ian Alberts
- Department of Molecular Imaging and Therapy, BC Cancer, Vancouver, Canada
| | - Madjid Soltani
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, Canada
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran, Iran
- Department of Electrical and Computer Engineering, University of Waterloo, ON, Canada
| | - Carlos Uribe
- Department of Radiology, University of British Columbia, Vancouver, Canada
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, Canada
- Department of Molecular Imaging and Therapy, BC Cancer, Vancouver, Canada
| | - Babak Saboury
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, Canada
- Department of Radiology and Imaging Sciences, Clinical Center, National Institutes of Health, Bethesda, USA
| | - Arman Rahmim
- Department of Radiology, University of British Columbia, Vancouver, Canada
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, Canada
- Department of Biomedical Engineering, University of British Columbia, Vancouver, Canada
- Department of Physics and Astronomy, University of British Columbia, Vancouver, Canada
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10
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Flynn CD, Chang D. Artificial Intelligence in Point-of-Care Biosensing: Challenges and Opportunities. Diagnostics (Basel) 2024; 14:1100. [PMID: 38893627 PMCID: PMC11172335 DOI: 10.3390/diagnostics14111100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
The integration of artificial intelligence (AI) into point-of-care (POC) biosensing has the potential to revolutionize diagnostic methodologies by offering rapid, accurate, and accessible health assessment directly at the patient level. This review paper explores the transformative impact of AI technologies on POC biosensing, emphasizing recent computational advancements, ongoing challenges, and future prospects in the field. We provide an overview of core biosensing technologies and their use at the POC, highlighting ongoing issues and challenges that may be solved with AI. We follow with an overview of AI methodologies that can be applied to biosensing, including machine learning algorithms, neural networks, and data processing frameworks that facilitate real-time analytical decision-making. We explore the applications of AI at each stage of the biosensor development process, highlighting the diverse opportunities beyond simple data analysis procedures. We include a thorough analysis of outstanding challenges in the field of AI-assisted biosensing, focusing on the technical and ethical challenges regarding the widespread adoption of these technologies, such as data security, algorithmic bias, and regulatory compliance. Through this review, we aim to emphasize the role of AI in advancing POC biosensing and inform researchers, clinicians, and policymakers about the potential of these technologies in reshaping global healthcare landscapes.
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Affiliation(s)
- Connor D. Flynn
- Department of Chemistry, Weinberg College of Arts & Sciences, Northwestern University, Evanston, IL 60208, USA
| | - Dingran Chang
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL 60208, USA
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11
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Liang G, Cao W, Tang D, Zhang H, Yu Y, Ding J, Karges J, Xiao H. Nanomedomics. ACS NANO 2024; 18:10979-11024. [PMID: 38635910 DOI: 10.1021/acsnano.3c11154] [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: 04/20/2024]
Abstract
Nanomaterials have attractive physicochemical properties. A variety of nanomaterials such as inorganic, lipid, polymers, and protein nanoparticles have been widely developed for nanomedicine via chemical conjugation or physical encapsulation of bioactive molecules. Superior to traditional drugs, nanomedicines offer high biocompatibility, good water solubility, long blood circulation times, and tumor-targeting properties. Capitalizing on this, several nanoformulations have already been clinically approved and many others are currently being studied in clinical trials. Despite their undoubtful success, the molecular mechanism of action of the vast majority of nanomedicines remains poorly understood. To tackle this limitation, herein, this review critically discusses the strategy of applying multiomics analysis to study the mechanism of action of nanomedicines, named nanomedomics, including advantages, applications, and future directions. A comprehensive understanding of the molecular mechanism could provide valuable insight and therefore foster the development and clinical translation of nanomedicines.
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Affiliation(s)
- Ganghao Liang
- Beijing National Laboratory for Molecular Sciences, Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Wanqing Cao
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, P. R. China
| | - Dongsheng Tang
- Beijing National Laboratory for Molecular Sciences, Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Hanchen Zhang
- Beijing National Laboratory for Molecular Sciences, Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yingjie Yu
- State Key Laboratory of Organic-Inorganic Composites, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Jianxun Ding
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, P. R. China
| | - Johannes Karges
- Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Haihua Xiao
- Beijing National Laboratory for Molecular Sciences, Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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12
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Zhang W, Mou M, Hu W, Lu M, Zhang H, Zhang H, Luo Y, Xu H, Tao L, Dai H, Gao J, Zhu F. MOINER: A Novel Multiomics Early Integration Framework for Biomedical Classification and Biomarker Discovery. J Chem Inf Model 2024; 64:2720-2732. [PMID: 38373720 DOI: 10.1021/acs.jcim.4c00013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
In the context of precision medicine, multiomics data integration provides a comprehensive understanding of underlying biological processes and is critical for disease diagnosis and biomarker discovery. One commonly used integration method is early integration through concatenation of multiple dimensionally reduced omics matrices due to its simplicity and ease of implementation. However, this approach is seriously limited by information loss and lack of latent feature interaction. Herein, a novel multiomics early integration framework (MOINER) based on information enhancement and image representation learning is thus presented to address the challenges. MOINER employs the self-attention mechanism to capture the intrinsic correlations of omics-features, which make it significantly outperform the existing state-of-the-art methods for multiomics data integration. Moreover, visualizing the attention embedding and identifying potential biomarkers offer interpretable insights into the prediction results. All source codes and model for MOINER are freely available https://github.com/idrblab/MOINER.
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Affiliation(s)
- Wei Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Minjie Mou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Wei Hu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Mingkun Lu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Hanyu Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Hongning Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Luo
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Hongquan Xu
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Lin Tao
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Haibin Dai
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Jianqing Gao
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
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13
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Demirbaş KC, Yıldız M, Saygılı S, Canpolat N, Kasapçopur Ö. Artificial Intelligence in Pediatrics: Learning to Walk Together. Turk Arch Pediatr 2024; 59:121-130. [PMID: 38454219 PMCID: PMC11059951 DOI: 10.5152/turkarchpediatr.2024.24002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 02/02/2024] [Indexed: 03/09/2024]
Abstract
In this era of rapidly advancing technology, artificial intelligence (AI) has emerged as a transformative force, even being called the Fourth Industrial Revolution, along with gene editing and robotics. While it has undoubtedly become an increasingly important part of our daily lives, it must be recognized that it is not an additional tool, but rather a complex concept that poses a variety of challenges. AI, with considerable potential, has found its place in both medical care and clinical research. Within the vast field of pediatrics, it stands out as a particularly promising advancement. As pediatricians, we are indeed witnessing the impactful integration of AI-based applications into our daily clinical practice and research efforts. These tools are being used for simple to more complex tasks such as diagnosing clinically challenging conditions, predicting disease outcomes, creating treatment plans, educating both patients and healthcare professionals, and generating accurate medical records or scientific papers. In conclusion, the multifaceted applications of AI in pediatrics will increase efficiency and improve the quality of healthcare and research. However, there are certain risks and threats accompanying this advancement including the biases that may contribute to health disparities and, inaccuracies. Therefore, it is crucial to recognize and address the technical, ethical, and legal challenges as well as explore the benefits in both clinical and research fields.
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Affiliation(s)
- Kaan Can Demirbaş
- İstanbul University-Cerrahpaşa, Cerrahpaşa Faculty of Medicine, İstanbul, Turkey
| | - Mehmet Yıldız
- Department of Pediatric Rheumatology, İstanbul University-Cerrahpaşa, Cerrahpaşa Faculty of Medicine, İstanbul, Turkey
| | - Seha Saygılı
- Department of Pediatric Nephrology, İstanbul University-Cerrahpaşa, Cerrahpaşa Faculty of Medicine, İstanbul, Turkey
| | - Nur Canpolat
- Department of Pediatric Nephrology, İstanbul University-Cerrahpaşa, Cerrahpaşa Faculty of Medicine, İstanbul, Turkey
| | - Özgür Kasapçopur
- Department of Pediatric Rheumatology, İstanbul University-Cerrahpaşa, Cerrahpaşa Faculty of Medicine, İstanbul, Turkey
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14
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Zhang JS, Huang S, Chen Z, Chu CH, Takahashi N, Yu OY. Application of omics technologies in cariology research: A critical review with bibliometric analysis. J Dent 2024; 141:104801. [PMID: 38097035 DOI: 10.1016/j.jdent.2023.104801] [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: 09/19/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/19/2023] Open
Abstract
OBJECTIVES To review the application of omics technologies in the field of cariology research and provide critical insights into the emerging opportunities and challenges. DATA & SOURCES Publications on the application of omics technologies in cariology research up to December 2022 were sourced from online databases, including PubMed, Web of Science and Scopus. Two independent reviewers assessed the relevance of the publications to the objective of this review. STUDY SELECTION Studies that employed omics technologies to investigate dental caries were selected from the initial pool of identified publications. A total of 922 publications with one or more omics technologies adopted were included for comprehensive bibliographic analysis. (Meta)genomics (676/922, 73 %) is the predominant omics technology applied for cariology research in the included studies. Other applied omics technologies are metabolomics (108/922, 12 %), proteomics (105/922, 11 %), and transcriptomics (76/922, 8 %). CONCLUSION This study identified an emerging trend in the application of multiple omics technologies in cariology research. Omics technologies possess significant potential in developing strategies for the detection, staging evaluation, risk assessment, prevention, and management of dental caries. Despite the numerous challenges that lie ahead, the integration of multi-omics data obtained from individual biological samples, in conjunction with artificial intelligence technology, may offer potential avenues for further exploration in caries research. CLINICAL SIGNIFICANCE This review presented a comprehensive overview of the application of omics technologies in cariology research and discussed the advantages and challenges of using these methods to detect, assess, predict, prevent, and treat dental caries. It contributes to steering research for improved understanding of dental caries and advancing clinical translation of cariology research outcomes.
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Affiliation(s)
| | - Shi Huang
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, PR China
| | - Zigui Chen
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, PR China; Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Chun-Hung Chu
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, PR China
| | - Nobuhiro Takahashi
- Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Ollie Yiru Yu
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, PR China.
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15
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Adeoye J, Su YX. Artificial intelligence in salivary biomarker discovery and validation for oral diseases. Oral Dis 2024; 30:23-37. [PMID: 37335832 DOI: 10.1111/odi.14641] [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: 03/17/2023] [Revised: 05/19/2023] [Accepted: 05/28/2023] [Indexed: 06/21/2023]
Abstract
Salivary biomarkers can improve the efficacy, efficiency, and timeliness of oral and maxillofacial disease diagnosis and monitoring. Oral and maxillofacial conditions in which salivary biomarkers have been utilized for disease-related outcomes include periodontal diseases, dental caries, oral cancer, temporomandibular joint dysfunction, and salivary gland diseases. However, given the equivocal accuracy of salivary biomarkers during validation, incorporating contemporary analytical techniques for biomarker selection and operationalization from the abundant multi-omics data available may help improve biomarker performance. Artificial intelligence represents one such advanced approach that may optimize the potential of salivary biomarkers to diagnose and manage oral and maxillofacial diseases. Therefore, this review summarized the role and current application of techniques based on artificial intelligence for salivary biomarker discovery and validation in oral and maxillofacial diseases.
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Affiliation(s)
- John Adeoye
- Division of Oral and Maxillofacial Surgery, Faculty of Dentistry, University of Hong Kong, Hong Kong SAR, China
| | - Yu-Xiong Su
- Division of Oral and Maxillofacial Surgery, Faculty of Dentistry, University of Hong Kong, Hong Kong SAR, China
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16
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Saima, Latha S, Sharma R, Kumar A. Role of Network Pharmacology in Prediction of Mechanism of Neuroprotective Compounds. Methods Mol Biol 2024; 2761:159-179. [PMID: 38427237 DOI: 10.1007/978-1-0716-3662-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Network pharmacology is an emerging pioneering approach in the drug discovery process, which is used to predict the therapeutic mechanism of compounds using various bioinformatic tools and databases. Emerging studies have indicated the use of network pharmacological approaches in various research fields, particularly in the identification of possible mechanisms of herbal compounds/ayurvedic formulations in the management of various diseases. These techniques could also play an important role in the prediction of the possible mechanisms of neuroprotective compounds. The first part of the chapter includes an introduction on neuroprotective compounds based on literature. Further, network pharmacological approaches are briefly discussed. The use of network pharmacology in the prediction of the neuroprotective mechanism of compounds is discussed in detail with suitable examples. Finally, the chapter concludes with the current challenges and future prospectives.
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Affiliation(s)
- Saima
- Department of Pharmacology, Delhi Pharmaceutical Science and Research University (DPSRU), New Delhi, India
| | - S Latha
- Department of Pharmacology, Delhi Pharmaceutical Science and Research University (DPSRU), New Delhi, India
| | - Ruchika Sharma
- Centre for Precision Medicine and Pharmacy, Delhi Pharmaceutical Sciences and Research University (DPSRU), New Delhi, India
| | - Anoop Kumar
- Department of Pharmacology, Delhi Pharmaceutical Science and Research University (DPSRU), New Delhi, India
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17
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Jotshi A, Sukla KK, Haque MM, Bose C, Varma B, Koppiker CB, Joshi S, Mishra R. Exploring the human microbiome - A step forward for precision medicine in breast cancer. Cancer Rep (Hoboken) 2023; 6:e1877. [PMID: 37539732 PMCID: PMC10644338 DOI: 10.1002/cnr2.1877] [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: 03/08/2023] [Revised: 06/24/2023] [Accepted: 07/22/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND The second most frequent cancer in the world and the most common malignancy in women is breast cancer. Breast cancer is a significant health concern in India with a high mortality-to-incidence ratio and presentation at a younger age. RECENT FINDINGS Recent studies have identified gut microbiota as a significant factor that can have an influence on the development, treatment, and prognosis of breast cancer. This review article aims to describe the influence of microbial dysbiosis on breast cancer occurrence and the possible interactions between oncobiome and specific breast cancer molecular subtypes. The review further also discusses the role of epigenetics and diet/nutrition in the regulation of the gut and breast microbiome and its association with breast cancer prevention, therapy, and recurrence. Additionally, the recent technological advances in microbiome research, including next-generation sequencing (NGS) technologies, genome sequencing, single-cell sequencing, and microbial metabolomics along with recent advances in artificial intelligence (AI) have also been reviewed. This is an attempt to present a comprehensive status of the microbiome as a key cancer biomarker. CONCLUSION We believe that correlating microbiome and carcinogenesis is important as it can provide insights into the mechanisms by which microbial dysbiosis can influence cancer development and progression, leading to the potential use of the microbiome as a tool for prognostication and personalized therapy.
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Affiliation(s)
- Asmita Jotshi
- Centre for Translational Cancer Research: A Joint Initiative of Indian Institute of Science Education and Research (IISER) Pune and Prashanti Cancer Care Mission (PCCM)PuneIndia
| | | | | | - Chandrani Bose
- Life Sciences R&D, TCS Research, Tata Consultancy Services LimitedPuneIndia
| | - Binuja Varma
- TCS Genomics Lab, Tata Consultancy Services LimitedNew DelhiIndia
| | - C. B. Koppiker
- Centre for Translational Cancer Research: A Joint Initiative of Indian Institute of Science Education and Research (IISER) Pune and Prashanti Cancer Care Mission (PCCM)PuneIndia
- Prashanti Cancer Care Mission, Pune, India and Orchids Breast Health Centre, a PCCM initiativePuneIndia
| | - Sneha Joshi
- Centre for Translational Cancer Research: A Joint Initiative of Indian Institute of Science Education and Research (IISER) Pune and Prashanti Cancer Care Mission (PCCM)PuneIndia
| | - Rupa Mishra
- Centre for Translational Cancer Research: A Joint Initiative of Indian Institute of Science Education and Research (IISER) Pune and Prashanti Cancer Care Mission (PCCM)PuneIndia
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18
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Viana JN, Pilbeam C, Howard M, Scholz B, Ge Z, Fisser C, Mitchell I, Raman S, Leach J. Maintaining High-Touch in High-Tech Digital Health Monitoring and Multi-Omics Prognostication: Ethical, Equity, and Societal Considerations in Precision Health for Palliative Care. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:461-473. [PMID: 37861713 DOI: 10.1089/omi.2023.0120] [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: 10/21/2023]
Abstract
Advances in digital health, systems biology, environmental monitoring, and artificial intelligence (AI) continue to revolutionize health care, ushering a precision health future. More than disease treatment and prevention, precision health aims at maintaining good health throughout the lifespan. However, how can precision health impact care for people with a terminal or life-limiting condition? We examine here the ethical, equity, and societal/relational implications of two precision health modalities, (1) integrated systems biology/multi-omics analysis for disease prognostication and (2) digital health technologies for health status monitoring and communication. We focus on three main ethical and societal considerations: benefits and risks associated with integration of these modalities into the palliative care system; inclusion of underrepresented and marginalized groups in technology development and deployment; and the impact of high-tech modalities on palliative care's highly personalized and "high-touch" practice. We conclude with 10 recommendations for ensuring that precision health technologies, such as multi-omics prognostication and digital health monitoring, for palliative care are developed, tested, and implemented ethically, inclusively, and equitably.
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Affiliation(s)
- John Noel Viana
- Australian National Centre for the Public Awareness of Science, College of Science, The Australian National University, Canberra, Australia
- Responsible Innovation Future Science Platform, Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia
| | - Caitlin Pilbeam
- School of Medicine and Psychology, College of Health and Medicine, The Australian National University, Canberra, Australia
| | - Mark Howard
- Monash Data Futures Institute, Monash University, Clayton, Australia
- Department of Philosophy, School of Philosophical, Historical and International Studies, Monash University, Clayton, Australia
| | - Brett Scholz
- School of Medicine and Psychology, College of Health and Medicine, The Australian National University, Canberra, Australia
| | - Zongyuan Ge
- Monash Data Futures Institute, Monash University, Clayton, Australia
- Department of Data Science & AI, Monash University, Clayton, Australia
| | - Carys Fisser
- Australian National Centre for the Public Awareness of Science, College of Science, The Australian National University, Canberra, Australia
- School of Medicine and Psychology, College of Health and Medicine, The Australian National University, Canberra, Australia
| | - Imogen Mitchell
- School of Medicine and Psychology, College of Health and Medicine, The Australian National University, Canberra, Australia
- Intensive Care Unit, Canberra Hospital, Canberra, Australia
| | - Sujatha Raman
- Australian National Centre for the Public Awareness of Science, College of Science, The Australian National University, Canberra, Australia
| | - Joan Leach
- Australian National Centre for the Public Awareness of Science, College of Science, The Australian National University, Canberra, Australia
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El Naqa I, Karolak A, Luo Y, Folio L, Tarhini AA, Rollison D, Parodi K. Translation of AI into oncology clinical practice. Oncogene 2023; 42:3089-3097. [PMID: 37684407 DOI: 10.1038/s41388-023-02826-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023]
Abstract
Artificial intelligence (AI) is a transformative technology that is capturing popular imagination and can revolutionize biomedicine. AI and machine learning (ML) algorithms have the potential to break through existing barriers in oncology research and practice such as automating workflow processes, personalizing care, and reducing healthcare disparities. Emerging applications of AI/ML in the literature include screening and early detection of cancer, disease diagnosis, response prediction, prognosis, and accelerated drug discovery. Despite this excitement, only few AI/ML models have been properly validated and fewer have become regulated products for routine clinical use. In this review, we highlight the main challenges impeding AI/ML clinical translation. We present different clinical use cases from the domains of radiology, radiation oncology, immunotherapy, and drug discovery in oncology. We dissect the unique challenges and opportunities associated with each of these cases. Finally, we summarize the general requirements for successful AI/ML implementation in the clinic, highlighting specific examples and points of emphasis including the importance of multidisciplinary collaboration of stakeholders, role of domain experts in AI augmentation, transparency of AI/ML models, and the establishment of a comprehensive quality assurance program to mitigate risks of training bias and data drifts, all culminating toward safer and more beneficial AI/ML applications in oncology labs and clinics.
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Affiliation(s)
- Issam El Naqa
- Department of Machine Learning, Moffitt Cancer Center, Tampa, FL, 33612, USA.
| | - Aleksandra Karolak
- Department of Machine Learning, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Yi Luo
- Department of Machine Learning, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Les Folio
- Diagnostic Imaging & Interventional Radiology, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Ahmad A Tarhini
- Cutaneous Oncology and Immunology, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Dana Rollison
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Katia Parodi
- Department of Medical Physics, Ludwig-Maximilians-Universität München, Munich, Germany
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20
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Cembrowska-Lech D, Krzemińska A, Miller T, Nowakowska A, Adamski C, Radaczyńska M, Mikiciuk G, Mikiciuk M. An Integrated Multi-Omics and Artificial Intelligence Framework for Advance Plant Phenotyping in Horticulture. BIOLOGY 2023; 12:1298. [PMID: 37887008 PMCID: PMC10603917 DOI: 10.3390/biology12101298] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023]
Abstract
This review discusses the transformative potential of integrating multi-omics data and artificial intelligence (AI) in advancing horticultural research, specifically plant phenotyping. The traditional methods of plant phenotyping, while valuable, are limited in their ability to capture the complexity of plant biology. The advent of (meta-)genomics, (meta-)transcriptomics, proteomics, and metabolomics has provided an opportunity for a more comprehensive analysis. AI and machine learning (ML) techniques can effectively handle the complexity and volume of multi-omics data, providing meaningful interpretations and predictions. Reflecting the multidisciplinary nature of this area of research, in this review, readers will find a collection of state-of-the-art solutions that are key to the integration of multi-omics data and AI for phenotyping experiments in horticulture, including experimental design considerations with several technical and non-technical challenges, which are discussed along with potential solutions. The future prospects of this integration include precision horticulture, predictive breeding, improved disease and stress response management, sustainable crop management, and exploration of plant biodiversity. The integration of multi-omics and AI holds immense promise for revolutionizing horticultural research and applications, heralding a new era in plant phenotyping.
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Affiliation(s)
- Danuta Cembrowska-Lech
- Department of Physiology and Biochemistry, Institute of Biology, University of Szczecin, Felczaka 3c, 71-412 Szczecin, Poland;
- Polish Society of Bioinformatics and Data Science BIODATA, Popiełuszki 4c, 71-214 Szczecin, Poland; (A.K.); (T.M.)
| | - Adrianna Krzemińska
- Polish Society of Bioinformatics and Data Science BIODATA, Popiełuszki 4c, 71-214 Szczecin, Poland; (A.K.); (T.M.)
- Institute of Biology, University of Szczecin, Wąska 13, 71-415 Szczecin, Poland;
| | - Tymoteusz Miller
- Polish Society of Bioinformatics and Data Science BIODATA, Popiełuszki 4c, 71-214 Szczecin, Poland; (A.K.); (T.M.)
- Institute of Marine and Environmental Sciences, University of Szczecin, Wąska 13, 71-415 Szczecin, Poland
| | - Anna Nowakowska
- Department of Physiology and Biochemistry, Institute of Biology, University of Szczecin, Felczaka 3c, 71-412 Szczecin, Poland;
| | - Cezary Adamski
- Institute of Biology, University of Szczecin, Wąska 13, 71-415 Szczecin, Poland;
| | | | - Grzegorz Mikiciuk
- Department of Horticulture, Faculty of Environmental Management and Agriculture, West Pomeranian University of Technology in Szczecin, Słowackiego 17, 71-434 Szczecin, Poland;
| | - Małgorzata Mikiciuk
- Department of Bioengineering, Faculty of Environmental Management and Agriculture, West Pomeranian University of Technology in Szczecin, Słowackiego 17, 71-434 Szczecin, Poland;
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21
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Gómez-Cebrián N, Gras-Colomer E, Poveda Andrés JL, Pineda-Lucena A, Puchades-Carrasco L. Omics-Based Approaches for the Characterization of Pompe Disease Metabolic Phenotypes. BIOLOGY 2023; 12:1159. [PMID: 37759559 PMCID: PMC10525434 DOI: 10.3390/biology12091159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023]
Abstract
Lysosomal storage disorders (LSDs) constitute a large group of rare, multisystemic, inherited disorders of metabolism, characterized by defects in lysosomal enzymes, accessory proteins, membrane transporters or trafficking proteins. Pompe disease (PD) is produced by mutations in the acid alpha-glucosidase (GAA) lysosomal enzyme. This enzymatic deficiency leads to the aberrant accumulation of glycogen in the lysosome. The onset of symptoms, including a variety of neurological and multiple-organ pathologies, can range from birth to adulthood, and disease severity can vary between individuals. Although very significant advances related to the development of new treatments, and also to the improvement of newborn screening programs and tools for a more accurate diagnosis and follow-up of patients, have occurred over recent years, there exists an unmet need for further understanding the molecular mechanisms underlying the progression of the disease. Also, the reason why currently available treatments lose effectiveness over time in some patients is not completely understood. In this scenario, characterization of the metabolic phenotype is a valuable approach to gain insights into the global impact of lysosomal dysfunction, and its potential correlation with clinical progression and response to therapies. These approaches represent a discovery tool for investigating disease-induced modifications in the complete metabolic profile, including large numbers of metabolites that are simultaneously analyzed, enabling the identification of novel potential biomarkers associated with these conditions. This review aims to highlight the most relevant findings of recently published omics-based studies with a particular focus on describing the clinical potential of the specific metabolic phenotypes associated to different subgroups of PD patients.
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Affiliation(s)
- Nuria Gómez-Cebrián
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain
| | - Elena Gras-Colomer
- Pharmacy Department, Hospital Manises of Valencia, 46940 Valencia, Spain
| | | | - Antonio Pineda-Lucena
- Molecular Therapeutics Program, Centro de Investigación Médica Aplicada, 31008 Pamplona, Spain
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22
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Wang Z, Kim W, Wang YW, Yakubovich E, Dong C, Trail F, Townsend JP, Yarden O. The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1214537. [PMID: 37746130 PMCID: PMC10512317 DOI: 10.3389/ffunb.2023.1214537] [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: 04/30/2023] [Accepted: 06/06/2023] [Indexed: 09/26/2023]
Abstract
Advances in genomics and transcriptomics accompanying the rapid accumulation of omics data have provided new tools that have transformed and expanded the traditional concepts of model fungi. Evolutionary genomics and transcriptomics have flourished with the use of classical and newer fungal models that facilitate the study of diverse topics encompassing fungal biology and development. Technological advances have also created the opportunity to obtain and mine large datasets. One such continuously growing dataset is that of the Sordariomycetes, which exhibit a richness of species, ecological diversity, economic importance, and a profound research history on amenable models. Currently, 3,574 species of this class have been sequenced, comprising nearly one-third of the available ascomycete genomes. Among these genomes, multiple representatives of the model genera Fusarium, Neurospora, and Trichoderma are present. In this review, we examine recently published studies and data on the Sordariomycetes that have contributed novel insights to the field of fungal evolution via integrative analyses of the genetic, pathogenic, and other biological characteristics of the fungi. Some of these studies applied ancestral state analysis of gene expression among divergent lineages to infer regulatory network models, identify key genetic elements in fungal sexual development, and investigate the regulation of conidial germination and secondary metabolism. Such multispecies investigations address challenges in the study of fungal evolutionary genomics derived from studies that are often based on limited model genomes and that primarily focus on the aspects of biology driven by knowledge drawn from a few model species. Rapidly accumulating information and expanding capabilities for systems biological analysis of Big Data are setting the stage for the expansion of the concept of model systems from unitary taxonomic species/genera to inclusive clusters of well-studied models that can facilitate both the in-depth study of specific lineages and also investigation of trait diversity across lineages. The Sordariomycetes class, in particular, offers abundant omics data and a large and active global research community. As such, the Sordariomycetes can form a core omics clade, providing a blueprint for the expansion of our knowledge of evolution at the genomic scale in the exciting era of Big Data and artificial intelligence, and serving as a reference for the future analysis of different taxonomic levels within the fungal kingdom.
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Affiliation(s)
- Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Wonyong Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Republic of Korea
| | - Yen-Wen Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Elizabeta Yakubovich
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Caihong Dong
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Frances Trail
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
- Department of Ecology and Evolutionary Biology, Program in Microbiology, and Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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23
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Ying W. Phenomic Studies on Diseases: Potential and Challenges. PHENOMICS (CHAM, SWITZERLAND) 2023; 3:285-299. [PMID: 36714223 PMCID: PMC9867904 DOI: 10.1007/s43657-022-00089-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 11/21/2022] [Accepted: 11/24/2022] [Indexed: 01/23/2023]
Abstract
The rapid development of such research field as multi-omics and artificial intelligence (AI) has made it possible to acquire and analyze the multi-dimensional big data of human phenomes. Increasing evidence has indicated that phenomics can provide a revolutionary strategy and approach for discovering new risk factors, diagnostic biomarkers and precision therapies of diseases, which holds profound advantages over conventional approaches for realizing precision medicine: first, the big data of patients' phenomes can provide remarkably richer information than that of the genomes; second, phenomic studies on diseases may expose the correlations among cross-scale and multi-dimensional phenomic parameters as well as the mechanisms underlying the correlations; and third, phenomics-based studies are big data-driven studies, which can significantly enhance the possibility and efficiency for generating novel discoveries. However, phenomic studies on human diseases are still in early developmental stage, which are facing multiple major challenges and tasks: first, there is significant deficiency in analytical and modeling approaches for analyzing the multi-dimensional data of human phenomes; second, it is crucial to establish universal standards for acquirement and management of phenomic data of patients; third, new methods and devices for acquirement of phenomic data of patients under clinical settings should be developed; fourth, it is of significance to establish the regulatory and ethical guidelines for phenomic studies on diseases; and fifth, it is important to develop effective international cooperation. It is expected that phenomic studies on diseases would profoundly and comprehensively enhance our capacity in prevention, diagnosis and treatment of diseases.
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Affiliation(s)
- Weihai Ying
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030 China
- Collaborative Innovation Center for Genetics and Development, Shanghai, 200043 China
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24
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Flores JE, Claborne DM, Weller ZD, Webb-Robertson BJM, Waters KM, Bramer LM. Missing data in multi-omics integration: Recent advances through artificial intelligence. Front Artif Intell 2023; 6:1098308. [PMID: 36844425 PMCID: PMC9949722 DOI: 10.3389/frai.2023.1098308] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
Biological systems function through complex interactions between various 'omics (biomolecules), and a more complete understanding of these systems is only possible through an integrated, multi-omic perspective. This has presented the need for the development of integration approaches that are able to capture the complex, often non-linear, interactions that define these biological systems and are adapted to the challenges of combining the heterogenous data across 'omic views. A principal challenge to multi-omic integration is missing data because all biomolecules are not measured in all samples. Due to either cost, instrument sensitivity, or other experimental factors, data for a biological sample may be missing for one or more 'omic techologies. Recent methodological developments in artificial intelligence and statistical learning have greatly facilitated the analyses of multi-omics data, however many of these techniques assume access to completely observed data. A subset of these methods incorporate mechanisms for handling partially observed samples, and these methods are the focus of this review. We describe recently developed approaches, noting their primary use cases and highlighting each method's approach to handling missing data. We additionally provide an overview of the more traditional missing data workflows and their limitations; and we discuss potential avenues for further developments as well as how the missing data issue and its current solutions may generalize beyond the multi-omics context.
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Affiliation(s)
- Javier E. Flores
- Pacific Northwest National Laboratory, Biological Sciences Division, Earth and Biological Sciences Directorate, Richland, WA, United States
| | - Daniel M. Claborne
- Pacific Northwest National Laboratory, Artificial Intelligence and Data Analytics Division, National Security Directorate, Richland, WA, United States
| | - Zachary D. Weller
- Pacific Northwest National Laboratory, Artificial Intelligence and Data Analytics Division, National Security Directorate, Richland, WA, United States
| | - Bobbie-Jo M. Webb-Robertson
- Pacific Northwest National Laboratory, Biological Sciences Division, Earth and Biological Sciences Directorate, Richland, WA, United States
| | - Katrina M. Waters
- Pacific Northwest National Laboratory, Biological Sciences Division, Earth and Biological Sciences Directorate, Richland, WA, United States
| | - Lisa M. Bramer
- Pacific Northwest National Laboratory, Biological Sciences Division, Earth and Biological Sciences Directorate, Richland, WA, United States,*Correspondence: Lisa M. Bramer ✉
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25
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Zhang N, Kandalai S, Zhou X, Hossain F, Zheng Q. Applying multi-omics toward tumor microbiome research. IMETA 2023; 2:e73. [PMID: 38868335 PMCID: PMC10989946 DOI: 10.1002/imt2.73] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/30/2022] [Accepted: 11/28/2022] [Indexed: 06/14/2024]
Abstract
Rather than a "short-term tenant," the tumor microbiome has been shown to play a vital role as a "permanent resident," affecting carcinogenesis, cancer development, metastasis, and cancer therapies. As the tumor microbiome has great potential to become a target for the early diagnosis and treatment of cancer, recent research on the relevance of the tumor microbiota has attracted a wide range of attention from various scientific fields, resulting in remarkable progress that benefits from the development of interdisciplinary technologies. However, there are still a great variety of challenges in this emerging area, such as the low biomass of intratumoral bacteria and unculturable character of some microbial species. Due to the complexity of tumor microbiome research (e.g., the heterogeneity of tumor microenvironment), new methods with high spatial and temporal resolution are urgently needed. Among these developing methods, multi-omics technologies (combinations of genomics, transcriptomics, proteomics, and metabolomics) are powerful approaches that can facilitate the understanding of the tumor microbiome on different levels of the central dogma. Therefore, multi-omics (especially single-cell omics) will make enormous impacts on the future studies of the interplay between microbes and tumor microenvironment. In this review, we have systematically summarized the advances in multi-omics and their existing and potential applications in tumor microbiome research, thus providing an omics toolbox for investigators to reference in the future.
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Affiliation(s)
- Nan Zhang
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
| | - Shruthi Kandalai
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
| | - Xiaozhuang Zhou
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
| | - Farzana Hossain
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
| | - Qingfei Zheng
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
- Department of Biological Chemistry and Pharmacology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
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26
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Targeted Quantification of Protein Phosphorylation and Its Contributions towards Mathematical Modeling of Signaling Pathways. Molecules 2023; 28:molecules28031143. [PMID: 36770810 PMCID: PMC9919559 DOI: 10.3390/molecules28031143] [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: 11/18/2022] [Revised: 01/12/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Post-translational modifications (PTMs) are key regulatory mechanisms that can control protein function. Of these, phosphorylation is the most common and widely studied. Because of its importance in regulating cell signaling, precise and accurate measurements of protein phosphorylation across wide dynamic ranges are crucial to understanding how signaling pathways function. Although immunological assays are commonly used to detect phosphoproteins, their lack of sensitivity, specificity, and selectivity often make them unreliable for quantitative measurements of complex biological samples. Recent advances in Mass Spectrometry (MS)-based targeted proteomics have made it a more useful approach than immunoassays for studying the dynamics of protein phosphorylation. Selected reaction monitoring (SRM)-also known as multiple reaction monitoring (MRM)-and parallel reaction monitoring (PRM) can quantify relative and absolute abundances of protein phosphorylation in multiplexed fashions targeting specific pathways. In addition, the refinement of these tools by enrichment and fractionation strategies has improved measurement of phosphorylation of low-abundance proteins. The quantitative data generated are particularly useful for building and parameterizing mathematical models of complex phospho-signaling pathways. Potentially, these models can provide a framework for linking analytical measurements of clinical samples to better diagnosis and treatment of disease.
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27
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Liao J, Li X, Gan Y, Han S, Rong P, Wang W, Li W, Zhou L. Artificial intelligence assists precision medicine in cancer treatment. Front Oncol 2023; 12:998222. [PMID: 36686757 PMCID: PMC9846804 DOI: 10.3389/fonc.2022.998222] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/22/2022] [Indexed: 01/06/2023] Open
Abstract
Cancer is a major medical problem worldwide. Due to its high heterogeneity, the use of the same drugs or surgical methods in patients with the same tumor may have different curative effects, leading to the need for more accurate treatment methods for tumors and personalized treatments for patients. The precise treatment of tumors is essential, which renders obtaining an in-depth understanding of the changes that tumors undergo urgent, including changes in their genes, proteins and cancer cell phenotypes, in order to develop targeted treatment strategies for patients. Artificial intelligence (AI) based on big data can extract the hidden patterns, important information, and corresponding knowledge behind the enormous amount of data. For example, the ML and deep learning of subsets of AI can be used to mine the deep-level information in genomics, transcriptomics, proteomics, radiomics, digital pathological images, and other data, which can make clinicians synthetically and comprehensively understand tumors. In addition, AI can find new biomarkers from data to assist tumor screening, detection, diagnosis, treatment and prognosis prediction, so as to providing the best treatment for individual patients and improving their clinical outcomes.
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Affiliation(s)
- Jinzhuang Liao
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Xiaoying Li
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Yu Gan
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Shuangze Han
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Pengfei Rong
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China,Cell Transplantation and Gene Therapy Institute, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China,*Correspondence: Pengfei Rong, ; Wei Wang, ; Wei Li, ; Li Zhou,
| | - Wei Wang
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China,Cell Transplantation and Gene Therapy Institute, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China,*Correspondence: Pengfei Rong, ; Wei Wang, ; Wei Li, ; Li Zhou,
| | - Wei Li
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China,Cell Transplantation and Gene Therapy Institute, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China,*Correspondence: Pengfei Rong, ; Wei Wang, ; Wei Li, ; Li Zhou,
| | - Li Zhou
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China,Cell Transplantation and Gene Therapy Institute, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Department of Pathology, The Xiangya Hospital of Central South University, Changsha, Hunan, China,*Correspondence: Pengfei Rong, ; Wei Wang, ; Wei Li, ; Li Zhou,
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28
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Srivastava R. Applications of artificial intelligence multiomics in precision oncology. J Cancer Res Clin Oncol 2023; 149:503-510. [PMID: 35796775 DOI: 10.1007/s00432-022-04161-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 06/17/2022] [Indexed: 02/06/2023]
Abstract
Cancer is the second leading worldwide disease that depends on oncogenic mutations and non-mutated genes for survival. Recent advancements in next-generation sequencing (NGS) have transformed the health care sector with big data and machine learning (ML) approaches. NGS data are able to detect the abnormalities and mutations in the oncogenes. These multi-omics analyses are used for risk prediction, early diagnosis, accurate prognosis, and identification of biomarkers in cancer patients. The availability of these cancer data and their analysis may provide insights into the biology of the disease, which can be used for the personalized treatment of cancer patients. Bioinformatics tools are delivering this promise by managing, integrating, and analyzing these complex datasets. The clinical outcomes of cancer patients are improved by the use of various innovative methods implicated particularly for diagnosis and therapeutics. ML-based artificial intelligence (AI) applications are solving these issues to a great extent. AI techniques are used to update the patients on a personalized basis about their treatment procedures, progress, recovery, therapies used, dietary changes in lifestyles patterns along with the survival summary of previously recovered cancer patients. In this way, the patients are becoming more aware of their diseases and the entire clinical treatment procedures. Though the technology has its own advantages and disadvantages, we hope that the day is not so far when AI techniques will provide personalized treatment to cancer patients tailored to their needs in much quicker ways.
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Affiliation(s)
- Ruby Srivastava
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
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29
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Santa Maria JP, Wang Y, Camargo LM. Perspective on the challenges and opportunities of accelerating drug discovery with artificial intelligence. FRONTIERS IN BIOINFORMATICS 2023; 3:1121591. [PMID: 36909937 PMCID: PMC9997711 DOI: 10.3389/fbinf.2023.1121591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/06/2023] [Indexed: 02/25/2023] Open
Affiliation(s)
- John P Santa Maria
- Data and Translational Sciences, UCB Biosciences Inc., Cambridge, MA, United States
| | - Yuan Wang
- Data and Translational Sciences, UCB Biosciences Inc., Cambridge, MA, United States
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30
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Kumar K, Bhowmik D, Mandloi S, Gautam A, Lahiri A, Biswas N, Paul S, Chakrabarti S. Integrating Multi-Omics Data to Construct Reliable Interconnected Models of Signaling, Gene Regulatory, and Metabolic Pathways. Methods Mol Biol 2023; 2634:139-151. [PMID: 37074577 DOI: 10.1007/978-1-0716-3008-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Alteration of the status of the metabolic enzymes could be a probable way to regulate metabolic reprogramming, which is a critical cellular adaptation mechanism especially for cancer cells. Coordination among biological pathways, such as gene-regulatory, signaling, and metabolic pathways is crucial for regulating metabolic adaptation. Also, incorporation of resident microbial metabolic potential in human body can influence the interplay between the microbiome and the systemic or tissue metabolic environments. Systemic framework for model-based integration of multi-omics data can ultimately improve our understanding of metabolic reprogramming at holistic level. However, the interconnectivity and novel meta-pathway regulatory mechanisms are relatively lesser explored and understood. Hence, we propose a computational protocol that utilizes multi-omics data to identify probable cross-pathway regulatory and protein-protein interaction (PPI) links connecting signaling proteins or transcription factors or miRNAs to metabolic enzymes and their metabolites using network analysis and mathematical modeling. These cross-pathway links were shown to play important roles in metabolic reprogramming in cancer scenarios.
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Affiliation(s)
- Krishna Kumar
- Structural Biology and Bioinformatics Division, Council for Scientific and Industrial Research (CSIR) - Indian Institute of Chemical Biology (IICB), Kolkata, West Bengal, India
| | - Debaleena Bhowmik
- Structural Biology and Bioinformatics Division, Council for Scientific and Industrial Research (CSIR) - Indian Institute of Chemical Biology (IICB), Kolkata, West Bengal, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Sapan Mandloi
- Structural Biology and Bioinformatics Division, Council for Scientific and Industrial Research (CSIR) - Indian Institute of Chemical Biology (IICB), Kolkata, West Bengal, India
| | - Anupam Gautam
- Algorithms in Bioinformatics, Institute for Bioinformatics and Medical Informatics, University of Tübingen,, Tübingen, Germany
- International Max Planck Research School "From Molecules to Organisms," Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, University of Tübingen, Tübingen, Germany
| | - Abhishake Lahiri
- Structural Biology and Bioinformatics Division, Council for Scientific and Industrial Research (CSIR) - Indian Institute of Chemical Biology (IICB), Kolkata, West Bengal, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Nupur Biswas
- Structural Biology and Bioinformatics Division, Council for Scientific and Industrial Research (CSIR) - Indian Institute of Chemical Biology (IICB), Kolkata, West Bengal, India
| | - Sandip Paul
- JIS Institute of Advanced Studies and Research, JIS University, Kolkata, India.
| | - Saikat Chakrabarti
- Structural Biology and Bioinformatics Division, Council for Scientific and Industrial Research (CSIR) - Indian Institute of Chemical Biology (IICB), Kolkata, West Bengal, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
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31
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Krittanawong C, Singh NK, Scheuring RA, Urquieta E, Bershad EM, Macaulay TR, Kaplin S, Dunn C, Kry SF, Russomano T, Shepanek M, Stowe RP, Kirkpatrick AW, Broderick TJ, Sibonga JD, Lee AG, Crucian BE. Human Health during Space Travel: State-of-the-Art Review. Cells 2022; 12:cells12010040. [PMID: 36611835 PMCID: PMC9818606 DOI: 10.3390/cells12010040] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
The field of human space travel is in the midst of a dramatic revolution. Upcoming missions are looking to push the boundaries of space travel, with plans to travel for longer distances and durations than ever before. Both the National Aeronautics and Space Administration (NASA) and several commercial space companies (e.g., Blue Origin, SpaceX, Virgin Galactic) have already started the process of preparing for long-distance, long-duration space exploration and currently plan to explore inner solar planets (e.g., Mars) by the 2030s. With the emergence of space tourism, space travel has materialized as a potential new, exciting frontier of business, hospitality, medicine, and technology in the coming years. However, current evidence regarding human health in space is very limited, particularly pertaining to short-term and long-term space travel. This review synthesizes developments across the continuum of space health including prior studies and unpublished data from NASA related to each individual organ system, and medical screening prior to space travel. We categorized the extraterrestrial environment into exogenous (e.g., space radiation and microgravity) and endogenous processes (e.g., alteration of humans' natural circadian rhythm and mental health due to confinement, isolation, immobilization, and lack of social interaction) and their various effects on human health. The aim of this review is to explore the potential health challenges associated with space travel and how they may be overcome in order to enable new paradigms for space health, as well as the use of emerging Artificial Intelligence based (AI) technology to propel future space health research.
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Affiliation(s)
- Chayakrit Krittanawong
- Department of Medicine and Center for Space Medicine, Section of Cardiology, Baylor College of Medicine, Houston, TX 77030, USA
- Translational Research Institute for Space Health, Houston, TX 77030, USA
- Department of Cardiovascular Diseases, New York University School of Medicine, New York, NY 10016, USA
- Correspondence: or (C.K.); (B.E.C.); Tel.: +1-713-798-4951 (C.K.); +1-281-483-0123 (B.E.C.)
| | - Nitin Kumar Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | | | - Emmanuel Urquieta
- Translational Research Institute for Space Health, Houston, TX 77030, USA
- Department of Emergency Medicine and Center for Space Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric M. Bershad
- Department of Neurology, Center for Space Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Scott Kaplin
- Department of Cardiovascular Diseases, New York University School of Medicine, New York, NY 10016, USA
| | - Carly Dunn
- Department of Dermatology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stephen F. Kry
- Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Marc Shepanek
- Office of the Chief Health and Medical Officer, NASA, Washington, DC 20546, USA
| | | | - Andrew W. Kirkpatrick
- Department of Surgery and Critical Care Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | | | - Jean D. Sibonga
- Division of Biomedical Research and Environmental Sciences, NASA Lyndon B. Johnson Space Center, Houston, TX 77058, USA
| | - Andrew G. Lee
- Department of Ophthalmology, University of Texas Medical Branch School of Medicine, Galveston, TX 77555, USA
- Department of Ophthalmology, Blanton Eye Institute, Houston Methodist Hospital, Houston, TX 77030, USA
- Department of Ophthalmology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Ophthalmology, Texas A and M College of Medicine, College Station, TX 77807, USA
- Department of Ophthalmology, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
- Departments of Ophthalmology, Neurology, and Neurosurgery, Weill Cornell Medicine, New York, NY 10021, USA
| | - Brian E. Crucian
- National Aeronautics and Space Administration (NASA) Johnson Space Center, Human Health and Performance Directorate, Houston, TX 77058, USA
- Correspondence: or (C.K.); (B.E.C.); Tel.: +1-713-798-4951 (C.K.); +1-281-483-0123 (B.E.C.)
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Soni M, Pratap JV. Development of Novel Anti-Leishmanials: The Case for Structure-Based Approaches. Pathogens 2022; 11:pathogens11080950. [PMID: 36015070 PMCID: PMC9414883 DOI: 10.3390/pathogens11080950] [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: 05/06/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
The neglected tropical disease (NTD) leishmaniasis is the collective name given to a diverse group of illnesses caused by ~20 species belonging to the genus Leishmania, a majority of which are vector borne and associated with complex life cycles that cause immense health, social, and economic burdens locally, but individually are not a major global health priority. Therapeutic approaches against leishmaniasis have various inadequacies including drug resistance and a lack of effective control and eradication of the disease spread. Therefore, the development of a rationale-driven, target based approaches towards novel therapeutics against leishmaniasis is an emergent need. The utilization of Artificial Intelligence/Machine Learning methods, which have made significant advances in drug discovery applications, would benefit the discovery process. In this review, following a summary of the disease epidemiology and available therapies, we consider three important leishmanial metabolic pathways that can be attractive targets for a structure-based drug discovery approach towards the development of novel anti-leishmanials. The folate biosynthesis pathway is critical, as Leishmania is auxotrophic for folates that are essential in many metabolic pathways. Leishmania can not synthesize purines de novo, and salvage them from the host, making the purine salvage pathway an attractive target for novel therapeutics. Leishmania also possesses an organelle glycosome, evolutionarily related to peroxisomes of higher eukaryotes, which is essential for the survival of the parasite. Research towards therapeutics is underway against enzymes from the first two pathways, while the third is as yet unexplored.
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Affiliation(s)
- Mohini Soni
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - J. Venkatesh Pratap
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Correspondence:
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Akinyelu AA, Zaccagna F, Grist JT, Castelli M, Rundo L. Brain Tumor Diagnosis Using Machine Learning, Convolutional Neural Networks, Capsule Neural Networks and Vision Transformers, Applied to MRI: A Survey. J Imaging 2022; 8:205. [PMID: 35893083 PMCID: PMC9331677 DOI: 10.3390/jimaging8080205] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 06/20/2022] [Accepted: 07/12/2022] [Indexed: 02/01/2023] Open
Abstract
Management of brain tumors is based on clinical and radiological information with presumed grade dictating treatment. Hence, a non-invasive assessment of tumor grade is of paramount importance to choose the best treatment plan. Convolutional Neural Networks (CNNs) represent one of the effective Deep Learning (DL)-based techniques that have been used for brain tumor diagnosis. However, they are unable to handle input modifications effectively. Capsule neural networks (CapsNets) are a novel type of machine learning (ML) architecture that was recently developed to address the drawbacks of CNNs. CapsNets are resistant to rotations and affine translations, which is beneficial when processing medical imaging datasets. Moreover, Vision Transformers (ViT)-based solutions have been very recently proposed to address the issue of long-range dependency in CNNs. This survey provides a comprehensive overview of brain tumor classification and segmentation techniques, with a focus on ML-based, CNN-based, CapsNet-based, and ViT-based techniques. The survey highlights the fundamental contributions of recent studies and the performance of state-of-the-art techniques. Moreover, we present an in-depth discussion of crucial issues and open challenges. We also identify some key limitations and promising future research directions. We envisage that this survey shall serve as a good springboard for further study.
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Affiliation(s)
- Andronicus A. Akinyelu
- NOVA Information Management School (NOVA IMS), Universidade NOVA de Lisboa, Campus de Campolide, 1070-312 Lisboa, Portugal;
- Department of Computer Science and Informatics, University of the Free State, Phuthaditjhaba 9866, South Africa
| | - Fulvio Zaccagna
- Department of Biomedical and Neuromotor Sciences, Alma Mater Studiorum-University of Bologna, 40138 Bologna, Italy;
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Functional and Molecular Neuroimaging Unit, 40139 Bologna, Italy
| | - James T. Grist
- Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3PT, UK;
- Department of Radiology, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
- Oxford Centre for Clinical Magnetic Research Imaging, University of Oxford, Oxford OX3 9DU, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2SY, UK
| | - Mauro Castelli
- NOVA Information Management School (NOVA IMS), Universidade NOVA de Lisboa, Campus de Campolide, 1070-312 Lisboa, Portugal;
| | - Leonardo Rundo
- Department of Information and Electrical Engineering and Applied Mathematics, University of Salerno, 84084 Fisciano, Italy
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When artificial intelligence meets PD-1/PD-L1 inhibitors: Population screening, response prediction and efficacy evaluation. Comput Biol Med 2022; 145:105499. [DOI: 10.1016/j.compbiomed.2022.105499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/26/2022] [Accepted: 04/03/2022] [Indexed: 02/07/2023]
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Noor F, Tahir ul Qamar M, Ashfaq UA, Albutti A, Alwashmi ASS, Aljasir MA. Network Pharmacology Approach for Medicinal Plants: Review and Assessment. Pharmaceuticals (Basel) 2022; 15:572. [PMID: 35631398 PMCID: PMC9143318 DOI: 10.3390/ph15050572] [Citation(s) in RCA: 107] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 12/13/2022] Open
Abstract
Natural products have played a critical role in medicine due to their ability to bind and modulate cellular targets involved in disease. Medicinal plants hold a variety of bioactive scaffolds for the treatment of multiple disorders. The less adverse effects, affordability, and easy accessibility highlight their potential in traditional remedies. Identifying pharmacological targets from active ingredients of medicinal plants has become a hot topic for biomedical research to generate innovative therapies. By developing an unprecedented opportunity for the systematic investigation of traditional medicines, network pharmacology is evolving as a systematic paradigm and becoming a frontier research field of drug discovery and development. The advancement of network pharmacology has opened up new avenues for understanding the complex bioactive components found in various medicinal plants. This study is attributed to a comprehensive summary of network pharmacology based on current research, highlighting various active ingredients, related techniques/tools/databases, and drug discovery and development applications. Moreover, this study would serve as a protocol for discovering novel compounds to explore the full range of biological potential of traditionally used plants. We have attempted to cover this vast topic in the review form. We hope it will serve as a significant pioneer for researchers working with medicinal plants by employing network pharmacology approaches.
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Affiliation(s)
- Fatima Noor
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan; (F.N.); (M.T.u.Q.)
| | - Muhammad Tahir ul Qamar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan; (F.N.); (M.T.u.Q.)
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan; (F.N.); (M.T.u.Q.)
| | - Aqel Albutti
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Ameen S. S. Alwashmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (A.S.S.A.); (M.A.A.)
| | - Mohammad Abdullah Aljasir
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (A.S.S.A.); (M.A.A.)
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Chen Z, Ye N, Teng C, Li X. Alternations and Applications of the Structural and Functional Connectome in Gliomas: A Mini-Review. Front Neurosci 2022; 16:856808. [PMID: 35478847 PMCID: PMC9035851 DOI: 10.3389/fnins.2022.856808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/28/2022] [Indexed: 12/12/2022] Open
Abstract
In the central nervous system, gliomas are the most common, but complex primary tumors. Genome-based molecular and clinical studies have revealed different classifications and subtypes of gliomas. Neuroradiological approaches have non-invasively provided a macroscopic view for surgical resection and therapeutic effects. The connectome is a structural map of a physical object, the brain, which raises issues of spatial scale and definition, and it is calculated through diffusion magnetic resonance imaging (MRI) and functional MRI. In this study, we reviewed the basic principles and attributes of the structural and functional connectome, followed by the alternations of connectomes and their influences on glioma. To extend the applications of connectome, we demonstrated that a series of multi-center projects still need to be conducted to systemically investigate the connectome and the structural-functional coupling of glioma. Additionally, the brain-computer interface based on accurate connectome could provide more precise structural and functional data, which are significant for surgery and postoperative recovery. Besides, integrating the data from different sources, including connectome and other omics information, and their processing with artificial intelligence, together with validated biological and clinical findings will be significant for the development of a personalized surgical strategy.
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Affiliation(s)
- Ziyan Chen
- Department of Neurosurgery, Xiangya Hospital, Central South University, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
| | - Ningrong Ye
- Department of Neurosurgery, Xiangya Hospital, Central South University, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
| | - Chubei Teng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
- Department of Neurosurgery, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Xuejun Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
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Qiu H, Ding S, Liu J, Wang L, Wang X. Applications of Artificial Intelligence in Screening, Diagnosis, Treatment, and Prognosis of Colorectal Cancer. Curr Oncol 2022; 29:1773-1795. [PMID: 35323346 PMCID: PMC8947571 DOI: 10.3390/curroncol29030146] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/28/2022] [Accepted: 03/03/2022] [Indexed: 12/29/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers worldwide. Accurate early detection and diagnosis, comprehensive assessment of treatment response, and precise prediction of prognosis are essential to improve the patients’ survival rate. In recent years, due to the explosion of clinical and omics data, and groundbreaking research in machine learning, artificial intelligence (AI) has shown a great application potential in clinical field of CRC, providing new auxiliary approaches for clinicians to identify high-risk patients, select precise and personalized treatment plans, as well as to predict prognoses. This review comprehensively analyzes and summarizes the research progress and clinical application value of AI technologies in CRC screening, diagnosis, treatment, and prognosis, demonstrating the current status of the AI in the main clinical stages. The limitations, challenges, and future perspectives in the clinical implementation of AI are also discussed.
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Affiliation(s)
- Hang Qiu
- Big Data Research Center, University of Electronic Science and Technology of China, Chengdu 611731, China;
- School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China
- Correspondence: (H.Q.); (X.W.)
| | - Shuhan Ding
- School of Electrical and Computer Engineering, Cornell University, Ithaca, NY 14853, USA;
| | - Jianbo Liu
- West China School of Medicine, Sichuan University, Chengdu 610041, China;
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Liya Wang
- Big Data Research Center, University of Electronic Science and Technology of China, Chengdu 611731, China;
| | - Xiaodong Wang
- West China School of Medicine, Sichuan University, Chengdu 610041, China;
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
- Correspondence: (H.Q.); (X.W.)
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Arjmand B, Hamidpour SK, Tayanloo-Beik A, Goodarzi P, Aghayan HR, Adibi H, Larijani B. Machine Learning: A New Prospect in Multi-Omics Data Analysis of Cancer. Front Genet 2022; 13:824451. [PMID: 35154283 PMCID: PMC8829119 DOI: 10.3389/fgene.2022.824451] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/10/2022] [Indexed: 12/11/2022] Open
Abstract
Cancer is defined as a large group of diseases that is associated with abnormal cell growth, uncontrollable cell division, and may tend to impinge on other tissues of the body by different mechanisms through metastasis. What makes cancer so important is that the cancer incidence rate is growing worldwide which can have major health, economic, and even social impacts on both patients and the governments. Thereby, the early cancer prognosis, diagnosis, and treatment can play a crucial role at the front line of combating cancer. The onset and progression of cancer can occur under the influence of complicated mechanisms and some alterations in the level of genome, proteome, transcriptome, metabolome etc. Consequently, the advent of omics science and its broad research branches (such as genomics, proteomics, transcriptomics, metabolomics, and so forth) as revolutionary biological approaches have opened new doors to the comprehensive perception of the cancer landscape. Due to the complexities of the formation and development of cancer, the study of mechanisms underlying cancer has gone beyond just one field of the omics arena. Therefore, making a connection between the resultant data from different branches of omics science and examining them in a multi-omics field can pave the way for facilitating the discovery of novel prognostic, diagnostic, and therapeutic approaches. As the volume and complexity of data from the omics studies in cancer are increasing dramatically, the use of leading-edge technologies such as machine learning can have a promising role in the assessments of cancer research resultant data. Machine learning is categorized as a subset of artificial intelligence which aims to data parsing, classification, and data pattern identification by applying statistical methods and algorithms. This acquired knowledge subsequently allows computers to learn and improve accurate predictions through experiences from data processing. In this context, the application of machine learning, as a novel computational technology offers new opportunities for achieving in-depth knowledge of cancer by analysis of resultant data from multi-omics studies. Therefore, it can be concluded that the use of artificial intelligence technologies such as machine learning can have revolutionary roles in the fight against cancer.
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Affiliation(s)
- Babak Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- *Correspondence: Babak Arjmand, ; Bagher Larijani,
| | - Shayesteh Kokabi Hamidpour
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Akram Tayanloo-Beik
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Parisa Goodarzi
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamid Reza Aghayan
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Adibi
- Diabetes Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- *Correspondence: Babak Arjmand, ; Bagher Larijani,
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Abstract
Biological dosimetry is an internationally recognized method for quantifying and estimating radiation dose following suspected or verified excessive exposure to ionising radiation. In severe radiation accidents where a large number of people are potentially affected, it is possible to distinguish irradiated from non-irradiated people in order to initiate appropriate medical care if necessary. In addition to severe incidents caused by technical failure, environmental disasters, military actions, or criminal abuse, there are also radiation accidents in which only one or a few individuals are affected in the frame of occupational or medical exposure. The requirements for biological dosimetry are fundamentally different for these two scenarios. In particular, for large-scale radiation accidents, pre-screening methods are necessary to increase the throughput of samples for a rough first-dose categorization. The rapid development and increasing use of omics methods in research as well as in individual applications provides new opportunities for biological dosimetry. In addition to the discovery and search for new biomarkers, dosimetry assays based on omics technologies are becoming increasingly interesting and hold great potential, especially for large-scale dosimetry. In the following review, the different areas of biological dosimetry, the problems in finding suitable biomarkers, the current status of biomarker research based on omics, the potential applications of assays using omics technologies, and also the limitations for the different areas of biological dosimetry are discussed.
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Diaz-Flores E, Meyer T, Giorkallos A. Evolution of Artificial Intelligence-Powered Technologies in Biomedical Research and Healthcare. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2022; 182:23-60. [DOI: 10.1007/10_2021_189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Chen D, Fulmer C, Gordon IO, Syed S, Stidham RW, Vande Casteele N, Qin Y, Falloon K, Cohen BL, Wyllie R, Rieder F. Application of Artificial Intelligence to Clinical Practice in Inflammatory Bowel Disease - What the Clinician Needs to Know. J Crohns Colitis 2021; 16:460-471. [PMID: 34558619 PMCID: PMC8919817 DOI: 10.1093/ecco-jcc/jjab169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Artificial intelligence [AI] techniques are quickly spreading across medicine as an analytical method to tackle challenging clinical questions. What were previously thought of as highly complex data sources, such as images or free text, are now becoming manageable. Novel analytical methods merge the latest developments in information technology infrastructure with advances in computer science. Once primarily associated with Silicon Valley, AI techniques are now making their way into medicine, including in the field of inflammatory bowel diseases [IBD]. Understanding potential applications and limitations of these techniques can be difficult, in particular for busy clinicians. In this article, we explain the basic terminologies and provide a particular focus on the foundations behind state-of-the-art AI methodologies in both imaging and text. We explore the growing applications of AI in medicine, with a specific focus on IBD to inform the practising gastroenterologist and IBD specialist. Finally, we outline possible future uses of these technologies in daily clinical practice.
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Affiliation(s)
- David Chen
- Medical Operations, Cleveland Clinic Foundation, Cleveland, OH, USA,Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Clifton Fulmer
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Ilyssa O Gordon
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Sana Syed
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, School of Medicine, University of Virginia, Charlottesville, VA, USA,School of Data Science, University of Virginia, Charlottesville, VA, USA
| | - Ryan W Stidham
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Michigan Medicine, Ann Arbor, MI, USA,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | | | - Yi Qin
- Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Katherine Falloon
- Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Benjamin L Cohen
- Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Robert Wyllie
- Medical Operations, Cleveland Clinic Foundation, Cleveland, OH, USA,Department of Pediatric Gastroenterology, Hepatology, and Nutrition, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Florian Rieder
- Corresponding author: Florian Rieder, MD, Department of Inflammation and Immunity, and Department of Gastroenterology, Hepatology, & Nutrition, Cleveland Clinic Foundation, 9500 Euclid Ave., Cleveland, OH 44195, USA. Tel: (216) 445-5631; Fax: (216) 636-0104; E-mail:
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Tanaka I, Furukawa T, Morise M. The current issues and future perspective of artificial intelligence for developing new treatment strategy in non-small cell lung cancer: harmonization of molecular cancer biology and artificial intelligence. Cancer Cell Int 2021; 21:454. [PMID: 34446006 PMCID: PMC8393743 DOI: 10.1186/s12935-021-02165-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/19/2021] [Indexed: 12/12/2022] Open
Abstract
Comprehensive analysis of omics data, such as genome, transcriptome, proteome, metabolome, and interactome, is a crucial technique for elucidating the complex mechanism of cancer onset and progression. Recently, a variety of new findings have been reported based on multi-omics analysis in combination with various clinical information. However, integrated analysis of multi-omics data is extremely labor intensive, making the development of new analysis technology indispensable. Artificial intelligence (AI), which has been under development in recent years, is quickly becoming an effective approach to reduce the labor involved in analyzing large amounts of complex data and to obtain valuable information that is often overlooked in manual analysis and experiments. The use of AI, such as machine learning approaches and deep learning systems, allows for the efficient analysis of massive omics data combined with accurate clinical information and can lead to comprehensive predictive models that will be desirable for further developing individual treatment strategies of immunotherapy and molecular target therapy. Here, we aim to review the potential of AI in the integrated analysis of omics data and clinical information with a special focus on recent advances in the discovery of new biomarkers and the future direction of personalized medicine in non-small lung cancer.
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Affiliation(s)
- Ichidai Tanaka
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
| | - Taiki Furukawa
- Center for Healthcare Information Technology (C-HiT), Nagoya University, Nagoya, Japan
| | - Masahiro Morise
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
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Koppad S, B A, Gkoutos GV, Acharjee A. Cloud Computing Enabled Big Multi-Omics Data Analytics. Bioinform Biol Insights 2021; 15:11779322211035921. [PMID: 34376975 PMCID: PMC8323418 DOI: 10.1177/11779322211035921] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/12/2021] [Indexed: 12/27/2022] Open
Abstract
High-throughput experiments enable researchers to explore complex multifactorial
diseases through large-scale analysis of omics data. Challenges for such
high-dimensional data sets include storage, analyses, and sharing. Recent
innovations in computational technologies and approaches, especially in cloud
computing, offer a promising, low-cost, and highly flexible solution in the
bioinformatics domain. Cloud computing is rapidly proving increasingly useful in
molecular modeling, omics data analytics (eg, RNA sequencing, metabolomics, or
proteomics data sets), and for the integration, analysis, and interpretation of
phenotypic data. We review the adoption of advanced cloud-based and big data
technologies for processing and analyzing omics data and provide insights into
state-of-the-art cloud bioinformatics applications.
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Affiliation(s)
- Saraswati Koppad
- Department of Computer Science and Engineering, National Institute of Technology Karnataka, Surathkal, India
| | - Annappa B
- Department of Computer Science and Engineering, National Institute of Technology Karnataka, Surathkal, India
| | - Georgios V Gkoutos
- Institute of Cancer and Genomic Sciences and Centre for Computational Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.,Institute of Translational Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.,NIHR Surgical Reconstruction and Microbiology Research Centre, University Hospitals Birmingham, Birmingham, UK.,MRC Health Data Research UK (HDR UK), London, UK.,NIHR Experimental Cancer Medicine Centre, Birmingham, UK.,NIHR Biomedical Research Centre, University Hospitals Birmingham, Birmingham, UK
| | - Animesh Acharjee
- Institute of Cancer and Genomic Sciences and Centre for Computational Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.,Institute of Translational Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.,NIHR Surgical Reconstruction and Microbiology Research Centre, University Hospitals Birmingham, Birmingham, UK
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Franceschini G, Mason EJ, Orlandi A, D'Archi S, Sanchez AM, Masetti R. How will artificial intelligence impact breast cancer research efficiency? Expert Rev Anticancer Ther 2021; 21:1067-1070. [PMID: 34214007 DOI: 10.1080/14737140.2021.1951240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Gianluca Franceschini
- Multidisciplinary Breast Center, Dipartimento Scienze della Salute della Donna e del Bambino e di Sanità Pubblica, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Elena Jane Mason
- Multidisciplinary Breast Center, Dipartimento Scienze della Salute della Donna e del Bambino e di Sanità Pubblica, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Armando Orlandi
- Division of Medical Oncology, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Sabatino D'Archi
- Multidisciplinary Breast Center, Dipartimento Scienze della Salute della Donna e del Bambino e di Sanità Pubblica, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Alejandro Martin Sanchez
- Multidisciplinary Breast Center, Dipartimento Scienze della Salute della Donna e del Bambino e di Sanità Pubblica, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Riccardo Masetti
- Multidisciplinary Breast Center, Dipartimento Scienze della Salute della Donna e del Bambino e di Sanità Pubblica, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
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Rafique R, Islam SR, Kazi JU. Machine learning in the prediction of cancer therapy. Comput Struct Biotechnol J 2021; 19:4003-4017. [PMID: 34377366 PMCID: PMC8321893 DOI: 10.1016/j.csbj.2021.07.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 12/15/2022] Open
Abstract
Resistance to therapy remains a major cause of cancer treatment failures, resulting in many cancer-related deaths. Resistance can occur at any time during the treatment, even at the beginning. The current treatment plan is dependent mainly on cancer subtypes and the presence of genetic mutations. Evidently, the presence of a genetic mutation does not always predict the therapeutic response and can vary for different cancer subtypes. Therefore, there is an unmet need for predictive models to match a cancer patient with a specific drug or drug combination. Recent advancements in predictive models using artificial intelligence have shown great promise in preclinical settings. However, despite massive improvements in computational power, building clinically useable models remains challenging due to a lack of clinically meaningful pharmacogenomic data. In this review, we provide an overview of recent advancements in therapeutic response prediction using machine learning, which is the most widely used branch of artificial intelligence. We describe the basics of machine learning algorithms, illustrate their use, and highlight the current challenges in therapy response prediction for clinical practice.
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Affiliation(s)
| | - S.M. Riazul Islam
- Department of Computer Science and Engineering, Sejong University, Seoul, South Korea
| | - Julhash U. Kazi
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Lund Stem Cell Center, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Corresponding author at: Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon village Building 404:C3, Scheelevägen 8, 22363 Lund, Sweden.
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Abstract
PURPOSE OF REVIEW Artificial intelligence has become popular in medical applications, specifically as a clinical support tool for computer-aided diagnosis. These tools are typically employed on medical data (i.e., image, molecular data, clinical variables, etc.) and used the statistical and machine-learning methods to measure the model performance. In this review, we summarized and discussed the most recent radiomic pipeline used for clinical analysis. RECENT FINDINGS Currently, limited management of cancers benefits from artificial intelligence, mostly related to a computer-aided diagnosis that avoids a biopsy analysis that presents additional risks and costs. Most artificial intelligence tools are based on imaging features, known as radiomic analysis that can be refined into predictive models in noninvasively acquired imaging data. This review explores the progress of artificial intelligence-based radiomic tools for clinical applications with a brief description of necessary technical steps. Explaining new radiomic approaches based on deep-learning techniques will explain how the new radiomic models (deep radiomic analysis) can benefit from deep convolutional neural networks and be applied on limited data sets. SUMMARY To consider the radiomic algorithms, further investigations are recommended to involve deep learning in radiomic models with additional validation steps on various cancer types.
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Affiliation(s)
- Ahmad Chaddad
- School of Artificial Intelligence, Guilin University of Electronic Technology, Guilin, China
| | - Yousef Katib
- Department of Radiology, Taibah University, Al-Madinah, Saudi Arabia
| | - Lama Hassan
- School of Artificial Intelligence, Guilin University of Electronic Technology, Guilin, China
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47
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Veenstra TD. Omics in Systems Biology: Current Progress and Future Outlook. Proteomics 2021; 21:e2000235. [PMID: 33320441 DOI: 10.1002/pmic.202000235] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/25/2020] [Indexed: 12/16/2022]
Abstract
Biological research has undergone tremendous changes over the past three decades. Research used to almost exclusively focus on a single aspect of a single molecule per experiment. Modern technologies have enabled thousands of molecules to be simultaneously analyzed and the way that these molecules influence each other to be discerned. The change is so dramatic that it has given rise to a whole new descriptive suffix (i.e., omics) to describe these fields of study. While genomics was arguably the initial driver of this new trend, it quickly spread to other biological entities resulting in the creation of transcriptomics, proteomics, metabolomics, etc. The development of these "big four omics" created a wave of other omic fields, such as epigenomics, glycomics, lipidomics, microbiomics, and even foodomics; all with the purpose of comprehensively studying all the molecular entities or processes within their respective domain. The large number of omic fields that are invented even led to the term "panomics" as a way to classify them all under one category. Ultimately, all of these omic fields are setting the foundation for developing systems biology; in which the focus will be on determining the complex interactions that occur within biological systems.
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Biswas N, Kumar K, Bose S, Bera R, Chakrabarti S. Analysis of Pan-omics Data in Human Interactome Network (APODHIN). Front Genet 2020; 11:589231. [PMID: 33363571 PMCID: PMC7753071 DOI: 10.3389/fgene.2020.589231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/11/2020] [Indexed: 12/24/2022] Open
Abstract
Analysis of Pan-omics Data in Human Interactome Network (APODHIN) is a platform for integrative analysis of transcriptomics, proteomics, genomics, and metabolomics data for identification of key molecular players and their interconnections exemplified in cancer scenario. APODHIN works on a meta-interactome network consisting of human protein-protein interactions (PPIs), miRNA-target gene regulatory interactions, and transcription factor-target gene regulatory relationships. In its first module, APODHIN maps proteins/genes/miRNAs from different omics data in its meta-interactome network and extracts the network of biomolecules that are differentially altered in the given scenario. Using this context specific, filtered interaction network, APODHIN identifies topologically important nodes (TINs) implementing graph theory based network topology analysis and further justifies their role via pathway and disease marker mapping. These TINs could be used as prospective diagnostic and/or prognostic biomarkers and/or potential therapeutic targets. In its second module, APODHIN attempts to identify cross pathway regulatory and PPI links connecting signaling proteins, transcription factors (TFs), and miRNAs to metabolic enzymes via utilization of single-omics and/or pan-omics data and implementation of mathematical modeling. Interconnections between regulatory components such as signaling proteins/TFs/miRNAs and metabolic pathways need to be elucidated more elaborately in order to understand the role of oncogene and tumor suppressors in regulation of metabolic reprogramming during cancer. APODHIN platform contains a web server component where users can upload single/multi omics data to identify TINs and cross-pathway links. Tabular, graphical and 3D network representations of the identified TINs and cross-pathway links are provided for better appreciation. Additionally, this platform also provides few example data analysis of cancer specific, single and/or multi omics dataset for cervical, ovarian, and breast cancers where meta-interactome networks, TINs, and cross-pathway links are provided. APODHIN platform is freely available at http://www.hpppi.iicb.res.in/APODHIN/home.html.
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Affiliation(s)
| | | | | | | | - Saikat Chakrabarti
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
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