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Fu X, Ma W, Zuo Q, Qi Y, Zhang S, Zhao Y. Application of machine learning for high-throughput tumor marker screening. Life Sci 2024; 348:122634. [PMID: 38685558 DOI: 10.1016/j.lfs.2024.122634] [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: 03/26/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
High-throughput sequencing and multiomics technologies have allowed increasing numbers of biomarkers to be mined and used for disease diagnosis, risk stratification, efficacy assessment, and prognosis prediction. However, the large number and complexity of tumor markers make screening them a substantial challenge. Machine learning (ML) offers new and effective ways to solve the screening problem. ML goes beyond mere data processing and is instrumental in recognizing intricate patterns within data. ML also has a crucial role in modeling dynamic changes associated with diseases. Used together, ML techniques have been included in automatic pipelines for tumor marker screening, thereby enhancing the efficiency and accuracy of the screening process. In this review, we discuss the general processes and common ML algorithms, and highlight recent applications of ML in tumor marker screening of genomic, transcriptomic, proteomic, and metabolomic data of patients with various types of cancers. Finally, the challenges and future prospects of the application of ML in tumor therapy are discussed.
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Affiliation(s)
- Xingxing Fu
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian 116600, China
| | - Wanting Ma
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian 116600, China
| | - Qi Zuo
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian 116600, China
| | - Yanfei Qi
- Centenary Institute, The University of Sydney, Sydney, NSW 2050, Australia
| | - Shubiao Zhang
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian 116600, China.
| | - Yinan Zhao
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian 116600, China
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2
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Rutter LA, Cope H, MacKay MJ, Herranz R, Das S, Ponomarev SA, Costes SV, Paul AM, Barker R, Taylor DM, Bezdan D, Szewczyk NJ, Muratani M, Mason CE, Giacomello S. Astronaut omics and the impact of space on the human body at scale. Nat Commun 2024; 15:4952. [PMID: 38862505 PMCID: PMC11166943 DOI: 10.1038/s41467-024-47237-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 03/22/2024] [Indexed: 06/13/2024] Open
Abstract
Future multi-year crewed planetary missions will motivate advances in aerospace nutrition and telehealth. On Earth, the Human Cell Atlas project aims to spatially map all cell types in the human body. Here, we propose that a parallel Human Cell Space Atlas could serve as an openly available, global resource for space life science research. As humanity becomes increasingly spacefaring, high-resolution omics on orbit could permit an advent of precision spaceflight healthcare. Alongside the scientific potential, we consider the complex ethical, cultural, and legal challenges intrinsic to the human space omics discipline, and how philosophical frameworks may benefit from international perspectives.
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Affiliation(s)
- Lindsay A Rutter
- Transborder Medical Research Center, University of Tsukuba, 305-8575, Tsukuba, Japan
- Department of Genome Biology, Institute of Medicine, University of Tsukuba, 305-8575, Tsukuba, Japan
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Henry Cope
- School of Medicine, University of Nottingham, Derby, DE22 3DT, UK
| | - Matthew J MacKay
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Raúl Herranz
- Centro de Investigaciones Biológicas "Margarita Salas" (CSIC), Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Saswati Das
- Department of Biochemistry, Atal Bihari Vajpayee Institute of Medical Sciences & Dr. Ram Manohar Lohia Hospital, New Delhi, 110001, India
| | - Sergey A Ponomarev
- Department of Immunology and Microbiology, Institute for the Biomedical Problems, Russian Academy of Sciences, 123007, Moscow, Russia
| | - Sylvain V Costes
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Amber M Paul
- Embry-Riddle Aeronautical University, Department of Human Factors and Behavioral Neurobiology, Daytona Beach, FL, 32114, USA
| | - Richard Barker
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Deanne M Taylor
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Daniela Bezdan
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, 72076, Germany
- yuri GmbH, Meckenbeuren, 88074, Germany
| | - Nathaniel J Szewczyk
- School of Medicine, University of Nottingham, Derby, DE22 3DT, UK
- Ohio Musculoskeletal and Neurological Institute (OMNI), Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, 45701, USA
| | - Masafumi Muratani
- Transborder Medical Research Center, University of Tsukuba, 305-8575, Tsukuba, Japan
- Department of Genome Biology, Institute of Medicine, University of Tsukuba, 305-8575, Tsukuba, Japan
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA.
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, 10065, USA.
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10065, USA.
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3
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Tarzi C, Zampieri G, Sullivan N, Angione C. Emerging methods for genome-scale metabolic modeling of microbial communities. Trends Endocrinol Metab 2024; 35:533-548. [PMID: 38575441 DOI: 10.1016/j.tem.2024.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 04/06/2024]
Abstract
Genome-scale metabolic models (GEMs) are consolidating as platforms for studying mixed microbial populations, by combining biological data and knowledge with mathematical rigor. However, deploying these models to answer research questions can be challenging due to the increasing number of available computational tools, the lack of universal standards, and their inherent limitations. Here, we present a comprehensive overview of foundational concepts for building and evaluating genome-scale models of microbial communities. We then compare tools in terms of requirements, capabilities, and applications. Next, we highlight the current pitfalls and open challenges to consider when adopting existing tools and developing new ones. Our compendium can be relevant for the expanding community of modelers, both at the entry and experienced levels.
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Affiliation(s)
- Chaimaa Tarzi
- School of Computing, Engineering and Digital Technologies, Teesside University, Southfield Rd, Middlesbrough, TS1 3BX, North Yorkshire, UK
| | - Guido Zampieri
- Department of Biology, University of Padova, Padova, 35122, Veneto, Italy
| | - Neil Sullivan
- Complement Genomics Ltd, Station Rd, Lanchester, Durham, DH7 0EX, County Durham, UK
| | - Claudio Angione
- School of Computing, Engineering and Digital Technologies, Teesside University, Southfield Rd, Middlesbrough, TS1 3BX, North Yorkshire, UK; Centre for Digital Innovation, Teesside University, Southfield Rd, Middlesbrough, TS1 3BX, North Yorkshire, UK; National Horizons Centre, Teesside University, 38 John Dixon Ln, Darlington, DL1 1HG, North Yorkshire, UK.
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4
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Wang FS, Zhang HX. Identification of Anticancer Enzymes and Biomarkers for Hepatocellular Carcinoma through Constraint-Based Modeling. Molecules 2024; 29:2594. [PMID: 38893469 PMCID: PMC11173608 DOI: 10.3390/molecules29112594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/26/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Hepatocellular carcinoma (HCC) results in the abnormal regulation of cellular metabolic pathways. Constraint-based modeling approaches can be utilized to dissect metabolic reprogramming, enabling the identification of biomarkers and anticancer targets for diagnosis and treatment. In this study, two genome-scale metabolic models (GSMMs) were reconstructed by employing RNA sequencing expression patterns of hepatocellular carcinoma (HCC) and their healthy counterparts. An anticancer target discovery (ACTD) framework was integrated with the two models to identify HCC targets for anticancer treatment. The ACTD framework encompassed four fuzzy objectives to assess both the suppression of cancer cell growth and the minimization of side effects during treatment. The composition of a nutrient may significantly affect target identification. Within the ACTD framework, ten distinct nutrient media were utilized to assess nutrient uptake for identifying potential anticancer enzymes. The findings revealed the successful identification of target enzymes within the cholesterol biosynthetic pathway using a cholesterol-free cell culture medium. Conversely, target enzymes in the cholesterol biosynthetic pathway were not identified when the nutrient uptake included a cholesterol component. Moreover, the enzymes PGS1 and CRL1 were detected in all ten nutrient media. Additionally, the ACTD framework comprises dual-group representations of target combinations, pairing a single-target enzyme with an additional nutrient uptake reaction. Additionally, the enzymes PGS1 and CRL1 were identified across the ten-nutrient media. Furthermore, the ACTD framework encompasses two-group representations of target combinations involving the pairing of a single-target enzyme with an additional nutrient uptake reaction. Computational analysis unveiled that cell viability for all dual-target combinations exceeded that of their respective single-target enzymes. Consequently, integrating a target enzyme while adjusting an additional exchange reaction could efficiently mitigate cell proliferation rates and ATP production in the treated cancer cells. Nevertheless, most dual-target combinations led to lower side effects in contrast to their single-target counterparts. Additionally, differential expression of metabolites between cancer cells and their healthy counterparts were assessed via parsimonious flux variability analysis employing the GSMMs to pinpoint potential biomarkers. The variabilities of the fluxes and metabolite flow rates in cancer and healthy cells were classified into seven categories. Accordingly, two secretions and thirteen uptakes (including eight essential amino acids and two conditionally essential amino acids) were identified as potential biomarkers. The findings of this study indicated that cancer cells exhibit a higher uptake of amino acids compared with their healthy counterparts.
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Affiliation(s)
- Feng-Sheng Wang
- Department of Chemical Engineering, National Chung Cheng University, Chiayi 621301, Taiwan;
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Yang L, Tang Q, Zhang M, Tian Y, Chen X, Xu R, Ma Q, Guo P, Zhang C, Han D. A spatially localized DNA linear classifier for cancer diagnosis. Nat Commun 2024; 15:4583. [PMID: 38811607 PMCID: PMC11136972 DOI: 10.1038/s41467-024-48869-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 05/14/2024] [Indexed: 05/31/2024] Open
Abstract
Molecular computing is an emerging paradigm that plays an essential role in data storage, bio-computation, and clinical diagnosis with the future trends of more efficient computing scheme, higher modularity with scaled-up circuity and stronger tolerance of corrupted inputs in a complex environment. Towards these goals, we construct a spatially localized, DNA integrated circuits-based classifier (DNA IC-CLA) that can perform neuromorphic architecture-based computation at a molecular level for medical diagnosis. The DNA-based classifier employs a two-dimensional DNA origami as the framework and localized processing modules as the in-frame computing core to execute arithmetic operations (e.g. multiplication, addition, subtraction) for efficient linear classification of complex patterns of miRNA inputs. We demonstrate that the DNA IC-CLA enables accurate cancer diagnosis in a faster (about 3 h) and more effective manner in synthetic and clinical samples compared to those of the traditional freely diffusible DNA circuits. We believe that this all-in-one DNA-based classifier can exhibit more applications in biocomputing in cells and medical diagnostics.
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Affiliation(s)
- Linlin Yang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
- School of Pharmacy, Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, 264003, Yantai, China
| | - Qian Tang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China
| | - Mingzhi Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Yuan Tian
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Xiaoxing Chen
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Rui Xu
- Intellinosis Biotech Co.Ltd., 201112, Shanghai, China
| | - Qian Ma
- Intellinosis Biotech Co.Ltd., 201112, Shanghai, China
| | - Pei Guo
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China.
| | - Chao Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China.
- Intellinosis Biotech Co.Ltd., 201112, Shanghai, China.
| | - Da Han
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China.
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China.
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Chen J, Ji Y, Liu Y, Cen Z, Chen Y, Zhang Y, Li X, Li X. Exhaled volatolomics profiling facilitates personalized screening for gastric cancer. Cancer Lett 2024; 590:216881. [PMID: 38614384 DOI: 10.1016/j.canlet.2024.216881] [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: 04/02/2024] [Accepted: 04/09/2024] [Indexed: 04/15/2024]
Abstract
Gastric cancer (GC) is one of the most fatal cancers, characterized by non-specific early symptoms and difficulty in detection. However, there are no valid non-invasive screening tools available for GC. Here we establish a non-invasive method that employs exhaled volatolomics and ensemble learning to detect GC. We developed a comprehensive mass spectrometry-based procedure and determined of a wide range of volatolomics from 314 breath samples. The discovery, identification and verification research screened a biomarker panel to distinguish GC from controls. This panel has achieved 0.90 (0.87-0.94, 95%CI) accuracy, with an area under curve (AUC) of 0.92 (0.89-0.94, 95%CI) in discovery cohort and 0.88 (0.83-0.91, 95%CI) accuracy with an AUC of 0.91 (0.87-0.93, 95%CI) in replication cohort, which outperformed traditional serum markers. Single-cell sequencing and gene set enrichment analysis revealed that these exhaled markers originated from aldehyde oxidation and pyruvate metabolism. Our approach advances the design of exhaled analysis for GC detection and holds promise as a non-invasive method to the clinic.
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Affiliation(s)
- Jian Chen
- Department of Environmental Science & Engineering, Fudan University, Shanghai, 200438, PR China
| | - Yongyan Ji
- Department of Environmental Science & Engineering, Fudan University, Shanghai, 200438, PR China
| | - Yongqian Liu
- Department of Environmental Science & Engineering, Fudan University, Shanghai, 200438, PR China
| | - Zhengnan Cen
- Department of Environmental Science & Engineering, Fudan University, Shanghai, 200438, PR China
| | - Yuanwen Chen
- Department of Gastroenterology, Huadong Hospital Affiliated to Fudan University, Shanghai, 200040, PR China
| | - Yixuan Zhang
- Department of Gastroenterology, Huadong Hospital Affiliated to Fudan University, Shanghai, 200040, PR China
| | - Xiaowen Li
- Department of Gastroenterology, Huadong Hospital Affiliated to Fudan University, Shanghai, 200040, PR China.
| | - Xiang Li
- Department of Environmental Science & Engineering, Fudan University, Shanghai, 200438, PR China.
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7
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Lee G, Lee SM, Lee S, Jeong CW, Song H, Lee SY, Yun H, Koh Y, Kim HU. Prediction of metabolites associated with somatic mutations in cancers by using genome-scale metabolic models and mutation data. Genome Biol 2024; 25:66. [PMID: 38468344 DOI: 10.1186/s13059-024-03208-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 02/28/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND Oncometabolites, often generated as a result of a gene mutation, show pro-oncogenic function when abnormally accumulated in cancer cells. Identification of such mutation-associated metabolites will facilitate developing treatment strategies for cancers, but is challenging due to the large number of metabolites in a cell and the presence of multiple genes associated with cancer development. RESULTS Here we report the development of a computational workflow that predicts metabolite-gene-pathway sets. Metabolite-gene-pathway sets present metabolites and metabolic pathways significantly associated with specific somatic mutations in cancers. The computational workflow uses both cancer patient-specific genome-scale metabolic models (GEMs) and mutation data to generate metabolite-gene-pathway sets. A GEM is a computational model that predicts reaction fluxes at a genome scale and can be constructed in a cell-specific manner by using omics data. The computational workflow is first validated by comparing the resulting metabolite-gene pairs with multi-omics data (i.e., mutation data, RNA-seq data, and metabolome data) from acute myeloid leukemia and renal cell carcinoma samples collected in this study. The computational workflow is further validated by evaluating the metabolite-gene-pathway sets predicted for 18 cancer types, by using RNA-seq data publicly available, in comparison with the reported studies. Therapeutic potential of the resulting metabolite-gene-pathway sets is also discussed. CONCLUSIONS Validation of the metabolite-gene-pathway set-predicting computational workflow indicates that a decent number of metabolites and metabolic pathways appear to be significantly associated with specific somatic mutations. The computational workflow and the resulting metabolite-gene-pathway sets will help identify novel oncometabolites and also suggest cancer treatment strategies.
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Affiliation(s)
- GaRyoung Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, 34141, Republic of Korea
| | - Sang Mi Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, 34141, Republic of Korea
| | - Sungyoung Lee
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, 03080, Republic of Korea
| | - Chang Wook Jeong
- Department of Urology, Seoul National University College of Medicine, and Seoul National University Hospital, Seoul, 03080, Republic of Korea
| | - Hyojin Song
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, 03080, Republic of Korea
| | - Sang Yup Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, 34141, Republic of Korea
- Graduate School of Engineering Biology, BioProcess Engineering Research Center, and BioInformatics Research Center, KAIST, Daejeon, 34141, Republic of Korea
| | - Hongseok Yun
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, 03080, Republic of Korea.
| | - Youngil Koh
- Department of Internal Medicine, Seoul National University Hospital, Seoul, 03080, Republic of Korea.
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, 34141, Republic of Korea.
- Graduate School of Engineering Biology, BioProcess Engineering Research Center, and BioInformatics Research Center, KAIST, Daejeon, 34141, Republic of Korea.
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Hasibi R, Michoel T, Oyarzún DA. Integration of graph neural networks and genome-scale metabolic models for predicting gene essentiality. NPJ Syst Biol Appl 2024; 10:24. [PMID: 38448436 PMCID: PMC10917767 DOI: 10.1038/s41540-024-00348-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/08/2024] [Indexed: 03/08/2024] Open
Abstract
Genome-scale metabolic models are powerful tools for understanding cellular physiology. Flux balance analysis (FBA), in particular, is an optimization-based approach widely employed for predicting metabolic phenotypes. In model microbes such as Escherichia coli, FBA has been successful at predicting essential genes, i.e. those genes that impair survival when deleted. A central assumption in this approach is that both wild type and deletion strains optimize the same fitness objective. Although the optimality assumption may hold for the wild type metabolic network, deletion strains are not subject to the same evolutionary pressures and knock-out mutants may steer their metabolism to meet other objectives for survival. Here, we present FlowGAT, a hybrid FBA-machine learning strategy for predicting essentiality directly from wild type metabolic phenotypes. The approach is based on graph-structured representation of metabolic fluxes predicted by FBA, where nodes correspond to enzymatic reactions and edges quantify the propagation of metabolite mass flow between a reaction and its neighbours. We integrate this information into a graph neural network that can be trained on knock-out fitness assay data. Comparisons across different model architectures reveal that FlowGAT predictions for E. coli are close to those of FBA for several growth conditions. This suggests that essentiality of enzymatic genes can be predicted by exploiting the inherent network structure of metabolism. Our approach demonstrates the benefits of combining the mechanistic insights afforded by genome-scale models with the ability of deep learning to infer patterns from complex datasets.
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Affiliation(s)
- Ramin Hasibi
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Tom Michoel
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Diego A Oyarzún
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
- School of Informatics, University of Edinburgh, Edinburgh, UK.
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Fei X, Du X, Wang J, Liu J, Gong Y, Zhao Z, Cao Z, Fu Q, Zhu Y, Dong L, Dong B, Pan J, Sun W, Xie S, Xue W. Precise diagnosis and risk stratification of prostate cancer by comprehensive serum metabolic fingerprints: a prediction model study. Int J Surg 2024; 110:1450-1462. [PMID: 38181121 PMCID: PMC10942223 DOI: 10.1097/js9.0000000000001033] [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: 08/03/2023] [Accepted: 12/11/2023] [Indexed: 01/07/2024]
Abstract
OBJECTIVES Prostate cancer (PCa) is one of the most common malignancies in men worldwide and has caused increasing clinical morbidity and mortality, making timely diagnosis and accurate staging crucial. The authors introduced a novel approach based on mass spectrometry for precise diagnosis and stratification of PCa to facilitate clinical decision-making. METHODS Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry analysis of trace blood samples was combined with machine learning algorithms to construct diagnostic and stratification models. A total of 367 subjects, comprising 181 with PCa and 186 with non-PCa were enrolled. Additional 60 subjects, comprising 30 with PCa and 30 with non-PCa were enrolled as an external cohort for validation. Subsequent metabolomic analysis was carried out using Autoflex MALDI-TOF, and the mass spectra were introduced into various algorithms to construct different models. RESULTS Serum metabolic fingerprints were successfully obtained from 181 patients with PCa and 186 patients with non-PCa. The diagnostic model based on the eight signals demonstrated a remarkable area under curve of 100% and was validated in the external cohort with the area under curve of 87.3%. Fifteen signals were selected for enrichment analysis, revealing the potential metabolic pathways that facilitate tumorigenesis. Furthermore, the stage prediction model with an overall accuracy of 85.9% precisely classified subjects with localized disease and those with metastasis. The risk stratification model, with an overall accuracy of 89.6%, precisely classified the subjects as low-risk and high-risk. CONCLUSIONS Our study facilitated the timely diagnosis and risk stratification of PCa and provided new insights into the underlying mechanisms of metabolic alterations in PCa.
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Affiliation(s)
| | | | | | | | | | - Zejun Zhao
- Department of Ultrasound, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine
| | - Zhibin Cao
- Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Shandong, People’s Republic of China
| | - Qibo Fu
- Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Shandong, People’s Republic of China
| | | | | | | | | | - Wenshe Sun
- Department of Urology, Jiading District Central Hospital, Shanghai University of Medicine and Health Sciences, Shanghai
| | - Shaowei Xie
- Department of Ultrasound, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine
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Wojakowska A, Marczak L, Zeman M, Chekan M, Zembala-Nożyńska E, Polanski K, Strugała A, Widlak P, Pietrowska M. Proteomic and metabolomic signatures of rectal tumor discriminate patients with different responses to preoperative radiotherapy. Front Oncol 2024; 14:1323961. [PMID: 38410100 PMCID: PMC10896604 DOI: 10.3389/fonc.2024.1323961] [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: 10/18/2023] [Accepted: 01/16/2024] [Indexed: 02/28/2024] Open
Abstract
Background Neoadjuvant radiotherapy (neo-RT) is widely used in locally advanced rectal cancer (LARC) as a component of radical treatment. Despite the advantages of neo-RT, which typically improves outcomes in LARC patients, the lack of reliable biomarkers that predict response and monitor the efficacy of therapy, can result in the application of unnecessary aggressive therapy affecting patients' quality of life. Hence, the search for molecular biomarkers for assessing the radio responsiveness of this cancer represents a relevant issue. Methods Here, we combined proteomic and metabolomic approaches to identify molecular signatures, which could discriminate LARC tumors with good and poor responses to neo-RT. Results The integration of data on differentially accumulated proteins and metabolites made it possible to identify disrupted metabolic pathways and signaling processes connected with response to irradiation, including ketone bodies synthesis and degradation, purine metabolism, energy metabolism, degradation of fatty acid, amino acid metabolism, and focal adhesion. Moreover, we proposed multi-component panels of proteins and metabolites which could serve as a solid base to develop biomarkers for monitoring and predicting the efficacy of preoperative RT in rectal cancer patients. Conclusion We proved that an integrated multi-omic approach presents a valid look at the analysis of the global response to cancer treatment from the perspective of metabolomic reprogramming.
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Affiliation(s)
- Anna Wojakowska
- Laboratory of Mass Spectrometry, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Lukasz Marczak
- Laboratory of Mass Spectrometry, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Marcin Zeman
- The Oncologic and Reconstructive Surgery Clinic, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice, Poland
| | - Mykola Chekan
- Department of Pathomorphology, University of Technology, Katowice, Poland
| | - Ewa Zembala-Nożyńska
- Tumor Pathology Department, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice, Poland
| | | | - Aleksander Strugała
- Laboratory of Mass Spectrometry, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Piotr Widlak
- 2nd Department of Radiology, Medical University of Gdańsk, Gdańsk, Poland
| | - Monika Pietrowska
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice, Poland
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Sha Y, Meng W, Luo G, Zhai X, Tong HHY, Wang Y, Li K. MetDIT: Transforming and Analyzing Clinical Metabolomics Data with Convolutional Neural Networks. Anal Chem 2024. [PMID: 38324756 DOI: 10.1021/acs.analchem.3c04607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Clinical metabolomics is growing as an essential tool for precision medicine. However, classical machine learning algorithms struggle to comprehensively encode and analyze the metabolomics data due to their high dimensionality and complex intercorrelations. This article introduces a new method called MetDIT, designed to analyze intricate metabolomics data effectively using deep convolutional neural networks (CNN). MetDIT comprises two components: TransOmics and NetOmics. Since CNN models have difficulty in processing one-dimensional (1D) sequence data efficiently, we developed TransOmics, a framework that transforms sequence data into two-dimensional (2D) images while maintaining a one-to-one correspondence between the sequences and images. NetOmics, the second component, leverages a CNN architecture to extract more discriminative representations from the transformed samples. To overcome the overfitting due to the small sample size and class imbalance, we introduced a feature augmentation module (FAM) and a loss function to improve the model performance. Furthermore, we systematically optimized the model backbone and image resolution to balance the model parameters and computational costs. To demonstrate the performance of the proposed MetDIT, we conducted extensive experiments using three different clinical metabolomics data sets and achieved better classification performance than classical machine learning methods used in metabolomics, including Random Forest, SVM, XGBoost, and LightGBM. The source code is available at the GitHub repository at https://github.com/Li-OmicsLab/MetDIT, and the WebApp can be found at http://metdit.bioinformatics.vip/.
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Affiliation(s)
- Yuyang Sha
- Center for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macau SR 999708, China
| | - Weiyu Meng
- Center for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macau SR 999708, China
| | - Gang Luo
- Center for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macau SR 999708, China
| | - Xiaobing Zhai
- Center for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macau SR 999708, China
| | - Henry H Y Tong
- Center for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macau SR 999708, China
| | - Yuefei Wang
- National Key Laboratory of Chinese Medicine Modernization, State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Kefeng Li
- Center for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macau SR 999708, China
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12
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Chang YT, Prompsy P, Kimeswenger S, Tsai YC, Ignatova D, Pavlova O, Iselin C, French LE, Levesque MP, Kuonen F, Bobrowicz M, Brunner PM, Pascolo S, Hoetzenecker W, Guenova E. MHC-I upregulation safeguards neoplastic T cells in the skin against NK cell-mediated eradication in mycosis fungoides. Nat Commun 2024; 15:752. [PMID: 38272918 PMCID: PMC10810852 DOI: 10.1038/s41467-024-45083-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 01/15/2024] [Indexed: 01/27/2024] Open
Abstract
Cancer-associated immune dysfunction is a major challenge for effective therapies. The emergence of antibodies targeting tumor cell-surface antigens led to advancements in the treatment of hematopoietic malignancies, particularly blood cancers. Yet their impact is constrained against tumors of hematopoietic origin manifesting in the skin. In this study, we employ a clonality-supervised deep learning methodology to dissect key pathological features implicated in mycosis fungoides, the most common cutaneous T-cell lymphoma. Our investigations unveil the prominence of the IL-32β-major histocompatibility complex (MHC)-I axis as a critical determinant in tumor T-cell immune evasion within the skin microenvironment. In patients' skin, we find MHC-I to detrimentally impact the functionality of natural killer (NK) cells, diminishing antibody-dependent cellular cytotoxicity and promoting resistance of tumor skin T-cells to cell-surface targeting therapies. Through murine experiments in female mice, we demonstrate that disruption of the MHC-I interaction with NK cell inhibitory Ly49 receptors restores NK cell anti-tumor activity and targeted T-cell lymphoma elimination in vivo. These findings underscore the significance of attenuating the MHC-I-dependent immunosuppressive networks within skin tumors. Overall, our study introduces a strategy to reinvigorate NK cell-mediated anti-tumor responses to overcome treatment resistance to existing cell-surface targeted therapies for skin lymphoma.
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Affiliation(s)
- Yun-Tsan Chang
- Department of Dermatology, Lausanne University Hospital (CHUV) and Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Pacôme Prompsy
- Department of Dermatology, Lausanne University Hospital (CHUV) and Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Susanne Kimeswenger
- Department of Dermatology and Venerology, Medical Faculty, Johannes Kepler University, Linz, Austria
| | - Yi-Chien Tsai
- Department of Dermatology, Lausanne University Hospital (CHUV) and Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Desislava Ignatova
- Department of Dermatology, University Hospital of Zurich and Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Olesya Pavlova
- Department of Dermatology, Lausanne University Hospital (CHUV) and Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Christoph Iselin
- Department of Dermatology, Lausanne University Hospital (CHUV) and Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Lars E French
- Department of Dermatology and Allergology, Ludwig-Maximilians-University of Munich, Munich, Germany
- Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Mitchell P Levesque
- Department of Dermatology, University Hospital of Zurich and Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - François Kuonen
- Department of Dermatology, Lausanne University Hospital (CHUV) and Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | | | - Patrick M Brunner
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Steve Pascolo
- Department of Dermatology, University Hospital of Zurich and Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Wolfram Hoetzenecker
- Department of Dermatology and Venerology, Medical Faculty, Johannes Kepler University, Linz, Austria.
| | - Emmanuella Guenova
- Department of Dermatology, Lausanne University Hospital (CHUV) and Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
- Department of Dermatology, University Hospital of Zurich and Faculty of Medicine, University of Zurich, Zurich, Switzerland.
- Department of Dermatology, Hospital 12 de Octubre, Medical School, University Complutense, Madrid, Spain.
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13
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Guo C, Yang X, Li L. Pyroptosis-Related Gene Signature Predicts Prognosis and Response to Immunotherapy and Medication in Pediatric and Young Adult Osteosarcoma Patients. J Inflamm Res 2024; 17:417-445. [PMID: 38269108 PMCID: PMC10807455 DOI: 10.2147/jir.s440425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 12/21/2023] [Indexed: 01/26/2024] Open
Abstract
Purpose Pyroptosis, a new form of inflammatory programmed cell death, has recently gained attention. However, the impact of the expression levels of pyroptosis-related genes (PRGs) on the overall survival (OS) of osteosarcoma patients remains unclear. This study aims to investigate the impact of the expression levels of PRGs on the OS of pediatric and young adult patients with osteosarcoma. Patients and Methods Transcriptome matrix datasets of normal muscle or skeletal tissues from the Genotype-Tissue Expression (GTEx) project and osteosarcoma specimen the National Cancer Institute's (NCI) Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database were used to identify pyroptosis-related genes (PRGs) associated with prognosis. The National Center for Biotechnology Information's (NCBI) GSE21257 dataset was employed to validate the predictive value of the pyroptosis-related signature (PRS). Additionally, reverse transcription polymerase chain reaction (RT-qPCR) experiment was performed in normal and osteosarcoma cell lines. Results The study identified 18 differentially expressed PRGs (DEPRGs) between normal muscle or skeletal tissues and tumor samples. Multiple machine learning techniques were used to select PRGs, resulting in the identification of four hub PRGs. A PRS-score was calculated for each sample based on the expression of these four hub PRGs, and samples were categorized into low and high PRS-score level groups. It was confirmed that metastatic status and PRS-score level are independent prognostic predictors. A nomogram model for predicting OS of osteosarcoma patients was constructed. Single-cell RNA-sequencing data display the expression patterns of the hub PRGs. RT-qPCR data results were found to be consistent with the differential expression analysis performed on TARGET and GTEx samples. Conclusion The study developed a novel pyroptosis-related gene signature that can stratify pediatric and young adult osteosarcoma patients into different risk groups, thus predicting their response to immunotherapy and chemotherapy.
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Affiliation(s)
- Chaofan Guo
- Department of Orthopedics, Shanxi Provincial People’s Hospital, Taiyuan, Shanxi Province, People’s Republic of China
- Department of Spine Surgery, Fifth Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, People’s Republic of China
| | - Xin Yang
- Department of Neurosurgery, Chongqing Fourth People’s Hospital, Chongqing, People’s Republic of China
| | - Lijun Li
- Department of Orthopedics, Shanxi Provincial People’s Hospital, Taiyuan, Shanxi Province, People’s Republic of China
- Department of Spine Surgery, Fifth Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, People’s Republic of China
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14
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Yang C, Dong H, Chen Y, Xu L, Chen G, Fan X, Wang Y, Tham YJ, Lin Z, Li M, Hong Y, Chen J. New Insights on the Formation of Nucleation Mode Particles in a Coastal City Based on a Machine Learning Approach. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:1187-1198. [PMID: 38117945 DOI: 10.1021/acs.est.3c07042] [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: 12/22/2023]
Abstract
Atmospheric particles have profound implications for the global climate and human health. Among them, ultrafine particles dominate in terms of the number concentration and exhibit enhanced toxic effects as a result of their large total surface area. Therefore, understanding the driving factors behind ultrafine particle behavior is crucial. Machine learning (ML) provides a promising approach for handling complex relationships. In this study, three ML models were constructed on the basis of field observations to simulate the particle number concentration of nucleation mode (PNCN). All three models exhibited robust PNCN reproduction (R2 > 0.80), with the random forest (RF) model excelling on the test data (R2 = 0.89). Multiple methods of feature importance analysis revealed that ultraviolet (UV), H2SO4, low-volatility oxygenated organic molecules (LOOMs), temperature, and O3 were the primary factors influencing PNCN. Bivariate partial dependency plots (PDPs) indicated that during nighttime and overcast conditions, the presence of H2SO4 and LOOMs may play a crucial role in influencing PNCN. Additionally, integrating additional detailed information related to emissions or meteorology would further enhance the model performance. This pilot study shows that ML can be a novel approach for simulating atmospheric pollutants and contributes to a better understanding of the formation and growth mechanisms of nucleation mode particles.
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Affiliation(s)
- Chen Yang
- Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, People's Republic of China
- Fujian Key Laboratory of Atmospheric Ozone Pollution Prevention, Chinese Academy of Sciences, Xiamen, Fujian 361021, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Hesong Dong
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, People's Republic of China
| | - Yuping Chen
- Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, People's Republic of China
- Fujian Key Laboratory of Atmospheric Ozone Pollution Prevention, Chinese Academy of Sciences, Xiamen, Fujian 361021, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Lingling Xu
- Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, People's Republic of China
- Fujian Key Laboratory of Atmospheric Ozone Pollution Prevention, Chinese Academy of Sciences, Xiamen, Fujian 361021, People's Republic of China
| | - Gaojie Chen
- Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, People's Republic of China
- Fujian Key Laboratory of Atmospheric Ozone Pollution Prevention, Chinese Academy of Sciences, Xiamen, Fujian 361021, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Xiaolong Fan
- Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, People's Republic of China
- Fujian Key Laboratory of Atmospheric Ozone Pollution Prevention, Chinese Academy of Sciences, Xiamen, Fujian 361021, People's Republic of China
| | - Yonghong Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Yee Jun Tham
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, Guangdong 519082, People's Republic of China
| | - Ziyi Lin
- Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, People's Republic of China
- Fujian Key Laboratory of Atmospheric Ozone Pollution Prevention, Chinese Academy of Sciences, Xiamen, Fujian 361021, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Mengren Li
- Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, People's Republic of China
- Fujian Key Laboratory of Atmospheric Ozone Pollution Prevention, Chinese Academy of Sciences, Xiamen, Fujian 361021, People's Republic of China
| | - Youwei Hong
- Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, People's Republic of China
- Fujian Key Laboratory of Atmospheric Ozone Pollution Prevention, Chinese Academy of Sciences, Xiamen, Fujian 361021, People's Republic of China
| | - Jinsheng Chen
- Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, People's Republic of China
- Fujian Key Laboratory of Atmospheric Ozone Pollution Prevention, Chinese Academy of Sciences, Xiamen, Fujian 361021, People's Republic of China
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15
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Chaturvedi G, Sarusi-Portuguez A, Loza O, Shimoni-Sebag A, Yoron O, Lawrence YR, Zach L, Hakim O. Dose-Dependent Transcriptional Response to Ionizing Radiation Is Orchestrated with DNA Repair within the Nuclear Space. Int J Mol Sci 2024; 25:970. [PMID: 38256047 PMCID: PMC10815587 DOI: 10.3390/ijms25020970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Radiation therapy is commonly used to treat glioblastoma multiforme (GBM) brain tumors. Ionizing radiation (IR) induces dose-specific variations in transcriptional programs, implicating that they are tightly regulated and critical components in the tumor response and survival. Yet, our understanding of the downstream molecular events triggered by effective vs. non-effective IR doses is limited. Herein, we report that variations in the genetic programs are positively and functionally correlated with the exposure to effective or non-effective IR doses. Genome architecture analysis revealed that gene regulation is spatially and temporally coordinated with DNA repair kinetics. The radiation-activated genes were pre-positioned in active sub-nuclear compartments and were upregulated following the DNA damage response, while the DNA repair activity shifted to the inactive heterochromatic spatial compartments. The IR dose affected the levels of DNA damage repair and transcription modulation, but not the order of the events, which was linked to their spatial nuclear positioning. Thus, the distinct coordinated temporal dynamics of DNA damage repair and transcription reprogramming in the active and inactive sub-nuclear compartments highlight the importance of high-order genome organization in synchronizing the molecular events following IR.
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Affiliation(s)
- Garima Chaturvedi
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat Gan 5290002, Israel; (A.S.-P.)
| | - Avital Sarusi-Portuguez
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat Gan 5290002, Israel; (A.S.-P.)
| | - Olga Loza
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat Gan 5290002, Israel; (A.S.-P.)
| | - Ariel Shimoni-Sebag
- Institute of Oncology, Sheba Medical Center, Ramat Gan 5262000, Israel; (A.S.-S.)
| | - Orly Yoron
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat Gan 5290002, Israel; (A.S.-P.)
| | | | - Leor Zach
- Institute of Oncology, Tel Aviv Soraski Medical Center, Tel Aviv 6423906, Israel
| | - Ofir Hakim
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat Gan 5290002, Israel; (A.S.-P.)
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16
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Akshay A, Katoch M, Shekarchizadeh N, Abedi M, Sharma A, Burkhard FC, Adam RM, Monastyrskaya K, Gheinani AH. Machine Learning Made Easy (MLme): a comprehensive toolkit for machine learning-driven data analysis. Gigascience 2024; 13:giad111. [PMID: 38206587 PMCID: PMC10783149 DOI: 10.1093/gigascience/giad111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/20/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Machine learning (ML) has emerged as a vital asset for researchers to analyze and extract valuable information from complex datasets. However, developing an effective and robust ML pipeline can present a real challenge, demanding considerable time and effort, thereby impeding research progress. Existing tools in this landscape require a profound understanding of ML principles and programming skills. Furthermore, users are required to engage in the comprehensive configuration of their ML pipeline to obtain optimal performance. RESULTS To address these challenges, we have developed a novel tool called Machine Learning Made Easy (MLme) that streamlines the use of ML in research, specifically focusing on classification problems at present. By integrating 4 essential functionalities-namely, Data Exploration, AutoML, CustomML, and Visualization-MLme fulfills the diverse requirements of researchers while eliminating the need for extensive coding efforts. To demonstrate the applicability of MLme, we conducted rigorous testing on 6 distinct datasets, each presenting unique characteristics and challenges. Our results consistently showed promising performance across different datasets, reaffirming the versatility and effectiveness of the tool. Additionally, by utilizing MLme's feature selection functionality, we successfully identified significant markers for CD8+ naive (BACH2), CD16+ (CD16), and CD14+ (VCAN) cell populations. CONCLUSION MLme serves as a valuable resource for leveraging ML to facilitate insightful data analysis and enhance research outcomes, while alleviating concerns related to complex coding scripts. The source code and a detailed tutorial for MLme are available at https://github.com/FunctionalUrology/MLme.
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Affiliation(s)
- Akshay Akshay
- Functional Urology Research Group, Department for BioMedical Research DBMR, University of Bern, 3008 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Mitali Katoch
- Institute of Neuropathology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Navid Shekarchizadeh
- Department of Medical Data Science, Leipzig University Medical Centre, 04107 Leipzig, Germany
- Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI) Dresden/Leipzig, 04105 Leipzig, Germany
| | - Masoud Abedi
- Department of Medical Data Science, Leipzig University Medical Centre, 04107 Leipzig, Germany
| | - Ankush Sharma
- KG Jebsen Centre for B-cell Malignancies, Institute for Clinical Medicine, University of Oslo, 0318 Oslo, Norway
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, 0310 Oslo, Norway
| | - Fiona C Burkhard
- Functional Urology Research Group, Department for BioMedical Research DBMR, University of Bern, 3008 Bern, Switzerland
- Department of Urology, Inselspital University Hospital, 3010 Bern, Switzerland
| | - Rosalyn M Adam
- Urological Diseases Research Center, Boston Children's Hospital, 02115 Boston, MA, USA
- Department of Surgery, Harvard Medical School, 02115 Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, 02142 MA, USA
| | - Katia Monastyrskaya
- Functional Urology Research Group, Department for BioMedical Research DBMR, University of Bern, 3008 Bern, Switzerland
- Department of Urology, Inselspital University Hospital, 3010 Bern, Switzerland
| | - Ali Hashemi Gheinani
- Functional Urology Research Group, Department for BioMedical Research DBMR, University of Bern, 3008 Bern, Switzerland
- Department of Urology, Inselspital University Hospital, 3010 Bern, Switzerland
- Urological Diseases Research Center, Boston Children's Hospital, 02115 Boston, MA, USA
- Department of Surgery, Harvard Medical School, 02115 Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, 02142 MA, USA
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17
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Uatay A, Gall L, Irons L, Tewari SG, Zhu XS, Gibbs M, Kimko H. Physiological Indirect Response Model to Omics-Powered Quantitative Systems Pharmacology Model. J Pharm Sci 2024; 113:11-21. [PMID: 37898164 DOI: 10.1016/j.xphs.2023.10.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/21/2023] [Accepted: 10/21/2023] [Indexed: 10/30/2023]
Abstract
Over the past several decades, mathematical modeling has been applied to increasingly wider scopes of questions in drug development. Accordingly, the range of modeling tools has also been evolving, as showcased by contributions of Jusko and colleagues: from basic pharmacokinetics/pharmacodynamics (PK/PD) modeling to today's platform-based approach of quantitative systems pharmacology (QSP) modeling. Aimed at understanding the mechanism of action of investigational drugs, QSP models characterize systemic effects by incorporating information about cellular signaling networks, which is often represented by omics data. In this perspective, we share a few examples illustrating approaches for the integration of omics into mechanistic QSP modeling. We briefly overview how the evolution of PK/PD modeling into QSP has been accompanied by an increase in available data and the complexity of mathematical methods that integrate it. We discuss current gaps and challenges of integrating omics data into QSP models and propose several potential areas where integrated QSP and omics modeling may benefit drug development.
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Affiliation(s)
- Aydar Uatay
- Clinical Pharmacology & Quantitative Pharmacology, R&D Biopharmaceuticals, Cambridge, United Kingdom.
| | - Louis Gall
- Clinical Pharmacology & Quantitative Pharmacology, R&D Biopharmaceuticals, Cambridge, United Kingdom
| | - Linda Irons
- Clinical Pharmacology & Quantitative Pharmacology, R&D Biopharmaceuticals, Waltham, MA, United States
| | - Shivendra G Tewari
- Clinical Pharmacology & Quantitative Pharmacology, R&D Biopharmaceuticals, Gaithersburg, MD, United States
| | - Xu Sue Zhu
- Clinical Pharmacology & Quantitative Pharmacology, R&D Biopharmaceuticals, Waltham, MA, United States
| | - Megan Gibbs
- Clinical Pharmacology & Quantitative Pharmacology, R&D Biopharmaceuticals, Waltham, MA, United States
| | - Holly Kimko
- Clinical Pharmacology & Quantitative Pharmacology, R&D Biopharmaceuticals, Gaithersburg, MD, United States.
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18
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Zhu J, Yin J, Chen J, Hu M, Lu W, Wang H, Zhang H, Chen W. Integrative analysis with microbial modelling and machine learning uncovers potential alleviators for ulcerative colitis. Gut Microbes 2024; 16:2336877. [PMID: 38563656 PMCID: PMC10989691 DOI: 10.1080/19490976.2024.2336877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/27/2024] [Indexed: 04/04/2024] Open
Abstract
Ulcerative colitis (UC) is a challenging form of inflammatory bowel disease, and its etiology is intricately linked to disturbances in the gut microbiome. To identify the potential alleviators of UC, we employed an integrative analysis combining microbial community modeling with advanced machine learning techniques. Using metagenomics data sourced from the Integrated Human Microbiome Project, we constructed individualized microbiome community models for each participant. Our analysis highlighted a significant decline in both α and β-diversity of strain-level microbial populations in UC subjects compared to controls. Distinct differences were also observed in the predicted fecal metabolite profiles and strain-to-metabolite contributions between the two groups. Using tree-based machine learning models, we successfully identified specific microbial strains and their associated metabolites as potential alleviators of UC. Notably, our experimental validation using a dextran sulfate sodium-induced UC mouse model demonstrated that the administration of Parabacteroides merdae ATCC 43,184 and N-acetyl-D-mannosamine provided notable relief from colitis symptoms. In summary, our study underscores the potential of an integrative approach to identify novel therapeutic avenues for UC, paving the way for future targeted interventions.
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Affiliation(s)
- Jinlin Zhu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Jialin Yin
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Jing Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Mingyi Hu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wenwei Lu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, China
| | - Hongchao Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi People’s Hospital, Wuxi, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
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19
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Georgouli K, Yeom JS, Blake RC, Navid A. Multi-scale models of whole cells: progress and challenges. Front Cell Dev Biol 2023; 11:1260507. [PMID: 38020904 PMCID: PMC10661945 DOI: 10.3389/fcell.2023.1260507] [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: 07/18/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
Whole-cell modeling is "the ultimate goal" of computational systems biology and "a grand challenge for 21st century" (Tomita, Trends in Biotechnology, 2001, 19(6), 205-10). These complex, highly detailed models account for the activity of every molecule in a cell and serve as comprehensive knowledgebases for the modeled system. Their scope and utility far surpass those of other systems models. In fact, whole-cell models (WCMs) are an amalgam of several types of "system" models. The models are simulated using a hybrid modeling method where the appropriate mathematical methods for each biological process are used to simulate their behavior. Given the complexity of the models, the process of developing and curating these models is labor-intensive and to date only a handful of these models have been developed. While whole-cell models provide valuable and novel biological insights, and to date have identified some novel biological phenomena, their most important contribution has been to highlight the discrepancy between available data and observations that are used for the parametrization and validation of complex biological models. Another realization has been that current whole-cell modeling simulators are slow and to run models that mimic more complex (e.g., multi-cellular) biosystems, those need to be executed in an accelerated fashion on high-performance computing platforms. In this manuscript, we review the progress of whole-cell modeling to date and discuss some of the ways that they can be improved.
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Affiliation(s)
- Konstantia Georgouli
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Jae-Seung Yeom
- Center for Applied Scientific Computing, Computing Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Robert C. Blake
- Center for Applied Scientific Computing, Computing Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Ali Navid
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
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Bailleul J, Vlashi E. Glioblastomas: Hijacking Metabolism to Build a Flexible Shield for Therapy Resistance. Antioxid Redox Signal 2023; 39:957-979. [PMID: 37022791 PMCID: PMC10655009 DOI: 10.1089/ars.2022.0088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 02/01/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023]
Abstract
Significance: Glioblastomas (GBMs) are among the most lethal tumors despite the almost exclusive localization to the brain. This is largely due to therapeutic resistance. Radiation and chemotherapy significantly increase the survival for GBM patients, however, GBMs always recur, and the median overall survival is just over a year. Proposed reasons for such intractable resistance to therapy are numerous and include tumor metabolism, in particular, the ability of tumor cells to reconfigure metabolic fluxes on demand (metabolic plasticity). Understanding how the hard-wired, oncogene-driven metabolic tendencies of GBMs intersect with flexible, context-induced metabolic rewiring promises to reveal novel approaches for combating therapy resistance. Recent Advances: Personalized genome-scale metabolic flux models have recently provided evidence that metabolic flexibility promotes radiation resistance in cancer and identified tumor redox metabolism as a major predictor for resistance to radiation therapy (RT). It was demonstrated that radioresistant tumors, including GBM, reroute metabolic fluxes to boost the levels of reducing factors of the cell, thus enhancing clearance of reactive oxygen species that are generated during RT and promoting survival. Critical Issues: The current body of knowledge from published studies strongly supports the notion that robust metabolic plasticity can act as a (flexible) shield against the cytotoxic effects of standard GBM therapies, thus driving therapy resistance. The limited understanding of the critical drivers of such metabolic plasticity hampers the rational design of effective combination therapies. Future Directions: Identifying and targeting regulators of metabolic plasticity, rather than specific metabolic pathways, in combination with standard-of-care treatments have the potential to improve therapeutic outcomes in GBM. Antioxid. Redox Signal. 39, 957-979.
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Affiliation(s)
- Justine Bailleul
- Department of Radiation Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Erina Vlashi
- Department of Radiation Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California, USA
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21
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Chen CJ, Lee DY, Yu J, Lin YN, Lin TM. Recent advances in LC-MS-based metabolomics for clinical biomarker discovery. MASS SPECTROMETRY REVIEWS 2023; 42:2349-2378. [PMID: 35645144 DOI: 10.1002/mas.21785] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/14/2021] [Accepted: 11/18/2021] [Indexed: 06/15/2023]
Abstract
The employment of liquid chromatography-mass spectrometry (LC-MS) untargeted and targeted metabolomics has led to the discovery of novel biomarkers and improved the understanding of various disease mechanisms. Numerous strategies have been reported to expand the metabolite coverage in LC-MS-untargeted and targeted metabolomics. To improve the sensitivity of low-abundance or poor-ionized metabolites for reducing the amount of clinical sample, chemical derivatization methods are used to target different functional groups. Proper sample preparation is beneficial for reducing the matrix effect, maintaining the stability of the LC-MS system, and increasing the metabolite coverage. Machine learning has recently been integrated into the workflow of LC-MS metabolomics to accelerate metabolite identification and data-processing automation, and increase the accuracy of disease classification and clinical outcome prediction. Due to the rapidly growing utility of LC-MS metabolomics in discovering disease markers, this review will address the recent advances in the field and offer perspectives on various strategies for expanding metabolite coverage, chemical derivatization, sample preparation, clinical disease markers, and machining learning for disease modeling.
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Affiliation(s)
- Chao-Jung Chen
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Der-Yen Lee
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Jiaxin Yu
- AI Innovation Center, China Medical University Hospital, Taichung, Taiwan
| | - Yu-Ning Lin
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Tsung-Min Lin
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
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22
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Makaremi M, Vafaei Sadr A, Marcy B, Chraibi Kaadoud I, Mohammad-Djafari A, Sadoun S, De Brondeau F, N'kaoua B. An interpretable machine learning approach to study the relationship beetwen retrognathia and skull anatomy. Sci Rep 2023; 13:18130. [PMID: 37875537 PMCID: PMC10597995 DOI: 10.1038/s41598-023-45314-w] [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: 02/02/2023] [Accepted: 10/18/2023] [Indexed: 10/26/2023] Open
Abstract
Mandibular retrognathia (C2Rm) is one of the most common oral pathologies. Acquiring a better understanding of the points of impact of C2Rm on the entire skull is of major interest in the diagnosis, treatment, and management of this dysmorphism, but also permits us to contribute to the debate on the changes undergone by the shape of the skull during human evolution. However, conventional methods have some limits in meeting these challenges, insofar as they require defining in advance the structures to be studied, and identifying them using landmarks. In this context, our work aims to answer these questions using AI tools and, in particular, machine learning, with the objective of relaying these treatments automatically. We propose an innovative methodology coupling convolutional neural networks (CNNs) and interpretability algorithms. Applied to a set of radiographs classified into physiological versus pathological categories, our methodology made it possible to: discuss the structures impacted by retrognathia and already identified in literature; identify new structures of potential interest in medical terms; highlight the dynamic evolution of impacted structures according to the level of gravity of C2Rm; provide for insights into the evolution of human anatomy. Results were discussed in terms of the major interest of this approach in the field of orthodontics and, more generally, in the field of automated processing of medical images.
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Affiliation(s)
- Masrour Makaremi
- Dentofacial Orthopedics Department (UFR de Sciences Odontologiques), University of Bordeaux, Bordeaux, France.
- Bordeaux Population Health (Team ACTIVE), INSERM U1219, University of Bordeaux, Talence, France.
| | - Alireza Vafaei Sadr
- Department of Public Health Sciences, College of Medicine, The Pennsylvania State University, Hershey, PA, 17033, USA
- Theoretical Physics Department, University of Geneva, 1211, Geneva, Switzerland
| | | | | | | | - Salomé Sadoun
- Dentofacial Orthopedics Department (UFR de Sciences Odontologiques), University of Bordeaux, Bordeaux, France
| | - François De Brondeau
- Dentofacial Orthopedics Department (UFR de Sciences Odontologiques), University of Bordeaux, Bordeaux, France
| | - Bernard N'kaoua
- Bordeaux Population Health (Team ACTIVE), INSERM U1219, University of Bordeaux, Talence, France
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Zhang G, Zhang Z, Pei Y, Hu W, Xue Y, Ning R, Guo X, Sun Y, Zhang Q. Biological and clinical significance of radiomics features obtained from magnetic resonance imaging preceding pre-carbon ion radiotherapy in prostate cancer based on radiometabolomics. Front Endocrinol (Lausanne) 2023; 14:1272806. [PMID: 38027108 PMCID: PMC10644841 DOI: 10.3389/fendo.2023.1272806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/27/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction We aimed to investigate the feasibility of metabolomics to explain the underlying biological implications of radiomics features obtained from magnetic resonance imaging (MRI) preceding carbon ion radiotherapy (CIRT) in patients with prostate cancer and to further explore the clinical significance of radiomics features on the prognosis of patients, based on their biochemical recurrence (BCR) status. Methods Metabolomic results obtained using high-performance liquid chromatography coupled with tandem mass spectrometry of urine samples, combined with pre-RT radiomic features extracted from MRI images, were evaluated to investigate their biological significance. Receiver operating characteristic (ROC) curve analysis was subsequently conducted to examine the correlation between these biological implications and clinical BCR status. Statistical and metabolic pathway analyses were performed using MetaboAnalyst and R software. Results Correlation analysis revealed that methionine alteration extent was significantly related to four radiomic features (Contrast, Difference Variance, Small Dependence High Gray Level Emphasis, and Mean Absolute Deviation), which were significantly correlated with BCR status. The area under the curve (AUC) for BCR prediction of these four radiomic features ranged from 0.704 to 0.769, suggesting that the higher the value of these four radiomic features, the greater the decrease in methionine levels after CIRT and the lower the probability of BCR. Pre-CIRT MRI radiomic features were associated with CIRT-suppressed metabolites. Discussion These radiomic features can be used to predict the alteration in the amplitude of methionine after CIRT and the BCR status, which may contribute to the optimization of the CIRT strategy and deepen the understanding of PCa.
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Affiliation(s)
- Guangyuan Zhang
- Department of Radiation Oncology, Shanghai Proton and Heavy Ion Center, Fudan University Cancer Hospital, Shanghai, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai, China
- Shanghai Engineering Research Center of Proton and Heavy Ion Radiation Therapy, Shanghai, China
| | - Zhenshan Zhang
- Department of Radiation Oncology, Shanghai Proton and Heavy Ion Center, Fudan University Cancer Hospital, Shanghai, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai, China
- Shanghai Engineering Research Center of Proton and Heavy Ion Radiation Therapy, Shanghai, China
| | - Yulei Pei
- Department of Radiation Oncology, Shanghai Proton and Heavy Ion Center, Fudan University Cancer Hospital, Shanghai, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai, China
- Shanghai Engineering Research Center of Proton and Heavy Ion Radiation Therapy, Shanghai, China
| | - Wei Hu
- Department of Radiation Oncology, Shanghai Proton and Heavy Ion Center, Fudan University Cancer Hospital, Shanghai, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai, China
- Shanghai Engineering Research Center of Proton and Heavy Ion Radiation Therapy, Shanghai, China
| | - Yushan Xue
- Department of Radiation Oncology, Shanghai Proton and Heavy Ion Center, Fudan University Cancer Hospital, Shanghai, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai, China
- Shanghai Engineering Research Center of Proton and Heavy Ion Radiation Therapy, Shanghai, China
| | - Renli Ning
- Shanghai Key Laboratory of Radiation Oncology, Shanghai, China
- Shanghai Engineering Research Center of Proton and Heavy Ion Radiation Therapy, Shanghai, China
- Department of Research and Development, Shanghai Proton and Heavy Ion Center, Fudan University Cancer Hospital, Shanghai, China
| | - Xiaomao Guo
- Department of Radiation Oncology, Shanghai Proton and Heavy Ion Center, Fudan University Cancer Hospital, Shanghai, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai, China
- Shanghai Engineering Research Center of Proton and Heavy Ion Radiation Therapy, Shanghai, China
| | - Yun Sun
- Shanghai Key Laboratory of Radiation Oncology, Shanghai, China
- Shanghai Engineering Research Center of Proton and Heavy Ion Radiation Therapy, Shanghai, China
- Department of Research and Development, Shanghai Proton and Heavy Ion Center, Fudan University Cancer Hospital, Shanghai, China
| | - Qing Zhang
- Department of Radiation Oncology, Shanghai Proton and Heavy Ion Center, Fudan University Cancer Hospital, Shanghai, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai, China
- Shanghai Engineering Research Center of Proton and Heavy Ion Radiation Therapy, Shanghai, China
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Qiu Y, Liu Y, Wu Z, Wang F, Meng X, Zhang Z, Man R, Huang D, Wang H, Gao Y, Huang C, Hu M. Predicting Atmospheric Particle Phase State Using an Explainable Machine Learning Approach Based on Particle Rebound Measurements. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:15055-15064. [PMID: 37774013 DOI: 10.1021/acs.est.3c05284] [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: 10/01/2023]
Abstract
The particle phase state plays a vital role in the gas-particle partitioning, multiphase reactions, ice nucleation activity, and particle growth in the atmosphere. However, the characterization of the atmospheric phase state remains challenging. Herein, based on measured aerosol chemical composition and ambient relative humidity (RH), a machine learning (ML) model with high accuracy (R2 = 0.952) and robustness (RMSE = 0.078) was developed to predict the particle rebound fraction, f, which is an indicator of the particle phase state. Using this ML model, the f of particles in the urban atmosphere was predicted based on seasonal average aerosol chemical composition and RH. Regardless of seasons, aerosols remain in the liquid state of mid-high latitude cities in the northern hemisphere and in the semisolid state over semiarid regions. In the East Asian megacities, the particles remain in the liquid state in spring and summer and in the semisolid state in other seasons. The effects of nitrate, which is becoming dominant in fine particles in several urban areas, on the particle phase state were evaluated. More nitrate led the particles to remain in the liquid state at an even lower RH. This study proposed a new approach to predict the particle phase state in the atmosphere based on RH and aerosol chemical composition.
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Affiliation(s)
- Yanting Qiu
- State Joint Key Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yuechen Liu
- State Joint Key Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Zhijun Wu
- State Joint Key Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Fuzhou Wang
- Department of Computer Science, City University of Hong Kong, Hong Kong, SAR 999077, China
| | - Xiangxinyue Meng
- State Joint Key Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Zirui Zhang
- State Joint Key Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Ruiqi Man
- State Joint Key Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Dandan Huang
- State Environmental Protection Key Laboratory of Formation and Prevention of Urban Air Pollution Complex, Shanghai Academy of Environmental Sciences, Shanghai 200233, China
| | - Hongli Wang
- State Environmental Protection Key Laboratory of Formation and Prevention of Urban Air Pollution Complex, Shanghai Academy of Environmental Sciences, Shanghai 200233, China
| | - Yaqin Gao
- State Environmental Protection Key Laboratory of Formation and Prevention of Urban Air Pollution Complex, Shanghai Academy of Environmental Sciences, Shanghai 200233, China
| | - Cheng Huang
- State Environmental Protection Key Laboratory of Formation and Prevention of Urban Air Pollution Complex, Shanghai Academy of Environmental Sciences, Shanghai 200233, China
| | - Min Hu
- State Joint Key Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
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25
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Wang Q, He M, Guo L, Chai H. AFEI: adaptive optimized vertical federated learning for heterogeneous multi-omics data integration. Brief Bioinform 2023; 24:bbad269. [PMID: 37497720 DOI: 10.1093/bib/bbad269] [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: 05/19/2023] [Revised: 06/26/2023] [Accepted: 07/04/2023] [Indexed: 07/28/2023] Open
Abstract
Vertical federated learning has gained popularity as a means of enabling collaboration and information sharing between different entities while maintaining data privacy and security. This approach has potential applications in disease healthcare, cancer prognosis prediction, and other industries where data privacy is a major concern. Although using multi-omics data for cancer prognosis prediction provides more information for treatment selection, collecting different types of omics data can be challenging due to their production in various medical institutions. Data owners must comply with strict data protection regulations such as European Union (EU) General Data Protection Regulation. To share patient data across multiple institutions, privacy and security issues must be addressed. Therefore, we propose an adaptive optimized vertical federated-learning-based framework adaptive optimized vertical federated learning for heterogeneous multi-omics data integration (AFEI) to integrate multi-omics data collected from multiple institutions for cancer prognosis prediction. AFEI enables participating parties to build an accurate joint evaluation model for learning more information related to cancer patients from different perspectives, based on the distributed and encrypted multi-omics features shared by multiple institutions. The experimental results demonstrate that AFEI achieves higher prediction accuracy (6.5% on average) than using single omics data by utilizing the encrypted multi-omics data from different institutions, and it performs almost as well as prognosis prediction by directly integrating multi-omics data. Overall, AFEI can be seen as an efficient solution for breaking down barriers to multi-institutional collaboration and promoting the development of cancer prognosis prediction.
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Affiliation(s)
- Qingyong Wang
- School of Information and Computer, Anhui Agricultural University, Hefei 230000, China
| | - Minfan He
- School of Mathematics and Big Data, Foshan University, Foshan 528000, China
| | - Longyi Guo
- Guangdong Provincial Hospital of Traditional Chinese Medical, Guangzhou 510000, China
| | - Hua Chai
- School of Mathematics and Big Data, Foshan University, Foshan 528000, China
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Gelbach PE, Finley SD. Genome-scale modeling predicts metabolic differences between macrophage subtypes in colorectal cancer. iScience 2023; 26:107569. [PMID: 37664588 PMCID: PMC10474475 DOI: 10.1016/j.isci.2023.107569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/24/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023] Open
Abstract
Colorectal cancer (CRC) shows high incidence and mortality, partly due to the tumor microenvironment (TME), which is viewed as an active promoter of disease progression. Macrophages are among the most abundant cells in the TME. These immune cells are generally categorized as M1, with inflammatory and anti-cancer properties, or M2, which promote tumor proliferation and survival. Although the M1/M2 subclassification scheme is strongly influenced by metabolism, the metabolic divergence between the subtypes remains poorly understood. Therefore, we generated a suite of computational models that characterize the M1- and M2-specific metabolic states. Our models show key differences between the M1 and M2 metabolic networks and capabilities. We leverage the models to identify metabolic perturbations that cause the metabolic state of M2 macrophages to more closely resemble M1 cells. Overall, this work increases understanding of macrophage metabolism in CRC and elucidates strategies to promote the metabolic state of anti-tumor macrophages.
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Affiliation(s)
- Patrick E. Gelbach
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Stacey D. Finley
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA 90089, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA
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Guo Y, Wang R, Shi J, Yang C, Ma P, Min J, Zhao T, Hua L, Song Y, Li J, Su H. Machine learning-based integration develops a metabolism-derived consensus model for improving immunotherapy in pancreatic cancer. J Immunother Cancer 2023; 11:e007466. [PMID: 37739440 PMCID: PMC10533800 DOI: 10.1136/jitc-2023-007466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND Pancreatic cancer (PAC) is one of the most malignant cancer types and immunotherapy has emerged as a promising treatment option. PAC cells undergo metabolic reprogramming, which is thought to modulate the tumor microenvironment (TME) and affect immunotherapy outcomes. However, the metabolic landscape of PAC and its association with the TME remains largely unexplored. METHODS We characterized the metabolic landscape of PAC based on 112 metabolic pathways and constructed a novel metabolism-related signature (MBS) using data from 1,188 patients with PAC. We evaluated the predictive performance of MBS for immunotherapy outcomes in 11 immunotherapy cohorts from both bulk-RNA and single-cell perspectives. We validated our results using immunohistochemistry, western blotting, colony-formation assays, and an in-house cohort. RESULTS MBS was found to be negatively associated with antitumor immunity, while positively correlated with cancer stemness, intratumoral heterogeneity, and immune resistant pathways. Notably, MBS outperformed other acknowledged signatures for predicting immunotherapy response in multiple immunotherapy cohorts. Additionally, MBS was a powerful and robust biomarker for predicting prognosis compared with 66 published signatures. Further, we identified dasatinib and epothilone B as potential therapeutic options for MBS-high patients, which were validated through experiments. CONCLUSIONS Our study provides insights into the mechanisms of immunotherapy resistance in PAC and introduces MBS as a robust metabolism-based indicator for predicting response to immunotherapy and prognosis in patients with PAC. These findings have significant implications for the development of personalized treatment strategies in patients with PAC and highlight the importance of considering metabolic pathways and immune infiltration in TME regulation.
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Affiliation(s)
- Yongdong Guo
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, Shaanxi, China
| | - Ronglin Wang
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, Shaanxi, China
| | - Jingjie Shi
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, Shaanxi, China
| | - Cheng Yang
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, Shaanxi, China
| | - Peixiang Ma
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, Shaanxi, China
| | - Jie Min
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, Shaanxi, China
| | - Ting Zhao
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, Shaanxi, China
| | - Lei Hua
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, Shaanxi, China
| | - Yang Song
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, Shaanxi, China
| | - Junqiang Li
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, Shaanxi, China
| | - Haichuan Su
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, Shaanxi, China
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Faure L, Mollet B, Liebermeister W, Faulon JL. A neural-mechanistic hybrid approach improving the predictive power of genome-scale metabolic models. Nat Commun 2023; 14:4669. [PMID: 37537192 PMCID: PMC10400647 DOI: 10.1038/s41467-023-40380-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 07/19/2023] [Indexed: 08/05/2023] Open
Abstract
Constraint-based metabolic models have been used for decades to predict the phenotype of microorganisms in different environments. However, quantitative predictions are limited unless labor-intensive measurements of media uptake fluxes are performed. We show how hybrid neural-mechanistic models can serve as an architecture for machine learning providing a way to improve phenotype predictions. We illustrate our hybrid models with growth rate predictions of Escherichia coli and Pseudomonas putida grown in different media and with phenotype predictions of gene knocked-out Escherichia coli mutants. Our neural-mechanistic models systematically outperform constraint-based models and require training set sizes orders of magnitude smaller than classical machine learning methods. Our hybrid approach opens a doorway to enhancing constraint-based modeling: instead of constraining mechanistic models with additional experimental measurements, our hybrid models grasp the power of machine learning while fulfilling mechanistic constrains, thus saving time and resources in typical systems biology or biological engineering projects.
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Affiliation(s)
- Léon Faure
- MICALIS Institute, INRAE, AgroParisTech, University of Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Bastien Mollet
- Ecole Normale Supérieure of Lyon, 69342, Lyon, France
- UMR MIA, INRAE, AgroParisTech, University of Paris-Saclay, 91120, Palaiseau, France
| | | | - Jean-Loup Faulon
- MICALIS Institute, INRAE, AgroParisTech, University of Paris-Saclay, 78350, Jouy-en-Josas, France.
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK.
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29
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Han Z, Gong Q, Huang S, Meng X, Xu Y, Li L, Shi Y, Lin J, Chen X, Li C, Ma H, Liu J, Zhang X, Chen D, Si J. Machine learning uncovers accumulation mechanism of flavonoid compounds in Polygonatum cyrtonema Hua. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107839. [PMID: 37352696 DOI: 10.1016/j.plaphy.2023.107839] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/05/2023] [Accepted: 06/13/2023] [Indexed: 06/25/2023]
Abstract
The compositions and yield of flavonoid compounds of Polygonatum cyrtonema Hua (PC) are important indices of the quality of medicinal materials. However, the flavonoids compositions and accumulation mechanism are still unclear in PC. Here, we identified 22 flavonoids using widely-targeted metabolome analysis in 15 genotypes of PC. Then weighted gene co-expression network analysis based on 45 transcriptome samples was performed to construct 12 co-expressed modules, in which blue module highly correlated with flavonoids was identified. Furthermore, 4 feature genes including PcCHS1, PcCHI, PcCHS2 and PcCHR5 were identified from 94 hub genes in blue module via machine learning methods support vector machine-recursive feature elimination (SVM-RFE) and random forest (RF), and their functions on metabolic flux of flavonoids pathway were confirmed by tobacco transient expression system. Our findings identified representative flavonoids and key enzymes in PC that provided new insight for elite breeding rich in flavonoids, and thus will be beneficial for rapid development of great potential economic and medicinal value of PC.
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Affiliation(s)
- Zhigang Han
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China.
| | - Qiqi Gong
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China.
| | - Suya Huang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, China.
| | - Xinyue Meng
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, China.
| | - Yi Xu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China.
| | - Lige Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China.
| | - Yan Shi
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China.
| | - Junhao Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China.
| | - Xueliang Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China.
| | - Cong Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China.
| | - Haijie Ma
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, China.
| | - Jingjing Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China.
| | - Xinfeng Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China.
| | - Donghong Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China.
| | - Jinping Si
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China.
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Sen P, Orešič M. Integrating Omics Data in Genome-Scale Metabolic Modeling: A Methodological Perspective for Precision Medicine. Metabolites 2023; 13:855. [PMID: 37512562 PMCID: PMC10383060 DOI: 10.3390/metabo13070855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Recent advancements in omics technologies have generated a wealth of biological data. Integrating these data within mathematical models is essential to fully leverage their potential. Genome-scale metabolic models (GEMs) provide a robust framework for studying complex biological systems. GEMs have significantly contributed to our understanding of human metabolism, including the intrinsic relationship between the gut microbiome and the host metabolism. In this review, we highlight the contributions of GEMs and discuss the critical challenges that must be overcome to ensure their reproducibility and enhance their prediction accuracy, particularly in the context of precision medicine. We also explore the role of machine learning in addressing these challenges within GEMs. The integration of omics data with GEMs has the potential to lead to new insights, and to advance our understanding of molecular mechanisms in human health and disease.
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Affiliation(s)
- Partho Sen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden
| | - Matej Orešič
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden
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31
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Erdem C, Gross SM, Heiser LM, Birtwistle MR. MOBILE pipeline enables identification of context-specific networks and regulatory mechanisms. Nat Commun 2023; 14:3991. [PMID: 37414767 PMCID: PMC10326020 DOI: 10.1038/s41467-023-39729-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 06/27/2023] [Indexed: 07/08/2023] Open
Abstract
Robust identification of context-specific network features that control cellular phenotypes remains a challenge. We here introduce MOBILE (Multi-Omics Binary Integration via Lasso Ensembles) to nominate molecular features associated with cellular phenotypes and pathways. First, we use MOBILE to nominate mechanisms of interferon-γ (IFNγ) regulated PD-L1 expression. Our analyses suggest that IFNγ-controlled PD-L1 expression involves BST2, CLIC2, FAM83D, ACSL5, and HIST2H2AA3 genes, which were supported by prior literature. We also compare networks activated by related family members transforming growth factor-beta 1 (TGFβ1) and bone morphogenetic protein 2 (BMP2) and find that differences in ligand-induced changes in cell size and clustering properties are related to differences in laminin/collagen pathway activity. Finally, we demonstrate the broad applicability and adaptability of MOBILE by analyzing publicly available molecular datasets to investigate breast cancer subtype specific networks. Given the ever-growing availability of multi-omics datasets, we envision that MOBILE will be broadly useful for identification of context-specific molecular features and pathways.
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Affiliation(s)
- Cemal Erdem
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, USA
| | - Sean M Gross
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - Laura M Heiser
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA.
| | - Marc R Birtwistle
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, USA.
- Department of Bioengineering, Clemson University, Clemson, SC, USA.
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32
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Karlsen ST, Rau MH, Sánchez BJ, Jensen K, Zeidan AA. From genotype to phenotype: computational approaches for inferring microbial traits relevant to the food industry. FEMS Microbiol Rev 2023; 47:fuad030. [PMID: 37286882 PMCID: PMC10337747 DOI: 10.1093/femsre/fuad030] [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: 02/28/2023] [Revised: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 06/09/2023] Open
Abstract
When selecting microbial strains for the production of fermented foods, various microbial phenotypes need to be taken into account to achieve target product characteristics, such as biosafety, flavor, texture, and health-promoting effects. Through continuous advances in sequencing technologies, microbial whole-genome sequences of increasing quality can now be obtained both cheaper and faster, which increases the relevance of genome-based characterization of microbial phenotypes. Prediction of microbial phenotypes from genome sequences makes it possible to quickly screen large strain collections in silico to identify candidates with desirable traits. Several microbial phenotypes relevant to the production of fermented foods can be predicted using knowledge-based approaches, leveraging our existing understanding of the genetic and molecular mechanisms underlying those phenotypes. In the absence of this knowledge, data-driven approaches can be applied to estimate genotype-phenotype relationships based on large experimental datasets. Here, we review computational methods that implement knowledge- and data-driven approaches for phenotype prediction, as well as methods that combine elements from both approaches. Furthermore, we provide examples of how these methods have been applied in industrial biotechnology, with special focus on the fermented food industry.
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Affiliation(s)
- Signe T Karlsen
- Bioinformatics & Modeling, R&D Digital Innovation, Chr. Hansen A/S, Bøge Allé 10-12, 2970 Hørsholm, Denmark
| | - Martin H Rau
- Bioinformatics & Modeling, R&D Digital Innovation, Chr. Hansen A/S, Bøge Allé 10-12, 2970 Hørsholm, Denmark
| | - Benjamín J Sánchez
- Bioinformatics & Modeling, R&D Digital Innovation, Chr. Hansen A/S, Bøge Allé 10-12, 2970 Hørsholm, Denmark
| | - Kristian Jensen
- Bioinformatics & Modeling, R&D Digital Innovation, Chr. Hansen A/S, Bøge Allé 10-12, 2970 Hørsholm, Denmark
| | - Ahmad A Zeidan
- Bioinformatics & Modeling, R&D Digital Innovation, Chr. Hansen A/S, Bøge Allé 10-12, 2970 Hørsholm, Denmark
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33
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O'Connor JD, Overton IM, McMahon SJ. Validation of In Vitro Trained Transcriptomic Radiosensitivity Signatures in Clinical Cohorts. Cancers (Basel) 2023; 15:3504. [PMID: 37444614 PMCID: PMC10340371 DOI: 10.3390/cancers15133504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/15/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Transcriptomic personalisation of radiation therapy has gained considerable interest in recent years. However, independent model testing on in vitro data has shown poor performance. In this work, we assess the reproducibility in clinical applications of radiosensitivity signatures. Agreement between radiosensitivity predictions from published signatures using different microarray normalization methods was assessed. Control signatures developed from resampled in vitro data were benchmarked in clinical cohorts. Survival analysis was performed using each gene in the clinical transcriptomic data, and gene set enrichment analysis was used to determine pathways related to model performance in predicting survival and recurrence. The normalisation approach impacted calculated radiosensitivity index (RSI) values. Indeed, the limits of agreement exceeded 20% with different normalisation approaches. No published signature significantly improved on the resampled controls for prediction of clinical outcomes. Functional annotation of gene models suggested that many overlapping biological processes are associated with cancer outcomes in RT treated and non-RT treated patients, including proliferation and immune responses. In summary, different normalisation methods should not be used interchangeably. The utility of published signatures remains unclear given the large proportion of genes relating to cancer outcome. Biological processes influencing outcome overlapped for patients treated with or without radiation suggest that existing signatures may lack specificity.
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Affiliation(s)
- John D O'Connor
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast BT9 7AE, UK
| | - Ian M Overton
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast BT9 7AE, UK
| | - Stephen J McMahon
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast BT9 7AE, UK
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Akshay A, Katoch M, Shekarchizadeh N, Abedi M, Sharma A, Burkhard FC, Adam RM, Monastyrskaya K, Gheinani AH. Machine Learning Made Easy (MLme): A Comprehensive Toolkit for Machine Learning-Driven Data Analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.04.546825. [PMID: 37461685 PMCID: PMC10349995 DOI: 10.1101/2023.07.04.546825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Background Machine learning (ML) has emerged as a vital asset for researchers to analyze and extract valuable information from complex datasets. However, developing an effective and robust ML pipeline can present a real challenge, demanding considerable time and effort, thereby impeding research progress. Existing tools in this landscape require a profound understanding of ML principles and programming skills. Furthermore, users are required to engage in the comprehensive configuration of their ML pipeline to obtain optimal performance. Results To address these challenges, we have developed a novel tool called Machine Learning Made Easy (MLme) that streamlines the use of ML in research, specifically focusing on classification problems at present. By integrating four essential functionalities, namely Data Exploration, AutoML, CustomML, and Visualization, MLme fulfills the diverse requirements of researchers while eliminating the need for extensive coding efforts. To demonstrate the applicability of MLme, we conducted rigorous testing on six distinct datasets, each presenting unique characteristics and challenges. Our results consistently showed promising performance across different datasets, reaffirming the versatility and effectiveness of the tool. Additionally, by utilizing MLme's feature selection functionality, we successfully identified significant markers for CD8+ naive (BACH2), CD16+ (CD16), and CD14+ (VCAN) cell populations. Conclusion MLme serves as a valuable resource for leveraging machine learning (ML) to facilitate insightful data analysis and enhance research outcomes, while alleviating concerns related to complex coding scripts. The source code and a detailed tutorial for MLme are available at https://github.com/FunctionalUrology/MLme.
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Affiliation(s)
- Akshay Akshay
- Functional Urology Research Group, Department for BioMedical Research DBMR, University of Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland
| | - Mitali Katoch
- Institute of Neuropathology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Navid Shekarchizadeh
- Department of Medical Data Science, Leipzig University Medical Centre, 04107 Leipzig, Germany
- Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI) Dresden/Leipzig, 04105 Leipzig, Germany
| | - Masoud Abedi
- Department of Medical Data Science, Leipzig University Medical Centre, 04107 Leipzig, Germany
| | - Ankush Sharma
- KG Jebsen Centre for B-cell malignancies, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Fiona C. Burkhard
- Functional Urology Research Group, Department for BioMedical Research DBMR, University of Bern, Switzerland
- Department of Urology, Inselspital University Hospital, 3010 Bern, Switzerland
| | - Rosalyn M. Adam
- Urological Diseases Research Center, Boston Children’s Hospital, MA, USA
- Harvard Medical School, Boston, Department of Surgery MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Katia Monastyrskaya
- Functional Urology Research Group, Department for BioMedical Research DBMR, University of Bern, Switzerland
- Department of Urology, Inselspital University Hospital, 3010 Bern, Switzerland
| | - Ali Hashemi Gheinani
- Functional Urology Research Group, Department for BioMedical Research DBMR, University of Bern, Switzerland
- Department of Urology, Inselspital University Hospital, 3010 Bern, Switzerland
- Urological Diseases Research Center, Boston Children’s Hospital, MA, USA
- Harvard Medical School, Boston, Department of Surgery MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Chicco D, Cumbo F, Angione C. Ten quick tips for avoiding pitfalls in multi-omics data integration analyses. PLoS Comput Biol 2023; 19:e1011224. [PMID: 37410704 DOI: 10.1371/journal.pcbi.1011224] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023] Open
Abstract
Data are the most important elements of bioinformatics: Computational analysis of bioinformatics data, in fact, can help researchers infer new knowledge about biology, chemistry, biophysics, and sometimes even medicine, influencing treatments and therapies for patients. Bioinformatics and high-throughput biological data coming from different sources can even be more helpful, because each of these different data chunks can provide alternative, complementary information about a specific biological phenomenon, similar to multiple photos of the same subject taken from different angles. In this context, the integration of bioinformatics and high-throughput biological data gets a pivotal role in running a successful bioinformatics study. In the last decades, data originating from proteomics, metabolomics, metagenomics, phenomics, transcriptomics, and epigenomics have been labelled -omics data, as a unique name to refer to them, and the integration of these omics data has gained importance in all biological areas. Even if this omics data integration is useful and relevant, due to its heterogeneity, it is not uncommon to make mistakes during the integration phases. We therefore decided to present these ten quick tips to perform an omics data integration correctly, avoiding common mistakes we experienced or noticed in published studies in the past. Even if we designed our ten guidelines for beginners, by using a simple language that (we hope) can be understood by anyone, we believe our ten recommendations should be taken into account by all the bioinformaticians performing omics data integration, including experts.
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Affiliation(s)
- Davide Chicco
- Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Fabio Cumbo
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Claudio Angione
- School of Computing Engineering and Digital Technologies, Teesside University, Middlesbrough, United Kingdom
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36
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Rydzewski NR, Helzer KT, Bootsma M, Shi Y, Bakhtiar H, Sjöström M, Zhao SG. Machine Learning & Molecular Radiation Tumor Biomarkers. Semin Radiat Oncol 2023; 33:243-251. [PMID: 37331779 DOI: 10.1016/j.semradonc.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Developing radiation tumor biomarkers that can guide personalized radiotherapy clinical decision making is a critical goal in the effort towards precision cancer medicine. High-throughput molecular assays paired with modern computational techniques have the potential to identify individual tumor-specific signatures and create tools that can help understand heterogenous patient outcomes in response to radiotherapy, allowing clinicians to fully benefit from the technological advances in molecular profiling and computational biology including machine learning. However, the increasingly complex nature of the data generated from high-throughput and "omics" assays require careful selection of analytical strategies. Furthermore, the power of modern machine learning techniques to detect subtle data patterns comes with special considerations to ensure that the results are generalizable. Herein, we review the computational framework of tumor biomarker development and describe commonly used machine learning approaches and how they are applied for radiation biomarker development using molecular data, as well as challenges and emerging research trends.
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Affiliation(s)
- Nicholas R Rydzewski
- Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD; Department of Human Oncology, University of Wisconsin, Madison, WI
| | - Kyle T Helzer
- Department of Human Oncology, University of Wisconsin, Madison, WI
| | - Matthew Bootsma
- Department of Human Oncology, University of Wisconsin, Madison, WI
| | - Yue Shi
- Department of Human Oncology, University of Wisconsin, Madison, WI
| | - Hamza Bakhtiar
- Department of Human Oncology, University of Wisconsin, Madison, WI
| | - Martin Sjöström
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA
| | - Shuang G Zhao
- Department of Human Oncology, University of Wisconsin, Madison, WI; Carbone Cancer Center, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital, Madison, WI.
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37
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Benavente S. Remodeling the tumor microenvironment to overcome treatment resistance in HPV-negative head and neck cancer. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2023; 6:291-313. [PMID: 37457128 PMCID: PMC10344731 DOI: 10.20517/cdr.2022.141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 05/02/2023] [Accepted: 05/22/2023] [Indexed: 07/18/2023]
Abstract
Despite intensive efforts and refined techniques, overall survival in HPV-negative head and neck cancer remains poor. Robust immune priming is required to elicit a strong and durable antitumor immune response in immunologically cold and excluded tumors like HPV-negative head and neck cancer. This review highlights how the tumor microenvironment could be affected by different immune and stromal cell types, weighs the need to integrate metabolic regulation of the tumor microenvironment into cancer treatment strategies and summarizes the emerging clinical applicability of personalized immunotherapeutic strategies in HPV-negative head and neck cancer.
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Affiliation(s)
- Sergi Benavente
- Correspondence to: Dr. Sergi Benavente, Department of Radiation Oncology, Vall d’Hebron University Hospital, Passeig Vall d’Hebron 119, Barcelona 08035, Spain. E-mail:
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38
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Angione C, Wang H, Burtt N. Editorial: Artificial intelligence for data discovery and reuse in endocrinology and metabolism. Front Endocrinol (Lausanne) 2023; 14:1180254. [PMID: 37214239 PMCID: PMC10196622 DOI: 10.3389/fendo.2023.1180254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 04/18/2023] [Indexed: 05/24/2023] Open
Affiliation(s)
- Claudio Angione
- School of Computing, Engineering and Digital Technologies, Teesside University, North Yorkshire, United Kingdom
- Centre for Digital Innovation, Teesside University, North Yorkshire, United Kingdom
- National Horizons Centre, Teesside University, North Yorkshire, United Kingdom
| | - Huajin Wang
- Open Science & Data Collaborations, Carnegie Mellon University, Pittsburgh, PA, United States
| | - Noël Burtt
- Medical and Population Genetics Program and Metabolism Program, The Broad Institute of MIT and Harvard, Cambridge, MA, United States
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Lee G, Lee SM, Kim HU. A contribution of metabolic engineering to addressing medical problems: Metabolic flux analysis. Metab Eng 2023; 77:283-293. [PMID: 37075858 DOI: 10.1016/j.ymben.2023.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/20/2023] [Accepted: 04/12/2023] [Indexed: 04/21/2023]
Abstract
Metabolic engineering has served as a systematic discipline for industrial biotechnology as it has offered systematic tools and methods for strain development and bioprocess optimization. Because these metabolic engineering tools and methods are concerned with the biological network of a cell with emphasis on metabolic network, they have also been applied to a range of medical problems where better understanding of metabolism has also been perceived to be important. Metabolic flux analysis (MFA) is a unique systematic approach initially developed in the metabolic engineering community, and has proved its usefulness and potential when addressing a range of medical problems. In this regard, this review discusses the contribution of MFA to addressing medical problems. For this, we i) provide overview of the milestones of MFA, ii) define two main branches of MFA, namely constraint-based reconstruction and analysis (COBRA) and isotope-based MFA (iMFA), and iii) present successful examples of their medical applications, including characterizing the metabolism of diseased cells and pathogens, and identifying effective drug targets. Finally, synergistic interactions between metabolic engineering and biomedical sciences are discussed with respect to MFA.
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Affiliation(s)
- GaRyoung Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Sang Mi Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon, 34141, Republic of Korea.
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40
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Qiu S, Cai Y, Yao H, Lin C, Xie Y, Tang S, Zhang A. Small molecule metabolites: discovery of biomarkers and therapeutic targets. Signal Transduct Target Ther 2023; 8:132. [PMID: 36941259 PMCID: PMC10026263 DOI: 10.1038/s41392-023-01399-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/22/2023] Open
Abstract
Metabolic abnormalities lead to the dysfunction of metabolic pathways and metabolite accumulation or deficiency which is well-recognized hallmarks of diseases. Metabolite signatures that have close proximity to subject's phenotypic informative dimension, are useful for predicting diagnosis and prognosis of diseases as well as monitoring treatments. The lack of early biomarkers could lead to poor diagnosis and serious outcomes. Therefore, noninvasive diagnosis and monitoring methods with high specificity and selectivity are desperately needed. Small molecule metabolites-based metabolomics has become a specialized tool for metabolic biomarker and pathway analysis, for revealing possible mechanisms of human various diseases and deciphering therapeutic potentials. It could help identify functional biomarkers related to phenotypic variation and delineate biochemical pathways changes as early indicators of pathological dysfunction and damage prior to disease development. Recently, scientists have established a large number of metabolic profiles to reveal the underlying mechanisms and metabolic networks for therapeutic target exploration in biomedicine. This review summarized the metabolic analysis on the potential value of small-molecule candidate metabolites as biomarkers with clinical events, which may lead to better diagnosis, prognosis, drug screening and treatment. We also discuss challenges that need to be addressed to fuel the next wave of breakthroughs.
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Affiliation(s)
- Shi Qiu
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China
| | - Ying Cai
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Hong Yao
- First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
| | - Chunsheng Lin
- Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin, 150001, China
| | - Yiqiang Xie
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
| | - Songqi Tang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
| | - Aihua Zhang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150040, China.
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41
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Gelbach PE, Finley SD. Ensemble-based genome-scale modeling predicts metabolic differences between macrophage subtypes in colorectal cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.09.532000. [PMID: 36993493 PMCID: PMC10052244 DOI: 10.1101/2023.03.09.532000] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
1Colorectal cancer (CRC) shows high incidence and mortality, partly due to the tumor microenvironment, which is viewed as an active promoter of disease progression. Macrophages are among the most abundant cells in the tumor microenvironment. These immune cells are generally categorized as M1, with inflammatory and anti-cancer properties, or M2, which promote tumor proliferation and survival. Although the M1/M2 subclassification scheme is strongly influenced by metabolism, the metabolic divergence between the subtypes remains poorly understood. Therefore, we generated a suite of computational models that characterize the M1- and M2-specific metabolic states. Our models show key differences between the M1 and M2 metabolic networks and capabilities. We leverage the models to identify metabolic perturbations that cause the metabolic state of M2 macrophages to more closely resemble M1 cells. Overall, this work increases understanding of macrophage metabolism in CRC and elucidates strategies to promote the metabolic state of anti-tumor macrophages.
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Affiliation(s)
- Patrick E. Gelbach
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Stacey D. Finley
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA 90089, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA
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42
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A General Hybrid Modeling Framework for Systems Biology Applications: Combining Mechanistic Knowledge with Deep Neural Networks under the SBML Standard. AI 2023. [DOI: 10.3390/ai4010014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
In this paper, a computational framework is proposed that merges mechanistic modeling with deep neural networks obeying the Systems Biology Markup Language (SBML) standard. Over the last 20 years, the systems biology community has developed a large number of mechanistic models that are currently stored in public databases in SBML. With the proposed framework, existing SBML models may be redesigned into hybrid systems through the incorporation of deep neural networks into the model core, using a freely available python tool. The so-formed hybrid mechanistic/neural network models are trained with a deep learning algorithm based on the adaptive moment estimation method (ADAM), stochastic regularization and semidirect sensitivity equations. The trained hybrid models are encoded in SBML and uploaded in model databases, where they may be further analyzed as regular SBML models. This approach is illustrated with three well-known case studies: the Escherichia coli threonine synthesis model, the P58IPK signal transduction model, and the Yeast glycolytic oscillations model. The proposed framework is expected to greatly facilitate the widespread use of hybrid modeling techniques for systems biology applications.
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Gonzales LISA, Qiao JW, Buffier AW, Rogers LJ, Suchowerska N, McKenzie DR, Kwan AH. An omics approach to delineating the molecular mechanisms that underlie the biological effects of physical plasma. BIOPHYSICS REVIEWS 2023; 4:011312. [PMID: 38510160 PMCID: PMC10903421 DOI: 10.1063/5.0089831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 02/24/2023] [Indexed: 03/22/2024]
Abstract
The use of physical plasma to treat cancer is an emerging field, and interest in its applications in oncology is increasing rapidly. Physical plasma can be used directly by aiming the plasma jet onto cells or tissue, or indirectly, where a plasma-treated solution is applied. A key scientific question is the mechanism by which physical plasma achieves selective killing of cancer over normal cells. Many studies have focused on specific pathways and mechanisms, such as apoptosis and oxidative stress, and the role of redox biology. However, over the past two decades, there has been a rise in omics, the systematic analysis of entire collections of molecules in a biological entity, enabling the discovery of the so-called "unknown unknowns." For example, transcriptomics, epigenomics, proteomics, and metabolomics have helped to uncover molecular mechanisms behind the action of physical plasma, revealing critical pathways beyond those traditionally associated with cancer treatments. This review showcases a selection of omics and then summarizes the insights gained from these studies toward understanding the biological pathways and molecular mechanisms implicated in physical plasma treatment. Omics studies have revealed how reactive species generated by plasma treatment preferentially affect several critical cellular pathways in cancer cells, resulting in epigenetic, transcriptional, and post-translational changes that promote cell death. Finally, this review considers the outlook for omics in uncovering both synergies and antagonisms with other common cancer therapies, as well as in overcoming challenges in the clinical translation of physical plasma.
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Affiliation(s)
- Lou I. S. A. Gonzales
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Jessica W. Qiao
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Aston W. Buffier
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | | | | | | | - Ann H. Kwan
- Author to whom correspondence should be addressed:
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Li J, Li L, You P, Wei Y, Xu B. Towards artificial intelligence to multi-omics characterization of tumor heterogeneity in esophageal cancer. Semin Cancer Biol 2023; 91:35-49. [PMID: 36868394 DOI: 10.1016/j.semcancer.2023.02.009] [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: 01/07/2023] [Revised: 02/21/2023] [Accepted: 02/28/2023] [Indexed: 03/05/2023]
Abstract
Esophageal cancer is a unique and complex heterogeneous malignancy, with substantial tumor heterogeneity: at the cellular levels, tumors are composed of tumor and stromal cellular components; at the genetic levels, they comprise genetically distinct tumor clones; at the phenotypic levels, cells in distinct microenvironmental niches acquire diverse phenotypic features. This heterogeneity affects almost every process of esophageal cancer progression from onset to metastases and recurrence, etc. Intertumoral and intratumoral heterogeneity are major obstacles in the treatment of esophageal cancer, but also offer the potential to manipulate the heterogeneity themselves as a new therapeutic strategy. The high-dimensional, multi-faceted characterization of genomics, epigenomics, transcriptomics, proteomics, metabonomics, etc. of esophageal cancer has opened novel horizons for dissecting tumor heterogeneity. Artificial intelligence especially machine learning and deep learning algorithms, are able to make decisive interpretations of data from multi-omics layers. To date, artificial intelligence has emerged as a promising computational tool for analyzing and dissecting esophageal patient-specific multi-omics data. This review provides a comprehensive review of tumor heterogeneity from a multi-omics perspective. Especially, we discuss the novel techniques single-cell sequencing and spatial transcriptomics, which have revolutionized our understanding of the cell compositions of esophageal cancer and allowed us to determine novel cell types. We focus on the latest advances in artificial intelligence in integrating multi-omics data of esophageal cancer. Artificial intelligence-based multi-omics data integration computational tools exert a key role in tumor heterogeneity assessment, which will potentially boost the development of precision oncology in esophageal cancer.
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Affiliation(s)
- Junyu Li
- Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang 330029, Jiangxi, China; Jiangxi Health Committee Key (JHCK) Laboratory of Tumor Metastasis, Jiangxi Cancer Hospital, Nanchang 330029, Jiangxi, China
| | - Lin Li
- Department of Thoracic Oncology, Jiangxi Cancer Hospital, Nanchang 330029, Jiangxi, China
| | - Peimeng You
- Nanchang University, Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang 330029, Jiangxi, China
| | - Yiping Wei
- Department of Thoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China.
| | - Bin Xu
- Jiangxi Health Committee Key (JHCK) Laboratory of Tumor Metastasis, Jiangxi Cancer Hospital, Nanchang 330029, Jiangxi, China.
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Bidzińska J, Szurowska E. See Lung Cancer with an AI. Cancers (Basel) 2023; 15:cancers15041321. [PMID: 36831662 PMCID: PMC9954317 DOI: 10.3390/cancers15041321] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
A lot has happened in the field of lung cancer screening in recent months. The ongoing discussion and documentation published by the scientific community and policymakers are of great importance to the entire European community and perhaps beyond. Lung cancer is the main worldwide killer. Low-dose computed tomography-based screening, together with smoking cessation, is the only tool to fight lung cancer, as it has already been proven in the United States of America but also European randomized controlled trials. Screening requires a lot of well-organized specialized work, but it can be supported by artificial intelligence (AI). Here we discuss whether and how to use AI for patients, radiologists, pulmonologists, thoracic surgeons, and all hospital staff supporting screening process benefits.
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Neuroinflammation, Energy and Sphingolipid Metabolism Biomarkers Are Revealed by Metabolic Modeling of Autistic Brains. Biomedicines 2023; 11:biomedicines11020583. [PMID: 36831124 PMCID: PMC9953696 DOI: 10.3390/biomedicines11020583] [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: 01/08/2023] [Revised: 02/03/2023] [Accepted: 02/08/2023] [Indexed: 02/18/2023] Open
Abstract
Autism spectrum disorders (ASD) are a heterogeneous group of neurodevelopmental disorders generally characterized by repetitive behaviors and difficulties in communication and social behavior. Despite its heterogeneous nature, several metabolic dysregulations are prevalent in individuals with ASD. This work aims to understand ASD brain metabolism by constructing an ASD-specific prefrontal cortex genome-scale metabolic model (GEM) using transcriptomics data to decipher novel neuroinflammatory biomarkers. The healthy and ASD-specific models are compared via uniform sampling to identify ASD-exclusive metabolic features. Noticeably, the results of our simulations and those found in the literature are comparable, supporting the accuracy of our reconstructed ASD model. We identified that several oxidative stress, mitochondrial dysfunction, and inflammatory markers are elevated in ASD. While oxidative phosphorylation fluxes were similar for healthy and ASD-specific models, and the fluxes through the pathway were nearly undisturbed, the tricarboxylic acid (TCA) fluxes indicated disruptions in the pathway. Similarly, the secretions of mitochondrial dysfunction markers such as pyruvate are found to be higher, as well as the activities of oxidative stress marker enzymes like alanine and aspartate aminotransferases (ALT and AST) and glutathione-disulfide reductase (GSR). We also detected abnormalities in the sphingolipid metabolism, which has been implicated in many inflammatory and immune processes, but its relationship with ASD has not been thoroughly explored in the existing literature. We suggest that important sphingolipid metabolites, such as sphingosine-1-phosphate (S1P), ceramide, and glucosylceramide, may be promising biomarkers for the diagnosis of ASD and provide an opportunity for the adoption of early intervention for young children.
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Assessing Metabolic Markers in Glioblastoma Using Machine Learning: A Systematic Review. Metabolites 2023; 13:metabo13020161. [PMID: 36837779 PMCID: PMC9958885 DOI: 10.3390/metabo13020161] [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: 12/26/2022] [Revised: 01/14/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
Glioblastoma (GBM) is a common and deadly brain tumor with late diagnoses and poor prognoses. Machine learning (ML) is an emerging tool that can create highly accurate diagnostic and prognostic prediction models. This paper aimed to systematically search the literature on ML for GBM metabolism and assess recent advancements. A literature search was performed using predetermined search terms. Articles describing the use of an ML algorithm for GBM metabolism were included. Ten studies met the inclusion criteria for analysis: diagnostic (n = 3, 30%), prognostic (n = 6, 60%), or both (n = 1, 10%). Most studies analyzed data from multiple databases, while 50% (n = 5) included additional original samples. At least 2536 data samples were run through an ML algorithm. Twenty-seven ML algorithms were recorded with a mean of 2.8 algorithms per study. Algorithms were supervised (n = 24, 89%), unsupervised (n = 3, 11%), continuous (n = 19, 70%), or categorical (n = 8, 30%). The mean reported accuracy and AUC of ROC were 95.63% and 0.779, respectively. One hundred six metabolic markers were identified, but only EMP3 was reported in multiple studies. Many studies have identified potential biomarkers for GBM diagnosis and prognostication. These algorithms show promise; however, a consensus on even a handful of biomarkers has not yet been made.
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Pinto J, Costa RS, Alexandre L, Ramos J, Oliveira R. SBML2HYB: a Python interface for SBML compatible hybrid modeling. Bioinformatics 2023; 39:6994184. [PMID: 36661327 PMCID: PMC9889961 DOI: 10.1093/bioinformatics/btad044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/03/2023] [Accepted: 01/19/2023] [Indexed: 01/21/2023] Open
Abstract
SUMMARY Here, we present sbml2hyb, an easy-to-use standalone Python tool that facilitates the conversion of existing mechanistic models of biological systems in Systems Biology Markup Language (SBML) into hybrid semiparametric models that combine mechanistic functions with machine learning (ML). The so-formed hybrid models can be trained and stored back in databases in SBML format. The tool supports a user-friendly export interface with an internal format validator. Two case studies illustrate the use of the sbml2hyb tool. Additionally, we describe HMOD, a new model format designed to support and facilitate hybrid models building. It aggregates the mechanistic model information with the ML information and follows as close as possible the SBML rules. We expect the sbml2hyb tool and HMOD to greatly facilitate the widespread usage of hybrid modeling techniques for biological systems analysis. AVAILABILITY AND IMPLEMENTATION The Python interface, source code and the example models used for the case studies are accessible at: https://github.com/r-costa/sbml2hyb. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Leonardo Alexandre
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica 2829-516, Portugal,INESC-ID, Lisboa, Portugal
| | - João Ramos
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica 2829-516, Portugal
| | - Rui Oliveira
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica 2829-516, Portugal
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Wei C, Xiang X, Zhou X, Ren S, Zhou Q, Dong W, Lin H, Wang S, Zhang Y, Lin H, He Q, Lu Y, Jiang X, Shuai J, Jin X, Xie C. Development and validation of an interpretable radiomic nomogram for severe radiation proctitis prediction in postoperative cervical cancer patients. Front Microbiol 2023; 13:1090770. [PMID: 36713206 PMCID: PMC9877536 DOI: 10.3389/fmicb.2022.1090770] [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: 11/06/2022] [Accepted: 12/28/2022] [Indexed: 01/13/2023] Open
Abstract
Background Radiation proctitis is a common complication after radiotherapy for cervical cancer. Unlike simple radiation damage to other organs, radiation proctitis is a complex disease closely related to the microbiota. However, analysis of the gut microbiota is time-consuming and expensive. This study aims to mine rectal information using radiomics and incorporate it into a nomogram model for cheap and fast prediction of severe radiation proctitis prediction in postoperative cervical cancer patients. Methods The severity of the patient's radiation proctitis was graded according to the RTOG/EORTC criteria. The toxicity grade of radiation proctitis over or equal to grade 2 was set as the model's target. A total of 178 patients with cervical cancer were divided into a training set (n = 124) and a validation set (n = 54). Multivariate logistic regression was used to build the radiomic and non-raidomic models. Results The radiomics model [AUC=0.6855(0.5174-0.8535)] showed better performance and more net benefit in the validation set than the non-radiomic model [AUC=0.6641(0.4904-0.8378)]. In particular, we applied SHapley Additive exPlanation (SHAP) method for the first time to a radiomics-based logistic regression model to further interpret the radiomic features from case-based and feature-based perspectives. The integrated radiomic model enables the first accurate quantitative assessment of the probability of radiation proctitis in postoperative cervical cancer patients, addressing the limitations of the current qualitative assessment of the plan through dose-volume parameters only. Conclusion We successfully developed and validated an integrated radiomic model containing rectal information. SHAP analysis of the model suggests that radiomic features have a supporting role in the quantitative assessment of the probability of radiation proctitis in postoperative cervical cancer patients.
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Affiliation(s)
- Chaoyi Wei
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang Province, China
| | - Xinli Xiang
- The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Xiaobo Zhou
- Medical and Radiation Oncology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Siyan Ren
- Medical and Radiation Oncology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Qingyu Zhou
- Medical and Radiation Oncology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Wenjun Dong
- Medical and Radiation Oncology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Haizhen Lin
- Medical and Radiation Oncology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Saijun Wang
- Medical and Radiation Oncology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Yuyue Zhang
- Medical and Radiation Oncology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Hai Lin
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang Province, China
| | - Qingzu He
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang Province, China
| | - Yuer Lu
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang Province, China
| | - Xiaoming Jiang
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang Province, China
| | - Jianwei Shuai
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang Province, China
| | - Xiance Jin
- Radiotherapy Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China,School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China,*Correspondence: Xiance Jin, ✉
| | - Congying Xie
- Medical and Radiation Oncology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China,Congying Xie, ✉
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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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