151
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Ng QX, Yau CE, Yaow CYL, Chong RIH, Chong NZY, Teoh SE, Lim YL, Soh AYS, Ng WK, Thumboo J. What Has Longitudinal ‘Omics’ Studies Taught Us about Irritable Bowel Syndrome? A Systematic Review. Metabolites 2023; 13:metabo13040484. [PMID: 37110143 PMCID: PMC10142038 DOI: 10.3390/metabo13040484] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023] Open
Abstract
Irritable bowel syndrome is a prototypical disorder of the brain–gut–microbiome axis, although the underlying pathogenesis and mechanisms remain incompletely understood. With the recent advances in ‘omics’ technologies, studies have attempted to uncover IBS-specific variations in the host–microbiome profile and function. However, no biomarker has been identified to date. Given the high inter-individual and day-to-day variability of the gut microbiota, and a lack of agreement across the large number of microbiome studies, this review focused on omics studies that had sampling at more than one time point. A systematic literature search was performed using various combinations of the search terms “Irritable Bowel Syndrome” and “Omics” in the Medline, EMBASE, and Cochrane Library up to 1 December 2022. A total of 16 original studies were reviewed. These multi-omics studies have implicated Bacteroides, Faecalibacterium prausnitzii, Ruminococcus spp., and Bifidobacteria in IBS and treatment response, found altered metabolite profiles in serum, faecal, or urinary samples taken from IBS patients compared to the healthy controls, and revealed enrichment in the immune and inflammation-related pathways. They also demonstrated the possible therapeutic mechanisms of diet interventions, for example, synbiotics and low fermentable oligosaccharides, disaccharides, monosaccharides, and polyol (FODMAP) diets on microbial metabolites. However, there was significant heterogeneity among the studies and no uniform characteristics of IBS-related gut microbiota. There is a need to further study these putative mechanisms and also ensure that they can be translated to therapeutic benefits for patients with IBS.
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152
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Turgman O, Schinkel M, Wiersinga WJ. Host Response Biomarkers for Sepsis in the Emergency Room. Crit Care 2023; 27:97. [PMID: 36941681 PMCID: PMC10027585 DOI: 10.1186/s13054-023-04367-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
This article is one of ten reviews selected from the Annual Update in Intensive Care and Emergency Medicine 2023. Other selected articles can be found online at https://www.biomedcentral.com/collections/annualupdate2023 . Further information about the Annual Update in Intensive Care and Emergency Medicine is available from https://link.springer.com/bookseries/8901 .
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Affiliation(s)
- Oren Turgman
- Center for Experimental and Molecular Medicine, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Michiel Schinkel
- Center for Experimental and Molecular Medicine, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Division of Infectious Diseases, Department of Medicine, Amsterdam UMC, Location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Willem Joost Wiersinga
- Center for Experimental and Molecular Medicine, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
- Division of Infectious Diseases, Department of Medicine, Amsterdam UMC, Location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
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153
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Khadirnaikar S, Shukla S, Prasanna SRM. Machine learning based combination of multi-omics data for subgroup identification in non-small cell lung cancer. Sci Rep 2023; 13:4636. [PMID: 36944673 PMCID: PMC10030850 DOI: 10.1038/s41598-023-31426-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 03/11/2023] [Indexed: 03/23/2023] Open
Abstract
Non-small Cell Lung Cancer (NSCLC) is a heterogeneous disease with a poor prognosis. Identifying novel subtypes in cancer can help classify patients with similar molecular and clinical phenotypes. This work proposes an end-to-end pipeline for subgroup identification in NSCLC. Here, we used a machine learning (ML) based approach to compress the multi-omics NSCLC data to a lower dimensional space. This data is subjected to consensus K-means clustering to identify the five novel clusters (C1-C5). Survival analysis of the resulting clusters revealed a significant difference in the overall survival of clusters (p-value: 0.019). Each cluster was then molecularly characterized to identify specific molecular characteristics. We found that cluster C3 showed minimal genetic aberration with a high prognosis. Next, classification models were developed using data from each omic level to predict the subgroup of unseen patients. Decision‑level fused classification models were then built using these classifiers, which were used to classify unseen patients into five novel clusters. We also showed that the multi-omics-based classification model outperformed single-omic-based models, and the combination of classifiers proved to be a more accurate prediction model than the individual classifiers. In summary, we have used ML models to develop a classification method and identified five novel NSCLC clusters with different genetic and clinical characteristics.
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Affiliation(s)
- Seema Khadirnaikar
- Department of Electrical Engineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Sudhanshu Shukla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India.
| | - S R M Prasanna
- Department of Electrical Engineering, Indian Institute of Technology Dharwad, Dharwad, India
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154
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Aharoni A, Goodacre R, Fernie AR. Plant and microbial sciences as key drivers in the development of metabolomics research. Proc Natl Acad Sci U S A 2023; 120:e2217383120. [PMID: 36930598 PMCID: PMC10041103 DOI: 10.1073/pnas.2217383120] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
This year marks the 25th anniversary of the coinage of the term metabolome [S. G. Oliver et al., Trends Biotech. 16, 373-378 (1998)]. As the field rapidly advances, it is important to take stock of the progress which has been made to best inform the disciplines future. While a medical-centric perspective on metabolomics has recently been published [M. Giera et al., Cell Metab. 34, 21-34 (2022)], this largely ignores the pioneering contributions made by the plant and microbial science communities. In this perspective, we provide a contemporary overview of all fields in which metabolomics is employed with particular emphasis on both methodological and application breakthroughs made in plant and microbial sciences that have shaped this evolving research discipline from the very early days of its establishment. This will not cover all types of metabolomics assays currently employed but will focus mainly on those utilizing mass spectrometry-based measurements since they are currently by far the most prominent. Having established the historical context of metabolomics, we will address the key challenges currently facing metabolomics and offer potential approaches by which these can be faced. Most salient among these is the fact that the vast majority of mass features are as yet not annotated with high confidence; what we may refer to as definitive identification. We discuss the potential of both standard compound libraries and artificial intelligence technologies to address this challenge and the use of natural variance-based approaches such as genome-wide association studies in attempt to assign specific functions to the myriad of structurally similar and complex specialized metabolites. We conclude by stating our contention that as these challenges are epic and that they will need far greater cooperative efforts from biologists, chemists, and computer scientists with an interest in all kingdoms of life than have been made to date. Ultimately, a better linkage of metabolome and genome data will likely also be needed particularly considering the Earth BioGenome Project.
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Affiliation(s)
- Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot76100, Israel
| | - Royston Goodacre
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, LiverpoolL69 7BE, UK
| | - Alisdair R. Fernie
- Max-Planck-Institute for Molecular Plant Physiology, Potsdam14476, Germany
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155
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Zhan L, Tian X, Lin J, Zhang Y, Zheng H, Peng X, Zhao G. Honokiol reduces fungal burden and ameliorate inflammation lesions of Aspergillus fumigatus keratitis via Dectin-2 down-regulation. Int Immunopharmacol 2023; 118:109849. [PMID: 36933490 DOI: 10.1016/j.intimp.2023.109849] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 01/29/2023] [Accepted: 02/03/2023] [Indexed: 03/18/2023]
Abstract
PURPOSE To screen and identify the mechanism of honokiol on anti-fungi and anti-inflammation in fungal keratitis (FK) through bioinformatic analysis and biological experiments. METHODS Transcriptome profile demonstrated differential expression genes (DEGs) of Aspergillus fumigatus keratitis between PBS-treated and honokiol-treated groups via bioinformatics analyses. Inflammatory substances were quantified by qRT-PCR, Western blot and ELISA, and macrophage polarization was examined by flow cytometry. Periodic acid Schiff staining and morphological interference assay were used to detect hyphal distribution in vivo and fungal germination in vitro, respectively. Electron microscopy was to illustrate hyphal microstructure. RESULTS Illumina sequencing demonstrated that compared with the honokiol group, 1175 up-regulated and 383 down-regulated genes were induced in C57BL/6 mice Aspergillus fumigatus keratitis with PBS treatment. Through GO analysis, some differential expression proteins (DEPs) played major roles in biological processes, especially fungal defense and immune activation. KEGG analysis provided fungus-related signaling pathways. PPI analysis demonstrated that DEPs from multiple pathways form a close-knit network, providing a broader context for FK treatment. In biological experiments, Dectin-2, NLRP3 and IL-1β were upregulated by Aspergillus fumigatus to evaluate immune response. Honokiol could reverse the trend, comparable to Dectin-2 siRNA interference. Meanwhile, honokiol could also play an anti-inflammatory role via promoting M2 phenotype polarization. Moreover, honokiol reduced hyphal distribution in the stroma, delayed germination, and destroyed the hyphal cell membrane in-vitro. CONCLUSIONS Honokiol possesses anti-fungal and anti-inflammatory effects in Aspergillus fumigatus keratitis and may develop a potential and safe therapeutic modality for FK.
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Affiliation(s)
- Lu Zhan
- Department of Ophthalmology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xue Tian
- Department of Ophthalmology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jing Lin
- Department of Ophthalmology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yingxue Zhang
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine 540 E. Canfield Avenue Detroit, MI 48201, USA
| | - Hengrui Zheng
- Department of Ophthalmology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xudong Peng
- Department of Ophthalmology, The Affiliated Hospital of Qingdao University, Qingdao, China; Department of Ophthalmology, University of Washington, Seattle WA98104, USA.
| | - Guiqiu Zhao
- Department of Ophthalmology, The Affiliated Hospital of Qingdao University, Qingdao, China.
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156
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Bostanci E, Kocak E, Unal M, Guzel MS, Acici K, Asuroglu T. Machine Learning Analysis of RNA-seq Data for Diagnostic and Prognostic Prediction of Colon Cancer. SENSORS (BASEL, SWITZERLAND) 2023; 23:3080. [PMID: 36991790 PMCID: PMC10052105 DOI: 10.3390/s23063080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/09/2023] [Accepted: 03/11/2023] [Indexed: 06/19/2023]
Abstract
Data from omics studies have been used for prediction and classification of various diseases in biomedical and bioinformatics research. In recent years, Machine Learning (ML) algorithms have been used in many different fields related to healthcare systems, especially for disease prediction and classification tasks. Integration of molecular omics data with ML algorithms has offered a great opportunity to evaluate clinical data. RNA sequence (RNA-seq) analysis has been emerged as the gold standard for transcriptomics analysis. Currently, it is being used widely in clinical research. In our present work, RNA-seq data of extracellular vesicles (EV) from healthy and colon cancer patients are analyzed. Our aim is to develop models for prediction and classification of colon cancer stages. Five different canonical ML and Deep Learning (DL) classifiers are used to predict colon cancer of an individual with processed RNA-seq data. The classes of data are formed on the basis of both colon cancer stages and cancer presence (healthy or cancer). The canonical ML classifiers, which are k-Nearest Neighbor (kNN), Logistic Model Tree (LMT), Random Tree (RT), Random Committee (RC), and Random Forest (RF), are tested with both forms of the data. In addition, to compare the performance with canonical ML models, One-Dimensional Convolutional Neural Network (1-D CNN), Long Short-Term Memory (LSTM), and Bidirectional LSTM (BiLSTM) DL models are utilized. Hyper-parameter optimizations of DL models are constructed by using genetic meta-heuristic optimization algorithm (GA). The best accuracy in cancer prediction is obtained with RC, LMT, and RF canonical ML algorithms as 97.33%. However, RT and kNN show 95.33% performance. The best accuracy in cancer stage classification is achieved with RF as 97.33%. This result is followed by LMT, RC, kNN, and RT with 96.33%, 96%, 94.66%, and 94%, respectively. According to the results of the experiments with DL algorithms, the best accuracy in cancer prediction is obtained with 1-D CNN as 97.67%. BiLSTM and LSTM show 94.33% and 93.67% performance, respectively. In classification of the cancer stages, the best accuracy is achieved with BiLSTM as 98%. 1-D CNN and LSTM show 97% and 94.33% performance, respectively. The results reveal that both canonical ML and DL models may outperform each other for different numbers of features.
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Affiliation(s)
- Erkan Bostanci
- Department of Computer Engineering, Faculty of Engineering, Ankara University, 06830 Ankara, Turkey
| | - Engin Kocak
- Department of Analytical Chemistry, Faculty of Gülhane Pharmacy, University of Health Sciences, 06018 Ankara, Turkey
| | - Metehan Unal
- Department of Computer Engineering, Faculty of Engineering, Ankara University, 06830 Ankara, Turkey
| | - Mehmet Serdar Guzel
- Department of Computer Engineering, Faculty of Engineering, Ankara University, 06830 Ankara, Turkey
| | - Koray Acici
- Department of Artificial Intelligence and Data Engineering, Faculty of Engineering, Ankara University, 06830 Ankara, Turkey
| | - Tunc Asuroglu
- Faculty of Medicine and Health Technology, Tampere University, 33720 Tampere, Finland
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157
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Zhao M, Liu J, Xin M, Yang K, Huang H, Zhang W, Zhang J, He S. Pulmonary arterial hypertension associated with congenital heart disease: An omics study. Front Cardiovasc Med 2023; 10:1037357. [PMID: 36970344 PMCID: PMC10036813 DOI: 10.3389/fcvm.2023.1037357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 02/24/2023] [Indexed: 03/12/2023] Open
Abstract
Pulmonary arterial hypertension associated with congenital heart disease (PAH-CHD) is a severely progressive condition with uncertain physiological course. Hence, it has become increasingly relevant to clarify the specific mechanisms of molecular modification, which is crucial to identify more treatment strategies. With the rapid development of high-throughput sequencing, omics technology gives access to massive experimental data and advanced techniques for systems biology, permitting comprehensive assessment of disease occurrence and progression. In recent years, significant progress has been made in the study of PAH-CHD and omics. To provide a comprehensive description and promote further in-depth investigation of PAH-CHD, this review attempts to summarize the latest developments in genomics, transcriptomics, epigenomics, proteomics, metabolomics, and multi-omics integration.
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Affiliation(s)
- Maolin Zhao
- Department of Cardiovascular Surgery, Affiliated Hospital of Southwest Jiaotong University, General Hospital of Western Theater Command, Chengdu, China
| | - Jian Liu
- Department of Cardiovascular Surgery, Affiliated Hospital of Southwest Jiaotong University, General Hospital of Western Theater Command, Chengdu, China
| | - Mei Xin
- Department of Cardiovascular Surgery, Affiliated Hospital of Southwest Jiaotong University, General Hospital of Western Theater Command, Chengdu, China
| | - Ke Yang
- Department of Cardiovascular Surgery, Affiliated Hospital of Southwest Jiaotong University, General Hospital of Western Theater Command, Chengdu, China
| | - Honghao Huang
- Department of Cardiovascular Surgery, Affiliated Hospital of Southwest Jiaotong University, General Hospital of Western Theater Command, Chengdu, China
| | - Wenxin Zhang
- Department of Cardiovascular Surgery, Affiliated Hospital of Southwest Jiaotong University, General Hospital of Western Theater Command, Chengdu, China
| | - Jinbao Zhang
- Department of Cardiovascular Surgery, Affiliated Hospital of Southwest Jiaotong University, General Hospital of Western Theater Command, Chengdu, China
| | - Siyi He
- Department of Cardiovascular Surgery, Affiliated Hospital of Southwest Jiaotong University, General Hospital of Western Theater Command, Chengdu, China
- Correspondence: Siyi He
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158
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Multi-omics analysis identifies potential mechanisms by which high glucose accelerates macrophage foaming. Mol Cell Biochem 2023; 478:665-678. [PMID: 36029453 DOI: 10.1007/s11010-022-04542-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 08/09/2022] [Indexed: 10/15/2022]
Abstract
Atherosclerotic morbidity is significantly higher in the diabetic population. Hyperglycemia, a typical feature of diabetes, has been proven to accelerate foam cell formation. However, the molecular mechanisms behind this process remain unclear. In this study, LPS and IFN-γ were used to convert THP-1-derived macrophages into M1 macrophages, which were then activated with ox-LDL in either high glucose or normal condition. We identified lipids within macrophages by Oil red O staining and total cholesterol detection. The genes involved in lipid absorption, efflux, inflammation, and metabolism were analyzed using qRT-PCR. The mechanisms of high glucose-induced foam cell formation were further investigated through metabolomics and transcriptomics analysis. We discovered that high glucose speed up lipid accumulation in macrophages (both lipid droplets and total cholesterol increased), diminished lipid efflux (ABCG1 down-regulation), and aggravated inflammation (IL1B and TNF up-regulation). Following multi-omics analysis, it was determined that glucose altered the metabolic and transcriptional profiles of macrophages, identifying 392 differently expressed metabolites and 293 differentially expressed genes, respectively. Joint pathway analysis suggested that glucose predominantly disrupted the glycerolipid, glycerophospholipid, and arachidonic acid metabolic pathways in macrophages. High glucose in the glyceride metabolic pathway, for instance, suppressed the transcription of triglyceride hydrolase (LIPG and LPL), causing cells to deposit excess triglycerides into lipid droplets and encouraging foam cell formation. More importantly, high glucose triggered the accumulation of pro-atherosclerotic lipids (7-ketocholesterol, lysophosphatidylcholine, and glycerophosphatidylcholine). In conclusion, this work elucidated mechanisms of glucose-induced foam cell formation via a multi-omics approach.
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159
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Su J, Cao J, Yang H, Xu W, Liu W, Wang R, Huang Y, Wu J, Gao X, Weng R, Pu J, Liu N, Gu Y, Qian K, Ni W. Diagnosis of Unruptured Intracranial Aneurysm by High-Performance Serum Metabolic Fingerprints. SMALL METHODS 2023; 7:e2201486. [PMID: 36634984 DOI: 10.1002/smtd.202201486] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Unruptured intracranial aneurysm (UIA) is a high-risk cerebrovascular saccular dilatation, the effective medical management of which depends on high-performance diagnosis. However, most UIAs are diagnosed incidentally during neurovascular imaging modalities, which are time-consuming and harmful (e.g., radiation). Serum metabolic fingerprints is a promising alternative for early diagnosis of UIA. Here, nanoparticle enhanced laser desorption/ionization mass spectrometry is applied to obtain high-performance UIA-specific serum metabolic fingerprints. Diagnostic performance with an area-under-the-curve (AUC) of 0.842 (95% confidence interval (CI): 0.783-0.891) is achieved by the constructed machine learning (ML) model, including ML algorithm selection and feature selection. Lactate, glutamine, homoarginine, and 3-methylglutaconic acid are identified as the metabolic biomarker panel, which showed satisfactory diagnosis (AUC of 0.812, 95% CI: 0.727-0.897) and effective growth risk assessment (p<0.05, two-tailed t-test) of UIAs. This work aims to promote the diagnostics of UIAs and metabolic biomarker screening for medical management.
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Affiliation(s)
- Jiabin Su
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, P. R. China
- National Center for Neurological Disorders, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, P. R. China
| | - Jing Cao
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, 160 Pujian Road, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Heng Yang
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, P. R. China
- National Center for Neurological Disorders, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, P. R. China
| | - Wei Xu
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, 160 Pujian Road, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Wanshan Liu
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, 160 Pujian Road, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Ruimin Wang
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, 160 Pujian Road, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Yida Huang
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, 160 Pujian Road, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Jiao Wu
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, 160 Pujian Road, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Xinjie Gao
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, P. R. China
- National Center for Neurological Disorders, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, P. R. China
| | - Ruiyuan Weng
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, P. R. China
| | - Jun Pu
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, 160 Pujian Road, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Ning Liu
- School of Electronics Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Yuxiang Gu
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, P. R. China
- National Center for Neurological Disorders, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, P. R. China
| | - Kun Qian
- State Key Laboratory for Oncogenes and Related Genes, Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, 160 Pujian Road, Shanghai, 200127, P. R. China
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Wei Ni
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, P. R. China
- National Center for Neurological Disorders, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, P. R. China
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160
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Ma R, Fan Y, Huang X, Wang J, Li S, Wang Y, Ye Q. Lipid dysregulation associated with progression of silica-induced pulmonary fibrosis. Toxicol Sci 2023; 191:296-307. [PMID: 36477571 DOI: 10.1093/toxsci/kfac124] [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] [Indexed: 12/12/2022] Open
Abstract
Silicosis is an irreversible, progressive, fibrotic lung disease caused by long-term exposure to dust-containing silica particles at the workplace. Despite the precautions enforced, the rising incidence of silicosis continues to occur globally, particularly in developing countries. A better understanding of the disease progression and potential metabolic reprogramming of silicosis is warranted. The low- or high-dose silica-induced pulmonary fibrosis in mice was constructed to mimic chronic or accelerated silicosis. Silica-induced mice lung fibrosis was analyzed by histology, lung function, and computed tomography scans. Non-targeted metabolomics of the lung tissues was conducted by ultra-high-performance liquid chromatography-mass spectrometry to show the temporal metabolic trajectory. The low-dose silica-induced silicosis characterized inflammation for up to 42 days, with the onset of cellular silicon nodules. Conversely, the high-dose silica-induced silicosis characterized inflammation for up to 14 days, after which the disease developed rapidly, with a large volume of collagen deposition, presenting progressive massive fibrosis. Both low- and high silica-induced fibrosis had aberrant lipid metabolism. Combined with the RNA-Seq data, this multiomics study demonstrated alterations in the enzymes involved in sphingolipid metabolism. Time-dependent metabolic reprogramming revealing abnormal glycerophospholipid metabolism was intimately associated with the process of inflammation, whereas sphingolipid metabolism was crucial during lung fibrosis. These findings suggest that lipid dysregulation, especially sphingolipid metabolism, was involved in the process of silicosis.
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Affiliation(s)
- Ruimin Ma
- Department of Occupational Medicine and Toxicology, Clinical Center for Interstitial Lung Diseases, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Yali Fan
- Department of Occupational Medicine and Toxicology, Clinical Center for Interstitial Lung Diseases, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Xiaoxi Huang
- Medical Research Center, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Jingwei Wang
- Department of Occupational Medicine and Toxicology, Clinical Center for Interstitial Lung Diseases, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Shuang Li
- Department of Occupational Medicine and Toxicology, Clinical Center for Interstitial Lung Diseases, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Yuanying Wang
- Department of Occupational Medicine and Toxicology, Clinical Center for Interstitial Lung Diseases, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Qiao Ye
- Department of Occupational Medicine and Toxicology, Clinical Center for Interstitial Lung Diseases, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
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161
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Paul I, Bolzan D, Youssef A, Gagnon KA, Hook H, Karemore G, Oliphant MUJ, Lin W, Liu Q, Phanse S, White C, Padhorny D, Kotelnikov S, Chen CS, Hu P, Denis GV, Kozakov D, Raught B, Siggers T, Wuchty S, Muthuswamy SK, Emili A. Parallelized multidimensional analytic framework applied to mammary epithelial cells uncovers regulatory principles in EMT. Nat Commun 2023; 14:688. [PMID: 36755019 PMCID: PMC9908882 DOI: 10.1038/s41467-023-36122-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 01/17/2023] [Indexed: 02/10/2023] Open
Abstract
A proper understanding of disease etiology will require longitudinal systems-scale reconstruction of the multitiered architecture of eukaryotic signaling. Here we combine state-of-the-art data acquisition platforms and bioinformatics tools to devise PAMAF, a workflow that simultaneously examines twelve omics modalities, i.e., protein abundance from whole-cells, nucleus, exosomes, secretome and membrane; N-glycosylation, phosphorylation; metabolites; mRNA, miRNA; and, in parallel, single-cell transcriptomes. We apply PAMAF in an established in vitro model of TGFβ-induced epithelial to mesenchymal transition (EMT) to quantify >61,000 molecules from 12 omics and 10 timepoints over 12 days. Bioinformatics analysis of this EMT-ExMap resource allowed us to identify; -topological coupling between omics, -four distinct cell states during EMT, -omics-specific kinetic paths, -stage-specific multi-omics characteristics, -distinct regulatory classes of genes, -ligand-receptor mediated intercellular crosstalk by integrating scRNAseq and subcellular proteomics, and -combinatorial drug targets (e.g., Hedgehog signaling and CAMK-II) to inhibit EMT, which we validate using a 3D mammary duct-on-a-chip platform. Overall, this study provides a resource on TGFβ signaling and EMT.
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Affiliation(s)
- Indranil Paul
- Department of Biochemistry, Boston University School of Medicine, Boston University, 71 East Concord Street, Boston, MA, 02118, USA
| | - Dante Bolzan
- Department of Computer Science, University of Miami, 1356 Memorial Drive, Coral Gables, FL, 33146, USA
| | - Ahmed Youssef
- Graduate Program in Bioinformatics, Boston University, 24 Cummington Mall, Boston, MA, 02215, USA
| | - Keith A Gagnon
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA, 02215, USA
| | - Heather Hook
- Department of Biology, Boston University, 24 Cummington Mall, Boston, MA, 02115, USA
- Biological Design Center, Boston University, 610 Commonwealth Avenue, Boston, MA, 02215, USA
| | - Gopal Karemore
- Advanced Analytics, Novo Nordisk A/S, 2760, Måløv, Denmark
| | - Michael U J Oliphant
- Cancer Research Institute, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Weiwei Lin
- Department of Biochemistry, Boston University School of Medicine, Boston University, 71 East Concord Street, Boston, MA, 02118, USA
| | - Qian Liu
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada
| | - Sadhna Phanse
- Department of Biochemistry, Boston University School of Medicine, Boston University, 71 East Concord Street, Boston, MA, 02118, USA
| | - Carl White
- Department of Biochemistry, Boston University School of Medicine, Boston University, 71 East Concord Street, Boston, MA, 02118, USA
| | - Dzmitry Padhorny
- Department of Applied Mathematics and Statistics, Stony Brook University, 11794, Stony Brook, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Sergei Kotelnikov
- Department of Applied Mathematics and Statistics, Stony Brook University, 11794, Stony Brook, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Christopher S Chen
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA, 02215, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA, 02115, USA
| | - Pingzhao Hu
- Department of Biochemistry, Western University, London, ON, N6A 5C1, Canada
| | - Gerald V Denis
- Boston Medical Center Cancer Center, Boston University, Boston University, 72 East Concord Street, Boston, MA, 02118, USA
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, 11794, Stony Brook, NY, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Brian Raught
- Discovery Tower (TMDT), 101 College St, Rm. 9-701A, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Trevor Siggers
- Department of Biology, Boston University, 24 Cummington Mall, Boston, MA, 02115, USA
- Biological Design Center, Boston University, 610 Commonwealth Avenue, Boston, MA, 02215, USA
| | - Stefan Wuchty
- Department of Computer Science, University of Miami, 1356 Memorial Drive, Coral Gables, FL, 33146, USA
| | - Senthil K Muthuswamy
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Andrew Emili
- Department of Biochemistry, Boston University School of Medicine, Boston University, 71 East Concord Street, Boston, MA, 02118, USA.
- Department of Biology, Charles River Campus, Boston University, Life Science & Engineering (LSEB-602), 24 Cummington Mall, Boston, MA, 02215, USA.
- Division of Oncological Sciences, Knight Cancer Institute, Oregon Health and Science University, Portland, USA.
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Smith MR, Hu X, Jarrell ZR, He X, Orr M, Fernandes J, Chandler JD, Walker DI, Esper A, Marts L, Neujahr DC, Jones DP, Go YM. Study on the Relationship between Selenium and Cadmium in Diseased Human Lungs. ADVANCES IN REDOX RESEARCH 2023; 7. [PMID: 37034445 PMCID: PMC10078579 DOI: 10.1016/j.arres.2023.100065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Cadmium (Cd) is a toxic environmental metal that interacts with selenium (Se) and contributes to many lung diseases. Humans have widespread exposures to Cd through diet and cigarette smoking, and studies in rodent models show that Se can protect against Cd toxicities. We sought to identify whether an antagonistic relationship existed between Se and Cd burdens and determine whether this relationship may associate with metabolic variation within human lungs. We performed metabolomics of 31 human lungs, including 25 with end-stage lung disease due to idiopathic pulmonary fibrosis, cystic fibrosis, chronic obstructive lung disease (COPD)/emphysema and other causes, and 6 non-diseased lungs. Results showed pathway associations with Cd including amino acid, lipid and energy-related pathways. Metabolic pathways varying with Se had considerable overlap with these pathways. Hierarchical cluster analysis (HCA) of individuals according to metabolites associated with Cd showed partial separation of disease types, with COPD/emphysema in the cluster with highest Cd, and non-diseased lungs in the cluster with the lowest Cd. When compared to HCA of metabolites associated with Se, the results showed that the cluster containing COPD/emphysema had the lowest Se, and the non-diseased lungs had the highest Se. A greater number of pathway associations occurred for Cd to Se ratio than either Cd or Se alone, indicating that metabolic patterns were more dependent on Cd to Se ratio than on either alone. Network analysis of interactions of Cd and Se showed network centrality was associated with pathways linked to polyunsaturated fatty acids involved in inflammatory signaling. Overall, the data show that metabolic pathway responses in human lung vary with Cd and Se in a pattern suggesting that Se is antagonistic to Cd toxicity in humans.
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Affiliation(s)
- Matthew Ryan Smith
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine at Emory University, Atlanta, GA, USA
- Atlanta Department of Veterans Affairs Medical Center, Decatur, GA, USA
| | - Xin Hu
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine at Emory University, Atlanta, GA, USA
| | - Zachery R Jarrell
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine at Emory University, Atlanta, GA, USA
| | - Xiaojia He
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine at Emory University, Atlanta, GA, USA
| | - Michael Orr
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine at Emory University, Atlanta, GA, USA
| | - Jolyn Fernandes
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine at Emory University, Atlanta, GA, USA
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Joshua D. Chandler
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine at Emory University, Atlanta, GA, USA
- Department of Pediatrics, School of Medicine at Emory University, Atlanta, GA, USA
| | - Douglas I. Walker
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine at Emory University, Atlanta, GA, USA
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Annette Esper
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine at Emory University, Atlanta, GA, USA
| | - Lucian Marts
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine at Emory University, Atlanta, GA, USA
| | - David C. Neujahr
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine at Emory University, Atlanta, GA, USA
| | - Dean P. Jones
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine at Emory University, Atlanta, GA, USA
- Corresponding authors at: Whitehead Biomedical Research Building, 615 Michael St, Room 225, Atlanta, GA, 30322, USA. (D.P. Jones), (Y.-M. Go)
| | - Young-Mi Go
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine at Emory University, Atlanta, GA, USA
- Corresponding authors at: Whitehead Biomedical Research Building, 615 Michael St, Room 225, Atlanta, GA, 30322, USA. (D.P. Jones), (Y.-M. Go)
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Cao J, Xiao Y, Zhang M, Huang L, Wang Y, Liu W, Wang X, Wu J, Huang Y, Wang R, Zhou L, Li L, Zhang Y, Ren L, Qian K, Wang J. Deep Learning of Dual Plasma Fingerprints for High-Performance Infection Classification. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206349. [PMID: 36470664 DOI: 10.1002/smll.202206349] [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: 10/15/2022] [Revised: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Infection classification is the key for choosing the proper treatment plans. Early determination of the causative agents is critical for disease control. Host responses analysis can detect variform and sensitive host inflammatory responses to ascertain the presence and type of the infection. However, traditional host-derived inflammatory indicators are insufficient for clinical infection classification. Fingerprints-based omic analysis has attracted increasing attention globally for analyzing the complex host systemic immune response. A single type of fingerprints is not applicable for infection classification (area under curve (AUC) of 0.550-0.617). Herein, an infection classification platform based on deep learning of dual plasma fingerprints (DPFs-DL) is developed. The DPFs with high reproducibility (coefficient of variation <15%) are obtained at low sample consumption (550 nL native plasma) using inorganic nanoparticle and organic matrix assisted laser desorption/ionization mass spectrometry. A classifier (DPFs-DL) for viral versus bacterial infection discrimination (AUC of 0.775) and coronavirus disease 2019 (COVID-2019) diagnosis (AUC of 0.917) is also built. Furthermore, a metabolic biomarker panel of two differentially regulated metabolites, which may serve as potential biomarkers for COVID-19 management (AUC of 0.677-0.883), is constructed. This study will contribute to the development of precision clinical care for infectious diseases.
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Affiliation(s)
- Jing Cao
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering and Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore, 117583, Singapore
| | - Yan Xiao
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Mengji Zhang
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering and Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Lin Huang
- Country Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Ying Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Wanshan Liu
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering and Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Xinming Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Jiao Wu
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering and Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Yida Huang
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering and Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Ruimin Wang
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering and Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Li Zhou
- Beijing health biotech co. Ltd, Beijing, 100193, P. R. China
| | - Lin Li
- Beijing health biotech co. Ltd, Beijing, 100193, P. R. China
| | - Yong Zhang
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore, 117583, Singapore
| | - Lili Ren
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Kun Qian
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering and Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
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164
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Chen YW, Wu GH, Lee BS, Liu CT, Li HY, Cheng SJ, Kuo WT, Jeng JH, Chang PC, Lin CP, Chou HYE, Hou HH. Third-generation sequencing-selected Scardovia wiggsiae promotes periodontitis progression in mice. J Periodontal Res 2023; 58:155-164. [PMID: 36451314 DOI: 10.1111/jre.13077] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/01/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022]
Abstract
BACKGROUNDS Periodontitis is an oral-bacteria-directed disease that occurs worldwide. Currently, periodontal pathogens are mostly determined using traditional culture techniques, next-generation sequencing, and microbiological screening system. In addition to the well-known and cultivatable periodontal bacteria, we aimed to discover a novel periodontal pathogen by using DNA sequencing and investigate its role in the progression of periodontitis. OBJECTIVE This study identified pathogens from subgingival dental plaque in patients with periodontitis by using the Oxford Nanopore Technology (ONT) third-generation sequencing system and validated the impact of selected pathogen in periodontitis progression by ligature-implanted mice. METHODS Twenty-five patients with periodontitis and 25 healthy controls were recruited in this study. Subgingival plaque samples were collected for metagenomic analysis. The ONT third-generation sequencing system was used to confirm the dominant bacteria. A mouse model with ligature implantation and bacterial injection verified the pathogenesis of periodontitis. Neutrophil infiltration and osteoclast activity were evaluated using immunohistochemistry and tartrate-resistant acid phosphatase assays in periodontal tissue. Gingival inflammation was evaluated using pro-inflammatory cytokines in gingival crevicular fluids. Alveolar bone destruction in the mice was evaluated using micro-computed tomography and hematoxylin and eosin staining. RESULTS Scardovia wiggsiae (S. wiggsiae) was dominant in the subgingival plaque of the patients with periodontitis. S. wiggsiae significantly deteriorated ligature-induced neutrophil infiltration, osteoclast activation, alveolar bone destruction, and the secretion of interleukin-6, monocyte chemoattractant protein-1, and tumor necrosis factor-α in the mouse model. CONCLUSION Our metagenome results suggested that S. wiggsiae is a dominant flora in patients with periodontitis. In mice, the induction of neutrophil infiltration, proinflammatory cytokine secretion, osteoclast activation, and alveolar bone destruction further verified the pathogenic role of S. wiggsiae in the progress of periodontitis. Future studies investigating the metabolic interactions between S. wiggsiae and other periodontopathic bacteria are warranted.
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Affiliation(s)
- Yi-Wen Chen
- Department of Dentistry, National Taiwan University Hospital, Taipei, Taiwan.,Graduate Institute of Clinical Dentistry, School of Dentistry, National Taiwan University, Taipei, Taiwan
| | - Guan-Hua Wu
- Graduate Institute of Oral Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Bor-Shiunn Lee
- Department of Dentistry, National Taiwan University Hospital, Taipei, Taiwan.,Graduate Institute of Oral Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chung-Te Liu
- Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Huei-Ying Li
- Medical Microbiota Center of the First Core Laboratory, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shih-Jung Cheng
- Department of Dentistry, National Taiwan University Hospital, Taipei, Taiwan.,Graduate Institute of Oral Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wei-Ting Kuo
- Graduate Institute of Oral Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Jiiang-Huei Jeng
- School of Dentistry, College of Dental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Dentistry, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Po-Chun Chang
- Department of Dentistry, National Taiwan University Hospital, Taipei, Taiwan.,Graduate Institute of Clinical Dentistry, School of Dentistry, National Taiwan University, Taipei, Taiwan.,School of Dentistry, College of Dental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chun-Pin Lin
- Department of Dentistry, National Taiwan University Hospital, Taipei, Taiwan.,Graduate Institute of Clinical Dentistry, School of Dentistry, National Taiwan University, Taipei, Taiwan
| | - Han-Yi E Chou
- Department of Dentistry, National Taiwan University Hospital, Taipei, Taiwan.,Graduate Institute of Clinical Dentistry, School of Dentistry, National Taiwan University, Taipei, Taiwan.,Graduate Institute of Oral Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsin-Han Hou
- Department of Dentistry, National Taiwan University Hospital, Taipei, Taiwan.,Graduate Institute of Clinical Dentistry, School of Dentistry, National Taiwan University, Taipei, Taiwan.,Graduate Institute of Oral Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
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165
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Mohammadi-Shemirani P, Sood T, Paré G. From 'Omics to Multi-omics Technologies: the Discovery of Novel Causal Mediators. Curr Atheroscler Rep 2023; 25:55-65. [PMID: 36595202 PMCID: PMC9807989 DOI: 10.1007/s11883-022-01078-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2022] [Indexed: 01/04/2023]
Abstract
PURPOSE OF REVIEW 'Omics studies provide a comprehensive characterisation of a biological entity, such as the genome, epigenome, transcriptome, proteome, metabolome, or microbiome. This review covers the unique properties of these types of 'omics and their roles as causal mediators in cardiovascular disease. Moreover, applications and challenges of integrating multiple types of 'omics data to increase predictive power, improve causal inference, and elucidate biological mechanisms are discussed. RECENT FINDINGS Multi-omics approaches are growing in adoption as they provide orthogonal evidence and overcome the limitations of individual types of 'omics data. Studies with multiple types of 'omics data have improved the diagnosis and prediction of disease states and afforded a deeper understanding of underlying pathophysiological mechanisms, beyond any single type of 'omics data. For instance, disease-associated loci in the genome can be supplemented with other 'omics to prioritise causal genes and understand the function of non-coding variants. Alternatively, techniques, such as Mendelian randomisation, can leverage genetics to provide evidence supporting a causal role for disease-associated molecules, and elucidate their role in disease pathogenesis. As technologies improve, costs for 'omics studies will continue to fall and datasets will become increasingly accessible to researchers. The intrinsically unbiased nature of 'omics data is well-suited to exploratory analyses that discover causal mediators of disease, and multi-omics is an emerging discipline that leverages the strengths of each type of 'omics data to provide insights greater than the sum of its parts.
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Affiliation(s)
- Pedrum Mohammadi-Shemirani
- Population Health Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, ON Canada
- Thrombosis and Atherosclerosis Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, ON Canada
| | - Tushar Sood
- Temerty Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Guillaume Paré
- Population Health Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, ON Canada
- Thrombosis and Atherosclerosis Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, ON Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON Canada
- Department of Pathology and Molecular Medicine, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON Canada
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166
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Baldi Antognini A, Novelli M, Zagoraiou M. Simulated annealing for balancing covariates. Stat Med 2023; 42:1323-1337. [PMID: 37078360 DOI: 10.1002/sim.9672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 11/09/2022] [Accepted: 01/16/2023] [Indexed: 01/30/2023]
Abstract
Covariate balance is one of the fundamental issues in designing experiments for treatment comparisons, especially in randomized clinical trials. In this article, we introduce a new class of covariate-adaptive procedures based on the Simulated Annealing algorithm aimed at balancing the allocations of two competing treatments across a set of pre-specified covariates. Due to the nature of the simulated annealing, these designs are intrinsically randomized, thus completely unpredictable, and very flexible: they can manage both quantitative and qualitative factors and be implemented in a static version as well as sequentially. The properties of the suggested proposal are described, showing a significant improvement in terms of covariate balance and inferential accuracy with respect to all the other procedures proposed in the literature. An illustrative example based on real data is also discussed.
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Affiliation(s)
| | - Marco Novelli
- Department of Statistics University of Bologna Bologna Italy
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167
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Wang S, Zhao Y, Chan AWH, Yao M, Chen Z, Abbatt JPD. Organic Peroxides in Aerosol: Key Reactive Intermediates for Multiphase Processes in the Atmosphere. Chem Rev 2023; 123:1635-1679. [PMID: 36630720 DOI: 10.1021/acs.chemrev.2c00430] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Organic peroxides (POs) are organic molecules with one or more peroxide (-O-O-) functional groups. POs are commonly regarded as chemically labile termination products from gas-phase radical chemistry and therefore serve as temporary reservoirs for oxidative radicals (HOx and ROx) in the atmosphere. Owing to their ubiquity, active gas-particle partitioning behavior, and reactivity, POs are key reactive intermediates in atmospheric multiphase processes determining the life cycle (formation, growth, and aging), climate, and health impacts of aerosol. However, there remain substantial gaps in the origin, molecular diversity, and fate of POs due to their complex nature and dynamic behavior. Here, we summarize the current understanding on atmospheric POs, with a focus on their identification and quantification, state-of-the-art analytical developments, molecular-level formation mechanisms, multiphase chemical transformation pathways, as well as environmental and health impacts. We find that interactions with SO2 and transition metal ions are generally the fast PO transformation pathways in atmospheric liquid water, with lifetimes estimated to be minutes to hours, while hydrolysis is particularly important for α-substituted hydroperoxides. Meanwhile, photolysis and thermolysis are likely minor sinks for POs. These multiphase PO transformation pathways are distinctly different from their gas-phase fates, such as photolysis and reaction with OH radicals, which highlights the need to understand the multiphase partitioning of POs. By summarizing the current advances and remaining challenges for the investigation of POs, we propose future research priorities regarding their origin, fate, and impacts in the atmosphere.
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Affiliation(s)
- Shunyao Wang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai200240, China
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai200444, China
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, OntarioM5S 3E5, Canada
| | - Yue Zhao
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Arthur W H Chan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, OntarioM5S 3E5, Canada
- School of the Environment, University of Toronto, Toronto, OntarioM5S 3E8, Canada
| | - Min Yao
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Zhongming Chen
- State Key Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing100871, China
| | - Jonathan P D Abbatt
- Department of Chemistry, University of Toronto, Toronto, OntarioM5S 3H6, Canada
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168
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Shen J, Li H, Yu X, Bai L, Dong Y, Cao J, Lu K, Tang Z. Efficient feature extraction from highly sparse binary genotype data for cancer prognosis prediction using an auto-encoder. Front Oncol 2023; 12:1091767. [PMID: 36703783 PMCID: PMC9872139 DOI: 10.3389/fonc.2022.1091767] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
Genomics involving tens of thousands of genes is a complex system determining phenotype. An interesting and vital issue is how to integrate highly sparse genetic genomics data with a mass of minor effects into a prediction model for improving prediction power. We find that the deep learning method can work well to extract features by transforming highly sparse dichotomous data to lower-dimensional continuous data in a non-linear way. This may provide benefits in risk prediction-associated genotype data. We developed a multi-stage strategy to extract information from highly sparse binary genotype data and applied it for cancer prognosis. Specifically, we first reduced the size of binary biomarkers via a univariable regression model to a moderate size. Then, a trainable auto-encoder was used to learn compact features from the reduced data. Next, we performed a LASSO problem process to select the optimal combination of extracted features. Lastly, we applied such feature combination to real cancer prognostic models and evaluated the raw predictive effect of the models. The results indicated that these compressed transformation features could better improve the model's original predictive performance and might avoid an overfitting problem. This idea may be enlightening for everyone involved in cancer research, risk reduction, treatment, and patient care via integrating genomics data.
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Affiliation(s)
- Junjie Shen
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, China,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, China
| | - Huijun Li
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, China,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, China
| | - Xinghao Yu
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, China,Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Lu Bai
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, China,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, China
| | - Yongfei Dong
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, China,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, China
| | - Jianping Cao
- School of Radiation Medicine and Protection and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Ke Lu
- Department of Orthopedics, Affiliated Kunshan Hospital of Jiangsu University, Suzhou, China,*Correspondence: Zaixiang Tang, ; Ke Lu,
| | - Zaixiang Tang
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, China,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, China,*Correspondence: Zaixiang Tang, ; Ke Lu,
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169
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Schork NJ, Beaulieu-Jones B, Liang WS, Smalley S, Goetz LH. Exploring human biology with N-of-1 clinical trials. CAMBRIDGE PRISMS. PRECISION MEDICINE 2023; 1:e12. [PMID: 37255593 PMCID: PMC10228692 DOI: 10.1017/pcm.2022.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/12/2022] [Accepted: 12/26/2022] [Indexed: 06/01/2023]
Abstract
Studies on humans that exploit contemporary data-intensive, high-throughput 'omic' assay technologies, such as genomics, transcriptomics, proteomics and metabolomics, have unequivocally revealed that humans differ greatly at the molecular level. These differences, which are compounded by each individual's distinct behavioral and environmental exposures, impact individual responses to health interventions such as diet and drugs. Questions about the best way to tailor health interventions to individuals based on their nuanced genomic, physiologic, behavioral, etc. profiles have motivated the current emphasis on 'precision' medicine. This review's purpose is to describe how the design and execution of N-of-1 (or personalized) multivariate clinical trials can advance the field. Such trials focus on individual responses to health interventions from a whole-person perspective, leverage emerging health monitoring technologies, and can be used to address the most relevant questions in the precision medicine era. This includes how to validate biomarkers that may indicate appropriate activity of an intervention as well as how to identify likely beneficial interventions for an individual. We also argue that multivariate N-of-1 and aggregated N-of-1 trials are ideal vehicles for advancing biomedical and translational science in the precision medicine era since the insights gained from them can not only shed light on how to treat or prevent diseases generally, but also provide insight into how to provide real-time care to the very individuals who are seeking attention for their health concerns in the first place.
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Affiliation(s)
- N. J. Schork
- Department of Quantitative Medicine, The Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
- Net.bio Inc., Los Angeles, CA, USA
| | - B. Beaulieu-Jones
- Net.bio Inc., Los Angeles, CA, USA
- University of Chicago, Chicago, IL, USA
| | | | - S. Smalley
- Net.bio Inc., Los Angeles, CA, USA
- The University of California Los Angeles, Los Angeles, CA, USA
| | - L. H. Goetz
- Department of Quantitative Medicine, The Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
- Net.bio Inc., Los Angeles, CA, USA
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170
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Wang D, Kumar V, Burnham KL, Mentzer AJ, Marsden B, Knight JC. COMBATdb: a database for the COVID-19 Multi-Omics Blood ATlas. Nucleic Acids Res 2023; 51:D896-D905. [PMID: 36353986 PMCID: PMC9825482 DOI: 10.1093/nar/gkac1019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 10/10/2022] [Accepted: 10/21/2022] [Indexed: 11/11/2022] Open
Abstract
Advances in our understanding of the nature of the immune response to SARS-CoV-2 infection, and how this varies within and between individuals, is important in efforts to develop targeted therapies and precision medicine approaches. Here we present a database for the COvid-19 Multi-omics Blood ATlas (COMBAT) project, COMBATdb (https://db.combat.ox.ac.uk). This enables exploration of multi-modal datasets arising from profiling of patients with different severities of illness admitted to hospital in the first phase of the pandemic in the UK prior to vaccination, compared with community cases, healthy controls, and patients with all-cause sepsis and influenza. These data include whole blood transcriptomics, plasma proteomics, epigenomics, single-cell multi-omics, immune repertoire sequencing, flow and mass cytometry, and cohort metadata. COMBATdb provides access to the processed data in a well-defined framework of samples, cell types and genes/proteins that allows exploration across the assayed modalities, with functionality including browse, search, download, calculation and visualisation via shiny apps. This advances the ability of users to leverage COMBAT datasets to understand the pathogenesis of COVID-19, and the nature of specific and shared features with other infectious diseases.
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Affiliation(s)
- Dapeng Wang
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Vinod Kumar
- Kennedy Institute for Rheumatology, University of Oxford, UK
| | | | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Brian D Marsden
- Kennedy Institute for Rheumatology, University of Oxford, UK
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford, OX3 7BN, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
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171
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Nelson MS, Liu Y, Wilson HM, Li B, Rosado-Mendez IM, Rogers JD, Block WF, Eliceiri KW. Multiscale Label-Free Imaging of Fibrillar Collagen in the Tumor Microenvironment. Methods Mol Biol 2023; 2614:187-235. [PMID: 36587127 DOI: 10.1007/978-1-0716-2914-7_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
With recent advances in cancer therapeutics, there is a great need for improved imaging methods for characterizing cancer onset and progression in a quantitative and actionable way. Collagen, the most abundant extracellular matrix protein in the tumor microenvironment (and the body in general), plays a multifaceted role, both hindering and promoting cancer invasion and progression. Collagen deposition can defend the tumor with immunosuppressive effects, while aligned collagen fiber structures can enable tumor cell migration, aiding invasion and metastasis. Given the complex role of collagen fiber organization and topology, imaging has been a tool of choice to characterize these changes on multiple spatial scales, from the organ and tumor scale to cellular and subcellular level. Macroscale density already aids in the detection and diagnosis of solid cancers, but progress is being made to integrate finer microscale features into the process. Here we review imaging modalities ranging from optical methods of second harmonic generation (SHG), polarized light microscopy (PLM), and optical coherence tomography (OCT) to the medical imaging approaches of ultrasound and magnetic resonance imaging (MRI). These methods have enabled scientists and clinicians to better understand the impact collagen structure has on the tumor environment, at both the bulk scale (density) and microscale (fibrillar structure) levels. We focus on imaging methods with the potential to both examine the collagen structure in as natural a state as possible and still be clinically amenable, with an emphasis on label-free strategies, exploiting intrinsic optical properties of collagen fibers.
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Affiliation(s)
- Michael S Nelson
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, USA.,Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Yuming Liu
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, USA
| | - Helen M Wilson
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, USA.,Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Bin Li
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, USA.,Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA.,Morgridge Institute for Research, Madison, WI, USA
| | - Ivan M Rosado-Mendez
- Department of Medical Physics, University of Wisconsin-Madison, Madison, WI, USA
| | - Jeremy D Rogers
- Morgridge Institute for Research, Madison, WI, USA.,McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Walter F Block
- Department of Medical Physics, University of Wisconsin-Madison, Madison, WI, USA
| | - Kevin W Eliceiri
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, USA. .,Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA. .,Morgridge Institute for Research, Madison, WI, USA. .,Department of Medical Physics, University of Wisconsin-Madison, Madison, WI, USA. .,McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, USA.
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172
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Shrestha B, Tang L, Hood RL. Nanotechnology for Personalized Medicine. Nanomedicine (Lond) 2023. [DOI: 10.1007/978-981-16-8984-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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173
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Chen S, Xin Y, Tang K, Wu Y, Guo Y. Nardosinone and aurantio-obtusin, two medicine food homology natural compounds, are anti-influenza agents as indicated by transcriptome signature reversion. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 108:154515. [PMID: 36347176 DOI: 10.1016/j.phymed.2022.154515] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 10/06/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Medicine food homology (MFH) refers to food that can be used as medicine, and compounds isolated from MFH materials are valuable in novel drug discovery due to their good safety. Transcriptome signature reversion (TSR) is an attractive method for discovering drugs through transcriptional reverse matching; namely, the changes in transcriptional signatures induced by compounds are matched to a certain disease. This strategy can be used to discover anti-influenza agents among MFH natural compounds. PURPOSE MFH natural compounds with anti-influenza activities were identified through analyses of the reversal in the expression of multiple informative genes followed by in vitro evaluation of the cytopathic effect (CPE) caused by influenza infection and relative quantification of the nucleoprotein (NP) gene in viral RNA (vRNA). The combined effect of active compounds was determined through network-based separation score prediction followed by quantification of the viral hemagglutinin (HA) level. METHODS The transcriptome profiles of 4 lung or airway cell lines infected with 7 influenza virus strains were analyzed by robust rank aggregation (RRA) to identify informative genes in the signature of influenza virus infection. The identified informative genes were then matched to a transcriptomic profile library of MFH natural compounds. The anti-influenza activities of MFH natural compounds with negative enrichment scores (ESs) were evaluated in vitro using a CPE assay and relative quantification of the NP gene in the vRNA in the supernatant and cytoplasm to identify anti-influenza agents. The effects of combinations of active compounds were analyzed using network-based calculations followed by confirmation through bioassays for quantifying the viral HA levels. RESULTS Among the 159 MFH natural compounds, 54 compounds had negative ESs, as determined through TSR, and the anti-influenza activities of nardosinone and aurantio-obtusin were confirmed by bioassays. The half-maximal effective concentrations (EC50) of nardosinone and aurantio-obtusin were 4.3-84.4 μM and 31.9-113.6 μM, respectively. The separation score between the informative genes with expression that was negatively regulated by nardosinone and aurantio-obtusin in the human protein-protein interaction (PPI) network was calculated to be 0.10, which indicated that the two compounds potentially exert a synergistic effect, and this effect was confirmed by the finding that the combination indexes (CIs) were calculated to equal 0.86 at inhibition level of 50% and 0.44 at inhibition level of 90%. CONCLUSION The TSR analysis and in vitro evaluation identified nardosinone and aurantio-obtusin as anti-influenza agents. Their antiviral activities were exerted by reversing the expression of multiple informative genes of the host cells. The separation analysis between the informative genes that were reversely regulated by nardosinone and aurantio-obtusin indicated that their combination may exert a synergistic effect, which was confirmed in vitro.
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Affiliation(s)
- Shubing Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; Department of Pharmacology, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Yijing Xin
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; Department of Pharmacology, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Ke Tang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; Department of Pharmacology, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - You Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; Department of Pharmacology, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Ying Guo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; Department of Pharmacology, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
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174
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Niebla-Cárdenas A, Bareke H, Juanes-Velasco P, Landeira-Viñuela A, Hernández ÁP, Montalvillo E, Góngora R, Arroyo-Anlló E, Silvia Puente-González A, Méndez-Sánchez R, Fuentes M. Translational research into frailty from bench to bedside: Salivary biomarkers for inflammaging. Exp Gerontol 2023; 171:112040. [PMID: 36455696 DOI: 10.1016/j.exger.2022.112040] [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: 06/07/2022] [Revised: 11/22/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022]
Abstract
Frailty is a complex physiological syndrome associated with adverse ageing and decreased physiological reserves. Frailty leads to cognitive and physical disability and is a significant cause of morbidity, mortality and economic costs. The underlying cause of frailty is multifaceted, including immunosenescence and inflammaging, changes in microbiota and metabolic dysfunction. Currently, salivary biomarkers are used as early predictors for some clinical diseases, contributing to the effective prevention and treatment of diseases, including frailty. Sample collection for salivary analysis is non-invasive and simple, which are paramount factors for testing in the vulnerable frail population. The aim of this review is to describe the current knowledge on the association between frailty and the inflammatory process and discuss methods to identify putative biomarkers in salivary fluids to predict this syndrome. This study describes the relationship between i.-inflammatory process and frailty; ii.-infectious, chronic, skeletal, metabolic and cognitive diseases with inflammation and frailty; iii.-inflammatory biomarkers and salivary fluids. There is a limited number of previous studies focusing on the analysis of inflammatory salivary biomarkers and frailty syndrome; hence, the study of salivary fluids as a source for biomarkers is an open area of research with the potential to address the increasing demands for frailty-associated biomarkers.
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Affiliation(s)
- Alfonssina Niebla-Cárdenas
- Department of Nursing and Physiotherapy, Faculty of Nursing and Physiotherapy, University of Salamanca, 37007 Salamanca, Spain
| | - Halin Bareke
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Institute of Health Sciences, Marmara University, Istanbul, Turkey; Department of Medicine and Cytometry General Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Pablo Juanes-Velasco
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Alicia Landeira-Viñuela
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Ángela-Patricia Hernández
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; Department of Pharmaceutical Sciences: Organic Chemistry, Faculty of Pharmacy, University of Salamanca, CIETUS, IBSAL, 37007 Salamanca, Spain
| | - Enrique Montalvillo
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Rafael Góngora
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Eva Arroyo-Anlló
- Department of Psychobiology, Neuroscience Institute of Castilla-León, Faculty of Psychology, University of Salamanca, 37007 Salamanca, Spain
| | - Ana Silvia Puente-González
- Department of Nursing and Physiotherapy, Faculty of Nursing and Physiotherapy, University of Salamanca, 37007 Salamanca, Spain; Institute of Biomedical Research of Salamanca. Primary Care, Public Health and Pharmacology Area, 37007 Salamanca, Spain.
| | - Roberto Méndez-Sánchez
- Department of Nursing and Physiotherapy, Faculty of Nursing and Physiotherapy, University of Salamanca, 37007 Salamanca, Spain; Institute of Biomedical Research of Salamanca. Primary Care, Public Health and Pharmacology Area, 37007 Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain.
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175
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Saeed RF, Awan UA, Saeed S, Mumtaz S, Akhtar N, Aslam S. Targeted Therapy and Personalized Medicine. Cancer Treat Res 2023; 185:177-205. [PMID: 37306910 DOI: 10.1007/978-3-031-27156-4_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Targeted therapy and personalized medicine are novel emerging disciplines of cancer research intended for treatment and prevention. One of the most significant advancements in modern oncology is the shift from an organ-centric strategy to a personalized strategy guided by deep molecular analysis. This shift in view, which focuses on the tumour's precise molecular changes, has paved the way for individualized treatment. Researchers and clinicians are using targeted therapies to select the best treatment available based on the molecular characterization of malignant cancer. In the treatment of a cancer, personalized medicine entails the use of genetic, immunological, and proteomic profiling to provide therapeutic alternatives as well as prognostic information about cancer. In this book, targeted therapies and personalized medicine have been covered for specific malignancies, including latest FDA-approved targeted therapies and it also sheds light on effective anti-cancer regimens and drug resistance. This will help to enhance our ability to conduct individualized health planning, make early diagnoses, and choose optimal medications for each cancer patient with predictable side effects and outcomes in a quickly evolving era. Various applications and tools' capacity have been improved for early diagnosis of cancer and the growing number of clinical trials that choose specific molecular targets reflects this predicament. Nevertheless, there are several limitations that must need to be addressed. Hence, in this chapter, we will discuss recent advancements, challenges, and opportunities in personalized medicine for various cancers, with a specific emphasis on target therapies in diagnostics and therapeutics.
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Affiliation(s)
- Rida Fatima Saeed
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan.
| | - Uzma Azeem Awan
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | | | - Sara Mumtaz
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Nosheen Akhtar
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Shaista Aslam
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
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176
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Hassan T, Firdous P, Nissar K, Ahmad MB, Imtiyaz Z. Role of proteomics in surgical oncology. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00012-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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177
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Chemotherapy-Induced Peripheral Neuropathy. Handb Exp Pharmacol 2023; 277:299-337. [PMID: 36253554 DOI: 10.1007/164_2022_609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Chemotherapy-induced peripheral neuropathy (CIPN) is a debilitating side effect of many common anti-cancer agents that can lead to dose reduction or treatment discontinuation, which decrease chemotherapy efficacy. Long-term CIPN can interfere with activities of daily living and diminish the quality of life. The mechanism of CIPN is not yet fully understood, and biomarkers are needed to identify patients at high risk and potential treatment targets. Metabolomics can capture the complex behavioral and pathophysiological processes involved in CIPN. This chapter is to review the CIPN metabolomics studies to find metabolic pathways potentially involved in CIPN. These potential CIPN metabolites are then investigated to determine whether there is evidence from studies of other neuropathy etiologies such as diabetic neuropathy and Leber hereditary optic neuropathy to support the importance of these pathways in peripheral neuropathy. Six potential biomarkers and their putative mechanisms in peripheral neuropathy were reviewed. Among these biomarkers, histidine and phenylalanine have clear roles in neurotransmission or neuroinflammation in peripheral neuropathy. Further research is needed to discover and validate CIPN metabolomics biomarkers in large clinical studies.
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178
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Forny P, Bonilla X, Lamparter D, Shao W, Plessl T, Frei C, Bingisser A, Goetze S, van Drogen A, Harshman K, Pedrioli PGA, Howald C, Poms M, Traversi F, Bürer C, Cherkaoui S, Morscher RJ, Simmons L, Forny M, Xenarios I, Aebersold R, Zamboni N, Rätsch G, Dermitzakis ET, Wollscheid B, Baumgartner MR, Froese DS. Integrated multi-omics reveals anaplerotic rewiring in methylmalonyl-CoA mutase deficiency. Nat Metab 2023; 5:80-95. [PMID: 36717752 PMCID: PMC9886552 DOI: 10.1038/s42255-022-00720-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 12/01/2022] [Indexed: 01/31/2023]
Abstract
Methylmalonic aciduria (MMA) is an inborn error of metabolism with multiple monogenic causes and a poorly understood pathogenesis, leading to the absence of effective causal treatments. Here we employ multi-layered omics profiling combined with biochemical and clinical features of individuals with MMA to reveal a molecular diagnosis for 177 out of 210 (84%) cases, the majority (148) of whom display pathogenic variants in methylmalonyl-CoA mutase (MMUT). Stratification of these data layers by disease severity shows dysregulation of the tricarboxylic acid cycle and its replenishment (anaplerosis) by glutamine. The relevance of these disturbances is evidenced by multi-organ metabolomics of a hemizygous Mmut mouse model as well as through identification of physical interactions between MMUT and glutamine anaplerotic enzymes. Using stable-isotope tracing, we find that treatment with dimethyl-oxoglutarate restores deficient tricarboxylic acid cycling. Our work highlights glutamine anaplerosis as a potential therapeutic intervention point in MMA.
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Affiliation(s)
- Patrick Forny
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ximena Bonilla
- Biomedical Informatics, Department of Computer Science, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
| | - David Lamparter
- Health 2030 Genome Center, Geneva, Switzerland
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
| | - Wenguang Shao
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
- Institute of Translational Medicine, Department of Health Science and Technology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
| | - Tanja Plessl
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Caroline Frei
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Anna Bingisser
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sandra Goetze
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
- Institute of Translational Medicine, Department of Health Science and Technology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Audrey van Drogen
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
- Institute of Translational Medicine, Department of Health Science and Technology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
| | - Keith Harshman
- Health 2030 Genome Center, Geneva, Switzerland
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
| | - Patrick G A Pedrioli
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
- Institute of Translational Medicine, Department of Health Science and Technology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
| | | | - Martin Poms
- Division of Clinical Chemistry, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Florian Traversi
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Céline Bürer
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sarah Cherkaoui
- Division of Oncology and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Center, Université Paris-Saclay, Villejuif, France
| | - Raphael J Morscher
- Division of Oncology and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Luke Simmons
- Division of Child Neurology, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Merima Forny
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ioannis Xenarios
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
- Agora Center, Lausanne, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
| | - Nicola Zamboni
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
| | - Gunnar Rätsch
- Biomedical Informatics, Department of Computer Science, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Medical Informatics Unit, University Hospital Zurich, Zurich, Switzerland.
- AI Center, ETH Zurich, Zurich, Switzerland.
| | - Emmanouil T Dermitzakis
- Health 2030 Genome Center, Geneva, Switzerland.
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland.
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.
| | - Bernd Wollscheid
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland.
- Institute of Translational Medicine, Department of Health Science and Technology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Matthias R Baumgartner
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland.
| | - D Sean Froese
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland.
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179
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Qu X, Ma J, Gao H, Zhang Y, Zhai J, Gong J, Song Y, Hu T. Integration of metabolomics and proteomics analysis to explore the mechanism of neurotoxicity induced by receipt of isoniazid and rifampicin in mice. Neurotoxicology 2023; 94:24-34. [PMID: 36347327 DOI: 10.1016/j.neuro.2022.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/06/2022]
Abstract
Isoniazid (INH) and rifampicin (RIF) are co-administered in tuberculosis treatment but can cause neurotoxicity, and the mechanism is not known. To explore this mechanism, we employed an integrated approach using metabolomics analysis (MA) and proteomics analysis (PA). Male mice were divided into three groups and administered vehicle (control group), or co-administered INH (120 mg/kg) and RIF (240 mg/kg), for 7 or 14 days. Mice brains were collected for mass spectrometry-based PA and MA plus lipidomics analysis. Measurement of brain levels of malondialdehyde and superoxide dismutase revealed time-dependent brain injury after exposure to INH+RIF for 7 and 14 days. Also, 422 proteins, 35 metabolites, and 21 lipids were dysregulated and identified. MA demonstrated "purine metabolism," "phenylalanine, tyrosine and tryptophan biosynthesis," "biosynthesis of unsaturated fatty acids," "phenylalanine metabolism," and "arginine biosynthesis" to be disturbed significantly. PA demonstrated pathways such as "lipids," "amino acids," and "energy metabolism" to be disrupted. Peroxisome proliferator-activated receptor (PPAR) pathways were changed in energy metabolism, which led to the neurotoxicity induced by INH+RIF. Immunohistochemical analyses of PPARs in mice brains verified that PPAR-α and -γ expression was downregulated. PPAR-α and -γ activation might be a key target for alleviating INH+RIF-induced neurotoxicity.
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Affiliation(s)
- Xiaoyu Qu
- Department of Pharmacy, The First Hospital of Jilin University, 130021 Changchun, China
| | - Jie Ma
- Department of Pharmacy, The First Hospital of Jilin University, 130021 Changchun, China
| | - Huan Gao
- Department of Pharmacy, The First Hospital of Jilin University, 130021 Changchun, China
| | - Yueming Zhang
- Department of Pharmacy, The First Hospital of Jilin University, 130021 Changchun, China
| | - Jinghui Zhai
- Department of Pharmacy, The First Hospital of Jilin University, 130021 Changchun, China
| | - Jiawei Gong
- Department of Pharmacy, The First Hospital of Jilin University, 130021 Changchun, China
| | - Yanqing Song
- Department of Pharmacy, The First Hospital of Jilin University, 130021 Changchun, China.
| | - Tingting Hu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 130021 Changchun, China.
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180
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Trifonova OP, Maslov DL, Balashova EE, Lokhov PG. Current State and Future Perspectives on Personalized Metabolomics. Metabolites 2023; 13:metabo13010067. [PMID: 36676992 PMCID: PMC9863827 DOI: 10.3390/metabo13010067] [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: 12/05/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
Metabolomics is one of the most promising 'omics' sciences for the implementation in medicine by developing new diagnostic tests and optimizing drug therapy. Since in metabolomics, the end products of the biochemical processes in an organism are studied, which are under the influence of both genetic and environmental factors, the metabolomics analysis can detect any changes associated with both lifestyle and pathological processes. Almost every case-controlled metabolomics study shows a high diagnostic accuracy. Taking into account that metabolomics processes are already described for most nosologies, there are prerequisites that a high-speed and comprehensive metabolite analysis will replace, in near future, the narrow range of chemical analyses used today, by the medical community. However, despite the promising perspectives of personalized metabolomics, there are currently no FDA-approved metabolomics tests. The well-known problem of complexity of personalized metabolomics data analysis and their interpretation for the end-users, in addition to a traditional need for analytical methods to address the quality control, standardization, and data treatment are reported in the review. Possible ways to solve the problems and change the situation with the introduction of metabolomics tests into clinical practice, are also discussed.
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181
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Gu N, Sheng J. Introduction to Nanomedicine. Nanomedicine (Lond) 2023. [DOI: 10.1007/978-981-16-8984-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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182
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Sheng B, Wang Z, Qiao Y, Xie SQ, Tao J, Duan C. Detecting latent topics and trends of digital twins in healthcare: A structural topic model-based systematic review. Digit Health 2023; 9:20552076231203672. [PMID: 37846404 PMCID: PMC10576938 DOI: 10.1177/20552076231203672] [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: 04/28/2023] [Accepted: 09/08/2023] [Indexed: 10/18/2023] Open
Abstract
Objective Digital twins (DTs) have received widespread attention recently, providing new ideas and possibilities for future healthcare. This review aims to provide a quantitative review to analyze specific study contents, research focus, and trends of DT in healthcare. Simultaneously, this review intends to expand the connotation of "healthcare" into two directions, namely "Disease treatment" and "Health enhancement" to analyze the content within the "DT + healthcare" field thoroughly. Methods A data mining method named Structure Topic Modeling (STM) was used as the analytical tool due to its topic analysis ability and versatility. Google Scholar, Web of Science, and China National Knowledge Infrastructure supplied the material papers in this review. Results A total of 94 high-quality papers published between 2018 and 2022 were gathered and categorized into eight topics, collectively covering the transformative impact across a broader spectrum in healthcare. Three main findings have emerged: (1) papers published in healthcare predominantly concentrate on technology development (artificial intelligence, Internet of Things, etc.) and application scenarios(personalized, precise, and real-time health service); (2) the popularity of research topics is influenced by various factors, including policies, COVID-19, and emerging technologies; and (3) the preference for topics is diverse, with a general inclination toward the attribute of "Health enhancement." Conclusions This review underscores the significance of real-time capability and accuracy in shaping the future of DT, where algorithms and data transmission methods assume central importance in achieving these goals. Moreover, technological advancements, such as omics and Metaverse, have opened up new possibilities for DT in healthcare. These findings contribute to the existing literature by offering quantitative insights and valuable guidance to keep researchers ahead of the curve.
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Affiliation(s)
- Bo Sheng
- School of Mechatronic Engineering and Automation, Shanghai University, Shanghai, China
- Shanghai Key Laboratory of Intelligent Manufacturing and Robotics, Shanghai University, Shanghai, China
| | - Zheyu Wang
- School of Mechatronic Engineering and Automation, Shanghai University, Shanghai, China
| | - Yujiao Qiao
- ShanghaiTech University Center for Innovative Teaching and Learning, ShanghaiTech University, Shanghai, China
| | - Sheng Quan Xie
- School of Electronic and Electrical Engineering, University of Leeds, Leeds, UK
| | - Jing Tao
- School of Mechatronic Engineering and Automation, Shanghai University, Shanghai, China
| | - Chaoqun Duan
- School of Mechatronic Engineering and Automation, Shanghai University, Shanghai, China
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183
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Hao X, Cheng S, Jiang B, Xin S. Applying multi-omics techniques to the discovery of biomarkers for acute aortic dissection. Front Cardiovasc Med 2022; 9:961991. [PMID: 36588568 PMCID: PMC9797526 DOI: 10.3389/fcvm.2022.961991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Acute aortic dissection (AAD) is a cardiovascular disease that manifests suddenly and fatally. Due to the lack of specific early symptoms, many patients with AAD are often overlooked or misdiagnosed, which is undoubtedly catastrophic for patients. The particular pathogenic mechanism of AAD is yet unknown, which makes clinical pharmacological therapy extremely difficult. Therefore, it is necessary and crucial to find and employ unique biomarkers for Acute aortic dissection (AAD) as soon as possible in clinical practice and research. This will aid in the early detection of AAD and give clear guidelines for the creation of focused treatment agents. This goal has been made attainable over the past 20 years by the quick advancement of omics technologies and the development of high-throughput tissue specimen biomarker screening. The primary histology data support and add to one another to create a more thorough and three-dimensional picture of the disease. Based on the introduction of the main histology technologies, in this review, we summarize the current situation and most recent developments in the application of multi-omics technologies to AAD biomarker discovery and emphasize the significance of concentrating on integration concepts for integrating multi-omics data. In this context, we seek to offer fresh concepts and recommendations for fundamental investigation, perspective innovation, and therapeutic development in AAD.
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Affiliation(s)
- Xinyu Hao
- Department of Vascular Surgery, The First Affiliated Hospital of China Medical University, China Medical University, Shenyang, China,Key Laboratory of Pathogenesis, Prevention and Therapeutics of Aortic Aneurysm, Shenyang, Liaoning, China
| | - Shuai Cheng
- Department of Vascular Surgery, The First Affiliated Hospital of China Medical University, China Medical University, Shenyang, China,Key Laboratory of Pathogenesis, Prevention and Therapeutics of Aortic Aneurysm, Shenyang, Liaoning, China
| | - Bo Jiang
- Department of Vascular Surgery, The First Affiliated Hospital of China Medical University, China Medical University, Shenyang, China,Key Laboratory of Pathogenesis, Prevention and Therapeutics of Aortic Aneurysm, Shenyang, Liaoning, China
| | - Shijie Xin
- Department of Vascular Surgery, The First Affiliated Hospital of China Medical University, China Medical University, Shenyang, China,Key Laboratory of Pathogenesis, Prevention and Therapeutics of Aortic Aneurysm, Shenyang, Liaoning, China,*Correspondence: Shijie Xin,
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184
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Qian S, Han Y, Zhang Y, Du Y, Li J, Yang X, Kang J. Discovery of AHCY as an Off-Target of Doxorubicin by Integrative Analysis of Photoaffinity Labeling Chemoproteomics and Untargeted Metabolomics. Anal Chem 2022; 94:17121-17130. [PMID: 36445716 DOI: 10.1021/acs.analchem.2c03377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Target identification is critically important for understanding the mechanism of action of drugs. Here, we reported a new strategy for deconvolution of drug targets (or off-targets) with photoaffinity labeling chemoproteomics in combination with untargeted metabolomics by using doxorubicin (DOX) as a model. The DOX-derived photoaffinity probes were prepared and applied to capture DOX-interacting proteins in living cells. The captured DOX-interacting proteins were then identified by label-free quantitative proteomics. Totally, 151 significant proteins were identified with high confidence (fold change >4, p-value < 0.005). The gene ontology enrichment analysis suggested that the proteins were mainly involved in carbon metabolism, citrate cycle, fatty acid metabolism, and metabolic pathways. Therefore, untargeted metabolomics was applied to quantify the significantly altered metabolites in cells upon drug treatment. The pathway enrichment analysis suggested that DOX mainly interrupted with the processes of pyrimidine and purine metabolism, carbon metabolism, methionine metabolism, and phosphatidylcholine biosynthesis. Integrative analysis of chemoproteomics and metabolomics indicated that adenosylhomocysteinase (AHCY) is a new target (off-target) of DOX leading to the accumulation of S-adenosyl homocysteine. This deduced DOX target was confirmed by the cellular thermal shift assay, affinity competitive pull-down assay, biochemical assay, and siRNA knock down experiments. Our result suggested that AHCY is the uncovered off-target of DOX.
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Affiliation(s)
- Shanshan Qian
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai200032, China.,University of Chinese Academy of Sciences, Yuquan Road 19, Beijing100049, China
| | - Ying Han
- School of Life Science and Technology, ShanghaiTech University, Haike Road 100, Shanghai200120, China
| | - Yue Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai200032, China.,University of Chinese Academy of Sciences, Yuquan Road 19, Beijing100049, China
| | - Yanan Du
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai200032, China.,School of Physical Science and Technology, ShanghaiTech University, Haike Road 100, Shanghai200120, China
| | - Jing Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai200032, China.,School of Physical Science and Technology, ShanghaiTech University, Haike Road 100, Shanghai200120, China
| | - Xin Yang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai200032, China.,School of Physical Science and Technology, ShanghaiTech University, Haike Road 100, Shanghai200120, China
| | - Jingwu Kang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai200032, China.,School of Physical Science and Technology, ShanghaiTech University, Haike Road 100, Shanghai200120, China
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185
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Zhang W, Wan Z, Li X, Li R, Luo L, Song Z, Miao Y, Li Z, Wang S, Shan Y, Li Y, Chen B, Zhen H, Sun Y, Fang M, Ding J, Yan Y, Zong Y, Wang Z, Zhang W, Yang H, Yang S, Wang J, Jin X, Wang R, Chen P, Min J, Zeng Y, Li T, Xu X, Nie C. A population-based study of precision health assessments using multi-omics network-derived biological functional modules. Cell Rep Med 2022; 3:100847. [PMID: 36493776 PMCID: PMC9798030 DOI: 10.1016/j.xcrm.2022.100847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 10/05/2022] [Accepted: 11/11/2022] [Indexed: 12/13/2022]
Abstract
Recent technological advances in multi-omics and bioinformatics provide an opportunity to develop precision health assessments, which require big data and relevant bioinformatic methods. Here we collect multi-omics data from 4,277 individuals. We calculate the correlations between pairwise features from cross-sectional data and then generate 11 biological functional modules (BFMs) in males and 12 BFMs in females using a community detection algorithm. Using the features in the BFM associated with cardiometabolic health, carotid plaques can be predicted accurately in an independent dataset. We developed a model by comparing individual data with the health baseline in BFMs to assess health status (BFM-ash). Then we apply the model to chronic patients and modify the BFM-ash model to assess the effects of consuming grape seed extract as a dietary supplement. Finally, anomalous BFMs are identified for each subject. Our BFMs and BFM-ash model have huge prospects for application in precision health assessment.
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Affiliation(s)
- Wei Zhang
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Ziyun Wan
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Xiaoyu Li
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China,BGI Education Center, University of the Chinese Academy of Sciences, Shenzhen 518083, China
| | - Rui Li
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Lihua Luo
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China,BGI Education Center, University of the Chinese Academy of Sciences, Shenzhen 518083, China
| | - Zijun Song
- The First Affiliated Hospital, Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yu Miao
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China,BGI Education Center, University of the Chinese Academy of Sciences, Shenzhen 518083, China
| | - Zhiming Li
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Shiyu Wang
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China,BGI Education Center, University of the Chinese Academy of Sciences, Shenzhen 518083, China
| | - Ying Shan
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Yan Li
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Bangwei Chen
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China,School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Hefu Zhen
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Yuzhe Sun
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Mingyan Fang
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Jiahong Ding
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Yizhen Yan
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Yang Zong
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Zhen Wang
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Wenwei Zhang
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Shuang Yang
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Ru Wang
- School of Exercise and Health, Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, Shanghai University of Sport, Shanghai, China
| | - Peijie Chen
- School of Exercise and Health, Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, Shanghai University of Sport, Shanghai, China
| | - Junxia Min
- The First Affiliated Hospital, Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yi Zeng
- Center for Healthy Aging and Development Studies, National School of Development, Peking University, Beijing, China
| | - Tao Li
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China
| | - Chao Nie
- BGI-Shenzhen, Shenzhen 518083, China,China National GeneBank, Shenzhen 518120, China,Corresponding author
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186
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Song Y, Qu X, Tao L, Gao H, Zhang Y, Zhai J, Gong J, Hu T. Exploration of the underlying mechanisms of isoniazid/rifampicin-induced liver injury in mice using an integrated proteomics and metabolomics approach. J Biochem Mol Toxicol 2022; 36:e23217. [PMID: 36111668 DOI: 10.1002/jbt.23217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 06/22/2022] [Accepted: 08/30/2022] [Indexed: 11/02/2023]
Abstract
The hepatotoxic mechanism resulting from coadministration of isoniazid (INH) and rifampicin (RIF) are complex and studies remain inconclusive. To systematically explore the underlying mechanisms, an integrated mass-based untargeted metabolomics and label-free quantitative proteomics approach was used to clarify the mechanism of INH/RIF-induced liver injury. Thirty male mice were randomly divided into three groups: control (receiving orally administered vehicle solution), INH (150 mg/kg) + RIF (300 mg/kg) orally administered for either 7 or 14 days, respectively. Serum was collected for the analysis of biochemical parameters and liver samples were obtained for mass spectrum-based proteomics, metabolomics, and lipidomics analysis. Overall, 511 proteins, 31 metabolites, and 23 lipids were dysregulated and identified, and disordered biological pathways were identified. The network of integrated multiomics showed that glucose, lipid, and amino acid metabolism as well as energy metabolism were mainly dysregulated and led to oxidative stress, inflammation, liver steatosis, and cell death induced by INH and RIF. Coadministration of INH and RIF can induce liver injury by oxidative stress, inflammation, liver steatosis, and cell death, and the reduction in glutathione levels may play a critical role in these systematic changes and warrants further study.
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Affiliation(s)
- Yanqing Song
- Department of Pharmacy, The First Hospital of Jilin University, Changchun, China
| | - Xiaoyu Qu
- Department of Pharmacy, The First Hospital of Jilin University, Changchun, China
| | - Lina Tao
- Department of Pharmacy, The First Hospital of Jilin University, Changchun, China
| | - Huan Gao
- Department of Pharmacy, The First Hospital of Jilin University, Changchun, China
| | - Yueming Zhang
- Department of Pharmacy, The First Hospital of Jilin University, Changchun, China
| | - Jinghui Zhai
- Department of Pharmacy, The First Hospital of Jilin University, Changchun, China
| | - Jiawei Gong
- Department of Pharmacy, The First Hospital of Jilin University, Changchun, China
| | - Tingting Hu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, China
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187
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Kreutzer L, Weber P, Heider T, Heikenwälder M, Riedl T, Baumeister P, Klauschen F, Belka C, Walch A, Zitzelsberger H, Hess J, Unger K. Simultaneous metabolite MALDI-MSI, whole exome and transcriptome analysis from formalin-fixed paraffin-embedded tissue sections. J Transl Med 2022; 102:1400-1405. [PMID: 36045222 PMCID: PMC9708593 DOI: 10.1038/s41374-022-00829-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 11/09/2022] Open
Abstract
Matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) allows spatial analysis of proteins, metabolites, or small molecules from tissue sections. Here, we present the simultaneous generation and analysis of MALDI-MSI, whole-exome sequencing (WES), and RNA-sequencing data from the same formalin-fixed paraffin-embedded (FFPE) tissue sections. Genomic DNA and total RNA were extracted from (i) untreated, (ii) hematoxylin-eosin (HE) stained, and (iii) MALDI-MSI-analyzed FFPE tissue sections from three head and neck squamous cell carcinomas. MALDI-MSI data were generated by a time-of-flight analyzer prior to preprocessing and visualization. WES data were generated using a low-input protocol followed by detection of single-nucleotide variants (SNVs), tumor mutational burden, and mutational signatures. The transcriptome was determined using 3'-RNA sequencing and was examined for similarities and differences between processing stages. All data met the commonly accepted quality criteria. Besides SNVs commonly identified between differently processed tissues, FFPE-typical artifactual variants were detected. Tumor mutational burden was in the same range for tissues from the same patient and mutational signatures were highly overlapping. Transcriptome profiles showed high levels of correlation. Our data demonstrate that simultaneous molecular profiling of MALDI-MSI-processed FFPE tissue sections at the transcriptome and exome levels is feasible and reliable.
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Affiliation(s)
- Lisa Kreutzer
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, Neuherberg, Germany
- Clinical Cooperation Group Personalized Radiotherapy in Head and Neck Cancer, Helmholtz Zentrum München, Neuherberg, Germany
| | - Peter Weber
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, Neuherberg, Germany
- Clinical Cooperation Group Personalized Radiotherapy in Head and Neck Cancer, Helmholtz Zentrum München, Neuherberg, Germany
| | - Theresa Heider
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, Neuherberg, Germany
- Clinical Cooperation Group Personalized Radiotherapy in Head and Neck Cancer, Helmholtz Zentrum München, Neuherberg, Germany
| | - Mathias Heikenwälder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tobias Riedl
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp Baumeister
- Department of Otorhinolaryngology, University Hospital, LMU Munich, München, Germany
| | - Frederick Klauschen
- Faculty of Medicine, Ludwig-Maximilians-University of Munich, Institute of Pathology, München, Germany
| | - Claus Belka
- Clinical Cooperation Group Personalized Radiotherapy in Head and Neck Cancer, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Radiation Oncology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Axel Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Horst Zitzelsberger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, Neuherberg, Germany
- Clinical Cooperation Group Personalized Radiotherapy in Head and Neck Cancer, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Radiation Oncology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Julia Hess
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, Neuherberg, Germany
- Clinical Cooperation Group Personalized Radiotherapy in Head and Neck Cancer, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Radiation Oncology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Kristian Unger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, Neuherberg, Germany.
- Clinical Cooperation Group Personalized Radiotherapy in Head and Neck Cancer, Helmholtz Zentrum München, Neuherberg, Germany.
- Department of Radiation Oncology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany.
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188
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Corral A, Alcala M, Carmen Duran-Ruiz M, Arroba AI, Ponce-Gonzalez JG, Todorčević M, Serra D, Calderon-Dominguez M, Herrero L. Role of long non-coding RNAs in adipose tissue metabolism and associated pathologies. Biochem Pharmacol 2022; 206:115305. [DOI: 10.1016/j.bcp.2022.115305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/17/2022]
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189
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Woodward AA, Urbanowicz RJ, Naj AC, Moore JH. Genetic heterogeneity: Challenges, impacts, and methods through an associative lens. Genet Epidemiol 2022; 46:555-571. [PMID: 35924480 PMCID: PMC9669229 DOI: 10.1002/gepi.22497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 01/07/2023]
Abstract
Genetic heterogeneity describes the occurrence of the same or similar phenotypes through different genetic mechanisms in different individuals. Robustly characterizing and accounting for genetic heterogeneity is crucial to pursuing the goals of precision medicine, for discovering novel disease biomarkers, and for identifying targets for treatments. Failure to account for genetic heterogeneity may lead to missed associations and incorrect inferences. Thus, it is critical to review the impact of genetic heterogeneity on the design and analysis of population level genetic studies, aspects that are often overlooked in the literature. In this review, we first contextualize our approach to genetic heterogeneity by proposing a high-level categorization of heterogeneity into "feature," "outcome," and "associative" heterogeneity, drawing on perspectives from epidemiology and machine learning to illustrate distinctions between them. We highlight the unique nature of genetic heterogeneity as a heterogeneous pattern of association that warrants specific methodological considerations. We then focus on the challenges that preclude effective detection and characterization of genetic heterogeneity across a variety of epidemiological contexts. Finally, we discuss systems heterogeneity as an integrated approach to using genetic and other high-dimensional multi-omic data in complex disease research.
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Affiliation(s)
- Alexa A. Woodward
- Department of Biostatistics, Epidemiology and InformaticsUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Ryan J. Urbanowicz
- Department of Computational BiomedicineCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
| | - Adam C. Naj
- Department of Biostatistics, Epidemiology and InformaticsUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Jason H. Moore
- Department of Computational BiomedicineCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
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190
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Multi-omics to predict changes during cold pressor test. BMC Genomics 2022; 23:759. [PMCID: PMC9675059 DOI: 10.1186/s12864-022-08981-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 10/31/2022] [Indexed: 11/21/2022] Open
Abstract
Background The cold pressor test (CPT) is a widely used pain provocation test to investigate both pain tolerance and cardiovascular responses. We hypothesize, that performing multi-omic analyses during CPT gives the opportunity to home in on molecular mechanisms involved. Twenty-two females were phenotypically assessed before and after a CPT, and blood samples were taken. RNA-Sequencing, steroid profiling and untargeted metabolomics were performed. Each ‘omic level was analyzed separately at both single-feature and systems-level (principal component [PCA] and partial least squares [PLS] regression analysis) and all ‘omic levels were combined using an integrative multi-omics approach, all using the paired-sample design. Results We showed that PCA was not able to discriminate time points, while PLS did significantly distinguish time points using metabolomics and/or transcriptomic data, but not using conventional physiological measures. Transcriptomic and metabolomic data revealed at feature-, systems- and integrative- level biologically relevant processes involved during CPT, e.g. lipid metabolism and stress response. Conclusion Multi-omics strategies have a great potential in pain research, both at feature- and systems- level. Therefore, they should be exploited in intervention studies, such as pain provocation tests, to gain knowledge on the biological mechanisms involved in complex traits. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08981-z.
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191
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Agamah FE, Bayjanov JR, Niehues A, Njoku KF, Skelton M, Mazandu GK, Ederveen THA, Mulder N, Chimusa ER, 't Hoen PAC. Computational approaches for network-based integrative multi-omics analysis. Front Mol Biosci 2022; 9:967205. [PMID: 36452456 PMCID: PMC9703081 DOI: 10.3389/fmolb.2022.967205] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 10/20/2022] [Indexed: 08/27/2023] Open
Abstract
Advances in omics technologies allow for holistic studies into biological systems. These studies rely on integrative data analysis techniques to obtain a comprehensive view of the dynamics of cellular processes, and molecular mechanisms. Network-based integrative approaches have revolutionized multi-omics analysis by providing the framework to represent interactions between multiple different omics-layers in a graph, which may faithfully reflect the molecular wiring in a cell. Here we review network-based multi-omics/multi-modal integrative analytical approaches. We classify these approaches according to the type of omics data supported, the methods and/or algorithms implemented, their node and/or edge weighting components, and their ability to identify key nodes and subnetworks. We show how these approaches can be used to identify biomarkers, disease subtypes, crosstalk, causality, and molecular drivers of physiological and pathological mechanisms. We provide insight into the most appropriate methods and tools for research questions as showcased around the aetiology and treatment of COVID-19 that can be informed by multi-omics data integration. We conclude with an overview of challenges associated with multi-omics network-based analysis, such as reproducibility, heterogeneity, (biological) interpretability of the results, and we highlight some future directions for network-based integration.
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Affiliation(s)
- Francis E. Agamah
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI-Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jumamurat R. Bayjanov
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Anna Niehues
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Kelechi F. Njoku
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Michelle Skelton
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI-Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Gaston K. Mazandu
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI-Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- African Institute for Mathematical Sciences, Cape Town, South Africa
| | - Thomas H. A. Ederveen
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI-Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Emile R. Chimusa
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, United Kingdom
| | - Peter A. C. 't Hoen
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
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192
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Gerussi A, Scaravaglio M, Cristoferi L, Verda D, Milani C, De Bernardi E, Ippolito D, Asselta R, Invernizzi P, Kather JN, Carbone M. Artificial intelligence for precision medicine in autoimmune liver disease. Front Immunol 2022; 13:966329. [PMID: 36439097 PMCID: PMC9691668 DOI: 10.3389/fimmu.2022.966329] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 10/13/2022] [Indexed: 09/10/2023] Open
Abstract
Autoimmune liver diseases (AiLDs) are rare autoimmune conditions of the liver and the biliary tree with unknown etiology and limited treatment options. AiLDs are inherently characterized by a high degree of complexity, which poses great challenges in understanding their etiopathogenesis, developing novel biomarkers and risk-stratification tools, and, eventually, generating new drugs. Artificial intelligence (AI) is considered one of the best candidates to support researchers and clinicians in making sense of biological complexity. In this review, we offer a primer on AI and machine learning for clinicians, and discuss recent available literature on its applications in medicine and more specifically how it can help to tackle major unmet needs in AiLDs.
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Affiliation(s)
- Alessio Gerussi
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Miki Scaravaglio
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Laura Cristoferi
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
- Bicocca Bioinformatics Biostatistics and Bioimaging Centre - B4, School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | | | - Chiara Milani
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Elisabetta De Bernardi
- Department of Medicine and Surgery and Tecnomed Foundation, University of Milano - Bicocca, Monza, Italy
| | | | - Rosanna Asselta
- Humanitas Clinical and Research Center, Rozzano, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
| | - Pietro Invernizzi
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Jakob Nikolas Kather
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Marco Carbone
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
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193
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Buvall L, Menzies RI, Williams J, Woollard KJ, Kumar C, Granqvist AB, Fritsch M, Feliers D, Reznichenko A, Gianni D, Petrovski S, Bendtsen C, Bohlooly-Y M, Haefliger C, Danielson RF, Hansen PBL. Selecting the right therapeutic target for kidney disease. Front Pharmacol 2022; 13:971065. [DOI: 10.3389/fphar.2022.971065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Kidney disease is a complex disease with several different etiologies and underlying associated pathophysiology. This is reflected by the lack of effective treatment therapies in chronic kidney disease (CKD) that stop disease progression. However, novel strategies, recent scientific breakthroughs, and technological advances have revealed new possibilities for finding novel disease drivers in CKD. This review describes some of the latest advances in the field and brings them together in a more holistic framework as applied to identification and validation of disease drivers in CKD. It uses high-resolution ‘patient-centric’ omics data sets, advanced in silico tools (systems biology, connectivity mapping, and machine learning) and ‘state-of-the-art‘ experimental systems (complex 3D systems in vitro, CRISPR gene editing, and various model biological systems in vivo). Application of such a framework is expected to increase the likelihood of successful identification of novel drug candidates based on strong human target validation and a better scientific understanding of underlying mechanisms.
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194
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Scaravaglio M, Carbone M. Prognostic Scoring Systems in Primary Biliary Cholangitis: An Update. Clin Liver Dis 2022; 26:629-642. [PMID: 36270720 DOI: 10.1016/j.cld.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Primary biliary cholangitis (PBC) is a complex, chronic disease with a heterogeneous presentation, disease progression, and response to therapy. Several prognostic models based on disease stage and/or treatment response enhance risk stratification and therapeutic management. Recent work on disease modeling proposed early prediction of outcomes at PBC onset, yet this has not been implemented in clinical practice. Although early stratification of patients based on their individual risk of developing end-stage liver disease may prove cost-effective and actually become matter of medical deontology to timely offer the best therapeutic option, given the forthcoming availability of novel, disease-modifying drugs. This review outlines established and novel prognostic systems in PBC and provides some perspectives on the potential role of omics-derived biomarkers in developing reliable risk prediction models and promoting the implementation of personalized medicine in PBC.
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Affiliation(s)
- Miki Scaravaglio
- Division of Gastroenterology and Hepatology, Department of Medicine and Surgery, University of Milano-Bicocca, Via Cadore 48, 20900 Monza (MB), Italy.
| | - Marco Carbone
- Division of Gastroenterology and Hepatology, Department of Medicine and Surgery, University of Milano-Bicocca, Via Cadore 48, 20900 Monza (MB), Italy.
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195
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Lunasin peptide promotes lysosome-mitochondrial mediated apoptosis and mitotic termination in MDA-MB-231 cells. FOOD SCIENCE AND HUMAN WELLNESS 2022. [DOI: 10.1016/j.fshw.2022.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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196
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Shan Z, Ding L, Zhu C, Sun R, Hong W. Medical care of rare and undiagnosed diseases: Prospects and challenges. FUNDAMENTAL RESEARCH 2022; 2:851-858. [PMID: 38933390 PMCID: PMC11197738 DOI: 10.1016/j.fmre.2022.08.018] [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: 06/28/2022] [Revised: 08/18/2022] [Accepted: 08/23/2022] [Indexed: 11/25/2022] Open
Abstract
Rare and undiagnosed diseases tend to be diverse, misdiagnosed, and difficult to diagnose. In some cases, the disease is progressive and life-threatening. Yet, to date, an estimated 95% of rare diseases have no approved therapy. Therefore, rare and undiagnosed diseases are considered the ultimate challenges for understanding human diseases. Here, we review the research progress, research frontiers, and important scientific issues related to rare and undiagnosed diseases. We mainly focus on five topics: (1) the identification and functional analysis of disease-causing genes; (2) the construction of cells, organoids, and animal models for mechanism validation; (3) subtyping and diagnosis; (4) treatment and drug screening based on causative genes and mutations; and (5) new technologies and methods for studying rare and undiagnosed diseases. In this review, we briefly update and discuss the pathogenic mechanisms and precision medicine for rare and undiagnosed diseases.
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Affiliation(s)
- Zhiyan Shan
- Department of Health Sciences, National Natural Science Foundation of China, Beijing 100085, China
- Department of Histology and Embryology, Harbin Medical University, Harbin 150081, China
| | - Lijun Ding
- Department of Health Sciences, National Natural Science Foundation of China, Beijing 100085, China
- Center for Reproductive Medicine and Obstetrics and Gynecology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu 210008, China
| | - Caiyun Zhu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Ruijuan Sun
- Department of Health Sciences, National Natural Science Foundation of China, Beijing 100085, China
| | - Wei Hong
- Department of Health Sciences, National Natural Science Foundation of China, Beijing 100085, China
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197
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Liu Y, Deng Y, Wang F, Liu X, Wang J, Xiao J, Zhang C, Zhang Q. A New Mechanism for Ginsenoside Rb1 to Promote Glucose Uptake, Regulating Riboflavin Metabolism and Redox Homeostasis. Metabolites 2022; 12:1011. [PMID: 36355094 PMCID: PMC9698532 DOI: 10.3390/metabo12111011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 09/29/2023] Open
Abstract
Glucose absorption promoters perform insulin mimic functions to enhance blood glucose transport to skeletal muscle cells and accelerate glucose consumption, thereby reducing blood glucose levels. In our screening exploration of food ingredients for improving glucose transportation and metabolism, we found that the saponins in American ginseng (Panaxquinquefolius L.) showed potential activity to promote glucose uptake, which can be used for stabilizing levels of postprandial blood glucose. The aim of this study was to identify key components of American ginseng with glucose uptake-promoting activity and to elucidate their metabolic regulatory mechanisms. Bio-guided isolation using zebrafish larvae and 2-NBDG indicator identified ginsenoside Rb1 (GRb1) as the most potential promotor of glucose uptake. Using UPLC-QTOF-MS/MS combined with RT-qPCR and phenotypic verification, we found that riboflavin metabolism is the hinge for GRb1-mediated facilitation of glucose transport. GRb1-induced restoration of redox homeostasis was mediated by targeting riboflavin transporters (SLC52A1 and SLC52A3) and riboflavin kinase (RFK).
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Affiliation(s)
- Yihan Liu
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Xianyang 712100, China
| | - Yuchan Deng
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Xianyang 712100, China
| | - Fengyu Wang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Xianyang 712100, China
| | - Xiaoyi Liu
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Xianyang 712100, China
| | - Jiaqi Wang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Xianyang 712100, China
| | - Jian Xiao
- Shaanxi Key Laboratory of Phytochemistry, College of Chemistry and Chemical Engineering, Baoji University of Arts and Sciences, Baoji 721013, China
| | - Cunli Zhang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Xianyang 712100, China
| | - Qiang Zhang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Xianyang 712100, China
- Shaanxi Key Laboratory of Phytochemistry, College of Chemistry and Chemical Engineering, Baoji University of Arts and Sciences, Baoji 721013, China
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198
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Oldoni E, Saunders G, Bietrix F, Garcia Bermejo ML, Niehues A, ’t Hoen PAC, Nordlund J, Hajduch M, Scherer A, Kivinen K, Pitkänen E, Mäkela TP, Gut I, Scollen S, Kozera Ł, Esteller M, Shi L, Ussi A, Andreu AL, van Gool AJ. Tackling the translational challenges of multi-omics research in the realm of European personalised medicine: A workshop report. Front Mol Biosci 2022; 9:974799. [PMID: 36310597 PMCID: PMC9608444 DOI: 10.3389/fmolb.2022.974799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Personalised medicine (PM) presents a great opportunity to improve the future of individualised healthcare. Recent advances in -omics technologies have led to unprecedented efforts characterising the biology and molecular mechanisms that underlie the development and progression of a wide array of complex human diseases, supporting further development of PM. This article reflects the outcome of the 2021 EATRIS-Plus Multi-omics Stakeholder Group workshop organised to 1) outline a global overview of common promises and challenges that key European stakeholders are facing in the field of multi-omics research, 2) assess the potential of new technologies, such as artificial intelligence (AI), and 3) establish an initial dialogue between key initiatives in this space. Our focus is on the alignment of agendas of European initiatives in multi-omics research and the centrality of patients in designing solutions that have the potential to advance PM in long-term healthcare strategies.
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Affiliation(s)
- Emanuela Oldoni
- European Infrastructure for Translational Medicine (EATRIS), Amsterdam, Netherlands
- *Correspondence: Gary Saunders, ; Emanuela Oldoni,
| | - Gary Saunders
- European Infrastructure for Translational Medicine (EATRIS), Amsterdam, Netherlands
- *Correspondence: Gary Saunders, ; Emanuela Oldoni,
| | - Florence Bietrix
- European Infrastructure for Translational Medicine (EATRIS), Amsterdam, Netherlands
| | - Maria Laura Garcia Bermejo
- Biomarkers and Therapeutic Targets Group, Ramon and Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Anna Niehues
- Translational Metabolomic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Peter A. C. ’t Hoen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jessica Nordlund
- Department of Medical Sciences, Molecular Precision Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Olomouc, Czechia
| | - Andreas Scherer
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Katja Kivinen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
- HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Esa Pitkänen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
- HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Tomi Pekka Mäkela
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
- HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | | | - Łukasz Kozera
- Biobanking and BioMolecular Resources Research Infrastructure-European Research Infrastructure Consortium (BBMRI-ERIC), Graz, Austria
| | - Manel Esteller
- Josep Carreras Leukemia Research Institute (IJC), Badalona, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Spain
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Anton Ussi
- European Infrastructure for Translational Medicine (EATRIS), Amsterdam, Netherlands
| | - Antonio L. Andreu
- European Infrastructure for Translational Medicine (EATRIS), Amsterdam, Netherlands
| | - Alain J. van Gool
- Translational Metabolomic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
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199
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Spick M, Campbell A, Baricevic-Jones I, von Gerichten J, Lewis HM, Frampas CF, Longman K, Stewart A, Dunn-Walters D, Skene DJ, Geifman N, Whetton AD, Bailey MJ. Multi-Omics Reveals Mechanisms of Partial Modulation of COVID-19 Dysregulation by Glucocorticoid Treatment. Int J Mol Sci 2022; 23:12079. [PMID: 36292938 PMCID: PMC9602480 DOI: 10.3390/ijms232012079] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/22/2022] [Accepted: 10/07/2022] [Indexed: 12/15/2022] Open
Abstract
Treatments for COVID-19 infections have improved dramatically since the beginning of the pandemic, and glucocorticoids have been a key tool in improving mortality rates. The UK's National Institute for Health and Care Excellence guidance is for treatment to be targeted only at those requiring oxygen supplementation, however, and the interactions between glucocorticoids and COVID-19 are not completely understood. In this work, a multi-omic analysis of 98 inpatient-recruited participants was performed by quantitative metabolomics (using targeted liquid chromatography-mass spectrometry) and data-independent acquisition proteomics. Both 'omics datasets were analysed for statistically significant features and pathways differentiating participants whose treatment regimens did or did not include glucocorticoids. Metabolomic differences in glucocorticoid-treated patients included the modulation of cortisol and bile acid concentrations in serum, but no alleviation of serum dyslipidemia or increased amino acid concentrations (including tyrosine and arginine) in the glucocorticoid-treated cohort relative to the untreated cohort. Proteomic pathway analysis indicated neutrophil and platelet degranulation as influenced by glucocorticoid treatment. These results are in keeping with the key role of platelet-associated pathways and neutrophils in COVID-19 pathogenesis and provide opportunity for further understanding of glucocorticoid action. The findings also, however, highlight that glucocorticoids are not fully effective across the wide range of 'omics dysregulation caused by COVID-19 infections.
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Affiliation(s)
- Matt Spick
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Amy Campbell
- Stoller Biomarker Discovery Centre, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9NQ, UK
| | - Ivona Baricevic-Jones
- Stoller Biomarker Discovery Centre, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9NQ, UK
| | - Johanna von Gerichten
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford GU2 7XH, UK
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Holly-May Lewis
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Cecile F. Frampas
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford GU2 7XH, UK
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Katie Longman
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Alexander Stewart
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Deborah Dunn-Walters
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Debra J. Skene
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Nophar Geifman
- School of Health Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Anthony D. Whetton
- School of Veterinary Medicine, School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, UK
| | - Melanie J. Bailey
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford GU2 7XH, UK
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Amini AP, Kirkpatrick JD, Wang CS, Jaeger AM, Su S, Naranjo S, Zhong Q, Cabana CM, Jacks T, Bhatia SN. Multiscale profiling of protease activity in cancer. Nat Commun 2022; 13:5745. [PMID: 36192379 PMCID: PMC9530178 DOI: 10.1038/s41467-022-32988-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 08/24/2022] [Indexed: 11/09/2022] Open
Abstract
Diverse processes in cancer are mediated by enzymes, which most proximally exert their function through their activity. High-fidelity methods to profile enzyme activity are therefore critical to understanding and targeting the pathological roles of enzymes in cancer. Here, we present an integrated set of methods for measuring specific protease activities across scales, and deploy these methods to study treatment response in an autochthonous model of Alk-mutant lung cancer. We leverage multiplexed nanosensors and machine learning to analyze in vivo protease activity dynamics in lung cancer, identifying significant dysregulation that includes enhanced cleavage of a peptide, S1, which rapidly returns to healthy levels with targeted therapy. Through direct on-tissue localization of protease activity, we pinpoint S1 cleavage to the tumor vasculature. To link protease activity to cellular function, we design a high-throughput method to isolate and characterize proteolytically active cells, uncovering a pro-angiogenic phenotype in S1-cleaving cells. These methods provide a framework for functional, multiscale characterization of protease dysregulation in cancer.
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Affiliation(s)
- Ava P Amini
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Program in Biophysics, Harvard University, Boston, MA, USA
- Microsoft Research New England, Cambridge, MA, USA
| | - Jesse D Kirkpatrick
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Cathy S Wang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alex M Jaeger
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Susan Su
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Santiago Naranjo
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Qian Zhong
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christina M Cabana
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tyler Jacks
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Harvard MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
- Wyss Institute at Harvard University, Boston, MA, USA.
- Howard Hughes Medical Institute, Cambridge, MA, USA.
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