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Li W, Zhang Z, Xie B, He Y, He K, Qiu H, Lu Z, Jiang C, Pan X, He Y, Hu W, Liu W, Que T, Hu Y. HiOmics: A cloud-based one-stop platform for the comprehensive analysis of large-scale omics data. Comput Struct Biotechnol J 2024; 23:659-668. [PMID: 38292471 PMCID: PMC10824657 DOI: 10.1016/j.csbj.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/01/2024] [Accepted: 01/02/2024] [Indexed: 02/01/2024] Open
Abstract
Analyzing the vast amount of omics data generated comprehensively by high-throughput sequencing technology is of utmost importance for scientists. In this context, we propose HiOmics, a cloud-based platform equipped with nearly 300 plugins designed for the comprehensive analysis and visualization of omics data. HiOmics utilizes the Element Plus framework to craft a user-friendly interface and harnesses Docker container technology to ensure the reliability and reproducibility of data analysis results. Furthermore, HiOmics employs the Workflow Description Language and Cromwell engine to construct workflows, ensuring the portability of data analysis and simplifying the examination of intricate data. Additionally, HiOmics has developed DataCheck, a tool based on Golang, which verifies and converts data formats. Finally, by leveraging the object storage technology and batch computing capabilities of public cloud platforms, HiOmics enables the storage and processing of large-scale data while maintaining resource independence among users.
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Affiliation(s)
- Wen Li
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Biological Molecular Medicine Research (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
| | - Zhining Zhang
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Bo Xie
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Yunlin He
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Kangming He
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Hong Qiu
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Zhiwei Lu
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Chunlan Jiang
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Xuanyu Pan
- School of Basic Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Yuxiao He
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Wenyu Hu
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
| | - Wenjian Liu
- Faculty of Data Science, City University of Macau, Macau, China
| | - Tengcheng Que
- Faculty of Data Science, City University of Macau, Macau, China
- Youjiang Medical University for Nationalities, Baise, Guangxi, China
- Guangxi Zhuang Autonomous Terrestrial Wildlife Rescue Research and Epidemic Diseases Monitoring Center, Nanning, Guangxi, China
| | - Yanling Hu
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, China
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Key Laboratory of Biological Molecular Medicine Research (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
- Guangxi Henbio Biotechnology Co., Ltd., Nanning, Guangxi, China
- Faculty of Data Science, City University of Macau, Macau, China
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2
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Meng X, Zhang S, Zhou S, Ma Y, Yu X, Guan L. Putative Risk Biomarkers of Bipolar Disorder in At-risk Youth. Neurosci Bull 2024:10.1007/s12264-024-01219-w. [PMID: 38710851 DOI: 10.1007/s12264-024-01219-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: 11/23/2023] [Accepted: 03/08/2024] [Indexed: 05/08/2024] Open
Abstract
Bipolar disorder is a highly heritable and functionally impairing disease. The recognition and intervention of BD especially that characterized by early onset remains challenging. Risk biomarkers for predicting BD transition among at-risk youth may improve disease prognosis. We reviewed the more recent clinical studies to find possible pre-diagnostic biomarkers in youth at familial or (and) clinical risk of BD. Here we found that putative biomarkers for predicting conversion to BD include findings from multiple sample sources based on different hypotheses. Putative risk biomarkers shown by perspective studies are higher bipolar polygenetic risk scores, epigenetic alterations, elevated immune parameters, front-limbic system deficits, and brain circuit dysfunction associated with emotion and reward processing. Future studies need to enhance machine learning integration, make clinical detection methods more objective, and improve the quality of cohort studies.
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Affiliation(s)
- Xinyu Meng
- Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
| | - Shengmin Zhang
- Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
| | - Shuzhe Zhou
- Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
| | - Yantao Ma
- Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
| | - Xin Yu
- Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China
| | - Lili Guan
- Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, 100191, China.
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3
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Wang M, Yang N, Laterrière M, Gagné D, Omonijo F, Ibeagha-Awemu EM. Multi-omics integration identifies regulatory factors underlying bovine subclinical mastitis. J Anim Sci Biotechnol 2024; 15:46. [PMID: 38481273 PMCID: PMC10938844 DOI: 10.1186/s40104-024-00996-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/14/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Mastitis caused by multiple factors remains one of the most common and costly disease of the dairy industry. Multi-omics approaches enable the comprehensive investigation of the complex interactions between multiple layers of information to provide a more holistic view of disease pathogenesis. Therefore, this study investigated the genomic and epigenomic signatures and the possible regulatory mechanisms underlying subclinical mastitis by integrating RNA sequencing data (mRNA and lncRNA), small RNA sequencing data (miRNA) and DNA methylation sequencing data of milk somatic cells from 10 healthy cows and 20 cows with naturally occurring subclinical mastitis caused by Staphylococcus aureus or Staphylococcus chromogenes. RESULTS Functional investigation of the data sets through gene set analysis uncovered 3458 biological process GO terms and 170 KEGG pathways with altered activities during subclinical mastitis, provided further insights into subclinical mastitis and revealed the involvement of multi-omics signatures in the altered immune responses and impaired mammary gland productivity during subclinical mastitis. The abundant genomic and epigenomic signatures with significant alterations related to subclinical mastitis were observed, including 30,846, 2552, 1276 and 57 differential methylation haplotype blocks (dMHBs), differentially expressed genes (DEGs), lncRNAs (DELs) and miRNAs (DEMs), respectively. Next, 5 factors presenting the principal variation of differential multi-omics signatures were identified. The important roles of Factor 1 (DEG, DEM and DEL) and Factor 2 (dMHB and DEM), in the regulation of immune defense and impaired mammary gland functions during subclinical mastitis were revealed. Each of the omics within Factors 1 and 2 explained about 20% of the source of variation in subclinical mastitis. Also, networks of important functional gene sets with the involvement of multi-omics signatures were demonstrated, which contributed to a comprehensive view of the possible regulatory mechanisms underlying subclinical mastitis. Furthermore, multi-omics integration enabled the association of the epigenomic regulatory factors (dMHBs, DELs and DEMs) of altered genes in important pathways, such as 'Staphylococcus aureus infection pathway' and 'natural killer cell mediated cytotoxicity pathway', etc., which provides further insights into mastitis regulatory mechanisms. Moreover, few multi-omics signatures (14 dMHBs, 25 DEGs, 18 DELs and 5 DEMs) were identified as candidate discriminant signatures with capacity of distinguishing subclinical mastitis cows from healthy cows. CONCLUSION The integration of genomic and epigenomic data by multi-omics approaches in this study provided a better understanding of the molecular mechanisms underlying subclinical mastitis and identified multi-omics candidate discriminant signatures for subclinical mastitis, which may ultimately lead to the development of more effective mastitis control and management strategies.
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Affiliation(s)
- Mengqi Wang
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
- Department of Animal Science, Université Laval, Quebec City, QC, Canada
| | - Naisu Yang
- Department of Animal Science, Université Laval, Quebec City, QC, Canada
| | - Mario Laterrière
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec City, QC, Canada
| | - David Gagné
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec City, QC, Canada
| | - Faith Omonijo
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
| | - Eveline M Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada.
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4
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Lopez-Jaramillo C. Advancing psychiatric care: The transition from symptom-based diagnosis to personalized psychiatry. Eur Neuropsychopharmacol 2024; 80:36-37. [PMID: 38310747 DOI: 10.1016/j.euroneuro.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 10/30/2023] [Indexed: 02/06/2024]
Affiliation(s)
- Carlos Lopez-Jaramillo
- Department of Psychiatry, Faculty of Medicine, Universidad de Antioquia, Medellin, Colombia.
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5
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Baune BT, Minelli A, Carpiniello B, Contu M, Domínguez Barragán J, Donlo C, Ferensztajn-Rochowiak E, Glaser R, Kelch B, Kobelska P, Kolasa G, Kopeć D, Martínez de Lagrán Cabredo M, Martini P, Mayer MA, Menesello V, Paribello P, Perera Bel J, Perusi G, Pinna F, Pinna M, Pisanu C, Sierra C, Stonner I, Wahner VTH, Xicota L, Zang JCS, Gennarelli M, Manchia M, Squassina A, Potier MC, Rybakowski F, Sanz F, Dierssen M. An integrated precision medicine approach in major depressive disorder: a study protocol to create a new algorithm for the prediction of treatment response. Front Psychiatry 2024; 14:1279688. [PMID: 38348362 PMCID: PMC10859920 DOI: 10.3389/fpsyt.2023.1279688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/21/2023] [Indexed: 02/15/2024] Open
Abstract
Major depressive disorder (MDD) is the most common psychiatric disease worldwide with a huge socio-economic impact. Pharmacotherapy represents the most common option among the first-line treatment choice; however, only about one third of patients respond to the first trial and about 30% are classified as treatment-resistant depression (TRD). TRD is associated with specific clinical features and genetic/gene expression signatures. To date, single sets of markers have shown limited power in response prediction. Here we describe the methodology of the PROMPT project that aims at the development of a precision medicine algorithm that would help early detection of non-responder patients, who might be more prone to later develop TRD. To address this, the project will be organized in 2 phases. Phase 1 will involve 300 patients with MDD already recruited, comprising 150 TRD and 150 responders, considered as extremes phenotypes of response. A deep clinical stratification will be performed for all patients; moreover, a genomic, transcriptomic and miRNomic profiling will be conducted. The data generated will be exploited to develop an innovative algorithm integrating clinical, omics and sex-related data, in order to predict treatment response and TRD development. In phase 2, a new naturalistic cohort of 300 MDD patients will be recruited to assess, under real-world conditions, the capability of the algorithm to correctly predict the treatment outcomes. Moreover, in this phase we will investigate shared decision making (SDM) in the context of pharmacogenetic testing and evaluate various needs and perspectives of different stakeholders toward the use of predictive tools for MDD treatment to foster active participation and patients' empowerment. This project represents a proof-of-concept study. The obtained results will provide information about the feasibility and usefulness of the proposed approach, with the perspective of designing future clinical trials in which algorithms could be tested as a predictive tool to drive decision making by clinicians, enabling a better prevention and management of MDD resistance.
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Affiliation(s)
- Bernhard T. Baune
- Department of Mental Health, University of Münster, Münster, Germany
- Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia
- Department of Psychiatry, University of Melbourne, Parkville, VIC, Australia
| | - Alessandra Minelli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
- Genetics Unit, San Giovanni di Dio Fatebenefratelli Center (IRCCS), Brescia, Italy
| | - Bernardo Carpiniello
- Section of Psychiatry, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Martina Contu
- Section of Psychiatry, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | | | - Chus Donlo
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | | | - Rosa Glaser
- Department of Mental Health, University Hospital Münster, Münster, Germany
| | - Britta Kelch
- Department of Mental Health, University Hospital Münster, Münster, Germany
| | - Paulina Kobelska
- Department of Science, Grants and International Cooperation, Poznan University of Medical Sciences, Poznan, Poland
| | - Grzegorz Kolasa
- Department of Adult Psychiatry, Poznan University of Medical Sciences, Poznan, Poland
| | - Dobrochna Kopeć
- Department of Adult Psychiatry, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Paolo Martini
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Miguel-Angel Mayer
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Valentina Menesello
- Genetics Unit, San Giovanni di Dio Fatebenefratelli Center (IRCCS), Brescia, Italy
| | - Pasquale Paribello
- Section of Psychiatry, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Júlia Perera Bel
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Giulia Perusi
- Department of Mental Health and Addiction Services, ASST Spedali Civili of Brescia, Brescia, Italy
| | - Federica Pinna
- Section of Psychiatry, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Marco Pinna
- Section of Psychiatry, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Claudia Pisanu
- Section of Neuroscience and Clinical Pharmacology, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Cesar Sierra
- Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Inga Stonner
- Department of Mental Health, University Hospital Münster, Münster, Germany
| | | | - Laura Xicota
- Gertrude H. Sergievsky Center, Columbia University Irving Medical Center, New York, NY, United States
| | | | - Massimo Gennarelli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
- Genetics Unit, San Giovanni di Dio Fatebenefratelli Center (IRCCS), Brescia, Italy
| | - Mirko Manchia
- Section of Psychiatry, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
- Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | - Alessio Squassina
- Section of Neuroscience and Clinical Pharmacology, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
- Department of Psychiatry, Dalhousie University, Halifax, NS, Canada
| | - Marie-Claude Potier
- Paris Brain Institute (ICM), National Centre for Scientific Research (CNRS), Paris, France
| | - Filip Rybakowski
- Department of Adult Psychiatry, Poznan University of Medical Sciences, Poznan, Poland
| | - Ferran Sanz
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Mara Dierssen
- Centre for Genomic Regulation (CRG), Barcelona, Spain
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Mengelkoch S, Gassen J, Lev-Ari S, Alley JC, Schüssler-Fiorenza Rose SM, Snyder MP, Slavich GM. Multi-omics in stress and health research: study designs that will drive the field forward. Stress 2024; 27:2321610. [PMID: 38425100 DOI: 10.1080/10253890.2024.2321610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 02/16/2024] [Indexed: 03/02/2024] Open
Abstract
Despite decades of stress research, there still exist substantial gaps in our understanding of how social, environmental, and biological factors interact and combine with developmental stressor exposures, cognitive appraisals of stressors, and psychosocial coping processes to shape individuals' stress reactivity, health, and disease risk. Relatively new biological profiling approaches, called multi-omics, are helping address these issues by enabling researchers to quantify thousands of molecules from a single blood or tissue sample, thus providing a panoramic snapshot of the molecular processes occurring in an organism from a systems perspective. In this review, we summarize two types of research designs for which multi-omics approaches are best suited, and describe how these approaches can help advance our understanding of stress processes and the development, prevention, and treatment of stress-related pathologies. We first discuss incorporating multi-omics approaches into theory-rich, intensive longitudinal study designs to characterize, in high-resolution, the transition to stress-related multisystem dysfunction and disease throughout development. Next, we discuss how multi-omics approaches should be incorporated into intervention research to better understand the transition from stress-related dysfunction back to health, which can help inform novel precision medicine approaches to managing stress and fostering biopsychosocial resilience. Throughout, we provide concrete recommendations for types of studies that will help advance stress research, and translate multi-omics data into better health and health care.
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Affiliation(s)
- Summer Mengelkoch
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Jeffrey Gassen
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Shahar Lev-Ari
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Health Promotion, Tel Aviv University, Tel Aviv, Israel
| | - Jenna C Alley
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | | | | | - George M Slavich
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
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7
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Oraki Kohshour M, Heilbronner U. The significance of an integrated multi-omics approach in psychiatric disorders: A pharmacological perspective. Eur Neuropsychopharmacol 2024; 78:64-66. [PMID: 37977087 DOI: 10.1016/j.euroneuro.2023.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 11/19/2023]
Affiliation(s)
- Mojtaba Oraki Kohshour
- Institute of Psychiatric Phenomics and Genomics (IPPG), LMU University Hospital, LMU Munich, 80336, Munich, Germany; Department of Immunology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Urs Heilbronner
- Institute of Psychiatric Phenomics and Genomics (IPPG), LMU University Hospital, LMU Munich, 80336, Munich, Germany.
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8
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Elhadi K, Daiwile AP, Cadet JL. Modeling methamphetamine use disorder and relapse in animals: short- and long-term epigenetic, transcriptional., and biochemical consequences in the rat brain. Neurosci Biobehav Rev 2023; 155:105440. [PMID: 38707245 PMCID: PMC11068368 DOI: 10.1016/j.neubiorev.2023.105440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Methamphetamine use disorder (MUD) is a neuropsychiatric disorder characterized by binge drug taking episodes, intervals of abstinence, and relapses to drug use even during treatment. MUD has been modeled in rodents and investigators are attempting to identify its molecular bases. Preclinical experiments have shown that different schedules of methamphetamine self-administration can cause diverse transcriptional changes in the dorsal striatum of Sprague-Dawley rats. In the present review, we present data on differentially expressed genes (DEGs) identified in the rat striatum following methamphetamine intake. These include genes involved in transcription regulation, potassium channel function, and neuroinflammation. We then use the striatal data to discuss the potential significance of the molecular changes induced by methamphetamine by reviewing concordant or discordant data from the literature. This review identified potential molecular targets for pharmacological interventions. Nevertheless, there is a need for more research on methamphetamine-induced transcriptional consequences in various brain regions. These data should provide a more detailed neuroanatomical map of methamphetamine-induced changes and should better inform therapeutic interventions against MUD.
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Affiliation(s)
- Khalid Elhadi
- Molecular Neuropsychiatry Research Branch, NIH/NIDA Intramural Research Program, Baltimore, MD, 21224
| | - Atul P. Daiwile
- Molecular Neuropsychiatry Research Branch, NIH/NIDA Intramural Research Program, Baltimore, MD, 21224
| | - Jean Lud Cadet
- Molecular Neuropsychiatry Research Branch, NIH/NIDA Intramural Research Program, Baltimore, MD, 21224
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9
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Liu M, Ma W, He Y, Sun Z, Yang J. Recent Progress in Mass Spectrometry-Based Metabolomics in Major Depressive Disorder Research. Molecules 2023; 28:7430. [PMID: 37959849 PMCID: PMC10647556 DOI: 10.3390/molecules28217430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/24/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023] Open
Abstract
Major depressive disorder (MDD) is a serious mental illness with a heavy social burden, but its underlying molecular mechanisms remain unclear. Mass spectrometry (MS)-based metabolomics is providing new insights into the heterogeneous pathophysiology, diagnosis, treatment, and prognosis of MDD by revealing multi-parametric biomarker signatures at the metabolite level. In this comprehensive review, recent developments of MS-based metabolomics in MDD research are summarized from the perspective of analytical platforms (liquid chromatography-MS, gas chromatography-MS, supercritical fluid chromatography-MS, etc.), strategies (untargeted, targeted, and pseudotargeted metabolomics), key metabolite changes (monoamine neurotransmitters, amino acids, lipids, etc.), and antidepressant treatments (both western and traditional Chinese medicines). Depression sub-phenotypes, comorbid depression, and multi-omics approaches are also highlighted to stimulate further advances in MS-based metabolomics in the field of MDD research.
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Affiliation(s)
- Mingxia Liu
- Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders, National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing 100088, China; (M.L.)
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Wen Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yi He
- Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders, National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing 100088, China; (M.L.)
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Zuoli Sun
- Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders, National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing 100088, China; (M.L.)
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Jian Yang
- Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders, National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing 100088, China; (M.L.)
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
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10
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Mengelkoch S, Miryam Schüssler-Fiorenza Rose S, Lautman Z, Alley JC, Roos LG, Ehlert B, Moriarity DP, Lancaster S, Snyder MP, Slavich GM. Multi-omics approaches in psychoneuroimmunology and health research: Conceptual considerations and methodological recommendations. Brain Behav Immun 2023; 114:475-487. [PMID: 37543247 DOI: 10.1016/j.bbi.2023.07.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/04/2023] [Accepted: 07/30/2023] [Indexed: 08/07/2023] Open
Abstract
The field of psychoneuroimmunology (PNI) has grown substantially in both relevance and prominence over the past 40 years. Notwithstanding its impressive trajectory, a majority of PNI studies are still based on a relatively small number of analytes. To advance this work, we suggest that PNI, and health research in general, can benefit greatly from adopting a multi-omics approach, which involves integrating data across multiple biological levels (e.g., the genome, proteome, transcriptome, metabolome, lipidome, and microbiome/metagenome) to more comprehensively profile biological functions and relate these profiles to clinical and behavioral outcomes. To assist investigators in this endeavor, we provide an overview of multi-omics research, highlight recent landmark multi-omics studies investigating human health and disease risk, and discuss how multi-omics can be applied to better elucidate links between psychological, nervous system, and immune system activity. In doing so, we describe how to design high-quality multi-omics studies, decide which biological samples (e.g., blood, stool, urine, saliva, solid tissue) are most relevant, incorporate behavioral and wearable sensing data into multi-omics research, and understand key data quality, integration, analysis, and interpretation issues. PNI researchers are addressing some of the most interesting and important questions at the intersection of psychology, neuroscience, and immunology. Applying a multi-omics approach to this work will greatly expand the horizon of what is possible in PNI and has the potential to revolutionize our understanding of mind-body medicine.
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Affiliation(s)
- Summer Mengelkoch
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA.
| | | | - Ziv Lautman
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Jenna C Alley
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Lydia G Roos
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Benjamin Ehlert
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Daniel P Moriarity
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | | | | | - George M Slavich
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA.
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11
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Kumsta R. The role of stress in the biological embedding of experience. Psychoneuroendocrinology 2023; 156:106364. [PMID: 37586308 DOI: 10.1016/j.psyneuen.2023.106364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 08/08/2023] [Indexed: 08/18/2023]
Abstract
Exposure to early adversity is one of the most important and pervasive risk factors for the development of nearly all major mental disorders across the lifespan. In the search for the mediating mechanisms and processes that underlie long-term stability of these effects, changes to stress-associated hormonal and cellular signalling have emerged as prime candidates. This review summarises evidence showing that experience of early adversity in the form of childhood abuse or neglect and exposure to severe institutional deprivation influences multiple interconnected bio-behavioural, physiological and cellular processes. This paper focusses on dysregulations of hormonal stress regulation, altered DNA methylation pattern, changes to transcriptomic profiles in the context of stress-immune interplay, and mitochondrial biology. Consistent findings that have emerged include a relative cortisol hypoactivity and hyporeactivity in response to challenge, increased activity of pro-inflammatory genes, and altered mitochondrial function. The majority of investigations have focussed on single outcomes, but there is a clear rationale of conceiving the implicated physiological processes as interconnected parts of a wider stress-associated regulatory network, which in turn is connected to behaviour and mental disorders. This calls for integrated and longitudinal investigations to come to a more comprehensive understanding of the role of stress in the biological embedding of experience. The review concludes with considerations of how stress research can contribute to translational efforts through characterising subtypes of mental disorders which arise as a function of early adversity, and have distinct features of behavioral and biological stress processing.
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Affiliation(s)
- Robert Kumsta
- Department of Behavioural and Cognitive Sciences, Faculty of Humanities, Education and Social Sciences, Laboratory for Stress and Gene-Environment Interplay, University of Luxemburg, Esch-sur-Alzette, Luxemburg; Faculty of Psychology, Institute for Health and Development, Ruhr University Bochum, Bochum, Germany; German Center for Mental Health (DZPG), partner site Bochum/Marburg, Germany.
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Arachchige ASPM, Verma Y. Revolutionizing stress-related disorder regulation through neuroinformatics and data analysis: An editorial. AIMS Neurosci 2023; 10:252-254. [PMID: 37841345 PMCID: PMC10567583 DOI: 10.3934/neuroscience.2023019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 08/30/2023] [Indexed: 10/17/2023] Open
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13
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Felsky D, Cannitelli A, Pipitone J. Whole Person Modeling: a transdisciplinary approach to mental health research. DISCOVER MENTAL HEALTH 2023; 3:16. [PMID: 37638348 PMCID: PMC10449734 DOI: 10.1007/s44192-023-00041-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 08/10/2023] [Indexed: 08/29/2023]
Abstract
The growing global burden of mental illness has prompted calls for innovative research strategies. Theoretical models of mental health include complex contributions of biological, psychosocial, experiential, and other environmental influences. Accordingly, neuropsychiatric research has self-organized into largely isolated disciplines working to decode each individual contribution. However, research directly modeling objective biological measurements in combination with cognitive, psychological, demographic, or other environmental measurements is only now beginning to proliferate. This review aims to (1) to describe the landscape of modern mental health research and current movement towards integrative study, (2) to provide a concrete framework for quantitative integrative research, which we call Whole Person Modeling, (3) to explore existing and emerging techniques and methods used in Whole Person Modeling, and (4) to discuss our observations about the scarcity, potential value, and untested aspects of highly transdisciplinary research in general. Whole Person Modeling studies have the potential to provide a better understanding of multilevel phenomena, deliver more accurate diagnostic and prognostic tests to aid in clinical decision making, and test long standing theoretical models of mental illness. Some current barriers to progress include challenges with interdisciplinary communication and collaboration, systemic cultural barriers to transdisciplinary career paths, technical challenges in model specification, bias, and data harmonization, and gaps in transdisciplinary educational programs. We hope to ease anxiety in the field surrounding the often mysterious and intimidating world of transdisciplinary, data-driven mental health research and provide a useful orientation for students or highly specialized researchers who are new to this area.
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Affiliation(s)
- Daniel Felsky
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, 250 College Street, Toronto, ON M5T 1R8 Canada
- Department of Psychiatry, Faculty of Medicine, University of Toronto, Toronto, ON Canada
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON Canada
- Rotman Research Institute, Baycrest Hospital, Toronto, ON Canada
- Faculty of Medicine, McMaster University, Hamilton, ON Canada
| | - Alyssa Cannitelli
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, 250 College Street, Toronto, ON M5T 1R8 Canada
- Faculty of Medicine, McMaster University, Hamilton, ON Canada
| | - Jon Pipitone
- Department of Psychiatry, Queen’s University, Kingston, ON Canada
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Shuryak I, Ghandhi SA, Laiakis EC, Garty G, Wu X, Ponnaiya B, Kosowski E, Pannkuk E, Kaur SP, Harken AD, Deoli N, Fornace AJ, Brenner DJ, Amundson SA. Biomarker integration for improved biodosimetry of mixed neutron + photon exposures. Sci Rep 2023; 13:10936. [PMID: 37414809 PMCID: PMC10325958 DOI: 10.1038/s41598-023-37906-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023] Open
Abstract
There is a persistent risk of a large-scale malicious or accidental exposure to ionizing radiation that may affect a large number of people. Exposure will consist of both a photon and neutron component, which will vary in magnitude between individuals and is likely to have profound impacts on radiation-induced diseases. To mitigate these potential disasters, there exists a need for novel biodosimetry approaches that can estimate the radiation dose absorbed by each person based on biofluid samples, and predict delayed effects. Integration of several radiation-responsive biomarker types (transcripts, metabolites, blood cell counts) by machine learning (ML) can improve biodosimetry. Here we integrated data from mice exposed to various neutron + photon mixtures, total 3 Gy dose, using multiple ML algorithms to select the strongest biomarker combinations and reconstruct radiation exposure magnitude and composition. We obtained promising results, such as receiver operating characteristic curve area of 0.904 (95% CI: 0.821, 0.969) for classifying samples exposed to ≥ 10% neutrons vs. < 10% neutrons, and R2 of 0.964 for reconstructing photon-equivalent dose (weighted by neutron relative biological effectiveness) for neutron + photon mixtures. These findings demonstrate the potential of combining various -omic biomarkers for novel biodosimetry.
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Affiliation(s)
- Igor Shuryak
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168Th Street, VC-11-234/5, New York, NY, 10032, USA.
| | - Shanaz A Ghandhi
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168Th Street, VC-11-234/5, New York, NY, 10032, USA
| | - Evagelia C Laiakis
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA
| | - Guy Garty
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168Th Street, VC-11-234/5, New York, NY, 10032, USA
| | - Xuefeng Wu
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168Th Street, VC-11-234/5, New York, NY, 10032, USA
| | - Brian Ponnaiya
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168Th Street, VC-11-234/5, New York, NY, 10032, USA
| | - Emma Kosowski
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Evan Pannkuk
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA
| | - Salan P Kaur
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168Th Street, VC-11-234/5, New York, NY, 10032, USA
| | - Andrew D Harken
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168Th Street, VC-11-234/5, New York, NY, 10032, USA
| | - Naresh Deoli
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168Th Street, VC-11-234/5, New York, NY, 10032, USA
| | - Albert J Fornace
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA
| | - David J Brenner
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168Th Street, VC-11-234/5, New York, NY, 10032, USA
| | - Sally A Amundson
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168Th Street, VC-11-234/5, New York, NY, 10032, USA
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Valli I, McGuire P. Genetic and obstetric risk in psychosis: Towards a hypothesis-based probe of different noxae. Eur Neuropsychopharmacol 2023; 72:6-8. [PMID: 36958231 DOI: 10.1016/j.euroneuro.2023.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/25/2023]
Affiliation(s)
- Isabel Valli
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, UK.
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Fernandes BS, Zhao Z. Improving drug development in precision psychiatry by ameliorating cognitive biases. Eur Neuropsychopharmacol 2023; 70:14-16. [PMID: 36796294 DOI: 10.1016/j.euroneuro.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/16/2023]
Affiliation(s)
- Brisa S Fernandes
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
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