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Chen B, Sun X, Huang H, Feng C, Chen W, Wu D. An integrated machine learning framework for developing and validating a diagnostic model of major depressive disorder based on interstitial cystitis-related genes. J Affect Disord 2024; 359:22-32. [PMID: 38754597 DOI: 10.1016/j.jad.2024.05.061] [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: 10/16/2023] [Revised: 03/24/2024] [Accepted: 05/12/2024] [Indexed: 05/18/2024]
Abstract
BACKGROUND Major depressive disorder (MDD) and interstitial cystitis (IC) are two highly debilitating conditions that often coexist with reciprocal effect, significantly exacerbating patients' suffering. However, the molecular underpinnings linking these disorders remain poorly understood. METHODS Transcriptomic data from GEO datasets including those of MDD and IC patients was systematically analyzed to develop and validate our model. Following removal of batch effect, differentially expressed genes (DEGs) between respective disease and control groups were identified. Shared DEGs of the conditions then underwent functional enrichment analyses. Additionally, immune infiltration analysis was quantified through ssGSEA. A diagnostic model for MDD was constructed by exploring 113 combinations of 12 machine learning algorithms with 10-fold cross-validation on the training sets following by external validation on test sets. Finally, the "Enrichr" platform was utilized to identify potential drugs for MDD. RESULTS Totally, 21 key genes closely associated with both MDD and IC were identified, predominantly involved in immune processes based on enrichment analyses. Immune infiltration analysis revealed distinct profiles of immune cell infiltration in MDD and IC compared to healthy controls. From these genes, a robust 11-gene (ABCD2, ATP8B4, TNNT1, AKR1C3, SLC26A8, S100A12, PTX3, FAM3B, ITGA2B, OLFM4, BCL7A) diagnostic signature was constructed, which exhibited superior performance over existing MDD diagnostic models both in training and testing cohorts. Additionally, epigallocatechin gallate and 10 other drugs emerged as potential targets for MDD. CONCLUSION Our work developed a diagnostic model for MDD employing a combination of bioinformatic techniques and machine learning methods, focusing on shared genes between MDD and IC.
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Affiliation(s)
- Bohong Chen
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061 Xi'an, Shaanxi, China
| | - Xinyue Sun
- Department of neurology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061 Xi'an, Shaanxi, China
| | - Haoxiang Huang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061 Xi'an, Shaanxi, China
| | - Cong Feng
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061 Xi'an, Shaanxi, China
| | - Wei Chen
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061 Xi'an, Shaanxi, China.
| | - Dapeng Wu
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061 Xi'an, Shaanxi, China.
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Usta Saglam NG, Duz MB, Salman Yilmaz S, Ozen M, Balcioglu I. Comparison of microRNA expression levels in patients with schizophrenia before and after electroconvulsive therapy. Psychiatr Genet 2024; 34:79-85. [PMID: 38842000 DOI: 10.1097/ypg.0000000000000371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
OBJECTIVE Exploring the role of microRNAs in the antipsychotic efficacy of electroconvulsive therapy (ECT) will contribute to understanding the underlying mechanism through which ECT exerts its therapeutic effects. The primary objective of this study was to identify microRNA alterations before and after ECT in patients with schizophrenia. METHODS We compared microarray-based microRNA profiles in peripheral blood from eight patients with schizophrenia before and after ECT and eight healthy controls. Then, we aimed to validate selected differentially expressed microRNAs in 30 patients with schizophrenia following a course of ECT, alongside 30 healthy controls by using quantitative reverse-transcription PCR. RESULTS Microarray-based expression profiling revealed alterations in 681 microRNAs when comparing pre- and post-ECT samples. Subsequent quantitative reverse-transcription PCR analysis of the selected microRNAs (miR-20a-5p and miR-598) did not reveal any statistical differences between pre- and post-ECT samples nor between pre-ECT samples and those of healthy controls. CONCLUSION As neuroepigenetic studies on ECT are still in their infancy, the results reported in this study are best interpreted as exploratory outcomes. Additional studies are required to explore the potential epigenetic mechanisms underlying the therapeutic efficacy of ECT.
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Affiliation(s)
| | - Mehmet Bugrahan Duz
- Department of Medical Genetics, Istanbul Memorial Hospital
- Department of Medical Genetics, Istanbul Arel University
| | - Seda Salman Yilmaz
- Department of Medical Genetics, Cerrahpaşa Faculty of Medicine, Istanbul University-Cerrahpaşa
- Department of Medical Services and Techniques Medical Monitoring Techniques Pr., Vocational School of Health Services, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Mustafa Ozen
- Department of Medical Genetics, Cerrahpaşa Faculty of Medicine, Istanbul University-Cerrahpaşa
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
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Cai L, Xu J, Liu J, Luo H, Yang R, Gui X, Wei L. miRNAs in treatment-resistant depression: a systematic review. Mol Biol Rep 2024; 51:638. [PMID: 38727891 DOI: 10.1007/s11033-024-09554-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 04/15/2024] [Indexed: 07/12/2024]
Abstract
BACKGROUND Treatment-resistant depression (TRD) is a condition in a subset of depressed patients characterized by resistance to antidepressant medications. The global prevalence of TRD has been steadily increasing, yet significant advancements in its diagnosis and treatment remain elusive despite extensive research efforts. The precise underlying pathogenic mechanisms are still not fully understood. Epigenetic mechanisms play a vital role in a wide range of diseases. In recent years, investigators have increasingly focused on the regulatory roles of miRNAs in the onset and progression of TRD. miRNAs are a class of noncoding RNA molecules that regulate the translation and degradation of their target mRNAs via interaction, making the exploration of their functions in TRD essential for elucidating their pathogenic mechanisms. METHODS AND RESULTS A systematic search was conducted in four databases, namely PubMed, Web of Science, Cochrane Library, and Embase, focusing on studies related to treatment-resistant depression and miRNAs. The search was performed using terms individually or in combination, such as "treatment-resistant depression," "medication-resistant depression," and "miRNAs." The selected articles were reviewed and collated, covering the time period from the inception of each database to the end of February 2024. We found that miRNAs play a crucial role in the pathophysiology of TRD through three main aspects: 1) involvement in miRNA-mediated inflammatory responses (including miR-155, miR-345-5p, miR-146a, and miR-146a-5p); 2) influence on 5-HT transport processes (including miR-674,miR-708, and miR-133a); and 3) regulation of synaptic plasticity (including has-miR-335-5p,has-miR- 1292-3p, let-7b, and let-7c). Investigating the differential expression and interactions of these miRNAs could contribute to a deeper understanding of the molecular mechanisms underlying TRD. CONCLUSIONS miRNAs might play a pivotal role in the pathogenesis of TRD. Gaining a deeper understanding of the roles and interrelations of miRNAs in TRD will contribute to elucidating disease pathogenesis and potentially provide avenues for the development of novel diagnostic and therapeutic strategies.
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Affiliation(s)
- Lun Cai
- Department of Neurology, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Guangxi University of Chinese Medicine, Nanning, 530023, People's Republic of China
| | - Jingwen Xu
- Department of Neurology, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Guangxi University of Chinese Medicine, Nanning, 530023, People's Republic of China
| | - Jie Liu
- Department of Neurology, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Guangxi University of Chinese Medicine, Nanning, 530023, People's Republic of China
| | - Huazheng Luo
- Department of Neurology, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Guangxi University of Chinese Medicine, Nanning, 530023, People's Republic of China
| | - Rongrong Yang
- Department of Neurology, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Guangxi University of Chinese Medicine, Nanning, 530023, People's Republic of China
| | - Xiongbin Gui
- Department of Surgery, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Guangxi University of Chinese Medicine, No. 89-9 Dongge Road, Nanning, 530000, Guangxi, People's Republic of China.
| | - Liping Wei
- Department of Surgery, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Guangxi University of Chinese Medicine, No. 89-9 Dongge Road, Nanning, 530000, Guangxi, People's Republic of China
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Moaddel R, Farmer CA, Yavi M, Kadriu B, Zhu M, Fan J, Chen Q, Lehrmann E, Fantoni G, De S, Mazucanti CH, Acevedo-Diaz EE, Yuan P, Gould TD, Park LT, Egan JM, Ferrucci L, Zarate CA. Cerebrospinal fluid exploratory proteomics and ketamine metabolite pharmacokinetics in human volunteers after ketamine infusion. iScience 2023; 26:108527. [PMID: 38162029 PMCID: PMC10755719 DOI: 10.1016/j.isci.2023.108527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/13/2023] [Accepted: 11/20/2023] [Indexed: 01/03/2024] Open
Abstract
Ketamine is a treatment for both refractory depression and chronic pain syndromes. In order to explore ketamine's potential mechanism of action and whether ketamine or its metabolites cross the blood brain barrier, we examined the pharmacokinetics of ketamine and its metabolites-norketamine (NK), dehydronorketamine (DHNK), and hydroxynorketamines (HNKs)-in cerebrospinal fluid (CSF) and plasma, as well as in an exploratory proteomic analysis in the CSF of nine healthy volunteers who received ketamine intravenously (0.5 mg/kg IV). We found that ketamine, NK, and (2R,6R;2S,6S)-HNK readily crossed the blood brain barrier. Additionally, 354 proteins were altered in the CSF in at least two consecutive timepoints (p < 0.01). Proteins in the classes of tyrosine kinases, cellular adhesion molecules, and growth factors, including insulin, were most affected, suggesting an interplay of altered neurotransmission, neuroplasticity, neurogenesis, synaptogenesis, and neural network functions following ketamine administration.
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Affiliation(s)
- Ruin Moaddel
- Biomedical Research Center, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Cristan A. Farmer
- Experimental Therapeutics and Pathophysiology Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Mani Yavi
- Experimental Therapeutics and Pathophysiology Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Bashkim Kadriu
- Experimental Therapeutics and Pathophysiology Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Min Zhu
- Biomedical Research Center, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jinshui Fan
- Biomedical Research Center, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Qinghua Chen
- Biomedical Research Center, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Elin Lehrmann
- Biomedical Research Center, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Giovanna Fantoni
- Biomedical Research Center, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Supriyo De
- Biomedical Research Center, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Caio H. Mazucanti
- Biomedical Research Center, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Elia E. Acevedo-Diaz
- Experimental Therapeutics and Pathophysiology Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Peixiong Yuan
- Experimental Therapeutics and Pathophysiology Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Todd D. Gould
- Departments of Psychiatry, Pharmacology, and Neurobiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Veterans Affairs Maryland Health Care System, Baltimore, MD 21201, USA
| | - Lawrence T. Park
- Experimental Therapeutics and Pathophysiology Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Josephine M. Egan
- Biomedical Research Center, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Luigi Ferrucci
- Biomedical Research Center, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Carlos A. Zarate
- Experimental Therapeutics and Pathophysiology Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
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Castro SCC, Bicca C, Bicca B, Araujo S, Viola TW. A systematic mini-review of epigenetic mechanisms associated with electroconvulsive therapy in humans. Front Hum Neurosci 2023; 17:1143332. [PMID: 36968786 PMCID: PMC10033581 DOI: 10.3389/fnhum.2023.1143332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/06/2023] [Indexed: 03/11/2023] Open
Abstract
IntroductionElectroconvulsive therapy (ECT) is one of the most effective strategies for treating resistant major depression. Although the mechanism of action is not fully understood and studies are limited, epigenetics is a promising area for the development of biomarkers associated with ECT treatment response.AimWe reviewed studies available in the literature that explored the epigenetics of ECT in peripheral samples from patients with major depressive disorder (MDD).MethodsA systematic review was performed following The PRISMA guidelines. The search was performed in seven electronic databases: Scopus, Web of Science, Medline, PsycINFO, Embase, Cochrane, and Cinahl.ResultsNine studies were included. Seven assessed DNA methylation and three investigated microRNAs (miR). Overall, most studies were exploratory, with small sample sizes, and we found high heterogeneity between the study’s design, ECT protocols, molecular biology methods, and epigenetic findings. Investigated candidates with some evidence of association with ECT treatment response were BDNF, S100A10, RNF213M, TNKS, FKBP5, miR-126, miR-106a, and miR-24.ConclusionThe present findings seem to support previous preclinical research, suggesting that epigenetic mechanisms play an important role in the molecular mechanism underlying ECT effects.
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Roy B, Dwivedi Y. An insight into the sprawling microverse of microRNAs in depression pathophysiology and treatment response. Neurosci Biobehav Rev 2023; 146:105040. [PMID: 36639069 PMCID: PMC9974865 DOI: 10.1016/j.neubiorev.2023.105040] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/06/2023] [Accepted: 01/08/2023] [Indexed: 01/12/2023]
Abstract
Stress-related neuropathologies are pivotal in developing major depressive disorder (MDD) and are often governed by gene-regulatory changes. Being a stress-responsive gene-regulatory factor, microRNAs (miRNAs) have tremendous biomolecular potential to define an altered gene-regulatory landscape in the MDD brain. MiRNAs' regulatory roles in the MDD brain are closely aligned with changes in plasticity, neurogenesis, and stress-axis functions. MiRNAs act at the epigenetic interface between stress-induced environmental stimuli and cellular pathologies by triggering large-scale gene expression changes in a highly coordinated fashion. The parallel changes in peripheral circulation may provide an excellent opportunity for miRNA to devise more effective treatment strategies and help explore their potential as biomarkers in treatment response. This review discusses the role of miRNAs as epigenetic modifiers in the etiopathogenesis of MDD. Concurrently, key research is highlighted to show the progress in using miRNAs as predictive biomarkers for treatment response.
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Affiliation(s)
- Bhaskar Roy
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yogesh Dwivedi
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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Amasi-Hartoonian N, Pariante CM, Cattaneo A, Sforzini L. Understanding treatment-resistant depression using "omics" techniques: A systematic review. J Affect Disord 2022; 318:423-455. [PMID: 36103934 DOI: 10.1016/j.jad.2022.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/26/2022] [Accepted: 09/07/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Treatment-resistant depression (TRD) results in huge healthcare costs and poor patient clinical outcomes. Most studies have adopted a "candidate mechanism" approach to investigate TRD pathogenesis, however this is made more challenging due to the complex and heterogeneous nature of this condition. High-throughput "omics" technologies can provide a more holistic view and further insight into the underlying mechanisms involved in TRD development, expanding knowledge beyond already-identified mechanisms. This systematic review assessed the information from studies that examined TRD using hypothesis-free omics techniques. METHODS PubMed, MEDLINE, Embase, APA PsycInfo, Scopus and Web of Science databases were searched on July 2022. 37 human studies met the eligibility criteria, totalling 17,518 TRD patients, 571,402 healthy controls and 62,279 non-TRD depressed patients (including antidepressant responders and untreated MDD patients). RESULTS Significant findings were reported that implicate the role in TRD of various molecules, including polymorphisms, genes, mRNAs and microRNAs. The pathways most commonly reported by the identified studies were involved in immune system and inflammation, neuroplasticity, calcium signalling and neurotransmitters. LIMITATIONS Small sample sizes, variability in defining TRD, and heterogeneity in study design and methodology. CONCLUSIONS These findings provide insight into TRD pathophysiology, proposing future research directions for novel drug targets and potential biomarkers for clinical staging and response to antidepressants (citalopram/escitalopram in particular) and electroconvulsive therapy (ECT). Further validation is warranted in large prospective studies using standardised TRD criteria. A multi-omics and systems biology strategy with a collaborative effort will likely deliver robust findings for translation into the clinic.
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Affiliation(s)
- Nare Amasi-Hartoonian
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, Department of Psychological Medicine, London, UK.
| | - Carmine Maria Pariante
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, Department of Psychological Medicine, London, UK; National Institute for Health and Research Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King's College London, UK
| | - Annamaria Cattaneo
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy; Laboratory of Biological Psychiatry, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Luca Sforzini
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, Department of Psychological Medicine, London, UK
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