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Hu Y, Oleshko S, Firmani S, Zhu Z, Cheng H, Ulmer M, Arnold M, Colomé-Tatché M, Tang J, Xhonneux S, Marsico A. Path-based reasoning for biomedical knowledge graphs with BioPathNet. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.17.599219. [PMID: 39149355 PMCID: PMC11326122 DOI: 10.1101/2024.06.17.599219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Understanding complex interactions in biomedical networks is crucial for advancements in biomedicine, but traditional link prediction (LP) methods are limited in capturing this complexity. Representation-based learning techniques improve prediction accuracy by mapping nodes to low-dimensional embeddings, yet they often struggle with interpretability and scalability. We present BioPathNet, a novel graph neural network framework based on the Neural Bellman-Ford Network (NBFNet), addressing these limitations through path-based reasoning for LP in biomedical knowledge graphs. Unlike node-embedding frameworks, BioPathNet learns representations between node pairs by considering all relations along paths, enhancing prediction accuracy and interpretability. This allows visualization of influential paths and facilitates biological validation. BioPathNet leverages a background regulatory graph (BRG) for enhanced message passing and uses stringent negative sampling to improve precision. In evaluations across various LP tasks, such as gene function annotation, drug-disease indication, synthetic lethality, and lncRNA-mRNA interaction prediction, BioPathNet consistently outperformed shallow node embedding methods, relational graph neural networks and task-specific state-of-the-art methods, demonstrating robust performance and versatility. Our study predicts novel drug indications for diseases like acute lymphoblastic leukemia (ALL) and Alzheimer's, validated by medical experts and clinical trials. We also identified new synthetic lethality gene pairs and regulatory interactions involving lncRNAs and target genes, confirmed through literature reviews. BioPathNet's interpretability will enable researchers to trace prediction paths and gain molecular insights, making it a valuable tool for drug discovery, personalized medicine and biology in general.
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Affiliation(s)
- Yue Hu
- Computational Health Center, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, Neuherberg, 85764, Bavaria, Germany
- School of Life Sciences, Technical University of Munich, Alte Akademie 8, Freising, 85354, Bavaria, Germany
| | - Svitlana Oleshko
- Computational Health Center, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, Neuherberg, 85764, Bavaria, Germany
- School of Computation, Information and Technology, Technical University of Munich, Arcisstrasse 21, Munich, 80333, Bavaria, Germany
| | - Samuele Firmani
- Computational Health Center, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, Neuherberg, 85764, Bavaria, Germany
| | - Zhaocheng Zhu
- Department, Mila - Québec AI Institute, 6666 St-Urbain, Montréal, QC H2S 3H1, Quebec, Canada
- Department, Université de Montréal, 2900, boul. Édouard-Montpetit, Montréal, QC H3T 1J4, Quebec, Canada
| | - Hui Cheng
- School of Computation, Information and Technology, Technical University of Munich, Arcisstrasse 21, Munich, 80333, Bavaria, Germany
| | - Maria Ulmer
- Computational Health Center, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, Neuherberg, 85764, Bavaria, Germany
- School of Life Sciences, Technical University of Munich, Alte Akademie 8, Freising, 85354, Bavaria, Germany
| | - Matthias Arnold
- Computational Health Center, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, Neuherberg, 85764, Bavaria, Germany
- Department of Psychiatry and Behavioural Sciences, Duke University, 905 W Main St., Durham, NC 27701, North Carolina, United States
| | - Maria Colomé-Tatché
- Computational Health Center, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, Neuherberg, 85764, Bavaria, Germany
- School of Life Sciences, Technical University of Munich, Alte Akademie 8, Freising, 85354, Bavaria, Germany
- Faculty of Biology, Ludwig-Maximilian University of Munich, Grosshaderner Str. 2, Planegg-Martinsried, 82152, Bavaria, Germany
| | - Jian Tang
- Department, Mila - Québec AI Institute, 6666 St-Urbain, Montréal, QC H2S 3H1, Quebec, Canada
- Department, CIFAR AI Chair, 661 University Ave, Toronto, ON M5G 1M1, Ontario, Canada
- Department, HEC Montréal, 3000 Chem. de la Côte-Sainte-Catherine, Montréal, QC H3T 2A7, Quebec, Canada
| | - Sophie Xhonneux
- Department, Mila - Québec AI Institute, 6666 St-Urbain, Montréal, QC H2S 3H1, Quebec, Canada
- Department, Université de Montréal, 2900, boul. Édouard-Montpetit, Montréal, QC H3T 1J4, Quebec, Canada
| | - Annalisa Marsico
- Computational Health Center, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, Neuherberg, 85764, Bavaria, Germany
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Weston F, Carter B, Powell N, Young AH, Moulton CD. Antidepressant treatment in inflammatory bowel disease: a systematic review and meta-analysis. Eur J Gastroenterol Hepatol 2024; 36:850-860. [PMID: 38625827 PMCID: PMC11136269 DOI: 10.1097/meg.0000000000002768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/28/2024] [Indexed: 04/18/2024]
Abstract
Around 25% of patients with inflammatory bowel disease (IBD) have depressive symptoms, yet antidepressants have been poorly studied in IBD. We systematically searched IBD studies testing antidepressants in four databases. Outcomes were depressive symptoms, anxiety, IBD disease activity, quality of life (QoL) and adverse events. For randomized controlled trials (RCTs), we performed random-effects meta-analysis of the standardized mean difference (SMD) in posttreatment scores between antidepressant and placebo groups. Risk of bias was assessed using the Cochrane Common Mental Disorders Depression Anxiety and Neurosis Group tool (clinical trials) and Newcastle-Ottawa scale (cohort studies). We included 11 studies ( n = 327): three placebo-controlled RCTs, two nonrandomized trials, and six other study types. In the pooled analysis, antidepressants improved depressive symptoms [SMD = -0.71 (95% confidence interval (CI) -1.32 to -0.10), P = 0.02, I2 = 51%] and QoL [SMD = 0.88 (95% CI 0.30-1.45), P = 0.003, I2 = 44%] more than placebo. Serotonin and noradrenaline reuptake inhibitors (SNRIs) alone improved depressive symptoms [SMD = -0.95 (95% CI -1.45 to -0.45, P < 0.001, I2 = 11%], anxiety [SMD = -0.92 (95% CI 1.72 to -0.13), P = 0.023, I2 = 65%] and QoL [SMD = 1.14 (95% CI 0.66-1.62), P < 0.001, I2 = 0%]. The three RCTs were of good quality. In conclusion, based on three small but good-quality studies, antidepressants improve depressive symptoms and QoL compared to placebo in IBD. SNRI antidepressants may also improve anxiety. A fully powered study of antidepressants in IBD is needed.
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Affiliation(s)
| | - Ben Carter
- Department of Biostatistics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London
| | - Nick Powell
- Department of Digestion, Metabolism and Reproduction, Imperial College London
| | - Allan H. Young
- Centre for Affective Disorders
- National Affective Disorders Service, South London and Maudsley NHS Foundation Trust
| | - Calum D. Moulton
- Centre for Affective Disorders
- Division of Psychiatry, Department of Brain Sciences, Imperial College
- Psychological Medicine Unit, St Mark’s Hospital, London, UK
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Jiang Q, Velu P, Sohouli MH, Ziamanesh F, Shojaie S, Fatahi S, Li Q. The effects of bupropion alone and combined with naltrexone on blood pressure and CRP concentration: A systematic review and meta-regression analysis of randomized controlled trials. Eur J Clin Invest 2024; 54:e14118. [PMID: 37924302 DOI: 10.1111/eci.14118] [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: 08/23/2023] [Revised: 10/03/2023] [Accepted: 10/18/2023] [Indexed: 11/06/2023]
Abstract
BACKGROUND Considering the conflicting effects of bupropion on parameters related to cardiovascular system including blood pressure and inflammation, in this meta-analysis study, we investigated the effects of this drug alone or in combination with naltrexone on systolic (SBP) and diastolic blood pressure (DBP) and C-reactive protein (CRP). METHODS Scopus, PubMed/Medline, Web of Science and Embase databases were searched using standard keywords to identify all controlled trials investigating effects of bupropion alone and combined with naltrexone on the BP and CRP. Pooled weighted mean difference and 95% confidence intervals (CIs) were achieved by random-effects model analysis for the best estimation of outcomes. RESULTS The pooled findings showed that that bupropion alone or in combination with naltrexone would significantly increase SBP (weighted mean difference (WMD): 1.34 mmHg, 95% CI: 0.38-2.29) and DBP (WMD: 0.93 mmHg, 95% CI 0.88-0.99) as well as decrease CRP (WMD: -0.89 mg/L, 95% CI -1.09 to -0.70). The findings of the subgroup also show the greater effect of bupropion on blood pressure (SBP and DBP) increase in a dose greater than 360 mg and a duration of intervention less equal to 26 weeks. In addition, the subgroup analysis showed that changes in SBP after receiving bupropion together with naltrexone were more compared to bupropion alone. CONCLUSIONS The addition of combination therapies such as bupropion and naltrexone can significantly improve CRP levels. However, its effect on blood pressure requires proper management of this drug.
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Affiliation(s)
- Qidong Jiang
- Intensive Care Unit, The Affiliated Hospital of Southwest Medical University, Luzhou City, China
| | - Periyannan Velu
- Department of Biochemistry and Biotechnology, Faculty of Science, Annamalai University, Chidambaram, Tamil Nadu, India
| | - Mohammad Hassan Sohouli
- Student Research Committee, Department of Clinical Nutrition and Dietetics, Faculty of Nutrition and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fateme Ziamanesh
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Shima Shojaie
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Somaye Fatahi
- Pediatric Gastroenterology, Hepatology, and Nutrition Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Qin Li
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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Arockiaraj N, Gupta R, Ahmad R, Halder S, Bhatia MS. Sertraline with desvenlafaxine and sertraline with mirtazapine as treatment initiation in MDD patients with moderate to severe depression and effect on inflammatory markers. Int J Psychiatry Clin Pract 2024; 28:9-16. [PMID: 38019131 DOI: 10.1080/13651501.2023.2287754] [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: 04/17/2023] [Accepted: 09/11/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND This study evaluated the effect of sertraline with desvenlafaxine and sertraline with mirtazapine on HAM-D score and inflammatory markers (IL-6 and TNF-α levels) in major depressive disorder. METHODS Patients (18-60 years) with MDD diagnosed by DSM-V criteria and HAM-D score 18 or more were included (n = 60). Group A patients (n = 30) received sertraline 50 mg/day and desvenlafaxine 50 mg/day. Group B patients (n = 30) received sertraline 50 mg/day and mirtazapine 30 mg/day. All patients were followed up for 8 weeks for the evaluation of clinical efficacy, safety, serum IL-6, and TNF-α levels. RESULTS Our study showed a comparatively similar and statistically significant (p < 0.05) reduction in HAM-D score in both groups in the 4th and 8th week of the treatment. Both drug combinations significantly (p < 0.05) decreased serum IL-6 and TNF-α after 8 weeks of treatment. CONCLUSION The present study suggests that the combination therapy (as treatment initiation) with sertraline and desvenlafaxine, and sertraline with mirtazapine is effective and well tolerated in MDD patients with moderate to severe depression, and their therapeutic efficacy is accompanied by decreased inflammatory markers (serum IL-6 and TNF-α).
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Affiliation(s)
- Norman Arockiaraj
- Department of Pharmacology, University College of Medical Sciences (University of Delhi) and Guru Teg Bahadur Hospital, New Delhi, India
| | - Rachna Gupta
- Department of Pharmacology, University College of Medical Sciences (University of Delhi) and Guru Teg Bahadur Hospital, New Delhi, India
| | - Rafat Ahmad
- Department of Biochemistry, University College of Medical Sciences (University of Delhi) and Guru Teg Bahadur Hospital, New Delhi, India
| | - Sumita Halder
- Department of Pharmacology, University College of Medical Sciences (University of Delhi) and Guru Teg Bahadur Hospital, New Delhi, India
| | - M S Bhatia
- Department of Psychiatry, University College of Medical Sciences (University of Delhi) and Guru Teg Bahadur Hospital, New Delhi, India
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Jaiswal A, Umesh S, Goyal N. Research on treatment-related aspects of depression from India in the preceding decade (2014-2023): An updated systematic review. Indian J Psychiatry 2023; 65:1112-1121. [PMID: 38249143 PMCID: PMC10795667 DOI: 10.4103/indianjpsychiatry.indianjpsychiatry_810_23] [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: 10/25/2023] [Revised: 11/07/2023] [Accepted: 11/11/2023] [Indexed: 01/23/2024] Open
Abstract
Background The National Mental Health Survey reports a prevalence of 2.7% for depressive disorders in India. The services for depression patients may be organized differently in India as compared to Western countries. It is important to consider studies conducted in India to determine effective interventions for depression catered specifically to the needs of the Indian population. We intended to systematically review the articles studying the usefulness of various treatment modalities in the management of depression in the Indian context. Materials and Methods We searched PubMed, Google Scholar, and ScienceDirect to identify studies published in peer-reviewed English language journals. All articles from India evaluating the clinical efficacy of anti-depressants, electro-convulsive therapy, repetitive transcranial magnetic stimulation, and psychological interventions for the management of depression were evaluated. Data were extracted using standard procedures. Results A total of 36 studies were included in the review. Out of those, 15 were studies on drug efficacy, five on neuro-modulation, nine on psycho-social interventions, four on adverse effects, and three on miscellaneous studies. Innovations were seen in the field of neuro-modulation and psycho-social intervention. Trials on drug efficacy and adverse drug reactions require larger sample sizes, more studies on newer agents, and more robust study designs. Conclusion More research is needed to understand the effectiveness and potential negative effects of depression treatments in India. Studies on ketamine have been inconclusive, and existing research on pharmacological agents is limited. Neuro-modulation studies show promise, but larger-scale studies are needed. Innovative psychological interventions tailored to the Indian population include community-based and digital technology-driven care.
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Affiliation(s)
- Alankrit Jaiswal
- Department of Psychiatry, Central Institute of Psychiatry, Ranchi, Jharkhand, India
| | - S Umesh
- Department of Psychiatry, Central Institute of Psychiatry, Ranchi, Jharkhand, India
| | - Nishant Goyal
- Centre for Child and Adolescent Psychiatry, Central Institute of Psychiatry, Ranchi, Jharkhand, India
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Colwell MJ, Tagomori H, Chapman S, Gillespie AL, Cowen PJ, Harmer CJ, Murphy SE. Pharmacological targeting of cognitive impairment in depression: recent developments and challenges in human clinical research. Transl Psychiatry 2022; 12:484. [PMID: 36396622 PMCID: PMC9671959 DOI: 10.1038/s41398-022-02249-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 11/18/2022] Open
Abstract
Impaired cognition is often overlooked in the clinical management of depression, despite its association with poor psychosocial functioning and reduced clinical engagement. There is an outstanding need for new treatments to address this unmet clinical need, highlighted by our consultations with individuals with lived experience of depression. Here we consider the evidence to support different pharmacological approaches for the treatment of impaired cognition in individuals with depression, including treatments that influence primary neurotransmission directly as well as novel targets such as neurosteroid modulation. We also consider potential methodological challenges in establishing a strong evidence base in this area, including the need to disentangle direct effects of treatment on cognition from more generalised symptomatic improvement and the identification of sensitive, reliable and objective measures of cognition.
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Affiliation(s)
- Michael J Colwell
- University Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, UK
- Oxford Health NHS Foundation Trust, Warneford Hospital, Oxford, UK
| | - Hosana Tagomori
- University Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, UK
- Oxford Health NHS Foundation Trust, Warneford Hospital, Oxford, UK
| | - Sarah Chapman
- University Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, UK
| | - Amy L Gillespie
- University Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, UK
- Oxford Health NHS Foundation Trust, Warneford Hospital, Oxford, UK
| | - Philip J Cowen
- University Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, UK
- Oxford Health NHS Foundation Trust, Warneford Hospital, Oxford, UK
| | - Catherine J Harmer
- University Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, UK
- Oxford Health NHS Foundation Trust, Warneford Hospital, Oxford, UK
| | - Susannah E Murphy
- University Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, UK.
- Oxford Health NHS Foundation Trust, Warneford Hospital, Oxford, UK.
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