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Martins D, Abbasi M, Egas C, Arrais JP. Detecting outliers in case-control cohorts for improving deep learning networks on Schizophrenia prediction. J Integr Bioinform 2024; 21:jib-2023-0042. [PMID: 39004922 PMCID: PMC11377398 DOI: 10.1515/jib-2023-0042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 06/06/2024] [Indexed: 07/16/2024] Open
Abstract
This study delves into the intricate genetic and clinical aspects of Schizophrenia, a complex mental disorder with uncertain etiology. Deep Learning (DL) holds promise for analyzing large genomic datasets to uncover new risk factors. However, based on reports of non-negligible misdiagnosis rates for SCZ, case-control cohorts may contain outlying genetic profiles, hindering compelling performances of classification models. The research employed a case-control dataset sourced from the Swedish populace. A gene-annotation-based DL architecture was developed and employed in two stages. First, the model was trained on the entire dataset to highlight differences between cases and controls. Then, samples likely to be misclassified were excluded, and the model was retrained on the refined dataset for performance evaluation. The results indicate that SCZ prevalence and misdiagnosis rates can affect case-control cohorts, potentially compromising future studies reliant on such datasets. However, by detecting and filtering outliers, the study demonstrates the feasibility of adapting DL methodologies to large-scale biological problems, producing results more aligned with existing heritability estimates for SCZ. This approach not only advances the comprehension of the genetic background of SCZ but also opens doors for adapting DL techniques in complex research for precision medicine in mental health.
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Affiliation(s)
- Daniel Martins
- Centre for Informatics and Systems, Department of Informatics Engineering, University of Coimbra, Coimbra, Portugal
- Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Maryam Abbasi
- Polytechnic Institute of Coimbra, Applied Research Institute, Coimbra, Portugal
- Research Centre for Natural Resources Environment and Society, Polytechnic Institute of Coimbra, Coimbra, Portugal
| | - Conceição Egas
- Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
- Biocant - Transfer Technology Association, Cantanhede, Portugal
| | - Joel P Arrais
- Centre for Informatics and Systems, Department of Informatics Engineering, University of Coimbra, Coimbra, Portugal
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Peleg LC, Rabinovitch D, Lavie Y, Rabbie DM, Horowitz I, Fruchter E, Gruenwald I. Post-SSRI Sexual Dysfunction (PSSD): Biological Plausibility, Symptoms, Diagnosis, and Presumed Risk Factors. Sex Med Rev 2021; 10:91-98. [PMID: 34627736 DOI: 10.1016/j.sxmr.2021.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 06/24/2021] [Accepted: 07/06/2021] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Post-SSRI sexual-dysfunction (PSSD) is an iatrogenicsyndrome, the underlying neurobiological mechanisms of which areunclear. Symptom onset follows cessation of serotonergicantidepressants i.e. Selective Serotonin and Norepinephrine ReuptakeInhibitors (SSRI's, SNRI's), and Tricyclic antidepressants (TCA's). PSSDsymptoms include genital anesthesia, erectile dysfunction andorgasmic/ejaculatory anhedonia, and should be differentiated fromdepression-related sexual-dysfunction. Recently, accumulated data of numerous case-reports suggest additional non-sexual symptoms including, anhedonia, apathy, and blunted affect. PSSD gained official recognition after the European medical agency concluded that PSSD is a medical condition that persists after discontinuation of SSRI's and SNRI's. OBJECTIVE To review possible underlying neurobiological mechanisms ofthis syndrome, update information on the pathophysiology, present a listof potential risk-factors and discuss potential management options forPSSD. METHODS Extensive literature review on the main symptom-patterns ofthis disorder was undertaken using PubMed. It includes introductoryexplications of relevant neurobiology with the objective of generatinghypothesis. RESULTS Precipitating factors for PSSD include previous exposure to certain drugs, genetic predisposition, psychological stress or chemical stressful reaction to antidepressants along pre-existing medical conditions affecting neuroplasticity. Different theories have been proposed to explain the pathophysiology of PSSD: epigenetic gene expression, dopamine-serotonin interactions, serotonin neurotoxicity and hormonal changes. The diagnosis of PSSD is by excluding all other etiologies of sexual-dysfunction. Treatment is challenging, and many strategies have been suggested without definitive outcomes. We offerthe contours of a future neurobiological research agenda, and propose several underlying mechanisms for the various symptoms of PSSD which could be the foundation for a future treatment algorithm. CONCLUSION There is a need for well-designed neurobiological research in this domain, as well as in the prevalence, pathophysiology, and treatment of PSSD. Practitioners should be alert to the distinctive features of PSSD. Misdiagnosing this syndrome might lead to harmful Sexual Medicine Reviews. Peleg LC, Rabinovitch D, Lavie Y, et al. Post-SSRI Sexual Dysfunction (PSSD): Biological Plausibility, Symptoms, Diagnosis, and Presumed Risk Factors. Sex Med Rev 2021;XX:XXX-XXX.
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Affiliation(s)
| | | | | | - Deya M Rabbie
- Ahram Canadian University, Neuropharmacology, 6th of October City, Egypt
| | - Itai Horowitz
- Rambam Healthcare Campus, Psychiatry Department, Haifa, Israel
| | | | - Ilan Gruenwald
- Rambam Healthcare Campus, Neuro-Urology Unit, Haifa, Israel.
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Gasnier M, Ellul P, Plaze M, Ahad PA. A New Look on an Old Issue: Comprehensive Review of Neurotransmitter Studies in Cerebrospinal Fluid of Patients with Schizophrenia and Antipsychotic Effect on Monoamine's Metabolism. CLINICAL PSYCHOPHARMACOLOGY AND NEUROSCIENCE 2021; 19:395-410. [PMID: 34294610 PMCID: PMC8316661 DOI: 10.9758/cpn.2021.19.3.395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/30/2020] [Accepted: 12/28/2020] [Indexed: 11/18/2022]
Abstract
Neurotransmitters metabolism has a key role in the physiopathology of schizophrenia as demonstrated by studies measuring monoamine metabolites in patient’s cerebrospinal fluid (CSF) since the beginning of the antipsychotic use. This comprehensive review aims to understand the anomalies of CSF monoamines in schizophrenia and their correlation with clinical and paraclinical features. We also review the influence of antipsychotic treatment on CSF monoamines and discuss the connection with metabolic and inflammatory processes. Studies comparing CSF homovanillic acid (HVA) levels between patients and controls are miscellaneous, due to the heterogeneity of samples studies. However, low HVA is associated with more positive symptoms and a poorer outcome and negatively correlated with brain ventricle size. Based on humans and animals’ studies, antipsychotic treatments increase HVA during the first week of administration and decrease progressively over the time with a fall-off after withdrawal. 5‐hydroxyindolacetic acetic acid levels do not seem to be different in the patient’s CSF compared to controls. Considering metabolic co-factors of neurotrans-mitters synthesis, there is evidence supporting an increase of kynurenic acid in the CSF of patients with schizophrenia. Few studies explore folate metabolism in CSF. Literature also emphasizes the relationship between folate metabolism, inflammation and monoamine’s metabolism. Those results suggest that the CSF monoamines could be correlated with schizophrenia symptoms and treatment outcome. However, further studies, exploring the role of CSF monoamines as biomarkers of disease severity and response to treatment are needed. They should assess the antipsychotic prescription, inflammatory markers and folate metabolism as potential confounding factors.
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Affiliation(s)
- Matthieu Gasnier
- Department of Psychiatry, MOODS Team, Paris Saclay University, Bicetre Hospital, AP-HP, Paris, France
| | - Pierre Ellul
- Department of Child and Adolescent Psychiatry, Robert Debré Hospital, AP-HP, Paris, France
| | - Marion Plaze
- Department of Psychiatry, Service Hospitalo Universitaire, Sainte Anne Hospital, Paris, France
| | - Pierre Abdel Ahad
- Department of Psychiatry, Service Hospitalo Universitaire, Sainte Anne Hospital, Paris, France
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Forster J, Duis J, Butler MG. Pharmacodynamic Gene Testing in Prader-Willi Syndrome. Front Genet 2020; 11:579609. [PMID: 33329716 PMCID: PMC7715001 DOI: 10.3389/fgene.2020.579609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/20/2020] [Indexed: 01/14/2023] Open
Abstract
Prader-Willi syndrome (PWS) is a rare genetic disorder with a complex neurobehavioral phenotype associated with considerable psychiatric co-morbidity. This clinical case series, for the first time, describes the distribution and frequency of polymorphisms of pharmacodynamic genes (serotonin transporter, serotonin 2A and 2C receptors, catechol-o-methyltransferase, adrenergic receptor 2A, methylene tetrahydrofolate reductase, and human leucocytic antigens) across the two major molecular classes of PWS in a cohort of 33 referred patients who met medical criteria for testing. When results were pooled across PWS genetic subtypes, genotypic and allelic frequencies did not differ from normative population data. However, when the genetic subtype of PWS was examined, there were differences observed across all genes tested that may affect response to psychotropic medication. Due to small sample size, no statistical significance was found, but results suggest that pharmacodynamic gene testing should be considered before initiating pharmacotherapy in PWS. Larger scale studies are warranted.
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Affiliation(s)
| | - Jessica Duis
- Section of Genetics and Inherited Metabolic Disease, Department of Pediatrics, Children's Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Merlin G Butler
- Division of Research and Genetics, Department of Psychiatry and Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, KS, United States
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Irimie AI, Braicu C, Pasca S, Magdo L, Gulei D, Cojocneanu R, Ciocan C, Olariu A, Coza O, Berindan-Neagoe I. Role of Key Micronutrients from Nutrigenetic and Nutrigenomic Perspectives in Cancer Prevention. ACTA ACUST UNITED AC 2019; 55:medicina55060283. [PMID: 31216637 PMCID: PMC6630934 DOI: 10.3390/medicina55060283] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 05/28/2019] [Accepted: 06/13/2019] [Indexed: 02/06/2023]
Abstract
Regarding cancer as a genetic multi-factorial disease, a number of aspects need to be investigated and analyzed in terms of cancer's predisposition, development and prognosis. One of these multi-dimensional factors, which has gained increased attention in the oncological field due to its unelucidated role in risk assessment for cancer, is diet. Moreover, as studies advance, a clearer connection between diet and the molecular alteration of patients is becoming identifiable and quantifiable, thereby replacing the old general view associating specific phenotypical changes with the differential intake of nutrients. Respectively, there are two major fields concentrated on the interrelation between genome and diet: nutrigenetics and nutrigenomics. Nutrigenetics studies the effects of nutrition at the gene level, whereas nutrigenomics studies the effect of nutrients on genome and transcriptome patterns. By precisely evaluating the interaction between the genomic profile of patients and their nutrient intake, it is possible to envision a concept of personalized medicine encompassing nutrition and health care. The list of nutrients that could have an inhibitory effect on cancer development is quite extensive, with evidence in the scientific literature. The administration of these nutrients showed significant results in vitro and in vivo regarding cancer inhibition, although more studies regarding administration in effective doses in actual patients need to be done.
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Affiliation(s)
- Alexandra Iulia Irimie
- Department of Prosthetic Dentistry and Dental Materials, Division Dental Propaedeutics, Aesthetic, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Cornelia Braicu
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Sergiu Pasca
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Lorand Magdo
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Diana Gulei
- MEDFUTURE-Research Center for Advanced Medicine, University of Medicine and Pharmacy Iuliu Hatieganu, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Roxana Cojocneanu
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Cristina Ciocan
- MEDFUTURE-Research Center for Advanced Medicine, University of Medicine and Pharmacy Iuliu Hatieganu, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Andrei Olariu
- Nordlogic Software, 10-12, Rene Descartes Street 400486 Cluj-Napoca, Romania.
| | - Ovidiu Coza
- Department of Radiotherapy with High Energies and Brachytherapy, Oncology Institute "Prof. Dr. Ion Chiricuta", Street Republicii, No. 34-36, 400015 Cluj-Napoca, Romania.
- Department of Radiotherapy and Medical Oncology, "Iuliu Hatieganu" University of Medicine and Pharmacy, Street Louis Pasteur, No. 4, 400349 Cluj-Napoca, Romania.
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
- MEDFUTURE-Research Center for Advanced Medicine, University of Medicine and Pharmacy Iuliu Hatieganu, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
- Department of Functional Genomics and Experimental Pathology, "Prof. Dr. Ion Chiricuta" The Oncology Institute, 34-36 Republicii Street, 400015 Cluj-Napoca, Romania.
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Parra M, Stahl S, Hellmann H. Vitamin B₆ and Its Role in Cell Metabolism and Physiology. Cells 2018; 7:cells7070084. [PMID: 30037155 PMCID: PMC6071262 DOI: 10.3390/cells7070084] [Citation(s) in RCA: 207] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 12/11/2022] Open
Abstract
Vitamin B6 is one of the most central molecules in cells of living organisms. It is a critical co-factor for a diverse range of biochemical reactions that regulate basic cellular metabolism, which impact overall physiology. In the last several years, major progress has been accomplished on various aspects of vitamin B6 biology. Consequently, this review goes beyond the classical role of vitamin B6 as a cofactor to highlight new structural and regulatory information that further defines how the vitamin is synthesized and controlled in the cell. We also discuss broader applications of the vitamin related to human health, pathogen resistance, and abiotic stress tolerance. Overall, the information assembled shall provide helpful insight on top of what is currently known about the vitamin, along with addressing currently open questions in the field to highlight possible approaches vitamin B6 research may take in the future.
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Affiliation(s)
- Marcelina Parra
- Hellmann Lab, School of Biological Sciences, College of Liberal Arts and Sciences, Washington State University, Pullman, 99164-6234 WA, USA.
| | - Seth Stahl
- Hellmann Lab, School of Biological Sciences, College of Liberal Arts and Sciences, Washington State University, Pullman, 99164-6234 WA, USA.
| | - Hanjo Hellmann
- Hellmann Lab, School of Biological Sciences, College of Liberal Arts and Sciences, Washington State University, Pullman, 99164-6234 WA, USA.
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