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Tedesco S, Reyes K, Meiselman AI, Secondino JA, Tarnoverskyy N. Bipolar Disorder Predisposition in a Greek Male With β-Thalassemia Trait: External Factors, Including COVID-19, and Other Clinical Implications. Cureus 2024; 16:e59303. [PMID: 38813331 PMCID: PMC11136509 DOI: 10.7759/cureus.59303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2024] [Indexed: 05/31/2024] Open
Abstract
The present case study examines an adult male of Greek descent diagnosed with the β-thalassemia trait during adulthood. The individual had psychiatric symptoms after the sudden cessation of anabolic steroid injections, which had been utilized improperly for nearly a decade. Furthermore, the administration of an increased dosage of bupropion in conjunction with the absence of treatment for manic symptoms may have contributed to worsening his illness. The individual's contraction of COVID-19 and the subsequent discontinuation of steroid medication resulted in a notable psychosis despite the absence of any prior psychiatric conditions. Following initial therapy and hospitalization, which resulted in a stable discharge, the patient experienced a relapse due to later alterations in his medication. Consequently, this relapse necessitated a second admission to the hospital. The patient's therapeutic regimen consisted of a concurrent administration of lithium, antipsychotics, and an intense program of psychiatric counseling. This particular example highlights the distinctive connection between β-thalassemia and bipolar disorder, focusing on a Greek patient with the β-thalassemia trait and a genetic predisposition to mood disorders. The present study provides a comprehensive narrative of the patient's clinical progression, with particular emphasis on the impact of the β-thalassemia trait on his mental health trajectory. This observation highlights the limited availability of data about the interplay between hemoglobinopathies and mood disorders, hence emphasizing the need for further research in this niche intersection of genetics and psychiatry.
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Affiliation(s)
- Sarah Tedesco
- Psychiatry, Richmond University Medical Center, Staten Island, USA
| | | | - Alec I Meiselman
- Psychiatry, Richmond University Medical Center, Staten Island, USA
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van Beuningen N, Alkema S, Hijlkema N, Ulfhake B, Frias R, Ritskes-Hoitinga M, Alkema W. The 3Ranker: An AI-based Algorithm for Finding Non-animal Alternative Methods. Altern Lab Anim 2023; 51:376-386. [PMID: 37864460 DOI: 10.1177/02611929231210777] [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] [Indexed: 10/22/2023]
Abstract
The search for existing non-animal alternative methods for use in experiments is currently challenging because of the lack of both comprehensive structured databases and balanced keyword-based search strategies to mine unstructured textual databases. In this paper we describe 3Ranker, which is a fast, keyword-independent algorithm for finding non-animal alternative methods for use in biomedical research. The 3Ranker algorithm was created by using a machine learning approach, consisting of a Random Forest model built on a dataset of 35 million abstracts and constructed with weak supervision, followed by iterative model improvement with expert curated data. We found a satisfactory trade-off between sensitivity and specificity, with Area Under the Curve (AUC) values ranging from 0.85-0.95. Trials showed that the AI-based classifier was able to identify articles that describe potential alternatives to animal use, among the thousands of articles returned by generic PubMed queries on dermatitis and Parkinson's disease. Application of the classification models on time series data showed the earlier implementation and acceptance of Three Rs principles in the area of cosmetics and skin research, as compared to the area of neurodegenerative disease research. The 3Ranker algorithm is freely available at www.open3r.org; the future goal is to expand this framework to cover multiple research domains and to enable its broad use by researchers, policymakers, funders and ethical review boards, in order to promote the replacement of animal use in research wherever possible.
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Affiliation(s)
| | | | | | - Brun Ulfhake
- Department of Laboratory Medicine, Karolinska Institute, Solna, Sweden
| | - Rafael Frias
- Department of Comparative Medicine, Karolinska Institute, Solna, Sweden
| | - Merel Ritskes-Hoitinga
- Department Population Health Sciences - IRAS Toxicology, Utrecht University, Utrecht, The Netherlands
- Department Clinical Medicine, Aarhus University, Denmark
| | - Wynand Alkema
- TenWise BV, Leiden, The Netherlands
- Institute for Life Science and Technology, Centre for Biobased Economy, Hanze University of Applied Sciences, Groningen, The Netherlands
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Rasskazov D, Chadaeva I, Sharypova E, Zolotareva K, Khandaev B, Ponomarenko P, Podkolodnyy N, Tverdokhleb N, Vishnevsky O, Bogomolov A, Podkolodnaya O, Savinkova L, Zemlyanskaya E, Golubyatnikov V, Kolchanov N, Ponomarenko M. Plant_SNP_TATA_Z-Tester: A Web Service That Unequivocally Estimates the Impact of Proximal Promoter Mutations on Plant Gene Expression. Int J Mol Sci 2022; 23:ijms23158684. [PMID: 35955817 PMCID: PMC9369029 DOI: 10.3390/ijms23158684] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/01/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
Synthetic targeted optimization of plant promoters is becoming a part of progress in mainstream postgenomic agriculture along with hybridization of cultivated plants with wild congeners, as well as marker-assisted breeding. Therefore, here, for the first time, we compiled all the experimental data—on mutational effects in plant proximal promoters on gene expression—that we could find in PubMed. Some of these datasets cast doubt on both the existence and the uniqueness of the sought solution, which could unequivocally estimate effects of proximal promoter mutation on gene expression when plants are grown under various environmental conditions during their development. This means that the inverse problem under study is ill-posed. Furthermore, we found experimental data on in vitro interchangeability of plant and human TATA-binding proteins allowing the application of Tikhonov’s regularization, making this problem well-posed. Within these frameworks, we created our Web service Plant_SNP_TATA_Z-tester and then determined the limits of its applicability using those data that cast doubt on both the existence and the uniqueness of the sought solution. We confirmed that the effects (of proximal promoter mutations on gene expression) predicted by Plant_SNP_TATA_Z-tester correlate statistically significantly with all the experimental data under study. Lastly, we exemplified an application of Plant_SNP_TATA_Z-tester to agriculturally valuable mutations in plant promoters.
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Affiliation(s)
| | - Irina Chadaeva
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia
| | | | | | - Bato Khandaev
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia
| | | | - Nikolay Podkolodnyy
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia
- Institute of Computational Mathematics and Mathematical Geophysics, 630090 Novosibirsk, Russia
| | | | - Oleg Vishnevsky
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia
| | - Anton Bogomolov
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia
| | | | | | | | | | | | - Mikhail Ponomarenko
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia
- Correspondence: ; Tel.: +7-(383)-363-4963 (ext. 1311)
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Sharypova EB, Drachkova IA, Chadaeva IV, Ponomarenko MP, Savinkova LK. An experimental study of the effects of SNPs in the TATA boxes of the <i>GRIN1, ASCL3</i> and <i>NOS1</i> genes on interactions with the TATA-binding protein. Vavilovskii Zhurnal Genet Selektsii 2022; 26:227-233. [PMID: 35774364 PMCID: PMC9167820 DOI: 10.18699/vjgb-22-29] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/27/2021] [Accepted: 12/30/2021] [Indexed: 12/12/2022] Open
Abstract
The GRIN1, ASCL3, and NOS1 genes are associated with various phenotypes of neuropsychiatric disorders. For instance, these genes contribute to the development of schizophrenia, Alzheimer’s and Parkinson’s diseases, and epilepsy. These genes are also associated with various cancers. For example, ASCL3 is overexpressed in breast cancer, and NOS1, in ovarian cancer cell lines. Based on our findings and literature data, we had previously obtained results suggesting that the single-nucleotide polymorphisms (SNPs) that disrupt erythropoiesis are highly likely to be associated with cognitive and neuropsychiatric disorders in humans. In the present work, using SNP_TATA_Z-tester, we investigated the influence of unannotated SNPs in the TATA boxes of the promoters of the GRIN1, ASCL3, and NOS1 genes (which are involved in neuropsychiatric disorders and cancers) on the interaction of the TATA boxes with the TATA-binding protein (TBP). Double-stranded oligodeoxyribonucleotides identical to the TATA-containing promoter regions of the GRIN1, ASCL3, and NOS1 genes (reference and minor alleles) and recombinant human TBP were employed to study in vitro (by an electrophoretic mobility shift assay) kinetic characteristics of the formation of TBP–TATA complexes and their affinity. It was found, for example, that allele A of rs1402667001 in the GRIN1 promoter increases TBP–TATA affinity 1.4-fold, whereas allele C in the TATA box of the ASCL3 promoter decreases the affinity 1.4-fold. The lifetime of the complexes in both cases decreased by ~20 % due to changes in the rates of association and dissociation of the complexes (ka and kd, respectively). Our experimental results are consistent with the literature showing GRIN1 underexpression in schizophrenic disorders as well as an increased risk of cervical, bladder, and kidney cancers and lymphoma during ASCL3 underexpression. The effect of allele A of the –27G>A SNP (rs1195040887) in the NOS1 promoter is suggestive of an increased risk of ischemic damage to the brain in carriers. A comparison of experimental TBP–TATA affinity values (KD) of wild-type and minor alleles with predicted ones showed that the data correlate well (linear correlation coefficient r = 0.94, p < 0.01).
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Affiliation(s)
- E. B. Sharypova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - I. A. Drachkova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - I. V. Chadaeva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - M. P. Ponomarenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - L. K. Savinkova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
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Baranova AV, Leberfarb EY, Lebedev GS, Orlov YL. Medical genetics studies at the SBB-2019 and MGNGS-2019 conferences. BMC MEDICAL GENETICS 2020; 21:186. [PMID: 33092553 PMCID: PMC7579857 DOI: 10.1186/s12881-020-01109-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Ancha V. Baranova
- George Mason University, Fairfax, VA 22030 USA
- Research Centre for Medical Genetics, 115522 Moscow, Russia
| | | | - Georgy S. Lebedev
- The Digital Health Institute, I.M.Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
| | - Yuriy L. Orlov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- The Digital Health Institute, I.M.Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
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