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Iori S, D'Onofrio C, Laham-Karam N, Mushimiyimana I, Lucatello L, Montanucci L, Lopparelli RM, Bonsembiante F, Capolongo F, Pauletto M, Dacasto M, Giantin M. Generation and characterization of cytochrome P450 3A74 CRISPR/Cas9 knockout bovine foetal hepatocyte cell line (BFH12). Biochem Pharmacol 2024; 224:116231. [PMID: 38648904 DOI: 10.1016/j.bcp.2024.116231] [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: 12/05/2023] [Revised: 04/04/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
In human, the cytochrome P450 3A (CYP3A) subfamily of drug-metabolizing enzymes (DMEs) is responsible for a significant number of phase I reactions, with the CYP3A4 isoform superintending the hepatic and intestinal metabolism of diverse endobiotic and xenobiotic compounds. The CYP3A4-dependent bioactivation of chemicals may result in hepatotoxicity and trigger carcinogenesis. In cattle, four CYP3A genes (CYP3A74, CYP3A76, CYP3A28 and CYP3A24) have been identified. Despite cattle being daily exposed to xenobiotics (e.g., mycotoxins, food additives, drugs and pesticides), the existing knowledge about the contribution of CYP3A in bovine hepatic metabolism is still incomplete. Nowadays, CRISPR/Cas9 mediated knockout (KO) is a valuable method to generate in vivo and in vitro models for studying the metabolism of xenobiotics. In the present study, we successfully performed CRISPR/Cas9-mediated KO of bovine CYP3A74, human CYP3A4-like, in a bovine foetal hepatocyte cell line (BFH12). After clonal expansion and selection, CYP3A74 ablation was confirmed at the DNA, mRNA, and protein level. The subsequent characterization of the CYP3A74 KO clone highlighted significant transcriptomic changes (RNA-sequencing) associated with the regulation of cell cycle and proliferation, immune and inflammatory response, as well as metabolic processes. Overall, this study successfully developed a new CYP3A74 KO in vitro model by using CRISPR/Cas9 technology, which represents a novel resource for xenobiotic metabolism studies in cattle. Furthermore, the transcriptomic analysis suggests a key role of CYP3A74 in bovine hepatocyte cell cycle regulation and metabolic homeostasis.
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Affiliation(s)
- Silvia Iori
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy
| | - Caterina D'Onofrio
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy
| | - Nihay Laham-Karam
- University of Eastern Finland, A.I. Virtanen Institute for Molecular Sciences, Neulaniementie 2, 70211 Kuopio, Finland
| | - Isidore Mushimiyimana
- University of Eastern Finland, A.I. Virtanen Institute for Molecular Sciences, Neulaniementie 2, 70211 Kuopio, Finland
| | - Lorena Lucatello
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy
| | - Ludovica Montanucci
- Department of Neurology, University of Texas Health Science Center, 6431 Fannin Street, Houston, TX, OH 44106, USA
| | - Rosa Maria Lopparelli
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy
| | - Federico Bonsembiante
- Department of Animal Medicine, Production and Health, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy
| | - Francesca Capolongo
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy
| | - Marianna Pauletto
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy
| | - Mauro Dacasto
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy
| | - Mery Giantin
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy.
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Shnayder NA, Grechkina VV, Trefilova VV, Kissin MY, Narodova EA, Petrova MM, Al-Zamil M, Garganeeva NP, Nasyrova RF. Ethnic Aspects of Valproic Acid P-Oxidation. Biomedicines 2024; 12:1036. [PMID: 38790997 PMCID: PMC11117587 DOI: 10.3390/biomedicines12051036] [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: 04/10/2024] [Revised: 04/29/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
The safety of the use of psychotropic drugs, widely used in neurological and psychiatric practice, is an urgent problem in personalized medicine. This narrative review demonstrated the variability in allelic frequencies of low-functioning and non-functional single nucleotide variants in genes encoding key isoenzymes of valproic acid P-oxidation in the liver across different ethnic/racial groups. The sensitivity and specificity of pharmacogenetic testing panels for predicting the rate of metabolism of valproic acid by P-oxidation can be increased by prioritizing the inclusion of the most common risk allele characteristic of a particular population (country).
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Affiliation(s)
- Natalia A. Shnayder
- Institute of Personalized Psychiatry and Neurology, Shared Core Facilities, V.M. Bekhterev National Medical Research Centre for Psychiatry and Neurology, 192019 Saint Petersburg, Russia; (V.V.G.); (V.V.T.)
- Shared Core Facilities “Molecular and Cell Technologies”, V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia; (E.A.N.); (M.M.P.)
| | - Violetta V. Grechkina
- Institute of Personalized Psychiatry and Neurology, Shared Core Facilities, V.M. Bekhterev National Medical Research Centre for Psychiatry and Neurology, 192019 Saint Petersburg, Russia; (V.V.G.); (V.V.T.)
| | - Vera V. Trefilova
- Institute of Personalized Psychiatry and Neurology, Shared Core Facilities, V.M. Bekhterev National Medical Research Centre for Psychiatry and Neurology, 192019 Saint Petersburg, Russia; (V.V.G.); (V.V.T.)
| | - Mikhail Ya. Kissin
- Department of Psychiatry and Addiction, I.P. Pavlov First St. Petersburg State Medical University, 197022 Saint Petersburg, Russia;
| | - Ekaterina A. Narodova
- Shared Core Facilities “Molecular and Cell Technologies”, V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia; (E.A.N.); (M.M.P.)
| | - Marina M. Petrova
- Shared Core Facilities “Molecular and Cell Technologies”, V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia; (E.A.N.); (M.M.P.)
| | - Mustafa Al-Zamil
- Department of Physiotherapy, Faculty of Continuing Medical Education, Peoples’ Friendship University of Russia, 117198 Moscow, Russia;
| | - Natalia P. Garganeeva
- Department of General Medical Practice and Outpatient Therapy, Siberian State Medical University, 634050 Tomsk, Russia;
| | - Regina F. Nasyrova
- Institute of Personalized Psychiatry and Neurology, Shared Core Facilities, V.M. Bekhterev National Medical Research Centre for Psychiatry and Neurology, 192019 Saint Petersburg, Russia; (V.V.G.); (V.V.T.)
- International Centre for Education and Research in Neuropsychiatry, Samara State Medical University, 443016 Samara, Russia
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Yang L, Yu S, Qin X, Li Z. Analysis of inter-individual variability of antitussive effect of Farfarae Flos and its fecal metabolites based on gut microbiota. J Pharm Biomed Anal 2022; 217:114836. [DOI: 10.1016/j.jpba.2022.114836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 04/27/2022] [Accepted: 05/13/2022] [Indexed: 10/18/2022]
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Hypermethylation-Mediated Silencing of CIDEA, MAL and PCDH17 Tumour Suppressor Genes in Canine DLBCL: From Multi-Omics Analyses to Mechanistic Studies. Int J Mol Sci 2022; 23:ijms23074021. [PMID: 35409379 PMCID: PMC9000013 DOI: 10.3390/ijms23074021] [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: 03/10/2022] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 11/23/2022] Open
Abstract
Gene expression is controlled by epigenetic deregulation, a hallmark of cancer. The DNA methylome of canine diffuse large B-cell lymphoma (cDLBCL), the most frequent malignancy of B-lymphocytes in dog, has recently been investigated, suggesting that aberrant hypermethylation of CpG loci is associated with gene silencing. Here, we used a multi-omics approach (DNA methylome, transcriptome and copy number variations) combined with functional in vitro assays, to identify putative tumour suppressor genes subjected to DNA methylation in cDLBCL. Using four cDLBCL primary cell cultures and CLBL-1 cells, we found that CiDEA, MAL and PCDH17, which were significantly suppressed in DLBCL samples, were hypermethylated and also responsive (at the DNA, mRNA and protein level) to pharmacological unmasking with hypomethylating drugs and histone deacetylase inhibitors. The regulatory mechanism underneath the methylation-dependent inhibition of those target genes expression was then investigated through luciferase and in vitro methylation assays. In the most responsive CpG-rich regions, an in silico analysis allowed the prediction of putative transcription factor binding sites influenced by DNA methylation. Interestingly, regulatory elements for AP2, MZF1, NF-kB, PAX5 and SP1 were commonly identified in all three genes. This study provides a foundation for characterisation and experimental validation of novel epigenetically-dysregulated pathways in cDLBCL.
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Othman H, da Rocha JEB, Hazelhurst S. Single Nucleotide Polymorphism Induces Divergent Dynamic Patterns in CYP3A5: A Microsecond Scale Biomolecular Simulation of Variants Identified in Sub-Saharan African Populations. Int J Mol Sci 2021; 22:7786. [PMID: 34360551 PMCID: PMC8346100 DOI: 10.3390/ijms22157786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/19/2021] [Accepted: 06/23/2021] [Indexed: 11/17/2022] Open
Abstract
Pharmacogenomics aims to reveal variants associated with drug response phenotypes. Genes whose roles involve the absorption, distribution, metabolism, and excretion of drugs, are highly polymorphic between populations. High coverage whole genome sequencing showed that a large proportion of the variants for these genes are rare in African populations. This study investigated the impact of such variants on protein structure to assess their functional importance. We used genetic data of CYP3A5 from 458 individuals from sub-Saharan Africa to conduct a structural bioinformatics analysis. Five missense variants were modeled and microsecond scale molecular dynamics simulations were conducted for each, as well as for the CYP3A5 wildtype and the Y53C variant, which has a known deleterious impact on enzyme activity. The binding of ritonavir and artemether to CYP3A5 variant structures was also evaluated. Our results showed different conformational characteristics between all the variants. No significant structural changes were noticed. However, the genetic variability seemed to act on the plasticity of the protein. The impact on drug binding might be drug dependant. We concluded that rare variants hold relevance in determining the pharmacogenomics properties of populations. This could have a significant impact on precision medicine applications in sub-Saharan Africa.
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Affiliation(s)
- Houcemeddine Othman
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2001, South Africa; (J.E.B.d.R.); (S.H.)
| | - Jorge E. B. da Rocha
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2001, South Africa; (J.E.B.d.R.); (S.H.)
- Division of Human Genetics, National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2001, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2001, South Africa; (J.E.B.d.R.); (S.H.)
- School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg 2001, South Africa
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Talebi M, Talebi M, Farkhondeh T, Samarghandian S. Molecular mechanism-based therapeutic properties of honey. Biomed Pharmacother 2020; 130:110590. [DOI: 10.1016/j.biopha.2020.110590] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 07/24/2020] [Accepted: 07/28/2020] [Indexed: 12/14/2022] Open
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Nassi A, Quintieri L, Merlanti R, Pezzato F, Capolongo F, Pauletto M, Dacasto M, Giantin M. Midazolam oxidation in cattle liver microsomes: The role of cytochrome P450 3A. J Vet Pharmacol Ther 2020; 43:608-613. [PMID: 32893906 DOI: 10.1111/jvp.12906] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/24/2020] [Accepted: 08/13/2020] [Indexed: 11/30/2022]
Abstract
In humans, the cytochrome P450 3A (CYP3A) subfamily is involved in midazolam (MDZ) biotransformation into 1'- and 4-hydroxy metabolites, and the former serves as a probe for CYP3A catalytic activity. In veterinary species is still crucial to identify enzyme- and species-specific CYP substrates; thus, the aim of this study was to characterize MDZ oxidation in cattle liver. A HPLC-UV method was used to measure 1'- and 4-hydroxy MDZ (1'- and 4-OHMDZ, respectively) formation in cattle liver microsomes and assess the role of CYP3A by an immunoinhibition study. Moreover, MDZ hydroxylation was evaluated in 300 cattle liver samples and results were correlated with testosterone hydroxylation. Formation of both metabolites conformed to a single-enzyme Michaelis-Menten kinetics. Values of Vmax and Km were 0.67 nmol/min/mg protein and 6.16 μM for 4-OHMDZ, and 0.06 nmol/min/mg protein and 10.08 μM for 1'-OHMDZ. An anti-rat CYP3A1 polyclonal antibody inhibited up to 50% and 94% 1'- and 4-OHMDZ formation, respectively. MDZ oxidation in liver microsomes was poorly correlated with testosterone hydroxylation. In conclusion, cattle metabolized MDZ to 1'-OHMDZ and 4-OHMDZ. The immunoinhibition results indicated a major contribution of CYP3As to 4-OHMDZ formation and the involvement of other CYPs in 1'-OHMDZ production, paving the way for further investigations.
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Affiliation(s)
- Alberto Nassi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy
| | - Luigi Quintieri
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy
| | - Roberta Merlanti
- Department of Comparative Biomedicine and Food Science, University of Padua, Padua, Italy
| | - Francesca Pezzato
- Department of Comparative Biomedicine and Food Science, University of Padua, Padua, Italy
| | - Francesca Capolongo
- Department of Comparative Biomedicine and Food Science, University of Padua, Padua, Italy
| | - Marianna Pauletto
- Department of Comparative Biomedicine and Food Science, University of Padua, Padua, Italy
| | - Mauro Dacasto
- Department of Comparative Biomedicine and Food Science, University of Padua, Padua, Italy
| | - Mery Giantin
- Department of Comparative Biomedicine and Food Science, University of Padua, Padua, Italy
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Pauletto M, Tolosi R, Dacasto M, Giantin M. Missense single nucleotide variants affecting CYP3A catalytic activity are present in Limousine cattle. ITALIAN JOURNAL OF ANIMAL SCIENCE 2020. [DOI: 10.1080/1828051x.2020.1808100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Marianna Pauletto
- Dipartimento di Biomedicina Comparata e Alimentazione, Area di Farmacologia e Tossicologia Veterinaria, Università di Padova, Padova, Italy
| | - Roberta Tolosi
- Dipartimento di Biomedicina Comparata e Alimentazione, Area di Farmacologia e Tossicologia Veterinaria, Università di Padova, Padova, Italy
| | - Mauro Dacasto
- Dipartimento di Biomedicina Comparata e Alimentazione, Area di Farmacologia e Tossicologia Veterinaria, Università di Padova, Padova, Italy
| | - Mery Giantin
- Dipartimento di Biomedicina Comparata e Alimentazione, Area di Farmacologia e Tossicologia Veterinaria, Università di Padova, Padova, Italy
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