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Jelovac M, Kotur N, Ristivojevic B, Pavlovic D, Spasovski V, Damjanov N, Pavlovic S, Zukic B. Can Pharmacogenetic Variants in TPMT, MTHFR and SLCO1B1 Genes Be Used as Potential Markers of Outcome Prediction in Systemic Sclerosis Patients? Int J Mol Sci 2023; 24:ijms24108538. [PMID: 37239884 DOI: 10.3390/ijms24108538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Systemic sclerosis (SSc) is a rare connective tissue disorder with highest morbidity and mortality among rheumatologic diseases. Disease progression is highly heterogeneous between patients, implying a strong need for individualization of therapy. Four pharmacogenetic variants, namely TPMT rs1800460, TPMT rs1142345, MTHFR rs1801133 and SLCO1B1 rs4149056 were tested for association with severe disease outcomes in 102 patients with SSc from Serbia treated either with immunosuppressants azathioprine (AZA) and methotrexate (MTX) or with other types of medications. Genotyping was performed using PCR-RFLP and direct Sanger sequencing. R software was used for statistical analysis and development of polygenic risk score (PRS) model. Association was found between MTHFR rs1801133 and higher risk for elevated systolic pressure in all patients except those prescribed with MTX, and higher risk for kidney insufficiency in patients prescribed with other types of drugs. In patients treated with MTX, variant SLCO1B1 rs4149056 was protective against kidney insufficiency. For patients receiving MTX a trend was shown for having a higher PRS rank and elevated systolic pressure. Our results open a door wide for more extensive research on pharmacogenomics markers in patients with SSc. Altogether, pharmacogenomics markers could predict the outcome of patients with SSc and help in prevention of adverse drug reactions.
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Affiliation(s)
- Marina Jelovac
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia
| | - Nikola Kotur
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia
| | - Bojan Ristivojevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia
| | - Djordje Pavlovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia
| | - Vesna Spasovski
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia
| | - Nemanja Damjanov
- Institute of Rheumatology, 11000 Belgrade, Serbia
- Medical School, University of Belgrade, 11000 Belgrade, Serbia
| | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia
| | - Branka Zukic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia
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2
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van Schaik RH, Manolopoulos VG, Daly AK, Niemi M, Zukic B, Patrinos GP, Primorac D, Swen JJ, Ingelman-Sundberg M, Morris T, Molden E, Müller D, Pavlovic S, Russmann S, Ansari M, Henricks LM, den Broek WV, Florindi F, Bozina N, Akin D, Christrup L, Llerena A, Sipeky C, Stankovic S. The Sixth European Society of Pharmacogenomics and Personalised Therapy Congress (Belgrade, 8-9 November 2022). Pharmacogenomics 2023; 24:243-246. [PMID: 37014361 DOI: 10.2217/pgs-2023-0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
Abstract
On 8-9 November 2022, the European Society of Pharmacogenomics and Personalised Therapy organized its sixth biennial congress, in Belgrade, Serbia (congress website: www.sspt.rs). The congress aimed to address the current status and future perspectives of pharmacogenomics, share latest knowledge in the field of precision medicine and showcase the implementation of clinical applications in pharmacogenomics/pharmacogenetics. The 2 day congress consisted of 17 lectures given by key-opinion leaders and included a poster session plus discussions. The meeting was a great success by generating an informal environment and enabling the exchange of information between 162 participants from 16 different countries.
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Affiliation(s)
- Ron Hn van Schaik
- Department of Clinical Chemistry, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | | | - Ann K Daly
- Translational & Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Mikko Niemi
- Department of Clinical Pharmacology, University of Helsinki, Helsinki, Finland
| | - Branka Zukic
- Institute of Molecular Genetics & Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - George P Patrinos
- Laboratory of Pharmacogenomics & Individualised Therapy, University of Patras, Department of Pharmacy, Patras, Greece
- Department of Genetics & Genomics, United Arab Emirates University, College of Medicine & Health Sciences, Al Ain, Abu Dhabi, UAE
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
| | | | - Jesse J Swen
- Department of Clinical Pharmacology & Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Tiffany Morris
- Precision Health & Pharmacogenomics, Illumina, Cambridge, UK
| | - Espen Molden
- Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Daniel Müller
- Department of Psychiatry, University of Toronto, Toronto, Canada
| | - Sonja Pavlovic
- Institute of Molecular Genetics & Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Stefan Russmann
- ETH Zürich, Hirslanden Hospitals & drugsafety.ch, Switzerland
| | - Marc Ansari
- Cansearch Research Platform for Pediatric Oncology & Hematology, Faculty of Medicine, Department of Pediatrics, Gynecology & Obstetrics, University of Geneva, Switzerland
| | - Linda M Henricks
- Division of Pediatric Oncology & Hematology, Department of Women, Child & Adolescent, University Geneva Hospitals, Geneva, Switzerland
| | - Wout van den Broek
- Department of Clinical Chemistry, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Nada Bozina
- Department of Pharmacology, University of Zagreb, Zagreb, Croatia
| | - Demet Akin
- Department of Pharmacology, Bahcesehir University, Istanbul, Türkiye
| | - Lona Christrup
- Department of Drug Design & Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Adrian Llerena
- INUBE Biosanitary University Research Institute, University of Extramedura, Spain
| | - Cilla Sipeky
- Department of Translational Medicine, UCB Biopharma, Waterloo, Belgium
| | - Sanja Stankovic
- Department of Medical Biochemistry, University Clinical Center of Serbia, Belgrade, Serbia
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3
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Gasic V, Karan-Djurasevic T, Pavlovic D, Zukic B, Pavlovic S, Tosic N. Diagnostic and Therapeutic Implications of Long Non-Coding RNAs in Leukemia. Life (Basel) 2022; 12:1770. [PMID: 36362925 PMCID: PMC9695865 DOI: 10.3390/life12111770] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/27/2022] [Accepted: 10/29/2022] [Indexed: 08/26/2023] Open
Abstract
Leukemia is a heterogenous group of hematological malignancies categorized in four main types (acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), chronic myeloid leukemia (CML) and chronic lymphocytic leukemia (CLL). Several cytogenetic and molecular markers have become a part of routine analysis for leukemia patients. These markers have been used in diagnosis, risk-stratification and targeted therapy application. Recent studies have indicated that numerous regulatory RNAs, such as long non-coding RNAs (lncRNAs), have a role in tumor initiation and progression. When it comes to leukemia, data for lncRNA involvement in its etiology, progression, diagnosis, treatment and prognosis is limited. The aim of this review is to summarize research data on lncRNAs in different types of leukemia, on their expression pattern, their role in leukemic transformation and disease progression. The usefulness of this information in the clinical setting, i.e., for diagnostic and prognostic purposes, will be emphasized. Finally, how particular lncRNAs could be used as potential targets for the application of targeted therapy will be considered.
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Affiliation(s)
- Vladimir Gasic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia
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4
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Zecevic M, Kotur N, Ristivojevic B, Gasic V, Skodric-Trifunovic V, Stjepanovic M, Stevanovic G, Lavadinovic L, Zukic B, Pavlovic S, Stankovic B. Genome-Wide Association Study of COVID-19 Outcomes Reveals Novel Host Genetic Risk Loci in the Serbian Population. Front Genet 2022; 13:911010. [PMID: 35910207 PMCID: PMC9329799 DOI: 10.3389/fgene.2022.911010] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/21/2022] [Indexed: 11/16/2022] Open
Abstract
Host genetics, an important contributor to the COVID-19 clinical susceptibility and severity, currently is the focus of multiple genome-wide association studies (GWAS) in populations affected by the pandemic. This is the first study from Serbia that performed a GWAS of COVID-19 outcomes to identify genetic risk markers of disease severity. A group of 128 hospitalized COVID-19 patients from the Serbian population was enrolled in the study. We conducted a GWAS comparing (1) patients with pneumonia (n = 80) against patients without pneumonia (n = 48), and (2) severe (n = 34) against mild disease (n = 48) patients, using a genotyping array followed by imputation of missing genotypes. We have detected a significant signal associated with COVID-19 related pneumonia at locus 13q21.33, with a peak residing upstream of the gene KLHL1 (p = 1.91 × 10−8). Our study also replicated a previously reported COVID-19 risk locus at 3p21.31, identifying lead variants in SACM1L and LZTFL1 genes suggestively associated with pneumonia (p = 7.54 × 10−6) and severe COVID-19 (p = 6.88 × 10−7), respectively. Suggestive association with COVID-19 pneumonia has also been observed at chromosomes 5p15.33 (IRX, NDUFS6, MRPL36, p = 2.81 × 10−6), 5q11.2 (ESM1, p = 6.59 × 10−6), and 9p23 (TYRP1, LURAP1L, p = 8.69 × 10−6). The genes located in or near the risk loci are expressed in neural or lung tissues, and have been previously associated with respiratory diseases such as asthma and COVID-19 or reported as differentially expressed in COVID-19 gene expression profiling studies. Our results revealed novel risk loci for pneumonia and severe COVID-19 disease which could contribute to a better understanding of the COVID-19 host genetics in different populations.
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Affiliation(s)
- Marko Zecevic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
- Seven Bridges, Boston, MA, United States
| | - Nikola Kotur
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Bojan Ristivojevic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Vladimir Gasic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Vesna Skodric-Trifunovic
- Clinic of Pulmonology, Clinical Centre of Serbia, Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Mihailo Stjepanovic
- Clinic of Pulmonology, Clinical Centre of Serbia, Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Goran Stevanovic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
- Clinic for Infectious and Tropical Diseases, Clinical Centre of Serbia, Belgrade, Serbia
| | - Lidija Lavadinovic
- Clinic for Infectious and Tropical Diseases, Clinical Centre of Serbia, Belgrade, Serbia
| | - Branka Zukic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Sonja Pavlovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Biljana Stankovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
- *Correspondence: Biljana Stankovic,
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5
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Drljaca T, Zukic B, Kovacevic V, Gemovic B, Klaassen-Ljubicic K, Perovic V, Lazarevic M, Pavlovic S, Veljkovic N. The first insight into the genetic structure of the population of modern Serbia. Sci Rep 2021; 11:13995. [PMID: 34234178 PMCID: PMC8263702 DOI: 10.1038/s41598-021-93129-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 06/18/2021] [Indexed: 11/16/2022] Open
Abstract
The complete understanding of the genomic contribution to complex traits, diseases, and response to treatments, as well as genomic medicine application to the well-being of all humans will be achieved through the global variome that encompasses fine-scale genetic diversity. Despite significant efforts in recent years, uneven representation still characterizes genomic resources and among the underrepresented European populations are the Western Balkans including the Serbian population. Our research addresses this gap and presents the first ever targeted sequencing dataset of variants in clinically relevant genes. By measuring population differentiation and applying the Principal Component and Admixture analysis we demonstrated that the Serbian population differs little from other European populations, yet we identified several novel and more frequent variants that appear as its unique genetic determinants. We explored thoroughly the functional impact of frequent variants and its correlation with the health burden of the population of Serbia based on a sample of 144 individuals. Our variants catalogue improves the understanding of genetics of modern Serbia, contributes to research on ancestry, and aids in improvements of well-being and health equity. In addition, this resource may also be applicable in neighboring regions and valuable in worldwide functional analyses of genetic variants in individuals of European descent.
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Affiliation(s)
- Tamara Drljaca
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Branka Zukic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | | | - Branislava Gemovic
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | | | - Vladimir Perovic
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | | | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia.
| | - Nevena Veljkovic
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia.
- Heliant Ltd, Belgrade, Serbia.
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6
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Kotur N, Skakic A, Klaassen K, Gasic V, Zukic B, Skodric-Trifunovic V, Stjepanovic M, Zivkovic Z, Ostojic O, Stevanovic G, Lavadinovic L, Pavlovic S, Stankovic B. Association of Vitamin D, Zinc and Selenium Related Genetic Variants With COVID-19 Disease Severity. Front Nutr 2021; 8:689419. [PMID: 34150833 PMCID: PMC8211741 DOI: 10.3389/fnut.2021.689419] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/11/2021] [Indexed: 12/13/2022] Open
Abstract
Background: COVID-19 pandemic has proved to be an unrelenting health threat for more than a year now. The emerging amount of data indicates that vitamin D, zinc and selenium could be important for clinical presentation of COVID-19. Here, we investigated association of genetic variants related to the altered level and bioavailability of vitamin D, zinc and selenium with clinical severity of COVID-19. Methods: We analyzed variants in genes significant for the status of vitamin D (DHCR7/NADSYN1 rs12785878, GC rs2282679, CYP2R1 rs10741657, and VDR rs2228570), zinc (PPCDC rs2120019) and selenium (DMGDH rs17823744) in 120 Serbian adult and pediatric COVID-19 patients using allelic discrimination. Furthermore, we carried out comparative population genetic analysis among European and other worldwide populations to investigate variation in allelic frequencies of selected variants. Results: Study showed that DHCR7/NADSYN rs12785878 and CYP2R1 rs10741657 variants were associated with severe COVID-19 in adults (p = 0.03, p = 0.017, respectively); carriers of DHCR7/NADSYN TG+GG and CYP2R1 GG genotypes had 0.21 and 5.9 the odds for developing severe disease, OR 0.21 (0.05-0.9) and OR 5.9 (1.4-25.2), respectively. There were no associations between selected genetic variants and disease severity in pediatric patients. Comparative population genetic analysis revealed that Serbian population had the lowest frequency of CYP2R1 rs10741657 G allele compared to other non-Finish Europeans (0.58 compared to 0.69 and 0.66 in Spanish and Italian population, respectively), suggesting that other populations should also investigate the relationship of CYP2R1 variant and the COVID-19 disease course. Conclusion: The results of the study indicated that vitamin D related genetic variants were implicated in severe COVID-19 in adults. This could direct prevention strategies based on population specific nutrigenetic profiles.
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Affiliation(s)
- Nikola Kotur
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Anita Skakic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Kristel Klaassen
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Vladimir Gasic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Branka Zukic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Vesna Skodric-Trifunovic
- Clinic of Pulmonology, Clinical Center of Serbia, Belgrade, Serbia
- Medical Faculty, University of Belgrade, Belgrade, Serbia
| | - Mihailo Stjepanovic
- Clinic of Pulmonology, Clinical Center of Serbia, Belgrade, Serbia
- Medical Faculty, University of Belgrade, Belgrade, Serbia
| | - Zorica Zivkovic
- Children's Hospital for Lung Diseases and Tbc, MC Dr Dragisa Misovic, Belgrade, Serbia
- Faculty of Pharmacy Novi Sad, Business Academy, Novi Sad, Serbia
| | - Olivera Ostojic
- Children's Hospital for Lung Diseases and Tbc, MC Dr Dragisa Misovic, Belgrade, Serbia
| | - Goran Stevanovic
- Medical Faculty, University of Belgrade, Belgrade, Serbia
- Clinic for Infectious and Tropical Diseases, Clinical Centre of Serbia, Belgrade, Serbia
| | - Lidija Lavadinovic
- Clinic for Infectious and Tropical Diseases, Clinical Centre of Serbia, Belgrade, Serbia
| | - Sonja Pavlovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Biljana Stankovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
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7
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Mihaljevic M, Franic D, Soldatovic I, Lukic I, Petrovic SA, Mirjanic T, Stankovic B, Zukic B, Zeljic K, Gasic V, Novakovic I, Pavlovic S, Adzic M, Maric NP. The FKBP5 genotype and childhood trauma effects on FKBP5 DNA methylation in patients with psychosis, their unaffected siblings, and healthy controls. Psychoneuroendocrinology 2021; 128:105205. [PMID: 33933892 DOI: 10.1016/j.psyneuen.2021.105205] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/19/2021] [Accepted: 03/19/2021] [Indexed: 01/08/2023]
Abstract
Hypothalamic-pituitary-adrenal (HPA) axis activity mediates the relationship between childhood trauma (CT) and psychosis. The FKBP5 gene, one of the key regulators of HPA axis activity after stress exposure, has been found associated with psychosis. Allele-specific and CT related FKBP5 demethylation in intron 7 was revealed in different psychiatric disorders. However, no studies have investigated FKBP5 methylation in subjects with different genetic liability for psychosis. A total of 144 participants were included in the study: 48 patients with psychotic disorders, 50 unaffected siblings, and 46 healthy controls. CT was assessed by Childhood Trauma Questionnaire. The FKBP5 rs1360780 was genotyped and FKBP5 methylation analyses were performed using bisulfite conversion followed by Sanger sequencing at three CpG sites in intron 7. Mixed linear model was used to assess group differences depending on rs1360780 T allele and CT. Results showed a significant T allele-dependent decrease of FKBP5 methylation in patients compared to unaffected siblings and controls. Effect of interaction between T allele and CT exposure on FKBP5 demethylation was found in controls. No effect of both risk factors (T allele and CT) on FKBP5 methylation level was found in unaffected siblings. We confirmed previous evidence of the association between the FKBP5 rs1360780 T allele, CT, and decreased FKBP5 methylation in intron 7. Allele-specific FKBP5 demethylation found in patients could shed a light on altered HPA axis activity in a subgroup of patients related to stress-induced psychosis. FKBP5 methylation and potential protective mechanisms in unaffected siblings after trauma exposure require further investigation.
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Affiliation(s)
- Marina Mihaljevic
- Clinic for Psychiatry, Clinical Centre of Serbia, Pasterova 2, Belgrade 11000, Serbia; Faculty of Medicine, University of Belgrade, Dr Subotica 8, Belgrade 11000, Serbia.
| | - Dusanka Franic
- Department of Molecular Biology and Endocrinology, "VINČA" Institute of Nuclear Sciences - National Institute of thе Republic of Serbia, University of Belgrade, Belgrade 1100, Serbia
| | - Ivan Soldatovic
- Faculty of Medicine, University of Belgrade, Dr Subotica 8, Belgrade 11000, Serbia; Institute for Biostatistics, Medical Informatics and Research in Medicine, Faculty of Medicine, University of Belgrade, Dr Subotica, Belgrade 11000, Serbia
| | - Iva Lukic
- Department of Molecular Biology and Endocrinology, "VINČA" Institute of Nuclear Sciences - National Institute of thе Republic of Serbia, University of Belgrade, Belgrade 1100, Serbia
| | - Sanja Andric Petrovic
- Clinic for Psychiatry, Clinical Centre of Serbia, Pasterova 2, Belgrade 11000, Serbia
| | - Tijana Mirjanic
- Special Hospital for Psychiatric Disorders Kovin, Cara Lazara 253, Kovin 26220, Serbia
| | - Biljana Stankovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade 11010, Serbia
| | - Branka Zukic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade 11010, Serbia
| | - Katarina Zeljic
- Genetics & Evolution Department, Faculty of Biology, University of Belgrade, Studentski trg 3, Belgrade 11000, Serbia
| | - Vladimir Gasic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade 11010, Serbia
| | - Ivana Novakovic
- Faculty of Medicine, University of Belgrade, Dr Subotica 8, Belgrade 11000, Serbia; Institute of Human Genetics, Faculty of Medicine, University of Belgrade, Visegradska 26, Belgrade 11000, Serbia
| | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade 11010, Serbia
| | - Miroslav Adzic
- Department of Molecular Biology and Endocrinology, "VINČA" Institute of Nuclear Sciences - National Institute of thе Republic of Serbia, University of Belgrade, Belgrade 1100, Serbia
| | - Nadja P Maric
- Clinic for Psychiatry, Clinical Centre of Serbia, Pasterova 2, Belgrade 11000, Serbia; Faculty of Medicine, University of Belgrade, Dr Subotica 8, Belgrade 11000, Serbia
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8
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Klaassen K, Stankovic B, Zukic B, Kotur N, Gasic V, Pavlovic S, Stojiljkovic M. Functional prediction and comparative population analysis of variants in genes for proteases and innate immunity related to SARS-CoV-2 infection. Infect Genet Evol 2020; 84:104498. [PMID: 32771700 PMCID: PMC7410821 DOI: 10.1016/j.meegid.2020.104498] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/27/2020] [Accepted: 08/05/2020] [Indexed: 01/12/2023]
Abstract
New coronavirus SARS-CoV-2 is capable to infect humans and cause a novel disease COVID-19. Aiming to understand a host genetic component of COVID-19, we focused on variants in genes encoding proteases and genes involved in innate immunity that could be important for susceptibility and resistance to SARS-CoV-2 infection. Analysis of sequence data of coding regions of FURIN, PLG, PRSS1, TMPRSS11a, MBL2 and OAS1 genes in 143 unrelated individuals from Serbian population identified 22 variants with potential functional effect. In silico analyses (PolyPhen-2, SIFT, MutPred2 and Swiss-Pdb Viewer) predicted that 10 variants could impact the structure and/or function of proteins. These protein-altering variants (p.Gly146Ser in FURIN; p.Arg261His and p.Ala494Val in PLG; p.Asn54Lys in PRSS1; p.Arg52Cys, p.Gly54Asp and p.Gly57Glu in MBL2; p.Arg47Gln, p.Ile99Val and p.Arg130His in OAS1) may have predictive value for inter-individual differences in the response to the SARS-CoV-2 infection. Next, we performed comparative population analysis for the same variants using extracted data from the 1000 Genomes project. Population genetic variability was assessed using delta MAF and Fst statistics. Our study pointed to 7 variants in PLG, TMPRSS11a, MBL2 and OAS1 genes with noticeable divergence in allelic frequencies between populations worldwide. Three of them, all in MBL2 gene, were predicted to be damaging, making them the most promising population-specific markers related to SARS-CoV-2 infection. Comparing allelic frequencies between Serbian and other populations, we found that the highest level of genetic divergence related to selected loci was observed with African, followed by East Asian, Central and South American and South Asian populations. When compared with European populations, the highest divergence was observed with Italian population. In conclusion, we identified 4 variants in genes encoding proteases (FURIN, PLG and PRSS1) and 6 in genes involved in the innate immunity (MBL2 and OAS1) that might be relevant for the host response to SARS-CoV-2 infection.
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Affiliation(s)
- Kristel Klaassen
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Biljana Stankovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Branka Zukic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Nikola Kotur
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Vladimir Gasic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Sonja Pavlovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Maja Stojiljkovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia.
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9
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Stankovic B, Dragasevic S, Klaassen K, Kotur N, Srzentic Drazilov S, Zukic B, Sokic Milutinovic A, Milovanovic T, Lukic S, Popovic D, Pavlovic S, Nikcevic G. Exploring inflammatory and apoptotic signatures in distinct Crohn's disease phenotypes: Way towards molecular stratification of patients and targeted therapy. Pathol Res Pract 2020; 216:152945. [PMID: 32279918 DOI: 10.1016/j.prp.2020.152945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 03/21/2020] [Accepted: 03/23/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND Crohn's disease (CD) is chronic inflammatory bowel disease with different phenotypic characteristics influencing disease prognosis and therapeutic strategies. The aim of this pilot study was to analyze selected inflammatory and apoptotic markers in non-inflamed and inflamed samples of ileal mucosa of non-stricturing/non-penetrating (NS/NP) and stricturing (S) CD mucosal phenotypes in order to characterize their distinct profiles. METHODS From twenty CD patients (9 NS/NP, 11 S) paired non-inflamed and inflamed ileal biopsies were collected and used for analysis of cytokine (TNF and IL6) and apoptotic (Bcl2, Bax, Fas and FasL) genes' expression levels by real-time PCR, while NFκB transcriptional potency was assessed by electromobility gel shift assay. RESULTS Our results demonstrated significant upregulation of TNF and IL6 in inflamed area of both NS/NP (p = 0.03, p = 0.01) and S phenotypes (p = 0.04, p = 0.04), respectively. However, TNF increase was more prominent in NS/NP compared to S inflamed mucosa (p = 0.02). Also, level of proapoptotic Bax was significantly higher in NS/NP compared to S inflamed mucosa (p = 0.01). Opposing transcription potency of NFκB has been detected between two phenotypes: being decreased in NS/NP (p = 0.07) and increased in S (p = 0.1) inflamed compared to non-inflamed mucosa, demonstrating trend towards statistical significance. CONCLUSIONS We found that two distinct CD phenotypes have specific molecular signatures. Obtained results could direct improvement of current and development of new therapeutic strategies based on more specific molecular stratification of CD patients.
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Affiliation(s)
- Biljana Stankovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia.
| | - Sanja Dragasevic
- Clinic for Gastroenterology and Hepatology, Clinical Center of Serbia, Koste Todorovica 2, 11000 Belgrade, Serbia; School of Medicine, University of Belgrade, Dr Subotica 8, 11000 Belgrade, Serbia.
| | - Kristel Klaassen
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia.
| | - Nikola Kotur
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia.
| | - Sanja Srzentic Drazilov
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia.
| | - Branka Zukic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia.
| | - Aleksandra Sokic Milutinovic
- Clinic for Gastroenterology and Hepatology, Clinical Center of Serbia, Koste Todorovica 2, 11000 Belgrade, Serbia; School of Medicine, University of Belgrade, Dr Subotica 8, 11000 Belgrade, Serbia.
| | - Tamara Milovanovic
- Clinic for Gastroenterology and Hepatology, Clinical Center of Serbia, Koste Todorovica 2, 11000 Belgrade, Serbia; School of Medicine, University of Belgrade, Dr Subotica 8, 11000 Belgrade, Serbia.
| | - Snezana Lukic
- Clinic for Gastroenterology and Hepatology, Clinical Center of Serbia, Koste Todorovica 2, 11000 Belgrade, Serbia; School of Medicine, University of Belgrade, Dr Subotica 8, 11000 Belgrade, Serbia.
| | - Dragan Popovic
- Clinic for Gastroenterology and Hepatology, Clinical Center of Serbia, Koste Todorovica 2, 11000 Belgrade, Serbia; School of Medicine, University of Belgrade, Dr Subotica 8, 11000 Belgrade, Serbia.
| | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia.
| | - Gordana Nikcevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia.
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Pavlovic S, Kotur N, Stankovic B, Gasic V, Lucafo M, Decorti G, Zukic B. Clinical Application of Thiopurine Pharmacogenomics in Pediatrics. Curr Drug Metab 2020; 21:53-62. [PMID: 32124692 DOI: 10.2174/1389200221666200303113456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/06/2020] [Accepted: 02/20/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Thiopurine drugs are used for the treatment of pediatric diseases. Inter-individual differences in the metabolism of these drugs greatly influence the risk of thiopurine induced toxicity and therapy failure. These differences are the consequence of genomic, epigenomic and transcriptomic variability among patients. Pharmacogenomics aims to individualize therapy according to the specific genetic signature of a patient. Treatment protocols based on thiopurine drugs have already been improved by applying pharmacogenomics in pediatric clinical practice. OBJECTIVE The aim of this review was to summarize the application of thiopurine pharmacogenomics in pediatric patients suffering from acute leukemias, different types of autoimmune and inflammatory diseases, as well as in posttransplant care. METHODS We searched PubMed/Medline database to identify thiopurine pharmacogenomic markers clinically relevant in pediatric diseases. RESULTS TPMT and NUDT15 pharmacogenomic testing is done in pediatric care, contributing to the reduction of thiopurine induced toxicity. Data on numerous novel potential pharmacogenomic markers relevant for optimization of thiopurine treatment are still controversial (ITPA, ABCC4, NT5C2, PRPS1, GSTM1, FTO gene variants). Majority of evidences regarding thiopurine pharmacogenomics in pediatrics have been acquired by studying acute lymphoblastic leukemia and inflammatory bowel disease. For other pediatric diseases, namely acute myeloid leukemia, non-Hodgkin lymphoma, juvenile idiopathic arthritis, atopic dermatitis, juvenile autoimmune hepatitis and renal allograft transplantation, data are still scarce. CONCLUSION Thiopurine pharmacogenomics has shown to be one of the best examples of successful application of pharmacogenomics in pediatrics.
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Affiliation(s)
- Sonja Pavlovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Nikola Kotur
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Biljana Stankovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Vladimir Gasic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Marianna Lucafo
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Giuliana Decorti
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy.,Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Branka Zukic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
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11
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Milosevic G, Kotur N, Lazic J, Krstovski N, Stankovic B, Zukic B, Janic D, Jurisic V, Pavlovic S, Dokmanovic L. Influence of variants in folate metabolism genes on 6-mercaptopurine induced toxicity during treatment for childhood acute lymphocytic leukemia. J BUON 2019; 24:2075-2083. [PMID: 31786878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
PURPOSE To analyze influence of variants in TYMS, MTHFR, SLC19A1 and DHFR genes on 6-mercaptopurine (MP) induced toxicity during maintenance phase of treatment for childhood acute lymphocytic leukemia (ALL). METHODS One-hundred twenty-seven children with ALL that received maintenance therapy were involved in this study. All patients were treated according to Berlin-Frankfurt-Muenster (BFM) based protocols. Myelotoxicity and hepatotoxicity were evaluated using surrogate markers (median 6-MP dose, number of leukopenic episodes and levels of bilirubin and transaminases on each visit). RESULTS Higher number of leukopenic episodes, as a surrogate marker of 6-MP myelotoxicity, was found in carriers of TYMS 3R3R and 3R4R genotypes (p=0.067) as well as in TYMS 3R6bp+ (28bp VNTR, 6bp indel) haplotype carriers (p=0.015). Carriers of DHFR CATAG (-680, -675, -556, -464, -317) haplotype were also found to have higher number of leukopenic episodes (p=0.070). SLC19A1 c.80A allele (p=0.079) and TYMS 2R6bp+ (5'UTR VNTR, 6bp indel) haplotype carriers (p=0.078) had fewer leukopenic episodes. No difference in genotype frequencies between the control group of volunteered blood donors and childhood ALL patients was found. CONCLUSIONS Variants in TYMS, SLC19A1 and DHFR genes are potential biomarkers of myelotoxicity and could be used for 6-MP therapy individualization in maintenance phase of childhood ALL treatment, alongside with well-established TPMT variants.
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Jordovic J, Simonovic-Babic J, Gasic V, Kotur N, Zukic B, Pavlovic S, Lazarevic I, Karalic D, Katanic N, Nikolic N, Urosevic A, Nestorov J, Delic D, Bojovic K. IL-28B genotypes as predictors of long-term outcome in patients with hepatitis C-related severe liver injury. J Infect Dev Ctries 2019; 13:526-535. [PMID: 32058988 DOI: 10.3855/jidc.11351] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 03/03/2019] [Indexed: 10/31/2022] Open
Abstract
INTRODUCTION Patients with severe fibrosis or cirrhosis are at high risk for liver-related complications, even after successful antiviral treatment and/or regression of fibrosis. These are the first published results concerning the role of IL-28B genotypes as predictors of the durability of sustained virological response (SVR) and long-term outcome, in patients with baseline severe fibrosis and cirrhosis caused by hepatitis C (HCV) infection. METHODOLOGY Genetic testing for three different single nucleotide polymorphisms (SNP) near the IL28B gene, rs12979860, rs12980275 and rs8099917, was performed in 42 patients with HCV-related advanced fibrosis and cirrhosis, who achieved SVR after successful interferon-based treatment. Baseline clinical and laboratory parameters were analysed, as well as IL28B genotype association with late virological relapse, fibrosis progression and clinical outcomes. RESULTS The most prevalent genotypes in all three tested SNP positions were: CCrs12979860 genotype in 69% of patients, GTrs8099917 in 78.6% and GGrs12980275 in 47.6% of patients. The presence of IL28B CCrs12979860 genotype was identified as a negative predictor of late virological relapse. Further analysis did not confirm the association of other IL28B genotypes with the progression of fibrosis and clinical outcomes. CONCLUSIONS Varying long-term prognosis in patients with HCV-related severe fibrosis and cirrhosis is due to multiple interactions between host genetic factors, virus and environment. These are first published results demonstrating the significance of IL28B CCrs12979860 genotype as a negative predictor of late virological relapse. A further investigation concerning genetic factors is necessary to identify patients under risk for late relapse, complications and unfavorable outcomes, so that they can be reevaluated and offered new treatment options.
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Affiliation(s)
- Jelena Jordovic
- Clinic for Infectious and Tropical Diseases, Clinical Centre of Serbia, Belgrade, Serbia.
| | | | - Vladimir Gasic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia.
| | - Nikola Kotur
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade.
| | - Branka Zukic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade.
| | - Sonja Pavlovic
- Medical Faculty, University of Belgrade, Belgrade, Serbia.
| | | | | | - Natasa Katanic
- Clinic for Infectious and Tropical Diseases, Clinical Centre of Serbia, Belgrade, Serbia.
| | - Natasa Nikolic
- Clinic for Infectious and Tropical Diseases, Clinical Centre of Serbia, Belgrade, Serbia.
| | - Aleksandar Urosevic
- Clinic for Infectious and Tropical Diseases, Clinical Centre of Serbia, Belgrade, Serbia.
| | | | - Dragan Delic
- Clinic for Infectious and Tropical Diseases, Clinical Centre of Serbia, Belgrade, Serbia.
| | - Ksenija Bojovic
- Clinic for Infectious and Tropical Diseases, Clinical Centre of Serbia, Belgrade, Serbia.
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Pavlovic S, Kotur N, Stankovic B, Zukic B, Gasic V, Dokmanovic L. Pharmacogenomic and Pharmacotranscriptomic Profiling of Childhood Acute Lymphoblastic Leukemia: Paving the Way to Personalized Treatment. Genes (Basel) 2019; 10:E191. [PMID: 30832275 PMCID: PMC6471971 DOI: 10.3390/genes10030191] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 02/23/2019] [Accepted: 02/25/2019] [Indexed: 02/07/2023] Open
Abstract
Personalized medicine is focused on research disciplines which contribute to the individualization of therapy, like pharmacogenomics and pharmacotranscriptomics. Acute lymphoblastic leukemia (ALL) is the most common malignancy of childhood. It is one of the pediatric malignancies with the highest cure rate, but still a lethal outcome due to therapy accounts for 1%⁻3% of deaths. Further improvement of treatment protocols is needed through the implementation of pharmacogenomics and pharmacotranscriptomics. Emerging high-throughput technologies, including microarrays and next-generation sequencing, have provided an enormous amount of molecular data with the potential to be implemented in childhood ALL treatment protocols. In the current review, we summarized the contribution of these novel technologies to the pharmacogenomics and pharmacotranscriptomics of childhood ALL. We have presented data on molecular markers responsible for the efficacy, side effects, and toxicity of the drugs commonly used for childhood ALL treatment, i.e., glucocorticoids, vincristine, asparaginase, anthracyclines, thiopurines, and methotrexate. Big data was generated using high-throughput technologies, but their implementation in clinical practice is poor. Research efforts should be focused on data analysis and designing prediction models using machine learning algorithms. Bioinformatics tools and the implementation of artificial i Lack of association of the CEP72 rs924607 TT genotype with intelligence are expected to open the door wide for personalized medicine in the clinical practice of childhood ALL.
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Affiliation(s)
- Sonja Pavlovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia.
| | - Nikola Kotur
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia.
| | - Biljana Stankovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia.
| | - Branka Zukic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia.
| | - Vladimir Gasic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia.
| | - Lidija Dokmanovic
- University Children's Hospital, 11000 Belgrade, Serbia.
- University of Belgrade, Faculty of Medicine, 11000 Belgrade, Serbia.
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14
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Lucafò M, Stankovic B, Kotur N, Di Silvestre A, Martelossi S, Ventura A, Zukic B, Pavlovic S, Decorti G. Pharmacotranscriptomic Biomarkers in Glucocorticoid Treatment of Pediatric Inflammatory Bowel Disease. Curr Med Chem 2018; 25:2855-2871. [PMID: 28933291 DOI: 10.2174/0929867324666170920145337] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 06/14/2017] [Accepted: 06/22/2017] [Indexed: 11/22/2022]
Abstract
BACKGROUND Pharmacotranscriptomics aims to reach more accurate drug dosing based on interindividual transcriptome variations. Here, we provide an overview of RNA biomarkers that could predict the response to glucocorticoids (GCs), considered the standard for treatment of inflammatory bowel diseases (IBD), both in adult and pediatric patients. Although new biological agents are very effective in IBD treatment, GCs are still widely used for induction of remission in patients with moderate to severe disease. It is important to identify patients that are poor responders to GCs therapy, because suboptimal response is frequent and associated with various side effects. A number of genetic variants related to GC mechanism of action has been studied. However, the majority of reported associations are not consistent. In this regard, pharmacogenomic research is now exploring the world of RNAs. An appropriate regulation of the transcriptome, which mainly comprises mRNAs and non-coding RNAs that control gene expression, has a strong impact in the modulation of GC activity. AIM The aim of this review is to present the current knowledge of the role of the transcriptome in modulating GC response in pediatric IBD. RESULTS We will discuss the available literature, concerning the development of pharmacotranscriptomic biomarkers, focusing particularly on non-coding RNAs, and present the results in this field that elucidate a concrete benefit of translating the knowledge gained in the "omics" studies into clinical practice.
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Affiliation(s)
- Marianna Lucafò
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Biljana Stankovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Nikola Kotur
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Alessia Di Silvestre
- PhD School in Science of Reproduction and Development, University of Trieste, Trieste, Italy
| | - Stefano Martelossi
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Alessandro Ventura
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy.,Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Branka Zukic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Giuliana Decorti
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy.,Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
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15
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Milosevic G, Kotur N, Krstovski N, Lazic J, Zukic B, Stankovic B, Janic D, Katsila T, Patrinos GP, Pavlovic S, Dokmanovic L. Variants in TPMT, ITPA, ABCC4 and ABCB1 Genes As Predictors of 6-mercaptopurine Induced Toxicity in Children with Acute Lymphoblastic Leukemia. J Med Biochem 2018; 37:320-327. [PMID: 30598629 PMCID: PMC6298470 DOI: 10.1515/jomb-2017-0060] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 12/18/2017] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Acute lymphoblastic leukemia is the most common childhood malignancy. Optimal use of anti leukemic drugs has led to less toxicity and adverse reactions, and a higher survival rate. Thiopurine drugs, including 6-mercaptopurine, are mostly used as antileukemic medications in the maintenance phase of treatment for children with acute lymphoblastic leukemia. For those patients, TPMT genotype- tailored 6-mercaptopurine therapy is already implemented in the treatment protocols. We investigated the role of TPMT, ITPA, ABCC4 and ABCB1 genetic variants as predictors of outcome and 6-mercaptopurine induced toxicity during the maintenance phase of treatment in pediatric acute lymphoblastic leukemia. METHODS Sixty-eight children with acute lymphoblastic leukemia were enrolled in this study. Patients have been treated according to ALL IC-BFM 2002 or ALL IC-BFM 2009 protocols. Toxicity and adverse events have been monitored via surrogate markers (off-therapy weeks, episodes of leu - ko penia and average 6-mercaptopurine dose) and a prob- abilistic model was employed to predict overall 6-mercaptopurine related toxicity. RESULTS We confirmed that patients with acute lymphoblastic leukemia that carry inactive TPMT allele(s) require 6- mercaptopurine dose reduction. ITPA and ABCC4 genetic variants failed to show an association with 6-mercapto - purine induced toxicity during the maintenance phase. Carriers of ABCB1 variant allele experienced greater hepatotoxicity. The probabilistic model Neural net which considered all the analysed genetic variants was assessed to be the best prediction model. It was able to discriminate ALL patients with good and poor 6-mercaptopurin tolerance in 71% of cases (AUC=0.71). CONCLUSIONS This study contributes to the design of a panel of pharmacogenetic markers for predicting thiopurineinduced toxicity in pediatric ALL.
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Affiliation(s)
| | - Nikola Kotur
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Nada Krstovski
- University Children’s Hospital, Belgrade, Serbia
- University of Belgrade, Faculty of Medicine, Belgrade, Serbia
| | - Jelena Lazic
- University Children’s Hospital, Belgrade, Serbia
- University of Belgrade, Faculty of Medicine, Belgrade, Serbia
| | - Branka Zukic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Biljana Stankovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Dragana Janic
- University Children’s Hospital, Belgrade, Serbia
- University of Belgrade, Faculty of Medicine, Belgrade, Serbia
| | - Theodora Katsila
- University of Patras School of Health Sciences, Department of Pharmacy, Patras, Greece
| | - George P. Patrinos
- University of Patras School of Health Sciences, Department of Pharmacy, Patras, Greece
- United Arab Emirates University, College of Medicine and Health Sciences, Department of Pathology, Al-Ain, United Arab Emirates
| | - Sonja Pavlovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Lidija Dokmanovic
- University Children’s Hospital, Belgrade, Serbia
- University of Belgrade, Faculty of Medicine, Belgrade, Serbia
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Mizzi C, Dalabira E, Kumuthini J, Dzimiri N, Balogh I, Başak N, Böhm R, Borg J, Borgiani P, Bozina N, Bruckmueller H, Burzynska B, Carracedo A, Cascorbi I, Deltas C, Dolzan V, Fenech A, Grech G, Kasiulevicius V, Kádaši Ľ, Kučinskas V, Khusnutdinova E, Loukas YL, Macek M, Makukh H, Mathijssen R, Mitropoulos K, Mitropoulou C, Novelli G, Papantoni I, Pavlovic S, Saglio G, Sertić J, Stojiljkovic M, Stubbs AP, Squassina A, Torres M, Turnovec M, van Schaik RH, Voskarides K, Wakil SM, Werk A, Del Zompo M, Zukic B, Katsila T, Lee MTM, Motsinger-Rief A, Mc Leod HL, van der Spek PJ, Patrinos GP. Correction: A European Spectrum of Pharmacogenomic Biomarkers: Implications for Clinical Pharmacogenomics. PLoS One 2017; 12:e0172595. [PMID: 28207884 PMCID: PMC5313168 DOI: 10.1371/journal.pone.0172595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
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17
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Balasopoulou A, Stanković B, Panagiotara A, Nikčevic G, Peters BA, John A, Mendrinou E, Stratopoulos A, Legaki AI, Stathakopoulou V, Tsolia A, Govaris N, Govari S, Zagoriti Z, Poulas K, Kanariou M, Constantinidou N, Krini M, Spanou K, Radlovic N, Ali BR, Borg J, Drmanac R, Chrousos G, Pavlovic S, Roma E, Zukic B, Patrinos GP, Katsila T. Novel genetic risk variants for pediatric celiac disease. Hum Genomics 2016; 10:34. [PMID: 27836013 PMCID: PMC5105295 DOI: 10.1186/s40246-016-0091-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/16/2016] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Celiac disease is a complex chronic immune-mediated disorder of the small intestine. Today, the pathobiology of the disease is unclear, perplexing differential diagnosis, patient stratification, and decision-making in the clinic. METHODS Herein, we adopted a next-generation sequencing approach in a celiac disease trio of Greek descent to identify all genomic variants with the potential of celiac disease predisposition. RESULTS Analysis revealed six genomic variants of prime interest: SLC9A4 c.1919G>A, KIAA1109 c.2933T>C and c.4268_4269delCCinsTA, HoxB6 c.668C>A, HoxD12 c.418G>A, and NCK2 c.745_746delAAinsG, from which NCK2 c.745_746delAAinsG is novel. Data validation in pediatric celiac disease patients of Greek (n = 109) and Serbian (n = 73) descent and their healthy counterparts (n = 111 and n = 32, respectively) indicated that HoxD12 c.418G>A is more prevalent in celiac disease patients in the Serbian population (P < 0.01), while NCK2 c.745_746delAAinsG is less prevalent in celiac disease patients rather than healthy individuals of Greek descent (P = 0.03). SLC9A4 c.1919G>A and KIAA1109 c.2933T>C and c.4268_4269delCCinsTA were more abundant in patients; nevertheless, they failed to show statistical significance. CONCLUSIONS The next-generation sequencing-based family genomics approach described herein may serve as a paradigm towards the identification of novel functional variants with the aim of understanding complex disease pathobiology.
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Affiliation(s)
- Angeliki Balasopoulou
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, 265 04, Patras, Greece
| | - Biljana Stanković
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Angeliki Panagiotara
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, 265 04, Patras, Greece
| | - Gordana Nikčevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Brock A Peters
- Complete Genomics Inc., Mountain View, CA, USA.,BGI Shenzhen, Shenzhen, 51803, China
| | - Anne John
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Effrosyni Mendrinou
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, 265 04, Patras, Greece
| | - Apostolos Stratopoulos
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, 265 04, Patras, Greece
| | - Aigli Ioanna Legaki
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, 265 04, Patras, Greece
| | - Vasiliki Stathakopoulou
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, 265 04, Patras, Greece
| | - Aristoniki Tsolia
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, 265 04, Patras, Greece
| | - Nikolaos Govaris
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, 265 04, Patras, Greece
| | - Sofia Govari
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, 265 04, Patras, Greece
| | - Zoi Zagoriti
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, 265 04, Patras, Greece
| | - Konstantinos Poulas
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, 265 04, Patras, Greece
| | - Maria Kanariou
- Department of Immunology and Histocompatibility, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Nikki Constantinidou
- Department of Immunology and Histocompatibility, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Maro Krini
- First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Kleopatra Spanou
- Department of Immunology and Histocompatibility, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Nedeljko Radlovic
- Department of Gastroenterology and Nutrition, University Children's Hospital, Medical Faculty, University of Belgrade, Belgrade, Serbia
| | - Bassam R Ali
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Joseph Borg
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta
| | - Radoje Drmanac
- Complete Genomics Inc., Mountain View, CA, USA.,BGI Shenzhen, Shenzhen, 51803, China
| | - George Chrousos
- First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Eleftheria Roma
- First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Branka Zukic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, 265 04, Patras, Greece.,Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Theodora Katsila
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, 265 04, Patras, Greece.
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18
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Viennas E, Komianou A, Mizzi C, Stojiljkovic M, Mitropoulou C, Muilu J, Vihinen M, Grypioti P, Papadaki S, Pavlidis C, Zukic B, Katsila T, van der Spek PJ, Pavlovic S, Tzimas G, Patrinos GP. Expanded national database collection and data coverage in the FINDbase worldwide database for clinically relevant genomic variation allele frequencies. Nucleic Acids Res 2016; 45:D846-D853. [PMID: 27924022 PMCID: PMC5210643 DOI: 10.1093/nar/gkw949] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/12/2016] [Indexed: 01/20/2023] Open
Abstract
FINDbase (http://www.findbase.org) is a comprehensive data repository that records the prevalence of clinically relevant genomic variants in various populations worldwide, such as pathogenic variants leading mostly to monogenic disorders and pharmacogenomics biomarkers. The database also records the incidence of rare genetic diseases in various populations, all in well-distinct data modules. Here, we report extensive data content updates in all data modules, with direct implications to clinical pharmacogenomics. Also, we report significant new developments in FINDbase, namely (i) the release of a new version of the ETHNOS software that catalyzes development curation of national/ethnic genetic databases, (ii) the migration of all FINDbase data content into 90 distinct national/ethnic mutation databases, all built around Microsoft's PivotViewer (http://www.getpivot.com) software (iii) new data visualization tools and (iv) the interrelation of FINDbase with DruGeVar database with direct implications in clinical pharmacogenomics. The abovementioned updates further enhance the impact of FINDbase, as a key resource for Genomic Medicine applications.
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Affiliation(s)
- Emmanouil Viennas
- University of Patras, Faculty of Engineering, Department of Computer Engineering and Informatics, GR-26504, Patras, Greece
| | - Angeliki Komianou
- Department of Pharmacy, School of Health Sciences, University of Patras, GR-26504, Patras, Greece
| | - Clint Mizzi
- Erasmus University Medical Center, Faculty of Medicine and Health Sciences, Department of Bioinformatics, NL-3015 CN, Rotterdam, The Netherlands.,University of Malta, Faculty of Medicine and Surgery, Department of Physiology and Biochemistry, MSD 2090, Malta
| | - Maja Stojiljkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Laboratory of Molecular Biomedicine, 11010, Belgrade, Serbia
| | | | - Juha Muilu
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
| | - Mauno Vihinen
- Department of Experimental Medical Science, Lund University, SE-22100, Lund, Sweden
| | - Panagiota Grypioti
- Department of Pharmacy, School of Health Sciences, University of Patras, GR-26504, Patras, Greece
| | - Styliani Papadaki
- Department of Pharmacy, School of Health Sciences, University of Patras, GR-26504, Patras, Greece
| | - Cristiana Pavlidis
- Department of Pharmacy, School of Health Sciences, University of Patras, GR-26504, Patras, Greece
| | - Branka Zukic
- University of Malta, Faculty of Medicine and Surgery, Department of Physiology and Biochemistry, MSD 2090, Malta
| | - Theodora Katsila
- Department of Pharmacy, School of Health Sciences, University of Patras, GR-26504, Patras, Greece
| | - Peter J van der Spek
- Erasmus University Medical Center, Faculty of Medicine and Health Sciences, Department of Bioinformatics, NL-3015 CN, Rotterdam, The Netherlands
| | - Sonja Pavlovic
- University of Malta, Faculty of Medicine and Surgery, Department of Physiology and Biochemistry, MSD 2090, Malta
| | - Giannis Tzimas
- Department of Computer and Informatics Engineering, Technological Educational Institute of Western Greece, GR-30020, Patras, Greece
| | - George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, GR-26504, Patras, Greece .,Erasmus University Medical Center, Faculty of Medicine and Health Sciences, Department of Bioinformatics, NL-3015 CN, Rotterdam, The Netherlands
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19
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Mizzi C, Dalabira E, Kumuthini J, Dzimiri N, Balogh I, Başak N, Böhm R, Borg J, Borgiani P, Bozina N, Bruckmueller H, Burzynska B, Carracedo A, Cascorbi I, Deltas C, Dolzan V, Fenech A, Grech G, Kasiulevicius V, Kádaši Ľ, Kučinskas V, Khusnutdinova E, Loukas YL, Macek M, Makukh H, Mathijssen R, Mitropoulos K, Mitropoulou C, Novelli G, Papantoni I, Pavlovic S, Saglio G, Setric J, Stojiljkovic M, Stubbs AP, Squassina A, Torres M, Turnovec M, van Schaik RH, Voskarides K, Wakil SM, Werk A, del Zompo M, Zukic B, Katsila T, Lee MTM, Motsinger-Rief A, Mc Leod HL, van der Spek PJ, Patrinos GP. A European Spectrum of Pharmacogenomic Biomarkers: Implications for Clinical Pharmacogenomics. PLoS One 2016; 11:e0162866. [PMID: 27636550 PMCID: PMC5026342 DOI: 10.1371/journal.pone.0162866] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 08/30/2016] [Indexed: 12/26/2022] Open
Abstract
Pharmacogenomics aims to correlate inter-individual differences of drug efficacy and/or toxicity with the underlying genetic composition, particularly in genes encoding for protein factors and enzymes involved in drug metabolism and transport. In several European populations, particularly in countries with lower income, information related to the prevalence of pharmacogenomic biomarkers is incomplete or lacking. Here, we have implemented the microattribution approach to assess the pharmacogenomic biomarkers allelic spectrum in 18 European populations, mostly from developing European countries, by analyzing 1,931 pharmacogenomics biomarkers in 231 genes. Our data show significant inter-population pharmacogenomic biomarker allele frequency differences, particularly in 7 clinically actionable pharmacogenomic biomarkers in 7 European populations, affecting drug efficacy and/or toxicity of 51 medication treatment modalities. These data also reflect on the differences observed in the prevalence of high-risk genotypes in these populations, as far as common markers in the CYP2C9, CYP2C19, CYP3A5, VKORC1, SLCO1B1 and TPMT pharmacogenes are concerned. Also, our data demonstrate notable differences in predicted genotype-based warfarin dosing among these populations. Our findings can be exploited not only to develop guidelines for medical prioritization, but most importantly to facilitate integration of pharmacogenomics and to support pre-emptive pharmacogenomic testing. This may subsequently contribute towards significant cost-savings in the overall healthcare expenditure in the participating countries, where pharmacogenomics implementation proves to be cost-effective.
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Affiliation(s)
- Clint Mizzi
- Erasmus University Medical Center, Faculty of Medicine, Department of Bioinformatics, Rotterdam, the Netherlands
- University of Malta, Faculty of Medicine and Surgery, Department of Physiology and Biochemistry, Msida, Malta
| | - Eleni Dalabira
- University of Patras School of Health Sciences, Department of Pharmacy, Patras, Greece
| | - Judit Kumuthini
- Center for Proteomic and Genomic Research, Observatory, Cape Town, South Africa
| | - Nduna Dzimiri
- King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | | | | | - Ruwen Böhm
- University of Kiel, Institute for Experimental and Clinical Pharmacology, Kiel, Germany
| | - Joseph Borg
- University of Malta, Department of Applied Biomedical Science, Faculty of Health Sciences, Msida, Malta
| | - Paola Borgiani
- University of Rome “Tor Vergata”, Department of Biomedicine and Prevention, Rome, Italy
| | | | - Henrike Bruckmueller
- University of Kiel, Institute for Experimental and Clinical Pharmacology, Kiel, Germany
| | - Beata Burzynska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | - Ingolf Cascorbi
- University of Kiel, Institute for Experimental and Clinical Pharmacology, Kiel, Germany
| | - Constantinos Deltas
- University of Cyprus, Molecular Medicine Research Center, Department of Biological Sciences, Nicosia, Cyprus
| | - Vita Dolzan
- University of Ljubljana Faculty of Medicine, Ljubljana, Slovenia
| | - Anthony Fenech
- University of Malta, Faculty of Medicine, Department of Surgery, Msida, Malta
| | - Godfrey Grech
- University of Malta, Faculty of Medicine, Department of Surgery, Msida, Malta
| | - Vytautas Kasiulevicius
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Ľudevít Kádaši
- Comenius University, Faculty of Natural Sciences, Bratislava, Slovakia
- Center for Molecular Medicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Vaidutis Kučinskas
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center, Russian Academy of Sciences, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Yiannis L. Loukas
- University of Athens, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Athens, Greece
| | - Milan Macek
- Charles University, 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Halyna Makukh
- Institute of Hereditary Pathology, Ukrainian National Academy of Medical Sciences, Lviv, Ukraine
| | - Ron Mathijssen
- Erasmus University Medical Center, Department of Clinical Chemistry, Rotterdam, the Netherlands
| | | | - Christina Mitropoulou
- Erasmus University Medical Center, Department of Clinical Chemistry, Rotterdam, the Netherlands
| | - Giuseppe Novelli
- University of Rome “Tor Vergata”, Department of Biomedicine and Prevention, Rome, Italy
| | - Ioanna Papantoni
- University of Patras School of Health Sciences, Department of Pharmacy, Patras, Greece
| | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic Engineering University of Belgrade, Laboratory of Molecular Biomedicine, Belgrade, Serbia
| | | | - Jadranka Setric
- University Hospital Centre, Zagreb, Croatia
- University of Zagreb School of Medicine, Zagreb, Croatia
| | - Maja Stojiljkovic
- Institute of Molecular Genetics and Genetic Engineering University of Belgrade, Laboratory of Molecular Biomedicine, Belgrade, Serbia
| | - Andrew P. Stubbs
- Erasmus University Medical Center, Faculty of Medicine, Department of Bioinformatics, Rotterdam, the Netherlands
| | - Alessio Squassina
- University of Cagliari, Department of Biomedical Sciences, Cagliari, Italy
| | - Maria Torres
- University of Santiago de Compostela, Santiago, Spain
| | - Marek Turnovec
- Charles University, 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Ron H. van Schaik
- Erasmus University Medical Center, Department of Clinical Chemistry, Rotterdam, the Netherlands
| | - Konstantinos Voskarides
- University of Cyprus, Molecular Medicine Research Center, Department of Biological Sciences, Nicosia, Cyprus
| | - Salma M. Wakil
- King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Anneke Werk
- University of Kiel, Institute for Experimental and Clinical Pharmacology, Kiel, Germany
| | - Maria del Zompo
- University of Cagliari, Department of Biomedical Sciences, Cagliari, Italy
| | - Branka Zukic
- Institute of Molecular Genetics and Genetic Engineering University of Belgrade, Laboratory of Molecular Biomedicine, Belgrade, Serbia
| | - Theodora Katsila
- University of Patras School of Health Sciences, Department of Pharmacy, Patras, Greece
| | - Ming Ta Michael Lee
- RIKEN Institute, Center for Genomic Medicine, Laboratory for International Alliance, Yokohama, Japan
| | - Alison Motsinger-Rief
- North Carolina State University, Department of Statistics, Raleigh, NC, United States of America
| | | | - Peter J. van der Spek
- Erasmus University Medical Center, Faculty of Medicine, Department of Bioinformatics, Rotterdam, the Netherlands
| | - George P. Patrinos
- Erasmus University Medical Center, Faculty of Medicine, Department of Bioinformatics, Rotterdam, the Netherlands
- University of Patras School of Health Sciences, Department of Pharmacy, Patras, Greece
- * E-mail:
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20
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Klaassen K, Stankovic B, Kotur N, Djordjevic M, Zukic B, Nikcevic G, Ugrin M, Spasovski V, Srzentic S, Pavlovic S, Stojiljkovic M. New PAH gene promoter KLF1 and 3'-region C/EBPalpha motifs influence transcription in vitro. J Appl Genet 2016; 58:79-85. [PMID: 27447460 DOI: 10.1007/s13353-016-0359-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 06/01/2016] [Accepted: 06/30/2016] [Indexed: 11/28/2022]
Abstract
Phenylketonuria (PKU) is a metabolic disease caused by mutations in the phenylalanine hydroxylase (PAH) gene. Although the PAH genotype remains the main determinant of PKU phenotype severity, genotype-phenotype inconsistencies have been reported. In this study, we focused on unanalysed sequences in non-coding PAH gene regions to assess their possible influence on the PKU phenotype. We transiently transfected HepG2 cells with various chloramphenicol acetyl transferase (CAT) reporter constructs which included PAH gene non-coding regions. Selected non-coding regions were indicated by in silico prediction to contain transcription factor binding sites. Furthermore, electrophoretic mobility shift assay (EMSA) and supershift assays were performed to identify which transcriptional factors were engaged in the interaction. We found novel KLF1 motif in the PAH promoter, which decreases CAT activity by 50 % in comparison to basal transcription in vitro. The cytosine at the c.-170 promoter position creates an additional binding site for the protein complex involving KLF1 transcription factor. Moreover, we assessed for the first time the role of a multivariant variable number tandem repeat (VNTR) region located in the 3'-region of the PAH gene. We found that the VNTR3, VNTR7 and VNTR8 constructs had approximately 60 % of CAT activity. The regulation is mediated by the C/EBPalpha transcription factor, present in protein complex binding to VNTR3. Our study highlighted two novel promoter KLF1 and 3'-region C/EBPalpha motifs in the PAH gene which decrease transcription in vitro and, thus, could be considered as PAH expression modifiers. New transcription motifs in non-coding regions will contribute to better understanding of the PKU phenotype complexity and may become important for the optimisation of PKU treatment.
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Affiliation(s)
- Kristel Klaassen
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010, Belgrade, Serbia
| | - Biljana Stankovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010, Belgrade, Serbia
| | - Nikola Kotur
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010, Belgrade, Serbia
| | - Maja Djordjevic
- Mother and Child Health Care Institute of Serbia "Dr Vukan Cupic", School of Medicine, University of Belgrade, Radoja Dakića 6-8, 11070, Belgrade, Serbia
| | - Branka Zukic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010, Belgrade, Serbia
| | - Gordana Nikcevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010, Belgrade, Serbia
| | - Milena Ugrin
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010, Belgrade, Serbia
| | - Vesna Spasovski
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010, Belgrade, Serbia
| | - Sanja Srzentic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010, Belgrade, Serbia
| | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010, Belgrade, Serbia
| | - Maja Stojiljkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010, Belgrade, Serbia.
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21
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Stankovic B, Dragasevic S, Popovic D, Zukic B, Kotur N, Sokic-Milutinovic A, Alempijevic T, Lukic S, Milosavljevic T, Nikcevic G, Pavlovic S. Variations in inflammatory genes as molecular markers for prediction of inflammatory bowel disease occurrence. J Dig Dis 2015; 16:723-33. [PMID: 26316104 DOI: 10.1111/1751-2980.12281] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 06/26/2015] [Accepted: 08/03/2015] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Research on inflammatory bowel disease (IBD) has highlighted genes involved in the regulation of inflammatory responses as contributors to disease pathogenesis. This study aimed to evaluate the associations between IBD and variations in NOD2, TLR4, TNF-α, IL-6, IL-1β and IL-1RN genes, and to use the genetic data obtained in predictive modeling. METHODS A total of 167 IBD patients and 101 healthy controls were genotyped by polymerase chain reaction-restriction fragment length polymorphism. Using the genotype data attained as the input to various classification algorithms, IBD prediction models were designed. The area under the receiver operating characteristic curve (AUROC) was used to measure their performance. RESULTS Significant associations were found between Crohn's disease (CD) and minor NOD2 variants, as well as TLR4 299Gly, TNF-α G-308A, IL-6 G-174C and IL-1RN VNTR A2 variants, while ulcerative colitis (UC) was associated only with IL-1RN VNTR A2 variants. CD and UC showed highly significant difference in the allelic distribution of TNF-α G-308A, where the A allele was found to be related to CD, and the G allele to UC. A combined effect of patients' gender and TLR4 variants was observed among CD patients. When all analyzed genotype and gender data were used, prediction performance achieved a maximum AUROC of 0.690 for CD and 0.601 for UC dataset. CONCLUSION Variations in the genes involved in immune regulation are genetic factors of importance in IBD susceptibility that could potentially be used as predictors of disease development.
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Affiliation(s)
- Biljana Stankovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Sanja Dragasevic
- Clinic for Gastroenterology and Hepatology, Clinical Center of Serbia, Belgrade, Serbia
| | - Dragan Popovic
- School of Medicine, University of Belgrade, Belgrade, Serbia.,Clinic for Gastroenterology and Hepatology, Clinical Center of Serbia, Belgrade, Serbia
| | - Branka Zukic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Nikola Kotur
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Aleksandra Sokic-Milutinovic
- School of Medicine, University of Belgrade, Belgrade, Serbia.,Clinic for Gastroenterology and Hepatology, Clinical Center of Serbia, Belgrade, Serbia
| | - Tamara Alempijevic
- School of Medicine, University of Belgrade, Belgrade, Serbia.,Clinic for Gastroenterology and Hepatology, Clinical Center of Serbia, Belgrade, Serbia
| | - Snezana Lukic
- School of Medicine, University of Belgrade, Belgrade, Serbia.,Clinic for Gastroenterology and Hepatology, Clinical Center of Serbia, Belgrade, Serbia
| | - Tomica Milosavljevic
- School of Medicine, University of Belgrade, Belgrade, Serbia.,Clinic for Gastroenterology and Hepatology, Clinical Center of Serbia, Belgrade, Serbia
| | - Gordana Nikcevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
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22
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Ugrin M, Stojiljkovic M, Zukic B, Klaassen K, Katsila T, Vasiljevic J, Dokmanovic L, Janic D, Patrinos GP, Pavlovic S. Functional Analysis of anAγ-Globin Gene Promoter Variant (HBG1: g.-225_-222delAGCA) Underlines Its Role in Increasing Fetal Hemoglobin Levels Under Erythropoietic Stress. Hemoglobin 2015; 40:48-52. [DOI: 10.3109/03630269.2015.1107842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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23
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Kotur N, Dokmanovic L, Janic D, Stankovic B, Krstovski N, Tosic N, Katsila T, Patrinos GP, Zukic B, Pavlovic S. TPMT gene expression is increased during maintenance therapy in childhood acute lymphoblastic leukemia patients in a TPMT gene promoter variable number of tandem repeat-dependent manner. Pharmacogenomics 2015; 16:1701-12. [PMID: 26411491 DOI: 10.2217/pgs.15.109] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
AIMS 6-mercaptopurine influences in vitro TPMT gene expression in a TPMT promoter variable number of tandem repeats (VNTR)-dependent manner. We studied TPMT expression following 6-mercaptopurine and methotrexate administration in childhood acute lymphoblastic leukemia (ALL) patients and the pharmacogenomic potential of the VNTR architecture. MATERIALS & METHODS TPMT gene expression was determined in childhood ALL patients at diagnosis (n = 57) and during the maintenance therapy (n = 27). RESULTS A threefold increase of TPMT gene expression was obtained during maintenance therapy, modulated by the architecture of the VNTR region. CONCLUSION The TPMT promoter genetic variants need to be considered at the very beginning of the maintenance therapy for childhood ALL patients. The TPMT promoter VNTR region may serve as a pharmacogenomic biomarker when introducing thiopurine therapy.
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Affiliation(s)
- Nikola Kotur
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics & Genetic Engineering, University of Belgrade, Serbia
| | - Lidija Dokmanovic
- University Children's Hospital, School of Medicine, University of Belgrade, Serbia
| | - Dragana Janic
- University Children's Hospital, School of Medicine, University of Belgrade, Serbia
| | - Biljana Stankovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics & Genetic Engineering, University of Belgrade, Serbia
| | - Nada Krstovski
- University Children's Hospital, School of Medicine, University of Belgrade, Serbia
| | - Natasa Tosic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics & Genetic Engineering, University of Belgrade, Serbia
| | - Theodora Katsila
- Department of Pharmacy, University of Patras, School of Health Sciences, Patras, Greece
| | - George P Patrinos
- Department of Pharmacy, University of Patras, School of Health Sciences, Patras, Greece
| | - Branka Zukic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics & Genetic Engineering, University of Belgrade, Serbia
| | - Sonja Pavlovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics & Genetic Engineering, University of Belgrade, Serbia
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24
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Stojiljkovic M, Klaassen K, Djordjevic M, Sarajlija A, Kecman B, Ugrin M, Zukic B, Desviat LR, Pavlovic S, Perez B. Tetrahydrobiopterin deficiency among Serbian patients presenting with hyperphenylalaninemia. J Pediatr Endocrinol Metab 2015; 28:477-80. [PMID: 25418970 DOI: 10.1515/jpem-2014-0297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 09/29/2014] [Indexed: 11/15/2022]
Abstract
Hyperphenylalaninemia (HPA) [phenylketonuria (PKU) and tetrahydrobiopterin (BH4) deficiencies] is rare inborn metabolic disease characterized by elevated phenylalanine level in body fluids. In Serbia, 62 HPA patients have been identified through newborn screening since 1983. However, pterin pattern analysis is not performed. We present a patient initially diagnosed and treated as classical PKU. At 3 years of age, during infection with H1N1 influenza A virus, the patient first developed a neurologic crisis with encephalopathy and dystonic movements. We suspected that the patient is the first case of BH4 deficiency identified in Serbia. Genetic analyses showed that the patient does not have disease-causing variants of the PAH gene and carries a p.Asp136Val mutation in homozygous state in the PTS gene. For patients with treatable rare diseases, like PKU and BH4 deficiencies, correct diagnosis is crucial for the implementation of optimal treatment. If biochemical tests needed for differential diagnosis are not available, our experience emphasizes the necessity of immediate genetic testing after newborn screening.
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25
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Stanković B, Radlović N, Leković Z, Ristić D, Radlović V, Nikčević G, Kotur N, Vučićević K, Kostić T, Pavlović S, Zukic B. HLA genotyping in pediatric celiac disease patients. Bosn J Basic Med Sci 2014; 14:171-6. [PMID: 25172978 DOI: 10.17305/bjbms.2014.3.28] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 07/21/2014] [Indexed: 12/12/2022] Open
Abstract
Celiac disease (CD) is a chronic inflammatory disease in the small intestine triggered by gluten uptake that occurs in genetically susceptible individuals. HLA-DQ2 protein encoded by HLA-DQA1*05 and DQB1*02 alleles is found in 90-95% of CD patients. All of the remaining patients carry HLA-DQ8 protein encoded by HLA-DQA1*03 and DQB1*03:02 alleles. Specific HLA-DQ genotypes define different risk for CD incidence. Presence of susceptible HLA-DQ genotypes does not predict certain disease development, but their absence makes CD very unlikely, close to 100%. Here we presented for the first time the distribution of HLA-DQ genotypes in the group of pediatric celiac patients from the University Children's Hospital, Belgrade, Serbia and estimated risk for CD development that these genotypes confer. Seventy three celiac disease patients and 62 healthy individuals underwent genotyping for DQA1, DQB alleles and DRB1 allele. 94.5% of patients carried alleles that encode DQ2 protein variant and 2.7% carried alleles that encode DQ8 protein variant. Two patients carried single DQB1*02 allele. No patients were negative for all the alleles predisposing to CD. The highest HLA-DQ genotype risk for CD development was found in group of patients homozygous for DQ2.5 haplotype, followed by the group of heterozygous carriers of DQ2.5 haplotype in combination with DQB1*02 allele within the other haplotype. The lowest risk was observed in carriers of a single copy of DQB1*02 or DQA1*05 allele or other non-predisposing alleles. HLA genotyping, more informative than serological testing commonly used, proved to be a useful diagnostic tool for excluding CD development.
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Affiliation(s)
- Biljana Stanković
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade.
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Tafrali C, Paizi A, Borg J, Radmilovic M, Bartsakoulia M, Giannopoulou E, Giannakopoulou O, Stojiljkovic-Petrovic M, Zukic B, Poulas K, Stavrou EF, Lambropoulou P, Kourakli A, Felice AE, Papachatzopoulou A, Philipsen S, Pavlovic S, Georgitsi M, Patrinos GP. Genomic variation in the MAP3K5 gene is associated with β-thalassemia disease severity and hydroxyurea treatment efficacy. Pharmacogenomics 2013; 14:469-83. [PMID: 23556445 DOI: 10.2217/pgs.13.31] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
AIM In this study we explored the association between genetic variations in MAP3K5 and PDE7B genes, residing on chromosome 6q23, and disease severity in β-hemoglobinopathy patients, as well as the association between these variants with response to hydroxyurea (HU) treatment. Furthermore, we examined MAP3K5 expression in the context of high fetal hemoglobin (HbF) and upon HU treatment in erythroid progenitor cells from healthy and KLF1 haploinsufficient individuals. MATERIALS & METHODS For this purpose, we genotyped β-thalassemia intermedia and major patients and healthy controls, as well as a cohort of compound heterozygous sickle cell disease/β-thalassemia patients receiving HU as HbF augmentation treatment. Furthermore, we examined MAP3K5 expression in the context of high HbF and upon HU treatment in erythroid progenitor cells from healthy and KLF1 haploinsufficient individuals. RESULTS A short tandem repeat in the MAP3K5 promoter and two intronic MAP3K5 gene variants, as well as a PDE7B variant, are associated with low HbF levels and a severe disease phenotype. Moreover, MAP3K5 mRNA expression levels are altered in the context of high HbF and are affected by the presence of HU. Lastly, the abovementioned MAP3K5 variants are associated with HU treatment efficacy. CONCLUSION Our data suggest that these MAP3K5 variants are indicative of β-thalassemia disease severity and response to HU treatment.
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Affiliation(s)
- Christina Tafrali
- University of Patras, School of Health Sciences, Department of Pharmacy, University Campus, Rion, Patras, Greece
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Spasovski V, Tosic N, Nikcevic G, Stojiljkovic M, Zukic B, Radmilovic M, Karan-Djurasevic T, Srzentic S, Colovic M, Pavlovic S. The influence of novel transcriptional regulatory element in intron 14 on the expression of Janus kinase 2 gene in myeloproliferative neoplasms. J Appl Genet 2012. [PMID: 23188718 DOI: 10.1007/s13353-012-0125-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The expression of Janus kinase 2 (JAK2) gene is altered in myeloproliferative neoplasms (MPN) and the regulation of transcription could be a mechanism that modulates JAK2 gene expression. We analyzed the transcriptional potential of single-nucleotide polymorphism (SNP) rs12343867 T > C in JAK2 intron 14, tagging 46/1 haplotype, and its influence on JAK2 gene expression. Functional analysis of JAK2 intron 14 was performed using the pBLCAT5 reporter system in K562 cells. Identification of the proteins binding to the intron 14 regulatory element was accomplished by electrophoretic mobility shift assay (EMSA) and supershift assays. Quantification of the expression of JAK2 gene in a cohort of 51 MPN patients and 12 healthy controls was performed by real-time quantitative polymerase chain reaction (RQ-PCR). Functional analysis revealed that the intronic DNA element harboring SNP rs12343867 T > C acts as a transcriptional repressor in vitro. The repressor activity was significantly attenuated by the presence of nucleotide C. Supershift analysis showed the enrolment of transcriptional factor Meis1 in this process. RQ-PCR experiments showed increased JAK2 expression in patients with the JAK2V617F mutation, with a significant difference between essential thrombocythemia (ET), polycythemia vera (PV), and myelofibrosis (MF) patients. SNP rs12343867 showed no statistically significant influence on the expression of JAK2 gene in MNP patients.
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Affiliation(s)
- Vesna Spasovski
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
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Radmilovic M, Zukic B, Petrovic MS, Bartsakoulia M, Stankovic B, Kotur N, Dokmanovic L, Georgitsi M, Patrinos GP, Pavlovic S. Functional analysis of a novel KLF1 gene promoter variation associated with hereditary persistence of fetal hemoglobin. Ann Hematol 2012; 92:53-8. [PMID: 23161389 DOI: 10.1007/s00277-012-1625-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 11/05/2012] [Indexed: 11/30/2022]
Abstract
Hereditary persistence of fetal hemoglobin (HPFH) is a rare hereditary condition resulting in elevated levels of fetal hemoglobin (HbF) in adults. Typical HPFH is associated with promoter mutations or large deletions affecting the human fetal globin (HBG1 and HBG2) genes, while genetic defects in other genes involved in human erythropoiesis, e.g. KLF1, also result in atypical HPFH. Here, we report the first KLF1 gene promoter mutation (KLF1:g.-148G > A) that is associated with increased HbF level. This mutation was shown to result in drastically reduced CAT reporter gene expression in K562 cells, compared to the wild-type sequence (p = 0.009) and also in reduced KLF1 gene expression in vivo. Furthermore, consistent with in silico analysis, electrophoretic mobility shift analysis showed that the KLF1:g.-148G > A mutation resides in a Sp1 binding site and further that this mutation leads to the ablation of Sp1 binding in vitro. These data suggest that the KLF1:g-148G > A mutation could play a role in increasing HbF levels in adults and further underlines the role of KLF1 as one of the key transcription factors involved in human fetal globin gene switching.
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Affiliation(s)
- Milena Radmilovic
- Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Hematology, University of Belgrade, Vojvode Stepe 444a, 11010, Belgrade, Serbia
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29
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Abstract
Interindividual variable drug response is correlated with sequence alterations in genes encoding drug-metabolizing enzymes and transporters, affecting drug absorption, distribution, metabolism and excretion. This variable drug response may have an impact on disease therapeutic outcomes, tolerance to adverse drug reactions and even survival. Sequence alterations may occur not only within the coding region of a gene, but in its regulatory elements too, affecting gene transcription and gene-expression levels. Here, we provide a compilation of the current knowledge of pharmacogenomics related to transcription, with a focus on the effect of SNPs and short tandem repeats residing in cis-regulatory elements of 11 genes encoding for drug-metabolizing enzymes and drug transporters. In addition, we comment on two genes encoding enzymes that are drug targets themselves. Finally, we briefly discuss the currently available methodologies for clinically assessing pharmacogenomic profiles, which could potentially in the future facilitate drug treatment-individualization via the identification of molecular signatures in specific patient groups.
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Affiliation(s)
- Marianthi Georgitsi
- Department of Pharmacy, School of Health Sciences, University of Patras, 26504 Rion, Patras, Greece
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30
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Kotur N, Stankovic B, Kassela K, Georgitsi M, Vicha A, Leontari I, Dokmanovic L, Janic D, Krstovski N, Klaassen K, Radmilovic M, Stojiljkovic M, Nikcevic G, Simeonidis A, Sivolapenko G, Pavlovic S, Patrinos GP, Zukic B. 6-mercaptopurine influences TPMT gene transcription in a TPMT gene promoter variable number of tandem repeats-dependent manner. Pharmacogenomics 2012; 13:283-95. [DOI: 10.2217/pgs.11.153] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Aim: TPMT activity is characterized by a trimodal distribution, namely low, intermediate and high methylator. TPMT gene promoter contains a variable number of GC-rich tandem repeats (VNTRs), namely A, B and C, ranging from three to nine repeats in length in an AnBmC architecture. We have previously shown that the VNTR architecture in the TPMT gene promoter affects TPMT gene transcription. Materials, methods & results: Here we demonstrate, using reporter assays, that 6-mercaptopurine (6-MP) treatment results in a VNTR architecture-dependent decrease of TPMT gene transcription, mediated by the binding of newly recruited protein complexes to the TPMT gene promoter, upon 6-MP treatment. We also show that acute lymphoblastic leukemia patients undergoing 6-MP treatment display a VNTR architecture-dependent response to 6-MP. Conclusion: These data suggest that the TPMT gene promoter VNTR architecture can be potentially used as a pharmacogenomic marker to predict toxicity due to 6-MP treatment in acute lymphoblastic leukemia patients. Original submitted 27 July 2011; Revision submitted 24 October 2011
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Affiliation(s)
- Nikola Kotur
- Institute of Molecular Genetics & Genetic Engineering, University of Belgrade, Laboratory for Molecular Hematology, Belgrade, 11010, Serbia
| | - Biljana Stankovic
- Institute of Molecular Genetics & Genetic Engineering, University of Belgrade, Laboratory for Molecular Hematology, Belgrade, 11010, Serbia
| | - Katerina Kassela
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, GR-26504, Greece
| | - Marianthi Georgitsi
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, GR-26504, Greece
| | - Anna Vicha
- Hematology Division, School of Health Sciences, Faculty of Medicine, University of Patras, Patras, GR-26504, Greece
| | - Iliana Leontari
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, GR-26504, Greece
| | - Lidija Dokmanovic
- University Children’s Hospital, School of Medicine, University of Belgrade, Belgrade, 11000, Serbia
| | - Dragana Janic
- University Children’s Hospital, School of Medicine, University of Belgrade, Belgrade, 11000, Serbia
| | - Nada Krstovski
- University Children’s Hospital, School of Medicine, University of Belgrade, Belgrade, 11000, Serbia
| | - Kristel Klaassen
- Institute of Molecular Genetics & Genetic Engineering, University of Belgrade, Laboratory for Molecular Hematology, Belgrade, 11010, Serbia
| | - Milena Radmilovic
- Institute of Molecular Genetics & Genetic Engineering, University of Belgrade, Laboratory for Molecular Hematology, Belgrade, 11010, Serbia
| | - Maja Stojiljkovic
- Institute of Molecular Genetics & Genetic Engineering, University of Belgrade, Laboratory for Molecular Hematology, Belgrade, 11010, Serbia
| | - Gordana Nikcevic
- Institute of Molecular Genetics & Genetic Engineering, University of Belgrade, Laboratory for Molecular Hematology, Belgrade, 11010, Serbia
| | - Argiris Simeonidis
- Hematology Division, School of Health Sciences, Faculty of Medicine, University of Patras, Patras, GR-26504, Greece
| | - Gregory Sivolapenko
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, GR-26504, Greece
| | - Sonja Pavlovic
- Institute of Molecular Genetics & Genetic Engineering, University of Belgrade, Laboratory for Molecular Hematology, Belgrade, 11010, Serbia
| | - George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, GR-26504, Greece
| | - Branka Zukic
- Institute of Molecular Genetics & Genetic Engineering, University of Belgrade, Laboratory for Molecular Hematology, Belgrade, 11010, Serbia
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Radmilovic M, Zukic B, Stankovic B, Karan-Djurasevic T, Stojiljkovic M, Spasovski V, Tosic N, Dokmanovic L, Janic D, Pavlovic S. Thalassemia Syndromes in Serbia: An update. Hemoglobin 2010; 34:477-85. [DOI: 10.3109/03630269.2010.513637] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Stojiljkovic M, Zukic B, Tosic N, Karan-Djurasevic T, Spasovski V, Nikcevic G, Pavlovic S. Novel transcriptional regulatory element in the phenylalanine hydroxylase gene intron 8. Mol Genet Metab 2010; 101:81-3. [PMID: 20599406 DOI: 10.1016/j.ymgme.2010.05.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 05/17/2010] [Accepted: 05/17/2010] [Indexed: 01/03/2023]
Abstract
We present the first transcriptional regulatory element found in a PAH gene intron. The element is located in the PAH gene intron 8, acts as an enhancer specifically in the hepatoma cell line, and binds GATA-1 transcription factor. Herein the presented data could unlock a new area for the analysis of PAH gene expression and could contribute to refining genotype-phenotype correlation.
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Affiliation(s)
- Maja Stojiljkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, Belgrade, Serbia.
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33
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Zukic B, Radmilovic M, Stojiljkovic M, Tosic N, Pourfarzad F, Dokmanovic L, Janic D, Colovic N, Philipsen S, Patrinos GP, Pavlovic S. Functional analysis of the role of the TPMT gene promoter VNTR polymorphism in TPMT gene transcription. Pharmacogenomics 2010; 11:547-57. [PMID: 20350137 DOI: 10.2217/pgs.10.7] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIMS Thiopurine S-methyltransferase (TPMT) activity is polymorphic, and a trimodal distribution has been demonstrated in Caucasians (low, intermediate and high methylator groups). The TPMT gene promoter contains a variable number of three GC-rich tandem repeats, namely A, B and C, ranging from three to nine in length in a A(n)B(m)C architecture. MATERIALS & METHODS Here, we investigated the influence of number and type of TPMT gene promoter tandem repeats on human TPMT gene transcription in K562 cells transiently transfected with reporter constructs bearing various variable number of tandem repeats (VNTR) and addressed the interaction of transcription factor binding to the VNTRs by electrophoretic mobility shift assays. RESULTS We found that the distribution patterns of VNTR alleles do not significantly differ among acute lymphoblastic leukemia patients, acute myeloid leukemia patients and normal individuals. We also demonstrated that the A repeat has a negative effect in TPMT gene transcription and that a positive regulatory element, identified immediately upstream to the VNTR region of the TPMT gene promoter, is indispensable for TPMT gene transcription. Our electrophoretic mobility shift assay analysis indicated that the Sp1 and Sp3 transcription factors bind to the VNTR repeats. CONCLUSION Overall, our data underline that both the number and type of VNTRs, as well as the upstream regulatory region of the TPMT gene promoter, determine the overall level of TPMT gene transcription. It remains to be seen whether these VNTRs can be employed as pharmacogenetic markers to individualize thiopurine therapy.
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Affiliation(s)
- Branka Zukic
- Institute for Molecular Genetics & Genetic Engineering, Laboratory of Molecular Hematology, Vojvode Stepe 444a, 11010 Belgrade, Serbia
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