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Mondal T, Loffredo CA, Trnovec T, Palkovicova Murinova L, Noreen Z, Nnanabu T, Conka K, Drobna B, Ghosh S. Gene expression signatures in PCB-exposed Slovak children in relation to their environmental exposures and socio-physical characteristics. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:60531-60541. [PMID: 35420343 PMCID: PMC9427901 DOI: 10.1007/s11356-022-20018-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Our previous gene expression studies in a PCB-exposed cohort of young children in Slovakia revealed that early-life exposures to PCBs and other organochlorine compounds were associated with significant alterations across several pathogenetic pathways. The present study was undertaken to further explore the high-throughput qRT-PCR-based gene expression effects by using TaqMan low-density array (TLDA) for selected genes in a sample of 55 children from the cohort. We analyzed the transcriptional changes of 11 genes in relation to PCB and organochlorine pesticide exposure levels (including DDT, DDE, HCH, and HCB), and to BMI and ethnicity in this cohort. The results indicated an overall downregulation of expression of these genes. Maximum downregulation (in fold change) was observed in the ENTPD3 gene, and the minimum level of downregulation was in CYP2D6. As per our multinomial regression model study, downregulation of LEPR gene was significantly directly correlated with all the exposure variables. Downregulation of APC, ARNT, CYP2D6, LEPR, LRP12, and MYC genes was directly correlated with BMI (kg/m2) of the individuals. Gender-specific differences in gene expression were observed in CYP2D6 (p-value 0.0001) and LEPR (p-value 0.028), while downregulation of CYP2D6 (p-value 0.01), LEPR (p-value 0.02), LRP12 (p-value 0.04), and MYC (p-value 0.02) genes was consistently observed in Roma children compared to Caucasians. The investigation of such health disparities must be emphasized in future research, together with interventions to reduce the health consequences of PCB exposures. In this context, we emphasize the importance of biomarker-based approaches to future research on genetic susceptibility to the effects of these compounds.
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Affiliation(s)
- Tanmoy Mondal
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Salt Lake, Kolkata, 700064, India
| | | | - Tomas Trnovec
- Department of Environmental Medicine, Faculty of Public Health, Slovak Medical University, Bratislava, Slovak Republic
| | - Lubica Palkovicova Murinova
- Department of Environmental Medicine, Faculty of Public Health, Slovak Medical University, Bratislava, Slovak Republic
| | - Zarish Noreen
- Department of Healthcare Biotechnology, National University of Sciences and Technology (NUST), Islamabad, 44000, Pakistan
| | - Thomas Nnanabu
- Departments of Biology, Howard University, 415 College Street, NW, Room 408, EE Just Hall, Washington, DC, 20059, USA
| | - Kamil Conka
- Department of Toxic Organic Pollutants, Faculty of Medicine, Slovak Medical University, Bratislava, Slovak Republic
| | - Beata Drobna
- Department of Toxic Organic Pollutants, Faculty of Medicine, Slovak Medical University, Bratislava, Slovak Republic
| | - Somiranjan Ghosh
- Departments of Biology, Howard University, 415 College Street, NW, Room 408, EE Just Hall, Washington, DC, 20059, USA.
- Departments of Pediatrics and Child Health, College of Medicine, Howard University, Washington, DC, 20059, USA.
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Lipphardt V, Rappold GA, Surdu M. Representing vulnerable populations in genetic studies: The case of the Roma. SCIENCE IN CONTEXT 2021; 34:69-100. [PMID: 36050807 DOI: 10.1017/s0269889722000023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Moreau () has raised concerns about the use of DNA data obtained from vulnerable populations, such as the Uighurs in China. We discuss another case, situated in Europe and with a research history dating back 100 years: genetic investigations of Roma. In our article, we focus on problems surrounding representativity in these studies. We claim that many of the circa 440 publications in our sample neglect the methodological and conceptual challenges of representativity. Moreover, authors do not account for problematic misrepresentations of Roma resulting from the conceptual frameworks and sampling schemes they use. We question the representation of Roma as a "genetic isolate" and the underlying rationales, with a strong focus on sampling strategies. We discuss our results against the optimistic prognosis that the "new genetics" could help to overcome essentialist understandings of groups.
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Mašindová I, Šoltýsová A, Varga L, Mátyás P, Ficek A, Hučková M, Sůrová M, Šafka-Brožková D, Anwar S, Bene J, Straka S, Janicsek I, Ahmed ZM, Seeman P, Melegh B, Profant M, Klimeš I, Riazuddin S, Kádasi Ľ, Gašperíková D. MARVELD2 (DFNB49) mutations in the hearing impaired Central European Roma population--prevalence, clinical impact and the common origin. PLoS One 2015; 10:e0124232. [PMID: 25885414 PMCID: PMC4401708 DOI: 10.1371/journal.pone.0124232] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 02/27/2015] [Indexed: 01/26/2023] Open
Abstract
Background In the present study we aimed: 1) To establish the prevalence and clinical impact of DFNB49 mutations in deaf Roma from 2 Central European countries (Slovakia and Hungary), and 2) to analyze a possible common origin of the c.1331+2T>C mutation among Roma and Pakistani mutation carriers identified in the present and previous studies. Methods We sequenced 6 exons of the MARVELD2 gene in a group of 143 unrelated hearing impaired Slovak Roma patients. Simultaneously, we used RFLP to detect the c.1331+2T>C mutation in 85 Hungarian deaf Roma patients, control groups of 702 normal hearing Romanies from both countries and 375 hearing impaired Slovak Caucasians. We analyzed the haplotype using 21 SNPs spanning a 5.34Mb around the mutation c.1331+2T>C. Results One pathogenic mutation (c.1331+2T>C) was identified in 12 homozygous hearing impaired Roma patients. Allele frequency of this mutation was higher in Hungarian (10%) than in Slovak (3.85%) Roma patients. The identified common haplotype in Roma patients was defined by 18 SNP markers (3.89 Mb). Fourteen common SNPs were also shared among Pakistani and Roma homozygotes. Biallelic mutation carriers suffered from prelingual bilateral moderate to profound sensorineural hearing loss. Conclusions We demonstrate different frequencies of the c.1331+2T>C mutation in hearing impaired Romanies from 3 Central European countries. In addition, our results provide support for the hypothesis of a possible common ancestor of the Slovak, Hungarian and Czech Roma as well as Pakistani deaf patients. Testing for the c.1331+2T>C mutation may be recommended in GJB2 negative Roma cases with early-onset sensorineural hearing loss.
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Affiliation(s)
- Ivica Mašindová
- Laboratory of Diabetes and Metabolic Disorders & DIABGENE, Institute of Experimental Endocrinology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Andrea Šoltýsová
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
- Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lukáš Varga
- Laboratory of Diabetes and Metabolic Disorders & DIABGENE, Institute of Experimental Endocrinology, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Otorhinolaryngology—Head and Neck Surgery, Faculty of Medicine and University Hospital, Comenius University, Bratislava, Slovakia
| | - Petra Mátyás
- Department of Medical Genetics, University of Pécs, Clinical Centre, Pécs, Hungary
| | - Andrej Ficek
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Miloslava Hučková
- Laboratory of Diabetes and Metabolic Disorders & DIABGENE, Institute of Experimental Endocrinology, Slovak Academy of Sciences, Bratislava, Slovakia
- Center for Molecular Medicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Martina Sůrová
- Laboratory of Diabetes and Metabolic Disorders & DIABGENE, Institute of Experimental Endocrinology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Dana Šafka-Brožková
- DNA Laboratory, Department of Paediatric Neurology, Charles University 2nd Medical School and University Hospital Motol, Prague, Czech Republic
| | - Saima Anwar
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, Maryland, United States of America
| | - Judit Bene
- Department of Medical Genetics, University of Pécs, Clinical Centre, Pécs, Hungary
- Szentagothai Research Centre, University of Pécs, Pécs, Hungary
| | - Slavomír Straka
- Department of Otorhinolaryngology—Head and Neck Surgery, Faculty Hospital of J. A. Reiman, Prešov, Slovakia
| | - Ingrid Janicsek
- Department of Medical Genetics, University of Pécs, Clinical Centre, Pécs, Hungary
| | - Zubair M. Ahmed
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, Maryland, United States of America
| | - Pavel Seeman
- DNA Laboratory, Department of Paediatric Neurology, Charles University 2nd Medical School and University Hospital Motol, Prague, Czech Republic
| | - Béla Melegh
- Department of Medical Genetics, University of Pécs, Clinical Centre, Pécs, Hungary
- Szentagothai Research Centre, University of Pécs, Pécs, Hungary
| | - Milan Profant
- Department of Otorhinolaryngology—Head and Neck Surgery, Faculty of Medicine and University Hospital, Comenius University, Bratislava, Slovakia
| | - Iwar Klimeš
- Laboratory of Diabetes and Metabolic Disorders & DIABGENE, Institute of Experimental Endocrinology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Saima Riazuddin
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, Maryland, United States of America
| | - Ľudevít Kádasi
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
- Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Daniela Gašperíková
- Laboratory of Diabetes and Metabolic Disorders & DIABGENE, Institute of Experimental Endocrinology, Slovak Academy of Sciences, Bratislava, Slovakia
- Center for Molecular Medicine, Slovak Academy of Sciences, Bratislava, Slovakia
- * E-mail:
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Polak E, Ficek A, Radvanszky J, Soltysova A, Urge O, Cmelova E, Kantarska D, Kadasi L. Phenylalanine hydroxylase deficiency in the Slovak population: genotype-phenotype correlations and genotype-based predictions of BH4-responsiveness. Gene 2013; 526:347-55. [PMID: 23764561 DOI: 10.1016/j.gene.2013.05.057] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 05/08/2013] [Accepted: 05/20/2013] [Indexed: 10/26/2022]
Abstract
We investigated the mutation spectrum of the phenylalanine hydroxylase gene (PAH) in a cohort of patients from 135 Slovak PKU families. Mutational screening of the known coding region, including conventional intron splice sites, was performed using high-resolution melting analysis, with subsequent sequencing analysis of the samples showing deviated melting profiles compared to control samples. The PAH gene was also screened for deletions and duplications using MLPA analysis. Forty-eight different disease causing mutations were identified in our patient group, including 30 missense, 8 splicing, 7 nonsense, 2 large deletions and 1 small deletion with frameshift; giving a detection rate of 97.6%. The most prevalent mutation was the p.R408W, occurring in 47% of all alleles, which concurs with results from neighboring and other Slavic countries. Other frequent mutations were: p.R158Q (5.3%), IVS12+1G>A (5.3%), p.R252W (5.1%), p.R261Q (3.9%) and p.A403V (3.6%). We also identified three novel missense mutations: p.F233I, p.R270I, p.F331S and one novel variant: c.-30A>T in the proximal part of the PAH gene promoter. A spectrum of 84 different genotypes was observed and a genotype based predictions of BH4-responsiveness were assessed. Among all genotypes, 36 were predicted to be BH4-responsive represented by 51 PKU families. In addition, genotype-phenotype correlations were performed.
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Affiliation(s)
- Emil Polak
- Comenius University, Faculty of Natural Sciences, Department of Molecular Biology, Mlynska Dolina, 842 15 Bratislava, Slovak Republic.
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Gabrikova D, Mistrik M, Bernasovska J, Bozikova A, Behulova R, Tothova I, Macekova S. Founder mutations in NDRG1 and HK1 genes are common causes of inherited neuropathies among Roma/Gypsies in Slovakia. J Appl Genet 2013; 54:455-60. [PMID: 23996628 DOI: 10.1007/s13353-013-0168-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 08/13/2013] [Accepted: 08/20/2013] [Indexed: 11/29/2022]
Abstract
Autosomal recessive forms of Charcot-Marie-Tooth disease (CMT) account for less than 10 % of all CMT cases, but are more frequent in the populations with a high rate of consanguinity. Roma (Gypsies) are a transnational minority with an estimated population of 10 to 14 million, in which a high degree of consanguineous marriages is a generally known fact. Similar to the other genetically isolated founder populations, the Roma harbour a number of unique or rare autosomal recessive disorders, caused by "private" founder mutations. There are three subtypes of autosomal recessive CMT with mutations private to the Roma population: CMT4C, CMT4D and CMT4G. We report on the molecular examination of four families of Roma origin in Slovakia with early-onset demyelinating neuropathy and autosomal recessive inheritance. We detected mutation p.R148X (g.631C>T) in the NDRG1 (NM_006096.3) gene in two families and mutation g.9712G>C in the HK1 (NM_033498) gene in the other two families. These mutations cause CMT4D and CMT4G, respectively. The success of molecular genetic analysis in all families confirms that autosomal recessive forms of CMT caused by mutations on the NDRG1 and HK1 genes are common causes of inherited neuropathies among Slovak Roma. Providing genetic analysis of these genes for patients with Roma origin as a common part of diagnostic procedure would contribute to a better rate of diagnosed cases of demyelinating neuropathy in Slovakia and in other countries with a Roma minority.
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Affiliation(s)
- Dana Gabrikova
- Department of Biology, Faculty of Humanities and Natural Sciences, University of Presov, Ul. 17. Novembra 1, 08116, Presov, Slovakia,
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Claramunt R, Sevilla T, Lupo V, Cuesta A, Millán JM, Vílchez JJ, Palau F, Espinós C. The p.R1109X mutation in SH3TC2 gene is predominant in Spanish Gypsies with Charcot-Marie-Tooth disease type 4. Clin Genet 2007; 71:343-9. [PMID: 17470135 DOI: 10.1111/j.1399-0004.2007.00774.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Charcot-Marie-Tooth (CMT) disease type 4 (CMT4) is the name given to autosomal recessive forms of hereditary motor and sensory neuropathy (HMSN). When we began this study, three genes or loci associated with inherited peripheral neuropathies had already been identified in the European Gypsy population: HMSN-Lom (MIM 601455), HMSN-Russe (MIM 605285) and the congenital cataracts facial dysmorphism neuropathy syndrome (MIM 604168). We have carried out genetic analyses in a series of 20 Spanish Gypsy families diagnosed with a demyelinating CMT disease compatible with an autosomal recessive trait. We found the p.R148X mutation in the N-myc downstream-regulated gene 1 gene to be responsible for the HMSN-Lom in four families and also possible linkage to the HMSN-Russe locus in three others. We have also studied the CMT4C locus because of the clinical similarities and showed that in 10 families, the disease is caused by mutations located on the SH3 domain and tetratricopeptide repeats 2 (SH3TC2) gene: p.R1109X in 20 out of 21 chromosomes and p.C737_P738delinsX in only one chromosome. Moreover, the SH3TC2 p.R1109X mutation is associated with a conserved haplotype and, therefore, may be a private founder mutation for the Gypsy population. Estimation of the allelic age revealed that the SH3TC2 p.R1109X mutation may have arisen about 225 years ago, probably as the consequence of a bottleneck.
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Affiliation(s)
- R Claramunt
- Instituto de Biomedicina, Consejo Superior de Investigaciones Científicas, Valencia, Spain
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Abstract
Phenylketonuria (PKU) is heterogeneous. More than 400 different mutations in the phenylalanine hydroxylase (PAH) gene have been identified. In a systematic review of the molecular genetics of PKU in Europe we identified 29 mutations that may be regarded as prevalent in European populations. Comprehensive regional data for these mutations were collated from all available studies. The spectrum of mutations found in individual regions results from a combination of factors including founder effect, range expansion and migration, genetic drift, and probably heterozygote advantage. Common mutations include R408W on a haplotype 2 background in Eastern Europe, IVS10-11G>A in the Mediterranean, IVS12+1G>A in Denmark and England, Y414C in Scandinavia, I65T in Western Europe, and R408W on haplotype 1 in the British Isles. Molecular data from mild hyperphenylalaninemia (MHP) patients are available from a number of countries, but it is currently not possible to calculate relative allele frequencies. The available data on PAH mutations are useful for the understanding of both the clinical features and the population genetics of PAH deficiency in Europe.
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Affiliation(s)
- Johannes Zschocke
- Institut für Humangenetik, Ruprecht-Karls-Universität, Heidelberg, Germany.
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Kalaydjieva L, Gresham D, Calafell F. Genetic studies of the Roma (Gypsies): a review. BMC MEDICAL GENETICS 2001; 2:5. [PMID: 11299048 PMCID: PMC31389 DOI: 10.1186/1471-2350-2-5] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2001] [Accepted: 04/02/2001] [Indexed: 11/10/2022]
Abstract
BACKGROUND Data provided by the social sciences as well as genetic research suggest that the 8-10 million Roma (Gypsies) who live in Europe today are best described as a conglomerate of genetically isolated founder populations. The relationship between the traditional social structure observed by the Roma, where the Group is the primary unit, and the boundaries, demographic history and biological relatedness of the diverse founder populations appears complex and has not been addressed by population genetic studies. RESULTS Recent medical genetic research has identified a number of novel, or previously known but rare conditions, caused by private founder mutations. A summary of the findings, provided in this review, should assist diagnosis and counselling in affected families, and promote future collaborative research. The available incomplete epidemiological data suggest a non-random distribution of disease-causing mutations among Romani groups. CONCLUSION Although far from systematic, the published information indicates that medical genetics has an important role to play in improving the health of this underprivileged and forgotten people of Europe. Reported carrier rates for some Mendelian disorders are in the range of 5-15%, sufficient to justify newborn screening and early treatment, or community-based education and carrier testing programs for disorders where no therapy is currently available. To be most productive, future studies of the epidemiology of single gene disorders should take social organisation and cultural anthropology into consideration, thus allowing the targeting of public health programs and contributing to the understanding of population structure and demographic history of the Roma.
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Affiliation(s)
- Luba Kalaydjieva
- Centre for Human Genetics, Edith Cowan University, Perth, Australia
- Western Australian Institute for Medical Research, Perth, Australia
| | - David Gresham
- Centre for Human Genetics, Edith Cowan University, Perth, Australia
| | - Francesc Calafell
- Unitat de Biologia Evolutiva, Facultat de Ciencies de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
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Affiliation(s)
- L R Desviat
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Universidad Autónoma de Madrid, Spain
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