Evaluation of the influence of single-nucleotide polymorphisms of vitamin D receptor (rs2228570), BDNF (rs6265), and NMDA (rs4880213) genes on gene expression in different tissues
Background. Questions regarding the association of individual and combined gene variations and mutations with thyroid disease and nervous system disorders remain insufficiently researched and require further study to facilitate early diagnosis of nervous system damage on the background of thyroid pa...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Zaslavsky O.Yu.
2023-04-01
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| Series: | Mìžnarodnij Endokrinologìčnij Žurnal |
| Subjects: | |
| Online Access: | https://iej.zaslavsky.com.ua/index.php/journal/article/view/1250 |
| _version_ | 1797811215451291648 |
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| author | I. Kamyshna L. Pavlovych I. Pankiv V. Pankiv A. Kamyshnyi |
| author_facet | I. Kamyshna L. Pavlovych I. Pankiv V. Pankiv A. Kamyshnyi |
| author_sort | I. Kamyshna |
| collection | DOAJ |
| description | Background. Questions regarding the association of individual and combined gene variations and mutations with thyroid disease and nervous system disorders remain insufficiently researched and require further study to facilitate early diagnosis of nervous system damage on the background of thyroid pathology, disease prognosis, and timely treatment and prevention. An important issue is the identification of the influence of individual polymorphisms in these genes on the functional activity of cells, including gene expression. Currently, gene expression genetics largely depends on the identification of expression quantitative trait loci (eQTL), which are the links between gene expression and genotype at a locus. The purpose of the study was to search for eQTL in single nucleotide polymorphisms (SNPs) of the BDNF gene (rs6265), VDR gene (rs2228570), and NMDA gene (rs4880213). The results were presented as nominal p-values for each SNP of the BDNF, VDR, and NMDA genes. Materials and methods. We use publicly available databases (QTLbase: http://www.mulinlab.org/qtlbase/index.html, GTExPortal: https://gtexportal.org). Results. Using the QTLbase, we identified statistically significant (p ≤ 0.05) associations of rs6265 with the expression of 17 genes (BDNF-AS, BDNF, LDHC, AC104563.1, BBOX1, SPTY2D1OS, YWHABP2, LINC00678, LIN7C, GTF2H1, METTL15, IMMP1L, KIF18A, HPS5, NAV2, LGR4, CCDC34) in various tissues. For rs4880213, we found a significant association with the expression levels of 49 genes (ARRDC1-AS1, TPRN, SSNA1, SAPCD2, UAP1L1, NPDC1, MAN1B1, PTGDS, SNHG7, NDOR1, TRAF2, PHPT1, EGFL7, EHMT1, RNF208, PNPLA7, LCNL1, DPP7, LCN12, STPG3, CCDC183-AS1, ABCA2, RNF224, ENTPD2, PAXX, CLIC3, C9orf163, LCN15, MAN1B1-DT, FAM166A, FAM166A, LRRC26, STPG3-AS1, AGPAT2, ANAPC2, DPH7, ZMYND19, NSMF, MRPL41, EXD3, TUBB4B, NELFB, ARRDC1, EDF1, FBXW5, DIPK1B, MAMDC4, RABL6, TMEM141, TMEM203) in 16 different tissues. Additionally, we identified statistically significant (p ≤ 0.05) associations of rs2228570 with the expression of 29 genes (ASB8, TMEM106C, KANSL2, DDX23, CCNT1, HDAC7, RPAP3, PFKM, SENP1, RND1, PCED1B, AC004466.1, AMIGO2, ZNF641, ENDOU, RAPGEF3, VDR, AC004241.1, AC004801.2, AC121338.1, LINC02354, SNORA2A, LINC02416, AC074029.3, AC004241.5, AC008083.3, COL2A1, CCDC184, SLC48A1) in 17 different tissues. Conclusions. Single nucleotide polymorphisms of the BDNF (rs6265), VDR (rs2228570), and NMDA genes (rs4880213) affect gene expression in various cells and tissues. The use of this extensive eQTL catalog provides an important resource for understanding the molecular basis of common genetic diseases. |
| first_indexed | 2024-03-13T07:19:22Z |
| format | Article |
| id | doaj.art-a280fc0af15247d3bae8a604077b81e4 |
| institution | Directory Open Access Journal |
| issn | 2224-0721 2307-1427 |
| language | English |
| last_indexed | 2024-03-13T07:19:22Z |
| publishDate | 2023-04-01 |
| publisher | Zaslavsky O.Yu. |
| record_format | Article |
| series | Mìžnarodnij Endokrinologìčnij Žurnal |
| spelling | doaj.art-a280fc0af15247d3bae8a604077b81e42023-06-04T19:53:39ZengZaslavsky O.Yu.Mìžnarodnij Endokrinologìčnij Žurnal2224-07212307-14272023-04-01192838810.22141/2224-0721.19.2.2023.12501248Evaluation of the influence of single-nucleotide polymorphisms of vitamin D receptor (rs2228570), BDNF (rs6265), and NMDA (rs4880213) genes on gene expression in different tissuesI. Kamyshna0https://orcid.org/0000-0002-4483-1856L. Pavlovych1https://orcid.org/0000-0002-7261-6141I. Pankiv2https://orcid.org/0000-0001-5576-636XV. Pankiv3https://orcid.org/0000-0002-9205-9530A. Kamyshnyi4https://orcid.org/0000-0003-3141-4436I. Horbachevsky Ternopil National Medical University, Ternopil, UkraineBukovinian State Medical University, Chernivtsi, UkraineBukovinian State Medical University, Chernivtsi, UkraineUkrainian Scientific and Practical Center for Endocrine Surgery, Transplantation of Endocrine Organsand Tissues of the Ministry of Health of Ukraine, Kyiv, UkraineI. Horbachevsky Ternopil National Medical University, Ternopil, UkraineBackground. Questions regarding the association of individual and combined gene variations and mutations with thyroid disease and nervous system disorders remain insufficiently researched and require further study to facilitate early diagnosis of nervous system damage on the background of thyroid pathology, disease prognosis, and timely treatment and prevention. An important issue is the identification of the influence of individual polymorphisms in these genes on the functional activity of cells, including gene expression. Currently, gene expression genetics largely depends on the identification of expression quantitative trait loci (eQTL), which are the links between gene expression and genotype at a locus. The purpose of the study was to search for eQTL in single nucleotide polymorphisms (SNPs) of the BDNF gene (rs6265), VDR gene (rs2228570), and NMDA gene (rs4880213). The results were presented as nominal p-values for each SNP of the BDNF, VDR, and NMDA genes. Materials and methods. We use publicly available databases (QTLbase: http://www.mulinlab.org/qtlbase/index.html, GTExPortal: https://gtexportal.org). Results. Using the QTLbase, we identified statistically significant (p ≤ 0.05) associations of rs6265 with the expression of 17 genes (BDNF-AS, BDNF, LDHC, AC104563.1, BBOX1, SPTY2D1OS, YWHABP2, LINC00678, LIN7C, GTF2H1, METTL15, IMMP1L, KIF18A, HPS5, NAV2, LGR4, CCDC34) in various tissues. For rs4880213, we found a significant association with the expression levels of 49 genes (ARRDC1-AS1, TPRN, SSNA1, SAPCD2, UAP1L1, NPDC1, MAN1B1, PTGDS, SNHG7, NDOR1, TRAF2, PHPT1, EGFL7, EHMT1, RNF208, PNPLA7, LCNL1, DPP7, LCN12, STPG3, CCDC183-AS1, ABCA2, RNF224, ENTPD2, PAXX, CLIC3, C9orf163, LCN15, MAN1B1-DT, FAM166A, FAM166A, LRRC26, STPG3-AS1, AGPAT2, ANAPC2, DPH7, ZMYND19, NSMF, MRPL41, EXD3, TUBB4B, NELFB, ARRDC1, EDF1, FBXW5, DIPK1B, MAMDC4, RABL6, TMEM141, TMEM203) in 16 different tissues. Additionally, we identified statistically significant (p ≤ 0.05) associations of rs2228570 with the expression of 29 genes (ASB8, TMEM106C, KANSL2, DDX23, CCNT1, HDAC7, RPAP3, PFKM, SENP1, RND1, PCED1B, AC004466.1, AMIGO2, ZNF641, ENDOU, RAPGEF3, VDR, AC004241.1, AC004801.2, AC121338.1, LINC02354, SNORA2A, LINC02416, AC074029.3, AC004241.5, AC008083.3, COL2A1, CCDC184, SLC48A1) in 17 different tissues. Conclusions. Single nucleotide polymorphisms of the BDNF (rs6265), VDR (rs2228570), and NMDA genes (rs4880213) affect gene expression in various cells and tissues. The use of this extensive eQTL catalog provides an important resource for understanding the molecular basis of common genetic diseases.https://iej.zaslavsky.com.ua/index.php/journal/article/view/1250genotypeexpressionnucleotide polymorphismsbdnf gene (rs6265)vdr gene (rs2228570)nmda gene (rs4880213) |
| spellingShingle | I. Kamyshna L. Pavlovych I. Pankiv V. Pankiv A. Kamyshnyi Evaluation of the influence of single-nucleotide polymorphisms of vitamin D receptor (rs2228570), BDNF (rs6265), and NMDA (rs4880213) genes on gene expression in different tissues Mìžnarodnij Endokrinologìčnij Žurnal genotype expression nucleotide polymorphisms bdnf gene (rs6265) vdr gene (rs2228570) nmda gene (rs4880213) |
| title | Evaluation of the influence of single-nucleotide polymorphisms of vitamin D receptor (rs2228570), BDNF (rs6265), and NMDA (rs4880213) genes on gene expression in different tissues |
| title_full | Evaluation of the influence of single-nucleotide polymorphisms of vitamin D receptor (rs2228570), BDNF (rs6265), and NMDA (rs4880213) genes on gene expression in different tissues |
| title_fullStr | Evaluation of the influence of single-nucleotide polymorphisms of vitamin D receptor (rs2228570), BDNF (rs6265), and NMDA (rs4880213) genes on gene expression in different tissues |
| title_full_unstemmed | Evaluation of the influence of single-nucleotide polymorphisms of vitamin D receptor (rs2228570), BDNF (rs6265), and NMDA (rs4880213) genes on gene expression in different tissues |
| title_short | Evaluation of the influence of single-nucleotide polymorphisms of vitamin D receptor (rs2228570), BDNF (rs6265), and NMDA (rs4880213) genes on gene expression in different tissues |
| title_sort | evaluation of the influence of single nucleotide polymorphisms of vitamin d receptor rs2228570 bdnf rs6265 and nmda rs4880213 genes on gene expression in different tissues |
| topic | genotype expression nucleotide polymorphisms bdnf gene (rs6265) vdr gene (rs2228570) nmda gene (rs4880213) |
| url | https://iej.zaslavsky.com.ua/index.php/journal/article/view/1250 |
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