Beyond Repeats: Intragenic Variants in FMR1 and Their Contribution to Fragile X Syndrome Pathogenesis
DOI:
https://doi.org/10.54548/چکیده
Fragile X Syndrome (FXS), the most common inherited cause of intellectual disability, is typically caused by expansion of a CGG triplet repeat in the 5′ untranslated region (5′-UTR) of the FMR1 gene. Growing evidence indicates that intragenic mutations in FMR1, including single-nucleotide variants (SNVs) and structural changes, can also alter FMR1 function without the classical pathogenic expansion of CGG repeats. This study re-analysed publicly available next-generation sequencing (NGS) data from BioProject PRJNA745542 using a reproducible Galaxy-based bioinformatics workflow to identify non-repeat intragenic FMR1 variants. Of 18 available datasets, 11 paired-end Illumina samples passing quality control (Phred > 30) were analysed for non-repeat intragenic FMR1 variants. Ninety-one unique variants were identified: 61 single-nucleotide variants (SNVs), 26 insertions/deletions (indels), three mixed (complex) variants, and one multi-nucleotide polymorphism (MNP), producing 1,107 predicted gene effects. SnpEff predicted sixteen variants to have high or moderate impact, predominantly within the KH1 and KH2 RNA-binding domains of FMRP. Most predicted effects (94.3%) were intronic or non-coding, suggesting a possible regulatory role in the expression or processing of FMR1 transcripts. These preliminary findings warrant validation in larger cohorts of subjects with verified disease status. High-impact KH-domain variants are predicted to disrupt hydrogen bonding required for FMRP RNA-binding and mRNA transport. This study extends the known mutation spectrum of FMR1 and supports the development of comprehensive NGS-based diagnostic assays that combine intragenic SNV and indel detection with quantitative CGG repeat analysis. Further studies using cellular or animal models are needed to validate the candidate variants identified and their potential role in Fragile X syndrome pathogenesis
مراجع
Ascano, M., Mukherjee, N., Bandaru, P., Miller, J.B., Nusbaum, J.D., Corcoran, D.L., Langlois, C., Munschauer, M., Dewell, S., Hafner, M., Williams, Z., Ohler, U. and Tuschl, T. (2012). FMRP targets distinct mRNA sequence elements to regulate protein expression. Nature, 492(7429), 382–386. https://doi.org/10.1038/nature11737
Bagni, C., and Zukin, R. S. (2019). A synaptic perspective of fragile X syndrome and autism spectrum disorders. Neuron, 101(6), 1070–1088. https://doi.org/10.1016/j.neuron.2019.02.041
Chen, E., and Joseph, S. (2015). Fragile X mental retardation protein: A paradigm for translational control by RNA-binding proteins. Biochimie, 114, 147–154.
Cingolani, P., Platts, A., Wang, L.L., Coon, M., Nguyen, T., Wang, L., Land, S.J., Lu, X. and Ruden, D.M. (2012). A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly, 6(2), 80–92. https://doi.org/10.4161/fly.19695
Coffee, B., Zhang, F., Ceman, S., Warren, S. T., and Reines, D. (2009). Histone modifications depict an aberrantly heterochromatinized FMR1 gene in fragile X syndrome. American Journal of Human Genetics, 85(6), 866–872.
Collins, S. C., Bray, S. M., and Suhl, J. A. (2010). Identification of novel FMR1 variants by next-generation sequencing. Human Mutation, 31(5), 595–600.
Darnell, J.C., Van Driesche, S.J., Zhang, C., Hung, K.Y.S., Mele, A., Fraser, C.E., Stone, E.F., Chen, C., Fak, J.J., Chi, S.W., Licatalosi, D.D., Richter, J.D. and Darnell, R.B. (2011). FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism. Cell, 146(2), 247–261. https://doi.org/10.1016/j.cell.2011.06.013
Garrison, E., and Marth, G. (2012). Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907.
Geng, Y., Hsu, R., and Zhu, Y. (2018). Functional consequences of FMR1 truncating mutations. Human Molecular Genetics, 27(10), 1727–1738.
Hagerman, R. J., and Hagerman, P. J. (2016). Fragile X-associated tremor/ataxia syndrome. Annals of the New York Academy of Sciences, 1338(1), 58–70.
Karczewski, K.J., Francioli, L.C., Tiao, G., Cummings, B.B., Alföldi, J., Wang, Q., Collins, R.L., Laricchia, K.M., Ganna, A., Birnbaum, D.P., Gauthier, L.D., Brand, H., Solomonson, M., Watts, N.A., Rhodes, D., Singer-Berk, M., England, E.M., Seaby, E.G., Kosmicki, J.A. and Walters, R.K., et al. (2020). The mutational constraint spectrum quantified from variation in 141,456 humans. Nature, 581(7809), 434–443. https://doi.org/10.1038/s41586-020-2308-7
Kim, D., Paggi, J. M., Park, C., Bennett, C., and Salzberg, S. L. (2019). Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature Biotechnology, 37(8), 907–915. https://doi.org/10.1038/s41587-019-0201-4
Kumar, S., Ambrosini, G., and Bucher, P. (2019). SNP distribution in regulatory regions of neurodevelopmental genes. Genome Research, 29(5), 720–730.
Lek, M., Karczewski, K.J., Minikel, E.V., Samocha, K.E., Banks, E., Fennell, T., O'Donnell-Luria, A.H., Ware, J.S., Hill, A.J., Cummings, B.B., Tukiainen, T., Birnbaum, D.P., Kosmicki, J.A., Duncan, L.E., Estrada, K., Zhao, F., Zou, J., Pierce-Hoffman, E., Berghout, J., Cooper, D.N., Deflaux, N., DePristo, M., Do, R., Flannick, J., Fromer, M., Gauthier, L., Goldstein, J., Gupta, N., Howrigan, D., Kiezun, A., Kurki, M.I., Moonshine, A.L., Natarajan, P., Orozco, L., Peloso, G.M., Poplin, R., Rivas, M.A., Ruano-Rubio, V., Rose, S.A., Ruderfer, D.M., Shakir, K., Stenson, P.D., Stevens, C., Thomas, B.P., Tiao, G., Tusie-Luna, M.T., Weisburd, B., Won, H.-H., Yu, D., Altshuler, D.M., Ardissino, D., Boehnke, M., Danesh, J., Donnelly, S., Elosua, R., Florez, J.C., Gabriel, S.B., Getz, G., Glatt, S.J., Hultman, C.M., Kathiresan, S., Laakso, M., McCarroll, S., McCarthy, M.I., McGovern, D., McPherson, R., Neale, B.M., Palotie, A., Purcell, S.M., Saleheen, D., Scharf, J.M., Sklar, P., Sullivan, P.F., Tuomilehto, J., Tsuang, M.T., Watkins, H.C., Wilson, J.G., Daly, M.J. and MacArthur, D.G., (2016). Analysis of protein-coding genetic variation in 60,706 humans. Nature, 536(7616), 285–291. https://doi.org/10.1038/nature19057
Landrum, M.J., Lee, J.M., Benson, M., Brown, G.R., Chao, C., Chitipiralla, S., Gu, B., Hart, J., Hoffman, D., Hoover, J., Jang, W., Katz, K., Ovetsky, M., Riley, G., Sethi, A., Tully, R., Villamarin-Salomon, R., Rubinstein, W.S. and Maglott, D.R. (2018). ClinVar: Improving access to variant interpretations and supporting evidence. Nucleic Acids Research, 46(D1), D1062–D1067.
Luo, Y., Shan, G., Guo, W., Smrt, R.D., Johnson, E.B., Li, X., Pfeiffer, R.L., Szulwach, K.E., Duan, R., Barkho, B.Z., Li, W., Liu, C., Jin, P. and Zhao, X., (2010). Fragile X mental retardation protein regulates proliferation and differentiation of adult neural stem/progenitor cells. PLoS Genetics, 6(4), e1000898.
Myrick, L.K., Deng, P.-Y., Hashimoto, H., Oh, Y.M., Cho, Y., Poidevin, M.J., Suhl, J.A., Visootsak, J., Cavalli, V., Jin, P., Cheng, X., Warren, S.T. and Klyachko, V.A., 2015. Independent role for presynaptic FMRP revealed by an FMR1 missense mutation associated with intellectual disability and seizures. Proceedings of the National Academy of Sciences of the United States of America, 112(4), pp.949–956.
Okeke, I.N. and Ihekweazu, C., (2021). The importance of molecular diagnostics for infectious diseases in low-resource settings. Nature Reviews Microbiology, 19(9), pp.547–548.
Oostra, B. A., and Willemsen, R. (2009). FMR1: A gene with three faces. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, 1790(6), 467–477.
Pirooznia, M., Goes, F. S., and Zandi, P. P. (2021). Whole-genome sequencing in psychiatric disorders: The role of rare variants. Neuropsychopharmacology, 46(1), 64–75.
Richards, S., Aziz, N., Bale, S., Bick, D., Das, S., Gastier-Foster, J., Grody, W.W., Hegde, M., Lyon, E., Spector, E., Voelkerding, K. and Rehm, H.L., on behalf of the ACMG Laboratory Quality Assurance Committee. (2015). Standards and guidelines for the interpretation of sequence variants. Genetics in Medicine, 17(5), 405–424.
Sauna, Z. E., and Kimchi-Sarfaty, C. (2011). Understanding the contribution of synonymous mutations to human disease. Nature Reviews Genetics, 12(10), 683–691.
Sherman, S.L., Kidd, S.A., Riley, C., Berry-Kravis, E., Andrews, H.F., Miller, R.M., Lincoln, S., Swanson, M., Kaufmann, W.E. and Brown, W.T., 2017. FORWARD: A Registry and Longitudinal Clinical Database to Study Fragile X Syndrome. Pediatrics, 139(Suppl. 3), pp.S183–S193.
Supek, F., Miñana, B., Valcárcel, J., Gabaldón, T., and Lehner, B. (2014). Synonymous mutations frequently act as driver mutations in human cancers. Cell, 156(6), 1324–1335.
Tassone, F., Iong, K. P., Tong, T. H., Lo, J., Gane, L. W., Berry-Kravis, E., and Hagerman, R. J. (2012). FMR1 CGG allele size and prevalence ascertained through newborn screening. American Journal of Medical Genetics Part A, 158A(8), 2033–2040.
Tekendo-Ngongang, C., Grochowsky, A., Solomon, B. D., and Yano, S. T. (2021). Beyond trinucleotide repeat expansion in Fragile X syndrome: Rare coding and noncoding variants in FMR1 and associated phenotypes. Genes, 12(11), 1669.
Valentina, R., et al. (2021). Public NGS dataset for Fragile X-associated regions. NCBI BioProject PRJNA745542.
Verkerk, A. J. M. H., Pieretti, M., Sutcliffe, J. S., Fu, Y. H., Kuhl, D. P. A., Pizzuti, A., … Warren, S. T. (1991). Identification of a gene (FMR1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome. Cell, 65(5), 905–914.
Wheeler, A. C., Bailey, D. B., and Berry-Kravis, E. (2014). Associated features in Fragile X syndrome. Journal of Neurodevelopmental Disorders, 6(1), 1–10.
دانلودها
چاپ شده
شماره
نوع مقاله
مجوز
حق نشر 2026 Nigerian Journal of Physiological Sciences
این پروژه تحت مجوز بین المللی Creative Commons Attribution 4.0 می باشد.
