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Open Access 01-12-2013 | Research

Lack of association of rare functional variants in TSC1/TSC2 genes with autism spectrum disorder

Authors: Samira Bahl, Colby Chiang, Roberta L Beauchamp, Benjamin M Neale, Mark J Daly, James F Gusella, Michael E Talkowski, Vijaya Ramesh

Published in: Molecular Autism | Issue 1/2013

Abstract

Background

Autism spectrum disorder (ASD) is reported in 30 to 60% of patients with tuberous sclerosis complex (TSC) but shared genetic mechanisms that exist between TSC-associated ASD and idiopathic ASD have yet to be determined. Through the small G-protein Rheb, the TSC proteins, hamartin and tuberin, negatively regulate mammalian target of rapamycin complex 1 (mTORC1) signaling. It is well established that mTORC1 plays a pivotal role in neuronal translation and connectivity, so dysregulation of mTORC1 signaling could be a common feature in many ASDs. Pam, an E3 ubiquitin ligase, binds to TSC proteins and regulates mTORC1 signaling in the CNS, and the FBXO45-Pam ubiquitin ligase complex plays an essential role in neurodevelopment by regulating synapse formation and growth. Since mounting evidence has established autism as a disorder of the synapses, we tested whether rare genetic variants in TSC1, TSC2, MYCBP2, RHEB and FBXO45, genes that regulate mTORC1 signaling and/or play a role in synapse development and function, contribute to the pathogenesis of idiopathic ASD.

Methods

Exons and splice junctions of TSC1, TSC2, MYCBP2, RHEB and FBXO45 were resequenced for 300 ASD trios from the Simons Simplex Collection (SSC) using a pooled PCR amplification and next-generation sequencing strategy, targeted to the discovery of deleterious coding variation. These detected, potentially functional, variants were confirmed by Sanger sequencing of the individual samples comprising the pools in which they were identified.

Results

We identified a total of 23 missense variants in MYCBP2, TSC1 and TSC2. These variants exhibited a near equal distribution between the proband and parental pools, with no statistical excess in ASD cases (P > 0.05). All proband variants were inherited. No putative deleterious variants were confirmed in RHEB and FBXO45. Three intronic variants, identified as potential splice defects in MYCBP2 did not show aberrant splicing upon RNA assay. Overall, we did not find an over-representation of ASD causal variants in the genes studied to support them as contributors to autism susceptibility.

Conclusions

We did not observe an enrichment of rare functional variants in TSC1 and TSC2 genes in our sample set of 300 trios.

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Betancur C: Etiological heterogeneity in autism spectrum disorders: more than 100 genetic and genomic disorders and still counting. Brain Res. 2011, 1380: 42-77.CrossRefPubMed

Bourgeron T: A synaptic trek to autism. Curr Opin Neurobiol. 2009, 19: 231-234. 10.1016/j.conb.2009.06.003.CrossRefPubMed

Toro R, Konyukh M, Delorme R, Leblond C, Chaste P, Fauchereau F, Coleman M, Leboyer M, Gillberg C, Bourgeron T: Key role for gene dosage and synaptic homeostasis in autism spectrum disorders. Trends Genet. 2010, 26: 363-372. 10.1016/j.tig.2010.05.007.CrossRefPubMed

Cohen D, Pichard N, Tordjman S, Baumann C, Burglen L, Excoffier E, Lazar G, Mazet P, Pinquier C, Verloes A, Héron D: Specific genetic disorders and autism: clinical contribution towards their identification. J Autism Dev Disord. 2005, 35: 103-116. 10.1007/s10803-004-1038-2.CrossRefPubMed

Crino PB, Nathanson KL, Henske EP: The tuberous sclerosis complex. N Engl J Med. 2006, 355: 1345-1356. 10.1056/NEJMra055323.CrossRefPubMed

Han JM, Sahin M: TSC1/TSC2 signaling in the CNS. FEBS Lett. 2011, 585: 973-980. 10.1016/j.febslet.2011.02.001.PubMedCentralCrossRefPubMed

Huang J, Manning BD: The TSC1-TSC2 complex: a molecular switchboard controlling cell growth. Biochem J. 2008, 412: 179-190. 10.1042/BJ20080281.PubMedCentralCrossRefPubMed

Costa-Mattioli M, Sossin WS, Klann E, Sonenberg N: Translational control of long-lasting synaptic plasticity and memory. Neuron. 2009, 61: 10-26. 10.1016/j.neuron.2008.10.055.CrossRefPubMed

Hoeffer CA, Klann E: mTOR signaling: at the crossroads of plasticity, memory and disease. Trends Neurosci. 2010, 33: 67-75. 10.1016/j.tins.2009.11.003.PubMedCentralCrossRefPubMed

10.

Tavazoie SF, Alvarez VA, Ridenour DA, Kwiatkowski DJ, Sabatini BL: Regulation of neuronal morphology and function by the tumor suppressors Tsc1 and Tsc2. Nat Neurosci. 2005, 8: 1727-1734. 10.1038/nn1566.CrossRefPubMed

11.

Ehninger D, Han S, Shilyansky C, Zhou Y, Li W, Kwiatkowski DJ, Ramesh V, Silva AJ: Reversal of learning deficits in a Tsc2+/− mouse model of tuberous sclerosis. Nat Med. 2008, 14: 843-848. 10.1038/nm1788.PubMedCentralCrossRefPubMed

12.

Kelleher RJ, Geigenmüller U, Hovhannisyan H, Trautman E, Pinard R, Rathmell B, Carpenter R, Margulies D: High-throughput sequencing of mGluR signaling pathway genes reveals enrichment of rare variants in autism. PLoS One. 2012, 7: 1-9.CrossRef

13.

Schaaf CP, Sabo A, Sakai Y, Crosby J, Muzny D, Hawes A, Lewis L, Akbar H, Varghese R, Boerwinkle E, Gibbs RA, Zoghbi HY: Oligogenic heterozygosity in individuals with high-functioning autism spectrum disorders. Hum Mol Genet. 2011, 20: 3366-3375. 10.1093/hmg/ddr243.PubMedCentralCrossRefPubMed

14.

Garami A, Zwartkruis FJ, Nobukuni T, Joaquin M, Roccio M, Stocker H, Kozma SC, Hafen E, Bos JL, Thomas G: Insulin activation of Rheb, a mediator of mTOR/S6K/4E-BP signaling, is inhibited by TSC1 and 2. Mol Cell. 2003, 11: 1457-1466. 10.1016/S1097-2765(03)00220-X.CrossRefPubMed

15.

Zhang Y, Gao X, Saucedo LJ, Ru B, Edgar BA, Pan D: Rheb is a direct target of the tuberous sclerosis tumour suppressor proteins. Nat Cell Biol. 2003, 5: 578-581. 10.1038/ncb999.CrossRefPubMed

16.

Yamagata K, Sanders LK, Kaufmann WE, Yee W, Barnes CA, Nathans D, Worley PF: rheb, a growth factor- and synaptic activity-regulated gene, encodes a novel Ras-related protein. J Biol Chem. 1994, 269: 16333-16339.PubMed

17.

Murthy V, Han S, Beauchamp RL, Smith N, Haddad LA, Ito N, Ramesh V: Pam and its ortholog highwire interact with and may negatively regulate the TSC1.TSC2 complex. J Biol Chem. 2004, 279: 1351-1358.CrossRefPubMed

18.

Po MD, Hwang C, Zheng M: PHRs: bridging axon guidance, outgrowth and synapse development. Curr Opin Neurobiol. 2010, 20: 100-107. 10.1016/j.conb.2009.12.007.CrossRefPubMed

19.

Han S, Witt RM, Santos TM, Polizzano C, Sabatini BL, Ramesh V: Pam (Protein associated with Myc) functions as an E3 ubiquitin ligase and regulates TSC/mTOR signaling. Cell Signal. 2008, 20: 1084-1091. 10.1016/j.cellsig.2008.01.020.PubMedCentralCrossRefPubMed

20.

Han S, Kim S, Bahl S, Li L, Burande CF, Smith N, James M, Beauchamp RL, Bhide P, Diantonio A, Ramesh V: The E3 ubiquitin ligase protein associated with Myc (Pam) regulates mammalian/mechanistic target of rapamycin complex 1 (mTORC1) signaling in vivo through N- and C-terminal domains. J Biol Chem. 2012, 287: 30063-30072. 10.1074/jbc.M112.353987.PubMedCentralCrossRefPubMed

21.

Saiga T, Fukuda T, Matsumoto M, Tada H, Okano HJ, Okano H, Nakayama KI: Fbxo45 forms a novel ubiquitin ligase complex and is required for neuronal development. Mol Cell Biol. 2009, 29: 3529-3543. 10.1128/MCB.00364-09.PubMedCentralCrossRefPubMed

22.

Fischbach GD, Lord C: The Simons Simplex Collection: a resource for identification of autism genetic risk factors. Neuron. 2010, 68: 192-195. 10.1016/j.neuron.2010.10.006.CrossRefPubMed

23.

Rivas MA, Beaudoin M, Gardet A, Stevens C, Sharma Y, Zhang CK, Boucher G, Ripke S, Ellinghaus D, Burtt N, Fennell T, Kirby A, Latiano A, Goyette P, Green T, Halfvarson J, Haritunians T, Korn JM, Kuruvilla F, Lagacé C, Neale B, Lo KS, Schumm P, Törkvist L, National Institute of Diabetes and Digestive and Kidney Diseases, and Inflammatory Bowel Disease Genetics Consortium (NIDDK IBDGC), United Kingdom Inflammatory Bowel Disease Genetics Consortium, International Inflammatory Bowel Disease Genetics Consortium, Dubinsky MC, Brant SR, Silverberg MS, Duerr RH, et al: Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease. Nat Genet. 2011, 43: 1066-1073. 10.1038/ng.952.PubMedCentralCrossRefPubMed

24.

Calvo SE, Tucker EJ, Compton AG, Kirby DM, Crawford G, Burtt NP, Rivas M, Guiducci C, Bruno DL, Goldberger OA, Redman MC, Wiltshire E, Wilson CJ, Altshuler D, Gabriel SB, Daly MJ, Thorburn DR, Mootha VK: High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency. Nat Genet. 2010, 42: 851-858. 10.1038/ng.659.PubMedCentralCrossRefPubMed

25.

McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA: The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010, 20: 1297-1303. 10.1101/gr.107524.110.PubMedCentralCrossRefPubMed

26.

DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ: A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011, 43: 491-498. 10.1038/ng.806.PubMedCentralCrossRefPubMed

27.

Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR: A method and server for predicting damaging missense mutations. Nat Methods. 2010, 7: 248-249. 10.1038/nmeth0410-248.PubMedCentralCrossRefPubMed

28.

Desmet FO, Hamroun D, Lalande M, Collod-Béroud G, Claustres M, Béroud C: Human splicing finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res. 2009, 37: 1-14. 10.1093/nar/gkn923.CrossRef

29.

Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP: Integrative genomics viewer. Nat Biotechnol. 2011, 29: 24-26. 10.1038/nbt.1754.PubMedCentralCrossRefPubMed

30.

Hoogeveen-Westerveld M, Wentink M, van den Heuvel D, Mozaffari M, Ekong R, Povey S, den Dunnen JT, Metcalfe K, Vallee S, Krueger S, Bergoffen J, Shashi V, Elmslie F, Kwiatkowski D, Sampson J, Vidales C, Dzarir J, Garcia-Planells J, Dies K, Maat-Kievit A, van den Ouweland A, Halley D, Nellist M: Functional assessment of variants in the TSC1 and TSC2 genes identified in individuals with tuberous sclerosis complex. Hum Mutat. 2011, 32: 424-435. 10.1002/humu.21451.CrossRefPubMed

31.

Hoogeveen-Westerveld M, Ekong R, Povey S, Karbassi I, Batish SD, den Dunnen JT, van Eeghen A, Thiele E, Mayer K, Dies K, Wen L, Thompson C, Sparagana SP, Davies P, Aalfs C, van den Ouweland A, Halley D, Nellist M: Functional assessment of TSC1 missense variants identified in individuals with tuberous sclerosis complex. Hum Mutat. 2012, 33: 476-479. 10.1002/humu.22007.CrossRefPubMed

32.

Hoogeveen-Westerveld M, Ekong R, Povey S, Mayer K, Lannoy N, Elmslie F, Bebin M, Dies K, Thompson C, Sparagana SP, Davies P, van den Ouweland A, Halley D, Nellist M: Functional assessment of TSC2 variants identified in individuals with tuberous sclerosis complex. Hum Mutat. 2013, 34: 167-175. 10.1002/humu.22202.CrossRefPubMed

33.

Sahin M: Targeted treatment trials for tuberous sclerosis and autism: no longer a dream. Curr Opin Neurobiol. 2012, 22: 1-7. 10.1016/j.conb.2012.01.004.CrossRef

34.

Bloom AJ, Miller BR, Sanes JR, DiAntonio A: The requirement for Phr1 in CNS axon tract formation reveals the corticostriatal boundary as a choice point for cortical axons. Genes Dev. 2007, 21: 2593-2606. 10.1101/gad.1592107.PubMedCentralCrossRefPubMed

35.

Lewcock JW, Genoud N, Lettieri K, Pfaff SL: The ubiquitin ligase Phr1 regulates axon outgrowth through modulation of microtubule dynamics. Neuron. 2007, 56: 604-620. 10.1016/j.neuron.2007.09.009.CrossRefPubMed

36.

Nejentsev S, Walker N, Riches D, Egholm M, Todd JA: Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes. Science. 2009, 324: 387-389. 10.1126/science.1167728.PubMedCentralCrossRefPubMed

37.

Neale BM, Kou Y, Liu L, Ma'ayan A, Samocha KE, Sabo A, Lin CF, Stevens C, Wang LS, Makarov V, Polak P, Yoon S, Maguire J, Crawford EL, Campbell NG, Geller ET, Valladares O, Schafer C, Liu H, Zhao T, Cai G, Lihm J, Dannenfelser R, Jabado O, Peralta Z, Nagaswamy U, Muzny D, Reid JG, Newsham I, Wu Y: Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature. 2012, 485: 242-245. 10.1038/nature11011.PubMedCentralCrossRefPubMed

38.

Sanders SJ, Murtha MT, Gupta AR, Murdoch JD, Raubeson MJ, Willsey AJ, Ercan-Sencicek AG, DiLullo NM, Parikshak NN, Stein JL, Walker MF, Ober GT, Teran NA, Song Y, El-Fishawy P, Murtha RC, Choi M, Overton JD, Bjornson RD, Carriero NJ, Meyer KA, Bilguvar K, Mane SM, Sestan N, Lifton RP, Günel M, Roeder K, Geschwind DH, Devlin B, State MW: De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature. 2012, 485: 237-241. 10.1038/nature10945.PubMedCentralCrossRefPubMed

39.

O'Roak BJ, Vives L, Girirajan S, Karakoc E, Krumm N, Coe BP, Levy R, Ko A, Lee C, Smith JD, Turner EH, Stanaway IB, Vernot B, Malig M, Baker C, Reilly B, Akey JM, Borenstein E, Rieder MJ, Nickerson DA, Bernier R, Shendure J, Eichler EE: Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature. 2012, 485: 246-250. 10.1038/nature10989.PubMedCentralCrossRefPubMed

40.

Hsu PP, Kang SA, Rameseder J, Zhang Y, Ottina KA, Lim D, Peterson TR, Choi Y, Gray NS, Yaffe MB, Marto JA, Sabatini DM: The mTOR-regulated phosphoproteome reveals a mechanism of mTORC1-mediated inhibition of growth factor signaling. Science. 2011, 332: 1317-1322. 10.1126/science.1199498.PubMedCentralCrossRefPubMed

41.

Yu Y, Yoon SO, Poulogiannis G, Yang Q, Ma XM, Villén J, Kubica N, Hoffman GR, Cantley LC, Gygi SP, Blenis J: Phosphoproteomic analysis identifies Grb10 as an mTORC1 substrate that negatively regulates insulin signaling. Science. 2011, 332: 1322-1326. 10.1126/science.1199484.PubMedCentralCrossRefPubMed

42.

Darnell JC, Van Driesche SJ, Zhang C, Hung KY, Mele A, Fraser CE, Stone EF, Chen C, Fak JJ, Chi SW, Licatalosi DD, Richter JD, Darnell RB: FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism. Cell. 2011, 146: 247-261. 10.1016/j.cell.2011.06.013.PubMedCentralCrossRefPubMed

43.

Muhle R, Trentacoste SV, Rapin I: The genetics of autism. Pediatrics. 2004, 113: e472-486. 10.1542/peds.113.5.e472.CrossRefPubMed

44.

Fombonne E, du Mazaubrun C: Prevalence of infantile autism in four French regions. Soc Psychiatry Psychiatr Epidemiol. 1992, 27: 203-210. 10.1007/BF00789007.CrossRefPubMed

45.

Fombonne E, Du Mazaubrun C, Cans C, Grandjean H: Autism and associated medical disorders in a French epidemiological survey. J Am Acad Child Adolesc Psychiatry. 1997, 36: 1561-1569.PubMed

46.

Chakrabarti S, Fombonne E: Pervasive developmental disorders in preschool children. JAMA. 2001, 285: 3093-3099. 10.1001/jama.285.24.3093.CrossRefPubMed

47.

Chudley AE, Gutierrez E, Jocelyn LJ, Chodirker BN: Outcomes of genetic evaluation in children with pervasive developmental disorder. J Dev Behav Pediatr. 1998, 19: 321-325. 10.1097/00004703-199810000-00001.CrossRefPubMed

Title: Lack of association of rare functional variants in TSC1/TSC2 genes with autism spectrum disorder
Authors: Samira Bahl
Colby Chiang
Roberta L Beauchamp
Benjamin M Neale
Mark J Daly
James F Gusella
Michael E Talkowski
Vijaya Ramesh
Publication date: 01-12-2013
Publisher: BioMed Central
Published in: Molecular Autism / Issue 1/2013
Electronic ISSN: 2040-2392
DOI: https://doi.org/10.1186/2040-2392-4-5

2024 ASCO Annual Meeting

Springer Medicine

Lack of association of rare functional variants in TSC1/TSC2 genes with autism spectrum disorder

Abstract

Background

Methods

Results

Conclusions

2024 ASCO Annual Meeting

Springer Medicine

Abstract

Background

Methods

Results

Conclusions

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