Abrahams, B.S., Arking, D.E., Campbell, D.B., Mefford, H.C., Morrow, E.M., Weiss, L.A., Menashe, I., Wadkins, T., Banerjee-Basu, S., Packer, A., 2013. SFARI Gene 2.0:a community-driven knowledgebase for the autism spectrum disorders (ASDs). Mol. Autism. 4, 1-3.
|
Aibar, S., González-Blas, C.B., Moerman, T., Huynh-Thu, V.A., Imrichova, H., Hulselmans, G., Rambow, F., Marine, J.C., Geurts, P., Aerts, J., van den Oord, J., et al., 2017. SCENIC:single-cell regulatory network inference and clustering. Nat. Methods 14, 1083-1086.
|
Akintunde, M.E., Rose, M., Krakowiak, P., Heuer, L., Ashwood, P., Hansen, R., Hertz-Picciotto, I., Van de Water, J., 2015. Increased production of IL-17 in children with autism spectrum disorders and co-morbid asthma. J. Neuroimmunol. 286, 33-41.
|
Allen-Brady, K., Miller, J., Matsunami, N., Stevens, J., Block, H., Farley, M., Krasny, L., Pingree, C., Lainhart, J., Leppert, M., et al., 2009. A high-density SNP genome-wide linkage scan in a large autism extended pedigree. Mol. Psychiatry 14, 590-600.
|
Amaral, D.G., Schumann, C.M., Nordahl, C.W., 2008. Neuroanatomy of autism. Trends Neurosci. 31, 137-145.
|
Arnold, M., Saijo, K., 2021. Estrogen receptor β as a candidate regulator of sex differences in the maternal immune activation model of ASD. Front. Mol. Neurosci. 14, 717411.
|
Bargiela, S., Steward, R., Mandy, W., 2016. The experiences of late-diagnosed women with autism spectrum conditions:an investigation of the female autism phenotype. J. Autism Dev. Disord. 46, 3281-3294.
|
Baron-Cohen, S., Lombardo, M.V., Auyeung, B., Ashwin, E., Chakrabarti, B., Knickmeyer, R., 2011. Why are autism spectrum conditions more prevalent in males? PLoS Biol. 9, e1001081.
|
Becht, E., McInnes, L., Healy, J., Dutertre, C.A., Kwok, I.W.H., Ng, L.G., Ginhoux, F., Newell, E.W., 2019. Dimensionality reduction for visualizing single-cell data using UMAP. Nat. Biotechnol. 37, 38.
|
Brewer, G.J., Torricelli, J.R., 2007. Isolation and culture of adult neurons and neurospheres. Nat. Protoc. 2, 1490.
|
Brumback, A.C., Ellwood, I., Kjaerby, C., Iafrati, J., Robinson, S., Lee, A., Patel, T., Nagaraj, S., Davatolhagh, F., Sohal, V.S., 2018. Identifying specific prefrontal neurons that contribute to autism-associated abnormalities in physiology and social behavior. Mol. Psychiatry 23, 2078-2089.
|
Chaste, P., Leboyer, M., 2012. Autism risk factors:genes, environment, and gene-environment interactions. Dialogues Clin. Neurosci. 14, 281.
|
Chen, J., Alberts, I., Li, X., 2014. Dysregulation of the IGF-I/PI3K/AKT/mTOR signaling pathway in autism spectrum disorders. Int. J. Dev. Neurosci. 35, 35-41.
|
Corbett, B., Kantor, A.B., Schulman, H., Walker, W.L., Lit, L., Ashwood, P., Rocke, D.M., Sharp, F.R., 2007. A proteomic study of serum from children with autism showing differential expression of apolipoproteins and complement proteins. Mol. Psychiatry 12, 292-306.
|
Dougherty, J.D., Marrus, N., Maloney, S.E., Yip, B., Sandin, S., Turner, T.N., Selmanovic, D., Kroll, K.L., Gutmann, D.H., Constantino, J.N., 2022. Can the "female protective effect" liability threshold model explain sex differences in autism spectrum disorder? Neuron 110, 3243-3262.
|
Efremova, M., Vento-Tormo, M., Teichmann, S.A., Vento-Tormo, R., 2020. CellPhoneDB:inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes. Nat. Protoc. 15, 1484-1506.
|
Esteban, F.J., Wall, D.P., 2011. Using game theory to detect genes involved in autism spectrum disorder. Top. 19, 121-129.
|
Fatemi, S.H., Folsom, T.D., Reutiman, T.J., Abu-Odeh, D., Mori, S., Huang, H., Oishi, K., 2009. Abnormal expression of myelination genes and alterations in white matter fractional anisotropy following prenatal viral influenza infection at E16 in mice. Schizophr. Res. 112, 46-53.
|
Felder, B., Radlwimmer, B., Benner, A., Mincheva, A., Tödt, G., Beyer, K.S., Schuster, C., Bölte, S., Schmötzer, G., Klauck, S.M., et al., 2009. FARP2, HDLBP and PASK are down-regulated in a patient with autism and 2q37. 3 deletion syndrome. Am. J. Med. Genet. A. 149, 952-959.
|
Feleke, R., Jazayeri, D., Abouzeid, M., Powell, K.L., Srivastava, P.K., O'Brien, T.J., Jones, N.C., Johnson, M.R., 2022. Integrative genomics reveals pathogenic mediator of valproate-induced neurodevelopmental disability. Brain 145, 3832-3842.
|
Ferri, S.L., Abel, T., Brodkin, E.S., 2018. Sex differences in autism spectrum disorder:a review. Curr. Psychiatry Rep. 20, 1-17.
|
Fombonne, E., 2005. The changing epidemiology of autism. J. Appl. Res. Intellect. Disabil. 18, 281-294.
|
Fujita-Jimbo, E., Yu, Z.L., Li, H., Yamagata, T., Mori, M., Momoi, T., Momoi, M.Y., 2012. Mutation in Parkinson disease-associated, G-protein-coupled receptor 37(GPR37/PaelR) is related to autism spectrum disorder. PLoS ONE. 7, e51155.
|
Garbett, K., Ebert, P.J., Mitchell, A., Lintas, C., Manzi, B., Mirnics, K., Persico, A.M., 2008. Immune transcriptome alterations in the temporal cortex of subjects with autism. Neurobiol. Dis. 30, 303-311.
|
Gupta, S., Ellis, S.E., Ashar, F.N., Moes, A., Bader, J.S., Zhan, J., West, A.B., Arking, D.E., 2014. Transcriptome analysis reveals dysregulation of innate immune response genes and neuronal activity-dependent genes in autism. Nat. Commun. 5, 5748.
|
Hadley, D., Wu, Z.L., Kao, C., Kini, A., Mohamed-Hadley, A., Thomas, K., Vazquez, L., Qiu, H., Mentch, F., Pellegrino, R., et al., 2014. The impact of the metabotropic glutamate receptor and other gene family interaction networks on autism. Nat. Commun. 5, 1-10.
|
Herz, J., Chen, Y., 2006. Reelin lipoprotein receptors and synaptic plasticity. Nat. Rev. Neurosci. 7, 850-859.
|
Hettinger, J.A., 2008. A PPP1R1B Polymorphism is Associated with Risk for Autism Spectrum Disorders in Male-only Affected Sib-pair Families.
|
Hu, V.W., 2012. Subphenotype-dependent disease markers for diagnosis and personalized treatment of autism spectrum disorders. Dis. Markers. 33, 277-288.
|
Ito, Y., Nakamura, Y., Takahashi, N., Saito, S., Aleksic, B., Iwata, N., Inada, T., Ozaki, N., 2008. A genetic association study of the FXYD domain containing ion transport regulator 6 (FXYD6) gene, encoding phosphohippolin, in susceptibility to schizophrenia in a Japanese population. Neurosci. Lett. 438, 70-75.
|
Lombardo, M.V., 2021. Ribosomal protein genes in post-mortem cortical tissue and iPSC-derived neural progenitor cells are commonly up-regulated in expression in autism. Mol. Psychiatry 26, 1432-1435.
|
Lucchina, L., Depino, A.M., 2014. Altered peripheral and central inflammatory responses in a mouse model of autism. Autism Res. 7, 273-289.
|
May, P., Rohlmann, A., Bock, H.H., Zurhove, K., Marth, J.D., Schomburg, E.D., Noebels, J.L., Beffert, U., Sweatt, J.D., Weeber, E.J., et al., 2004. Neuronal LRP1 functionally associates with postsynaptic proteins and is required for normal motor function in mice. Mol. Cell. Biol. 24, 8872-8883.
|
Morgan, J.T., Chana, G., Pardo, C.A., Achim, C., Semendeferi, K., Buckwalter, J., Courchesne, E., Everall, I.P., 2010. Microglial activation and increased microglial density observed in the dorsolateral prefrontal cortex in autism. Biol. Psychiatry 68, 368-376.
|
Mostafa, G.A., Al-Ayadhi, L.Y., 2012. Reduced serum concentrations of 25-hydroxy vitamin D in children with autism:relation to autoimmunity. J. Neuroinflamm. 9, 1-7.
|
Nadeem, A., Ahmad, S.F., Attia, S.M., Bakheet, S.A., Al-Harbi, N.O., Al-Ayadhi, L.Y., 2018. Activation of IL-17 receptor leads to increased oxidative inflammation in peripheral monocytes of autistic children. Brain Behav. Immun. 67, 335-344.
|
Nadler, J., Moy, S.S., Dold, G., Trang, D., Simmons, N., Perez, A., Young, N.B., Barbaro, R.P., Piven, J., Magnuson, T.R., et al., 2004. Automated apparatus for quantitation of social approach behaviors in mice. Genes Brain Behav. 3, 303-314.
|
Nassir, N., Bankapur, A., Samara, B., Ali, A., Ahmed, A., Inuwa, I.M., Zarrei, M., Safizadeh Shabestari, S.A., AlBanna, A., Howe, J.L., et al., 2021. Single-cell transcriptome identifies molecular subtype of autism spectrum disorder impacted by de novo loss-of-function variants regulating glial cells. Hum. Genomics. 15, 1-16.
|
Ngounou Wetie, A.G., Wormwood, K., Thome, J., Dudley, E., Taurines, R., Gerlach, M., Woods, A.G., Darie, C.C., 2014. A pilot proteomic study of protein markers in autism spectrum disorder. Electrophoresis. 35, 2046-2054.
|
Ornoy, A., 2009. Valproic acid in pregnancy:how much are we endangering the embryo and fetus? Reprod. Toxicol. 28, 1-10.
|
Parikshak, N.N., Swarup, V., Belgard, T.G., Irimia, M., Ramaswami, G., Gandal, M.J., Hartl, C., Leppa, V., Ubieta, L.d.l.T., Huang, J., 2016. Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism. Nature 540, 423-427.
|
Paulsen, B., Velasco, S., Kedaigle, A.J., Pigoni, M., Quadrato, G., Deo, A.J., Adiconis, X., Uzquiano, A., Sartore, R., Yang, S.M., 2022. Autism genes converge on asynchronous development of shared neuron classes. Nature 602, 268-273.
|
Prasad, A., Merico, D., Thiruvahindrapuram, B., Wei, J., Lionel, A.C., Sato, D., Rickaby, J., Lu, C., Szatmari, P., Roberts, W., et al., 2012. A discovery resource of rare copy number variations in individuals with autism spectrum disorder. G3 (Bethesda). 2, 1665-1685.
|
Rasalam, A.D., Hailey, H., Williams, J.H., Moore, S.J., Turnpenny, P.D., Lloyd, D.J., Dean, J.C., 2005. Characteristics of fetal anticonvulsant syndrome associated autistic disorder. Dev. Med. Child Neurol. 47, 551-555.
|
Satterstrom, F.K., Kosmicki, J.A., Wang, J., Breen, M.S., De Rubeis, S., An, J.Y., Peng, M., Collins, R., Grove, J., Klei, L., et al., 2020. Large-scale exome sequencing study implicates both developmental and functional changes in the neurobiology of autism. Cell. 180, 568-584. e523.
|
Schafer, D.P., Lehrman, E.K., Kautzman, A.G., Koyama, R., Mardinly, A.R., Yamasaki, R., Ransohoff, R.M., Greenberg, M.E., Barres, B.A., Stevens, B., 2012. Microglia sculpt postnatal neural circuits in an activity and complement-dependent manner. Neuron 74, 691-705.
|
Schumann, C.M., Hamstra, J., Goodlin-Jones, B.L., Lotspeich, L.J., Kwon, H., Buonocore, M.H., Lammers, C.R., Reiss, A.L., Amaral, D.G., 2004. The amygdala is enlarged in children but not adolescents with autism; the hippocampus is enlarged at all ages. J. Neurosci. 24, 6392-6401.
|
Shimamoto, C., Ohnishi, T., Maekawa, M., Watanabe, A., Ohba, H., Arai, R., Iwayama, Y., Hisano, Y., Toyota, T., Toyoshima, M., et al., 2015. Functional characterization of FABP3, 5 and 7 gene variants identified in schizophrenia and autism spectrum disorder and mouse behavioral studies. Hum. Mol. Genet. 24, 2409-2409.
|
Stoica, G.E., Kuo, A., Aigner, A., Sunitha, I., Souttou, B., Malerczyk, C., Caughey, D.J., Wen, D., Karavanov, A., Riegel, A.T., et al., 2001. Identification of anaplastic lymphoma kinase as a receptor for the growth factor pleiotrophin. J. Biol. Chem. 276, 16772-16779.
|
Suzuki, K., Sugihara, G., Ouchi, Y., Nakamura, K., Futatsubashi, M., Takebayashi, K., Yoshihara, Y., Omata, K., Matsumoto, K., Tsuchiya, K.J., Iwata, Y., Tsujii, M., Sugiyama, T., Mori, N., 2013. Microglial activation in young adults with autism spectrum disorder. JAMA Psychiatry 70, 49-58.
|
Tian, S.-S., Tsoulfas, P., Zinn, K., 1991. Three receptor-linked protein-tyrosine phosphatases are selectively expressed on central nervous system axons in the Drosophila embryo. Cell. 67, 675-685.
|
Tick, B., Bolton, P., Happé, F., Rutter, M., Rijsdijk, F., 2016. Heritability of autism spectrum disorders:a meta-analysis of twin studies. J. Child Psychol Psychiatry 57, 585-595.
|
Torres, A.R., Westover, J.B., Rosenspire, A.J., 2012. HLA immune function genes in autism. Autism Res. Treat. 2012, 959073.
|
van der Maaten, L., Hinton, G., 2008. Visualizing data using t-SNE. J. Mach. Learn. Res. 9, 2579-2605.
|
Velmeshev, D., Schirmer, L., Jung, D., Haeussler, M., Perez, Y., Mayer, S., Bhaduri, A., Goyal, N., Rowitch, D.H., Kriegstein, A.R., 2019. Single-cell genomics identifies cell type-specific molecular changes in autism. Science. 364, 685-689.
|
Voineagu, I., Wang, X., Johnston, P., Lowe, J.K., Tian, Y., Horvath, S., Mill, J., Cantor, R.M., Blencowe, B.J., Geschwind, D.H., 2011. Transcriptomic analysis of autistic brain reveals convergent molecular pathology. Nature. 474, 380-384.
|
Werling, D.M., 2016. The role of sex-differential biology in risk for autism spectrum disorder. Biol. Sex Differ. 7, 58.
|
Werling, D.M., Parikshak, N.N., Geschwind, D.H., 2016. Gene expression in human brain implicates sexually dimorphic pathways in autism spectrum disorders. Nat. Commun. 7, 1-11.
|
Yochum, C.L., Bhattacharya, P., Patti, L., Mirochnitchenko, O., Wagner, G.C., 2010. Animal model of autism using GSTM1 knockout mice and early post-natal sodium valproate treatment. Behav. Brain Res. 210, 202-210.
|
Zhang, Y., Li, N., Li, C., Zhang, Z., Teng, H., Wang, Y., Zhao, T., Shi, L., Zhang, K., Xia, K., 2020. Genetic evidence of gender difference in autism spectrum disorder supports the female-protective effect. Transl. Psychiatry 10, 4.
|
Zhao, H., Wang, Q., Yan, T., Zhang, Y., Xu, H.J., Yu, H.P., Tu, Z., Guo, X., Jiang, Y.H., Li, X.J., et al., 2019. Maternal valproic acid exposure leads to neurogenesis defects and autism-like behaviors in non-human primates. Transl. Psychiatry 9, 1-13.
|