Neuron 83, 518532 (2014). A new study highlights a strategy to link SNPs implicated in human complex traits and diseases with probable causal genes. The main strength of this study is the integration of independent data sets, across distinct biological levels, that include cortex-specific 3D genome structure, eQTL and PPI data with ASD-associated GWAS SNPs. We found 80 and 58 SNPs that mark regulatory regions (i.e. GWAS has been commonly used in identifying SNPs associated with diseases or clinical phenotypes or traits. This network illustrates potential evidence for gene regulation related to RA-associated SNPs, and may provide comprehensive information for subsequent functional analyses and experiments. (a) Of 344 ASD-associated SNPs represented in both fetal and adult cortex-specific eQTL databases, more SNPs (n=80) are involved in spatial eQTL-gene interactions in the fetal cortex than in the adult cortex (n=58). Pepper, K. L. et al. The proportion of ASD explained by SNPs has been estimated to be between 17 and 60%7,8, thus their contribution should not be neglected. 46, 881885 (2014). Furthermore, despite not having discussed them in detail, there are number of genes whose transcript levels are affected by ASD-eQTLs whose functions were not enriched within known pathways. Hi-C data) enables the identification of novel local and distal eQTL-gene connections. SNPs represent an important class of genetic variant, defined as a single-base change in the DNA sequence. Protoc. Python (version 3.6.9), R (version 4.0.2) and RStudio (version 1.2.5033) were used for data analysis and visualisation. TAP1 and TAP2); (b) decreased (HLA-DQB1); or (c) both increased and decreased depending on specific ASD-eQTLs (HLA-DMA; Fig. These mechanisms depend on the role o (b) Thirty ASD-associated SNPs are eQTLs in both fetal and adult cortical tissues. However, the functions of the genetic variants that are responsible for the association with ASD remain poorly characterized. Louvain clustering analysis identified seven highly connected PPI modules within fetal cortex. When present within a coding sequence and leading to an amino acid change (referred to as a non-synonymous SNP or mutation), they can modify the protein's activity. Polycomb proteins are known to be involved in transcriptional silencing43,44. There is no fundamental reason why the same regulatory elements must or must not impact on the same gene in different tissues, or at different stages of development. Abstract. Behav. 3, 1 (2011). Chang, X. The Gene module within AutDB is a manually curated reference set of ASD-linked genes that was first released in 2007. Stiles, J. Abnormalities in lipid metabolism may affect the proper functioning of the nervous system and, thus can contribute to ASD etiology48,49,50. Wang J, Su W, Zhang T, Zhang S, Lei H, Ma F, Shi M, Shi W, Xie X, Di C. Cell Death Dis. However, the potential contributions of cortex-specific developmental changes to these networks in ASD development have yet to be investigated. Godfrey, K. M. et al. The existence of changes within fetal cortex pathways for endogenous antigens (e.g. Maternal acute and chronic inflammation in pregnancy is associated with common neurodevelopmental disorders: A systematic review. In our study eQTL data represent composite datasets across critical periods of development (e.g. From these CSPPI networks we identified 42 ASD-associated PPIs within the fetal gene set, and 10 ASD-associated PPIs from the adult cortical tissue gene set (Fig. Li, F., An, Z. For a specific TF-gene pair, detailed information could be observed in the rSNP report page using a link from the SNP in the 'element-gene-related SNPs . It is estimated that the human genome contains more than 10 million different SNPs. Nasser, J. et al. This method prioritizes genes for functional characterization and helps address questions about the architecture of human phenotypes. These eQTLs were also linked to other psychiatric disorders (e.g. PubMed Central Cell 50, 184-196.e4 (2019). The butyrophilin genes encode proteins that belong to the immunoglobulin superfamily and help modulate the immune system23. When SNPs occur within a gene or in a regulatory region near a gene, they often play a more direct role in the disease by affecting the function of the gene, either causing it to make a protein that works too well, or has less activity than normal, or completely stops its production. 3). on gene regulation) of the ASD-associated SNPs and translating them to the affected biological pathways in fetal and adult cortical tissues may provide mechanistic insights into the etiology of ASD during neurodevelopment. Correspondence to All datasets and software used in the analysis are listed in Supplementary Table 1. When SNPs are located near a gene, then it is postulated that the gene contributes to the variation under investigation. HHS Vulnerability Disclosure, Help Only SNPs associated with ASD with a p<5108 were included in downstream analyses. The same reference genome and annotation files were used to calculate expression for fetal brain RNA-seq data. Since the output is an easily manipulated spreadsheet, the user can sort the SNPs to highlight different SNP features. Internet Explorer). Single nucleotide polymorphism (SNP) is the simplest form of DNA variation among individuals. 1). CAS At the same time, ASD-eQTLs are also associated with regulation of fatty acid metabolism, ribosome biogenesis, aminoacyl-tRNA biosynthesis and spliceosome pathways in fetal cortex. Clipboard, Search History, and several other advanced features are temporarily unavailable. In total, 663,956 variants passed QC filters. life cycle [1,2], population [3-5], species [6-8], tissue [9,10], and cell [11,12]) and this variation drives phenotypic divergence among species and populations [13,14].A long-standing goal in population genetics and evolutionary biology has been to identify and characterize this . How far from the SNP may the causative genes be?. Liggins Institute, University of Auckland, Auckland, New Zealand, E. Golovina,T. Fadason,M. H. Vickers&J. M. OSullivan, Maurice Wilkins Centre, University of Auckland, Auckland, New Zealand, T. Fadason,M. H. Vickers&J. M. OSullivan, School of Medical Science, University of Auckland, Auckland, New Zealand, School of Population Health, University of Auckland, Auckland, New Zealand, Brain Research New Zealand, University of Auckland, Auckland, New Zealand, MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK, Garvan Institute of Medical Research, Sydney, Australia, You can also search for this author in Of the 80 fetal and 58 adult eQTLs, 30 were observed in both fetal and adult cortical tissues (Fig. Here, we build on prior work to study a large set of anthropometric and biometric traits that could inform health differences by sex. Article Vannucchi, G., Perugi, G. & Masi, G. Bipolar disorder and ASD. We identified ASD-associated eQTLs that mark putative regulatory regions in fetal (n=80) and/or adult (n=80) cortical tissues. Malinowska, M., Tokarz-Deptua, B. Ernst, J. Wray, N. R., Wijmenga, C., Sullivan, P. F., Yang, J. There are studies connecting cortical dysfunctions and ASD using imaging14, cortical architecture15, or gene expression16. Enh enhancers, Het heterochromatin, Quies quiescent/low, ReprPC repressed PolyComb, ReprPCWk week repressed PolyComb, TssA active TSS, TssAFlnk flanking active TSS, Tx strong transcription, TxWk weak transcription. 48, 552555 (2016). Epidemiological studies estimate that approximately 1% of people worldwide have ASD2. A large number of genes associated with various cancer types contain single nucleotide polymorphisms (SNPs). Google Scholar. When SNPs occur within a gene or in a regulatory region near a gene, they may play a more direct role in disease by affecting the gene's function. An alternative explanation is that the existence of the shared eQTLs between the multimorbid conditions is due to ambiguity in the phenotyping that was used in the GWAS studies that characterised the phenotype associated-SNPs. Proteins that were not annotated in the expression datasets were also removed from the CSPPI network. 47, 165175 (2019). The patterns of transcript changes in the adult cortex PPI network were similar to those observed in the fetal cortex. Moreover, Trlungeanu et al. 1). Child Psychol. The authors declare no competing interests. Thank you for visiting nature.com. Commun. We identified 21 and 23 eQTLs that reduce the affinity of at least one TFBS in fetal and adult cortical tissues, respectively (Fig. Google Scholar. A compendium of chromatin contact maps reveals spatially active regions in the human genome. Gene expression is the outcome of numerous processes including transcription, co-transcriptional splicing, mRNA export, and translation. 3). However, this would require randomised control trials in animals prior to testing in humans. *Gene transcript levels are associated with the same eQTL in both the fetal and adult cortical tissues. & Crawford, D. A. Am. Autism 3, 9 (2012). Bioinformatics 32, 289291 (2016). https://doi.org/10.1038/s41588-022-01087-y (2022). How could so-called altruistic behaviors arise through natural selection? The identified gene sets were enriched for immune pathways, fatty acid metabolism, ribosome biogenesis, aminoacyl-tRNA biosynthesis and the spliceosome in the fetal cortex. dorsolateral prefrontal cortex cells) cortex-specific Hi-C libraries. 2c). Most of these fetal ASD-associated eQTLs located within the Polycomb-repressed eQTLs were not identified as eQTLs in the adult cortex (Fig. 4). Notably, eQTLs involving rs13218591 and rs2237234 regulate different butyrophilin alleles (i.e. Single nucleotide polymorphism, or SNP. Google Scholar. Sign up for the Nature Briefing: Translational Research newsletter top stories in biotechnology, drug discovery and pharma. The proteinprotein interaction (PPIs) network serves as a foundation for cellular signalling circuitry, which mediates cellular responses to environmental and genetic cues. 3, Supplementary Table 4). contributed to the eQTL analysis and commented on the manuscript. ASD is widely considered to be a neurodevelopmental disorder resulting from functional changes within the brain. *_merged_nodups.txt files) were processed to obtain Hi-C chromatin interaction libraries in the following format: read name, str1, chr1, pos1, frag1 mapq1, str2, chr2, pos2, frag2, mapq2 (str=strand, chr=chromosome, pos=position, frag=restriction site fragment, mapq=mapping quality score, 1 and 2 correspond to read ends in a pair). To identify existing and novel gene associations, we intersected our lists of genes, from fetal and adult cortical tissues, with a curated list of 1237 genes that had been previously implicated in autism development (AutDB31, accessed on 16/11/2020). The resulting expression (GTEx_Analysis_v8_eQTL_expression_matrices.tar) and covariates (GTEx_Analysis_v8_eQTL_covariates.tar.gz) data were downloaded from GTEx website (https://www.gtexportal.org/home/datasets, 01/05/2020). Tamiji, J. Notably, Polycomb repressive complexes have distinct regulatory roles in identity, proliferation and differentiation of neuronal progenitor cells during development29,30. PubMed Central The identified ASD-associated eQTLs were annotated using wANNOVAR tool77 (http://wannovar.wglab.org/, 10/08/2020) to obtain information about the locus they tagged (Supplementary Table 4). CAS 235, 40314045 (2020). 9, 5198 (2018). CAS Porokhovnik, L. Individual copy number of ribosomal genes as a factor of mental retardation and autism risk and severity. Neuron 89, 248268 (2016). rs10791097-SNX19, rs11191419-AS3MT, rs7085104-AS3MT, rs174592-FADS1; Supplementary Table 4). Szklarczyk, D. et al. There are several reasons for this: (1) there are multiple potential mechanisms through which a genetic variant can impact on a phenotype. The significance of these associations in the developing cortex and how they contribute to the etiology of ASD remains to be empirically determined. Scientific Reports (Sci Rep) [Structural variation in the human genome contributes to variation of traits]. 12, 405 (2018). J. Stat. de la Torre-Ubieta, L., Won, H., Stein, J. L. & Geschwind, D. H. Advancing the understanding of autism disease mechanisms through genetics. 1, Supplementary Fig. Sunwoo, M. et al. Schematic representation of the procedure to map SNPs to regulatory elements and target genes. Kanehisa, M. & Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. These differences can underlie susceptibility to common diseases, human traits, and differential responses to drugs. dorsolateral prefrontal cortex cells)12 Hi-C chromatin interaction libraries (Supplementary Table 1). Autism Spectr. NMB encodes the neuromedin B peptide that regulates physiological processes including cell growth, exocrine and endocrine secretion22; and (2) downregulates WDR73 in adult cortex. Autism, early psychosis, and social anxiety disorder: Understanding the role of social cognition and its relationship to disability in young adults with disorders characterized by social impairments. Accessibility Google Scholar. By contrast, the adult PPI gene set contained three highly connected modules, two of which were not associated with specific pathway, and one of which was enriched for immune pathways. Genet. Nat. Thousands of disease-associated SNPs (daSNPs) are located in intergenic regions (IGR), making it difficult to understand their association with disease phenotypes. volume54,pages 748749 (2022)Cite this article. Res. Identifying comorbid ADHD in autism: Attending to the inattentive presentation. The expression level in an indivisual is measured by the measuring the Trascribed mRNA, by the method of Northern blot . PRC2-associated chromatin contacts in the developing limb reveal a possible mechanism for the atypical role of PRC2 in HoxA gene expression. Thacker, S., Sefyi, M. & Eng, C. Alternative splicing landscape of the neural transcriptome in a cytoplasmic-predominant Pten expression murine model of autism-like Behavior. The STRING33 PPI network (version 11.0, protein.links.full.v11.0.txt.gz, https://string-db.org/) was downloaded on 24/09/2020. non-coding RNAs); (2) ASD is a spectrum disorder not a single highly characterised phenotype; and (3) like all polygenic disorders, ASD is likely to be a whole of body disorder with important etiological contributions from discrete and distant organs within the body. RNA-seq data)20,21 were mapped to gene identifiers, thus there was a potential loss of data specificity, since genes typically produce multiple transcripts and protein variants due to alternative splicing. How do SNPs occur? Edges are only present if both interacting proteins are expressed in the cortical tissue. Article EG is the recipient of a Liggins Ph.D. scholarship and was supported by MBIE Catalyst Grant (The New ZealandAustralia LifeCourse Collaboration on Genes, Environment, Nutrition and Obesity (GENO); UOAX1611). Briefly, merged fastq files were aligned to the GRCh38 reference genome (Homo_sapiens_assembly38_noALT_noHLA_noDecoy.fasta, gs://gtex-resources) using STAR (v2.5.3a). The SNPs located in enhancer elements may affect gene expression and lead to disease. As such, restriction fragments were used to identify regulatory interactions between SNPs and genes (Fig. SNP. Nat. 3). and co-wrote the manuscript. These spatial interactions are dynamic, developmentally and temporally dependent13. PubMed In the meantime, to ensure continued support, we are displaying the site without styles Schmitt, A. D. et al. & Paro, R. Transcriptional silencing by polycomb-group proteins. Aguet, F. et al. EBioMedicine 58, 102917 (2020). Genet. doi: 10.1136/bmjdrc-2022-003164. For example, rs35828350: (1) upregulates NMB in fetal cortex. Nucleic Acids Res. Neurosci. Cis-eQTL SNPs are the SNPs that are within or around the corresponding gene, and trans-eQTL SNPs are those that are far away or even on dierent chromosomes. Therefore, characterizing the functional impacts (i.e. By contrast, in the adult cortex they largely affect immune pathways. Fetal ASD-associated eQTLs were located within quiescent/low transcribed (n=31), weak transcription (n=18), week repressed Polycomb (n=14) and repressed Polycomb (n=10) regions (Fig. Backman, J. D. et al. miRNA) or by spatial associations of the regulatory element and target gene. We observed that schizophrenia has the largest significant overlap with ASD-associated eQTLs both in fetal (78 out of 80, bootstrapping p<0.01, n=10,000) and adult (57 out of 58, bootstrapping p<0.01, n=10,000) cortical tissues (Supplementary Fig. Huang C, Guo Y, Li W, Xiang B, Zeng J, Zhou F, She L, Zhang P, Wang S, Liu B, Dai Q, Yang M. BMJ Open Diabetes Res Care. An AUTS2-Polycomb complex activates gene expression in the CNS. Google Scholar. Five genes within this cluster (i.e. Until recently, there has been little if any functional follow-up of the actual role a given SNP or gene plays in the trait variation under study ( 22 ). However, gene expression-based methods use an arbitrary definition of which genes contribute to the SNP enrichment score at each locus and either select a single gene with the highest cell type specific gene expression or include all the genes within the locus (Hu et al., 2011). Brodie, A., Azaria, J. R. & Ofran, Y. Genetic and molecular features of seizure-freedom following surgical resections for focal epilepsy: A pilot study. chr1_61170_C_T_b38 where chr1 is chromosome name, 61170 is variant position on the chromosome, C is reference allele, T is alternate allele and b38 is genome build 38). Finucane, H. K. et al. 3). Paternally inherited cis-regulatory structural variants are associated with autism. 1). 51, 431444 (2019). Next, the CoDeS3D algorithm identified the restriction fragments interacting with the SNP-containing restriction fragments. 2009 May;37(5):977-91. doi: 10.1124/dmd.108.026047. We find that sex-het SNPs influence a large set of diseases and health-related . Basu, S. N., Kollu, R. & Banerjee-Basu, S. AutDB: A gene reference resource for autism research. Our findings highlight potential mechanisms through which ASD-associated variants potentially contribute to ASD development (fetal) and onset/maintenance (adult). PubMed Karczewski, K. J. et al. Adv. Integrative analysis of 111 reference human epigenomes. bioRxiv https://doi.org/10.1101/787903 (2019). The dynamic 3D genome in gametogenesis and early embryonic development. Article Genes depleted for null variants were defined as having pLI>0.9. 344 ASD-associated SNPs (p<5108) represented in both fetal and adult cortex-specific eQTL datasets were run through the CoDeS3D pipeline to identify 81 and 44 spatially regulated genes in fetal and adult cortical tissues, correspondingly. Nature Genetics However, studies have shown that Polycomb repressive complexes (PRC) can have a dual role in gene regulation during development45,46. Systematic identification of trans eQTLs as putative drivers of known disease associations. J. Rare genetic susceptibility variants assessment in autism spectrum disorder: Detection rate and practical use. The size of each node depends on the protein expression levels (no missing values and minimum expression level >0 TPM) in the corresponding cortical tissue. Louvain clustering identified seven PPI modules within the fetal cortex that were enriched for immune pathways, fatty acid metabolism, aminoacyl-tRNA biosynthesis, spliceosome, ribosome biogenesis in eukaryotes and two unknown modules. 16, 551563 (2015). 2023 Apr 6;14(4):244. doi: 10.1038/s41419-023-05763-7. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate. The p value was calculated as the sum of these instances divided by the total number of iterations n. If the p<0.01 we assume that the observed relationship is non-random. associated with an increase or reduction in transcript levels; Supplementary Fig. The integration of spatial and functional data represents a significant difference from other approaches where functional assignments for phenotype-associated SNPs are typically made to the gene that is closest to the phenotype-associated SNP72. By contrast, 9 fetal cortex-specific genes (i.e. Functional gene ontology enrichment analysis identified immune-related processes (e.g. Raudvere, U. et al. The results of our study should be interpreted in view of its strengths and limitations. 8600 Rockville Pike Knuesel, I. et al. Article To obtain Enrichment within active regulatory elements and histone modification marks was identified using the Roadmap Epigenomics Project 15-state ChromHMM models28,78 for adult dorsolateral prefrontal cortex (E073_15_coreMarks_hg38lift_mnemonics.bed.gz) and fetal brain (E081_15_coreMarks_hg38lift_mnemonics.bed.gz) (downloaded from https://egg2.wustl.edu/roadmap/data/byFileType/chromhmmSegmentations/ChmmModels/coreMarks/jointModel/final/, 22/11/2020) (Supplementary Table 1). Cell type- and differentiation-specific gene expression is precisely controlled by genomic non-coding regulatory elements (NCREs), which include promoters, enhancers, silencers and insulators. The remaining 60% of the identified eQTLs involve interactions with non-adjacent genes that can be >1Mb away in the linear DNA sequence or even on a different chromosome. Thank you for visiting nature.com. Of the 66 fetal cortex genes, transcript levels for 36 are upregulated in association with a change of the eQTL SNP to the minor allele, while 24 are reduced (Fig. Drug Metab Dispos. van Arensbergen, J. et al. The significance level was determined using the BH algorithm (FDR<0.05). To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The CSPPIs represents subnetworks of the STRING PPI network, in which a protein/node is only present if it is expressed in the cortical tissue (adult or fetal). The Kyoto Encyclopedia of Genes and Genomes (KEGG) database34 was used to query the most impacted biological pathways. Science 342, 253257 (2013). Nat. https://doi.org/10.1038/s41588-022-01093-0. Increasing role of maternal immune activation in neurodevelopmental disorders. Interestingly, most of the genes within immune-related pathways in fetal cortex are associated with Polycomb-repressed ASD-eQTLs. Single Nucleotide Polymorphism (SNP) SNPs are variations that involve a change in just one nucleotide. CAS Single-nucleotide polymorphisms (SNPs) associated with ASD (n=454) were downloaded from the GWAS Catalog (www.ebi.ac.uk/gwas/; 05/04/2020; Supplementary Table 2).