Identification of ultra-rare genetic variants in pediatric acute onset neuropsychiatric syndrome (PANS) by exome and whole genome sequencing

Abstract

Abrupt onset of severe neuropsychiatric symptoms including obsessive-compulsive disorder, tics, anxiety, mood swings, irritability, and restricted eating is described in children with Pediatric Acute-Onset Neuropsychiatric Syndrome (PANS). Symptom onset is often temporally associated with infections, suggesting an underlying autoimmune/autoinflammatory etiology, although direct evidence is often lacking. The pathological mechanisms are likely heterogeneous, but we hypothesize convergence on one or more biological pathways. Consequently, we conducted whole exome sequencing (WES) on a U.S. cohort of 386 cases, and whole genome sequencing (WGS) on ten cases from the European Union who were selected because of severe PANS. We focused on identifying potentially deleterious genetic variants that were de novo or ultra-rare (MAF) < 0.001. Candidate mutations were found in 11 genes (PPM1D, SGCE, PLCG2, NLRC4, CACNA1B, SHANK3, CHK2, GRIN2A, RAG1, GABRG2, and SYNGAP1) in 21 cases, which included two or more unrelated subjects with ultra-rare variants in four genes. These genes converge into two broad functional categories. One regulates peripheral immune responses and microglia (PPM1D, CHK2, NLRC4, RAG1, PLCG2). The other is expressed primarily at neuronal synapses (SHANK3, SYNGAP1, GRIN2A, GABRG2, CACNA1B, SGCE). Mutations in these neuronal genes are also described in autism spectrum disorder and myoclonus-dystonia. In fact, 12/21 cases developed PANS superimposed on a preexisting neurodevelopmental disorder. Genes in both categories are also highly expressed in the enteric nervous system and the choroid plexus. Thus, genetic variation in PANS candidate genes may function by disrupting peripheral and central immune functions, neurotransmission, and/or the blood-CSF/brain barriers following stressors such as infection.

Figure 1

Position of PANS ultra-rare variants within each candidate gene.

Figure 2

Connectivity network. A connectivity network was generated for each candidate gene using IPA software. Central to the network is the NF-κB complex transcriptional regulator hub, which connects to PPM1D, PLCG2, NLRC4, RAG1, BID, and CHK2. The PANS candidate genes not directly connected to NF-κB expression are those that are primarily expressed in the brain and cause neurodevelopmental disorders (CACNA1B, SYNGAP1, GRIN2A, SGCE, GABRG2, and SHANK3).

Figure 3

Heat map of LPS-mediated gene expression in microglia. Microarray gene expression data (GSE102482) from Greenhalgh et al. were analyzed to determine the expression pattern of a subset of 148 autism and pediatric immune disorder genes. The heat map shows the data obtained from RNA extracted from microglia grown on their own or co-cultured with peripheral macrophages. Arrows point to differentially expressed genes that are PANS candidates described in this report.

Figure 4

scRNA-seq expression pattern of each PANS candidate gene in mouse adolescent brains (open access article; CC BY license http://creativecommons.org/licenses/by/4.0/).