Susceptible genetic loci identification is crucial for better understanding the underlying mechanisms of autism, thus aiding the development of their treatment and management . Due to the high heritability of autism, various common genetic risk variants have surfaced, yet a long way to find rare variations showing the significance of heritability in autism . The homozygous haplotype mapping approach is complimentary to genome wide association studies and Next Generation Sequencing in studying the complexity and heterogeneity of autism . Homozygosity mapping analysis adds the missing pieces of the puzzle for complex disorders in terms of heritability and recessive gene burden . The present study reports the presence of rHH mapping study to identify candidate autism gene variants, particularly recessive gene loci involved in autism manifestation. The idea was to apply the concept of homozygosity mapping to the trios sample cohort and understand the role of haplotype blocks in unrelated subjects.
Studies have been performed to identify a genome-wide survey of runs of homozygosity for bone mineral density in Caucasian and Chinese populations . Similarly, an integrated approach of whole-genome genotyping and homozygosity mapping revealed the presence of 38 rHH regions with a much higher degree of haplotype-sharing. Oversharing of haplotype indicates a disease locus, an observation that forms the basis of the current study. The authors observed that these cases shared 18 homozygous blocks bearing 24 recessive genes related to autism. Previous studies have reported recessive autism genes such as ABHD14A, CADM2, CHRFAM7A, EPHA3, FGF10, GRIK2, GRM3, KCND2 PDZK1, present in the haplotype regions . ABHD14A genes have been identified in the present study as well, impairing autism pathophysiology.
eQTL analysis of polymorphisms in the homozygous blocks affected many downstream genes such as CEP290, KITLG, PTPRJ-JAK2, RERE, EMSY, CHD8, INS2, EP300, and MAPK3, identified in subcategories A1, A2, B1, and B2, known for autism manifestation. These nine genes have been exclusively identified in the current study. However, CNTN4, CADPS2, SUMF1, SLC9A9, and NTRK3 genes have been identified and implicated in autism elsewhere . These genes show affected binding of regulatory proteins, which deregulates autism genes and impairs the downstream gene functionality and processes. Among the regulatory proteins, CBX3  and BACH1  are functioning as repressors, while FOS, BACH1, MYC, JUND, MAFK, POU2F2, RBBP5, RUNX3, and SMARCA4 are functioning as activators. These are involved in the activation of autism genes through various cellular functions. These cellular functions include chromatin organization, G protein-coupled receptor (GPCR) signaling, cell cycle regulation, homeostasis, signaling pathways, and cellular stress response, which play a vital role in the severity of autism symptoms. Ubiquitination of calcium signaling pathway in endoplasmic reticulum across all body cells results in deficits observed in fibroblasts in autism subjects through neuronal functional impairment . Intracellular GPCRs, linked to synaptogenesis, memory and learning, behavior, and cognition for pathophysiological roles in autism . Cellular endoplasmic reticulum stress can lead to apoptosis, resulting in autism .
The establishment of the autism gene risk loci enrichment pathway led to identifying notable genes with a promising role in its pathogenesis. These include AUTS2, JMJD1C, PCGF5, PCGF3, CEP152, ABHD14A, CEACAM21, A4GALT, OPN1MW, CELSR1, RYK, ADGRA2, FZD3, FZD9, NF608, and RERE. These formed clustering at varied levels affecting downstream processes. ABHD14A has been implicated as a novel gene in a previous relevant autism haplotype study . In yet another study, a family was reported to carry two changes in ABHD14A, a gene involved in cerebellar development and diagnosed with intellectual disability and a male obligate carrier . Further studies need to be merited on each of these novel gene variants to decipher the complete cascade in haplotype analysis.
The pathway identified could be sliced down into seven gene pathway clusters: AUTS2, ADGRA2, CELSR1, FZD9, MBD1, RERE, and OPN1. Each of these genes physically interacts with autism-specific genes and bears receptors and ligands relevant to autism and affects the downstream cascade of processes like formation, morphology, hypoplasia, brain, and head development, development of a central nervous system, migration of Purkinje cells, and pervasive development disorder. ADGRA2 and CELSR1 share similar ectodomain structures, implicate in neural tube formation, as evident in network analysis in the current study as well . Extensive studies have established their role in these autism genes directly or indirectly as follows: (1) regulation of actin cytoskeleton is performed by cytoplasmic AUTS2 to control neuronal migration and neurite extension, vital to autism . (2). ADGRA2 plays a vital role during brain angiogenesis and has functionality as a WNT7A/7B-specific co-activator for beta-catenin signaling in the brain endothelium . (3). CELSR1 protein is involved in processes of the neural progenitor cells in the basal compartment to decide the fate for the development of the cerebral cortex . (4). Homozygous deletion in FZD9 resulted in an acute deficiency in learning and memory, leading to apoptosis in the dentate gyrus and lowered seizure cut-off . (5). Abnormal serotonin systems resulting from a deletion in MBD1 have been linked to autism due to its higher levels of receptor called Htr2c being synthesized. This system acts as an important link between MBD1 and autism-like behavior . (6). Based on a discovery resource of rare copy number variations in autism individuals. De novo mutations have been identified to be associated with proximal 1p36 deletions and various processes of transcriptional, synaptic, and chromatin gene disruptions in autism . (7). The OPN1 is a rho-linked protein for mental retardation, which controls synaptic vesicle endocytosis via endophilin A1, vital to autism .. These seven gene pathways bring out multiple population clusters with significant rHH genes suggesting the existence of common population-specific risk alleles.