Profiling of circulating microRNAs in body fluids from Autism Spectrum Disorder patients

Autism Spectrum Disorder is the name for a heterogeneous group of neurodevelopmental conditions, clinically defined by: defects in social interaction and communication; fixed interests and repetitive behaviors. Molecular basis of ASD is heterogeneous and only partially known. ASD-associated variants have been characterized in hundreds of genes and separate transcriptome studies have identified points of convergence among these loci, proving that common biological processes play a role in this disorder. However, no common ASD-associated variants with large effect size, that would be appropriate for its molecular diagnosis, have been identified to date, and therefore, diagnosis just relies on clinical assessment and confirmation. Many factors, including disorders comorbid with ASD, like Tourette Syndrome, complicate ASD behavior-based diagnosis and make it vulnerable to bias. Extracellular microRNAs have attracted researchers for their potential as non-invasive tools for diagnosis, prognosis, and treatment evaluation of human diseases and disorders. Circulating miRNAs can be detected in all mammalian body fluids, from serum to saliva. Stability and general consistency of levels among individuals, along with the existence of specific expression signatures in association with both physiological and pathological conditions, make circulating miRNAs appropriate biomarkers. To investigate ASD etiology and to identify potential biomarkers to support its diagnosis, we used TLDA technology to profile serum miRNAs from ASD, TS, and TS+ASD patients and NCs (unaffected controls). Through validation assays, we demonstrated that miR-140-3p is upregulated in ASD vs: NC, TS, and TS+ASD. We found that delta Ct values for miR-140-3p and YGTSS scores are positively correlated. Our network functional analysis showed that nodes controlled by miR-140-3p, especially CD38 and NRIP1, are involved in processes convergingly dysregulated in ASD, such as synaptic plasticity, immune response, and chromatin binding. Through biomarker analysis, we proved that serum miR-140-3p can discriminate among ASD and NC, ASD and TS, and ASD and TS+ASD, showing that it could be useful to strengthen the behavior-based diagnosis of either ASD or TS+ASD, which can be challenging in some clinical cases. Among all body fluids, saliva represents the most accessible and complete source of different types of molecules that could reflect genetic, epigenetic, environmental, metabolic, emotional, and behavioral alterations in ASD. Therefore, we also used NanoString nCounter technology to profile supernatant saliva circulating miRNAs from ASD patients and NCs. Through validation assays, we demonstrated that both miR-29a-3p and miR-141-3p are upregulated in ASD saliva compared to NC one. We observed that delta Ct values for both miRNAs are correlated with neuropsychiatric scores evaluating ASD defects in social interaction and verbal communication. Target genes of these miRNAs represent main components and regulators of pathways and processes known to be dysregulated in ASD. Through biomarker performance evaluation, we proved that saliva miR-29a-3p and miR-141-3p when used in combination could be useful and non-invasive tools for discriminating ASD patients. In particular, these miRNAs could be used as supportive means for the recognition of ASD verbal and social defects. Overall, our findings suggest that profiling of circulating miRNAs in body fluids can represent an easy and innovative approach to address important biomedical issues, such as the need for biomarkers and the necessity to investigate neurodevelopmental disorders through more accessible patient biopsies. In fact, through the characterization of miRNAs in ASD serum and saliva, we identified three miRNAs that could facilitate ASD clinical assessment and that are worth being further investigated for their potential role in neurodevelopment.