Identification of cell specific biomarkers for intellectual disability via single cell RNA sequencing and transcriptomic bioinformatics approaches.

PMID 40399537 | PMCID PMC12095737 | DOI 10.1038/s41598-025-85162-4 · Scientific reports · 2025 · View on PubMed ↗

Limitations in cognitive functioning and adaptive behavior are hallmarks of Intellectual Disability (ID), a neurodevelopmental disease. Specific genetic disorders that result in ID can also have immune system anomalies, such as changes in T (CD4+ and CD8+) cell activity. This work aimed to compare single-cell RNA-sequencing (scRNA-seq) and transcriptome data to find biomarkers linked to T cells that could potentially be utilized for the diagnosis and assessment of ID. After integrating genes and performing a comparative analysis 196 genes were identified as differentially expressed genes (DEGs). Furthermore, the DAVID online platform and FunRich software were utilized to detect signal transduction and translation, immune response, MHC (Major Histocompatibility Complex) class II, antigen processing and presentation, allograft rejection and important pathways of type I diabetes mellitus. In this investigation, six ribosomal proteins (RPS27A, RPS21, RPS18, RPS7, RPS5, and RPL9) have been identified as the hub genes of ID from PPI. Additionally, eleven topological algorithms discovered only one hub protein, namely RPS27A from the protein-protein interaction (PPI) network. Through the analysis of the regulatory network, we have identified several crucial transcriptional factors (TFs) including FOXC1, FOXL1, and GATA2; microRNAs such as mir-92a-3p, and mir-16-5p were investigated by procedural data analysis. This study used scRNA-seq and transcriptomics data analysis to define unique biomarkers associated with T cell types throughout the progression of ID. Ongoing research on the activity of ID genes is contributing to a greater understanding of the pathophysiology of ID and will become more scientific and research-based in future.