Transcriptome analysis of neural progenitor cells derived from Lowe syndrome induced pluripotent stem cells: identification of candidate genes for the neurodevelopmental and eye manifestations

Abstract

Background Lowe syndrome (LS) is caused by loss-of-function mutations in the X-linked gene OCRL, which codes for an inositol polyphosphate 5-phosphatase that plays a key role in endosome recycling, clathrin-coated pit formation, and actin polymerization. It is characterized by congenital cataracts, intellectual and developmental disability, and renal proximal tubular dysfunction. Patients are also at high risk for developing glaucoma and seizures. We recently developed induced pluripotent stem cell (iPSC) lines from three patients with LS who have hypomorphic variants affecting the 3′ end of the gene, and their neurotypical brothers to serve as controls. Methods In this study, we used RNA sequencing (RNA-seq) to obtain transcriptome profiles in LS and control neural progenitor cells (NPCs). Results In a comparison of the patient and control NPCs (n = 3), we found 16 differentially expressed genes (DEGs) at the multiple test adjusted p value (padj) < 0.1, with nine at padj < 0.05. Using nominal p value < 0.05, 319 DEGs were detected. The relatively small number of DEGs could be due to the fact that OCRL is not a transcription factor per se, although it could have secondary effects on gene expression through several different mechanisms. Although the number of DEGs passing multiple test correction was small, those that were found are quite consistent with some of the known molecular effects of OCRL protein, and the clinical manifestations of LS. Furthermore, using gene set enrichment analysis (GSEA), we found that genes increased expression in the patient NPCs showed enrichments of several gene ontology (GO) terms (false discovery rate < 0.25): telencephalon development, pallium development, NPC proliferation, and cortex development, which are consistent with a condition characterized by intellectual disabilities and psychiatric manifestations. In addition, a significant enrichment among the nominal DEGs for genes implicated in autism spectrum disorder (ASD) was found (e.g., AFF2, DNER, DPP6, DPP10, RELN, CACNA1C), as well as several that are strong candidate genes for the development of eye problems found in LS, including glaucoma. The most notable example is EFEMP1, a well-known candidate gene for glaucoma and other eye pathologies. Conclusion Overall, the RNA-seq findings present several candidate genes that could help explain the underlying basis for the neurodevelopmental and eye problems seen in boys with LS.

Transcriptomics Analysis of Lens from Patients with Posterior Subcapsular Congenital Cataract

“…To identify the candidate genes from the DEGs obtained via RNA-seq analysis that may be associated with the pathology of posterior congenital cataract, we next analysed the DEGs using the database resource of iSyTE2.0 [ 5 ], which represented the gene expression and lens enrichment data during the normal lens development. Previous studies have suggested that the database iSyTE could be a cataract gene prioritization resource [ 10 ] and 95% of known genes associated with cataract or lens defects are lens-enriched at one or more key embryonic stages [ 6 ].…”

“…The gene-specific primers for RT-qPCR are shown in Table 1 . The results were analysed using the 2 −ΔΔCt method as described previously [ 10 ].…”

Recent Developments in Autism Genetic Research: A Scientometric Review from 2018 to 2022

“…In Cluster #5, the major citing document is written by Al-Dewik et al [ 132 ] and has a coverage of 20 documents and a GCS of 5. As the term “Genomic Architectured” implies, many studies in this cluster make use of big data, such as genome-wide associations or transcriptome analyses, to uncover the genetic bases of ASD [ 133 , 134 , 135 , 136 , 137 , 138 , 139 , 140 ]. The top 10 citing papers of Cluster #5 are seen in Table 9 .…”

The Future of Genetic Disease Studies: Assembling an Updated Multidisciplinary Toolbox

“…These studies were complemented by biochemical and cell biological assays to assess the mutational impact on protein function and availability ( De Leo et al, 2016 ; Ramadesikan et al, 2021 ). Furthermore, models were prepared by various methods to gain mechanistic insight into LS such as KO/morpholino zebrafish lines ( Coon et al, 2012 ; Ramirez et al, 2012 ; Gliozzi et al, 2020 ), humanized mouse models ( Bothwell et al, 2011 ), Ocrl1-deficient cells by CRISPR ( Madhivanan et al, 2020 ) along with stable lines expressing specific variants ( Ramadesikan et al, 2021 ), and patient-derived iPSCs ( Barnes et al, 2018 ; Hsieh et al, 2018 ; Liu et al, 2020 ; Akhtar et al, 2022 ). Taken together, LS research has greatly benefitted from the assimilation of a variety of techniques and is rapidly moving towards understanding LS in a patient mutation-specific manner to better guide the design novel therapeutic approaches.…”