Understanding the gene expression differences between severe and mild forms of tuberous sclerosis (TSC) and the role of genetic modifiers to identify novel drug targets
Tuberous sclerosis complex (TSC) is an autosomal dominant neurogenetic disorder in which affected individuals are heterozygous for a mutation in either the TSC1 or TSC2 gene. Phenotypic variability (PV) in familial TSC is well recognized, but its molecular basis is not understood. PV clearly indicates that TSC1 or TSC2 mutation alone does not account for the observed phenotype and suggests a potential role for modifying factors. Mechanisms currently proposed for PV in monogenic disorders include modifying effects of unlinked genes (genetic modifiers), epigenetic factors, mosaicism, allelic skewing of gene expression, and environmental or other stochastic factors. At the Center for Rare Childhood Disorders (C4RCD), we have assembled a cohort of 16 TSC-afflicted families that exhibit phenotypic variability between parent and child. Using whole-exome (WES) and RNA sequencing, we aim to (1) define the aberrant gene expression in severe vs. mildly afflicted patients (2) identify genetic modifiers through WES that may be correlated with expression differences in severe vs. mildly afflicted patients. Preliminary results using the R tool DESeq2 have identified differentially expressed genes in the severe form of TSC in the child relative to the mild form of the disease in the parent who carries the same TSC genetic mutation. Overrepresentation Analysis (ORA) indicates that these genes are associated with protein processing in the endoplasmic reticulum and cell adhesion molecules. Within-family analysis of differentially expressed genes using the R tool edgeR in the parent-child pair with TSC mutations identified a unique set of differentially expressed genes, likely due to their unique genetic backgrounds. Further, in families that share mTOR mutations (genetic modifiers) in genes IRS1 and FZD1, we identified differentially expressed gene sets relevant to disease biology in severely affected patients, supporting the idea that genetic modifiers may impact gene expression and contribute to PV. Overall, our analysis demonstrates the correlation of aberrant expression of mTOR-related genes with disease severity in familial TSC and potentially influences the phenotypic variability observed within the family.