Axon guidance genes are regulated by TDP-43 and RGNEF through the rate of long-intron processing.

Rho guanine nucleotide exchange factor (RGNEF) is a guanine nucleotide exchange factor (GEF) mainly involved in regulating the activity of Rho-family GTPases. It is a bi-functional protein, acting both as a guanine exchange factor and as an RNA binding protein. RGNEF is known to act as a destabilising factor of neurofilament light chain mRNA (NEFL). Most importantly, RGNEF inclusions in the spinal motor neurons of ALS patients co-localise with TDP-43, the major RNA binding protein aggregating in the brain and spinal cord of ALS patients. Therefore, it can be hypothesized that loss-of-function of both proteins, following their aggregation, may contribute to motor neuron death/survival in ALS patients. To further characterise their relationship, we compared the transcriptomic profiles of neuronal-like cells depleted of TDP-43 and RGNEF demonstrating that these two factors predominantly act in an antagonistic manner when regulating the expression of axon guidance genes. From a mechanistic point of view, our experiments show that the effect of these genes on the processivity of long introns can explain their action. Taken together, our results show that the loss-of-function of factors co-aggregating with TDP-43 can potentially affect the expression of commonly regulated neuronal genes in a very significant manner, acting as potential disease modifiers. This finding further highlights that neurodegenerative processes at the RNA level are the result of combinatorial interactions between different RNA binding factors that can co-aggregate in neuronal cells. A deeper study of these complex scenarios may lead to a better understanding of pathogenic mechanisms occurring in patients, where more than one specific protein may be aggregated in their neurons.