Interactomics Analyses of Wild-Type and Mutant A1CF Reveal Diverged Functions in Regulating Cellular Lipid Metabolism

Population genetic
studies highlight a missense variant (G398S)
of A1CF that is strongly associated with higher levels of blood triglycerides
(TGs) and total cholesterol (TC). Functional analyses suggest that
the mutation accelerates the secretion of very low-density lipoprotein
(VLDL) from the liver by an unknown mechanism. Here, we used multiomics
approaches to interrogate the functional difference between the WT
and mutant A1CF. Using metabolomics analyses, we captured the cellular
lipid metabolite changes induced by transient expression of the proteins,
confirming that the mutant A1CF is able to relieve the TG accumulation
induced by WT A1CF. Using a proteomics approach, we obtained the interactomic
data of WT and mutant A1CF. Networking analyses show that WT A1CF
interacts with three functional protein groups, RNA/mRNA processing,
cytosolic translation, and, surprisingly, mitochondrial translation.
The mutation diminishes these interactions, especially with the group
of mitochondrial translation. Differential analyses show that the
WT A1CF-interacting proteins most significantly different from the
mutant are those for mitochondrial translation, whereas the most significant
interacting proteins with the mutant are those for cytoskeleton and
vesicle-mediated transport. RNA-seq analyses validate that the mutant,
but not the WT, A1CF increases the expression of the genes responsible
for cellular transport processes. On the contrary, WT A1CF affected
the expression of mitochondrial matrix proteins and increased cell
oxygen consumption. Thus, our studies confirm the previous hypothesis
that A1CF plays broader roles in regulating gene expression. The interactions
of the mutant A1CF with the vesicle-mediated transport machinery provide
mechanistic insight in understanding the increased VLDL secretion
in the A1CF mutation carriers.