# Identification of spastic ataxia-related proteins via comparative proteomic analysis of the cerebellum of conditional Ankfy1 knockout mice

## TL;DR

This study identifies proteins linked to spastic ataxia by comparing the cerebellum of mice with and without a specific gene knockout.

## Contribution

The study introduces a novel proteomic analysis of conditional Ankfy1 knockout mice to identify proteins associated with spastic ataxia.

## Key findings

- 69 differentially expressed proteins were identified in conditional knockout mice compared to controls.
- Itgb2 was the top hub gene in the protein–protein interaction analysis.
- ARHGDIB was upregulated and PCP2 was downregulated in the cerebellum of knockout mice.

## Abstract

Ankyrin repeat and FYVE domain containing 1 (ANKFY1) is an indispensable protein in the development of cerebellar Purkinje cells. Our preliminary study revealed that its absence caused progressive spastic ataxia, accompanied by the loss of Purkinje cells in mice. Here, we generated Ankfy1-floxed (Ankfy1f/f) mice, in which conditional inactivation of the Ankfy1 gene was achieved specifically in cerebellar Purkinje cells via crossing with a transgenic mouse strain expressing Cre recombinase under the regulatory control of the Purkinje cell protein 2 (PCP2) promoter. We employed data-independent acquisition (DIA) mass spectrometry to compare the protein expression profiles in cerebellar samples. The samples were obtained from two groups of male mice. The first group consisted of three Pcp2-Cre; Ankfy1f/f male mice, where the Ankfy1 gene was conditionally knocked out in Purkinje cells, and these mice were designated as the conditional knockout (CKO) group. The second group included three Cre-negative; Ankfy1f/f littermate male mice served as the wild-type (WT) control group. The results identified 69 (45 upregulated and 24 downregulated) differentially expressed proteins (DEPs) in CKO vs. WT male mice with a 1.5-fold change. Enrichment analyses of these DEPs based on the Gene Ontology (GO), Orthologous Groups of Proteins (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases revealed functional clusters associated with neuronal cell morphogenesis, extracellular structures, regulation of Rho-GTPase, calcium signaling pathway, etc. Itgb2, which was upregulated in CKO mice, was the top hub gene according to protein–protein interaction (PPI) analysis. We selected seven interesting differentially expressed genes (Arhgdib, Impa2, Pcp2, Pcp4, Ppp1r17, Rhobtb2, and Cdc123) for further validation. Arhgdib and Imp2a expression was increased in the cerebellum of CKO male and female mice, and Pcp2 and Pcp4 expression was decreased. Western blotting and immunofluorescence verified the upregulation of ARHGDIB and the downregulation of PCP2 in the cerebellum. Our proteomic analysis of conditional Ankfy1 knockout mice may guide future research to help develop treatments for progressive spastic ataxia.

The online version contains supplementary material available at 10.1038/s41598-025-06398-8.