Worth, C. S. | bioRxiv Science

bioRxiv2026

KDM6A is enzymatically active at the Golgi apparatus where it is necessary for maintenance of Golgi apparatus morphology

KDM6A and KDM6B, lysine demethylases, play a central role in regulation of transcription through their demethylation activity towards H3K27me3 and have also been shown to be dynamically regulated upon epithelial-mesenchymal transition (EMT). In particular, KDM6A has been implicated in a variety of malignancies and is frequently mutated in cancers including those in kidney, bladder, colorectal, and breast. KDM6A and KDM6B function as part of the COMPASS-like protein complex (CLC) which includes methyltransferases KMT2C/KMT2D and the regulatory WRAD-subcomplex. KDM6A total protein is known to be suppressed by TGF-{beta} in MCF10A breast cells; however, our examination of protein localization by immunofluorescence and LC-MS/MS reveals that KDM6A expression is lost in the nucleus but retained in the Golgi apparatus, independent of other CLC complex members. Importantly, KDM6A isolated from a biochemically-separated subcellular membranous fraction possesses the catalytic JmjC domain and is enzymatically active, indicating that KDM6A may have non-nuclear substrates. Further, knockdown of KDM6A and treatment with TGF-{beta} similarly alter Golgi apparatus morphology, in a cell type specific manner, suggesting context-dependent regulatory functions. These findings support a model in which KDM6A is necessary to maintain Golgi apparatus morphology and is enzymatically active outside of the nucleus.

cell biology↗

bioRxiv2024

Differences in Protein Capture by SP3 and SP4 Demonstrate Mechanistic Insights of Proteomics Clean-up Techniques

The goal of proteomics experiments is to identify proteins to observe changes in cellular processes and diseases. One challenge in proteomics is the removal of contaminants following protein extraction, which can limit protein identification. Single-pot, solid-phase-enhanced sample preparation (SP3) is a clean-up technique in which proteins are captured on carboxylate-modified particles through a proposed hydrophilic-interaction-liquid-chromatography (HILIC)-like mechanism. However, recent results have suggested that proteins are captured in SP3 due to a protein-aggregation mechanism. Thus, solvent precipitation, single-pot, solid-phase-enhanced sample preparation (SP4) is a newer clean-up technique that employs protein-aggregation to capture proteins without modified particles. SP4 has previously enriched low-solubility proteins, though differences in protein capture could affect which proteins are detected and identified. We hypothesize that the mechanisms of capture for SP3 and SP4 are distinct. Herein, we assess the proteins identified and enriched using SP3 versus SP4 for MCF7 subcellular fractions and correlate protein capture in each method to protein hydrophobicity. Our results indicate that SP3 captures more hydrophilic proteins through a combination of HILIC-like and protein-aggregation mechanisms, while SP4 captures more hydrophobic proteins through a protein-aggregation mechanism. From these results, we recommend clean-up techniques based on protein-sample hydrophobicity to yield high proteome coverage in biological samples.

biochemistry↗