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Insights into a Cancer-Target Demethylase: Substrate Prediction through Systematic Specificity Analysis for KDM3A
Anand Chopra1,2, William G Willmore1,2, Kyle K Biggar1,2
1Institute of Biochemistry, Carleton University, Ottawa, ON K1S 5B6, Canada.
Abstract:
Jumonji C (JmjC) lysine demethylases (KDMs) catalyze the removal of methyl (-CH3) groups from modified lysyl residues. Several JmjC KDMs promote cancerous properties and these findings have primarily been in relation to histone demethylation. However, the biological roles of these enzymes are increasingly being shown to also be attributed to non-histone demethylation. Notably, KDM3A has become relevant to tumour progression due to recent findings of this enzyme's role in promoting cancerous phenotypes, such as enhanced glucose consumption and upregulated mechanisms of chemoresistance. To aid in uncovering the mechanism(s) by which KDM3A imparts its oncogenic function(s), this study aimed to unravel KDM3A substrate specificity to predict high-confidence substrates. Firstly, substrate specificity was assessed by monitoring activity towards a peptide permutation library of histone H3 di-methylated at lysine-9 (i.e., H3K9me2). From this, the KDM3A recognition motif was established and used to define a set of high-confidence predictions of demethylation sites from within the KDM3A interactome. Notably, this led to the identification of three in vitro substrates (MLL1, p300, and KDM6B), which are relevant to the field of cancer progression. This preliminary data may be exploited in further tissue culture experiments to decipher the avenues by which KDM3A imparts cancerous phenotypes.
Insights
This study identifies the substrate specificity of KDM3A, a Jumonji C (JmjC) lysine demethylase (KDM) linked to cancer. Understanding KDM3A
Area of Science:
- Biochemistry and Molecular Biology
- Cancer Research
- Epigenetics
Background:
- Jumonji C (JmjC) lysine demethylases (KDMs) remove methyl groups from lysyl residues, influencing biological processes.
- While KDMs are known for histone demethylation, their non-histone roles are gaining attention in cancer progression.
- KDM3A is implicated in tumor progression, promoting phenotypes like increased glucose consumption and chemoresistance.
Purpose of the Study:
- To elucidate the mechanism of KDM3A's oncogenic function by determining its substrate specificity.
- To predict high-confidence KDM3A substrates and identify potential targets for therapeutic intervention.
Main Methods:
- Assessed KDM3A substrate specificity using a peptide permutation library targeting histone H3 di-methylated at lysine-9 (H3K9me2).
- Established the KDM3A recognition motif based on activity assays.
- Utilized the motif to predict demethylation sites within the KDM3A interactome.
Main Results:
- Defined the specific recognition motif for KDM3A activity.
- Identified three high-confidence in vitro substrates: MLL1, p300, and KDM6B.
- These substrates are known to be relevant to cancer progression pathways.
Conclusions:
- This study provides critical insights into KDM3A substrate specificity, revealing its potential non-histone targets.
- The identified substrates (MLL1, p300, KDM6B) offer avenues for further investigation into KDM3A's oncogenic roles.
- Preliminary data supports future tissue culture experiments to decipher KDM3A's contribution to cancer phenotypes.
