Background/Purpose:

Recent studies revealed that haplogroup J associates with a decreased rate of incident knee Osteoarthritis. Among the functional characteristics of this haplogroup, lower rates of apoptosis stand out. In this study we aimed to evaluate if this process is epigenetically regulated.

Methods:

DNA methylation profiling from a previous study performed in knee articular cartilage was obtained from Gene Expression Omnibus database (accession GSE-43191). In that study, cartilage DNA was isolated from 13 samples carrying the haplogroup J and 20 samples carrying the haplogroup H. The differential methylome between J and H haplogroups was obtained using Lumi and Methylumi packages (R bioconductor).

A subsequent validation by RNA-seq was performed in 7 haplogroup J cartilage samples and 9 haplogroup H cartilage samples. Differential expression data between haplogroups were analyzed using Kallisto package (R bioconductor). Gene ontology analyses from methylation and expression approaches were performed using DAVID (https://david.ncifcrf.gov/).

Results:

Gene ontology analysis of the 538 differentially methylated regions between haplogroups J and H revealed that genes involved in the negative regulation of apoptosis (p=0,021) and catalytic activity (p=0,036) were hypomethylated in haplogroup J cartilages. On the contrary, haplogroup H cartilages showed a enrichment of hypomethylated genes involved in the positive regulation of apoptosis (p=0,008); an enrichment of hypomethylated genes involved in the negative regulation of the metabolic processes of nitrogen compounds (p=0,03) and macromolecules (p=0,026) was detected in haplogroup H cartilages.

Subsequent validation by RNA-seq revealed 416 differentially expressed genes between haplogroups H and J, considering an adjusted p-value≤0,005 as well as a logFc≥±4 (Figure 1). Of these genes, 362 were up-regulated in haplogroup J cartilages and 54 up-regulated in haplogroup H. Among the most differentially altered biological processes, a enrichment of over-expressed genes involved in the positive regulation of apoptosis (p=0,047) and cellular adhesion (p=0,0018) was detected in haplogroup H cartilages. On the contrary, an enrichment of up-regulated genes involved in lipid synthesis (p=0,044), Calcium homeostasis (p=0,047), cell signaling (p=0,00031) and immune system development (p=0,0092) was detected in haplogroup J cartilages.

Conclusion:

Mitochondrial haplogroups J and H induce specific methylation and expression profiles in cartilage samples that lead to an epigenetic regulation of apoptosis, being more repressed in cartilages with J haplogroup and more active in cartilages with H haplogroup.