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Genome-wide analysis of DNA methylation profile identifies differentially methylated loci associated with human intervertebral disc degeneration


Autoři: Akihiro Ikuno aff001;  Koji Akeda aff002;  Shin-ichiro Takebayashi aff001;  Motomu Shimaoka aff003;  Katsuzumi Okumura aff001;  Akihiro Sudo aff002
Působiště autorů: Laboratory of Molecular & Cellular Biology, Graduate School of Bioresources, Mie University, Tsu, Japan aff001;  Department of Orthopaedic Surgery, Mie University Graduate School of Medicine, Tsu, Japan aff002;  Department of Molecular Pathobiology3, Mie University Graduate School of Medicine, Tsu, Japan aff003
Vyšlo v časopise: PLoS ONE 14(9)
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pone.0222188

Souhrn

Background

Environmental and endogenous factors under genetic predisposition are considered to initiate the human intervertebral disc (IVD) degeneration. DNA methylation is an essential mechanism to ensure cell-specific gene expression for normal development and tissue stability. Aberrant epigenetic alterations play a pivotal role in several diseases, including osteoarthritis. However, epigenetic alternations, including DNA methylation, in IVD degeneration have not been evaluated. The purpose of this study was to comprehensively compare the genome-wide DNA methylation profiles of human IVD tissues, specifically nucleus pulpous (NP) tissues, with early and advanced stages of disc degeneration.

Methods

Human NP tissues were used in this study. The samples were divided into two groups: early stage degeneration (n = 8, Pfirrmann’s MRI grade: I-III) and advanced stage degeneration (n = 8, grade: IV). Genomic DNA was processed for genome-wide DNA methylation profiling using the Infinium MethylationEPIC BeadChip array. Extraction of raw methylation data, clustering and scatter plot of each group values of each sample were performed using a methylation module in GenomeStudio software. The identification of differentially methylated loci (DMLs) and the Gene Ontology (GO) analysis were performed using R software with the ChAMP package.

Results

Unsupervised hierarchical clustering revealed that early and advanced stage degenerated IVD samples segregated into two main clusters by their DNA methylome. A total of 220 DMLs were identified between early and advanced disc degeneration stages. Among these, four loci were hypomethylated and 216 loci were hypermethylated in the advanced disc degeneration stage. The GO enrichment analysis of genes containing DMLs identified two significant GO terms for biological processes, hemophilic cell adhesion and cell-cell adhesion.

Conclusions

We conducted a genome-wide DNA methylation profile comparative study and observed significant differences in DNA methylation profiles between early and advanced stages of human IVD degeneration. These results implicate DNA methylation in the process of human IVD degeneration.

Klíčová slova:

Biology and life sciences – Cell biology – Chromosome biology – Chromatin – Chromatin modification – DNA methylation – Signal transduction – Cell signaling – Hedgehog signaling – Signaling cascades – Wnt signaling cascade – Cellular structures and organelles – Extracellular matrix – Genetics – Epigenetics – DNA modification – Gene expression – DNA – Genetic loci – Genomics – Genome analysis – Gene ontologies – Biochemistry – Nucleic acids – Computational biology – Medicine and health sciences – Rheumatology – Arthritis – Osteoarthritis – Diagnostic medicine – Diagnostic radiology – Magnetic resonance imaging – Radiology and imaging – Research and analysis methods – Imaging techniques


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