Integrated transcriptome and proteome analyses identify novel regulatory network of nucleus pulposus cells in intervertebral disc degeneration

Abstract

Background Degeneration of intervertebral disc is a major cause of lower back pain and neck pain. Studies have tried to unveil the regulatory network using either transcriptomic or proteomic analysis. However, neither have fully elucidated the exact mechanism of degeneration process. Since post-transcriptional regulation may affect gene expression by modulating the translational process of mRNA to protein product, a combined transcriptomic and proteomic study may provide more insight into the key regulatory network of Intervertebral disc degeneration. Methods In order to obtain the proteomic and transcriptomic data, we performed label-free proteome analysis on freshly isolated nucleus pulposus cells and obtained transcriptome profiling data from the Gene Expression Omnibus repository. To identify the key regulatory network of intervertebral disc degeneration in nucleus pulposus cells, we performed bioinformatic analyses and established a protein-RNA interacting network. To validate the candidate genes, we performed in vitro experimentation and immunochemistry labeling to identify their potential function during nucleus pulposus degeneration. Results The label-free proteome analysis identified altogether 656 proteins, and 503 of which were differentially expressed between nucleus pulposus cells from degenerated or normal disc cells. Using the existing nucleus pulposus transcriptomic profiling data, we integrated the proteomic and transcriptomic data of nucleus pulposus cells, and established a protein-RNA interacting network to show the combined regulatory network of intervertebral disc degeneration. In the network, we found 9 genes showed significant changes, and 6 of which (CHI3L1, KRT19, COL6A2, DPT, TNFAIP6 and COL11A2) showed concordant changes in both protein and mRNA level. Further functional analysis showed these candidates can significantly affect the degeneration of the nucleus pulposus cell when altering their expression. Conclusions This study is the first to use combined analysis of proteomic and transcriptomic profiling data to identify novel regulatory network of nucleus pulposus cells in intervertebral disc degeneration. Our established protein-RNA interacting network demonstrated novel regulatory mechanisms and key genes that may play vital roles in the pathogenesis of intervertebral disc degeneration.

Combined Transcriptomic and Proteomic Analyses Reveal the Different Responses to UVA and UVB Radiation in Human Keratinocytes

“…Although the correlation between the proteome and transcriptome was poor ( R = 0.225 and 0.05), a relatively higher positive correlation was identified ( R = 0.51 and 0.60) for the DEGs and DAPs, regulated in the same direction, in UVB_vs_Control and UVA_vs_Control, respectively (Figure S4c–f). These results were consistent with many previous studies, which integrated transcriptome and proteome to investigate molecular mechanisms in a variety of organisms, including Chinese hamster ovary cells, nucleus pulposus cells and plants (43–46). These were probably attributed to the complex post‐transcriptional or translational regulation (45,47).…”

“…These results were consistent with many previous studies, which integrated transcriptome and proteome to investigate molecular mechanisms in a variety of organisms, including Chinese hamster ovary cells, nucleus pulposus cells and plants (43–46). These were probably attributed to the complex post‐transcriptional or translational regulation (45,47). To a certain extent, the DAPs identified from comparative proteomic analysis implicated that these proteins might contribute to the changes in cell functions or phenotypes.…”

Identification of Core Genes and Screening of Potential Targets in Intervertebral Disc Degeneration Using Integrated Bioinformatics Analysis

“…First, the data used were downloaded from a public database, and it was not possible to assess whether there were entry errors. Also, there exist differences in the enriched gene functions and pathways of the differentially expressed genes between mRNA and protein data, and this study focused only on mRNA datasets ( Xu et al, 2021 ). Second, our study only focused on the genes that were identified as differentially expressed in datasets.…”

Immuno-Modulatory Effects of Intervertebral Disc Cells

“… Xu et al (2021) created a regulatory network behind IDD by combining transcriptomic and proteomic analysis. They hypothesized that post-transcriptional regulation could have an effect on protein content, thus, if a gene presents elevated mRNA and protein levels, it could be implicated in IDD.…”