TABLE 3.
Summary of omics studies in IVD research.
| Model | Tissue | Method | Findings | References |
|---|---|---|---|---|
| A. Transcriptomics | ||||
| Human | Notochordal cells derived from hESCs-H9 cell line | Pan-genomic high-throughput scRNA-seq | Identified transcription factor regulatory network consisting of notochordal differentiation drivers PAX6, GDF3, FOXD3, TDGF1, SOX5, LMX1A, LEFTY1 and LEFTY2 | Diaz-Hernandez et al. (2020) |
| IVDs dissected from healthy adult human donors. NP and AF cells isolated from tissue | scRNA-seq | Displayed high expression of SFRP1, BIRC5, CYTL1, ESM1 and CCNB2 genes in AF cells and COL2A1, DSC3, COL9A3, COL11A1, and ANGPTL7 in NP cells. Identified signature transcription factors for AF (FOXM1) and NP (KDM4E) | Fernandes et al. (2020) | |
| IVDs dissected from healthy adult human donors. Cells isolated from IVD tissue | Droplet-based scRNA-seq | Identified major cell clusters in human IVDs. Confirmed PDGFRA and PROCR marked progenitor cells in IVD. | Gan et al. (2021) | |
| Discs isolated from adult humans. Primary NP and AF cells isolated and immortalized | cDNA Microarray analysis | Identified of membrane-associated genes including AF-specific COLEC12, LPAR1 and CHIC1 and NP-specific CLDN1, TMEFF2, EFNsA1 and NETO2 | Minogue et al. (2010); van den Akker et al. (2020) | |
| AF and NP tissue surgically collected from adult IDD cervical discectomy patients | RNAseq | AF showed higher expression of genes including COL1A2, COL6A1, LAMA3, and DLL1. NP showed higher expression of COMP, LUM, COL2A1 and BGN. | Riester et al. (2018) | |
| Notochordal and sclerotomal cells isolated from human embryonic and fetal spines (7.5–14 WPC) | Microarray analysis followed by PCA | Identification of notochordal markers including CD24, STMN2, RTN1, PRPH, and CXCL12 | Rodrigues-Pinto et al. (2018) | |
| NP collected from adult human patients with IDD or spinal cord injury | RNA-seq followed by stringent algorithmic pipeline to identify lncRNA | Indicated that 1854 lncRNAs were differentially expressed in IDD including upregulation of EPB41L2, SH3BP2 and ATM and downregulation of SIPA1L2, KMT2E and PAAF1 | Zhao et al. (2016) | |
| Mouse | Notochords isolated from Shh-cre; ROSA:YFP mice at E12.5 and P0 days | Whole transcriptome RNA-Seq followed by PCA | Differential expression of Shh, TGF-β, and IGF pathways between E12.5 and P0. Lower mRNA abundance of Shh, Ptch1, Smo and Gli1 at P0 | Peck et al. (2017) |
| Cells isolated from dissected vertebral column tissue of E12.5 embryonic mice | In vivo high-throughput ChIP-Seq | Pax1 and Pax9 positively regulate key cartilage development genes including Sox5, 76an, Col2a1 and Wwp2 | Sivakamasundari et al. (2017) | |
| Tissue from adult Sox9cKO mice 5 days post-tamoxifen injection | Microarray analysis followed by PCA | Sox9 deletion resulted in downregulation of ECM-related genes Col2a1, Col11a1, Col9a2, and ion channel-encoding genes Trpm4, Trpm7 and Piezo2, as well as upregulation of matrix remodeling and inflammation genes including Timp1, Adam10, and Cxcr8 | Tsingas et al. (2020) | |
| Bovine | Coccygeal discs collected from 6mo to 12mo old calves | scRNA-seq and bulk RNA-seq | Identified 24 AF-specific markers including TIE1, CTGF, PCOLCE, and HSPA5. Identified 27 NP-specific markers including CD24, KRT8, CCN2, and HIGD2A | Calió et al. (2021) |
| Coccygeal discs collected from adult cows | RNA in situ hybridization and z proportion test | Identified 10 novel markers including Lam1 and Thy1 in the AF and Gli1, Gli3, Noto, Scx, Ptprc, Sox2, Zscan10 and LOC101904175 in the NP | Li et al. (2019) | |
| Caudal discs collected from 2 to 3yr old cows | scRNA-seq | Identified AF markers including MGP, COMP, SPP1, and GSN. Identified NP markers including CP, S100B, SNORC and CRELD2 | Panebianco et al. (2021) | |
| Rat | Cervical IVDs from healthy, adult, wild-type rats. AF and NP cells isolated from tissue | scRNA-seq | Identified highly specific marker genes including Bpifa2f, Mmmp3, and IL11 for IAF; Fibin, Myoc, and Igfbp5 for OAF; Krt7, Prrg4, and Akap12 for NP. | Wang et al. (2021a) |
| B. Proteomics | ||||
| Human | IVDs collected from healthy adult patients | LC-MS/MS and iTRAQ analysis | High levels of lubricin protein and lower levels of biglycan in IVDs compared to other cartilage subtypes | Önnerfjord et al. (2012) |
| IVDs collected from human fetal spines (24 WPC) | LC-MS/MS | Identified 1316 proteins and 10 significant protein clusters | Rajasekaran et al. (2020) | |
| IVDs collected from human fetal (less than 24 WPC) and adult spines | ESI-LC-MS/MS | Identified 14 proteins uniquely expressed or upregulated in fetal IVDs compared to adults. Proteins include P4HA1, P4HA2, Procollagen-lysine, PLOD1, SERPINH1, CD109, LGALS3, SERPINF1, and Annexin A1, A4 and A5 | Rajasekaran et al. (2021) | |
| IVDs collected from adult IDD patients. AF and NP tissues isolated from discs | FTMS/ITMSMS and iTRAQ analysis | In degenerated tissues, identified differential regulation on 73 proteins in the AF and 54 proteins in the NP. | Sarath Babu et al. (2016) | |
| AF cells collected from adult IDD and scoliosis patients | Silver stained 2-DE gels and MS | In degenerated AF cells, identified decrease in HSPA8Q, G6PD, and protocadherin-23 and increase in GNAI2, superoxide dismutase, TMEM51, adenosine receptor A3, 26S protease regulatory subunit 8, LPPR2, and FAR1 | Ye et al. (2015) | |
| IVDs collected from IDD, AIS and trauma patients (11–53years). AF, NP, and EP isolated from discs | LC-MS/MS and iTRAQ analysis | In degenerated tissues, revealed increased levels of HTRA1, COMP, and CILP in AF and CILP and CILP2 in NP tissue | Yee et al. (2016) | |
| Mouse | IVDs collected from healthy adult Foxa2 mNE -Cre/ZEG mice. NP and AF isolated from tissue | LC-MS/MS | NP cells displayed enrichment in proteins including Cdh2, Dsp, Gja1, Wnk1, Vamp3. AF cells displayed enrichment in proteins including Sod3 and Clu | Kudelko et al. (2021) |
| Intact IVDs collected from healthy adult mice | LC-ESI-MS/MS | Identified 1360 proteins in distinct categories. Confirmed presence of 14 previously identified IVD-associated markers | McCann et al. (2015) | |
| Bovine | Caudal discs collected from healthy fetal, 12mo old and 16–18years old cows | LC-MS/MS and iTRAQ analysis | Observed enrichment of Collagen XII and Collagen XIV in fetal NPs, Collagen XI in young NPs and Fibronectin and Prolargin in older NPs | Caldeira et al. (2017) |
| Caudal discs collected from 18mos to 24mo old cows | Differential in-gel electrophoresis proteomics (DIGE) | Identified 14 proteins specific to the disc or cartilage cells | Gilson et al. (2010) | |
| C. Metabolomics | ||||
| Human | IVDs collected from adult IDD patients. Tissue isolated from discs | 1H HR MAS NMR spectroscopy | Degraded discs had significantly higher concentrations of multiple metabolites including creatine, glycine, and leucine | Radek et al. (2016) |
PCA, principal component analysis; WPC, weeks post-conception; ECM, extracellular matrix; cKO, conditional knock-out; NP, nucleus pulposus; AF, annulus fibrosus; IAF, inner annulus fibrosus; OAF, outer annulus fibrosus; LC, liquid chromatography; MS, mass spectrometry; ESI-MS, electrospray ionization tandem mass spectrometry; 2-DE, 2-D electrophoresis; FTMS, Fourier transform mass spectrometry; ITMS, ion trap tandem mass spectrometry; HR MAS, high-resolution magic angle spinning; NMR, nuclear magnetic resonance.