DIPPER, a spatiotemporal proteomics atlas of human intervertebral discs for exploring ageing and degeneration dynamics

Abstract

The spatiotemporal proteome of the intervertebral disc (IVD) underpins its integrity and function. We present DIPPER, a deep and comprehensive IVD proteomic resource comprising 94 genome-wide profiles from 17 individuals. To begin with, protein modules defining key directional trends spanning the lateral and anteroposterior axes were derived from high-resolution spatial proteomes of intact young cadaveric lumbar IVDs. They revealed novel region-specific profiles of regulatory activities and displayed potential paths of deconstruction in the level- and location-matched aged cadaveric discs. Machine learning methods predicted a ‘hydration matrisome’ that connects extracellular matrix with MRI intensity. Importantly, the static proteome used as point-references can be integrated with dynamic proteome (SILAC/degradome) and transcriptome data from multiple clinical samples, enhancing robustness and clinical relevance. The data, findings, and methodology, available on a web interface (http://www.sbms.hku.hk/dclab/DIPPER/), will be valuable references in the field of IVD biology and proteomic analytics.

The Cellular Composition of Bovine Coccygeal Intervertebral Discs: A Comprehensive Single-Cell RNAseq Analysis

“…TAGLN ( SM22 ) has similarly been described in fibroblasts and dedifferentiated cultured chondrocytes [ 107 , 108 ]. Overall, our data match spatial proteomics findings from Tam V. 2020 in detecting structural specific genes both in the NP and AF, indicating the relevance and integrity of our data [ 21 ]. Discrepancies, however, might be due to the disc composition and remodeling of a sample, especially because with RNAseq data we only capture the cellular information and these only represent a small fraction of the disc volume [ 109 ].…”

“…In contrast to the NP, where only a couple of cell clusters expressing some collagens, most cell clusters in the AF contributed by expressing of a wide variety of collagens ( Figure S7 ). Among those highly expressed collagens, we found COL1A1, COL1A2, COL9A3, COL18A1 and COL4A1 , which have been widely reported [ 20 , 21 ].…”

“…Furthermore, our bulk RNA experiments could only support the overexpression of KRT8 and CD24 in the NP, indicating the potential limitations in detecting changes in gene expression in very heterogeneous cell populations. Novel NP markers such as CHRD [ 88 ], CHRDL2, SCUBE1 [ 89 ] and CLEC3B were both detected and differentially expressed in both our NP datasets [ 21 ]. Some of the novel detected NPC contributing genes are part of important signalling pathways and act as inhibitors of WNT ( FRZB and DKK3 ) and BMP signaling ( CHRD, CHRDL2 ).…”

“…Other matricellular genes involved in collagen fibrillogenesis were detected in our AF data and include PCOLCE , PCOLCE2 and MXRA5 [ 21 ]. Due to load bearing properties of the AF and similarities in mechanical functionalities, it was not surprising to find that AFC expressed tendon-related markers such as Tenacin C, tenomodulin and thrombosponins ( THBS1/3/4 ) as well as cartilage intermediate layer proteins ( CILP2 and CILP ), some of which have reported in previous studies [ 21 , 99 ]. Additionally, a wide variety of heat shock proteins ( HSPA5, HSPA6, HSPA8, HSP90AA1, HSP90AB1, HSP90B1, HSPB1, HSPH1 and HSPA1A ) were mostly detected in Clusters 4 and 5 in the AF, suggesting their role in the stress response to load bearing.…”

“…The annulus fibrosus is believed to retain the capacity to regenerate itself during the neonatal phase, and this is then lost during maturation [ 17 ]. Annulus fibrosus cell (APC) markers described in the literature include Col1a1, Col4, Lam1 and Thy1 , among others [ 10 , 18 , 19 , 20 , 21 , 22 , 23 , 24 ]. Instead, the young NP presents an abundant extracellular matrix (ECM) that separates NP cells (NPC) [ 8 ].…”