human IVD proteome resource
############# Introduction #############
The spatiotemporal proteome of the intervertebral disc (IVD) underpins its integrity and function. We present DIPPER, a comprehensive proteomic resource comprising IVD data from 17 individuals. To begin with, protein modules defining key directional trends along the lateral and anteroposterior axes were derived from high-resolution spatial proteomes of intact young cadaveric lumbar IVDs. They reveal novel region-specific regulatory activities and displayed potential paths of deconstruction in the level- and location-matched aged discs. Machine learning methods predict a “hydration matrisome” that connects extracellular matrix with MRI intensity. Importantly, results from the static proteome (as point-references) were shown to be integratable with dynamic proteome (SILAC/degradome) and transcriptome data from multiple clinical samples, enhancing robustness and boosting clinical relevance. The data, findings and methodology may be valuable references in the field of IVD biology and proteomic analytics.
############# Name #############
DIPPER (Disc Proteome Resource), also in reference to the Big Dipper, a group of seven point-reference stars important in guiding marine voyages since ancient times.
############# RAW data #############
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Vizcaino et al., 2016) repository with the following dataset identifiers for cadaver samples (PXD017774), SILAC samples (PXD018193), and degradome samples (PXD018298000). The RAW data for the transcriptome data has been deposited on NCBI GEO with accession number GSE147383. The custom scripts for processing and analysing the data were housed at github.com/hkudclab/human_disc_proteome. An interactive web interface for the data is available at http://www.sbms.hku.hk/dclab/DIPPER/ .
############# Team #############
Vivian Tam1,2*, Peikai Chen1*, Anita Yee1, Nestor Solis3, Theo Klein3, Mateusz Kudelko1, Rakesh Sharma4, Wilson Chan1,2,5, Anna Wang6, Christopher Overall3, Lisbet Haglund7, Ed Wu6, Pak C Sham8, Kathryn S E Cheah1, Danny Chan1,2
* These authors contributed equally to this manuscript
1 School of Biomedical Sciences, The University of Hong Kong, Hong Kong; 2 The University of Hong Kong Shenzhen of Research Institute and Innovation (HKU-SIRI), Shenzhen, China; 3 Centre for Blood Research, University of British Columbia, Vancouver, Canada; 4 Proteomics and Metabolomics Core Facility, The University of Hong Kong, Hong Kong; 5 Department of Orthopaedics Surgery and Traumatology, HKU-Shenzhen Hospital, Shenzhen, China; 6 Department of Electrical and Electronics Engineering, The University of Hong Kong, Hong Kong; 7 Department of Surgery, McGill University, Montreal, Canada; 8 Centre for PanorOmic Sciences (CPOS), The University of Hong Kong, Hong Kong.
############# Pre-print #############
See our pre-print: https://www.biorxiv.org/content/10.1101/2020.07.11.192948v3
############# Paper #############
(PMID: 33382035) Tam and Chen et al., 2020.