Unveiling inflammatory and prehypertrophic cell populations as key contributors to knee cartilage degeneration in osteoarthritis using multi-omics data integration.

OBJECTIVES: Single-cell and spatial transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome landscape and osteoarthritis (OA)-critical cell populations. METHODS: Single-cell RNA sequencing and spatially resolved transcriptomic technology have been applied to characterise the cellular heterogeneity of human knee articular cartilage which were collected from 8 OA donors, and 3 non-OA control donors, and a total of 19 samples. The novel chondrocyte population and marker genes of interest were validated by immunohistochemistry staining, quantitative real-time PCR, etc. The OA-critical cell populations were validated through integrative analyses of publicly available bulk RNA sequencing data and large-scale genome-wide association studies. RESULTS: We identified 33 cell population-specific marker genes that define 11 chondrocyte populations, including 9 known populations and 2 new populations, that is, pre-inflammatory chondrocyte population (preInfC) and inflammatory chondrocyte population (InfC). The novel findings that make this an important addition to the literature include: (1) the novel InfC activates the mediator MIF-CD74; (2) the prehypertrophic chondrocyte (preHTC) and hypertrophic chondrocyte (HTC) are potentially OA-critical cell populations; (3) most OA-associated differentially expressed genes reside in the articular surface and superficial zone; (4) the prefibrocartilage chondrocyte (preFC) population is a major contributor to the stratification of patients with OA, resulting in both an inflammatory-related subtype and a non-inflammatory-related subtype. CONCLUSIONS: Our results highlight InfC, preHTC, preFC and HTC as potential cell populations to target for therapy. Also, we conclude that profiling of those cell populations in patients might be used to stratify patient populations for defining cohorts for clinical trials and precision medicine.

SpatialMap: Spatial Mapping of Unmeasured Gene Expression Profiles in Spatial Transcriptomic Data Using Generalized Linear Spatial Models.

Recent advances in various single-cell RNA sequencing (scRNA-seq) technologies have enabled profiling the gene expression level with the whole transcriptome at a single-cell resolution. However, it lacks the spatial context of tissues. The image-based transcriptomics in situ studies (e.g., MERFISH and seqFISH) maintain the cell spatial context at individual cell levels but can only measure a limited number of genes or transcripts (up to roughly 1,000 genes). Therefore, integrating scRNA-seq data and image-based transcriptomics data can potentially gain the complementary benefits of both. Here, we develop a computational method, SpatialMap, to bridge the gap, which primarily facilitates spatial mapping of unmeasured gene profiles in spatial transcriptomic data via integrating with scRNA-seq data from the same tissue. SpatialMap directly models the count nature of spatial gene expression data through generalized linear spatial models, which accounts for the spatial correlation among spatial locations using conditional autoregressive (CAR) prior. With a newly developed computationally efficient penalized quasi-likelihood (PQL)-based algorithm, SpatialMap can scale up to performing large-scale spatial mapping analysis. Finally, we applied the SpatialMap to four publicly available tissue-paired studies (i.e., scRNA-seq studies and image-based transcriptomics studies). The results demonstrate that the proposed method can accurately predict unmeasured gene expression profiles across various spatial and scRNA-seq dataset pairs of different species and technologies.

Genome-Wide Differentially Methylated Region Analysis to Reveal Epigenetic Differences of Articular Cartilage in Kashin-Beck Disease and Osteoarthritis.

Kashin-Beck disease (KBD) is a degenerative osteoarticular disorder, and displays the significant differences with osteoarthritis (OA) regarding the etiology and molecular changes in articular cartilage. However, the underlying dysfunctions of molecular mechanisms in KBD and OA remain unclear. Here, we primarily performed the various genome-wide differential methylation analyses to reveal the distinct differentially methylated regions (DMRs) in conjunction with corresponding differentially methylated genes (DMGs), and enriched functional pathways in KBD and OA. We identified a total of 131 DMRs in KBD vs. Control, and 58 DMRs in OA vs. Controls, and the results demonstrate that many interesting DMRs are linked to DMGs, such as SMOC2 and HOXD3, which are all key genes to regulate cartilage/skeletal physiologic and pathologic process, and are further enriched in skeletal system and limb-associated pathways. Our DMR analysis indicates that KBD-associated DMRs has higher proportion than OA-associated DMRs in gene body regions. KBD-associated DMGs were enriched in wounding and coagulation-related functional pathways that may be stimulated by trace elements. The identified molecular features provide novel clues for understanding the pathogenetic and therapeutic studies of both KBD and OA.

[Construction and identification of recombinant adeno-associated virus shuttle vector expressing nerve growth factor beta gene].

OBJECTIVE: To construct a recombinant adeno-associated virus (AAV) shuttle vector expressing nerve growth factor beta (NGF-beta) gene. METHODS: By PCR amplification, the structural element of pAAV-multiple cloning site (MCS) and the functional element of pGenesil-1.1 were obtained and cloned into T-easy vector, respectively; the recombinant T-easy vectors were digested by restriction enzyme, then the target fragments were reclaimed and connected by DNA ligase, so the recombinant AAV shuttle vector pAAV-U6/CMV-enhanced green fluorescent protein (EGFP) containing U6 promoter and CMV promoter was obtained. The vector was transfected into 293 cells. The human Miapaca-2 cell line was cultured, and total RNA was extracted, then human NGF-beta gene was obtained by RT-PCR. T-easy-NGF-beta vector was constructed by cloning human NGF-beta gene into T-easy vector and identified by RT-PCR, digestion, and DNA sequencing. As NGF-beta gene was cloned into pAAV-U6/CMV-EGFP vector, the recombinant AAV shuttle vector expressing NGF-beta gene was obtained and identified by RT-PCR, digestion, and DNA sequencing. RESULTS: The bands of 800 bp and 4 250 bp were detected when pAAV-U6/CMV-EGFP was digested. The GFP was detected when pAAV-U6/CMV-EGFP was transfected into 293 cells. The bands of 736 bp and 3 015 bp were detected when T-easy-NGF-beta was digested; DNA sequencing result of T-easy-NGF-beta was fully consistent. The bands of 736 bp and 4 250 bp were detected when pAAV-U6/CMV-NGF-beta was digested. DNA sequencing result of pAAV-U6/ CMV-NGF-beta showed that sequences were completely correct. CONCLUSION: The AAV shuttle vector pAAV-U6/CMV-NGF-beta is successfully constructed, providing experimental basis for investigation of the repair of spinal cord injury.