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Bitterli T, Schmid D, Ettinger L, Krupkova O, Bach FC, Tryfonidou MA, Meij BP, Pozzi A, Steffen F, Wuertz‐Kozak K, Smolders LA. Targeted screening of inflammatory mediators in spontaneous degenerative disc disease in dogs reveals an upregulation of the tumor necrosis superfamily. JOR Spine 2024; 7:e1292. [PMID: 38222814 PMCID: PMC10782068 DOI: 10.1002/jsp2.1292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/28/2023] [Accepted: 09/26/2023] [Indexed: 01/16/2024] Open
Abstract
Background The regulation of inflammatory mediators in the degenerating intervertebral disc (IVD) and corresponding ligamentum flavum (LF) is a topic of emerging interest. The study aimed to investigate the expression of a broad array of inflammatory mediators in the degenerated LF and IVD using a dog model of spontaneous degenerative disc disease (DDD) to determine potential treatment targets. Methods LF and IVD tissues were collected from 22 normal dogs (Pfirrmann grades I and II) and 18 dogs affected by DDD (Pfirrmann grades III and IV). A qPCR gene array was used to investigate the expression of 80 inflammatory genes for LF and IVD tissues, whereafter targets of interest were investigated in additional tissue samples using qPCR, western blot (WB), and immunohistochemistry. Results Tumor necrosis factor superfamily (TNFSF) signaling was identified as a regulated pathway in DDD, based on the significant regulation (n-fold ± SD) of various TNFSF members in the degenerated IVD, including nerve growth factor (NGF; -8 ± 10), CD40LG (464 ± 442), CD70 (341 ± 336), TNFSF Ligand 10 (9 ± 8), and RANKL/TNFSF Ligand 11 (85 ± 74). In contrast, TNFSF genes were not significantly affected in the degenerated LF compared to the control LF. Protein expression of NGF (WB) was significantly upregulated in both the degenerated LF (4.4 ± 0.5) and IVD (11.3 ± 5.6) compared to the control group. RANKL immunopositivity was significantly upregulated in advanced stages of degeneration (Thompson grades IV and V) in the nucleus pulposus and annulus fibrosus of the IVD, but not in the LF. Conclusions DDD involves a significant upregulation of various TNFSF members, with tissue-specific expression profiles in LF and IVD tissues. The differential involvement of TNFSF members within multiple spinal tissues from the same individual provides new insights into the inflammatory processes involved in DDD and may provide a basis to formulate hypotheses for the determination of potential treatment targets.
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Affiliation(s)
- Thomas Bitterli
- Clinic for Small Animal Surgery, Department for Small Animals, Vetsuisse FacultyUniversity of ZurichZurichSwitzerland
| | - David Schmid
- Clinic for Small Animal Surgery, Department for Small Animals, Vetsuisse FacultyUniversity of ZurichZurichSwitzerland
| | - Ladina Ettinger
- Clinic for Small Animal Surgery, Department for Small Animals, Vetsuisse FacultyUniversity of ZurichZurichSwitzerland
| | - Olga Krupkova
- Clinic for Small Animal Surgery, Department for Small Animals, Vetsuisse FacultyUniversity of ZurichZurichSwitzerland
- Spine SurgeryUniversity Hospital BaselBaselSwitzerland
- Department of BiomedicineUniversity of Basel & University Hospital Basel, Tissue EngineeringBaselSwitzerland
| | - Frances C. Bach
- Department of Clinical Sciences, Faculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands
| | - Marianna A. Tryfonidou
- Department of Clinical Sciences, Faculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands
| | - Björn P. Meij
- Department of Clinical Sciences, Faculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands
| | - Antonio Pozzi
- Clinic for Small Animal Surgery, Department for Small Animals, Vetsuisse FacultyUniversity of ZurichZurichSwitzerland
| | - Frank Steffen
- Clinic for Small Animal Surgery, Department for Small Animals, Vetsuisse FacultyUniversity of ZurichZurichSwitzerland
| | - Karin Wuertz‐Kozak
- Institute for Biomechanics, ETH ZurichZurichSwitzerland
- Department of Biomedical EngineeringRochester Institute of Technology (RIT)RochesterNew YorkUSA
- Schön Clinic Munich Harlaching, Spine CenterAcademic Teaching Hospital and Spine Research Institute of the Paracelsus Medical University Salzburg (Austria)MunichGermany
| | - Lucas A. Smolders
- Clinic for Small Animal Surgery, Department for Small Animals, Vetsuisse FacultyUniversity of ZurichZurichSwitzerland
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Raghavan R, Coppola U, Wu Y, Ihewulezi C, Negrón-Piñeiro LJ, Maguire JE, Hong J, Cunningham M, Kim HJ, Albert TJ, Ali AM, Saint-Jeannet JP, Ristoratore F, Dahia CL, Di Gregorio A. Gene expression in notochord and nuclei pulposi: a study of gene families across the chordate phylum. BMC Ecol Evol 2023; 23:63. [PMID: 37891482 PMCID: PMC10605842 DOI: 10.1186/s12862-023-02167-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 08/08/2023] [Indexed: 10/29/2023] Open
Abstract
The transition from notochord to vertebral column is a crucial milestone in chordate evolution and in prenatal development of all vertebrates. As ossification of the vertebral bodies proceeds, involutions of residual notochord cells into the intervertebral discs form the nuclei pulposi, shock-absorbing structures that confer flexibility to the spine. Numerous studies have outlined the developmental and evolutionary relationship between notochord and nuclei pulposi. However, the knowledge of the similarities and differences in the genetic repertoires of these two structures remains limited, also because comparative studies of notochord and nuclei pulposi across chordates are complicated by the gene/genome duplication events that led to extant vertebrates. Here we show the results of a pilot study aimed at bridging the information on these two structures. We have followed in different vertebrates the evolutionary trajectory of notochord genes identified in the invertebrate chordate Ciona, and we have evaluated the extent of conservation of their expression in notochord cells. Our results have uncovered evolutionarily conserved markers of both notochord development and aging/degeneration of the nuclei pulposi.
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Affiliation(s)
- Rahul Raghavan
- Hospital for Special Surgery, Orthopedic Soft Tissue Research Program, New York, NY, 10021, USA
| | - Ugo Coppola
- Stazione Zoologica 'A. Dohrn', Villa Comunale 1, 80121, Naples, Italy
- Present Address: Molecular Cardiovascular Biology Division and Heart Institute, Cincinnati Children's Research Foundation, Cincinnati, OH, 45229, USA
| | - Yushi Wu
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Chibuike Ihewulezi
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Lenny J Negrón-Piñeiro
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Julie E Maguire
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Justin Hong
- Hospital for Special Surgery, Orthopedic Soft Tissue Research Program, New York, NY, 10021, USA
| | - Matthew Cunningham
- Hospital for Special Surgery, New York, NY, 10021, USA
- Weill Cornell Medical College, New York, NY, 10065, USA
| | - Han Jo Kim
- Hospital for Special Surgery, New York, NY, 10021, USA
- Weill Cornell Medical College, New York, NY, 10065, USA
| | - Todd J Albert
- Hospital for Special Surgery, New York, NY, 10021, USA
- Weill Cornell Medical College, New York, NY, 10065, USA
| | - Abdullah M Ali
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Jean-Pierre Saint-Jeannet
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | | | - Chitra L Dahia
- Hospital for Special Surgery, Orthopedic Soft Tissue Research Program, New York, NY, 10021, USA.
- Department of Cell and Developmental Biology, Weill Cornell Medicine, Graduate School of Medical Science, New York, NY, 10065, USA.
| | - Anna Di Gregorio
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA.
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Lu Z, Zheng Z. Integrated analysis of single-cell and bulk RNA sequencing data identifies the characteristics of ferroptosis in lumbar disc herniation. Funct Integr Genomics 2023; 23:289. [PMID: 37653201 DOI: 10.1007/s10142-023-01216-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/09/2023] [Accepted: 08/15/2023] [Indexed: 09/02/2023]
Abstract
Lumbar disc herniation (LDH) is the most common condition associated with low back pain, and it adversely impacts individuals' health. Ferroptosis has recently emerged as a novel factor in the pathogenesis of LDH; however, the specific impacts of ferroptosis on LDH have not been fully elucidated. Ferroptosis-related differentially expressed genes (FRDEGs) were identified from the transcriptomic datasets of LDH. Gene set enrichment analysis (GSEA) was conducted to identify biological mechanism and related pathways. LASSO and SVM-RFE algorithms were applied to detect signature genes. Function of the signature gene was confirmed by RT-qPCR. The CIBERSORT algorithm was used to compare immune infiltration between LDH and normal samples. Correlation analysis between MYB and immune cells was analyzed using the Pearson method. Additionally, we used scRNA-seq to dissect cell clusters and cellular interactions. AUCell scoring was used to analyze the ferroptosis scores of different cell types. We found that MYB, a highly expressed ferroptosis-related gene, was associated with LDH By leveraging bioinformatics analysis. In immune infiltration analysis, the abundance of monocytes and macrophages varied significantly between the LDH group and disc spondylolisthesis (DS) group. MYB was correlated with most immune cells. GSEA revealed MYB was significantly enriched in immune-related pathways. Furthermore, scRNA-seq analysis revealed the presence of eight distinct cell types. AUCell analysis showed that macrophages had a high ferroptosis score. Cell trajectory analysis revealed that chondrocyte 1 was at the beginning of the trajectory, while calcification inhibiting chondrocytes and fibrochondrocytes accumulated along the middle and tail end of the trajectory, respectively. Cell-cell communication analysis identified chondrocyte 1 had an extensive communication network with other clusters and interacted with nucleus pulposus through collagen signaling pathway. Our analysis demonstrated that MYB may be a potential therapeutic target for LDH. This study provides a resource for the orthopedics community that will facilitate additional discoveries directedly toward understanding the pathogenesis process of LDH.
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Affiliation(s)
- Ziqiang Lu
- Luoyang Orthopedic-Traumatological Hospital Of Henan Province, Luoyang, Henan, China.
| | - Zhenyu Zheng
- Luoyang Orthopedic-Traumatological Hospital Of Henan Province, Luoyang, Henan, China
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Zhang Y, Zhang J, Sun Z, Wang H, Ning R, Xu L, Zhao Y, Yang K, Xi X, Tian J. MAPK8 and CAPN1 as potential biomarkers of intervertebral disc degeneration overlapping immune infiltration, autophagy, and ceRNA. Front Immunol 2023; 14:1188774. [PMID: 37325630 PMCID: PMC10266224 DOI: 10.3389/fimmu.2023.1188774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/16/2023] [Indexed: 06/17/2023] Open
Abstract
Background Intervertebral disc degeneration (IDD) is one of the most common health problems in the elderly and a major causative factor in low back pain (LBP). An increasing number of studies have shown that IDD is closely associated with autophagy and immune dysregulation. Therefore, the aim of this study was to identify autophagy-related biomarkers and gene regulatory networks in IDD and potential therapeutic targets. Methods We obtained the gene expression profiles of IDD by downloading the datasets GSE176205 and GSE167931 from the Gene Expression Omnibus (GEO) public database. Subsequently, differentially expressed genes (DEGs) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, gene ontology (GO), and gene set enrichment analysis (GSEA) were performed to explore the biological functions of DEGs. Differentially expressed autophagy-related genes (DE-ARGs) were then crossed with the autophagy gene database. The hub genes were screened using the DE-ARGs protein-protein interaction (PPI) network. The correlation between the hub genes and immune infiltration and the construction of the gene regulatory network of the hub genes were confirmed. Finally, quantitative PCR (qPCR) was used to validate the correlation of hub genes in a rat IDD model. Results We obtained 636 DEGs enriched in the autophagy pathway. Our analysis revealed 30 DE-ARGs, of which six hub genes (MAPK8, CTSB, PRKCD, SNCA, CAPN1, and EGFR) were identified using the MCODE plugin. Immune cell infiltration analysis revealed that there was an increased proportion of CD8+ T cells and M0 macrophages in IDD, whereas CD4+ memory T cells, neutrophils, resting dendritic cells, follicular helper T cells, and monocytes were much less abundant. Subsequently, the competitive endogenous RNA (ceRNA) network was constructed using 15 long non-coding RNAs (lncRNAs) and 21 microRNAs (miRNAs). In quantitative PCR (qPCR) validation, two hub genes, MAPK8 and CAPN1, were shown to be consistent with the bioinformatic analysis results. Conclusion Our study identified MAPK8 and CAPN1 as key biomarkers of IDD. These key hub genes may be potential therapeutic targets for IDD.
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Affiliation(s)
- Yuxin Zhang
- School of Medicine, Shanghai University, Shanghai, China
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiahui Zhang
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhongyi Sun
- Department of Orthopedics, BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, China
| | - Hui Wang
- Department of Orthopaedics, Shanghai Changzheng Hospital, Shanghai, China
| | - Ruonan Ning
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Longyu Xu
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yichen Zhao
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kai Yang
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaobing Xi
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiwei Tian
- School of Medicine, Shanghai University, Shanghai, China
- Department of Orthopedics, BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, China
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5
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Whittal MC, Poynter SJ, Samms K, Briar KJ, Sinopoli SI, Millecamps M, Stone LS, DeWitte-Orr SJ, Gregory DE. TAK-242 treatment and its effect on mechanical properties and gene expression associated with IVD degeneration in SPARC-null mice. EUROPEAN SPINE JOURNAL : OFFICIAL PUBLICATION OF THE EUROPEAN SPINE SOCIETY, THE EUROPEAN SPINAL DEFORMITY SOCIETY, AND THE EUROPEAN SECTION OF THE CERVICAL SPINE RESEARCH SOCIETY 2022; 31:2801-2811. [PMID: 35816198 DOI: 10.1007/s00586-022-07310-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/09/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
PURPOSE Intervertebral disc (IVD) degeneration is accompanied by mechanical and gene expression changes to IVDs. SPARC-null mice display accelerated IVD degeneration, and treatment with (toll-like receptor 4 (TLR4) inhibitor) TAK-242 decreases proinflammatory cytokines and pain. This study examined if chronic TAK-242 treatment impacts mechanical properties and gene expression associated with IVD degeneration in SPARC-null mice. METHODS Male and female SPARC-null and WT mice aged 7-9 months were given intraperitoneal injections with TAK-242 or an equivalent saline vehicle for 8 weeks (3x/per week, M-W-F). L2-L5 spinal segments were tested in cyclic axial tension and compression. Gene expression analysis (RT-qPCR) was performed on male IVD tissues using Qiagen RT2 PCR arrays. RESULTS SPARC-null mice had decreased NZ length (p = 0.001) and increased NZ stiffness (p < 0.001) compared to WT mice. NZ length was not impacted by TAK-242 treatment (p = 0.967) despite increased hysteresis energy (p = 0.024). Tensile stiffness was greater in SPARC-null mice (p = 0.018), and compressive (p < 0.001) stiffness was reduced from TAK-242 treatment in WT but not SPARC-null mice (p = 0.391). Gene expression analysis found upregulation of 13 ECM and 5 inflammatory genes in SPARC-null mice, and downregulation of 2 inflammatory genes after TAK-242 treatment. CONCLUSIONS TAK-242 had limited impacts on SPARC-null mechanical properties and did not attenuate NZ mechanical changes associated with IVD degeneration. Expression analysis revealed an increase in ECM and inflammatory gene expression in SPARCnull mice with a reduction in inflammatory expression due to TAK-242 treatment. This study provides insight into the role of TLR4 in SPARC-null mediated IVD degeneration.
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Affiliation(s)
- Mitchel C Whittal
- Department of Kinesiology and Physical Education, Wilfrid Laurier University, 75 University Ave W, Waterloo, ON, N2L 3C5, Canada
| | - Sarah J Poynter
- Department of Health Sciences, Wilfrid Laurier University, 75 University Ave W, Waterloo, ON, N2L 3C5, Canada
| | - Kayla Samms
- Department of Health Sciences, Wilfrid Laurier University, 75 University Ave W, Waterloo, ON, N2L 3C5, Canada
| | - K Josh Briar
- Department of Kinesiology and Physical Education, Wilfrid Laurier University, 75 University Ave W, Waterloo, ON, N2L 3C5, Canada
| | - Sabrina I Sinopoli
- Department of Kinesiology and Physical Education, Wilfrid Laurier University, 75 University Ave W, Waterloo, ON, N2L 3C5, Canada
| | - Magali Millecamps
- McGill University, 845 Sherbrooke Street West, Montréal, QC, H3A 0G4, Canada
| | - Laura S Stone
- McGill University, 845 Sherbrooke Street West, Montréal, QC, H3A 0G4, Canada
- University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Stephanie J DeWitte-Orr
- Department of Health Sciences, Wilfrid Laurier University, 75 University Ave W, Waterloo, ON, N2L 3C5, Canada
| | - Diane E Gregory
- Department of Kinesiology and Physical Education, Wilfrid Laurier University, 75 University Ave W, Waterloo, ON, N2L 3C5, Canada.
- Department of Health Sciences, Wilfrid Laurier University, 75 University Ave W, Waterloo, ON, N2L 3C5, Canada.
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6
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Single-Cell RNA-Seq Analysis of Cells from Degenerating and Non-Degenerating Intervertebral Discs from the Same Individual Reveals New Biomarkers for Intervertebral Disc Degeneration. Int J Mol Sci 2022; 23:ijms23073993. [PMID: 35409356 PMCID: PMC8999935 DOI: 10.3390/ijms23073993] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 02/07/2023] Open
Abstract
In this study, we used single-cell transcriptomic analysis to identify new specific biomarkers for nucleus pulposus (NP) and inner annulus fibrosis (iAF) cells, and to define cell populations within non-degenerating (nD) and degenerating (D) human intervertebral discs (IVD) of the same individual. Cluster analysis based on differential gene expression delineated 14 cell clusters. Gene expression profiles at single-cell resolution revealed the potential functional differences linked to degeneration, and among NP and iAF subpopulations. GO and KEGG analyses discovered molecular functions, biological processes, and transcription factors linked to cell type and degeneration state. We propose two lists of biomarkers, one as specific cell type, including C2orf40, MGP, MSMP, CD44, EIF1, LGALS1, RGCC, EPYC, HILPDA, ACAN, MT1F, CHI3L1, ID1, ID3 and TMED2. The second list proposes predictive IVD degeneration genes, including MT1G, SPP1, HMGA1, FN1, FBXO2, SPARC, VIM, CTGF, MGST1, TAF1D, CAPS, SPTSSB, S100A1, CHI3L2, PLA2G2A, TNRSF11B, FGFBP2, MGP, SLPI, DCN, MT-ND2, MTCYB, ADIRF, FRZB, CLEC3A, UPP1, S100A2, PRG4, COL2A1, SOD2 and MT2A. Protein and mRNA expression of MGST1, vimentin, SOD2 and SYF2 (p29) genes validated our scRNA-seq findings. Our data provide new insights into disc cells phenotypes and biomarkers of IVD degeneration that could improve diagnostic and therapeutic options.
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Zamanian C, Bhandarkar AR, Monie DD, Moinuddin FM, Vile RG, Quiñones-Hinojosa A, Bydon M. Systems neuroimmunology: a review of multiomics methodologies to characterize neuroimmunological interactions in spinal and cranial diseases. Neurosurg Focus 2022; 52:E9. [PMID: 35104798 DOI: 10.3171/2021.11.focus21571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/19/2021] [Indexed: 01/01/2023]
Abstract
Neuroimmunology plays a critical role in our understanding of the pathophysiological processes that underlie a variety of diseases treated by neurosurgeons, including degenerative disc disease (DDD), glioblastoma (GBM), aneurysmal subarachnoid hemorrhage (aSAH), and others. Compared with traditional methods in neuroimmunology, which study one pathway or gene at a time, emerging multiomics methodologies allow for holistic interrogation of multiple immune-signaling pathways to test hypotheses and the effects of therapeutics at a systems level. In this review, the authors summarize key concepts for gathering and analyzing multiomics data so that neurosurgeons can contribute to the emerging field of systems neuroimmunology. Additionally, they describe 3 use cases, based on original research published by their group and others, that utilize transcriptomic, metabolomic, and proteomic analyses to study immune-signaling pathways in DDD, aSAH, and GBM. Through these use cases, techniques for performing machine learning and network-based analyses to generate new clinical insights from multiomics data are shared. The authors hope that neurosurgeons might use this review as a summary of common tools and principles in systems immunology to better engage in creating the immunotherapies of tomorrow.
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Affiliation(s)
| | - Archis R Bhandarkar
- 1Neuro-Informatics Laboratory.,2Department of Neurosurgery.,5Mayo Clinic Alix School of Medicine, Mayo Clinic, Rochester, Minnesota; and
| | - Dileep D Monie
- 2Department of Neurosurgery.,4Department of Immunology, and.,5Mayo Clinic Alix School of Medicine, Mayo Clinic, Rochester, Minnesota; and
| | - F M Moinuddin
- 1Neuro-Informatics Laboratory.,2Department of Neurosurgery
| | | | | | - Mohamad Bydon
- 1Neuro-Informatics Laboratory.,2Department of Neurosurgery
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8
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Davis JL, Thaler R, Cox L, Ricci B, Zannit HM, Wan F, Faccio R, Dudakovic A, van Wijnen AJ, Veis DJ. Constitutive activation of NF-κB inducing kinase (NIK) in the mesenchymal lineage using Osterix (Sp7)- or Fibroblast-specific protein 1 (S100a4)-Cre drives spontaneous soft tissue sarcoma. PLoS One 2021; 16:e0254426. [PMID: 34292968 PMCID: PMC8297882 DOI: 10.1371/journal.pone.0254426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 06/27/2021] [Indexed: 01/02/2023] Open
Abstract
Aberrant NF-κB signaling fuels tumor growth in multiple human cancer types including both hematologic and solid malignancies. Chronic elevated alternative NF-κB signaling can be modeled in transgenic mice upon activation of a conditional NF-κB-inducing kinase (NIK) allele lacking the regulatory TRAF3 binding domain (NT3). Here, we report that expression of NT3 in the mesenchymal lineage with Osterix (Osx/Sp7)-Cre or Fibroblast-Specific Protein 1 (FSP1)-Cre caused subcutaneous, soft tissue tumors. These tumors displayed significantly shorter latency and a greater multiple incidence rate in Fsp1-Cre;NT3 compared to Osx-Cre;NT3 mice, regardless of sex. Histological assessment revealed poorly differentiated solid tumors with some spindled patterns, as well as robust RelB immunostaining, confirming activation of alternative NF-κB. Even though NT3 expression also occurs in the osteolineage in Osx-Cre;NT3 mice, we observed no bony lesions. The staining profiles and pattern of Cre expression in the two lines pointed to a mesenchymal tumor origin. Immunohistochemistry revealed that these tumors stain strongly for alpha-smooth muscle actin (αSMA), although vimentin staining was uniform only in Osx-Cre;NT3 tumors. Negative CD45 and S100 immunostains precluded hematopoietic and melanocytic origins, respectively, while positive staining for cytokeratin 19 (CK19), typically associated with epithelia, was found in subpopulations of both tumors. Principal component, differential expression, and gene ontology analyses revealed that NT3 tumors are distinct from normal mesenchymal tissues and are enriched for NF-κB related biological processes. We conclude that constitutive activation of the alternative NF-κB pathway in the mesenchymal lineage drives spontaneous sarcoma and provides a novel mouse model for NF-κB related sarcomas.
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Affiliation(s)
- Jennifer L. Davis
- Musculoskeletal Research Center, Washington University School of Medicine, St. Louis, MO, United States of America
- Department of Medicine, Division of Bone and Mineral Diseases, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Roman Thaler
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, United States of America
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States of America
| | - Linda Cox
- Musculoskeletal Research Center, Washington University School of Medicine, St. Louis, MO, United States of America
- Department of Medicine, Division of Bone and Mineral Diseases, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Biancamaria Ricci
- Musculoskeletal Research Center, Washington University School of Medicine, St. Louis, MO, United States of America
- Department of Orthopaedic Surgery, Washington University School of Medicine, St Louis, MO, United States of America
| | - Heather M. Zannit
- Musculoskeletal Research Center, Washington University School of Medicine, St. Louis, MO, United States of America
- Department of Orthopaedic Surgery, Washington University School of Medicine, St Louis, MO, United States of America
| | - Fei Wan
- Department of Surgery, Division of Public Health Sciences, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Roberta Faccio
- Musculoskeletal Research Center, Washington University School of Medicine, St. Louis, MO, United States of America
- Department of Orthopaedic Surgery, Washington University School of Medicine, St Louis, MO, United States of America
- Shriners Hospitals for Children–St. Louis, St. Louis, MO, United States of America
| | - Amel Dudakovic
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, United States of America
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States of America
| | - Andre J. van Wijnen
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, United States of America
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States of America
| | - Deborah J. Veis
- Musculoskeletal Research Center, Washington University School of Medicine, St. Louis, MO, United States of America
- Department of Medicine, Division of Bone and Mineral Diseases, Washington University School of Medicine, St. Louis, MO, United States of America
- Shriners Hospitals for Children–St. Louis, St. Louis, MO, United States of America
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9
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Xia B, Xing J, Ai Q, Li H, Xu M, Hou T. [Expression profile of intervertebral disc degeneration-specific genes: a transcriptome sequencing-based analysis]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2021; 41:883-890. [PMID: 34238741 DOI: 10.12122/j.issn.1673-4254.2021.06.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To identify new therapeutic targets for intervertebral disc degeneration (IDD) by analyzing gene variations in IDD. OBJECTIVE We analyzed surgical samples of intervertebral disc from 4 patients with IDD and 3 patients with non-IDD using RNA sequencing (RNA-seq) technology to identify significant differentially expressed genes (DEGs) in IDD. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were utilized for gene enrichment studies to acquire the key genes and signal pathways during IDD progression. The differential expressions of the identified genes in IDD were validated in clinical samples with qRT-PCR. OBJECTIVE The transcriptome profile revealed 512 significant DEGs, which were enriched in terms of keratinization, extracellular matrix (ECM) components, growth factor binding, and inflammatory chemotaxis in GO analysis. The top 10 terms of KEGG enrichment included amoebiasis, viral protein interaction with cytokine and cytokine receptor, ECM-receptor interaction, IL-17 signaling pathway, cytokine-cytokine receptor interaction, TNF signaling pathway, AGE-RAGE signaling pathway in diabetic complications, PI3K-Akt signaling pathway, chemokine signaling pathway and estrogen signaling pathway. Thirteen DEGs selected as the targets for qRT-PCR validation showed significant differential expressions in IDD (P < 0.001), and their expression trends were all consistent with the results of RNA-seq. Among these genes, 10 genes showed significant intergroup fold change (Log2FoldChange>1). OBJECTIVE ECM, growth factors, collagen components, inflammatory chemokines and such signal pathways as TNF-α and PI3K-Akt all have important contributions to IDD progression and may thus serve as new therapeutic targets for treatment of IDD.
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Affiliation(s)
- B Xia
- Department of Orthopedics, First Affiliated Hospital of Army Medical University, Chongqing 400038, China
| | - J Xing
- Department of Orthopedics, First Affiliated Hospital of Army Medical University, Chongqing 400038, China
| | - Q Ai
- Department of Orthopedics, First Affiliated Hospital of Army Medical University, Chongqing 400038, China
| | - H Li
- Department of Orthopedics, First Affiliated Hospital of Army Medical University, Chongqing 400038, China
| | - M Xu
- Department of Orthopedics, First Affiliated Hospital of Army Medical University, Chongqing 400038, China
| | - T Hou
- Department of Orthopedics, First Affiliated Hospital of Army Medical University, Chongqing 400038, China
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Wang J, Huang Y, Huang L, Shi K, Wang J, Zhu C, Li L, Zhang L, Feng G, Liu L, Song Y. Novel biomarkers of intervertebral disc cells and evidence of stem cells in the intervertebral disc. Osteoarthritis Cartilage 2021; 29:389-401. [PMID: 33338640 DOI: 10.1016/j.joca.2020.12.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 10/23/2020] [Accepted: 12/09/2020] [Indexed: 02/08/2023]
Abstract
OBJECTIVE Rat intervertebral disc (IVD) is one of the most commonly used and cost-effective alternative models for human IVD. Many IVD related clinical studies need to be pre-tested on rat IVDs. However, studies on the heterogeneous cell clusters of the rat IVD are inadequate, and a further understanding of the marker genes and cell phenotypes of healthy mature IVD cells is essential. METHODS In this study, we used the 10X Genomics technology to analyze the single-cell transcriptome of purified wild-type rat IVDs. RESULTS We identified potentially new gene markers of IVDs via single-cell sequencing. Based on the unsupervised cluster analysis of 13,578 single-cell transcripts, 3 known IVD cell types were identified. We provided a complete single-cell gene expression map of the IVD. Immunohistochemical and immunofluorescence images of rat disc sections confirmed the new marker genes of all cell types. One group of heterologous cell groups expressed multi-functional stem cell (MSC)-specific genes, indicating the stem cell potential of IVD cells. CONCLUSION We provided the phenotype and marker genes of IVD cells at the single-cell level, reconfirmed existing data, and proposed new marker genes, including MSC marker genes. By identifying more accurate target cells and genes, our results pave the way for further study of the response of individual disc cells to disease states and provide the basis for future disc regeneration therapies.
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Affiliation(s)
- J Wang
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Y Huang
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - L Huang
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - K Shi
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - J Wang
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - C Zhu
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - L Li
- Department of Science and Technology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - L Zhang
- Analytical and Testing Center, State Key Laboratory of Oral Diseases, School of Materials Science and Engineering, Sichuan University, Chengdu, 610065, China.
| | - G Feng
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - L Liu
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Y Song
- Department of Orthopedic Surgery and Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
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Wang Y, Dai G, Jiang L, Liao S, Xia J. Microarray analysis reveals an inflammatory transcriptomic signature in peripheral blood for sciatica. BMC Neurol 2021; 21:50. [PMID: 33535986 PMCID: PMC7856817 DOI: 10.1186/s12883-021-02078-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 01/26/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Although the pathology of sciatica has been studied extensively, the transcriptional changes in the peripheral blood caused by sciatica have not been characterized. This study aimed to characterize the peripheral blood transcriptomic signature for sciatica. METHODS We used a microarray to identify differentially expressed genes in the peripheral blood of patients with sciatica compared with that of healthy controls, performed a functional analysis to reveal the peripheral blood transcriptomic signature for sciatica, and conducted a network analysis to identify key genes that contribute to the observed transcriptional changes. The expression levels of these key genes were assessed by qRT-PCR. RESULTS We found that 153 genes were differentially expressed in the peripheral blood of patients with sciatica compared with that of healthy controls, and 131 and 22 of these were upregulated and downregulated, respectively. A functional analysis revealed that these differentially expressed genes (DEGs) were strongly enriched for the inflammatory response or immunity. The network analysis revealed that a group of genes, most of which are related to the inflammatory response, played a key role in the dysregulation of these DEGs. These key genes are Toll-like receptor 4, matrix metallopeptidase 9, myeloperoxidase, cathelicidin antimicrobial peptide, resistin and Toll-like receptor 5, and a qRT-PCR analysis validated the higher transcript levels of these key genes in the peripheral blood of patients with sciatica than in that of healthy controls. CONCLUSION We revealed inflammatory characteristics that serve as a peripheral blood transcriptomic signature for sciatica and identified genes that are essential for mRNA dysregulation in the peripheral blood of patients with sciatica.
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Affiliation(s)
- Yi Wang
- Cervicodynia/Omalgia/Lumbago/Sciatica Department 2, Sichuan Provincial Orthopedics Hospital, No. 132 West First Section First Ring Road,Wuhou District, Chengdu, 610041, Sichuan Province, China.
| | - Guogang Dai
- Cervicodynia/Omalgia/Lumbago/Sciatica Department 2, Sichuan Provincial Orthopedics Hospital, No. 132 West First Section First Ring Road,Wuhou District, Chengdu, 610041, Sichuan Province, China
| | - Ling Jiang
- College Hospital, Sichuan Agricultural University-Chengdu Campus, NO. 211 Huimin Road, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Shichuan Liao
- Cervicodynia/Omalgia/Lumbago/Sciatica Department 2, Sichuan Provincial Orthopedics Hospital, No. 132 West First Section First Ring Road,Wuhou District, Chengdu, 610041, Sichuan Province, China
| | - Jiao Xia
- Cervicodynia/Omalgia/Lumbago/Sciatica Department 2, Sichuan Provincial Orthopedics Hospital, No. 132 West First Section First Ring Road,Wuhou District, Chengdu, 610041, Sichuan Province, China
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