Identification of Differential Genes Expression Profiles and Pathways of Bone Marrow Mesenchymal Stem Cells of Adolescent Idiopathic Scoliosis Patients by Microarray and Integrated Gene Network Analysis

Differential Gene Expression Profiles and Pathways Highlight the Role of Osteoimmunology in Neurofibromatosis Type 1-Related Dystrophic Scoliosis With Osteopenia

STUDY DESIGN

Microarray approach and integrated gene network analysis.

OBJECTIVE

To explore the differential genetic expression profile, Gene Ontology terms, and Kyoto Encyclopedia of Genes and Genomes pathways in human trabecular bone (HTB)-derived cells of dystrophic scoliosis secondary to neurofibromatosis type 1 (DS-NF1) and compare these to normal controls.

SUMMARY OF BACKGROUND DATA

The pathogenesis of DS-NF1 and the accompanying generalized osteopenia remain unclear. We hypothesized that HTBs may play a significant role in the etiology and pathogenesis of DS-NF1.

MATERIALS AND METHODS

Microarray analysis was used to identify differentially expressed genes of HTBs from patients with DS-NF1 compared with those from healthy individuals. Functional and pathway enrichment analysis were implemented through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway database. Then, the "search tool for the retrieval of interacting genes/proteins" database, Cytoscape, and "Molecular Complex Detection" were applied to construct the protein-protein interaction (PPI) network and screen hub genes. Pathway enrichment analysis was further performed for hub genes and gene clusters identified through module analysis. Six potential crucial genes were selected for validation by reverse transcription polymerase chain reaction.

RESULTS

Bioinformatic analysis revealed that there are 401 previously unrecognized differentially expressed genes (238 up and 163 downregulated genes) in HTBs from patients with DS-NF1, and they were mainly enriched in terms of immune response, type-I interferon (IFN) signaling, TNF signaling pathway and etinoic acid inducible gene I-like receptor signaling pathway. Five hub genes, including signal transducer and activator of transcription 1, 2'-5'-oligoadenylate synthetase-like, IFN induced with helicase C domain 1, IFN regulatory factor 7, and MX dynamin-like GTPase 1 were identified through PPI network, which were mainly enriched in terms of Jak-STAT and etinoic acid inducible gene I-like receptor signaling pathway. An independently dysregulated protein cluster containing CCL2, CXCL1, CXCL3, CX3CL1, TLR1 , and CXCL12 was also identified through the PPI network. This indicated that the upper abnormally expressed genes may play essential roles in DS-NF1 pathogenesis and accompanied osteopenia.

CONCLUSION

Six key genes were identified in the progression of DS-NF1-related osteopenia. Immune response might play a key role in the progression of osteopenia, whereas a CXCL12 -mediated osteogenic effect might play a protective role.

Research progress on the regulation of bone marrow stem cells by noncoding RNAs in adolescent idiopathic scoliosis

Adolescent idiopathic scoliosis (AIS) is a common spinal deformity in young women, but its pathogenesis remains unclear. The primary pathogenic factors contributing to its development include genetics, abnormal bone metabolism, and endocrine factors. Bone marrow stem cells (BMSCs) play a crucial role in the pathogenesis of AIS by regulating its occurrence and progression. Noncoding RNAs (ncRNAs) are also involved in the pathogenesis of AIS, and their role in regulating BMSCs in patients with AIS requires further evaluation. In this review, we discuss the relevant literature regarding the osteogenic, chondrogenic, and lipogenic differentiation of BMSCs. The corresponding mechanisms of ncRNA-mediated BMSC regulation in patients with AIS, recent advancements in AIS and ncRNA research, and the importance of ncRNA translation profiling and multiomics are highlighted.

Risk factors associated with low bone mineral density in children with idiopathic scoliosis: a scoping review

BACKGROUND

Children with idiopathic scoliosis (IS) have a high risk of osteoporosis and IS with low bone mineral density (BMD) are susceptible to curve progression. This review aims to explore the risk factors of low BMD in children with IS.

METHODS

Studies were retrieved from 5 databases that were published up to January 2022. Search terms are keywords in titles or abstracts, including subject headings related to "Scoliosis", "Bone Mineral Density", and "Risk Factors". Observational studies on risk factors of low BMD in children with IS were enrolled in this review. The number of studies, sample size, outcome measures, research type, endocrine, and lifestyle-related factors, gene/signal pathway, and other contents were extracted for qualitative analysis.

RESULTS

A total of 56 studies were included in this scoping review. Thirty studies involved genetic factors that may affect BMD, including the Vitamin-D receptor gene, RANK/RANKL signal pathway, the function of mesenchymal stem cells, Runx2, Interleukin-6 (IL-6), and miR-145/β-catenin pathway. Eight studies mentioned the influence of endocrine factors on BMD, and the results showed that serum levels of IL-6, leptin and its metabolites, and ghrelin in children with IS were different from the age-matched controls. In addition, there were 18 articles on lifestyle-related factors related to low BMD in children with IS, consisting of physical activity, calcium intake, Vitamin D level, and body composition.

CONCLUSIONS

Genetic, endocrine, and lifestyle-related factors might relate to low BMD and even osteoporosis in IS. To prevent osteoporosis, the effectiveness of regular screening for low BMD risk factors in children with IS needs to be investigated. Additionally, clear risk factors suggest strategies for bone intervention. Future studies should consider the effectiveness of calcium and vitamin D supplements and physical activity in BMD improvement.

The Potential Role of Dysregulated miRNAs in Adolescent Idiopathic Scoliosis and 22q11.2 Deletion Syndrome

Background: Adolescent idiopathic scoliosis (AIS), affecting 2-4% of adolescents, is a multifactorial spinal disease. Interactions between genetic and environmental factors can influence disease onset through epigenetic mechanisms, including DNA methylation, histone modifications and miRNA expression. Recent evidence reported that, among all clinical features in individuals with 22q11.2 deletion syndrome (DS), scoliosis can occur with a higher incidence than in the general population. Methods: A PubMed and Ovid Medline search was performed for idiopathic scoliosis in the setting of 22q11.2DS and miRNA according to PRISMA guidelines. Results: Four papers, accounting for 2841 individuals, reported clinical data about scoliosis in individuals with 22q11.2DS, showing that approximately 35.1% of the individuals with 22q11.2DS developed scoliosis. Conclusions: 22q11.2DS could be used as a model for the study of AIS. The DGCR8 gene seems to be essential for microRNA biogenesis, which is why we propose that a possible common pathological mechanism between scoliosis and 22q11.2DS could be the dysregulation of microRNA expression. In the current study, we identified two miRNAs that were altered in both 22q11.2DS and AIS, miR-93 and miR-1306, thus, corroborating the hypothesis that the two diseases share common molecular alterations.

Single-cell RNA Seq reveals cellular landscape-specific characteristics and potential etiologies for adolescent idiopathic scoliosis

BACKGROUNDS

Abnormal vertebral growth and development have been found in adolescent idiopathic scoliosis (AIS) patients, and the proliferation and differentiation of bone development-related cells play important roles in its pathogenesis. However, a comprehensive single-cell-level differentiation roadmap in AIS has not been achieved.

METHODS

The present study compared the single-cell level cellular landscapes of spinal cancellous bone tissues between AIS patients and healthy subjects using high throughput single-cell RNA sequencing (scRNA-seq), which covers multiple cellular lineages including osteoblast, chondrocyte, osteoclast and related immunocytes. We constructed the differentiation trajectories of bone development-related cell lineages through pseudotime analysis, and the intercellular-communication networks between bone development-related cells and immunocytes were further developed.

RESULTS

A total of 11 distinct cell clusters were identified according to the genome-wide transcriptome profiles. t-Distributed stochastic neighbor embedding (t-SNE) analysis showed that mesenchymal stem cells (MSC) were classified into three subtypes: MSC-LOXL2, MSC-IGFBP5, and MSC-GJA1. Gene ontology (GO) analysis showed that MSC-GJA1 might possess greater osteoblast differentiation potential than the others. MSC-IGFBP5 was the specific MSC subtype observed only in AIS. There were two distinct gene expression clusters: OB-DPT and OB-OLFML2B, and the counts of osteoblasts derived from AIS was significantly less than that of non-AIS subjects. In AIS patients, MSC-IGFBP5 failed to differentiate into osteoblasts and exhibited negative regulation of cell proliferation and enhanced cell death. CPC-PCNA was found to be the specific chondrocyte progenitor cell (CPC) subtype observed only in AIS patients. The cell counts of OC-BIRC3 in AIS were less than those in controls. Pseudotime analysis suggested two possible distinct osteoclast differentiation patterns in AIS and control subjects. Monocytes in AIS mainly differentiated into OC-CRISP3.

CONCLUSIONS

Our single-cell analysis first revealed differences existed in the cellular states between AIS patients and healthy subjects and found the differentiation disruption of specific MSC and CPC clusters in AIS. Cell communication analysis provided the possible pathogenesis of osteoblast and chondrocyte differentiation dysfunction in AIS.

Over-expression of the bottlenose dolphin Hoxd13 gene in zebrafish provides new insights into the cetacean flipper formation

Cetaceans have evolved elongated soft-tissue flipper with digits made of hyperphalangy. Cetaceans were found to have 2-3 more alanine residues in Hoxd13 than other mammals, which were suggested to be related to their flipper. However, how Hoxd13 regulates other genes and induces hyperphalangy in cetaceans remain poorly understood. Here, we overexpressed the bottlenose dolphin Hoxd13 in zebrafish (Danio rerio). Combined with transcriptome data and evolutionary analyses, our results revealed that the Wingless/Integrated (Wnt) and Hedgehog signaling pathways and multiple genes might regulate hyperphalangy development in cetaceans. Meanwhile, the Notch and mitogen-activated protein kinase (Mapk) signaling pathways and Fibroblast growth factor receptor 1 (Fgfr1) are probably correlated with interdigital tissues retained in the cetacean flipper. In conclusion, this is the first study to use a transgenic zebrafish to explore the molecular evolution of Hoxd13 in cetaceans, and it provides new insights into cetacean flipper formation.

Research progress on the etiology and pathogenesis of adolescent idiopathic scoliosis

Etiology of adolescent idiopathic scoliosis (AIS), a complicated three-dimensional spinal deformity with early-onset, receives continuous attention but remains unclear. To gain an insight into AIS pathogenesis, this review searched PubMed database up to June 2019, using key words or medical subject headings terms including "adolescent idiopathic scoliosis," "scoliosis," "pathogenesis," "etiology," "genetics," "mesenchymal stem cells," and their combinations, summarized existing literatures and categorized the theories or hypothesis into nine aspects. These aspects include bone marrow mesenchymal stem cell studies, genetic studies, tissue analysis, spine biomechanics measurements, neurologic analysis, hormone studies, biochemical analysis, environmental factor analysis, and lifestyle explorations. These categories could be a guidance for further etiology or treatment researches to gain inspiration.

From genetics to epigenetics to unravel the etiology of adolescent idiopathic scoliosis

Scoliosis is defined as the three-dimensional (3D) structural deformity of the spine with a radiological lateral Cobb angle (a measure of spinal curvature) of ≥10° that can be caused by congenital, developmental or degenerative problems. However, those cases whose etiology is still unknown, and affect healthy children and adolescents during growth, are the commonest form of spinal deformity, known as adolescent idiopathic scoliosis (AIS). In AIS management, early diagnosis and the accurate prediction of curve progression are most important because they can decrease negative long-term effects of AIS treatment, such as unnecessary bracing, frequent exposure to radiation, as well as saving the high costs of AIS treatment. Despite efforts made to identify a method or technique capable of predicting AIS progression, this challenge still remains unresolved. Genetics and epigenetics, and the application of machine learning and artificial intelligence technologies, open up new avenues to not only clarify AIS etiology, but to also identify potential biomarkers that can substantially improve the clinical management of these patients. This review presents the most relevant biomarkers to help explain the etiopathogenesis of AIS and provide new potential biomarkers to be validated in large clinical trials so they can be finally implemented into clinical settings.

In silico Analysis Excavates A Novel Competing Endogenous RNA Subnetwork in Adolescent Idiopathic Scoliosis

Background and Objective: Adolescent idiopathic scoliosis (AIS) is a complex three-dimensional deformity of the spine. Mesenchymal stem cells (MSCs) regulate bone mass homeostasis in AIS, which might be related to the pathogenesis of AIS. However, the mRNA–miRNA–lncRNA network linked to the regulation of the genetic pathogenesis of MSCs remains unknown.

Methods: We conducted an exhaustive literature search of PubMed, EMBASE, and the Gene Expression Omnibus database to find differentially expressed genes (DEGs), differentially expressed miRNAs (DE miRNAs), and differentially expressed lncRNAs (DE lncRNAs). Functional enrichment analysis was performed through Enrichr database. Protein–protein interaction (PPI) network was constructed using STRING database, and hub genes were identified by CytoHubba. Potential regulatory miRNAs and lncRNAs of mRNAs were predicted by miRTarBase and RNA22, respectively.

Results: We identified 551 upregulated and 476 downregulated genes, 42 upregulated and 12 downregulated miRNAs, and 345 upregulated and 313 downregulated lncRNAs as DEGs, DE miRNAs, and DE lncRNAs, respectively. Functional enrichment analysis revealed that they were significantly enriched in protein deglutamylation and regulation of endoplasmic reticulum unfolded protein response. According to node degree, one upregulated hub gene and eight downregulated hub genes were identified. After drawing the Venn diagrams and matching to Cytoscape, an mRNA–miRNA–lncRNA network linked to the pathogenesis of MSCs in AIS was constructed.

Conclusion: We established a novel triple regulatory network of mRNA–miRNA–lncRNA ceRNA, among which all RNAs may be utilized as the pathogenesis biomarker of MSCs in AIS.

Altered physiology of mesenchymal stem cells in the pathogenesis of adolescent idiopathic scoliosis

Adolescent idiopathic scoliosis is the most common spinal deformity during puberty, especially in females. It is characterized by aberrant skeletal growth and generalized reduced bone density, which is associated with impaired bone mineral metabolism. Despite recent progress in multidisciplinary research to support various hypotheses, the pathogenesis of Adolescent idiopathic scoliosis is still not clearly understood. One of the hypothesis is to study the role of mesenchymal stem cells due to its involvement in the above-mentioned bone metabolic abnormalities. In this review, we will summarize reported literatures on the role of mesenchymal stem cells, particularly in the pathogenesis of Adolescent idiopathic scoliosis. In addition, we will describe the research on mesenchymal stem cells of Adolescent idiopathic scoliosis performed using bioinformatics tools.

Whole-Genome Methylation Analysis of Phenotype Discordant Monozygotic Twins Reveals Novel Epigenetic Perturbation Contributing to the Pathogenesis of Adolescent Idiopathic Scoliosis

Background: Adolescent idiopathic scoliosis (AIS) is a complex disease affecting a large number of teenagers, especially in female. This study reveals novel epigenetic perturbation to the pathogenesis of AIS.

Methods: A female monozygotic (MZ) twin pair discordant for AIS were examined for whole-exome sequencing and epigenome difference. Sets of differentially methylated regions (DMRs) were validated using MethylTarget™ method in 20 AIS female patients and 20 healthy female controls.

Results: Few exome difference but several potential DMRs were found between the MZ twins. We identified 313 hypermethylated DMRs and 397 hypomethylated DMRs, respectively. Most of them were enriched in the MAPK and PI3K-Akt signaling pathway, which may contribute to the discordance of AIS. Several DMRs related to scoliosis genes were tested, and the NDN: TSS-DMR (chr15:23932133-23932304, hg19) was confirmed in additional samples. The methylation level of this DMR was significantly higher in the AIS group than in the control group (p = 0.04).

Conclusions: We described the epigenome difference in an AIS female discordant MZ twin pair using Whole Genome Bisulfite Sequencing (WGBS). The NDN: TSS-DMR had higher methylation level in female AIS, which can help elucidate the potential etiology of AIS.

SPRY4 is responsible for pathogenesis of adolescent idiopathic scoliosis by contributing to osteogenic differentiation and melatonin response of bone marrow-derived mesenchymal stem cells

Adolescent idiopathic scoliosis (AIS) is a complex, three-dimensional deformity of the spine that commonly occurs in pubescent girls. Decreased osteogenic differentiation and aberrant melatonin signalling have been demonstrated in mesenchymal stem cells (MSCs) from AIS patients and are implicated in the pathogenesis of AIS. However, the molecular mechanisms underlying these abnormal cellular features remain largely unknown. Our previous work comparing gene expression profiles between MSCs from AIS patients and healthy controls identified 1027 differentially expressed genes. In the present study, we focused on one of the most downregulated genes, SPRY4, in the MAPK signalling pathway and examined its role in osteogenic differentiation. We found that SPRY4 is markedly downregulated in AIS MSCs. Knockdown of SPRY4 impaired differentiation of healthy MSCs to osteoblasts, while SPRY4 overexpression in AIS MSCs enhanced osteogenic differentiation. Furthermore, melatonin treatment boosted osteogenic differentiation, whereas SPRY4 ablation ablated the promotional effects of melatonin. Moreover, SPRY4 was upregulated by melatonin exposure and contributed to osteogenic differentiation and melatonin response in a MEK-ERK1/2 dependent manner. Thus, loss of SPRY4 in bone marrow derived-MSCs results in reduced osteogenic differentiation, and these defects are further aggravated under the influence of melatonin. Our findings provide new insights for understanding the role of melatonin in AIS aetiology and highlight the importance of MSCs in AIS pathogenesis.

Long noncoding RNA lncAIS downregulation in mesenchymal stem cells is implicated in the pathogenesis of adolescent idiopathic scoliosis

Adolescent idiopathic scoliosis (AIS) is a complex, three dimensional deformity of the spine that commonly occurs in pubescent girls. Abnormal osteogenic differentiation of mesenchymal stem cells (MSCs) is implicated in the pathogenesis of AIS. However, the biological roles of long noncoding RNAs (lncRNAs) in the regulation of osteogenic differentiation of MSCs are unknown. Through microarray analyses of bone marrow (BM) MSCs from healthy donors and AIS patients, we identified 1483 differentially expressed lncRNAs in AIS BM-MSCs. We defined a novel lncAIS (gene symbol: ENST00000453347) is dramatically downregulated in AIS BM-MSCs. In normal BM-MSCs, lncAIS interacts with NF90 to promote HOXD8 mRNA stability that enhances RUNX2 transcription in BM-MSCs, leading to osteogenic differentiation of normal BM-MSCs. By contrast, lncAIS downregualtion in AIS BM-MSCs cannot recruit NF90 and abrogates HOXD8 mRNA stability, which impedes RUNX2 transcription for osteogenic differentiation. Thereby lncAIS downregualtion in BM-MSCs suppresses osteogenic differentiation that is implicated in the pathogenesis of AIS.

Differential miRNAs profile and bioinformatics analyses in bone marrow mesenchymal stem cells from adolescent idiopathic scoliosis patients

BACKGROUND CONTEXT

Coexistence of abnormal skeletal growth and reduced bone mineral density in the context of adolescent idiopathic scoliosis (AIS) suggests disturbed bone metabolism existing in such patients. Our previous study suggested increased proliferation ability and decreased osteogenic differentiation ability of bone marrow mesenchymal stem cells (BM-MSCs) of AIS.

PURPOSE

To explore the differential miRNA expression profile, Go (gene ontology) terms and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways in BM-MSCs of AIS and non-AIS controls were conducted using microarray approach and bioinformatics analyses.

STUDY DESIGN

miRNA microarray approach and bioinformatics analysis.

METHODS

The differentially expressed miRNAs (DEMs) of BM-MSCs from AIS patients compared with those from healthy individuals were analyzed using a microarray analysis. Comprehensive bioinformatics analyses were then used to enrich datasets for gene ontology and pathway. Based on the interaction network analysis of DEMs contained in significant pathways, 12 potential crucial miRNAs were selected for validation by RT-PCR.

RESULTS

The study identified 54 previously unrecognized DEMs (12 upregulated, 42 downregulated) in BM-MSCs from AIS patients. These miRNAs are involved in multiple biological processes, including small GTPase-mediated signal transduction, DNA-dependent transcription, cytokinesis, cell adhesion, transmembrane transport, response to hypoxia, etc. Pathway analysis of these new identified miRNAs revealed dysregulated MAPK signaling pathway, PI3K-Akt signaling pathway, calcium signaling pathway, Notch signaling pathway, and ubiquitin-mediated proteolysis pathway, all of which have been reported to play important role in regulating the osteogenic or adipogenic differentiation of MSCs. Furthermore, interaction networks analysis indicated that seven most significant central miRNAs, including miR-17-5p, miR-106a-5p, miR-106b-5p, miR-16-5p, miR-93-5p, miR-15a-5p, and miR-181b-5p may play essential roles in AIS pathogenesis and accompanied osteopenia.

CONCLUSION

The current study reports the differential miRNAs expression profiles of BM-MSCs from AIS patients and related pathways for the first time. The identification of these candidate miRNAs provides a deep insight into the pathogenesis of AIS and the accompanying generalized osteopenia.

Identification of core genes and prediction of miRNAs associated with osteoporosis using a bioinformatics approach

Osteoporosis (OP) is an age-related disease, and osteoporotic fracture is one of the major causes of disability and mortality in elderly patients (>70 years old). As the pathogenesis and molecular mechanism of OP remain unclear, the identification of disease biomarkers is important for guiding research and providing therapeutic targets. In the present study, core genes and microRNAs (miRNAs) associated with OP were identified. Differentially expressed genes (DEGs) between human mesenchymal stem cell specimens from normal osseous tissues and OP tissues were detected using the GEO2R tool of the Gene Expression Omnibus database and Morpheus. Network topological parameters were determined using NetworkAnalyzer. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed using the Database for Annotation, Visualization and Integrated Discovery, and ClueGO. Cytoscape with the Search Tool for the Retrieval of Interacting Genes and Molecular Complex Detection plug-in was used to visualize protein-protein interactions (PPIs). Additionally, miRNA-gene regulatory modules were predicted using CyTargetLinker in order to guide future research. In total, 915 DEGs were identified, including 774 upregulated and 141 downregulated genes. Enriched GO terms and pathways were determined, including 'nervous system development', 'regulation of molecular function', 'glutamatergic synapse pathway' and 'pathways in cancer'. The node degrees of DEGs followed power-law distributions. A PPI network with 541 nodes and 1,431 edges was obtained. Overall, 3 important modules were identified from the PPI network. The following 10 genes were identified as core genes based on high degrees of connectivity: Albumin, PH domain leucine-rich repeat-containing protein phosphatase 2 (PHLPP2), DNA topoisomerase 2-α, kininogen 1 (KNG1), interleukin 2 (IL2), leucine-rich repeats and guanylate kinase domain containing, phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit γ (PIK3CG), leptin, transferrin and RNA polymerase II subunit A (POLR2A). Additionally, 15 miRNA-target interactions were obtained using CyTargetLinker. Overall, 7 miRNAs co-regulated IL2, 3 regulated PHLPP2, 3 regulated KNG1, 1 regulated PIK3CG and 1 modulated POLR2A. These results indicate potential biomarkers in the pathogenesis of OP and therapeutic targets.