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Research • Adv. rheumatol. 63 • 2023 • https://doi.org/10.1186/s42358-023-00288-1   copy

Screening crucial lncRNAs and genes in osteoarthritis by integrated analysis

Authorship SCIMAGO INSTITUTIONS RANKINGS

Abstract

Background

Osteoarthritis (OA) is one of the most frequent chronic diseases with high morbidity worldwide, marked by degradation of the cartilage and bone, joint instability, stiffness, joint space stenosis and subchondral sclerosis. Due to the elusive mechanism of osteoarthritis (OA), we aimed to identify potential markers for OA and explore the molecular mechanisms underlying OA.

Methods

Expression profiles data of OA were collected from the Gene Expression Omnibus database to identify differentially expressed mRNAs (DEmRNAs) and differentially expressed lncRNAs (DElncRNAs) in OA. Functional annotation and protein–protein interaction (PPI) networks were performed. Then, nearby DEmRNAs of DElncRNAs was obtained. Moreover, GO and KEGG pathway enrichment analysis of nearby DEmRNAs of DElncRNAs was performed. Finally, expression validation of selected mRNAs and lncRNAs was performed by quantitative reverse transcriptase-polymerase chain reaction.

Results

In total, 2080 DEmRNAs and 664 DElncRNAs were determined in OA. PI3K-Akt signaling pathway, Endocytosis and Rap1 signaling pathway were significantly enriched KEGG pathways in OA. YWHAB, HSPA8, NEDD4L and SH3KBP1 were four hub proteins in PPI network. The AC093484.4/TRPV2 interact pair may be involved in the occurrence and development of OA.

Conclusion

Our study identified several DEmRNAs and DElncRNAs associated with OA. The molecular characters could provide more information for further study on OA.

Keywords
Osteoarthritis; GEO; lncRNA; mRNA; Bioinformatics; Diagnosis

Background

Osteoarthritis (OA) is one of the most frequent chronic diseases with high morbidity worldwide, marked by degradation of the cartilage and bone, joint instability, stiffness, joint space stenosis and subchondral sclerosis [11 Mathiessen A, Conaghan PG. Synovitis in osteoarthritis: current understanding with therapeutic implications. Arthritis Res Ther. 2017;19:18.].

Patients with OA would suffer some symptoms, such as stiffness, pain, swelling, and loss of mobility with occasional variable degrees of local inflammation, which would severely reduce the quality of life and create a heavy socioeconomic burden [22 Glyn-Jones S, Palmer AJ, Agricola R, Price AJ, Vincent TL, Weinans H, et al. Osteoarthritis. Lancet. 2015;386:376–87.]. However, the pathogenesis of OA is not completely understood. Therefore, it is essential to gain novel insights into biological mechanisms of OA and explore potential biomarkers for OA.

With advancement of next-generation sequencing technology, numerous research has increasingly recognized the important role of lncRNAs in the occurrence and development of OA [33 Xie F, Liu YL, Chen XY, Li Q, Zhong J, Dai BY, et al. Role of MicroRNA, LncRNA, and exosomes in the progression of osteoarthritis: a review of recent literature. Orthop Surg. 2020;12:708–16.]. LncRNAs are RNA molecules > 200 bp in length and participate in numerous biological processes, such as the proliferation, apoptosis, cell cycle, and chromatin remodeling [44 Ma L, Bajic VB, Zhang Z. On the classification of long non-coding RNAs. RNA Biol. 2013;10:925–33.]. DILC is reduced in OA and over expression of DILC inhibits the expression of IL-6 in chondrocytes [55 Huang J, Liu L, Yang J, Ding J, Xu X. lncRNA DILC is downregulated in osteoarthritis and regulates IL-6 expression in chondrocytes. J Cell Biochem. 2019;120:16019–24.]. Knockdown of MFI2-AS1 is found to increase cell viability but suppress apoptosis and inflammatory response to inhibit lipopolysaccharide-induced OA progression [66 Luo X, Wang J, Wei X, Wang S, Wang A. Knockdown of lncRNA MFI2-AS1 inhibits lipopolysaccharide-induced osteoarthritis progression by miR-130a-3p/TCF4. Life Sci. 2020;240: 117019.]. MALAT1 is reported to participate in cell proliferation, apoptosis, and ECM degradation of OA [77 Zhang Y, Wang F, Chen G, He R, Yang L. LncRNA MALAT1 promotes osteoarthritis by modulating miR-150-5p/AKT3 axis. Cell Biosci. 2019;9:54.]. TUG1 performed as a ceRNA through sponging miR-195 to increase MMP-13 expression to regulate ECM degradation in OA [88 Tang LP, Ding JB, Liu ZH, Zhou GJ. LncRNA TUG1 promotes osteoarthritisinduced degradation of chondrocyte extracellular matrix via miR-195/MMP-13 axis. Eur Rev Med Pharmacol Sci. 2018;22:8574–81.]. However, the results are not consistent and reliable due to the difference of samples and sequencing platform, which means we need more comprehensive approaches to identify the hub biomarkers.

Therefore, in this study, we analyzed the expression profiles of OA in the Gene Expression Omnibus database (GEO) database by bioinformatics tools to obtain differentially expressed mRNAs (DEmRNAs) and differentially expressed lncRNAs (DElncRNAs). This study aims to better understand the potential mechanisms in the occurrence and development of OA and may accelerate the improvement of the treatment level of OA.

Materials and methods

Microarray data

The mRNA/lncRNA expression profiles of OA were downloaded from GEO database. Three mRNA data-sets, GSE113825, GSE117999 and GSE114007, and one lncRNA dataset, GSE113825, were included in this study (Additional file 1: Table S1 Additional file 1: Table S1. List of mRNA/lncRNA study samples from GEO database. ).

Identification of DEmRNAs/DElncRNAs and functional analysis

With limma package and metaMA package, DEmRNAs and DElncRNAs in OA were obtained. The threshold for the significance was the false discovery rate (FDR) < 0.05. Metascape was employed to perform GO and KEGG pathway enrichment analysis to identify aberrantly regulated biological processes and signaling pathways in OA (p-value < 0.05).

Protein–protein interaction (PPI) network construction

In order to predict the function and explore the mechanism of mRNAs, top 200 up and down-regulated DEm- RNAs were searched with the BioGrid, and PPI network was constructed with Cytoscape software.

Identification of the nearby DEmRNAs of DElncRNAs

To explore the cis-regulated mechanism of lncRNAs, the nearby DEmRNAs were identified within a 100 kb window up- or down-stream of DElncRNAs in OA. GO and KEGG pathway enrichment analysis of nearby mRNAs of DElncRNAs was performed by Metascape (p-value < 0.05).

Quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) validation

Eight blood samples were obtained from 4 patients with OA and 4 normal controls. Samples were collected after obtaining written informed consent from every participant. This study was approved by the ethical committee of Honghui Hospital, Xi’an Jiaotong University Health Science Center (202,112,002) and performed in accordance with the Declaration of Helsinki. Total RNA was isolated with the Trizol reagent (Invitrogen, USA) following manufacturer's protocol. The qRT-PCR reactions were performed in ABI 7300 Real-time PCR Detection System with SuperReal PreMix Plus. GAPDH and ACTB were used as endogenous controls.

Expression validation in the GEO dataset and receiver operating characteristic (ROC) analysis

GSE82107 (involving synovial tissues), GSE55235 (involving synovial tissues), GSE63359 (involving peripheral blood leukocytes), GSE48556 (involving peripheral blood mononuclear cell) and GSE175960 (involving cartilage tissues) datasets were downloaded from the GEO database, which consisted of 175 patients with OA and 79 normal controls. The expression pattern of DEmRNAs and DElncRNAs was validated with these five datasets. Then, by using pROC package in R language, we performed the ROC analysis to assess the diagnostic value of DEmRNAs and DElncRNAs. The area under the curve (AUC) was further calculated.

Results

DEmRNAs and DElncRNAs in OA

After processing the raw data, 2080 (1146 up- and 934 down-regulated) DEmRNAs and 664 (522 up- and 142 down-regulated) DElncRNAs were acquired in OA. The top 10 up- and down-regulated DEmRNAs and DEl- ncRNAs are displayed in Table 1. Hierarchical clustering analysis of DEmRNAs and DElncRNAs is exhibited in Fig. 1A and B, respectively.

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Table 1
Top 10 up- and down-regulated DEmRNAs/DElncRNAs between patients with OA and normal controls
Fig. 1
The heatmap of top 100 up- and down-regulated DEmRNAs (A) and DElncRNAs (B) in OA

Functional analysis of DEmRNAs

GO analysis indicated that axon development (p-value = 1.00E-12), neuron projection morphogenesis (p-value = 1.00E-10) and plasma membrane bounded cell projection morphogenesis (p-value = 1.00E-10) were significantly enriched GO terms (Fig. 2A). KEGG pathway enrichment analysis showed that PI3K-Akt signaling pathway (p-value = 2.00E-06), endocytosis (p-value = 1.00E-05) and Rap1 signaling pathway (p-value = 5.01E-05) were several significantly enriched pathways (Fig. 2B).

Fig. 2
Significantly enriched GO terms and KEGG pathways of DEmRNAs between OA and normal controls. A BP, biological process; B KEGG pathways

PPI network of DEmRNAs

The PPI network of DEmRNAs contained 135 nodes and 135 edges (Fig. 3). MRNAs with higher degree were as follows: YWHAB (degree = 11), HSPA8 (degree = 8), NEDD4L (degree = 7) and SH3KBP1 (degree = 7).

Fig. 3
OA-specific PPI networks

Identification of the nearby DEmRNAs of DElncRNAs

A total of 46 DElncRNA-nearby DEmRNA pairs, involving 38 DElncRNAs and 45 DEmRNAs, were obtained in OA (Table 2). GO analysis indicated that these DEmR- NAs were significantly enriched in protein-DNA complex assembly (p-value = 1.26E-03), protein-DNA complex subunit organization (p-value = 2.00E-03) and head development (p-value = 3.16E-03) (Additional file 2: Fig. S1 Additional file 2: Fig. S1. Biological processes related to nearby DEmR- NAs of DElncRNAs in OA. ). In KEGG analysis of nearby DEmRNAs of DElncRNAs, only 3 mRNAs were significantly enriched in the cAMP signaling pathway.

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Table 2
Nearby targeted DEmRNAs of DElncRNAs

QRT-PCR validation

Seven DEmRNAs (TSPAN11, SULF1, YWHAB, AURKA, SH3KBP1, TRPV2 and ACP5) and two lncRNAs (CRNDE and LINC00152) were selected for qRT-PCR analysis. Based on our integrated analysis, TSPAN11, SULF1, YWHAB, AURKA, SH3KBP1, TRPV2, ACP5 and LINC00152 were up-regulated while CRNDE was down-regulated in OA. Except for CRNDE, the qRT-PCR results were basically in line with our integrated analysis results (Fig. 4).

Fig. 4
QRT-PCR results of the DEmRNAs and DElncRNAs in OA

Expression validation in the GEO dataset and ROC analysis

As shown in Fig. 5, the expression patterns of AURKA, PIK3IP1, SULF1 and TRPV2 in GSE48556, AURKA, B3GALT4, LIMK2, PIK3IP1, SULF1 and TRPV2 in GSE55235, AURKA, B3GALT4, LIMK2, PIK3IP1, SULF1 and TRPV2 in GSE63359, B3GALT4, LIMK2, SULF1, TRPV2, TSPAN11 and CRNDE in GSE82107, B3GALT4, LIMK2, SULF1, TSPAN11, CRNDE and LINC00152 in GSE175960 were displayed, which were consistent with our integrated analysis. We performed ROC curve analyses and calculated the AUC to assess the diagnostic value of these DEmRNAs and DElncRNAs. The results indicated that the AUC of SULF1 (1.000) and TRPV2 (0.900) in GSE55235, and LIMK2 (0.700), SULF1 (0.871) and TSPAN11 (0.829) in GSE82107, was more than 0.70, which indicated that these genes had a potential diagnostic value (Fig. 6).

Fig. 5
Expression validations of DEmRNAs and DElncRNAs in GSE48556 (A), GSE55235 (B), GSE63359 (C), GSE82107 (D) and GSE175960 (E) databases. The x-axis shows control and OA and the y-axis shows expression levels
Fig. 6
The ROC curves of DEmRNAs and DElncRNAs in GSE55235 (A) and GSE82107 (B) databases. The x-axes show 1-specificity (the proportion of false positives) and y-axes show sensitivity (the proportion of true positives)

Discussion

OA is a destructive joint disease, and increases in prevalence with age, marked by disordered cartilage homeostasis with subsequent inflammation and degradation, and seriously threatens human health [99 Zhang X, Bu Y, Zhu B, Zhao Q, Lv Z, Li B, et al. Global transcriptome analysis to identify critical genes involved in the pathology of osteoarthritis. Bone Jt Res. 2018;7:298–307.]. Therefore, more attention has been paid on exploring potential pathogenesis mechanisms of OA to facilitate diagnosis and prognosis.

TSPAN11 (CD 151-like) is a member of the tetraspanins family that has been linked to OA. Elevated TSPAN11 is detected in articular cartilage collected from knees undergoing total knee arthroplasty due to end-stage OA [1010 Rai MF, Tycksen ED, Cai L, Yu J, Wright RW, Brophy RH. Distinct degenerative phenotype of articular cartilage from knees with meniscus tear compared to knees with osteoarthritis. Osteoarthr Cartil. 2019;27:945–55.]. It has been suggested that the integrin clustering mediated by TSPAN11 determines the alignment of bone matrix architecture orthogonal to cell alignment [1111 Nakanishi Y, Matsugaki A, Kawahara K, Ninomiya T, Sawada H, Nakano T. Unique arrangement of bone matrix orthogonal to osteoblast alignment controlled by Tspan11-mediated focal adhesion assembly. Biomaterials. 2019;209:103–10.]. Human endo-O-sulfatases, including Sulf-1 and Sulf-2, regulate a multitude of cell-signaling events through heparan sulfate protein interactions and have been linked with the occurrence of OA [1212 Chiu LT, Sabbavarapu NM, Lin WC, Fan CY, Wu CC, Cheng TR, et al. Trisaccharide sulfate and its sulfonamide as an effective substrate and inhibitor of human endo-O-sulfatase-1. J Am Chem Soc. 2020;142:5282–92.]. SULF1 is a regulator of numerous growth factors in skeletal embryonic development [1313 Isidor B, Pichon O, Redon R, Day-Salvatore D, Hamel A, Siwicka KA, et al. Mesomelia-synostoses syndrome results from deletion of SULF1 and SLCO5A1 genes at 8q13. Am J Hum Genet. 2010;87:95–100.]. Increased mRNA and protein levels of SULF1 in the cartilage of the elderly patients with OA may alter the sulfation patterns of heparan sulfate proteoglycans and growth factor activities, leading to abnormal chondrocyte activation and cartilage degradation in OA [1414 Otsuki S, Taniguchi N, Grogan SP, D'Lima D, Kinoshita M, Lotz M. Expression of novel extracellular sulfatases Sulf-1 and Sulf-2 in normal and osteoarthritic articular cartilage. Arthritis Res Ther. 2008;10:R61.]. Jiang et al. indicated that SULF1 was associated with bone loss and the pathology of osteoporosis and OA in aging [1515 Jiang SS, Chen CH, Tseng KY, Tsai FY, Wang MJ, Chang IS, et al. Gene expression profiling suggests a pathological role of human bone marrow-derived mesenchymal stem cells in aging-related skeletal diseases. Aging (Albany NY). 2011;3:672–84.]. The increased expression of Sulf1 in differentiating osteoblasts was further confirmed by RT-PCR analysis of mRNA levels in rat calvarial osteoblast cultures [1616 Zaman G, Staines KA, Farquharson C, Newton PT, Dudhia J, Chenu C, et al. Expression of Sulf1 and Sulf2 in cartilage, bone and endochondral fracture healing. Histochem Cell Biol. 2016;145:67–79.]. In this study, both TSPAN11 and SULF1 were significantly high expressed, which was in accordance with previous observations, indicating the importance of TSPAN11 and SULF1 in OA.

As a type of Aurora kinase, Aurora kinase A (AURKA) is crucial for the successful execution of mitosis [1717 Bertolin G, Tramier M. Insights into the non-mitotic functions of Aurora kinase A: more than just cell division. Cell Mol Life Sci. 2020;77:1031–47.]. Highly expressed AURKA is detected in human osteo-arthritic chondrocytes and knocking-down AURKA significantly reduced the OARSI score [1818 Yang Q, Zhou Y, Cai P, Fu W, Wang J, Wei Q, et al. Up-regulated HIF-2α contributes to the osteoarthritis development through mediating the primary cilia loss. Int Immunopharmacol. 2019;75: 105762.]. AURKA ubiquitination affects mitochondrial dysfunction and inhibits the occurrence of OA by degradation of SOD2 [1919 Yang C, You D, Huang J, Yang B, Huang X, Ni J. Effects of AURKA-mediated degradation of SOD2 on mitochondrial dysfunction and cartilage homeostasis in osteoarthritis. J Cell Physiol. 2019;234:17727–38.]. AURKA is identified as a hub gene in osteoarthritic degenerative meniscal lesions based on GSE52042 data- set [2020 Huan X, Jinhe Y, Rongzong Z. Identification of pivotal genes and pathways in osteoarthritic degenerative meniscal lesions via bioinformatics analysis of the GSE52042 dataset. Med Sci Monit. 2019;25:8891–904.]. Similarly, we found that AURKA was identified not only as a significantly up-regulated DEmRNA, but also as a hub gene in this study, which added to evidence that AURKA is crucial for the development of OA.

CRNDE is closely associated with the proliferation of osteoclasts [2121 Li W, Zhu HM, Xu HD, Zhang B, Huang SM. CRNDE impacts the proliferation of osteoclast by estrogen deficiency in postmenopausal osteoporosis. Eur Rev Med Pharmacol Sci. 2018;22:5815–21.]. CRNDE regulates bone marrow mesenchymal stem cells chondrogenic differentiation to promote cartilage repair in OA [2222 Shi C, Zheng W, Wang J. lncRNA-CRNDE regulates BMSC chondrogenic differentiation and promotes cartilage repair in osteoarthritis through SIRT1/SOX9. Mol Cell Biochem. 2021;476:1881–90.]. CRNDE is a regulator of bone metabolism, and deletion of CRNDE in mice develops a low bone mass phenotype due to impaired bone formation [2323 Mulati M, Kobayashi Y, Takahashi A, Numata H, Saito M, Hiraoka Y, et al. The long noncoding RNA Crnde regulates osteoblast proliferation through the Wnt/β-catenin signaling pathway in mice. Bone. 2020;130: 115076.]. Overexpression of CRNDE alleviated cartilage damage and synovitis in OA rats [2424 Zhang Z, Yang P, Wang C, Tian R. LncRNA CRNDE hinders the progression of osteoarthritis by epigenetic regulation of DACT1. Cell Mol Life Sci. 2022;79:405.]. Wang et al. demonstrated that LINC00152 induced proliferation and suppressed apoptosis in rheumatoid arthritis fibroblast- like synoviocytes [2525 Wang W, Guo P, Chen M, Chen D, Cheng Y, He L. FOXM1/LINC00152 feedback loop regulates proliferation and apoptosis in rheumatoid arthritis fibroblast-like synoviocytes via Wnt/β-catenin signaling pathway. Biosci Rep. 2020;40(1):BSR20191900. https://doi.org/10.1042/BSR20191900.
https://doi.org/10.1042/BSR20191900... ]. Similarly, Zhang et al. suggested that LINC00152 was inflammation-related lncRNA and might be involved in the regulation of rheuma- toid arthritis fibroblast-like synoviocytes inflammation [2626 Zhang J, Gao FF, Xie J. LncRNA linc00152/NF-κB feedback loop promotes fibroblast-like synovial cells inflammation in rheumatoid arthritis via regulating miR-103a/TAK1 axis and YY1 expression. Immun Inflamm Dis. 2021;9:681–93.]. In addition, Hu et al. identified that CRNDE and LINC00152 were involved in age-related degeneration of articular cartilage [2727 Hu P, Sun F, Ran J, Wu L. Identify CRNDE and LINC00152 as the key lncRNAs in age-related degeneration of articular cartilage through comprehensive and integrative analysis. PeerJ. 2019;7: e7024.]. In agreement with previous studies, we also observed significantly down-regulated CRNDE and LINC00152 in this study.

LIM kinases (LIMKs), comprising LIMK1 and LIMK2, are common downstream effectors of several signalization pathways, and function as a signalling node that controls cytoskeleton dynamics through the phosphorylation of the cofilin family proteins [2828 Brion R, Regnier L, Mullard M, Amiaud J, Rédini F, Verrecchia F. LIM kinases in osteosarcoma development. Cells. 2021;10:3542.]. Li et al. suggested that LIMK2 is required for membrane cytoskeleton reorganization of contracting airway smooth muscle [2929 Li Y, Zhou Y, Wang P, Tao T, Wei L, Wang Y, et al. LIMK2 is required for membrane cytoskeleton reorganization of contracting airway smooth muscle. J Genet Genomics. 2021;48:452–62.]. LIMK2 plays an important role in the reorganization of actin cytoskeleton induced by fluid shear stress in murine osteoblast lines [3030 Fu Q, Wu C, Shen Y, Zheng S, Chen R. Effect of LIMK2 RNAi on reorganization of the actin cytoskeleton in osteoblasts induced by fluid shear stress. J Biomech. 2008;41:3225–8.]. LIMK2 silencing inhibits the fluid shear stress-induced reorganisation of the actin cytoskeleton of primary osteoblasts and demonstrates that the mechanosensitivity of osteoblasts in response to this stress is enhanced [3131 Yang Z, Tan S, Shen Y, Chen R, Wu C, Xu Y, et al. Inhibition of FSS-induced actin cytoskeleton reorganization by silencing LIMK2 gene increases the mechanosensitivity of primary osteoblasts. Bone. 2015;74:182–90.]. PIK3IP1 is reported as a negative regulator of the PI3K pathway [3232 Fruman DA, Chiu H, Hopkins BD, Bagrodia S, Cantley LC, Abraham RT. The PI3K pathway in human disease. Cell. 2017;170:605–35.]. PIK3IP1 has also been considered as a negative regulator of antitumor T cell response [3333 Chen Y, Wang J, Wang X, Li X, Song J, Fang J, et al. Pik3ip1 is a negative immune regulator that inhibits antitumor T-cell immunity. Clin Cancer Res. 2019;25:6180–94.]. PIK3IP1 is an important modulator for the tumor necrosis factor-driven inflammatory response in fibroblast-like synoviocytes [3434 Brandstetter B, Dalwigk K, Platzer A, Niederreiter B, Kartnig F, Fischer A, et al. FOXO3 is involved in the tumor necrosis factor-driven inflammatory response in fibroblast-like synoviocytes. Lab Invest. 2019;99:648–58.]. In addition, down-regulated PIK3IP1 is detected in rheuma- toid arthritis [3535 Badr MT, Häcker G. Gene expression profiling meta-analysis reveals novel gene signatures and pathways shared between tuberculosis and rheumatoid arthritis. PLoS ONE. 2019;14: e0213470.]. Both LIMK2 and PIK3IP1 interacted with LINC00152, which indicated that the LINC00152/- LIMK2 and LINC00152/PIK3IP1 interacted pairs may exert a critical function in OA.

TRPV2 encodes an ion channel which is a Ca2+ permeable channel and performs a function in mediating intracellular Ca2+ current via mechanical stimuli [3636 Nakamoto H, Katanosaka Y, Chijimatsu R, Mori D, Xuan F, Yano F, et al. Involvement of transient receptor potential vanilloid channel 2 in the induction of lubricin and suppression of ectopic endochondral ossification in mouse articular cartilage. Arthritis Rheumatol. 2021;73:1441–50.]. Bai et al. reported that TRPV2 modulated RANKL-dependent osteoclastic differentiation in multiple myeloma cells [3737 Bai H, Zhu H, Yan Q, Shen X, Lu X, Wang J, et al. TRPV2-induced Ca(2+)calcineurin-NFAT signaling regulates differentiation of osteoclast in multiple myeloma. Cell Commun Signal. 2018;16:68.]. Laragione et al. indicated that TRPV2 inhibited cell invasion, inflammatory cell infiltration, and angiogenesis, and reduced the severity of arthritis [3838 Laragione T, Cheng KF, Tanner MR, He M, Beeton C, Al-Abed Y, et al. The cation channel Trpv2 is a new suppressor of arthritis severity, joint damage, and synovial fibroblast invasion. Clin Immunol. 2015;158:183–92.]. TRPV2 is required for homeostasis of articular joints by induction of Prg4 and suppression of ectopic endochondral ossification in these joints [3636 Nakamoto H, Katanosaka Y, Chijimatsu R, Mori D, Xuan F, Yano F, et al. Involvement of transient receptor potential vanilloid channel 2 in the induction of lubricin and suppression of ectopic endochondral ossification in mouse articular cartilage. Arthritis Rheumatol. 2021;73:1441–50.]. In the present study, significantly up-regulated TRPV2 was detected in OA, which may suggest that TRPV2 is of great importance in OA. In addition, AC093484.4, as the most significant DElncRNA, interacted with TRPV2. Hence, more evidence should be obtained to determine the function of AC093484.4/TRPV2 interact pair on OA.

The β-1,3-galactosyltransferase-4 (B3GALT4) gene belongs to the β-1,3-galactosyltransferase (β3GalT) gene family, which is essential in the O-glycosylation process [3939 Wandall HH, Blixt O, Tarp MA, Pedersen JW, Bennett EP, Mandel U, et al. Cancer biomarkers defined by autoantibody signatures to aberrant O-glycopeptide epitopes. Cancer Res. 2010;70:1306–13.]. B3GALT4 has been linked to multiple tumors. For example, B3GALT4 is suggested to serve as a novel bio- marker for the diagnosis of gynecological cancers [4040 Seko A, Kataoka F, Aoki D, Sakamoto M, Nakamura T, Hatae M, et al. Beta 1,3-galactosyltransferases-4/5 are novel tumor markers for gynecological cancers. Tumour Biol. 2009;30:43–50.]. Zhang et al. revealed that B3GALT4 was a novel prognostic biomarker for colorectal cancer [4141 Zhang T, Wang F, Wu JY, Qiu ZC, Wang Y, Liu F, et al. Clinical correlation of B7–H3 and B3GALT4 with the prognosis of colorectal cancer. World J Gastroenterol. 2018;24:3538–46.]. Zhang et al. reported that higher expression levels of B3GALT4 predicted better overall survival rates, which might be potential predictors of recurrent osteosarcoma prognosis [4242 Zhang M, Liu Y, Kong D. Identifying biomolecules and constructing a prognostic risk prediction model for recurrence in osteosarcoma. J Bone Oncol. 2021;26: 100331.]. In addition, Verma et al. indicated that decreased B3GALT4 could increase cell vulnerability to potentially toxic stressors, which may contribute to dopaminergic neurodegeneration in Parkinson's disease [4343 Verma M, Schneider JS. siRNA-mediated knockdown of B3GALT4 decreases GM1 ganglioside expression and enhances vulnerability for neurodegeneration. Mol Cell Neurosci. 2019;95:25-30.]. Shi et al. indicated that HCG25 was significantly up-regulated in hepatocellular carcinoma and had great diagnostic value for hepatocellular carcinoma [4444 Shi B, Zhang X, Chao L, Zheng Y, Tan Y, Wang L, et al. Comprehensive analysis of key genes, microRNAs and long non-coding RNAs in hepatocellular carcinoma. FEBS Open Bio. 2018;8:1424-36.]. To date, there is no study report on the association between OA and HCG25/ B3GALT4. In this study, B3GALT4 was interacted with HCG25, which remind us to focus on the function of HCG25/B3GALT4 interact pair on OA.

Our study also has certain limitations. First, the data for this study was obtained from public databases with a small sample size. However, the external validation data- base confirmed the reliability of our analysis. Second, the sample size used for QRT-PCR validation was small. Third, molecular experiments as well as larger clinical samples are required to further validate the results.

Conclusion

In conclusion, we identified several DEmRNAs and DEl- ncRNAs associated with OA. This study thus provides further insights into the underlying molecular mechanism of OA, which may facilitate the diagnosis and treatment of OA.

  • Funding This research did not receive any specific Grant from funding agencies in the public, commercial, or not-for-profit sectors.
  • Declarations Ethics approval and consent to participate This study was approved by the ethical committee of Honghui Hospital, Xi’an Jiaotong University (202112002). All participants were informed as to the purpose ofthis study, and that this study complied with the Declaration of Helsinki. The written consent was obtained from the all patients.
  • Consent for publication The subjects gave written informed consent for the publication of any associated data and accompanying images.
  • Competing interests The authors declare that they have no competing interests.
  • Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Availability of data and materials

All data generated or analysed during this study are included in this published article.

Abbreviation Expansion
OA  Osteoarthritis
GEO  Gene expression omnibus database
DEmRNAs  Differentially expressed mRNAs
DElncRNAs  Differentially expressed lncRNAs
PPI  Protein–protein interaction
qRT-PCR  Quantitative reverse transcriptase-polymerase chain reaction
ROC  Receiver operating characteristic
AUC  Area under the curve
AURKA  Aurora kinase A
LIMKs  LIM kinases
B3GALT4  β-1,3-galactosyltransferase-4
β3GalT  β-1,3-galactosyltransferase
FDR  False discovery rate

Acknowledgements

Not applicable.

Supplementary Information

The online version contains supplementary material available at https://doi. org/10.1186/s42358-023-00288-1.

Additional file 1:

Table S1. List of mRNA/lncRNA study samples from GEO database.

Additional file 2:

Fig. S1. Biological processes related to nearby DEmR- NAs of DElncRNAs in OA.

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Publication Dates

  • Publication in this collection
    01 Sept 2023
  • Date of issue
    2023

History

  • Received
    13 July 2022
  • Accepted
    18 Feb 2023
  • Published
    27 Feb 2023
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