Functional & Integrative Genomics

, Volume 17, Issue 6, pp 739–749 | Cite as

Long noncoding RNA expression profiles in chondrogenic and hypertrophic differentiation of mouse mesenchymal stem cells

  • Zhen Cao
  • Song Huang
  • Jianmei Li
  • Yun Bai
  • Ce Dou
  • Chuan Liu
  • Fei Kang
  • Xiaoshan Gong
  • Haibin Ding
  • Tianyong Hou
  • Shiwu DongEmail author
Original Article


Long noncoding RNAs (lncRNAs) are important regulators for a variety of biological processes. Chondrogenic differentiation of mesenchymal stem cells (MSCs) is a crucial stage in chondrogenesis while chondrocyte hypertrophy is related to endochondral ossification and osteoarthritis. However, the effects of lncRNAs on chondrogenic and hypertrophic differentiation of mouse MSCs are unclear. To explore the potential mechanisms of lncRNAs during chondrogenesis and chondrocyte hypertrophy, microarray was performed to investigate the expression profiles of lncRNA and mRNA in MSCs, pre-chondrocytes, and hypertrophic chondrocytes. Then, we validated microarray data by RT-PCR and screened three lncRNAs from upregulating groups during chondrogenesis and chondrocyte hypertrophy respectively. After downregulating any of the above lncRNAs, we found that the expression of chondrogenesis-related genes such as Sox9 and Col2a1 and hypertrophy-related genes including Runx2 and Col10a1 was inhibited, respectively. Furthermore, the target genes of above lncRNAs were predicted by bioinformatics approaches. Gene ontology and Kyoto encyclopedia of genes and genome biological pathway analysis were also made to speculate the functions of above lncRNAs. In conclusion, the study first revealed the expression profile of lncRNAs in chondrogenic and hypertrophic differentiations of mouse MSCs and presented a new prospect for the underlying mechanisms of chondrogenesis and endochondral ossification.


Long noncoding RNA Microarray Mesenchymal stem cell Chondrogenesis Chondrocyte hypertrophy 



Long noncoding RNAs


Mesenchymal stem cells


Gene ontology


Matrix metalloproteinase 13


Kyoto encyclopedia of genes and genomes



This work was supported by grants from the Nature Science Foundation of China (81572164) and the National Key Technology Research and Development Program of China (2017YFC1103300).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

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Table S1 (DOCX 13 kb).
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Table S2 (DOCX 14 kb).
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Table S3 (DOCX 13 kb).
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Fig. S1 (DOCX 121 kb).
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Fig. S2 (DOCX 105 kb).


  1. Ahmed MR, Mehmood A, Bhatti FUR, Khan SN, Riazuddin S (2014) Combination of ADMSCs and chondrocytes reduces hypertrophy and improves the functional properties of osteoarthritic cartilage. Osteoarthr Cartil 22:1894–1901CrossRefPubMedGoogle Scholar
  2. Ahn R, Gupta R, Lai K, Chopra N, Arron ST, Liao W (2016) Network analysis of psoriasis reveals biological pathways and roles for coding and long non-coding RNAs. BMC Genomics 17:841CrossRefPubMedPubMedCentralGoogle Scholar
  3. Akkiraju H, Nohe A (2015) Role of chondrocytes in cartilage formation, progression of osteoarthritis and cartilage regeneration. J Dev Biol 3:177–192CrossRefPubMedPubMedCentralGoogle Scholar
  4. Azevedo-Pouly AC, Sutaria DS, Jiang J, Elgamal OA, Amari F, Allard D, Grippo PJ, Coppola V, Schmittgen TD (2017) miR-216 and miR-217 expression is reduced in transgenic mouse models of pancreatic adenocarcinoma, knockout of miR-216/miR-217 host gene is embryonic lethal. Funct Integr Genomics 17:203–212CrossRefPubMedGoogle Scholar
  5. Bianchi A, Guibert M, Cailotto F, Gasser A, Presle N, Mainard D, Netter P, Kempf H, Jouzeau JY, Reboul P (2016) Fibroblast Growth Factor 23 drives MMP13 expression in human osteoarthritic chondrocytes in a Klotho-independent manner. Osteoarthr Cartil 24:1961–1969CrossRefPubMedGoogle Scholar
  6. Chen S, Ma P, Li B, Zhu D, Chen X, Xiang Y, Wang T, Ren X, Liu C, Jin X (2017a) LncRNA CCAT1 inhibits cell apoptosis of renal cell carcinoma through up-regulation of Livin protein. Mol Cell Biochem. doi: 10.1007/s11010-017-3043-8
  7. Chen WK, Yu XH, Yang W, Wang C, He WS, Yan YG, Zhang J, Wang WJ (2017b) lncRNAs: novel players in intervertebral disc degeneration and osteoarthritis. Cell Prolif 50(1)Google Scholar
  8. Chen X, Li X, Guo J, Zhang P, Zeng W (2017c) The roles of microRNAs in regulation of mammalian spermatogenesis. J Anim Sci Biotechnol 8:35CrossRefPubMedPubMedCentralGoogle Scholar
  9. Cheng SH, Pourteymoor S, Alarcon C, Mohan S (2017) Conditional deletion of the Phd2 gene in articular chondrocytes accelerates differentiation and reduces articular cartilage thickness. Sci Rep 7Google Scholar
  10. Decambron A, Fournet A, Bensidhoum M, Manassero M, Sailhan F, Petite H, Logeart-Avramoglou D, Viateau V (2017) Low-dose BMP-2 and MSC dual delivery onto coral scaffold for critical-size bone defect regeneration in sheep. J Orthop Res. doi: 10.1002/jor.23577
  11. Deniz E, Erman B (2017) Long noncoding RNA (lincRNA), a new paradigm in gene expression control. Funct Integr Genomics 17:135–143CrossRefPubMedGoogle Scholar
  12. Dutkiewicz M, Stachowiak A, Swiatkowska A, Ciesiolka J (2016) Structure and function of RNA elements present in enteroviral genomes. Acta Biochim Pol 63:623–630CrossRefPubMedGoogle Scholar
  13. Farahani RM, Xaymardan M (2015) Platelet-derived growth factor receptor alpha as a marker of mesenchymal stem cells in development and stem cell biology. Stem Cells Int 2015:362753CrossRefPubMedPubMedCentralGoogle Scholar
  14. Feng Q, Lin S, Zhang K, Dong C, Wu T, Huang H, Yan X, Zhang L, Li G, Bian L (2017) Sulfated hyaluronic acid hydrogels with retarded degradation and enhanced growth factor retention promote hMSC chondrogenesis and articular cartilage integrity with reduced hypertrophy. Acta Biomater 53:329–342CrossRefPubMedGoogle Scholar
  15. Fruci D, Rota R, Gallo A (2017) The role of HCMV and HIV-1 microRNAs: processing, and mechanisms of action during viral infection. Front Microbiol 8:689CrossRefPubMedPubMedCentralGoogle Scholar
  16. Garg P, Mazur MM, Buck AC, Wandtke ME, Liu J, Ebraheim NA (2017) Prospective review of mesenchymal stem cells differentiation into osteoblasts. Orthop Surg 9:13–19CrossRefPubMedGoogle Scholar
  17. Guo W, Lei W, Yu D, Ge Y, Chen Y, Xue W, Li Q, Li S, Gao X, Yao W (2017) Involvement of lncRNA-1700040D17Rik in Th17 cell differentiation and the pathogenesis of EAE. Int Immunopharmacol 47:141–149CrossRefPubMedGoogle Scholar
  18. Han F, Wang C, Wang Y, Zhang L (2017) Long noncoding RNA ATB promotes osteosarcoma cell proliferation, migration and invasion by suppressing miR-200s. Am J Cancer Res 7:770–783PubMedPubMedCentralGoogle Scholar
  19. Hendijani F (2017) Explant culture: an advantageous method for isolation of mesenchymal stem cells from human tissues. Cell Prolif 50Google Scholar
  20. Hsuan YC, Lin CH, Chang CP, Lin MT (2016) Mesenchymal stem cell-based treatments for stroke, neural trauma, and heat stroke. Brain Behav 6:e00526CrossRefPubMedPubMedCentralGoogle Scholar
  21. Huh SW, Shetty AA, Ahmed S, Lee DH, Kim SJ (2016) Autologous bone-marrow mesenchymal cell induced chondrogenesis (MCIC). J Clin Orthop Trauma 7:153–156CrossRefPubMedPubMedCentralGoogle Scholar
  22. Im GI (2016) Regeneration of articular cartilage using adipose stem cells. J Biomed Mater Res A 104:1830–1844CrossRefPubMedGoogle Scholar
  23. Kasoju N, Wang H, Zhang B, George J, Gao S, Triffitt JT, Cui Z, Ye H (2017) Transcriptomics of human multipotent mesenchymal stromal cells: retrospective analysis and future prospects. Biotechnol Adv 35(4):407–418Google Scholar
  24. Kataruka S, Akhade VS, Kayyar B, Rao MRS (2017) Mrhl lncRNA mediates meiotic commitment of mouse spermatogonial cells by regulating Sox8 expression. Mol Cell Biol 29;37(14)Google Scholar
  25. Klingenberg M, Matsuda A, Diederichs S, Patel T (2017) Non-coding RNA in hepatocellular carcinoma: mechanisms, biomarkers and therapeutic targets. J Hepatol pii: S0168-8278(17)30250-7Google Scholar
  26. Lai Y, He S, Ma L, Lin H, Ren B, Ma J, Zhu X, Zhuang S (2017) HOTAIR functions as a competing endogenous RNA to regulate PTEN expression by inhibiting miR-19 in cardiac hypertrophy. Mol Cell Biochem. doi: 10.1007/s11010-017-3008-y
  27. Lammens T, Durinck K, Wallaert A, Speleman F, Van Vlierberghe P (2017) Long non-coding RNAs in leukemia: biology and clinical impact. Curr Opin Hematol 24(4):353–358Google Scholar
  28. Laneve P, Po A, Favia A, Legnini I, Alfano V, Rea J, Di Carlo V, Bevilacqua V, Miele E, Mastronuzzi A, Carai A, Locatelli F, Bozzoni I, Ferretti E, Caffarelli E (2017) The long noncoding RNA linc-NeD125 controls the expression of medulloblastoma driver genes by microRNA sponge activity. Oncotarget 8(19):31003–31015Google Scholar
  29. Lee JM, Kim JD, Oh EJ, Oh SH, Lee JH, Im GI (2014) PD98059-impregnated functional PLGA scaffold for direct tissue engineering promotes chondrogenesis and prevents hypertrophy from mesenchymal stem cells. Tissue Eng Part A 20:982–991CrossRefPubMedGoogle Scholar
  30. Lee DE, Ayoub N, Agrawal DK (2016) Mesenchymal stem cells and cutaneous wound healing: novel methods to increase cell delivery and therapeutic efficacy. Stem Cell Res Ther 7:37CrossRefPubMedPubMedCentralGoogle Scholar
  31. Lefebvre V, De Crombrugghe B (1998) Toward understanding SOX9 function in chondrocyte differentiation. Matrix Biol 16:529–540CrossRefPubMedGoogle Scholar
  32. Li FF, Mi R, Fan CL, Zhang P, Zhu T, Wang Q, Lu YJ, Gu JX, Zheng QP (2016) Runx2-interacting genes identified by yeast two-hybrid screening of libraries generated from hypertrophic chondrocytes. Am J Transl Res 8:5465–5474PubMedPubMedCentralGoogle Scholar
  33. Li J, Zhang Z, Xiong L, Guo C, Jiang T, Zeng L, Li G, Wang J (2017) SNHG1 lncRNA negatively regulates miR-199a-3p to enhance CDK7 expression and promote cell proliferation in prostate cancer. Biochem Biophys Res Commun 487:146–152CrossRefPubMedGoogle Scholar
  34. Lolli A, Penolazzi L, Narcisi R, van Osch G, Piva R (2017) Emerging potential of gene silencing approaches targeting anti-chondrogenic factors for cell-based cartilage repair. Cell Mol Life Sci. doi: 10.1007/s00018-017-2531-z
  35. Lu JW, Sun Y, Ge QT, Teng HJ, Jiang Q (2014) Histone deacetylase 4 alters cartilage homeostasis in human osteoarthritis. Bmc Musculoskelet Disord 15Google Scholar
  36. Luo G, Liu D, Huang C, Wang M, Xiao X, Zeng F, Wang L, Jiang G (2017) LncRNA GAS5 inhibits cellular proliferation by targeting P27Kip1. Mol Cancer Res 15(7):789–799Google Scholar
  37. Moradian H, Keshvari H, Fasehee H, Dinarvand R, Faghihi S (2017) Combining NT3-overexpressing MSCs and PLGA microcarriers for brain tissue engineering: a potential tool for treatment of Parkinson’s disease. Mater Sci Eng C Mater Biol Appl 76:934–943CrossRefPubMedGoogle Scholar
  38. Mueller MB, Tuan RS (2008) Functional characterization of hypertrophy in chondrogenesis of human mesenchymal stem cells. Arthritis Rheum 58:1377–1388CrossRefPubMedPubMedCentralGoogle Scholar
  39. Rai V, Dilisio MF, Dietz NE, Agrawal DK (2017) Recent strategies in cartilage repair: a systemic review of the scaffold development and tissue engineering. J Biomed Mater Res A 105(8):2343–2354Google Scholar
  40. Rossi B, Merlo B, Colleoni S, Iacono E, Tazzari PL, Ricci F, Lazzari G, Galli C (2014) Isolation and in vitro characterization of bovine amniotic fluid derived stem cells at different trimesters of pregnancy. Stem Cell Rev 10:712–724CrossRefPubMedGoogle Scholar
  41. Safari S, Malekvandfard F, Babashah S, Alizadehasl A, Sadeghizadeh M, Motavaf M (2016) Mesenchymal stem cell-derived exosomes: a novel potential therapeutic avenue for cardiac regeneration. Cell Mol Biol (Noisy-le-grand) 62:66–73Google Scholar
  42. Sahni A, Hajjari M, Raheb J, Foroughmand AM, Asgari M (2017) Cloning and over expression of non-coding RNA rprA in E. coli and its resistance to Kanamycin without osmotic shock. Bioinformation 13:21–24CrossRefPubMedPubMedCentralGoogle Scholar
  43. Saidi N, Ghalavand M, Hashemzadeh MS, Dorostkar R, Mohammadi H, Mahdian-Shakib A (2017) Dynamic changes of epigenetic signatures during chondrogenic and adipogenic differentiation of mesenchymal stem cells. Biomed Pharmacother 89:719–731CrossRefPubMedGoogle Scholar
  44. Shen B, Yuan Y, Zhang Y, Yu S, Peng W, Huang X, Feng J (2017) Long non-coding RNA FBXL19-AS1 plays oncogenic role in colorectal cancer by sponging miR-203. Biochem Biophys Res Commun 488(1):67–73Google Scholar
  45. Sun MM, Beier F (2014) Liver X receptor activation delays chondrocyte hypertrophy during endochondral bone growth. Osteoarthr Cartil 22:996–1006CrossRefPubMedGoogle Scholar
  46. Toh WS, Lai RC, Hui JH, Lim SK (2016) MSC exosome as a cell-free MSC therapy for cartilage regeneration: implications for osteoarthritis treatment. Semin Cell Dev Biol 67:56–64Google Scholar
  47. Vallot C, Patrat C, Collier AJ, Huret C, Casanova M, Liyakat Ali TM, Tosolini M, Frydman N, Heard E, Rugg-Gunn PJ, Rougeulle C (2017) XACT noncoding RNA competes with XIST in the control of X chromosome activity during human early development. Cell Stem Cell 20:102–111CrossRefPubMedPubMedCentralGoogle Scholar
  48. Wang Y, Liang T, Wang Y, Huang Y, Li Y (2017) Long non-coding RNA AK093407 promotes proliferation and inhibits apoptosis of human osteosarcoma cells via STAT3 activation. Am J Cancer Res 7:892–902PubMedPubMedCentralGoogle Scholar
  49. Wuelling M, Vortkamp A (2011) Chondrocyte proliferation and differentiation. Endocr Dev 21:1–11CrossRefPubMedGoogle Scholar
  50. Xin JW, Jiang YG (2017) Long noncoding RNA MALAT1 inhibits apoptosis induced by oxygen-glucose deprivation and reoxygenation in human brain microvascular endothelial cells. Exp Ther Med 13:1225–1234CrossRefPubMedPubMedCentralGoogle Scholar
  51. Yang B, Guo H, Zhang Y, Chen L, Ying D, Dong S (2011) MicroRNA-145 regulates chondrogenic differentiation of mesenchymal stem cells by targeting Sox9. PLoS One 6:e21679CrossRefPubMedPubMedCentralGoogle Scholar
  52. Yang J, Shrike Zhang Y, Yue K, Khademhosseini A (2017) Cell-laden hydrogels for osteochondral and cartilage tissue engineering. Acta Biomater 57:1–25Google Scholar
  53. Zhang J, Le TD, Liu L, Li J (2017) Inferring miRNA sponge co-regulation of protein-protein interactions in human breast cancer. BMC Bioinformatics 18:243CrossRefPubMedPubMedCentralGoogle Scholar
  54. Zhao Q, Li S, Li N, Yang X, Ma S, Yang A, Zhang H, Yang S, Mao C, Xu L, Gao T, Yang X, Zhang H, Jiang Y (2017) miR-34a targets HDAC1-regulated H3K9 acetylation on lipid accumulation induced by homocysteine in foam cells. J Cell Biochem. doi: 10.1002/jcb.26126
  55. Zhu M, Feng Q, Sun Y, Li G, Bian L (2016) Effect of cartilaginous matrix components on the chondrogenesis and hypertrophy of mesenchymal stem cells in hyaluronic acid hydrogels. J Biomed Mater Res B Appl Biomater. doi: 10.1002/jbm.b.33760

Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  1. 1.Department of Biomedical Materials Science, School of Biomedical EngineeringThird Military Medical UniversityChongqingChina
  2. 2.Department of AnatomyThird Military Medical UniversityChongqingChina
  3. 3.School of Pathology and Laboratory MedicineThe University of Western AustraliaNedlandsAustralia
  4. 4.National & Regional United Engineering Laboratory of Tissue Engineering, Department of Orthopedics, Southwest HospitalThird Military Medical UniversityChongqingChina

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