Construction of the miRNA–mRNA regulatory networks for both the cartilage formation and remodel zones in the antler tip in sika deer (Cervus nippon)
Ke Wang A , Ye Zhao A , Lele Cong A , Hongyan Sun A , Hengxing Ba
B , Chunyi Li B , Yimin Wang A * and Xianling Cong A *
+ Author Affiliations
- Author Affiliations
A China-Japan Union Hospital, Jilin University, No. 126, Xiantai Street, Erdao District, Changchun 130033, Jilin, P. R. China.
B Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun 130600, Jilin, P. R. China.
Animal Production Science 62(16) 1563-1572 https://doi.org/10.1071/AN22056
Submitted: 18 February 2022 Accepted: 25 April 2022 Published: 19 May 2022
© 2022 The Author(s) (or their employer(s)). Published by CSIRO Publishing
Abstract
Context: Deer antlers offer a premium model for investigating the mechanisms underlying arguably the most rapid cartilage formation and remodelling system. Although the cartilage formation process in the antler has been relatively intensively studied, thus far, at a molecular level, the cartilage remodelling has essentially been untouched.
Aims: To construct miRNA–mRNA regulatory networks for both the cartilage formation and remodel zones in the antler tip.
Methods: The tissues from both the cartilage formation zone (FZ) and remodel zone (RZ) in rapid growing antlers of sika deer were sampled, profiles of both mRNA and miRNA from these samples were sequenced and analysed, miRNA–mRNA regulatory networks for these two zones were constructed, and their encoded/targeted differentially expressed genes (DEGs) were identified through bioinformatics analysis.
Key results: In total, 3703 DEGs in the FZ over the RZ were identified, with 1615 being upregulated and 2088 downregulated. The upregulated DEGs in the FZ were found to be mainly enriched in cell proliferation and chondrogenesis/osteogenesis, whereas those in the RZ were enriched in the formation of chondroclasts and osteoclasts. In total, 308 unique mature miRNAs were detected including 110 significantly differentially expressed miRNAs. These miRNAs are predicted to target extracellular matrix proteins, growth factors and receptors, and transcriptional factors, all related to cartilage formation and remodelling. To verify the reliability of our datasets, we successfully tested the regulatory function of one of the top 10 hub miRNAs, miR-155, in vitro.
Conclusions: The miRNA–mRNA regulatory networks for cartilage formation zone (FZ) in relation to cartilage remodel zone (RZ) were successfully constructed, and validated, which has laid the foundation for the identification of potent growth factors and novel regulation system in bone formation through endochondral ossification.
Implications: We believe that our datasets are reliable for further mining potent growth factors and novel regulation systems for rapid cartilage formation, remodelling and bone fracture repair by using this unique model, the deer antler.
Keywords: antler, cartilage formation, miRNA, mRNA, regulatory networks, remodel zone, miR-155, FOXO3.
References
Agarwal V, Bell GW, Nam J-W, Bartel DP (2015) Predicting effective microRNA target sites in mammalian mRNAs. eLife 4, e05005| Predicting effective microRNA target sites in mammalian mRNAs.Crossref | GoogleScholarGoogle Scholar |
Ba H, Cai Z, Gao H, Qin T, Liu W, Xie L, Zhang Y, Jing B, Wang D, Li C (2020) Chromosome-level genome assembly of Tarim red deer, Cervus elaphus yarkandensis. Scientific Data 7, 187
| Chromosome-level genome assembly of Tarim red deer, Cervus elaphus yarkandensis.Crossref | GoogleScholarGoogle Scholar | 32561793PubMed |
Bai M, Yin H, Zhao J, Li Y, Wu Y (2019) miR-182-5p overexpression inhibits chondrogenesis by down-regulating PTHLH. Cell Biology International 43, 222–232.
| miR-182-5p overexpression inhibits chondrogenesis by down-regulating PTHLH.Crossref | GoogleScholarGoogle Scholar | 30095215PubMed |
Banks WJ, Newbrey JW (1983) Light microscopic studies of the ossification process in developing antlers. In ‘Antler development in Cervidae’. (Ed. RD Brown) pp. 231–260. (Caesar Kleberg Wildlife Research Institute)
Bean DM, Al-Chalabi A, Dobson RJB, Iacoangeli A (2020) A knowledge-based machine learning approach to gene prioritisation in amyotrophic lateral sclerosis. Genes 11, 668
| A knowledge-based machine learning approach to gene prioritisation in amyotrophic lateral sclerosis.Crossref | GoogleScholarGoogle Scholar |
Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, Lao KQ, Livak KJ, Guegler KJ (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Research 33, e179
| Real-time quantification of microRNAs by stem-loop RT-PCR.Crossref | GoogleScholarGoogle Scholar | 16314309PubMed |
Chen S, Zhou Y, Chen Y, Gu J (2018) fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890.
| fastp: an ultra-fast all-in-one FASTQ preprocessor.Crossref | GoogleScholarGoogle Scholar | 30423086PubMed |
Friedländer MR, Mackowiak SD, Li N, Chen W, Rajewsky N (2012) miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Research 40, 37–52.
| miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades.Crossref | GoogleScholarGoogle Scholar | 21911355PubMed |
Gopinath SD, Webb AE, Brunet A, Rando TA (2014) FOXO3 promotes quiescence in adult muscle stem cells during the process of self-renewal. Stem Cell Reports 2, 414–426.
| FOXO3 promotes quiescence in adult muscle stem cells during the process of self-renewal.Crossref | GoogleScholarGoogle Scholar | 24749067PubMed |
Goss RJ (1970) SECTION III. BASIC SCIENCES AND PATHOLOGY 24. Problems of antlerogesis. Clinical Orthopaedics and Related Research 69, 227–238.
| SECTION III. BASIC SCIENCES AND PATHOLOGY 24. Problems of antlerogesis.Crossref | GoogleScholarGoogle Scholar | 5462575PubMed |
Goss RJ (1983) ‘Deer antlers: regeneration, function, and evolution.’ (Academic Press: New York, NY, USA)
Gyurján I, Molnár A, Borsy A, Stéger V, Hackler L, Zomborszky Z, Papp P, Duda E, Deák F, Lakatos P, Puskás LG, Orosz L (2007) Gene expression dynamics in deer antler: mesenchymal differentiation toward chondrogenesis. Molecular Genetics and Genomics 277, 221–235.
| Gene expression dynamics in deer antler: mesenchymal differentiation toward chondrogenesis.Crossref | GoogleScholarGoogle Scholar | 17146666PubMed |
Hu W, Li T, Wu L, Li M, Meng X (2014) Identification of microRNA-18a as a novel regulator of the insulin-like growth factor-1 in the proliferation and regeneration of deer antler. Biotechnology Letters 36, 703–710.
| Identification of microRNA-18a as a novel regulator of the insulin-like growth factor-1 in the proliferation and regeneration of deer antler.Crossref | GoogleScholarGoogle Scholar | 24563285PubMed |
Hu W, Li M, Hu R, Li T, Meng X (2015) microRNA-18b modulates insulin-like growth factor-1 expression in deer antler cell proliferation by directly targeting its 3′ untranslated region. DNA and Cell Biology 34, 282–289.
| microRNA-18b modulates insulin-like growth factor-1 expression in deer antler cell proliferation by directly targeting its 3′ untranslated region.Crossref | GoogleScholarGoogle Scholar | 25756952PubMed |
Jia B, Zhang L, Zhang Y, Ge C, Yang F, Du R, Ba H (2021) Integrated analysis of miRNA and mRNA transcriptomic reveals antler growth regulatory network. Molecular Genetics and Genomics 296, 689–703.
| Integrated analysis of miRNA and mRNA transcriptomic reveals antler growth regulatory network.Crossref | GoogleScholarGoogle Scholar | 33770271PubMed |
Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nature Methods 12, 357–360.
| HISAT: a fast spliced aligner with low memory requirements.Crossref | GoogleScholarGoogle Scholar | 25751142PubMed |
Krüger J, Rehmsmeier M (2006) RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Research 34, W451–W454.
| RNAhybrid: microRNA target prediction easy, fast and flexible.Crossref | GoogleScholarGoogle Scholar | 16845047PubMed |
Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15–20.
| Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets.Crossref | GoogleScholarGoogle Scholar | 15652477PubMed |
Li C (2021) Residual antler periosteum holds the potential to partially regenerate lost antler tissue. Journal of Experimental Zoology Part A: Ecological and Integrative Physiology 335, 386–395.
| Residual antler periosteum holds the potential to partially regenerate lost antler tissue.Crossref | GoogleScholarGoogle Scholar |
Li C, Chu W (2016) The regenerating antler blastema: the derivative of stem cells resident in a pedicle stump. Frontiers in Biosciences (Landmark Ed) 21, 455–467.
| The regenerating antler blastema: the derivative of stem cells resident in a pedicle stump.Crossref | GoogleScholarGoogle Scholar |
Li C, Fennessy P (2021) The periosteum: a simple tissue with many faces, with special reference to the antler-lineage periostea. Biology Direct 16, 17
| The periosteum: a simple tissue with many faces, with special reference to the antler-lineage periostea.Crossref | GoogleScholarGoogle Scholar | 34663443PubMed |
Li C, Suttie JM (2003) Tissue collection methods for antler research. European Journal of Morphology 41, 23–30.
| Tissue collection methods for antler research.Crossref | GoogleScholarGoogle Scholar | 15121545PubMed |
Li C, Littlejohn RP, Suttie JM (1999) Effects of insulin-like growth factor 1 and testosterone on the proliferation of antlerogenic cells in vitro. Journal of Experimental Zoology 284, 82–90.
| Effects of insulin-like growth factor 1 and testosterone on the proliferation of antlerogenic cells in vitro.Crossref | GoogleScholarGoogle Scholar | 10368936PubMed |
Li C, Clark DE, Lord EA, Stanton J-AL, Suttie JM (2002) Sampling technique to discriminate the different tissue layers of growing antler tips for gene discovery. The Anatomical Record 268, 125–130.
| Sampling technique to discriminate the different tissue layers of growing antler tips for gene discovery.Crossref | GoogleScholarGoogle Scholar | 12221718PubMed |
Li C, Mills Z, Zheng Z (2021) Novel cell sources for bone regeneration. MedComm 2, 145–174.
| Novel cell sources for bone regeneration.Crossref | GoogleScholarGoogle Scholar | 34766140PubMed |
Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15, 550
| Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.Crossref | GoogleScholarGoogle Scholar | 25516281PubMed |
Lu J, Clark AG (2012) Impact of microRNA regulation on variation in human gene expression. Genome Research 22, 1243–1254.
| Impact of microRNA regulation on variation in human gene expression.Crossref | GoogleScholarGoogle Scholar | 22456605PubMed |
Ma C, Liu H, Wei Y, Li H, Miao D, Ren Y (2022) Exogenous PTH 1-34 attenuates impaired fracture healing in endogenous PTH deficiency mice via activating indian hedgehog signaling pathway and accelerating endochondral ossification. Frontiers in Cell and Developmental Biology 9, 750878
| Exogenous PTH 1-34 attenuates impaired fracture healing in endogenous PTH deficiency mice via activating indian hedgehog signaling pathway and accelerating endochondral ossification.Crossref | GoogleScholarGoogle Scholar | 35071224PubMed |
Martin TJ (2016) Parathyroid hormone-related protein, its regulation of cartilage and bone development, and role in treating bone diseases. Physiological Reviews 96, 831–871.
| Parathyroid hormone-related protein, its regulation of cartilage and bone development, and role in treating bone diseases.Crossref | GoogleScholarGoogle Scholar | 27142453PubMed |
Matsushita M, Kitoh H, Kaneko H, Mishima K, Kadono I, Ishiguro N, Nishimura G (2013) A novel SOX9 H169Q mutation in a family with overlapping phenotype of mild campomelic dysplasia and small patella syndrome. American Journal of Medical Genetics Part A 161A, 2528–2534.
| A novel SOX9 H169Q mutation in a family with overlapping phenotype of mild campomelic dysplasia and small patella syndrome.Crossref | GoogleScholarGoogle Scholar | 24038782PubMed |
Miyamoto T, Fukuda T, Nakashima M, Henzan T, Kusakabe S, Kobayashi N, Sugita J, Mori T, Kurokawa M, Mori S-i (2017) Donor lymphocyte infusion for relapsed hematological malignancies after unrelated allogeneic bone marrow transplantation facilitated by the Japan marrow donor program. Biology of Blood and Marrow Transplantation 23, 938–944.
| Donor lymphocyte infusion for relapsed hematological malignancies after unrelated allogeneic bone marrow transplantation facilitated by the Japan marrow donor program.Crossref | GoogleScholarGoogle Scholar | 28219836PubMed |
Molnár A, Gyurján I, Korpos E, Borsy A, Stéger V, Buzás Z, Kiss I, Zomborszky Z, Papp P, Deák F, Orosz L (2007) Identification of differentially expressed genes in the developing antler of red deer Cervus elaphus. Molecular Genetics and Genomics 277, 237–248.
| Identification of differentially expressed genes in the developing antler of red deer Cervus elaphus.Crossref | GoogleScholarGoogle Scholar | 17131158PubMed |
Pertea M, Pertea GM, Antonescu CM, Chang T-C, Mendell JT, Salzberg SL (2015) StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology 33, 290–295.
| StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.Crossref | GoogleScholarGoogle Scholar | 25690850PubMed |
Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL (2016) Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nature Protocols 11, 1650–1667.
| Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.Crossref | GoogleScholarGoogle Scholar | 27560171PubMed |
Renault VM, Rafalski VA, Morgan AA, Salih DAM, Brett JO, Webb AE, Villeda SA, Thekkat PU, Guillerey C, Denko NC, Palmer TD, Butte AJ, Brunet A (2009) FoxO3 regulates neural stem cell homeostasis. Cell Stem Cell 5, 527–539.
| FoxO3 regulates neural stem cell homeostasis.Crossref | GoogleScholarGoogle Scholar | 19896443PubMed |
Salih DAM, Brunet A (2008) FoxO transcription factors in the maintenance of cellular homeostasis during aging. Current Opinion in Cell Biology 20, 126–136.
| FoxO transcription factors in the maintenance of cellular homeostasis during aging.Crossref | GoogleScholarGoogle Scholar |
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 13, 2498–2504.
| Cytoscape: a software environment for integrated models of biomolecular interaction networks.Crossref | GoogleScholarGoogle Scholar | 14597658PubMed |
Tothova Z, Krill-Burger JM, Popova KD, Landers CC, Sievers QL, Yudovich D, Belizaire R, Aster JC, Morgan EA, Tsherniak A, Ebert BL (2017) Multiplex CRISPR/Cas9-based genome editing in human hematopoietic stem cells models clonal hematopoiesis and myeloid neoplasia. Cell Stem Cell 21, 547–555.e8.
| Multiplex CRISPR/Cas9-based genome editing in human hematopoietic stem cells models clonal hematopoiesis and myeloid neoplasia.Crossref | GoogleScholarGoogle Scholar | 28985529PubMed |
van Gastel N, Stegen S, Eelen G, Schoors S, Carlier A, Daniëls VW, Baryawno N, Przybylski D, Depypere M, Stiers P-J, Lambrechts D, Van Looveren R, Torrekens S, Sharda A, Agostinis P, Lambrechts D, Maes F, Swinnen JV, Geris L, Van Oosterwyck H, Thienpont B, Carmeliet P, Scadden DT, Carmeliet G (2020) Lipid availability determines fate of skeletal progenitor cells via SOX9. Nature 579, 111–117.
| Lipid availability determines fate of skeletal progenitor cells via SOX9.Crossref | GoogleScholarGoogle Scholar | 32103177PubMed |
Vortkamp A, Lee K, Lanske B, Segre GV, Kronenberg HM, Tabin CJ (1996) Regulation of rate of cartilage differentiation by Indian hedgehog and PTH-related protein. Science 273, 613–622.
| Regulation of rate of cartilage differentiation by Indian hedgehog and PTH-related protein.Crossref | GoogleScholarGoogle Scholar | 8662546PubMed |
Yao B, Zhao Y, Wang Q, Zhang M, Liu M, Liu H, Li J (2012) De novo characterization of the antler tip of Chinese Sika deer transcriptome and analysis of gene expression related to rapid growth. Molecular and Cellular Biochemistry 364, 93–100.
| De novo characterization of the antler tip of Chinese Sika deer transcriptome and analysis of gene expression related to rapid growth.Crossref | GoogleScholarGoogle Scholar | 22198337PubMed |
Yao B, Zhang M, Liu M, Lu B, Leng X, Hu Y, Zhao D, Zhao Y (2019) Identification of the miRNA–mRNA regulatory network of antler growth centers. Journal of Biosciences 44, 11
| Identification of the miRNA–mRNA regulatory network of antler growth centers.Crossref | GoogleScholarGoogle Scholar | 30837362PubMed |
