Calvaria Bone Transcriptome in Mouse Models of Osteogenesis Imperfecta
Abstract
:1. Introduction
2. Results
3. Discussion
4. Materials and Methods
4.1. Sample Preparation
4.2. Library Preparation and RNA Sequencing
Data Post-Processing and Statistical Evaluation
4.3. Real-Time PCR Validation
4.4. Micro-Computed Tomography (MicroCT)
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Conflicts of Interest
References
- Forlino, A.; Marini, J.C. Osteogenesis imperfecta. Lancet 2016, 387, 1657–1671. [Google Scholar] [CrossRef]
- Bardai, G.; Moffatt, P.; Glorieux, F.H.; Rauch, F. DNA sequence analysis in 598 individuals with a clinical diagnosis of osteogenesis imperfecta: Diagnostic yield and mutation spectrum. Osteoporos. Int. J. Establ. Result Coop. Eur. Found. Osteoporos. Natl. Osteoporos. Found. USA 2016, 27, 3607–3613. [Google Scholar] [CrossRef] [PubMed]
- Rauch, F.; Travers, R.; Parfitt, A.M.; Glorieux, F.H. Static and dynamic bone histomorphometry in children with osteogenesis imperfecta. Bone 2000, 26, 581–589. [Google Scholar] [CrossRef]
- Rauch, F.; Lalic, L.; Roughley, P.; Glorieux, F.H. Relationship between genotype and skeletal phenotype in children and adolescents with osteogenesis imperfecta. J. Bone Miner. Res. Off. J. Am. Soc. Bone Mineral. Res. 2010, 25, 1367–1374. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Chipman, S.D.; Sweet, H.O.; McBride, D.J.; Davisson, M.T.; Marks, S.C.; Shuldiner, A.R.; Wenstrup, R.J.; Rowe, D.W.; Shapiro, J.R. Defective pro alpha 2(I) collagen synthesis in a recessive mutation in mice: A model of human osteogenesis imperfecta. Proc. Natl. Acad. Sci. USA 1993, 90, 1701–1705. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Chen, F.; Guo, R.; Itoh, S.; Moreno, L.; Rosenthal, E.; Zappitelli, T.; Zirngibl, R.A.; Flenniken, A.; Cole, W.; Grynpas, M.; et al. First mouse model for combined osteogenesis imperfecta and Ehlers-Danlos syndrome. J. Bone Miner. Res. Off. J. Am. Soc. Bone Mineral. Res. 2014, 29, 1412–1423. [Google Scholar] [CrossRef]
- Zimmerman, S.M.; Dimori, M.; Heard-Lipsmeyer, M.E.; Morello, R. The osteocyte transcriptome is extensively dysregulated in mouse models of osteogenesis imperfecta. JBMR Plus 2019, 3, e10171. [Google Scholar] [CrossRef] [Green Version]
- Grafe, I.; Alexander, S.; Peterson, J.R.; Snider, T.N.; Levi, B.; Lee, B.; Mishina, Y. TGF-beta family signaling in mesenchymal differentiation. Cold Spring Harb. Perspect. Biol. 2018, 10. [Google Scholar] [CrossRef]
- Kim, H.N.; Iyer, S.; Ring, R.; Almeida, M. The role of FoxOs in bone health and disease. Curr. Top. Dev. Biol. 2018, 127, 149–163. [Google Scholar] [CrossRef]
- Roschger, A.; Roschger, P.; Keplingter, P.; Klaushofer, K.; Abdullah, S.; Kneissel, M.; Rauch, F. Effect of sclerostin antibody treatment in a mouse model of severe osteogenesis imperfecta. Bone 2014, 66, 182–188. [Google Scholar] [CrossRef]
- Tauer, J.T.; Abdullah, S.; Rauch, F. Effect of anti-TGF-beta treatment in a mouse model of severe osteogenesis imperfecta. J. Bone Miner. Res. Off. J. Am. Soc. Bone Mineral. Res. 2019, 34, 207–214. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Cardinal, M.; Tys, J.; Roels, T.; Lafont, S.; Ominsky, M.S.; Devogelaer, J.P.; Chappard, D.; Mabilleau, G.; Ammann, P.; Nyssen-Behets, C.; et al. Sclerostin antibody reduces long bone fractures in the oim/oim model of osteogenesis imperfecta. Bone 2019, 124, 137–147. [Google Scholar] [CrossRef] [PubMed]
- Grafe, I.; Yang, T.; Alexander, S.; Homan, E.P.; Lietman, C.; Jiang, M.M.; Bertin, T.; Munivez, E.; Chen, Y.; Dawson, B.; et al. Excessive transforming growth factor-beta signaling is a common mechanism in osteogenesis imperfecta. Nat. Med. 2014, 20, 670–675. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Seitz, H.K.; Mueller, S. Alcohol and cancer: An overview with special emphasis on the role of acetaldehyde and cytochrome P450 2E1. Adv. Exp. Med. Biol. 2015, 815, 59–70. [Google Scholar] [CrossRef]
- Hong, A.R.; Kim, K.; Lee, J.Y.; Yang, J.Y.; Kim, J.H.; Shin, C.S.; Kim, S.W. Transformation of Mature Osteoblasts into Bone Lining Cells and RNA Sequencing-Based Transcriptome Profiling of Mouse Bone during Mechanical Unloading. Endocrinol. Metab. 2020, 35, 456–469. [Google Scholar] [CrossRef]
- Pathak, J.L.; Liu, L.; Zhu, Y.Q.; Bureik, M. Cytochrome P450 expression patterns in human osteoblasts during osteogenic differentiation with or without TNFalpha treatment. Biopharm. Drug Dispos. 2020, 41, 184–191. [Google Scholar] [CrossRef]
- Matthews, B.G.; Roeder, E.; Wang, X.; Aguila, H.L.; Lee, S.K.; Grcevic, D.; Kalajzic, I. Splenomegaly, myeloid lineage expansion and increased osteoclastogenesis in osteogenesis imperfecta murine. Bone 2017, 103, 1–11. [Google Scholar] [CrossRef]
- Moffatt, P.; Boraschi-Diaz, I.; Bardai, G.; Rauch, F. Muscle transcriptome in mouse models of osteogenesis imperfecta. Bone 2021, 148, 115940. [Google Scholar] [CrossRef]
- Selch, S.; Chafai, A.; Sticht, H.; Birkenfeld, A.L.; Fromm, M.F.; Konig, J. Analysis of naturally occurring mutations in the human uptake transporter NaCT important for bone and brain development and energy metabolism. Sci. Rep. 2018, 8, 11330. [Google Scholar] [CrossRef] [PubMed]
- Hu, Y.Y.; Rawal, A.; Schmidt-Rohr, K. Strongly bound citrate stabilizes the apatite nanocrystals in bone. Proc. Natl. Acad. Sci. USA 2010, 107, 22425–22429. [Google Scholar] [CrossRef] [Green Version]
- Fratzl, P.; Paris, O.; Klaushofer, K.; Landis, W.J. Bone mineralization in an osteogenesis imperfecta mouse model studied by small-angle x-ray scattering. J. Clin. Investig. 1996, 97, 396–402. [Google Scholar] [CrossRef] [Green Version]
- Irizarry, A.R.; Yan, G.; Zeng, Q.; Lucchesi, J.; Hamang, M.J.; Ma, Y.L.; Rong, J.X. Defective enamel and bone development in sodium-dependent citrate transporter (NaCT) Slc13a5 deficient mice. PLoS ONE 2017, 12, e0175465. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Schossig, A.; Bloch-Zupan, A.; Lussi, A.; Wolf, N.I.; Raskin, S.; Cohen, M.; Giuliano, F.; Jurgens, J.; Krabichler, B.; Koolen, D.A.; et al. SLC13A5 is the second gene associated with Kohlschutter-Tonz syndrome. J. Med. Genet. 2017, 54, 54–62. [Google Scholar] [CrossRef] [PubMed]
- Deng, W.; Wang, L.; Xiong, Y.; Li, J.; Wang, Y.; Shi, T.; Ma, D. The novel secretory protein Cgref1 inhibits the activation of AP-1 transcriptional activity and cell proliferation. Int. J. Biochem. Cell Biol. 2015, 65, 32–39. [Google Scholar] [CrossRef]
- Gharibi, B.; Ghuman, M.S.; Cama, G.; Rawlinson, S.C.F.; Grigoriadis, A.E.; Hughes, F.J. Site-specific differences in osteoblast phenotype, mechanical loading response and estrogen receptor-related gene expression. Mol. Cell. Endocrinol. 2018, 477, 140–147. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Moffatt, P.; Gaumond, M.H.; Salois, P.; Sellin, K.; Bessette, M.C.; Godin, E.; de Oliveira, P.T.; Atkins, G.J.; Nanci, A.; Thomas, G. Bril: A novel bone-specific modulator of mineralization. J. Bone Miner. Res. Off. J. Am. Soc. Bone Mineral. Res. 2008, 23, 1497–1508. [Google Scholar] [CrossRef] [PubMed]
- Cho, T.J.; Lee, K.E.; Lee, S.K.; Song, S.J.; Kim, K.J.; Jeon, D.; Lee, G.; Kim, H.N.; Lee, H.R.; Eom, H.H.; et al. A single recurrent mutation in the 5’-UTR of IFITM5 causes osteogenesis imperfecta type V. Am. J. Hum. Genet. 2012, 91, 343–348. [Google Scholar] [CrossRef] [Green Version]
- Semler, O.; Garbes, L.; Keupp, K.; Swan, D.; Zimmermann, K.; Becker, J.; Iden, S.; Wirth, B.; Eysel, P.; Koerber, F.; et al. A mutation in the 5’-UTR of IFITM5 creates an in-frame start codon and causes autosomal-dominant osteogenesis imperfecta type V with hyperplastic callus. Am. J. Hum. Genet. 2012, 91, 349–357. [Google Scholar] [CrossRef] [Green Version]
- Greenblatt, M.B.; Ono, N.; Ayturk, U.M.; Debnath, S.; Lalani, S. The unmixing problem: A guide to applying single-cell RNA sequencing to bone. J. Bone Miner. Res. Off. J. Am. Soc. Bone Mineral. Res. 2019, 34, 1207–1219. [Google Scholar] [CrossRef]
- Aubin, I.; Adams, C.P.; Opsahl, S.; Septier, D.; Bishop, C.E.; Auge, N.; Salvayre, R.; Negre-Salvayre, A.; Goldberg, M.; Guenet, J.L.; et al. A deletion in the gene encoding sphingomyelin phosphodiesterase 3 (Smpd3) results in osteogenesis and dentinogenesis imperfecta in the mouse. Nat. Genet. 2005, 37, 803–805. [Google Scholar] [CrossRef]
- Jin, Y.R.; Stohn, J.P.; Wang, Q.; Nagano, K.; Baron, R.; Bouxsein, M.L.; Rosen, C.J.; Adarichev, V.A.; Lindner, V. Inhibition of osteoclast differentiation and collagen antibody-induced arthritis by CTHRC1. Bone 2017, 97, 153–167. [Google Scholar] [CrossRef]
- Cooling, L. Blood groups in infection and host susceptibility. Clin. Microbiol Rev. 2015, 28, 801–870. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Zimmerman, S.M.; Heard-Lipsmeyer, M.E.; Dimori, M.; Thostenson, J.D.; Mannen, E.M.; O’Brien, C.A.; Morello, R. Loss of RANKL in osteocytes dramatically increases cancellous bone mass in the osteogenesis imperfecta mouse (oim). Bone Rep. 2018, 9, 61–73. [Google Scholar] [CrossRef]
- Bolger, A.M.; Lohse, M.; Usadel, B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 2014, 30, 2114–2120. [Google Scholar] [CrossRef] [Green Version]
- Trapnell, C.; Hendrickson, D.G.; Sauvageau, M.; Goff, L.; Rinn, J.L.; Pachter, L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat. Biotechnol. 2013, 31, 46–53. [Google Scholar] [CrossRef] [PubMed]
- Anders, S.; Pyl, P.T.; Huber, W. HTSeq—A Python framework to work with high-throughput sequencing data. Bioinformatics 2015, 31, 166–169. [Google Scholar] [CrossRef] [PubMed]
- Anders, S.; Huber, W. Differential expression analysis for sequence count data. Genome Biol. 2010, 11, R106. [Google Scholar] [CrossRef] [Green Version]
- DeLuca, D.S.; Levin, J.Z.; Sivachenko, A.; Fennell, T.; Nazaire, M.D.; Williams, C.; Reich, M.; Winckler, W.; Getz, G. RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics 2012, 28, 1530–1532. [Google Scholar] [CrossRef]
- Subramanian, A.; Tamayo, P.; Mootha, V.K.; Mukherjee, S.; Ebert, B.L.; Gillette, M.A.; Paulovich, A.; Pomeroy, S.L.; Golub, T.R.; Lander, E.S.; et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 2005, 102, 15545–15550. [Google Scholar] [CrossRef] [Green Version]
- Zhang, B.; Kirov, S.; Snoddy, J. WebGestalt: An integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res. 2005, 33, W741–W748. [Google Scholar] [CrossRef]
- Liao, Y.; Wang, J.; Jaehnig, E.J.; Shi, Z.; Zhang, B. WebGestalt 2019: Gene set analysis toolkit with revamped UIs and APIs. Nucleic Acids Res. 2019, 47, W199–W205. [Google Scholar] [CrossRef] [PubMed] [Green Version]
Gene | Description | Fold Change | p |
---|---|---|---|
Cyp2e1 | Cytochrome P450, family 2, subfamily e, polypeptide 1 | 4.25 | 0.009 |
Bglap | Bone gamma carboxyglutamate protein | 3.44 | <0.001 |
Bglap2 | Bone gamma-carboxyglutamate protein 2 | 3.14 | <0.001 |
Cyp2f2 | Cytochrome P450, family 2, subfamily f, polypeptide 2 | 2.90 | <0.001 |
Ighg2c | 2.87 | 0.02 | |
Slc13a5 | Solute carrier family 13, member 5 | 2.59 | <0.001 |
Creb3l3 | cAMP responsive element binding protein 3-like 3 | 2.55 | 0.003 |
Tpsb2 | Tryptase beta 2 | 2.38 | 0.003 |
Col11a1 | Collagen, type XI, alpha 1 | 2.34 | 0.006 |
Col11a2 | Collagen, type XI, alpha 2 | 2.31 | 0.015 |
Lipc | Lipase, hepatic | 2.30 | <0.001 |
Cgref1 | Cell growth regulator with EF hand domain 1 | 2.29 | <0.001 |
Ifi27l2a | Interferon, alpha-inducible protein 27 like 2A | 2.24 | <0.001 |
Smpd3 | Sphingomyelin phosphodiesterase 3, neutral | 2.22 | <0.001 |
Ifitm5 | Interferon induced transmembrane protein 5 | 2.19 | <0.001 |
Ctsw | Cathepsin W | 2.14 | 0.04 |
Kazald1 | Kazal-type serine peptidase inhibitor domain 1 | 2.14 | <0.001 |
Cthrc1 | Collagen triple helix repeat containing 1 | 2.05 | <0.001 |
Rerg | RAS-like, estrogen-regulated, growth-inhibitor | 2.05 | 0.002 |
Adamts14 | A disintegrin-like and metallopeptidase with thrombospondin type 1 motif, 14 | 1.98 | <0.001 |
Gene | Description | Fold Change | p |
---|---|---|---|
Mt2 | Metallothionein 2 | 7.32 | 0.004 |
Edn1 | Endothelin 1 | 7.10 | <0.001 |
Aspg | Asparaginase | 6.37 | 0.002 |
Slc10a6 | Solute carrier family 10, member 6 | 5.71 | <0.001 |
Npas2 | Neuronal PAS domain protein 2 | 5.51 | <0.001 |
Cyp2e1 | Cytochrome P450, family 2, subfamily e, polypeptide 1 | 5.51 | <0.001 |
Angptl7 | Angiopoietin-like 7 | 5.27 | 0.005 |
Ddit4 | DNA-damage-inducible transcript 4 | 4.99 | <0.001 |
Arl4d | ADP-ribosylation factor-like 4D | 4.74 | <0.001 |
Cdkn1a | NUS1 dehydrodolichyl diphosphate synthase subunit | 4.74 | <0.001 |
Sult5a1 | Sulfotransferase family 5A, member 1 | 4.71 | <0.001 |
Cxcl13 | Chemokine (C-X-C motif) ligand 13 | 4.69 | <0.001 |
Zbtb16 | Zinc finger and BTB domain containing 16 | 4.67 | <0.001 |
Adamts15 | A disintegrin-like and metallopeptidase with thrombospondin type 1 motif, 15 | 4.66 | <0.001 |
Igfbp3 | Insulin-like growth factor binding protein 3 | 4.35 | <0.001 |
Mt1 | Metallothionein 1 | 4.35 | <0.001 |
Stc2 | Stanniocalcin 2 | 4.35 | <0.001 |
Syt13 | Synaptotagmin XIII | 4.33 | <0.001 |
Itga10 | Integrin, alpha 10 | 4.32 | <0.001 |
Adm | Adrenomedullin | 4.31 | 0.001 |
Gene | Description | Jrt | oim | ||
---|---|---|---|---|---|
Fold Change | p | Fold Change | p | ||
Upregulated | |||||
Cyp2e1 | Cytochrome P450, family 2, subfamily e, polypeptide 1 | 4.25 | 0.009 | 5.51 | <0.001 |
Slc13a5 | Solute carrier family 13, member 5 | 2.29 | <0.001 | 3.30 | <0.001 |
Cgref1 | Cell growth regulator with EF hand domain 1 | 2.05 | <0.001 | 2.87 | <0.001 |
Smpd3 | Sphingomyelin phosphodiesterase 3, neutral | 2.59 | <0.001 | 2.70 | 0.02 |
Ifitm5 | Interferon induced transmembrane protein 5 | 2.05 | <0.001 | 2.54 | <0.001 |
Cthrc1 | Collagen triple helix repeat containing 1 | 2.22 | <0.001 | 2.51 | <0.001 |
Rerg | RAS-like, estrogen-regulated, growth-inhibitor | 2.19 | 0.002 | 2.09 | <0.001 |
Downregulated | |||||
Gypa | Glycophorin A | 0.45 | <0.001 | 0.44 | 0.01 |
Gene Set | Description | FDR | Genes in Set |
---|---|---|---|
Upregulated | |||
GO:0001503 | ossification | <0.001 | Alpl; Aspn; Bglap; Bglap2; Bmp1; Bmp3; Bmp8a; Col11a1; Col11a2; Creb3l1; Cthrc1; Dkk1; Dmp1; Gdf10; Gja1; Ifitm5; Igsf10; Kazald1; Lrrc17; Mepe; Omd; Ostn; P3h1; Phex; Phospho1; Pth1r; Smad6; Sp7; Tmem119; Twist1 |
Downregulated | |||
GO:0030099 | myeloid cell differentiation | <0.001 | Alas2; Ank1; Bpgm; Car2; Dmtn; Epb42; Hmgb2; Myb; Rhag; Rhd; Spib; Tal1; Trim10; Trim58; Zfpm1 |
Gene Set | FDR | Genes in Set |
---|---|---|
Upregulated | ||
GO:0001503 (ossification) | <0.001 | Acvr1; Alpl; Ank; Ano6; Atraid; Axin2; Bcl2; Bmp1; Bmp2; Bmp3; Bmp4; Bmp8a; Bmpr1a; Bmpr2; Cd276; Cebpb; Cebpd; Chrdl1; Clec11a; Col11a1; Col11a2; Col13a1; Col5a2; Creb3l1; Cthrc1; Dchs1; Ddr2; Dlx5; Dmp1; Ecm1; Epha2; Ext1; Ext2; Fam20c; Fat4; Fgfr1; Fgfr2; Fndc3b; Foxc1; Foxc2; Fzd1; Gabbr1; Gja1; Gli1; Gpc3; Gpm6b; Gpnmb; Hspg2; Ibsp; Id3; Id4; Ifitm5; Igf2; Igfbp3; Igsf10; Il6st; Intu; Jag1; Kazald1; Kremen1; Lgr4; Lrp4; Lrp5; Lrp6; Lrrc17; Ltbp3; Mepe; Mgp; Mia3; Mmp14; Mmp2; Mn1; Nab2; Nog; Npnt; Npr2; Omd; P3h1; Phex; Pkdcc; Ptch1; Pth1r; Ptk2; S1pr1; Sfrp1; Sfrp2; Sh3pxd2b; Sik3; Six2; Smad1; Smad6; Smo; Smoc1; Snai1; Sost; Sp7; Tgfb2; Tgfbr3; Thbs3; Thra; Tmem119; Tnfsf11; Tnn; Trpm4; Twist1; Twsg1; Wnt10b; Wwtr1; Zbtb16; Zhx3 |
Downregulated | ||
GO:0030099 (myeloid cell differentiation) | <0.001 | B2m; Adar; Fes; Rcor1; G6pdx; Nrros; Itgb3; Casp8; Tyrobp; Ubd; Creb1; Pde1b; Tmem14c; Fcer1g; Pf4; Fli1; Wdr1; Tcf3; Senp1; Pml; Atpif1; Plscr1; Myh9; Pknox1; Ubash3b; Rb1; Spi1; Casp3; Kit; Adam8; Nckap1l; Smarca4; Ets1; Tspan2; Eif2ak1; Hcls1; Isg15; Ptbp3; Pabpc4; Inpp5d; Cd300lf; Lyn; Clec2i; Ptk2b; Ankle1; Mpl; Ltf; Ncapg2; Hmgb3; Clec1b; Ptpn6; Pilrb1; Cdk6; Irf8; Clec5a; Prtn3; Tfrc; Tesc; Ceacam1; Cd101; Lmo2; Irf4; Csf3r; Hhex; Stap1; Cebpe; Bpgm; Hmgb2; Ank1; Gfi1b; Gata1; Spib; Dmtn; Zfpm1; Rhd; Alas2; Rhag; Tal1; Dyrk3; Car2; Myb; Epb42; Trim10; Trim58 |
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. |
© 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Moffatt, P.; Boraschi-Diaz, I.; Marulanda, J.; Bardai, G.; Rauch, F. Calvaria Bone Transcriptome in Mouse Models of Osteogenesis Imperfecta. Int. J. Mol. Sci. 2021, 22, 5290. https://doi.org/10.3390/ijms22105290
Moffatt P, Boraschi-Diaz I, Marulanda J, Bardai G, Rauch F. Calvaria Bone Transcriptome in Mouse Models of Osteogenesis Imperfecta. International Journal of Molecular Sciences. 2021; 22(10):5290. https://doi.org/10.3390/ijms22105290
Chicago/Turabian StyleMoffatt, Pierre, Iris Boraschi-Diaz, Juliana Marulanda, Ghalib Bardai, and Frank Rauch. 2021. "Calvaria Bone Transcriptome in Mouse Models of Osteogenesis Imperfecta" International Journal of Molecular Sciences 22, no. 10: 5290. https://doi.org/10.3390/ijms22105290
APA StyleMoffatt, P., Boraschi-Diaz, I., Marulanda, J., Bardai, G., & Rauch, F. (2021). Calvaria Bone Transcriptome in Mouse Models of Osteogenesis Imperfecta. International Journal of Molecular Sciences, 22(10), 5290. https://doi.org/10.3390/ijms22105290