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Cellular and Molecular Bioengineering

, Volume 10, Issue 5, pp 433–450 | Cite as

Data-Modeling Identifies Conflicting Signaling Axes Governing Myoblast Proliferation and Differentiation Responses to Diverse Ligand Stimuli

  • Alexander M. Loiben
  • Sharon Soueid-Baumgarten
  • Ruth F. Kopyto
  • Debadrita Bhattacharya
  • Joseph C. Kim
  • Benjamin D. CosgroveEmail author
Article

Abstract

Introduction

Skeletal muscle tissue development and regeneration relies on the proliferation, maturation and fusion of muscle progenitor cells (myoblasts), which arise transiently from muscle stem cells (satellite cells). Following muscle damage, myoblasts proliferate and differentiate in response to temporally-varying inflammatory cytokines, growth factors, and extracellular matrix cues, which stimulate a shared network of intracellular signaling pathways. Here we present an integrated data-modeling approach to elucidate synergies and antagonisms among proliferation and differentiation signaling axes in myoblasts stimulated by regeneration-associated ligands.

Methods

We treated mouse primary myoblasts in culture with combinations of eight regeneration-associated growth factors and cytokines in mixtures that induced additive, synergistic, and antagonistic effects on myoblast proliferation and differentiation responses. For these combinatorial stimuli, we measured the activation dynamics of seven signal transduction pathways using multiplexed phosphoprotein assays and scored proliferation and differentiation responses based on expression of myogenic commitment factors to assemble a cue-signaling-response data compendium. We interrogated the relationship between these signals and responses by partial least-squares (PLS) regression modeling.

Results

Partial least-squares data-modeling accurately predicted response outcomes in cross-validation on the training compendium (cumulative R 2 = 0.96). The PLS model highlighted signaling axes that distinctly govern myoblast proliferation (MEK–ERK, Stat3) and differentiation (JNK) in response to these combinatorial cues, and we confirmed these signal-response associations with small molecule perturbations. Unexpectedly, we observed that a negative feedback circuit involving the phosphatase DUSP6/MKP-3 auto-regulates MEK–ERK signaling in myoblasts.

Conclusion

This data-modeling approach identified conflicting signaling axes that underlie muscle progenitor cell proliferation and differentiation.

Keywords

Cue-signal-response modeling Cytokines Growth factors Partial least-squares regression Skeletal muscle Systems biology 

Abbreviations

AUC

Area-under-the-curve

CSR

Cue-signal-response

DUSP

Dual specificity phosphatase

EGF

Epidermal growth factor

FGF2

Fibroblast growth factor 2

IGF1

Insulin-like growth factor 1

IL-1α

Interleukin-1α

IL-6

Interleukin-6

LIF

Leukemia inhibitor factor

MHC

Myosin heavy chain

OSM

Oncostatin-M

PC

Principal component

PLS

Partial-least squares

TNF-α

Tumor necrosis factor-α

Notes

Acknowledgments

This work was financially supported by the National Institute on Aging of the National Institutes of Health under Award R00AG042491 (to B.D.C), a US Department of Education Graduate Assistantship in Areas of National Need under Award P200A150273 (to A.M.L), a Roberta G. and John B. DeVries Graduate Fellowship (to A.M.L.), and Hunter R. Rawlings III Cornell Presidential Research Scholarship (to R.F.K. and J.K.). This work made use of the Nanobiotechnology Center (NBTC) shared research facilities at Cornell University. The authors acknowledge technical assistance from Teresa Porri, Penny Burke, Andrea De Micheli, Hilarie Sit, Muhammad Safwan Jalal, Nancy Mejia, Isabella Mercado, Ryan Ausmus, and Paula Fraczek. The authors thank the anonymous reviewers for their constructive reviews.

Animal Studies

All institutional and national guidelines for the care and use of laboratory animals were followed in a protocol approved by Cornell University’s Institutional Animal Care and Use Committee (IACUC).

Conflicts of interest

A. M. Loiben, S. Soueld-Baumgarten, D. Bhattacharya, R. F. Kopyto, J. C. Kim and B. D. Cosgrove declare that they have no conflicts of interest.

Human Studies

No human studies were carried out by the authors for this article.

Supplementary material

12195_2017_508_MOESM1_ESM.pdf (3.8 mb)
Supplementary material 1 (PDF 3868 kb)

References

  1. 1.
    Albeck, J. G., G. MacBeath, F. M. White, P. K. Sorger, D. A. Lauffenburger, and S. Gaudet. Collecting and organizing systematic sets of protein data. Nat. Rev. Mol. Cell Biol. 7(11):803–812, 2006.CrossRefGoogle Scholar
  2. 2.
    Belizario, J. E., C. C. Fontes-Oliveira, J. P. Borges, J. A. Kashiabara, and E. Vannier. Skeletal muscle wasting and renewal: a pivotal role of myokine il-6. Springerplus 5:619, 2016.CrossRefGoogle Scholar
  3. 3.
    Bennett, A. M., and N. K. Tonks. Regulation of distinct stages of skeletal muscle differentiation by mitogen-activated protein kinases. Science 278(5341):1288–1291, 1997.CrossRefGoogle Scholar
  4. 4.
    Bernet, J. D., J. D. Doles, J. K. Hall, K. Kelly Tanaka, T. A. Carter, and B. B. Olwin. P38 mapk signaling underlies a cell-autonomous loss of stem cell self-renewal in skeletal muscle of aged mice. Nat. Med. 20(3):265–271, 2014.CrossRefGoogle Scholar
  5. 5.
    Bliss, C. I. The toxicity of poisins applied jointly. Ann. Appl. Biol. 26(3):585–615, 1939.CrossRefGoogle Scholar
  6. 6.
    Broholm, C., M. J. Laye, C. Brandt, R. Vadalasetty, H. Pilegaard, B. K. Pedersen, and C. Scheele. LIF is a contraction-induced myokine stimulating human myocyte proliferation. J. Appl. Physiol. (1985) 111(1):251–259, 2011.CrossRefGoogle Scholar
  7. 7.
    Cheung, T. H., and T. A. Rando. Molecular regulation of stem cell quiescence. Nat. Rev. Mol. Cell Biol. 14(6):329–340, 2013.CrossRefGoogle Scholar
  8. 8.
    Cosgrove, B. D., L. G. Alexopoulos, T. C. Hang, B. S. Hendriks, P. K. Sorger, L. G. Griffith, and D. A. Lauffenburger. Cytokine-associated drug toxicity in human hepatocytes is associated with signaling network dysregulation. Mol. BioSyst. 6(7):1195–1206, 2010.CrossRefGoogle Scholar
  9. 9.
    Cosgrove, B. D., L. G. Alexopoulos, J. Saez-Rodriguez, L. G. Griffith, and D. A. Lauffenburger. A multipathway phosphoproteomic signaling network model of idiosyncratic drug- and inflammatory cytokine-induced toxicity in human hepatocytes. In: Conf Proc IEEE EMBS, 2009, pp. 5452–5455.Google Scholar
  10. 10.
    Cosgrove, B. D., P. M. Gilbert, E. Porpiglia, F. Mourkioti, S. P. Lee, S. Y. Corbel, M. E. Llewellyn, S. L. Delp, and H. M. Blau. Rejuvenation of the muscle stem cell population restores strength to injured aged muscles. Nat. Med. 20(3):255–264, 2014.CrossRefGoogle Scholar
  11. 11.
    Cosgrove, B. D., L. G. Griffith, and D. A. Lauffenburger. Fusing tissue engineering and systems biology toward fulfilling their promise. Cell. Mol. Bioeng. 1(1):33–41, 2008.CrossRefGoogle Scholar
  12. 12.
    Davies, S. P., H. Reddy, M. Caivano, and P. Cohen. Specificity and mechanism of action of some commonly used protein kinase inhibitors. Biochem. J. 351(Pt 1):95–105, 2000.CrossRefGoogle Scholar
  13. 13.
    Deshpande, R. S., and A. A. Spector. Modeling stem cell myogenic differentiation. Sci. Rep. 7:40639, 2017.CrossRefGoogle Scholar
  14. 14.
    Dumont, N. A., C. F. Bentzinger, M. C. Sincennes, and M. A. Rudnicki. Satellite cells and skeletal muscle regeneration. Compr. Physiol. 5(3):1027–1059, 2015.CrossRefGoogle Scholar
  15. 15.
    Fedorov, Y. V., R. S. Rosenthal, and B. B. Olwin. Oncogenic ras-induced proliferation requires autocrine fibroblast growth factor 2 signaling in skeletal muscle cells. J. Cell Biol. 152(6):1301–1305, 2001.CrossRefGoogle Scholar
  16. 16.
    Fu, X., J. Xiao, Y. Wei, S. Li, Y. Liu, J. Yin, K. Sun, H. Sun, H. Wang, Z. Zhang, B. T. Zhang, C. Sheng, H. Wang, and P. Hu. Combination of inflammation-related cytokines promotes long-term muscle stem cell expansion. Cell Res. 25(9):1082–1083, 2015.CrossRefGoogle Scholar
  17. 17.
    Gaudet, S., K. A. Janes, J. G. Albeck, E. A. Pace, D. A. Lauffenburger, and P. K. Sorger. A compendium of signals and responses triggered by prodeath and prosurvival cytokines. Mol. Cell. Proteom. 4(10):1569–1590, 2005.CrossRefGoogle Scholar
  18. 18.
    Heinemann, T., and A. Raue. Model calibration and uncertainty analysis in signaling networks. Curr. Opin. Biotechnol. 39:143–149, 2016.CrossRefGoogle Scholar
  19. 19.
    Janes, K. A. An analysis of critical factors for quantitative immunoblotting. Sci. Signal. 8(371):rs2, 2015.CrossRefGoogle Scholar
  20. 20.
    Janes, K. A., J. G. Albeck, S. Gaudet, P. K. Sorger, D. A. Lauffenburger, and M. B. Yaffe. A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis. Science 310(5754):1646–1653, 2005.CrossRefGoogle Scholar
  21. 21.
    Janes, K. A., and M. B. Yaffe. Data-driven modelling of signal-transduction networks. Nat. Rev. Mol. Cell Biol. 7(11):820–828, 2006.CrossRefGoogle Scholar
  22. 22.
    Joanisse, S., and G. Parise. Cytokine mediated control of muscle stem cell function. Adv. Exp. Med. Biol. 900:27–44, 2016.CrossRefGoogle Scholar
  23. 23.
    Jones, N. C., Y. V. Fedorov, R. S. Rosenthal, and B. B. Olwin. Erk1/2 is required for myoblast proliferation but is dispensable for muscle gene expression and cell fusion. J. Cell. Physiol. 186(1):104–115, 2001.CrossRefGoogle Scholar
  24. 24.
    Kellogg, R. A., and S. Tay. Noise facilitates transcriptional control under dynamic inputs. Cell 160(3):381–392, 2015.CrossRefGoogle Scholar
  25. 25.
    Kemp, M. L., L. Wille, C. L. Lewis, L. B. Nicholson, and D. A. Lauffenburger. Quantitative network signal combinations downstream of tcr activation can predict il-2 production response. J. Immunol. 178(8):4984–4992, 2007.CrossRefGoogle Scholar
  26. 26.
    Kreeger, P. K. Using partial least squares regression to analyze cellular response data. Sci. Signal. 6(271):tr7, 2013.CrossRefGoogle Scholar
  27. 27.
    Kumar, N., A. Wolf-Yadlin, F. M. White, and D. A. Lauffenburger. Modeling her2 effects on cell behavior from mass spectrometry phosphotyrosine data. PLoS Comput. Biol. 3(1):e4, 2007.CrossRefGoogle Scholar
  28. 28.
    Lagha, M., T. Sato, L. Bajard, P. Daubas, M. Esner, D. Montarras, F. Relaix, and M. Buckingham. Regulation of skeletal muscle stem cell behavior by pax3 and pax7. Cold Spring Harb. Symp. Quant. Biol. 73:307–315, 2008.CrossRefGoogle Scholar
  29. 29.
    Lawlor, M. A., X. Feng, D. R. Everding, K. Sieger, C. E. Stewart, and P. Rotwein. Dual control of muscle cell survival by distinct growth factor-regulated signaling pathways. Mol. Cell. Biol. 20(9):3256–3265, 2000.CrossRefGoogle Scholar
  30. 30.
    Miller-Jensen, K., K. A. Janes, J. S. Brugge, and D. A. Lauffenburger. Common effector processing mediates cell-specific responses to stimuli. Nature 448(7153):604–608, 2007.CrossRefGoogle Scholar
  31. 31.
    Mueck, T., F. Berger, I. Buechsler, R. S. Valchanova, L. Landuzzi, P. L. Lollini, K. Klingel, and B. Munz. Traf6 regulates proliferation and differentiation of skeletal myoblasts. Differentiation 81(2):99–106, 2011.CrossRefGoogle Scholar
  32. 32.
    Munoz-Canoves, P., C. Scheele, B. K. Pedersen, and A. L. Serrano. Interleukin-6 myokine signaling in skeletal muscle: a double-edged sword? FEBS J. 280:4131–4148, 2013.CrossRefGoogle Scholar
  33. 33.
    Nagata, Y., K. Ohashi, E. Wada, Y. Yuasa, M. Shiozuka, Y. Nonomura, and R. Matsuda. Sphingosine-1-phosphate mediates epidermal growth factor-induced muscle satellite cell activation. Exp. Cell Res. 326(1):112–124, 2014.CrossRefGoogle Scholar
  34. 34.
    Ogura, Y., S. M. Hindi, S. Sato, G. Xiong, S. Akira, and A. Kumar. TAK1 modulates satellite stem cell homeostasis and skeletal muscle repair. Nat. Commun. 6:10123, 2015.CrossRefGoogle Scholar
  35. 35.
    Palacios, D., C. Mozzetta, S. Consalvi, G. Caretti, V. Saccone, V. Proserpio, V. E. Marquez, S. Valente, A. Mai, S. V. Forcales, V. Sartorelli, and P. L. Puri. TNF/p38alpha/polycomb signaling to pax7 locus in satellite cells links inflammation to the epigenetic control of muscle regeneration. Cell Stem Cell 7(4):455–469, 2010.CrossRefGoogle Scholar
  36. 36.
    Patterson, K. I., T. Brummer, P. M. O’Brien, and R. J. Daly. Dual-specificity phosphatases: critical regulators with diverse cellular targets. Biochem. J. 418(3):475–489, 2009.CrossRefGoogle Scholar
  37. 37.
    Pawlikowski, B., T. Orion Vogler, K. Gadek, and B. Olwin. Regulation of skeletal muscle stem cells by fibroblast growth factors. Dev. Dyn. 2017. doi: 10.1002/dvdy.24495.Google Scholar
  38. 38.
    Price, F. D., J. von Maltzahn, C. F. Bentzinger, N. A. Dumont, H. Yin, N. C. Chang, D. H. Wilson, J. Frenette, and M. A. Rudnicki. Inhibition of JAK-STAT signaling stimulates adult satellite cell function. Nat. Med. 20(10):1174–1181, 2014.CrossRefGoogle Scholar
  39. 39.
    Puri, P. L., and V. Sartorelli. Regulation of muscle regulatory factors by DNA-binding, interacting proteins, and post-transcriptional modifications. J. Cell. Physiol. 185(2):155–173, 2000.CrossRefGoogle Scholar
  40. 40.
    Rando, T. A., and H. M. Blau. Primary mouse myoblast purification, characterization, and transplantation for cell-mediated gene therapy. J. Cell Biol. 125(6):1275–1287, 1994.CrossRefGoogle Scholar
  41. 41.
    Rudnicki, M. A., F. Le Grand, I. McKinnell, and S. Kuang. The molecular regulation of muscle stem cell function. CSH Symp. Quant. Biol. 73:323–331, 2008.CrossRefGoogle Scholar
  42. 42.
    Serra, C., D. Palacios, C. Mozzetta, S. V. Forcales, I. Morantte, M. Ripani, D. R. Jones, K. Du, U. S. Jhala, C. Simone, and P. L. Puri. Functional interdependence at the chromatin level between the MKK6/p38 and IGF1/PI3K/AKT pathways during muscle differentiation. Mol. Cell 28(2):200–213, 2007.CrossRefGoogle Scholar
  43. 43.
    Tidball, J. G. Regulation of muscle growth and regeneration by the immune system. Nat. Rev. Immunol. 17(3):165–178, 2017.CrossRefGoogle Scholar
  44. 44.
    Tierney, M. T., T. Aydogdu, D. Sala, B. Malecova, S. Gatto, P. L. Puri, L. Latella, and A. Sacco. Stat3 signaling controls satellite cell expansion and skeletal muscle repair. Nat. Med. 20(10):1182–1186, 2014.CrossRefGoogle Scholar
  45. 45.
    Wales, S., S. Hashemi, A. Blais, and J. C. McDermott. Global MEF2 target gene analysis in cardiac and skeletal muscle reveals novel regulation of DUSP6 by p38MAPK-MEF2 signaling. Nucleic Acids Res. 42(18):11349–11362, 2014.CrossRefGoogle Scholar
  46. 46.
    Xiao, F., H. Wang, X. Fu, Y. Li, K. Ma, L. Sun, X. Gao, and Z. Wu. Oncostatin m inhibits myoblast differentiation and regulates muscle regeneration. Cell Res. 21(2):350–364, 2011.CrossRefGoogle Scholar
  47. 47.
    Yin, H., F. Price, and M. A. Rudnicki. Satellite cells and the muscle stem cell niche. Physiol. Rev. 93(1):23–67, 2013.CrossRefGoogle Scholar

Copyright information

© Biomedical Engineering Society 2017

Authors and Affiliations

  1. 1.Meinig School of Biomedical EngineeringCornell UniversityIthacaUSA
  2. 2.Biological Sciences, College of Agriculture and Life SciencesCornell UniversityIthacaUSA
  3. 3.Graduate Field of Biochemistry, Molecular and Cell Biology, Department of Molecular Biology and GeneticsCornell UniversityIthacaUSA

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