Single-cell differences in matrix gene expression do not predict matrix deposition

Nature Communications

Volumn 7, Issue , 2016, Pages

  Cote, Allison J ^a   McLeod, Claire M ^a,b,c   Farrell, Megan J ^a,b   McClanahan, Patrick D ^a   Dunagin, Margaret C ^a   Raj, Arjun ^a   Mauck, Robert L ^a,b,c  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

^c VETERANS AFFAIRS MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AGGRECAN; LIPOPROTEIN LIPASE; MESSENGER RNA; OSTEOPONTIN; RNA; TRANSCRIPTOME; TRANSFORMING GROWTH FACTOR BETA; BIOLOGICAL MARKER;

CELLS AND CELL COMPONENTS; GENE EXPRESSION; GENETIC DIFFERENTIATION; GENETIC MARKER; HETEROGENEITY; PHENOTYPE; RNA;

ANIMAL CELL; ARTICLE; BOVINE; CARTILAGE CELL; CELL DIFFERENTIATION; FLUORESCENCE IN SITU HYBRIDIZATION; GENE EXPRESSION; IN VITRO STUDY; MESENCHYMAL STEM CELL; MICROSCOPY; NONHUMAN; PHENOTYPE; PROTEIN EXPRESSION; ANIMAL; CHONDROCYTE; EXTRACELLULAR MATRIX; GENE EXPRESSION REGULATION; MESENCHYMAL STROMA CELL; METABOLISM; PHYSIOLOGY;

ANIMALS; BIOMARKERS; CATTLE; CELL DIFFERENTIATION; CHONDROCYTES; EXTRACELLULAR MATRIX; GENE EXPRESSION REGULATION; IN SITU HYBRIDIZATION, FLUORESCENCE; MESENCHYMAL STROMAL CELLS; RNA, MESSENGER;

EID: 84960155525     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms10865     Document Type: Article

References (70)

1. Pittenger, M. F. et al. Multilineage potential of adult human mesenchymal stem cells. Science 284, 143-147 (1999).
2. Colter, D. C., Sekiya, I. & Prockop, D. J. Identification of a subpopulation of rapidly self-renewing and multipotential adult stem cells in colonies of human marrow stromal cells. Proc. Natl Acad. Sci. USA 98, 7841-7845 (2001).
3. Phinney, D. G. Functional heterogeneity of mesenchymal stem cells: implications for cell therapy. J. Cell. Biochem. 113, 2806-2812 (2012).
4. González-Cruz, R. D., Fonseca, V. C. & Darling, E. M. Cellular mechanical properties reflect the differentiation potential of adipose-derived mesenchymal stem cells. Proc. Natl Acad. Sci. USA 109, E1523-E1529 (2012).
5. Mareddy, S., Crawford, R., Brooke, G. & Xiao, Y. Clonal isolation and characterization of bone marrow stromal cells from patients with osteoarthritis. Tissue Eng. 13, 819-829 (2007).
6. Muraglia, A., Cancedda, R. & Quarto, R. Clonal mesenchymal progenitors from human bone marrow differentiate in vitro according to a hierarchical model. J. Cell Sci. 113, 1161-1166 (2000).
7. Russell, K. C. et al. In vitro high-capacity assay to quantify the clonal heterogeneity in trilineage potential of mesenchymal stem cells reveals a complex hierarchy of lineage commitment. Stem Cells 28, 788-798 (2010).
8. Song, L. Transdifferentiation potential of human mesenchymal stem cells derived from bone marrow. FASEB J. 18, 980-982 (2004).
9. Ponce, M. L. et al. Coexpression of osteogenic and adipogenic differentiation markers in selected subpopulations of primary human mesenchymal progenitor cells. J. Cell. Biochem. 104, 1342-1355 (2008).
10. Altschuler, S. J. & Wu, L. F. Cellular heterogeneity: do differences make a difference? Cell 141, 559-563 (2010).
11. Nimmo, R. A., May, G. E. & Enver, T. Primed and ready: understanding lineage commitment through single cell analysis. Trends Cell Biol. 25, 459-467 (2015).
12. Itzkovitz, S. & van Oudenaarden, A. Validating transcripts with probes and imaging technology. Nat. Methods 8, S12-S19 (2011).
13. Junker, J. P. & van Oudenaarden, A. Every cell is special: genome-wide studies add a new dimension to single-cell biology. Cell 157, 8-11 (2014).
14. Crosetto, N., Bienko, M. & van Oudenaarden, A. Spatially resolved transcriptomics and beyond. Nat. Rev. Genet. 16, 57-66 (2015).
15. Marble, H. D., Sutermaster, B. A., Kanthilal, M., Fonseca, V. C. & Darling, E. M. Gene expression-based enrichment of live cells from adipose tissue produces subpopulations with improved osteogenic potential. Stem Cell Res. Ther. 5, 145 (2014).
16. Huang, A. H., Farrell, M. J. & Mauck, R. L. Mechanics and mechanobiology of mesenchymal stem cell-based engineered cartilage. J. Biomech. 43, 128-136 (2010).
17. Femino, A. M., Fay, F. S., Fogarty, K. & Singer, R. H. Visualization of single RNA transcripts in situ. Science 280, 585-590 (1998).
18. Raj, A., van den Bogaard, P., Rifkin, S. A., van Oudenaarden, A. & Tyagi, S. Imaging individual mRNA molecules using multiple singly labeled probes. Nat. Methods 5, 877-879 (2008).
19. Frank, O. et al. Real-time quantitative RT-PCR analysis of human bone marrow stromal cells during osteogenic differentiation in vitro. J. Cell. Biochem. 85, 737-746 (2002).
20. Pelttari, K., Steck, E. & Richter, W. The use of mesenchymal stem cells for chondrogenesis. Injury 39 Suppl 1 S58-S65 (2008).
21. Sekiya, I., Larson, B. L., Vuoristo, J. T., Cui, J.-G. & Prockop, D. J. Adipogenic differentiation of human adult stem cells from bone marrow stroma (MSCs). J. Bone Miner. Res. 19, 256-264 (2003).
22. Puetzer, J. L., Petitte, J. N. & Loboa, E. G. Comparative review of growth factors for induction of three-dimensional in vitro chondrogenesis in human mesenchymal stem cells isolated from bone marrow and adipose tissue. Tissue Eng. B Rev. 16, 435-444 (2010).
23. Chan, C. K. F. et al. Identification and specification of the mouse skeletal stem cell. Cell 160, 285-298 (2015).
24. Barry, F., Boynton, R. E., Liu, B. & Murphy, J. M. Chondrogenic differentiation of mesenchymal stem cells from bone marrow: differentiationdependent gene expression of matrix components. Exp. Cell Res. 268, 189-200 (2001).
25. Mackay, A. M. et al. Chondrogenic differentiation of cultured human mesenchymal stem cells from marrow. Tissue Eng. 4, 415-428 (1998).
26. Vertel, B. M. The ins and outs of aggrecan. Trends Cell Biol. 5, 458-464 (1995).
27. Ma, B. et al. Gene expression profiling of dedifferentiated human articular chondrocytes in monolayer culture. Osteoarthritis Cartilage 21, 599-603 (2013).
28. Lin, Z. et al. Gene expression profiles of human chondrocytes during passaged monolayer cultivation. J. Orthop. Res. 26, 1230-1237 (2008).
29. Darling, E. M. & Athanasiou, K. A. Rapid phenotypic changes in passaged articular chondrocyte subpopulations. J. Orthop. Res. 23, 425-432 (2005).
30. Cheng, T., Maddox, N. C., Wong, A. W., Rahnama, R. & Kuo, A. C. Comparison of gene expression patterns in articular cartilage and dedifferentiated articular chondrocytes. J. Orthop. Res. 30, 234-245 (2012).
31. Elima, K. & Vuorio, E. Expression of mRNAs for collagens and other matrix components in dedifferentiating and redifferentiating human chondrocytes in culture. FEBS Lett. 258, 195-198 (1989).
32. Glowacki, J., Trepman, E. & Folkman, J. Cell shape and phenotypic expression in chondrocytes. Proc. Soc. Exp. Biol. Med. 172, 93-98 (1983).
33. Kumar, D. & Lassar, A. B. The transcriptional activity of Sox9 in chondrocytes is regulated by RhoA signaling and actin polymerization. Mol. Cell. Biol. 29, 4262-4273 (2009).
34. Schiltz, J. R., Mayne, R. & Holtzer, H. The synthesis of collagen and glycosaminoglycans by dedifferentiated chondroblasts in culture. Differentiation 1, 97-108 (1973).
35. Benya, P. D. & Shaffer, J. D. Dedifferentiated chondrocytes reexpress the differentiated collagen phenotype when cultured in agarose gels. Cell 30, 215-224 (1982).
36. Bonaventure, J. et al. Reexpression of cartilage-specific genes by dedifferentiated human articular chondrocytes cultured in alginate beads. Exp. Cell Res. 212, 97-104 (1994).
37. Stokes, D. G. et al. Regulation of type-II collagen gene expression during human chondrocyte de-differentiation and recovery of chondrocyte-specific phenotype in culture involves Sry-type high-mobility-group box (SOX) transcription factors. Biochem. J. 360, 461-470 (2001).
38. Padovan-Merhar, O. et al. Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms. Mol. Cell 58, 339-352 (2015).
39. Larsson, H. M. et al. Sorting live stem cells based on Sox2 mRNA expression. PLoS ONE 7, e49874 (2012).
40. King, F. W., Liszewski, W., Ritner, C. & Bernstein, H. S. High-throughput tracking of pluripotent human embryonic stem cells with dual fluorescence resonance energy transfer molecular beacons. Stem Cells Dev. 20, 475-484 (2011).
41. Lahm, H. et al. Live fluorescent RNA-based detection of pluripotency gene expression in embryonic and induced pluripotent stem cells of different species. Stem Cells 33, 392-402 (2015).
42. Raj, A., Peskin, C. S., Tranchina, D., Vargas, D. Y. & Tyagi, S. Stochastic mRNA synthesis in mammalian cells. PLoS Biol. 4, e309 (2006).
43. Chubb, J. R., Trcek, T., Shenoy, S. M. & Singer, R. H. Transcriptional pulsing of a developmental gene. Curr. Biol. 16, 1018-1025 (2006).
44. Golding, I., Paulsson, J., Zawilski, S. M. & Cox, E. C. Real-time kinetics of gene activity in individual bacteria. Cell 123, 1025-1036 (2005).
45. Raj, A. & van Oudenaarden, A. Single-molecule approaches to stochastic gene expression. Annu. Rev. Biophys. 38, 255-270 (2009).
46. Suter, D. M. et al. Mammalian genes are transcribed with widely different bursting kinetics. Science 332, 472-474 (2011).
47. Zenklusen, D., Larson, D. R. & Singer, R. H. Single-RNA counting reveals alternative modes of gene expression in yeast. Nat. Struct. Mol. Biol. 15, 1263-1271 (2008).
48. Dar, R. D. et al. Transcriptional burst frequency and burst size are equally modulated across the human genome. Proc. Natl Acad. Sci. USA 109, 17454-17459 (2012).
49. Octavio, L. M., Gedeon, K. & Maheshri, N. Epigenetic and conventional regulation is distributed among activators of FLO11 allowing tuning of population-level heterogeneity in its expression. PLoS Genet. 5, e1000673 (2009).
50. Zopf, C. J., Quinn, K., Zeidman, J. & Maheshri, N. Cell-cycle dependence of transcription dominates noise in gene expression. PLoS Comput. Biol. 9, e1003161 (2013).
51. Gandhi, S. J., Zenklusen, D., Lionnet, T. & Singer, R. H. Transcription of functionally related constitutive genes is not coordinated. Nat. Struct. Mol. Biol. 18, 27-34 (2011).
52. Shah, K. & Tyagi, S. Barriers to transmission of transcriptional noise in a c-fos c-jun pathway. Mol. Syst. Biol. 9, 687 (2013).
53. Molina, N. et al. Stimulus-induced modulation of transcriptional bursting in a single mammalian gene. Proc. Natl Acad. Sci. USA 110, 20563-20568 (2013).
54. Cai, L., Dalal, C. K. & Elowitz, M. B. Frequency-modulated nuclear localization bursts coordinate gene regulation. Nature 455, 485-490 (2008).
55. Kumar, R. M. et al. Deconstructing transcriptional heterogeneity in pluripotent stem cells. Nature 516, 56-61 (2014).
56. Maamar, H., Raj, A. & Dubnau, D. Noise in gene expression determines cell fate in Bacillus subtilis. Science 317, 526-529 (2007).
57. Choi, P. J., Cai, L., Frieda, K. & Xie, X. S. A stochastic single-molecule event triggers phenotype switching of a bacterial cell. Science 322, 442-446 (2008).
58. Raj, A. & van Oudenaarden, A. Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 135, 216-226 (2008).
59. Raj, A., Rifkin, S. A., Andersen, E. & van Oudenaarden, A. Variability in gene expression underlies incomplete penetrance. Nature 463, 913-918 (2010).
60. Wernet, M. F. et al. Stochastic spineless expression creates the retinal mosaic for colour vision. Nature 440, 174-180 (2006).
61. Eldar, A. & Elowitz, M. B. Functional roles for noise in genetic circuits. Nature 467, 167-173 (2010).
62. Süel, G. M., Kulkarni, R. P., Dworkin, J., Garcia-Ojalvo, J. & Elowitz, M. B. Tunability and noise dependence in differentiation dynamics. Science 315, 1716-1719 (2007).
63. Luo, W. et al. Aggrecan from start to finish. J. Bone Miner. Metab. 18, 51-56 (2000).
64. Knudson, C. B. Hyaluronan receptor-directed assembly of chondrocyte pericellular matrix. J. Cell Biol. 120, 825-834 (1993).
65. Caterson, B., Flannery, C. R., Hughes, C. E. & Little, C. B. Mechanisms involved in cartilage proteoglycan catabolism. Matrix Biol. 19, 333-344 (2000).
66. Mauck, R., Yuan, X. & Tuan, R. Chondrogenic differentiation and functional maturation of bovine mesenchymal stem cells in long-term agarose culture. Osteoarthritis Cartilage 14, 179-189 (2006).
67. Farrell, M. J., Shin, J. I., Smith, L. J. & Mauck, R. L. Functional consequences of glucose and oxygen deprivation on engineered mesenchymal stem cell-based cartilage constructs. Osteoarthritis Cartilage 23, 134-142 (2015).
68. Robin, X. et al. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinformatics 12, 77 (2011).
69. Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15-21 (2013).
70. Anders, S., Pyl, P. T. & Huber, W. HTSeq - a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166-169 (2015).