Epigenetic modulations rendering cell-to-cell variability and phenotypic metastability

Shawal Spencer; Agustina Gugliotta; Natascha Gödecke; Hansjörg Hauser; Dagmar Wirth

doi:10.1016/j.jgg.2016.05.008

Volume 43 Issue 8

Aug. 2016

Turn off MathJax

Article Contents

Article Navigation > Journal of Genetics and Genomics > 2016 > 43(8): 503-511

PDF( 2170 KB)

Epigenetic modulations rendering cell-to-cell variability and phenotypic metastability

doi: 10.1016/j.jgg.2016.05.008

a
Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, Braunschweig 38124, Germany
b
Experimental Hematology, Hannover Medical School, Hannover 30625, Germany

More Information

Corresponding author: E-mail address: dagmar.wirth@helmholtz-hzi.de (Dagmar Wirth)
Received Date: 2016-01-08
Accepted Date: 2016-05-25
Rev Recd Date: 2016-05-12

Available Online: 2016-05-27

Publish Date: 2016-08-20

Abstract

Abstract

Tumor cells display phenotypic plasticity and heterogeneity due to genetic and epigenetic variations which limit the predictability of therapeutic interventions. Chromatin modifications can arise stochastically but can also be a consequence of environmental influences such as the microenvironment of cancer cells. A better understanding of the impact and dynamics of epigenetic modulation at defined chromosomal sites is required to get access to the underlying mechanisms. We investigated the epigenetic modulations leading to cell-to-cell heterogeneity in a tumor cell line model. To this end, we analyzed expression variance in 80 genetically uniform cell populations having a single-copy reporter randomly integrated in the genome. Single-cell analysis showed high intraclonal heterogeneity. Epigenetic characterization revealed that expression heterogeneity was accompanied by differential histone marks whereas contribution of DNA methylation could be excluded. Strikingly, some clones revealed a highly dynamic, stochastically altered chromatin state of the transgene cassette which was accompanied with a metastable expression pattern. In contrast, other clones represented a robust chromatin state of the transgene cassette with a stable expression pattern. Together, these results elucidate locus-specific epigenetic modulation in gene expression that contributes to phenotypic heterogeneity of cells and might account for cellular plasticity.
- Intraclonal heterogeneity,
- Epigenetic regulation,
- DNA methylation,
- Differential histone marks,
- Metastable expression

Present address: Cell Culture Laboratory, Faculty of Biochemistry and Biological Sciences, National University of the Littoral, Santa Fe 3000, Argentina.

FullText(HTML)

References(59)

References

[1]	Angel, A., Song, J., Dean, C. et al. A polycomb-based switch underlying quantitative epigenetic memory Nature, 476 (2011),pp. 105-108
[2]	Bachman, K.E., Park, B.H., Rhee, I. et al. Histone modifications and silencing prior to DNA methylation of a tumor suppressor gene Cancer Cell, 3 (2003),pp. 89-95
[3]	Botezatu, L., Sievers, S., Gama-Norton, L. et al. Genetic aspects of cell line development from a synthetic biology perspective Adv. Biochem. Eng. Biotechnol., 127 (2012),pp. 251-284
[4]	Boudadi, E., Stower, H., Halsall, J.A. et al. The histone deacetylase inhibitor sodium valproate causes limited transcriptional change in mouse embryonic stem cells but selectively overrides polycomb-mediated Hoxb silencing Epigenetics Chromatin, 6 (2013),p. 11
[5]	Buck, M.J., Raaijmakers, L.M., Ramakrishnan, S. et al. Alterations in chromatin accessibility and DNA methylation in clear cell renal cell carcinoma Oncogene, 33 (2014),pp. 4961-4965
[6]	Butta, N., Larrucea, S., Alonso, S. et al. Role of transcription factor Sp1 and CpG methylation on the regulation of the human podocalyxin gene promoter BMC Mol. Biol., 7 (2006),p. 17
[7]	Cohen, Y., Merhavi-Shoham, E., Avraham, R.B. et al. Hypermethylation of CpG island loci of multiple tumor suppressor genes in retinoblastoma Exp. Eye Res., 86 (2008),pp. 201-206
[8]	Connolly, L.R., Smith, K.M., Freitag, M. The Fusarium graminearum histone H3 K27 methyltransferase KMT6 regulates development and expression of secondary metabolite gene clusters PLoS Genet., 9 (2013),p. e1003916
[9]	Corish, P., Tyler-Smith, C. Attenuation of green fluorescent protein half-life in mammalian cells Protein Eng., 12 (1999),pp. 1035-1040
[10]	Coulon, A., Chow, C.C., Singer, R.H. et al. Eukaryotic transcriptional dynamics: from single molecules to cell populations Nat. Rev. Genet., 14 (2013),pp. 572-584
[11]	Crider, K.S., Yang, T.P., Berry, R.J. et al. Folate and DNA methylation: a review of molecular mechanisms and the evidence for folate's role Adv. Nutr., 3 (2012),pp. 21-38
[12]	Cui, P., Li, J., Sun, B. et al. A quantitative analysis of the impact on chromatin accessibility by histone modifications and binding of transcription factors in DNase I hypersensitive sites Biomed. Res. Int., 2013 (2013),p. 914971
[13]	Dar, R.D., Razooky, B.S., Singh, A. et al. Transcriptional burst frequency and burst size are equally modulated across the human genome Proc. Natl. Acad. Sci. U. S. A., 109 (2012),pp. 17454-17459
[14]	Debeb, B.G., Zhang, X., Krishnamurthy, S. et al. Characterizing cancer cells with cancer stem cell-like features in 293T human embryonic kidney cells Mol. Cancer, 9 (2010),p. 180
[15]	Dokmanovic, M., Clarke, C., Marks, P.A. Histone deacetylase inhibitors: overview and perspectives Mol. Cancer Res., 5 (2007),pp. 981-989
[16]	Ellis, J. Silencing and variegation of gammaretrovirus and lentivirus vectors Hum. Gene Ther., 16 (2005),pp. 1241-1246
[17]	Esteller, M. CpG island hypermethylation and tumor suppressor genes: a booming present, a brighter future Oncogene, 21 (2002),pp. 5427-5440
[18]	Eszterhas, S.K., Bouhassira, E.E., Martin, D.I. et al. Transcriptional interference by independently regulated genes occurs in any relative arrangement of the genes and is influenced by chromosomal integration position Mol. Cell. Biol., 22 (2002),pp. 469-479
[19]	Falvo, J.V., Jasenosky, L.D., Kruidenier, L. et al. Epigenetic control of cytokine gene expression: regulation of the TNF/LT locus and T helper cell differentiation Adv. Immunol., 118 (2013),pp. 37-128
[20]	Feinberg, A.P., Ohlsson, R., Henikoff, S. The epigenetic progenitor origin of human cancer Nat. Rev. Genet., 7 (2006),pp. 21-33
[21]	Gacek, A., Strauss, J. The chromatin code of fungal secondary metabolite gene clusters Appl. Microbiol. Biotechnol., 95 (2012),pp. 1389-1404
[22]	Gama-Norton, L., Botezatu, L., Herrmann, S. et al. Lentivirus production is influenced by SV40 large T-antigen and chromosomal integration of the vector in HEK293 cells Hum. Gene Ther., 22 (2011),pp. 1269-1279
[23]	Garcia-Ramirez, M., Rocchini, C., Ausio, J. Modulation of chromatin folding by histone acetylation J. Biol. Chem., 270 (1995),pp. 17923-17928
[24]	Ghavifekr Fakhr, M., Farshdousti Hagh, M., Shanehbandi, D. et al. DNA methylation pattern as important epigenetic criterion in cancer Genet. Res. Int., 2013 (2013),p. 317569
[25]	Grassi, G., Maccaroni, P., Meyer, R. et al. Inhibitors of DNA methylation and histone deacetylation activate cytomegalovirus promoter-controlled reporter gene expression in human glioblastoma cell line U87 Carcinogenesis, 24 (2003),pp. 1625-1635
[26]	Guillemette, B., Drogaris, P., Lin, H.H. et al. H3 lysine 4 is acetylated at active gene promoters and is regulated by H3 lysine 4 methylation PLoS Genet., 7 (2011),p. e1001354
[27]	Hsu, C.C., Li, H.P., Hung, Y.H. et al. Targeted methylation of CMV and E1A viral promoters Biochem. Biophys. Res. Commun., 402 (2010),pp. 228-234
[28]	Huang, S. Genetic and non-genetic instability in tumor progression: link between the fitness landscape and the epigenetic landscape of cancer cells Cancer Metastasis Rev., 32 (2013),pp. 423-448
[29]	Jaenisch, R., Bird, A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals Nat. Genet., 33 (2003),pp. 245-254
[30]	Kaise, M., Yamasaki, T., Yonezawa, J. et al. Helicobacter, 13 (2008),pp. 35-41
[31]	Kirmizis, A., Bartley, S.M., Kuzmichev, A. et al. Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27 Genes Dev., 18 (2004),pp. 1592-1605
[32]	Knoechel, B., Roderick, J.E., Williamson, K.E. et al. An epigenetic mechanism of resistance to targeted therapy in T cell acute lymphoblastic leukemia Nat. Genet., 46 (2014),pp. 364-370
[33]	Krishnan, M., Park, J.M., Cao, F. et al. Effects of epigenetic modulation on reporter gene expression: implications for stem cell imaging FASEB J., 20 (2006),pp. 106-108
[34]	Lewis, A., Mitsuya, K., Umlauf, D. et al. Imprinting on distal chromosome 7 in the placenta involves repressive histone methylation independent of DNA methylation Nat. Genet., 36 (2004),pp. 1291-1295
[35]	Li, G.M. Decoding the histone code: role of H3K36me3 in mismatch repair and implications for cancer susceptibility and therapy Cancer Res., 73 (2013),pp. 6379-6383
[36]	Liu, W.B., Ao, L., Zhou, Z.Y. et al. CpG island hypermethylation of multiple tumor suppressor genes associated with loss of their protein expression during rat lung carcinogenesis induced by 3-methylcholanthrene and diethylnitrosamine Biochem. Biophys. Res. Commun., 402 (2010),pp. 507-514
[37]	Mancini, D.N., Singh, S.M., Archer, T.K. et al. Site-specific DNA methylation in the neurofibromatosis (NF1) promoter interferes with binding of CREB and SP1 transcription factors Oncogene, 18 (1999),pp. 4108-4119
[38]	Mariani, M.R., Carpaneto, E.M., Ulivi, M. et al. Correlation between butyrate-induced histone hyperacetylation turn-over and c-myc expression J. Steroid Biochem. Mol. Biol., 86 (2003),pp. 167-171
[39]	Marjanovic, N.D., Weinberg, R.A., Chaffer, C.L. Cell plasticity and heterogeneity in cancer Clin. Chem., 59 (2013),pp. 168-179
[40]	Marusyk, A., Almendro, V., Polyak, K. Intra-tumour heterogeneity: a looking glass for cancer? Nat. Rev. Cancer, 12 (2012),pp. 323-334
[41]	May, T., Eccleston, L., Herrmann, S. et al. Bimodal and hysteretic expression in mammalian cells from a synthetic gene circuit PLoS One, 3 (2008),p. e2372
[42]	McBurney, M.W., Mai, T., Yang, X. et al. Evidence for repeat-induced gene silencing in cultured mammalian cells: inactivation of tandem repeats of transfected genes Exp. Cell Res., 274 (2002),pp. 1-8
[43]	Mehta, A.K., Majumdar, S.S., Alam, P. et al. Epigenetic regulation of cytomegalovirus major immediate-early promoter activity in transgenic mice Gene, 428 (2009),pp. 20-24
[44]	Miranda, T.B., Jones, P.A. DNA methylation: the nuts and bolts of repression J. Cell. Physiol., 213 (2007),pp. 384-390
[45]	Misri, S., Pandita, S., Kumar, R. et al. Telomeres, histone code, and DNA damage response Cytogenet. Genome Res., 122 (2008),pp. 297-307
[46]	Mutskov, V., Felsenfeld, G. Silencing of transgene transcription precedes methylation of promoter DNA and histone H3 lysine 9 EMBO J., 23 (2004),pp. 138-149
[47]	Pauler, F.M., Sloane, M.A., Huang, R. et al. H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome Genome Res., 19 (2009),pp. 221-233
[48]	Peters, A.H., Kubicek, S., Mechtler, K. et al. Partitioning and plasticity of repressive histone methylation states in mammalian chromatin Mol. Cell, 12 (2003),pp. 1577-1589
[49]	Raj, A., Peskin, C.S., Tranchina, D. et al. Stochastic mRNA synthesis in mammalian cells PLoS Biol., 4 (2006),p. e309
[50]	Schucht, R., Coroadinha, A.S., Zanta-Boussif, M.A. et al. A new generation of retroviral producer cells: predictable and stable virus production by Flp-mediated site-specific integration of retroviral vectors Mol. Ther., 14 (2006),pp. 285-292
[51]	Smith, K.T., Workman, J.L. Chromatin proteins: key responders to stress PLoS Biol., 10 (2012),p. e1001371
[52]	Strunnikova, M., Schagdarsurengin, U., Kehlen, A. et al. Mol. Cell. Biol., 25 (2005),pp. 3923-3933
[53]	Tahara, T., Shibata, T., Nakamura, M. et al. Increased number of CpG island hypermethylation in tumor suppressor genes of non-neoplastic gastric mucosa correlates with higher risk of gastric cancer Digestion, 82 (2010),pp. 27-36
[54]	Tate, P.H., Bird, A.P. Effects of DNA methylation on DNA-binding proteins and gene expression Curr. Opin. Genet. Dev., 3 (1993),pp. 226-231
[55]	Umlauf, D., Goto, Y., Cao, R. et al. Imprinting along the Kcnq1 domain on mouse chromosome 7 involves repressive histone methylation and recruitment of polycomb group complexes Nat. Genet., 36 (2004),pp. 1296-1300
[56]	Weiner, A., Chen, H.V., Liu, C.L. et al. Systematic dissection of roles for chromatin regulators in a yeast stress response PLoS Biol., 10 (2012),p. e1001369
[57]	Williams, A., Spilianakis, C.G., Flavell, R.A. Trends Genet., 26 (2010),pp. 188-197
[58]	Wulhfard, S., Baldi, L., Hacker, D.L. et al. Valproic acid enhances recombinant mRNA and protein levels in transiently transfected Chinese hamster ovary cells J. Biotechnol., 148 (2010),pp. 128-132
[59]	Yu, J., Cao, Q., Mehra, R. et al. Integrative genomics analysis reveals silencing of beta-adrenergic signaling by polycomb in prostate cancer Cancer Cell, 12 (2007),pp. 419-431