Kinetics of HTLV-1 reactivation from latency quantified by single-molecule RNA FISH and stochastic modelling

English version

Autoři: Michi Miura ^aff001; Supravat Dey ^aff002; Saumya Ramanayake ^aff001; Abhyudai Singh ^aff002; David S. Rueda ^aff001; Charles R. M. Bangham ^aff001
Působiště autorů: Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, United Kingdom ^aff001; Department of Electrical and Computer Engineering, University of Delaware, Newark, Delaware, United States of America ^aff002; Single Molecule Imaging Group, MRC London Institute of Medical Sciences, Hammersmith Hospital, London, United Kingdom ^aff003
Vyšlo v časopise: Kinetics of HTLV-1 reactivation from latency quantified by single-molecule RNA FISH and stochastic modelling. PLoS Pathog 15(11): e32767. doi:10.1371/journal.ppat.1008164
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1008164

Souhrn

The human T cell leukemia virus HTLV-1 establishes a persistent infection in vivo in which the viral sense-strand transcription is usually silent at a given time in each cell. However, cellular stress responses trigger the reactivation of HTLV-1, enabling the virus to transmit to a new host cell. Using single-molecule RNA FISH, we measured the kinetics of the HTLV-1 transcriptional reactivation in peripheral blood mononuclear cells (PBMCs) isolated from HTLV-1⁺ individuals. The abundance of the HTLV-1 sense and antisense transcripts was quantified hourly during incubation of the HTLV-1-infected PBMCs ex vivo. We found that, in each cell, the sense-strand transcription occurs in two distinct phases: the initial low-rate transcription is followed by a phase of rapid transcription. The onset of transcription peaked between 1 and 3 hours after the start of in vitro incubation. The variance in the transcription intensity was similar in polyclonal HTLV-1⁺ PBMCs (with tens of thousands of distinct provirus insertion sites), and in samples with a single dominant HTLV-1⁺ clone. A stochastic simulation model was developed to estimate the parameters of HTLV-1 proviral transcription kinetics. In PBMCs from a leukemic subject with one dominant T-cell clone, the model indicated that the average duration of HTLV-1 sense-strand activation by Tax (i.e. the rapid transcription) was less than one hour. HTLV-1 antisense transcription was stable during reactivation of the sense-strand. The antisense transcript HBZ was produced at an average rate of ~0.1 molecules per hour per HTLV-1⁺ cell; however, between 20% and 70% of HTLV-1-infected cells were HBZ-negative at a given time, the percentage depending on the individual subject. HTLV-1-infected cells are exposed to a range of stresses when they are drawn from the host, which initiate the viral reactivation. We conclude that whereas antisense-strand transcription is stable throughout the stress response, the HTLV-1 sense-strand reactivation is highly heterogeneous and occurs in short, self-terminating bursts.

Klíčová slova:

Simulation and modeling – Messenger RNA – T cells – Viral replication – DNA transcription – Sense strands – HTLV-1

Zdroje

1. Bangham CRM, Matsuoka M. Human T-cell leukaemia virus type 1: parasitism and pathogenesis. Philos Trans R Soc Lond B Biol Sci. 2017;372(1732). Epub 2017/09/13. doi: 10.1098/rstb.2016.0272 28893939

2. Singh A, Weinberger LS. Stochastic gene expression as a molecular switch for viral latency. Curr Opin Microbiol. 2009;12(4):460–6. Epub 2009/07/15. doi: 10.1016/j.mib.2009.06.016 19595626

3. Darcis G, Van Driessche B, Van Lint C. HIV Latency: Should We Shock or Lock? Trends Immunol. 2017;38(3):217–28. Epub 2017/01/12. doi: 10.1016/j.it.2016.12.003 28073694.

4. Ho YC, Shan L, Hosmane NN, Wang J, Laskey SB, Rosenbloom DI, et al. Replication-competent noninduced proviruses in the latent reservoir increase barrier to HIV-1 cure. Cell. 2013;155(3):540–51. Epub 2013/11/19. doi: 10.1016/j.cell.2013.09.020 24243014

5. Kulkarni A, Taylor GP, Klose RJ, Schofield CJ, Bangham CR. Histone H2A monoubiquitylation and p38-MAPKs regulate immediate-early gene-like reactivation of latent retrovirus HTLV-1. JCI Insight. 2018;3(20). Epub 2018/10/20. doi: 10.1172/jci.insight.123196 30333309

6. Gessain A, Cassar O. Epidemiological Aspects and World Distribution of HTLV-1 Infection. Front Microbiol. 2012;3:388. Epub 2012/11/20. doi: 10.3389/fmicb.2012.00388 23162541

7. Gillet NA, Malani N, Melamed A, GormLey N, Carter R, Bentley D, et al. The host genomic environment of the provirus determines the abundance of HTLV-1-infected T-cell clones. Blood. 2011;117(11):3113–22. Epub 2011/01/14. doi: 10.1182/blood-2010-10-312926 21228324

8. Laydon DJ, Melamed A, Sim A, Gillet NA, Sim K, Darko S, et al. Quantification of HTLV-1 clonality and TCR diversity. PLoS Comput Biol. 2014;10(6):e1003646. Epub 2014/06/20. doi: 10.1371/journal.pcbi.1003646 24945836

9. Kulkarni A, Bangham CRM. HTLV-1: Regulating the Balance Between Proviral Latency and Reactivation. Front Microbiol. 2018;9:449. Epub 2018/04/05. doi: 10.3389/fmicb.2018.00449 29615991

10. Satou Y, Yasunaga J, Yoshida M, Matsuoka M. HTLV-I basic leucine zipper factor gene mRNA supports proliferation of adult T cell leukemia cells. Proc Natl Acad Sci U S A. 2006;103(3):720–5. Epub 2006/01/13. doi: 10.1073/pnas.0507631103 16407133

11. Jacobson S, Shida H, McFarlin DE, Fauci AS, Koenig S. Circulating CD8+ cytotoxic T lymphocytes specific for HTLV-I pX in patients with HTLV-I associated neurological disease. Nature. 1990;348(6298):245–8. Epub 1990/11/15. doi: 10.1038/348245a0 2146511.

12. Femino AM, Fay FS, Fogarty K, Singer RH. Visualization of single RNA transcripts in situ. Science. 1998;280(5363):585–90. Epub 1998/05/09. doi: 10.1126/science.280.5363.585 9554849.

13. Raj A, van den Bogaard P, Rifkin SA, van Oudenaarden A, Tyagi S. Imaging individual mRNA molecules using multiple singly labeled probes. Nat Methods. 2008;5(10):877–9. Epub 2008/09/23. doi: 10.1038/nmeth.1253 18806792

14. Billman MR, Rueda D, Bangham CRM. Single-cell heterogeneity and cell-cycle-related viral gene bursts in the human leukaemia virus HTLV-1. Wellcome Open Res. 2017;2:87. Epub 2017/10/25. doi: 10.12688/wellcomeopenres.12469.2 29062917

15. Igakura T, Stinchcombe JC, Goon PK, Taylor GP, Weber JN, Griffiths GM, et al. Spread of HTLV-I between lymphocytes by virus-induced polarization of the cytoskeleton. Science. 2003;299(5613):1713–6. Epub 2003/02/18. doi: 10.1126/science.1080115 12589003.

16. Hanon E, Hall S, Taylor GP, Saito M, Davis R, Tanaka Y, et al. Abundant tax protein expression in CD4+ T cells infected with human T-cell lymphotropic virus type I (HTLV-I) is prevented by cytotoxic T lymphocytes. Blood. 2000;95(4):1386–92. Epub 2000/02/09. 10666215.

17. Raj A, Peskin CS, Tranchina D, Vargas DY, Tyagi S. Stochastic mRNA synthesis in mammalian cells. PLoS Biol. 2006;4(10):e309. Epub 2006/10/20. doi: 10.1371/journal.pbio.0040309 17048983

18. Dar RD, Razooky BS, Singh A, Trimeloni TV, McCollum JM, Cox CD, et al. Transcriptional burst frequency and burst size are equally modulated across the human genome. Proc Natl Acad Sci U S A. 2012;109(43):17454–9. Epub 2012/10/16. doi: 10.1073/pnas.1213530109 23064634

19. Larsson AJM, Johnsson P, Hagemann-Jensen M, Hartmanis L, Faridani OR, Reinius B, et al. Genomic encoding of transcriptional burst kinetics. Nature. 2019;565(7738):251–4. Epub 2019/01/04. doi: 10.1038/s41586-018-0836-1 30602787.

20. Schwabe A, Bruggeman FJ. Single yeast cells vary in transcription activity not in delay time after a metabolic shift. Nat Commun. 2014;5:4798. Epub 2014/09/03. doi: 10.1038/ncomms5798 25178355.

21. Senecal A, Munsky B, Proux F, Ly N, Braye FE, Zimmer C, et al. Transcription factors modulate c-Fos transcriptional bursts. Cell Rep. 2014;8(1):75–83. Epub 2014/07/02. doi: 10.1016/j.celrep.2014.05.053 24981864

22. Furuta R, Yasunaga JI, Miura M, Sugata K, Saito A, Akari H, et al. Human T-cell leukemia virus type 1 infects multiple lineage hematopoietic cells in vivo. PLoS Pathog. 2017;13(11):e1006722. Epub 2017/12/01. doi: 10.1371/journal.ppat.1006722 29186194

23. Ma G, Yasunaga J, Matsuoka M. Multifaceted functions and roles of HBZ in HTLV-1 pathogenesis. Retrovirology. 2016;13:16. Epub 2016/03/17. doi: 10.1186/s12977-016-0249-x 26979059

24. Mitobe Y, Yasunaga J, Furuta R, Matsuoka M. HTLV-1 bZIP Factor RNA and Protein Impart Distinct Functions on T-cell Proliferation and Survival. Cancer Res. 2015;75(19):4143–52. Epub 2015/09/19. doi: 10.1158/0008-5472.CAN-15-0942 26383166.

25. Macnamara A, Rowan A, Hilburn S, Kadolsky U, Fujiwara H, Suemori K, et al. HLA class I binding of HBZ determines outcome in HTLV-1 infection. PLoS Pathog. 2010;6(9):e1001117. Epub 2010/10/05. doi: 10.1371/journal.ppat.1001117 20886101

26. Raval GU, Bidoia C, Forlani G, Tosi G, Gessain A, Accolla RS. Localization, quantification and interaction with host factors of endogenous HTLV-1 HBZ protein in infected cells and ATL. Retrovirology. 2015;12:59. Epub 2015/07/05. doi: 10.1186/s12977-015-0186-0 26140924

27. Mahgoub M, Yasunaga JI, Iwami S, Nakaoka S, Koizumi Y, Shimura K, et al. Sporadic on/off switching of HTLV-1 Tax expression is crucial to maintain the whole population of virus-induced leukemic cells. Proc Natl Acad Sci U S A. 2018;115(6):E1269–E78. Epub 2018/01/24. doi: 10.1073/pnas.1715724115 29358408

28. Cook LB, Rowan AG, Melamed A, Taylor GP, Bangham CR. HTLV-1-infected T cells contain a single integrated provirus in natural infection. Blood. 2012;120(17):3488–90. Epub 2012/09/08. doi: 10.1182/blood-2012-07-445593 22955925

29. Weinberger LS, Burnett JC, Toettcher JE, Arkin AP, Schaffer DV. Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity. Cell. 2005;122(2):169–82. Epub 2005/07/30. doi: 10.1016/j.cell.2005.06.006 16051143.

30. Razooky BS, Cao Y, Hansen MMK, Perelson AS, Simpson ML, Weinberger LS. Nonlatching positive feedback enables robust bimodality by decoupling expression noise from the mean. PLoS Biol. 2017;15(10):e2000841. Epub 2017/10/19. doi: 10.1371/journal.pbio.2000841 29045398

31. Aull KH, Tanner EJ, Thomson M, Weinberger LS. Transient Thresholding: A Mechanism Enabling Noncooperative Transcriptional Circuitry to Form a Switch. Biophys J. 2017;112(11):2428–38. Epub 2017/06/08. doi: 10.1016/j.bpj.2017.05.002 28591615

32. Nicot C, Dundr M, Johnson JM, Fullen JR, Alonzo N, Fukumoto R, et al. HTLV-1-encoded p30II is a post-transcriptional negative regulator of viral replication. Nat Med. 2004;10(2):197–201. Epub 2004/01/20. doi: 10.1038/nm984 14730358.

33. Rowan AG, Suemori K, Fujiwara H, Yasukawa M, Tanaka Y, Taylor GP, et al. Cytotoxic T lymphocyte lysis of HTLV-1 infected cells is limited by weak HBZ protein expression, but non-specifically enhanced on induction of Tax expression. Retrovirology. 2014;11:116. Epub 2014/12/17. doi: 10.1186/s12977-014-0116-6 25499803

34. Miura M, Miyazato P, Satou Y, Tanaka Y, Bangham CRM. Epigenetic changes around the pX region and spontaneous HTLV-1 transcription are CTCF-independent. Wellcome Open Res. 2018;3:105. Epub 20187/12/11. doi: 10.12688/wellcomeopenres.14741.2 30607369

35. Clerc I, Polakowski N, Andre-Arpin C, Cook P, Barbeau B, Mesnard JM, et al. An interaction between the human T cell leukemia virus type 1 basic leucine zipper factor (HBZ) and the KIX domain of p300/CBP contributes to the down-regulation of tax-dependent viral transcription by HBZ. J Biol Chem. 2008;283(35):23903–13. Epub 2008/07/05. doi: 10.1074/jbc.M803116200 18599479

36. D’Agostino DM, Cavallari I, Romanelli MG, Ciminale V. Post-transcriptional Regulation of HTLV Gene Expression: Rex to the Rescue. Front Microbiol. 2019;10:1958. Epub 2019/08/22. doi: 10.3389/fmicb.2019.01958 31507567.

37. Hnisz D, Shrinivas K, Young RA, Chakraborty AK, Sharp PA. A Phase Separation Model for Transcriptional Control. Cell. 2017;169(1):13–23. Epub 2017/03/25. doi: 10.1016/j.cell.2017.02.007 28340338

38. Boija A, Klein IA, Sabari BR, Dall’Agnese A, Coffey EL, Zamudio AV, et al. Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains. Cell. 2018;175(7):1842–55 e16. Epub 2018/11/20. doi: 10.1016/j.cell.2018.10.042 30449618

39. Boxus M, Twizere JC, Legros S, Dewulf JF, Kettmann R, Willems L. The HTLV-1 Tax interactome. Retrovirology. 2008;5:76. Epub 2008/08/16. doi: 10.1186/1742-4690-5-76 18702816

40. Semmes OJ, Jeang KT. Localization of human T-cell leukemia virus type 1 tax to subnuclear compartments that overlap with interchromatin speckles. J Virol. 1996;70(9):6347–57. Epub 1996/09/01. 8709263

41. Edelstein A, Amodaj N, Hoover K, Vale R, Stuurman N. Computer control of microscopes using microManager. Curr Protoc Mol Biol. 2010;Chapter 14:Unit14 20. Epub 2010/10/05. doi: 10.1002/0471142727.mb1420s92 20890901

42. Mueller F, Senecal A, Tantale K, Marie-Nelly H, Ly N, Collin O, et al. FISH-quant: automatic counting of transcripts in 3D FISH images. Nat Methods. 2013;10(4):277–8. Epub 2013/03/30. doi: 10.1038/nmeth.2406 23538861.

43. Gillespie DT. General Method for Numerically Simulating Stochastic Time Evolution of Coupled Chemical-Reactions. J Comput Phys. 1976;22(4):403–34. doi: 10.1016/0021-9991(76)90041-3

44. Rende F, Cavallari I, Corradin A, Silic-Benussi M, Toulza F, Toffolo GM, et al. Kinetics and intracellular compartmentalization of HTLV-1 gene expression: nuclear retention of HBZ mRNAs. Blood. 2011;117(18):4855–9. Epub 2011/03/11. doi: 10.1182/blood-2010-11-316463 21398577.