CoChat
Sign Up
Cited by 210Viral-associated cancers and disordersCytomegalovirus and herpesvirus researchHerpesvirus Infections and Treatments

Epstein–Barr virus reprograms human B lymphocytes immediately in the prelatent phase of infection

Open access
Mrozek-Gorska, Paulina, Buschle, Alexander, Pich, Dagmar, Schwarzmayr, Thomas, Fechtner, Ron, Scialdone, Antonio, Hammerschmidt, Wolfgang·2019·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.1901314116PMC PMC6690029

Published version of a preprint

Open this paper in CoChat — free accountOpen PDF

Abstract

Epstein–Barr virus (EBV) is a human tumor virus and a model of herpesviral latency. The virus efficiently infects resting human B lymphocytes and induces their continuous proliferation in vitro, which mimics certain aspects of EBV’s oncogenic potential in vivo. How lymphoblastoid cell lines (LCLs) evolve from the infected lymphocytes is uncertain. We conducted a systematic time-resolved longitudinal study of cellular functions and transcriptional profiles of newly infected naïve primary B lymphocytes. EBV reprograms the cells comprehensively and globally. Rapid and extensive transcriptional changes occur within 24 h and precede any metabolic and phenotypic changes. Within 72 h, the virus activates the cells, changes their phenotypes with respect to cell size, RNA, and protein content, and induces metabolic pathways to cope with the increased demand for energy, supporting an efficient cell cycle entry on day 3 postinfection. The transcriptional program that EBV initiates consists of 3 waves of clearly discernable clusters of cellular genes that peak on day 2, 3, or 4 and regulate RNA synthesis, metabolic pathways, and cell division, respectively. Upon onset of cell doublings on day 4, the cellular transcriptome appears to be completely reprogrammed to support the proliferating cells, but 3 additional clusters of EBV-regulated genes fine-tune cell signaling, migration, and immune response pathways, eventually. Our study reveals that more than 11,000 genes are regulated upon EBV infection as naïve B cells exit quiescence to enter a germinal center-like differentiation program, which culminates in immortalized, proliferating cells that partially resemble plasmablasts and early plasma cells.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1073/pnas.1901314116

Cites

3 of 3 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • RNA-Seq data indicate a time-dependent early increase in VLCFA synthesis around 2-3 days post EBV infection, indicated by transient robust induction of ELOVL1.

    “the RNA-Seq data22 also pointed to a time-dependent early increase in VLCFA synthesis around 2–3 dpi, as indicated by a transient but robust induction of ELOVL1 (Fig. 2f).”

    From Peroxisomal very long-chain fatty acid transport is targeted by herpesviruses and the antiviral host response (2022) · cites this paper as [22]

    The Results section on gene-expression clusters reports time-resolved RNA-seq findings, including a cellular-metabolism cluster that peaks on day 3 after EBV infection. It does not identify VLCFA synthesis or report transient, robust induction of ELOVL1; searches for ELOVL1, VLCFA, and fatty-acid synthesis found no supporting passage in our copy. (LLM, conf=0.77)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 56

  1. [1]Epstein M. A., Achong B. G., Barr Y. M., Virus particles in cultured lymphoblasts from Burkitt’s lymphoma. Lancet 1, 702– 703 (1964). 14107961
  2. [2]Pulvertaft J. V., Cytology of Burkitt’s tumour (African Lymphoma). Lancet 1, 238– 240 (1964). 14086209
  3. [3]Pope J. H., Establishment of cell lines from peripheral leucocytes in infectious mononucleosis. Nature 216, 810– 811 (1967). 6074953
  4. [4]Henle W., Evidence for viruses in acute leukemia and Burkitt’s tumor. Cancer 21, 580– 586 (1968). 4868472
  5. [5]Shannon-Lowe C., Rickinson A. B., Bell A. I., Epstein-Barr virus-associated lymphomas. Philos. Trans. R. Soc. Lond. B Biol. Sci. 372, 20160271 (2017). 28893938 PMC5597738
  6. [6]Young L. S., Yap L. F., Murray P. G., Epstein-Barr virus: More than 50 years old and still providing surprises. Nat. Rev. Cancer 16, 789– 802 (2016). 27687982
  7. [7]Young L. S., Rickinson A. B., Epstein-Barr virus: 40 years on. Nat. Rev. Cancer 4, 757– 768 (2004). 15510157
  8. [8]Woellmer A., Hammerschmidt W., Epstein-Barr virus and host cell methylation: Regulation of latency, replication and virus reactivation. Curr. Opin. Virol. 3, 260– 265 (2013). 23567077 PMC3799965
  9. [9]Jochum S., Ruiss R., Moosmann A., Hammerschmidt W., Zeidler R., RNAs in Epstein-Barr virions control early steps of infection. Proc. Natl. Acad. Sci. U.S.A. 109, E1396– E1404 (2012). 22543160 PMC3361417
  10. [10]Altmann M., Hammerschmidt W., Epstein-Barr virus provides a new paradigm: A requirement for the immediate inhibition of apoptosis. PLoS Biol. 3, e404 (2005). 16277553 PMC1283332
  11. [11]Kalla M., Göbel C., Hammerschmidt W., The lytic phase of Epstein-Barr virus requires a viral genome with 5-methylcytosine residues in CpG sites. J. Virol. 86, 447– 458 (2012). 22031942 PMC3255903
  12. [12]Kalla M., Hammerschmidt W., Human B cells on their route to latent infection—Early but transient expression of lytic genes of Epstein-Barr virus. Eur. J. Cell Biol. 91, 65– 69 (2012). 21450364
  13. [13]Zeidler R., Downregulation of TAP1 in B lymphocytes by cellular and Epstein-Barr virus-encoded interleukin-10. Blood 90, 2390– 2397 (1997). 9310490
  14. [14]Hislop A. D., A CD8+ T cell immune evasion protein specific to Epstein-Barr virus and its close relatives in Old World primates. J. Exp. Med. 204, 1863– 1873 (2007). 17620360 PMC2118677
  15. [15]Jochum S., Moosmann A., Lang S., Hammerschmidt W., Zeidler R., The EBV immunoevasins vIL-10 and BNLF2a protect newly infected B cells from immune recognition and elimination. PLoS Pathog. 8, e1002704 (2012). 22615564 PMC3355093
  16. [16]Albanese M., Tagawa T., Buschle A., Hammerschmidt W., MicroRNAs of Epstein-Barr virus control innate and adaptive anti-viral immunity. J. Virol. 91, e01667-16 (2017). 28592533 PMC5533892
  17. [17]Nikitin P. A., An ATM/Chk2-mediated DNA damage-responsive signaling pathway suppresses Epstein-Barr virus transformation of primary human B cells. Cell Host Microbe 8, 510– 522 (2010). 21147465 PMC3049316
  18. [18]Price A. M., Luftig M. A., Dynamic Epstein-Barr virus gene expression on the path to B-cell transformation. Adv. Virus Res. 88, 279– 313 (2014). 24373315 PMC4911173
  19. [19]Price A. M., Analysis of Epstein-Barr virus-regulated host gene expression changes through primary B-cell outgrowth reveals delayed kinetics of latent membrane protein 1-mediated NF-κB activation. J. Virol. 86, 11096– 11106 (2012). 22855490 PMC3457162
  20. [20]Fitzsimmons L., Kelly G. L., EBV and apoptosis: The viral master regulator of cell fate? Viruses 9, E339 (2017). 29137176 PMC5707546
  21. [21]Kaiser C., The proto-oncogene c-myc is a direct target gene of Epstein-Barr virus nuclear antigen 2. J. Virol. 73, 4481– 4484 (1999). 10196351 PMC104340
  22. [22]Zhao B., Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth. Proc. Natl. Acad. Sci. U.S.A. 108, 14902– 14907 (2011). 21746931 PMC3169132
  23. [23]Lu F., EBNA2 drives formation of new chromosome binding sites and target genes for B-cell master regulatory transcription factors RBP-jκ and EBF1. PLoS Pathog. 12, e1005339 (2016). 26752713 PMC4709166
  24. [24]Jiang S., Epstein-Barr virus nuclear antigen 3C binds to BATF/IRF4 or SPI1/IRF4 composite sites and recruits Sin3A to repress CDKN2A. Proc. Natl. Acad. Sci. U.S.A. 111, 421– 426 (2014). 24344258 PMC3890834
  25. [25]Strobl L. J., Both Epstein-Barr viral nuclear antigen 2 (EBNA2) and activated Notch1 transactivate genes by interacting with the cellular protein RBP-J kappa. Immunobiology 198, 299– 306 (1997). 9442401
  26. [26]Pich D., The first days in the life of naïve human B-lymphocytes infected with Epstein-Barr virus. biorXiv: 10.1101/666297v1 (11 June 2019). PMC6751056 31530670 · DOI
  27. [27]Steinbrück L., K1 and K15 of Kaposi’s sarcoma-associated herpesvirus are partial functional homologues of latent membrane protein 2A of Epstein-Barr virus. J. Virol. 89, 7248– 7261 (2015). 25948739 PMC4473585
  28. [28]Roederer M., Interpretation of cellular proliferation data: Avoid the panglossian. Cytometry A 79, 95– 101 (2011). 21265003
  29. [29]Delecluse H. J., Hilsendegen T., Pich D., Zeidler R., Hammerschmidt W., Propagation and recovery of intact, infectious Epstein-Barr virus from prokaryotic to human cells. Proc. Natl. Acad. Sci. U.S.A. 95, 8245– 8250 (1998). 9653172 PMC20961
  30. [30]Kassambara A., GenomicScape: An easy-to-use web tool for gene expression data analysis. Application to investigate the molecular events in the differentiation of B cells into plasma cells. PLoS Comput. Biol. 11, e1004077 (2015). 25633866 PMC4310610
  31. [31]Lex A., Gehlenborg N., Strobelt H., Vuillemot R., Pfister H., UpSet: Visualization of intersecting sets. IEEE Trans. Vis. Comput. Graph. 20, 1983– 1992 (2014). 26356912 PMC4720993
  32. [32]Jourdan M., An in vitro model of differentiation of memory B cells into plasmablasts and plasma cells including detailed phenotypic and molecular characterization. Blood 114, 5173– 5181 (2009). 19846886 PMC2834398
  33. [33]Nakayama T., Human B cells immortalized with Epstein-Barr virus upregulate CCR6 and CCR10 and downregulate CXCR4 and CXCR5. J. Virol. 76, 3072– 3077 (2002). 11861876 PMC135988
  34. [34]Ehlin-Henriksson B., Changes in chemokines and chemokine receptor expression on tonsillar B cells upon Epstein-Barr virus infection. Immunology 127, 549– 557 (2009). 19604305 PMC2729532
  35. [35]Yin Q., Wang X., McBride J., Fewell C., Flemington E., B-cell receptor activation induces BIC/miR-155 expression through a conserved AP-1 element. J. Biol. Chem. 283, 2654– 2662 (2008). 18048365 PMC2810639
  36. [36]Kholodnyuk I., Rudevica Z., Leonciks A., Ehlin-Henriksson B., Kashuba E., Expression of the chemokine receptors CCR1 and CCR2B is up-regulated in peripheral blood B cells upon EBV infection and in established lymphoblastoid cell lines. Virology 512, 1– 7 (2017). 28892735
  37. [37]Wen W., Epstein-Barr virus BZLF1 gene, a switch from latency to lytic infection, is expressed as an immediate-early gene after primary infection of B lymphocytes. J. Virol. 81, 1037– 1042 (2007). 17079287 PMC1797481
  38. [38]Kalla M., Schmeinck A., Bergbauer M., Pich D., Hammerschmidt W., AP-1 homolog BZLF1 of Epstein-Barr virus has two essential functions dependent on the epigenetic state of the viral genome. Proc. Natl. Acad. Sci. U.S.A. 107, 850– 855 (2010). 20080764 PMC2818922
  39. [39]Wang C., RNA sequencing analyses of gene expression during Epstein-Barr virus infection of primary B lymphocytes. J. Virol. 93, e00226-19 (2019). 31019051 PMC6580941
  40. [40]Murray P. J., Rathmell J., Pearce E., SnapShot: Immunometabolism. Cell Metab. 22, 190– 190.e1 (2015). 26154058
  41. [41]van Stipdonk M. J., Dynamic programming of CD8+ T lymphocyte responses. Nat. Immunol. 4, 361– 365 (2003). 12640451
  42. [42]Slack M., Wang T., Wang R., T cell metabolic reprogramming and plasticity. Mol. Immunol. 68, 507– 512 (2015). 26277274 PMC4679442
  43. [43]Wang R., Green D. R., Metabolic checkpoints in activated T cells. Nat. Immunol. 13, 907– 915 (2012). 22990888
  44. [44]Buck M. D., O’Sullivan D., Pearce E. L., T cell metabolism drives immunity. J. Exp. Med. 212, 1345– 1360 (2015). 26261266 PMC4548052
  45. [45]Almeida L., Lochner M., Berod L., Sparwasser T., Metabolic pathways in T cell activation and lineage differentiation. Semin. Immunol. 28, 514– 524 (2016). 27825556
  46. [46]Cao Y., Rathmell J. C., Macintyre A. N., Metabolic reprogramming towards aerobic glycolysis correlates with greater proliferative ability and resistance to metabolic inhibition in CD8 versus CD4 T cells. PLoS One 9, e104104 (2014). 25090630 PMC4121309
  47. [47]Doughty C. A., Antigen receptor-mediated changes in glucose metabolism in B lymphocytes: Role of phosphatidylinositol 3-kinase signaling in the glycolytic control of growth. Blood 107, 4458– 4465 (2006). 16449529 PMC1895797
  48. [48]Dufort F. J., Cutting edge: IL-4-mediated protection of primary B lymphocytes from apoptosis via Stat6-dependent regulation of glycolytic metabolism. J. Immunol. 179, 4953– 4957 (2007). 17911579
  49. [49]Mancao C., Hammerschmidt W., Epstein-Barr virus latent membrane protein 2A is a B-cell receptor mimic and essential for B-cell survival. Blood 110, 3715– 3721 (2007). 17682125 PMC2077319
  50. [50]Kieser A., Sterz K. R., The latent membrane protein 1 (LMP1). Curr. Top. Microbiol. Immunol. 391, 119– 149 (2015). 26428373
  51. [51]Rathmell J. C., T cell Myc-tabolism. Immunity 35, 845– 846 (2011). 22195738 PMC3267318
  52. [53]Stine Z. E., Walton Z. E., Altman B. J., Hsieh A. L., Dang C. V., MYC, metabolism, and cancer. Cancer Discov. 5, 1024– 1039 (2015). 26382145 PMC4592441
  53. [54]Kim J., Lee J. H., Iyer V. R., Global identification of Myc target genes reveals its direct role in mitochondrial biogenesis and its E-box usage in vivo. PLoS One 3, e1798 (2008). 18335064 PMC2258436
  54. [56]Liang J., Epstein-Barr virus super-enhancer eRNAs are essential for MYC oncogene expression and lymphoblast proliferation. Proc. Natl. Acad. Sci. U.S.A. 113, 14121– 14126 (2016). 27864512 PMC5150416
  55. [57]Sychev Z. E., Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism. PLoS Pathog. 13, e1006256 (2017). 28257516 PMC5352148
  56. [58]Lee D. Y., Sugden B., The LMP1 oncogene of EBV activates PERK and the unfolded protein response to drive its own synthesis. Blood 111, 2280– 2289 (2008). 18042799 PMC2234060

Cited by

Sorted by citations

Authors
Mrozek-Gorska, P., Buschle, A., Pich, D., Schwarzmayr, T., Fechtner, R., Scialdone, A., & Hammerschmidt, W.
Affiliations
  • Research Unit Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health and German Center for Infection Research, D-81377 Munich, Germany;
  • Helmholtz Munich (DE)
Corresponding author
  • Scialdone, Antonio
  • Hammerschmidt, Wolfgang
ORCID
Venue
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Published
2019-07-24
Volume
116
Issue
32
Pages
16046-16055
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
DOI
10.1073/pnas.1901314116
PMC
PMC6690029
OpenAlex
W2963954504
Cited by
210
References
3
Citations by year
2026: 18 · 2025: 31 · 2024: 26 · 2023: 27 · 2022: 39 · 2021: 40 · 2020: 23 · 2019: 5
FWCI
11.27
Type
journal article
Language
en
Open access
Licence
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion, cc-by-nc-nd)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • PuSH - Publication Server of Helmholtz Zentrum München (submittedVersion, cc-by-nc-nd)
  • Site cant be reached (submittedVersion, cc-by-nc-nd)
Funders
  • Deutsche Forschungsgemeinschaft (SFB/TR 36, TP-A04, TPA 13, SFB1064, SFB1064/TPA13, SFB‐TR36/TP A04)
  • Deutsche Krebshilfe (70112875)
  • National Cancer Institute (CA-70723)
Topics
  • Health Sciences › Medicine › Oncology › Viral-associated cancers and disorders
  • Health Sciences › Medicine › Epidemiology › Cytomegalovirus and herpesvirus research
  • Health Sciences › Medicine › Epidemiology › Herpesvirus Infections and Treatments
Keywords
Epstein-Barr virus, viral latency, transcriptional reprogramming, naive B cells, lymphoblastoid cell lines, cell cycle entry, metabolic reprogramming, plasmablasts, plasma cells, viral oncogenesis, gene expression dynamics
MeSH terms
B-Lymphocytes, Herpesvirus 4, Human, Multigene Family, Humans, Lymphocyte Activation, Phenotype, Time Factors, Gene Expression Regulation, Viral, Epstein-Barr Virus Infections, HEK293 Cells, Transcriptome

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review