Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Physiological and druggable skipping of immunoglobulin variable exons in plasma cells

Cellular & Molecular Immunology volume 16, pages 810–819 (2019)Cite this article

Abstract

The error-prone V(D)J recombination process generates considerable amounts of nonproductive immunoglobulin (Ig) pre-mRNAs. We recently demonstrated that aberrant Ig chains lacking variable (V) domains can be produced after nonsense-associated altered splicing (NAS) events. Remarkably, the expression of these truncated Ig polypeptides heightens endoplasmic reticulum stress and shortens plasma cell (PC) lifespan. Many questions remain regarding the molecular mechanisms underlying this new truncated Ig exclusion (TIE-) checkpoint and its restriction to the ultimate stage of B-cell differentiation. To address these issues, we evaluated the extent of NAS of Ig pre-mRNAs using an Ig heavy chain (IgH) knock-in model that allows for uncoupling of V exon skipping from TIE-induced apoptosis. We found high levels of V exon skipping in PCs compared with B cells, and this skipping was correlated with a biallelic boost in IgH transcription during PC differentiation. Chromatin analysis further revealed that the skipped V exon turned into a pseudo-intron. Finally, we showed that hypertranscription of Ig genes facilitated V exon skipping upon passive administration of splice-switching antisense oligonucleotides (ASOs). Thus, V exon skipping is coupled to transcription and increases as PC differentiation proceeds, likely explaining the late occurrence of the TIE-checkpoint and opening new avenues for ASO-mediated strategies in PC disorders.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  1. Li, S. & Wilkinson, M. F. Nonsense surveillance in lymphocytes? Immunity 8, 135–141 (1998).

    Article  CAS  Google Scholar 

  2. Deiss, T. C. et al. Immunogenetic factors driving formation of ultralong VH CDR3 in Bos taurus antibodies. Cell Mol. Immunol. https://doi.org/10.1038/cmi.2017.117 (2017).

  3. Baumann, B., Potash, M. J. & Köhler, G. Consequences of frameshift mutations at the immunoglobulin heavy chain locus of the mouse. EMBO J. 4, 351–359 (1985).

    Article  CAS  Google Scholar 

  4. Jäck, H. M., Berg, J. & Wabl, M. Translation affects immunoglobulin mRNA stability. Eur. J. Immunol. 19, 843–847 (1989).

    Article  Google Scholar 

  5. Chemin, G. et al. Multiple RNA surveillance mechanisms cooperate to reduce the amount of nonfunctional Ig kappa transcripts. J. Immunol. 184, 5009–5017 (2010).

    Article  CAS  Google Scholar 

  6. Tinguely, A. et al. Cross talk between immunoglobulin heavy-chain transcription and RNA surveillance during B cell development. Mol. Cell Biol. 32, 107–117 (2012).

    Article  CAS  Google Scholar 

  7. Valentine, C. R. The association of nonsense codons with exon skipping. Mutat. Res. 411, 87–117 (1998).

    Article  Google Scholar 

  8. Maquat, L. E. NASty effects on fibrillin pre-mRNA splicing: another case of ESE does it, but proposals for translation-dependent splice site choice live on. Genes Dev. 16, 1743–1753 (2002).

    Article  CAS  Google Scholar 

  9. Chang, Y.-F., Chan, W.-K., Imam, J. S. & Wilkinson, M. F. Alternatively spliced T-cell receptor transcripts are up-regulated in response to disruption of either splicing elements or reading frame. J. Biol. Chem. 282, 29738–29747 (2007).

    Article  CAS  Google Scholar 

  10. Srour, N. et al. A plasma cell differentiation quality control ablates B cell clones with biallelic Ig rearrangements and truncated Ig production. J. Exp. Med. 213, 109–122 (2016).

    Article  CAS  Google Scholar 

  11. Delpy, L., Le Bert, M., Cogné, M. & Khamlichi, A. A. Germ-line transcription occurs on both the functional and the non-functional alleles of immunoglobulin constant heavy chain genes. Eur. J. Immunol. 33, 2108–2113 (2003).

    Article  CAS  Google Scholar 

  12. Reynaud, S. et al. Interallelic class switch recombination contributes significantly to class switching in mouse B cells. J. Immunol. 174, 6176–6183 (2005).

    Article  CAS  Google Scholar 

  13. Casola, S. et al. B cell receptor signal strength determines B cell fate. Nat. Immunol. 5, 317–327 (2004).

    Article  CAS  Google Scholar 

  14. Lechouane, F. et al. B-cell receptor signal strength influences terminal differentiation. Eur. J. Immunol. 43, 619–628 (2013).

    Article  CAS  Google Scholar 

  15. Wesemann, D. R. et al. Microbial colonization influences early B-lineage development in the gut lamina propria. Nature 501, 112–115 (2013).

    Article  CAS  Google Scholar 

  16. Aouinti, S. et al. IMGT/StatClonotype for pairwise evaluation and visualization of NGS IG and TR IMGT clonotype (AA) diversity or expression from IMGT/HighV-QUEST. Front. Immunol. 7, 339 (2016).

    Article  Google Scholar 

  17. Pan, Q. et al. Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression. Genes Dev. 20, 153–158 (2006).

    Article  CAS  Google Scholar 

  18. de la Mata, M. et al. RNA polymerase II elongation at the crossroads of transcription and alternative splicing. Genet. Res. Int. 2011, 309865 (2011).

    PubMed  PubMed Central  Google Scholar 

  19. Schor, I. E., Rascovan, N., Pelisch, F., Alló, M. & Kornblihtt, A. R. Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing. Proc. Natl Acad. Sci. USA 106, 4325–4330 (2009).

    Article  CAS  Google Scholar 

  20. Park, S.-K., Xiang, Y., Feng, X. & Garrard, W. T. Pronounced cohabitation of active immunoglobulin genes from three different chromosomes in transcription factories during maximal antibody synthesis. Genes Dev. 28, 1159–1164 (2014).

    Article  CAS  Google Scholar 

  21. Kassambara, A. et al. 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).

    Article  Google Scholar 

  22. Kolasinska-Zwierz, P. et al. Differential chromatin marking of introns and expressed exons by H3K36me3. Nat. Genet. 41, 376–381 (2009).

    Article  CAS  Google Scholar 

  23. Meda, F., Folci, M., Baccarelli, A. & Selmi, C. The epigenetics of autoimmunity. Cell Mol. Immunol. 8, 226–236 (2011).

    Article  CAS  Google Scholar 

  24. Luco, R. F. et al. Regulation of alternative splicing by histone modifications. Science 327, 996–1000 (2010).

    Article  CAS  Google Scholar 

  25. Saint-André, V., Batsché, E., Rachez, C. & Muchardt, C. Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons. Nat. Struct. Mol. Biol. 18, 337–344 (2011).

    Article  Google Scholar 

  26. Zhou, H.-L., Luo, G., Wise, J. A. & Lou, H. Regulation of alternative splicing by local histone modifications: potential roles for RNA-guided mechanisms. Nucleic Acids Res. 42, 701–713 (2014).

    Article  CAS  Google Scholar 

  27. Benchaouir, R., Robin, V. & Goyenvalle, A. Gene and splicing therapies for neuromuscular diseases. Front. Biosci. Landmark Ed. 20, 1190–1233 (2015).

    Article  CAS  Google Scholar 

  28. Groen, E. J. N., Talbot, K., Gillingwater, T. H. Advances in therapy for spinal muscular atrophy: promises and challenges. Nat. Rev. Neurol. https://doi.org/10.1038/nrneurol.2018.4 (2018).

  29. Stein, C. A. & Castanotto, D. FDA-approved oligonucleotide therapies in 2017. Mol. Ther. J. Am. Soc. Gene Ther. 25, 1069–1075 (2017).

    Article  CAS  Google Scholar 

  30. Mostoslavsky, R., Alt, F. W. & Rajewsky, K. The lingering enigma of the allelic exclusion mechanism. Cell 118, 539–544 (2004).

    Article  CAS  Google Scholar 

  31. Blencowe, B. J. Alternative splicing: new insights from global analyses. Cell 126, 37–47 (2006).

    Article  CAS  Google Scholar 

  32. Johnson, K., Angelin-Duclos, C., Park, S. & Calame, K. L. Changes in histone acetylation are associated with differences in accessibility of V(H) gene segments to V-DJ recombination during B-cell ontogeny and development. Mol. Cell Biol. 23, 2438–2450 (2003).

    Article  CAS  Google Scholar 

  33. Wang, E. T. et al. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470–476 (2008).

    Article  CAS  Google Scholar 

  34. Aartsma-Rus, A. & van Ommen, G.-J. B. Progress in therapeutic antisense applications for neuromuscular disorders. Eur. J. Hum. Genet. 18, 146–153 (2010).

    Article  CAS  Google Scholar 

  35. Daly, J., Licence, S., Nanou, A., Morgan, G. & Mårtensson, I.-L. Transcription of productive and nonproductive VDJ-recombined alleles after IgH allelic exclusion. EMBO J. 26, 4273–4282 (2007).

    Article  CAS  Google Scholar 

  36. Delpy, L., Sirac, C., Le Morvan, C. & Cogné, M. Transcription-dependent somatic hypermutation occurs at similar levels on functional and nonfunctional rearranged IgH alleles. J. Immunol. 173, 1842–1848 (2004).

    Article  CAS  Google Scholar 

  37. Holwerda, S. J. B. et al. Allelic exclusion of the immunoglobulin heavy chain locus is independent of its nuclear localization in mature B cells. Nucleic Acids Res. 41, 6905–6916 (2013).

    Article  CAS  Google Scholar 

  38. Nogués, G. et al. Control of alternative pre-mRNA splicing by RNA Pol II elongation: faster is not always better. IUBMB Life 55, 235–241 (2003).

    Article  Google Scholar 

  39. Pandit, S., Wang, D. & Fu, X.-D. Functional integration of transcriptional and RNA processing machineries. Curr. Opin. Cell Biol. 20, 260–265 (2008).

    Article  CAS  Google Scholar 

  40. Shukla, S. & Oberdoerffer, S. Co-transcriptional regulation of alternative pre-mRNA splicing. Biochim. Biophys. Acta 1819, 673–683 (2012).

    Article  CAS  Google Scholar 

  41. Pinaud, E. et al. Localization of the 3’ IgH locus elements that effect long-distance regulation of class switch recombination. Immunity 15, 187–199 (2001).

    Article  CAS  Google Scholar 

  42. Sirac, C. et al. Role of the monoclonal kappa chain V domain and reversibility of renal damage in a transgenic model of acquired Fanconi syndrome. Blood 108, 536–543 (2006).

    Article  CAS  Google Scholar 

  43. Rouaud, P. et al. The IgH 3’ regulatory region controls somatic hypermutation in germinal center B cells. J. Exp. Med. 210, 1501–1507 (2013).

    Article  CAS  Google Scholar 

  44. Green, M. R. et al. Signatures of murine B-cell development implicate Yy1 as a regulator of the germinal center-specific program. Proc. Natl Acad. Sci. USA 108, 2873–2878 (2011).

    Article  CAS  Google Scholar 

  45. Eisen, M. B., Spellman, P. T., Brown, P. O. & Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA 95, 14863–14868 (1998).

    Article  CAS  Google Scholar 

  46. Tusher, V. G., Tibshirani, R. & Chu, G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA 98, 5116–5121 (2001).

    Article  CAS  Google Scholar 

  47. Li, S. et al. IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling. Nat. Commun. 4, 2333 (2013).

    Article  Google Scholar 

  48. Boice, M. et al. Loss of the HVEM tumor suppressor in lymphoma and restoration by modified CAR-T cells. Cell 167, 405–418.e13 (2016).

    Article  CAS  Google Scholar 

  49. Alamyar, E., Duroux, P., Lefranc, M.-P. & Giudicelli, V. IMGT(®) tools for the nucleotide analysis of immunoglobulin (IG) and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations: IMGT/V-QUEST and IMGT/HighV-QUEST for NGS. Methods Mol. Biol. 882, 569–604 (2012).

    Article  CAS  Google Scholar 

  50. Bischof, J. & Ibrahim, S. M. bcRep: R package for comprehensive analysis of B cell receptor repertoire data. PLoS ONE 11, e0161569 (2016).

    Article  Google Scholar 

Download references

Acknowledgements

We thank the staff of our animal facility as well as C. Carrion for technical assistance with microscopy and cell cytometry. We also thank K. Rajewsky (The Max Delbrück Center for Molecular Medicine, Berlin, Germany) and S. Casola (Institute of Molecular Oncology Foundation, Milano, Italy) for providing DH-LMP2A mice. We are grateful to N. Diallon (MRC Clinical Sciences Centre, London, UK) for providing the pγSat plasmid and M. Alizadeh (UMR S 917, Rennes, France) for repertoire sequencing. This work was supported by grants from Fondation ARC (PJA 20161204724/PGA120150202338), INCa (PLBIO15-256), ANR (2017-CE15-0024-01), Ligue Contre le Cancer (comités Corrèze, Haute-Vienne), Fondation Française pour la Recherche contre le Myélome et les Gammapathies monoclonales (FFRMG) and Comité d’Organisation de la Recherche sur le Cancer du Limousin (CORC). M.O.A. and N.S. were funded by Société Française d’Hématologie (SFH) and Région Limousin, respectively.

Author information

Author notes

  1. Nivine Srour

    Present address: Lady Davis Institute for Medical Research, McGill University, 3755 Cote Ste-Catherine Road, Montreal, QC, H3T 1E2, Canada

  2. These authors contributed equally: Mohamad Omar Ashi, Nivine Srour.

Authors and Affiliations

  1. Unité Mixte de Recherche Centre National de la Recherche Scientifique 7276, INSERM U1262—Contrôle de la Réponse Immune B et Lymphoproliférations, Université de Limoges, Limoges, France

    Mohamad Omar Ashi, Jean-Marie Lambert, Anne Marchalot, Ophélie Martin, Sandrine Le Noir, Eric Pinaud, Maria Victoria Ayala, Christophe Sirac, Jérôme Saulière, Michel Cogné & Laurent Delpy

  2. Institute of Human Genetics, CNRS-UM UMR9002, Department of Biological Haematology, CHU Montpellier, University of Montpellier, UFR Medecine, Montpellier, France

    Jérôme Moreaux

  3. Institut Universitaire de France, Université de Limoges, Limoges, France

    Michel Cogné

Authors
  1. Mohamad Omar Ashi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Nivine Srour
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jean-Marie Lambert
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Anne Marchalot
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ophélie Martin
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Sandrine Le Noir
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Eric Pinaud
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Maria Victoria Ayala
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Christophe Sirac
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Jérôme Saulière
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Jérôme Moreaux
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Michel Cogné
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Laurent Delpy
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

M.O.A. and N.S. designed and performed experiments, analyzed data and wrote the paper. J.-M.L. and A.M. contributed data to Fig. 6. O.M., S.L.N., and E.P. contributed 3D DNA-FISH data in Fig. 3. J.M. performed gene expression analysis in Fig. 4. M.V.A., J.S., C.S., and M.C. helped with the experiments and interpretation of the data. L.D. conceived the project, designed experiments, analyzed data and wrote the paper.

Corresponding author

Correspondence to Laurent Delpy.

Ethics declarations

Competing interests

The authors declare no competing interests.

Data availability

The data that support the findings of this study are available from the corresponding author upon reasonable request.

Additional information

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Ashi, M.O., Srour, N., Lambert, JM. et al. Physiological and druggable skipping of immunoglobulin variable exons in plasma cells. Cell Mol Immunol 16, 810–819 (2019). https://doi.org/10.1038/s41423-018-0160-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41423-018-0160-6

Keywords

This article is cited by

Search

Advanced search

Quick links