Oncogenic Rag GTPase signalling enhances B cell activation and drives follicular lymphoma sensitive to pharmacological inhibition of mTOR


The humoral immune response requires that B cells undergo a sudden anabolic shift and high cellular nutrient levels, which are required to sustain the subsequent proliferative burst. Follicular lymphoma (FL) originates from B cells that have participated in the humoral response, and 15% of FL samples harbour point-activating mutations in RRAGC, an essential activator of mTORC1 downstream of the sensing of cellular nutrients. The impact of recurrent RRAGC mutations in B cell function and lymphoma is unexplored. RRAGC mutations, targeted to the endogenous locus in mice, confer a partial insensitivity to nutrient deprivation, but strongly exacerbate B cell responses and accelerate lymphomagenesis, while creating a selective vulnerability to pharmacological inhibition of mTORC1. This moderate increase in nutrient signalling synergizes with paracrine cues from the supportive T cell microenvironment that activate B cells via the PI3K–Akt–mTORC1 axis. Hence, Rragc mutations sustain induced germinal centres and murine and human FL in the presence of decreased T cell help. Our results support a model in which activating mutations in the nutrient signalling pathway foster lymphomagenesis by corrupting a nutrient-dependent control over paracrine signals from the T cell microenvironment.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: RagC mutant cells are partially resistant to amino acid withdrawal.
Fig. 2: Accelerated lymphomagenesis by heterozygous expression of mutant RagC in mice with selective sensitivity to rapamycin.
Fig. 3: Exacerbated humoral response in RagC mutant mice.
Fig. 4: B cell-intrinsic activation and increased fitness by expression of RagC mutations.
Fig. 5: Impact of RagC mutations in Tfh-mediated B cell activation and apoptosis in FL.
Fig. 6: Consequences of RagC mutations for GC B cell and lymphomagenesis.

Data availability

Sequence data that support the findings of this study have been deposited in GEO, with the accession codes GSE125393 and GSE125394. The data that support the findings of this study are available from the corresponding author upon request. The data that support the plots within this paper and other findings of this study are available from the corresponding author upon reasonable request.


  1. 1.

    Kahl, B. D. & Yang, D. T. Follicular lymphoma: evolving therapeutic strategies. Blood 127, 2055–2063 (2016).

    CAS  Article  Google Scholar 

  2. 2.

    Victora, G. D. & Nussenzweig, M. C. Germinal centers. Annu. Rev. Immunol. 30, 429–457 (2012).

    CAS  Article  Google Scholar 

  3. 3.

    Shlomchik, M. J. & Weisel, F. Germinal center selection and the development of memory B and plasma cells. Immunol. Rev. 247, 52–63 (2012).

    Article  Google Scholar 

  4. 4.

    Mesin, L., Ersching, J. & Victora, G. D. Germinal center B cell dynamics. Immunity 45, 471–482 (2016).

    CAS  Article  Google Scholar 

  5. 5.

    Bannard, O. & Cyster, J. G. Germinal centers: programmed for affinity maturation and antibody diversification. Curr. Opin. Immunol. 45, 21–30 (2017).

    CAS  Article  Google Scholar 

  6. 6.

    Tas, J. et al. Visualizing antibody affinity maturation in germinal centers. Science 351, 1048–1054 (2016).

    CAS  Article  Google Scholar 

  7. 7.

    de Jong, D. & Fest, T. The microenvironment in follicular lymphoma. Best Pract. Res. Clin. Haematol. 24, 135–146 (2011).

    Article  Google Scholar 

  8. 8.

    Huet, S., Sujobert, P. & Salles, G. From genetics to the clinic: a translational perspective on follicular lymphoma. Nat. Rev. Cancer 18, 224–239 (2018).

    CAS  Article  Google Scholar 

  9. 9.

    Pasqualucci, L. et al. Genetics of follicular lymphoma transformation. Cell Rep. 6, 130–140 (2014).

    CAS  Article  Google Scholar 

  10. 10.

    Pasqualucci, L. et al. Inactivating mutations of acetyltransferase genes in B-cell lymphoma. Nature 471, 189–195 (2011).

    CAS  Article  Google Scholar 

  11. 11.

    Morin, R. D. et al. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature 476, 298–303 (2011).

    CAS  Article  Google Scholar 

  12. 12.

    Morin, R. D. et al. Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat. Genet. 42, 181–185 (2010).

    CAS  Article  Google Scholar 

  13. 13.

    Okosun, J. et al. Integrated genomic analysis identifies recurrent mutations and evolution patterns driving the initiation and progression of follicular lymphoma. Nat. Genet 46, 176–181 (2014).

    CAS  Article  Google Scholar 

  14. 14.

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

    CAS  Article  Google Scholar 

  15. 15.

    Challa-Malladi, M. et al. Combined genetic inactivation of β2-microglobulin and CD58 reveals frequent escape from immune recognition in diffuse large B cell lymphoma. Cancer Cell 20, 728–740 (2011).

    CAS  Article  Google Scholar 

  16. 16.

    Cheung, K. J. J. et al. Acquired TNFRSF14 mutations in follicular lymphoma are associated with worse prognosis. Cancer Res. 70, 9166–9174 (2010).

    CAS  Article  Google Scholar 

  17. 17.

    Kridel, R. et al. Histological transformation and progression in follicular lymphoma: a clonal evolution study. PLoS Med. 13, e1002197 (2016).

    Article  Google Scholar 

  18. 18.

    Launay, E. et al. High rate of TNFRSF14 gene alterations related to 1p36 region in de novo follicular lymphoma and impact on prognosis. Leukemia 26, 559–562 (2012).

    CAS  Article  Google Scholar 

  19. 19.

    Ying, Z. X. et al. Recurrent mutations in the MTOR regulator RRAGC in follicular lymphoma. Clin. Cancer Res. 22, 5383–5393 (2016).

    CAS  Article  Google Scholar 

  20. 20.

    Okosun, J. et al. Recurrent mTORC1-activating RRAGC mutations in follicular lymphoma. Nat. Genet. 48, 183–188 (2016).

    CAS  Article  Google Scholar 

  21. 21.

    Green, M. R. et al. Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation. Proc. Natl Acad. Sci. USA 112, E1116–E1125 (2015).

    CAS  Article  Google Scholar 

  22. 22.

    Ben-Sahra, I. & Manning, B. D. mTORC1 signaling and the metabolic control of cell growth. Curr. Opin. Cell Biol. 45, 72–82 (2017).

    CAS  Article  Google Scholar 

  23. 23.

    Efeyan, A., Comb, W. C. & Sabatini, D. M. Nutrient-sensing mechanisms and pathways. Nature 517, 302–310 (2015).

    CAS  Article  Google Scholar 

  24. 24.

    Kim, E., Goraksha-Hicks, P., Li, L., Neufeld, T. P. & Guan, K. L. Regulation of TORC1 by Rag GTPases in nutrient response. Nat. Cell Biol. 10, 935–945 (2008).

    CAS  Article  Google Scholar 

  25. 25.

    Sancak, Y. et al. The Rag GTPases bind raptor and mediate amino acid signaling to mTORC1. Science 320, 1496–1501 (2008).

    CAS  Article  Google Scholar 

  26. 26.

    Shen, K., Choe, A. & Sabatini, D. M. Intersubunit crosstalk in the Rag GTPase heterodimer enables mTORC1 to respond rapidly to amino acid availability. Mol. Cell 68, 552–565 (2017).

    CAS  Article  Google Scholar 

  27. 27.

    Shimobayashi, M. & Hall, M. N. Making new contacts: the mTOR network in metabolism and signalling crosstalk. Nat. Rev. Mol. Cell Biol. 15, 155–162 (2014).

    CAS  Article  Google Scholar 

  28. 28.

    Valvezan, A. J. & Manning, B. D. Molecular logic of mTORC1 signalling as a metabolic rheostat. Nat. Metab. 1, 321–333 (2019).

    Article  Google Scholar 

  29. 29.

    Tsun, Z. Y. et al. The folliculin tumor suppressor is a GAP for the RagC/D GTPases that signal amino acid levels to mTORC1. Mol. Cell 52, 495–505 (2013).

    CAS  Article  Google Scholar 

  30. 30.

    Wang, H. et al. One-step generation of mice carrying mutations in multiple genes by CRISPR/cas-mediated genome engineering. Cell 153, 910–918 (2013).

    CAS  Article  Google Scholar 

  31. 31.

    Efeyan, A. et al. Regulation of mTORC1 by the Rag GTPases is necessary for neonatal autophagy and survival. Nature 493, 679–683 (2013).

    CAS  Article  Google Scholar 

  32. 32.

    Hara, K. et al. Amino acid sufficiency and mTOR regulate p70 S6 kinase and eIF-4E BP1 through a common effector mechanism. J. Biol. Chem. 273, 14484–14494 (1998).

    CAS  Article  Google Scholar 

  33. 33.

    Wang, S. et al. Metabolism. Lysosomal amino acid transporter SLC38A9 signals arginine sufficiency to mTORC1. Science 347, 188–194 (2015).

    CAS  Article  Google Scholar 

  34. 34.

    Egle, A., Harris, A. W., Bath, M. L., O’Reilly, L. & Cory, S. VavP-Bcl2 transgenic mice develop follicular lymphoma preceded by germinal center hyperplasia. Blood 103, 2276–2283 (2004).

    CAS  Article  Google Scholar 

  35. 35.

    Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545–15550 (2005).

    CAS  Article  Google Scholar 

  36. 36.

    Ersching, J. et al. Germinal center selection and affinity maturation require dynamic regulation of mTORC1 kinase. Immunity 46, 1045–1058 (2017).

    CAS  Article  Google Scholar 

  37. 37.

    Kitamura, D., Roes, J., Kuhn, R. & Rajewsky, K. A. B cell-deficient mouse by targeted disruption of the membrane exon of the immunoglobulin μ chain gene. Nature 350, 423–426 (1991).

    CAS  Article  Google Scholar 

  38. 38.

    Calado, D. P. et al. The cell-cycle regulator c-Myc is essential for the formation and maintenance of germinal centers. Nat. Immunol. 13, 1092–1100 (2012).

    CAS  Article  Google Scholar 

  39. 39.

    Dominguez-Sola, D. et al. The proto-oncogene MYC is required for selection in the germinal center and cyclic reentry. Nat. Immunol. 13, 1083–1091 (2012).

    CAS  Article  Google Scholar 

  40. 40.

    Krysiak, K. et al. Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma. Blood 129, 473–483 (2017).

    CAS  Article  Google Scholar 

  41. 41.

    Peng, T., Golub, T. R. & Sabatini, D. M. The immunosuppressant rapamycin mimics a starvation-like signal distinct from amino acid and glucose deprivation. Mol. Cell Biol. 22, 5575–5584 (2002).

    CAS  Article  Google Scholar 

  42. 42.

    Murakami, M. et al. mTOR is essential for growth and proliferation in early mouse embryos and embryonic stem cells. Mol. Cell. Biol. 24, 6710–6718 (2004).

    CAS  Article  Google Scholar 

  43. 43.

    Thoreen, C. C. et al. An ATP-competitive mammalian target of rapamycin inhibitor reveals rapamycin-resistant functions of mTORC1. J. Biol. Chem. 284, 8023–8032 (2009).

    CAS  Article  Google Scholar 

  44. 44.

    Feldman, M. E. et al. Active-site inhibitors of mTOR target rapamycin-resistant outputs of mTORC1 and mTORC2. PLoS Biol. 7, e38 (2009).

    Article  Google Scholar 

  45. 45.

    Zoncu, R., Efeyan, A. & Sabatini, D. M. mTOR: from growth signal integration to cancer, diabetes and ageing. Nat. Rev. Mol. Cell Biol. 12, 21–35 (2011).

    CAS  Article  Google Scholar 

  46. 46.

    Luo, W., Weisel, F. & Shlomchik, M. J. B. B cell receptor and CD40 signaling are rewired for synergistic induction of the c-Myc transcription factor in germinal center B cells. Immunity 48, 313–326 (2018).

    CAS  Article  Google Scholar 

  47. 47.

    Han, S. et al. Cellular interaction in germinal centers. Roles of CD40 ligand and B7-2 in established germinal centers. J. Immunol. 155, 556–567 (1995).

    CAS  PubMed  Google Scholar 

  48. 48.

    Papa, I. & Vinuesa, C. G. Synaptic interactions in germinal centers. Front. Immunol. 9, 1858 (2018).

    Article  Google Scholar 

  49. 49.

    Vinuesa, C. G. & Cyster, J. G. How T cells earn the follicular rite of passage. Immunity 35, 671–680 (2011).

    CAS  Article  Google Scholar 

  50. 50.

    Vinuesa, C. G., Linterman, M. A., Yu, D. & MacLennan, I. C. M. Follicular helper T cells. Annu. Rev. Immunol. 34, 335–368 (2016).

    CAS  Article  Google Scholar 

  51. 51.

    Qi, H., Cannons, J. L., Klauschen, F., Schwartzberg, P. L. & Germain, R. N. SAP-controlled T–B cell interactions underlie germinal centre formation. Nature 455, 764–769 (2008).

    CAS  Article  Google Scholar 

  52. 52.

    Zoncu, R. et al. mTORC1 senses lysosomal aminoacids through an inside-out mechanism that requires the vacuolar H+-ATPase. Science 334, 678–683 (2011).

    CAS  Article  Google Scholar 

  53. 53.

    Efeyan, A. et al. RagA, but not RagB, is essential for embryonic development and adult mice. Dev. Cell 29, 321–329 (2014).

    CAS  Article  Google Scholar 

  54. 54.

    Boothby, M. & Rickert, R. C. Metabolic regulation of the immune humoral response. Immunity 46, 742–755 (2017).

    Article  Google Scholar 

  55. 55.

    Heise, N. et al. Germinal center B cell maintenance and differentiation are controlled by distinct NF-κB transcription factor subunits. J. Exp. Med. 211, 2103–2118 (2014).

    CAS  Article  Google Scholar 

  56. 56.

    Dowling, R. J. O. et al. mTORC1-mediated cell proliferation, but not cell growth, controlled by the 4E-BPs. Science 328, 1172–1176 (2010).

    CAS  Article  Google Scholar 

  57. 57.

    Barbet, N. C. et al. TOR controls translation initiation and early G1 progression in yeast. Mol. Biol. Cell 7, 25–42 (1996).

    CAS  Article  Google Scholar 

  58. 58.

    Smith, S. M. et al. Temsirolimus has activity in non-mantle cell non-Hodgkin’s lymphoma subtypes: The University of Chicago phase II consortium. J. Clin. Oncol. 28, 4740–4746 (2010).

    CAS  Article  Google Scholar 

  59. 59.

    Bannani, N. N. et al. Efficacy of the oral mTORC1 inhibitor everolimus in relapsed or refractory indolent lymphoma. Am. J. Hematol. 92, 448–453 (2017).

    Article  Google Scholar 

  60. 60.

    Witzig, T. E. et al. A phase II trial of the oral mTOR inhibitor everolimus in relapsed aggressive lymphoma. Leukemia 25, 341–347 (2011).

    CAS  Article  Google Scholar 

  61. 61.

    Willett, E. V. et al. Non‐Hodgkin lymphoma and obesity: a pooled analysis from the InterLymph Consortium. Int. J. Cancer 122, 2062–2070 (2008).

    CAS  Article  Google Scholar 

  62. 62.

    Renehan, A. G., Tyson, M., Egger, M., Heller, R. F. & Zwahlen, M. Body-mass index and incidence of cancer: a systematic review and meta-analysis of prospective observational studies. Lancet 371, 569–578 (2008).

    Article  Google Scholar 

  63. 63.

    Bhaskaran, K. et al. Body-mass index and risk of 22 specific cancers: a population-based cohort study of 5.24 million UK adults. Lancet 384, 755–765 (2014).

    Article  Google Scholar 

  64. 64.

    The Global BMI Mortality Collaboration Body-mass index and all-cause mortality: individual-participant-data meta-analysis of 239 prospective studies in four continentsThe Global BMI Mortality Collaboration Show footnotes. Lancet 388, 776–786 (2016).

    Article  Google Scholar 

  65. 65.

    Kosaraju, R. et al. B cell activity is impaired in human and mouse obesity and is responsive to an essential fatty acid upon murine influenza infection. J. Immunol. 198, 4738–4752 (2017).

    CAS  Article  Google Scholar 

  66. 66.

    Sheridan, P. A. et al. Obesity is associated with impaired immune response to influenza vaccination in humans. Int. J. Obes. (Lond.) 36, 1072–1077 (2012).

    CAS  Article  Google Scholar 

  67. 67.

    Zhang, J. et al. The CREBBP acetyltransferase is a haploinsufficient tumor suppressor in B-cell lymphoma. Cancer Discov. 7, 322–337 (2017).

    Article  Google Scholar 

  68. 68.

    Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7, 562–578 (2012).

    CAS  Article  Google Scholar 

  69. 69.

    Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).

    Article  Google Scholar 

  70. 70.

    Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    Article  Google Scholar 

  71. 71.

    Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).

    Article  Google Scholar 

  72. 72.

    Carreras, J. et al. High numbers of tumor-infiltrating programmed cell death 1-positive regulatory lymphocytes are associated with improved overall survival in follicular lymphoma. J. Clin. Oncol. 27, 1470–1476 (2009).

    Article  Google Scholar 

  73. 73.

    Carreras, J. et al. Genomic profile and pathologic features of diffuse large b-cell lymphoma subtype of methotrexate-associated lymphoproliferative disorder in rheumatoid arthritis patients. Am. J. Surg. Pathol. 42, 936–950 (2018).

    Article  Google Scholar 

Download references


We are indebted to D. M. Sabatini (R01 CA129105, R01 CA103866 and R37 AI047389) and thank R. Jaenisch, S. Markoulaki and the Whitehead Institute for Biomedical Research CRISPR facility for zygote injections. We thank A. Clear and K. Korfi for generating TMAs from lymphoma patients, and P. A. Katajisto for critical reading of the manuscript. We also thank CNIO Flow Cytometry, Histopathology, Animal Facility and Genomics Core Units for excellent technical support. Research was supported by the RETOS projects Programme of Spanish Ministry of Science, Innovation and Universities, Spanish State Research Agency, cofunded by the European Regional Development Fund (grant SAF2015-67538-R), EU-H2020 Programme (ERC-2014-STG-638891), Excellence Network Grant from MICIU/AEI (SAF2016-81975-REDT), a Ramon y Cajal Award from MICIU/AEI (RYC-2013-13546), Spanish Association Against Cancer Research Scientific Foundation Laboratory Grant, Beca de Investigación en Oncología Olivia Roddom, FERO Grant for Research in Oncology; Miguel Servet Fellowship and Grant Award (MS16/00112 and CP16/00112) and Project PI18/00816 within the Health Strategic Action from the ISCIII (to A.O.-M.), both cofunded by the European Regional Development Fund, Marcos Fernandez Fellowship from the Spanish Leukaemia and Lymphoma Foundation/Vistare Foundation (to A.O.-M.) and L’Oreal For Women in Science Award (to A.O.-M.). J.F. is a recipient of a Cancer Research UK Programme Award (15968) and J.O. is a recipient of a Cancer Research UK Clinician Scientist Fellowship (22742). N.M.-M. is a Ramon y Cajal Awardee MICIU/AEI (RYC-2016-20173). N.D.-S., C.C.A., A.B.P.-G. and K.T. are recipients of Ayudas de contratos predoctorales para la formacion de doctores from MICIU/AEI (BES-2016-077410, BES-2015-073776, BES-2017081381, BES-2016-078082).

Author information




A.O.-M. performed most experiments, contributed to experimental design, data analysis and writing of the manuscript. N.D.-S, A.S., C.L.-F, C.M., C.C.A., A.V., L.M.-A, B.F.-R, A.B.P-G. and N.M.-M. provided help with experimentation. K.T. and E.P.-Y. performed bioinformatics analysis of RNA-seq and meta-analysis of mutually exclusive mutations. E.C. and A.D.M. performed and diagnosed the histology and pathology. J.C. and N.N. performed and analysed immunohistochemistry studies on human samples. S.A., J.O. and J.F. performed the mutation analyses on the patient samples, provided the corresponding tissue microarrays and clinical information. J.O., J.F. and G.D.V. contributed critical intellectual input in design and interpretation of data. A.E. conceived and supervised the study, analysed the data, wrote the manuscript and secured funding. All authors read and commented on the manuscript and figures.

Corresponding author

Correspondence to Alejo Efeyan.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information: Primary Handling Editor: Ana Mateus.

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

Supplementary information

Supplementary Information

Supplementary Figs. 1–7 and Tables 1–3

Reporting Summary

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Ortega-Molina, A., Deleyto-Seldas, N., Carreras, J. et al. Oncogenic Rag GTPase signalling enhances B cell activation and drives follicular lymphoma sensitive to pharmacological inhibition of mTOR. Nat Metab 1, 775–789 (2019). https://doi.org/10.1038/s42255-019-0098-8

Download citation

Further reading