Abstract
Naive T cells are maintained under a quiescent state, and their exit from quiescence is a hallmark of antigen stimulation. Here we identify the RNA binding protein La-related protein 4 (LARP4) as an important checkpoint regulator of quiescence exit in naive CD4+ T cells. Conditional knockout of LARP4 in naive CD4+ T cells leads to an enhanced quiescence state and/or dampened quiescence exit due to altered stability of several messenger RNAs important for T-cell activation. The differentiation of naive CD4+ T cells into helper T-cell subsets is also impaired after conditional knockout, leading to ameliorated autoimmune and allergic responses. Lastly, we design a peptide inhibitor of LARP4 (LIPEP), and treatment with LIPEP could perfectly mimic LARP4 deficiency and alleviate the severity of autoimmune and allergic diseases in the corresponding mouse models. Our study reveals a link between RNA stability and CD4+ T-cell homeostasis/adaptive activation, highlighting the potential of LARP4 as a preventative and therapeutic target for autoimmune and allergic diseases although at quite high doses.
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Data availability
Data from the scRNA-seq, bulk RNA-seq, RIP-seq and RNA decay assays have been deposited in the Genome Sequence Archive (PRJCA009531)33. All other relevant data from this study are available from the corresponding authors upon reasonable request. Source data are provided with this paper.
References
Surh, C. D. & Sprent, J. Homeostasis of naive and memory T cells. Immunity 29, 848–862 (2008).
Hamilton, S. E. & Jameson, S. C. CD8 T cell quiescence revisited. Trends Immunol. 33, 224–230 (2012).
Zhang, S. et al. Newly generated CD4(+) T cells acquire metabolic quiescence after thymic egress. J. Immunol. 200, 1064–1077 (2018).
Chapman, N. M., Boothby, M. R. & Chi, H. Metabolic coordination of T cell quiescence and activation. Nat. Rev. Immunol. 20, 55–70 (2020).
Wildey, G. M. & Howe, P. H. Runx1 is a co-activator with FOXO3 to mediate transforming growth factor beta (TGFbeta)-induced Bim transcription in hepatic cells. J. Biol. Chem. 284, 20227–20239 (2009).
Liu, G. Y. et al. Low avidity recognition of self-antigen by T cells permits escape from central tolerance. Immunity 3, 407–415 (1995).
Kuo, C. T., Veselits, M. L. & Leiden, J. M. LKLF: a transcriptional regulator of single-positive T cell quiescence and survival. Science 277, 1986–1990 (1997).
Tzachanis, D. et al. Tob is a negative regulator of activation that is expressed in anergic and quiescent T cells. Nat. Immunol. 2, 1174–1182 (2001).
Yusuf, I. & Fruman, D. A. Regulation of quiescence in lymphocytes. Trends Immunol. 24, 380–386 (2003).
Hwang, S. S. et al. mRNA destabilization by BTG1 and BTG2 maintains T cell quiescence. Science 367, 1255–1260 (2020).
ElTanbouly, M. A. et al. VISTA is a checkpoint regulator for naive T cell quiescence and peripheral tolerance. Science 367, eaay0524 (2020).
Chapman, N. M. & Chi, H. Hallmarks of T-cell exit from quiescence. Cancer Immunol. Res. 6, 502–508 (2018).
Tian, Y. et al. Transcriptome-wide stability analysis uncovers LARP4-mediated NFkappaB1 mRNA stabilization during T cell activation. Nucleic Acids Res. 48, 8724–8739 (2020).
Mattijssen, S. & Maraia, R. J. LARP4 is regulated by tumor necrosis factor alpha in a tristetraprolin-dependent manner. Mol. Cell Biol. 36, 574–584 (2016).
Mattijssen, S., Kozlov, G., Fonseca, B. D., Gehring, K. & Maraia, R. J. LARP1 and LARP4: up close with PABP for mRNA 3’ poly(A) protection and stabilization. RNA Biol. 18, 259–274 (2021).
Mattijssen, S., Iben, J. R., Li, T., Coon, S. L. & Maraia, R. J. Single molecule poly(A) tail-seq shows LARP4 opposes deadenylation throughout mRNA lifespan with most impact on short tails. eLife 9, e59186 (2020).
Mattijssen, S. et al. LARP4 mRNA codon-tRNA match contributes to LARP4 activity for ribosomal protein mRNA poly(A) tail length protection. eLife 6, e28889 (2017).
Yang, R. et al. La-related protein 4 binds poly(A), interacts with the poly(A)-binding protein MLLE domain via a variant PAM2w motif, and can promote mRNA stability. Mol. Cell Biol. 31, 542–556 (2011).
Tian, Y. et al. SOX-5 activates a novel RORgammat enhancer to facilitate experimental autoimmune encephalomyelitis by promoting Th17 cell differentiation. Nat. Commun. 12, 481 (2021).
Gabrysova, L. et al. c-Maf controls immune responses by regulating disease-specific gene networks and repressing IL-2 in CD4(+) T cells. Nat. Immunol. 19, 497–507 (2018).
Debeuf, N., Haspeslagh, E., van Helden, M., Hammad, H. & Lambrecht, B. N. Mouse models of asthma. Curr. Protoc. Mouse Biol. 6, 169–184 (2016).
ElTanbouly, M. A. & Noelle, R. J. Rethinking peripheral T cell tolerance: checkpoints across a T cell’s journey. Nat. Rev. Immunol. 21, 257–267 (2021).
Cruz-Gallardo, I. et al. LARP4A recognizes polyA RNA via a novel binding mechanism mediated by disordered regions and involving the PAM2w motif, revealing interplay between PABP, LARP4A and mRNA. Nucleic Acids Res. 47, 4272–4291 (2019).
Bourgeois, C. F., Mortreux, F. & Auboeuf, D. The multiple functions of RNA helicases as drivers and regulators of gene expression. Nat. Rev. Mol. Cell Biol. 17, 426–438 (2016).
Shevach, E. M. & Thornton, A. M. tTregs, pTregs, and iTregs: similarities and differences. Immunol. Rev. 259, 88–102 (2014).
Kennedy, A. et al. The CTLA-4 immune checkpoint protein regulates PD-L1:PD-1 interaction via transendocytosis of its ligand CD80. EMBO J. 42, e111556 (2023).
Luoqian, J. et al. Ferroptosis promotes T-cell activation-induced neurodegeneration in multiple sclerosis. Cell Mol. Immunol. 19, 913–924 (2022).
Li, B. W. et al. T cells are necessary for ILC2 activation in house dust mite-induced allergic airway inflammation in mice. Eur. J. Immunol. 46, 1392–1403 (2016).
Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587 (2021).
Wu, S. F. et al. RIG-I regulates myeloid differentiation by promoting TRIM25-mediated ISGylation. Proc. Natl Acad. Sci. USA 117, 14395–14404 (2020).
Coomes, S. M. et al. CD4(+) Th2 cells are directly regulated by IL-10 during allergic airway inflammation. Mucosal Immunol. 10, 150–161 (2017).
Xu, L. et al. The transcription factor TCF-1 initiates the differentiation of T(FH) cells during acute viral infection. Nat. Immunol. 16, 991–999 (2015).
Tian, Y. & Zhou, J. Inhibition of LARP4-mediated quiescence exit of naïve CD4+ T cells ameliorates autoimmune and allergic diseases. GSA https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA009531 (2025).
Acknowledgements
We thank T. Ni and M. Y. Zhou (School of Life Sciences, Fudan University, China) for their helpful comments about data analysis. This work was supported by grants from the General Program of the National Natural Science Foundation of China (number 32170887), the Special Program of the National Natural Science Foundation of China (number 32141005) and the Major Research Plan of the National Natural Science Foundation of China (number 92269110), as well as the Chongqing Talent Program of China (cstc2022ycjh-bgzxm0020), the Natural Science Foundation of Chongqing (cstc2020jcyj-msxmX0909), the National College Students’ Innovation and Entrepreneurship Training Program (202190035003) and the Undergraduate Research Training Project of the Third Military Medical University (2021XBK09). This work was also supported by special fund for performance incentive guidance of research institutions in Chongqing (cstc2021jxjl130036) and Chongqing International Institute for Immunology Project (2022YJC01). The funders had no role in the study design, data analyses or the decision to publish.
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Contributions
Conceptualization: Y.T. and D.Y.; methodology: S.W. and X.L.; investigation: J. Zhou, D.Y., C.H., H.D., Z.W., S.X., C.X., Yiwei Zhang, X.W., J. Luo, Y.D., B.L., R.M. and M.Z.; writing—review and editing: R.L., J. Zhu, D.Y., X.Z., L.Y., B.N., X.C., J. Zhang, T.Z., J. Zhou, Y.T. and Y.W.; resources: J.H., C.W., J. Li, T.L. and Y.S.; supervision: Yi Zhang, Y.T. and Y.W.
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Y.T., Y.W., J. Zhou, Y.D., C.H., H.D., S.W., Yi Zhang, Yiwei Zhang, B.L., R.M. and J. Zhu have filed a patent application (Chinese patent application no. 202410491595.9) based on the data in this paper. The other authors declare no competing interests.
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Nature Biomedical Engineering thanks Jeffrey Hubbell and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.
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Extended data
Extended Data Fig. 1 LARP4 deficiency enforces the quiescent state in naïve T cells.
a, Flow cytometry to determine the frequencies of CD4 single-positive (CD4 SP) T cells in the thymus from the indicated mice. b, Flow cytometry to determine the frequencies of CD62L+CD44− (naïve) or CD62L−CD44+ (effector) T cells in equal numbers of splenic CD4+ T cells from the indicated mice. c, Cell cycle analyses with 4´,6-diamidino-2-phenylindole (DAPI) and Ki-67 staining and the percentage of Ki-67-positive cells in naïve CD4+ T cells. d, The size and granularity of control or CKO naïve T cells was measured by flow cytometry (MFI = Mean Fluorescence Intensity). e, The relative expression of Klf2, Klf6 and Foxp1 mRNAs in naïve CD4+ T cells was determined by RT-qPCR. GAPDH was used as the internal control. f, The protein levels of the KLF2, KLF6 and FOXP1 in naïve CD4+ T cells was measured by western blotting (WB). GAPDH and β-Tubulin was used as the internal control (n = 3 mice per group). Representative data from three independent experiments are shown in a-f. n = 5 mice per group in a-e. The mean ± SEM are shown in a-f. Two-sided Student’s t-tests were used for the comparisons in a-f. Experimental mice were between 6 and 10 weeks of age, with no preference for gender, and were maintained on a C57BL/6 J background.
Extended Data Fig. 2 The characteristics of LIPEP.
a, Data and plots showing measured plasma concentration (ng/mL) of LIPEP in ICR (CD-1) mice after s.c. administration of LIPEP 100 mg/kg of body weight per mice at indicated times. Data are presented as mean ± SD (n = 3). Plots for s.c. administration levels are plotted in a linear and logarithmic y-axis scale. hr=hour. b, Pharmacokinetic parameters for LIPEP: half-life (T1/2), maximum concentration (Cmax) at specific time (Tmax), area under the curve (AUC0-∞), mean residence time (MRT0-∞).
Extended Data Fig. 3 LIPEP could decrease the mRNA stability and expression of genes related to quiescence exit.
a, LIPEP treatment inhibited the interaction between LARP4 and PABPC1. HeLa cells were transfected with the pcDNA3.1-PABPC1 Flag vector together with the pcDNA3.1-LARP4 HA vector and then treated with LIPEP for 24 h at different concentrations. Whole-cell lysates from HeLa cells were subjected to IP with an anti-HA antibody or control mouse IgG and then IB with an anti-Flag or anti-HA HRP antibody. Input proteins (input) were also IB with an anti-Flag or anti-HA HRP antibody. GAPDH was used as the internal control. b, The interaction changes between LARP4 and Cd2, Cd3e, Cd44, Icos and Batf mRNAs in naïve CD4+ T cells after LIPEP treatment were verified by RIP-qPCR normalized to the Ct values of mRNAs encoding the housekeeping gene GAPDH, which was not bound by LARP4. c, The stability changes of Cd3e, Cd2, Cd44, Icos and Batf mRNAs in naïve CD4+ T cells after LIPEP treatment were determined by RT-qPCR using a label-free approach with a 3-point time course (0, 1, and 2 h after FLV treatment). GAPDH was used as the internal control. d, Relative expression changes in Cd2, Cd3e, Cd44, Icos and Batf mRNAs in naïve CD4+ T cells after LIPEP treatment were measured by RT-qPCR. GAPDH was used as the internal control. Representative data from three independent experiments are shown in a-d. n = 5 mice per group in b-d. The mean ± SEM are shown b-d. Two-sided Student’s t-tests were used for the comparisons in b-d. Experimental mice were between 6 and 10 weeks of age, with no preference for gender, and were maintained on a C57BL/6 J background.
Extended Data Fig. 4 LIPEP inhibits the differentiation of naïve T cells.
a, WT naïve CD4+ T cells were stimulated under Th17-polarizing conditions in the presence of LIPEP at different time points, and the frequency of CD4+IL-17A+ Th17 cells was measured by flow cytometry. b, WT naïve CD4+ T cells were stimulated under Th1-polarizing conditions in the presence of LIPEP at different time points, and the frequency of CD4+ IFN-γ+ Th1 cells was measured by flow cytometry. c, WT naïve CD4+ T cells were stimulated under Th2-polarizing conditions in the presence of LIPEP at different time points, and the frequency of CD4+IL-4+ Th2 cells was measured by flow cytometry. d, A total of 2 × 104 naïve CD45.1+ SMARTA cells treated with or without LIPEP were adoptively transferred into naïve wild-type (CD45.2+) recipient mice, which were infected intraperitoneally with the LCMV Armstrong strain the following day. The absolute numbers of CD4+CD45.1+Vα2+, CD45.1+Vα2+CD4+CD44+ and CD45.1+Vα2+CD4+CD69+ cells were assessed by flow cytometry in the host spleen on day 8 after infection. The mean ± SEM are shown in a-d. Representative data from three independent experiments are shown in a-d. n = 5 mice per group in a-d. Two-sided Student’s t-tests were used for the comparisons in a-d. Experimental mice were between 6 and 10 weeks of age, with no preference for gender, and were maintained on a C57BL/6 J background.
Extended Data Fig. 5 LIPEP treatment has the preventative potential in EAE mice.
a, Schematics of preventative potential of LIPEP treatment in an EAE disease model. Control mice were treated with 2% mannitol. b, The mean daily clinical scores of mice after EAE induction are shown (two-way analysis of variance, ANOVA). c, Spinal cords collected from the indicated mice on day 30 were stained with HE or LFB to assess inflammation and myelin content, respectively. The outlines indicate inflammatory or demyelinated foci. Scale bars, 200 or 100 µm (magnified panels). d, On day 30 after EAE induction, CD4+ T cells among leukocytes isolated from the spinal cord of the indicated mice were gated and further analysed to determine the frequencies of CD4+ T cells. In addition, the absolute numbers of spinal cord-infiltrated total CD4+ T cells were also evaluated by flow cytometry. e-h, On day 30 after EAE induction, CD4+ T cells among leukocytes isolated from the spinal cord of the indicated mice were gated and further analysed to determine the frequencies of CD4+IL-17A+ Th17 (e), CD4+ IFN-γ+ Th1 (f), CD4+IL-4+ Th2 (g) and CD4+FOXP3+ Treg cells (h) by flow cytometry. i, Mononuclear cells were collected on day 8 from the draining lymph nodes and further cultured ex vivo with MOG35-55 and LIPEP or mannitol for 3 days. The concentrations of IL-17A, IFN-γ, and IL-4 were measured by ELISA. Representative data from three independent experiments are shown in a-i. n = 5 mice per group in a-i. The mean ± SEM are shown b and d-i. Two-sided Student’s t-tests were used for the comparisons in d-i. Experimental mice were between 6 and 10 weeks of age, with no preference for gender, and were maintained on a C57BL/6 J background.
Extended Data Fig. 6 LIPEP treatment has the preventative potential in the mice model of allergic disease.
a, Schematics of preventative potential of LIPEP treatment in the HDM allergy model. Control mice were treated with 2% mannitol. b, Total cell and eosinophil cell counts in BAL fluids were measured by flow cytometry upon HDM challenge. c,d, Representative lung sections and cumulative total inflammation (H&E) and mucous (AB-PAS) scores Representative data from three independent experiments are shown in a-d. n = 5 mice per group in a-d. The mean ± SEM are shown in b and d. Two-sided Student’s t-tests were used for the comparisons in b and d. Experimental mice were between 6 and 10 weeks of age, with no preference for gender, and were maintained on a C57BL/6 J background.
Supplementary information
Supplementary Information
Supplementary Figs. 1–33, methods, unprocessed blots for the supplementary figures and gating strategy of flow cytometry.
Supplementary Tables
Supplementary Tables 1–6.
Supplementary Data
Statistical source data for the supplementary figures.
Source data
Source Data Figs. 1, 3, 4, 7 and 8 and Extended Data Figs. 1–6
Statistical source data.
Source Data Extended Data Figs. 1 and 3
Unprocessed western blots.
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Zhou, J., Yang, D., Han, C. et al. Inhibition of LARP4-mediated quiescence exit of naive CD4+ T cells ameliorates autoimmune and allergic diseases. Nat. Biomed. Eng (2025). https://doi.org/10.1038/s41551-025-01514-5
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DOI: https://doi.org/10.1038/s41551-025-01514-5
