Abstract
While T cell receptor (TCR) αβ+CD8α+CD8β– intraepithelial lymphocytes (CD8αα+ IELs) differentiate from thymic IEL precursors (IELps) and contribute to gut homeostasis, the transcriptional control of their development remains poorly understood. In the present study we showed that mouse thymocytes deficient for the transcription factor leukemia/lymphoma-related factor (LRF) failed to generate TCRαβ+CD8αα+ IELs and their CD8β-expressing counterparts, despite giving rise to thymus and spleen CD8αβ+ T cells. LRF-deficient IELps failed to migrate to the intestine and to protect against T cell-induced colitis, and had impaired expression of the gut-homing integrin α4β7. Single-cell RNA-sequencing found that LRF was necessary for the expression of genes characteristic of the most mature IELps, including Itgb7, encoding the β7 subunit of α4β7. Chromatin immunoprecipitation and gene-regulatory network analyses both defined Itgb7 as an LRF target. Our study identifies LRF as an essential transcriptional regulator of IELp maturation in the thymus and subsequent migration to the intestinal epithelium.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
Data availability
All sequence data reported in the present study are publicly available on the Gene Expression Omnibus, at accession nos. GSE149993, GSE149943, GSE149985, GSE186164 and GSE186291 for LRF ChIP–seq, RNA-seq, scRNA-seq and scATAC-seq, respectively. All datasets generated and/or analyzed during the present study are presented in this published article. Source data are provided with this paper. All the other relevant data are available upon request.
Code availability
No customized code was developed in the present study. Flow cytometry, statistical and bioinformatics analyses were performed using publicly available software packages, as indicated in Methods.
References
McDonald, B. D., Jabri, B. & Bendelac, A. Diverse developmental pathways of intestinal intraepithelial lymphocytes. Nat. Rev. Immunol. 18, 514–525 (2018).
Cheroutre, H., Lambolez, F. & Mucida, D. The light and dark sides of intestinal intraepithelial lymphocytes. Nat. Rev. Immunol. 11, 445–456 (2011).
Goodman, T. & Lefrancois, L. Expression of the gamma-delta T-cell receptor on intestinal CD8+ intraepithelial lymphocytes. Nature 333, 855–858 (1988).
Di Marco Barros, R. et al. Epithelia use butyrophilin-like molecules to shape organ-specific gammadelta T cell compartments. Cell 167, 203–218.e217 (2016).
Ruscher, R. & Hogquist, K. A. Development, ontogeny, and maintenance of TCRalphabeta+ CD8alphaalpha IEL. Curr. Opin. Immunol. 58, 83–88 (2019).
McDonald, B. D., Bunker, J. J., Ishizuka, I. E., Jabri, B. & Bendelac, A. Elevated T cell receptor signaling identifies a thymic precursor to the TCRalphabeta+CD4−CD8beta− intraepithelial lymphocyte lineage. Immunity 41, 219–229 (2014).
Pobezinsky, L. A. et al. Clonal deletion and the fate of autoreactive thymocytes that survive negative selection. Nat. Immunol. 13, 569–578 (2012).
McDonald, B. D., Bunker, J. J., Erickson, S. A., Oh-Hora, M. & Bendelac, A. Crossreactive alphabeta T cell receptors are the predominant targets of thymocyte negative selection. Immunity 43, 859–869 (2015).
Ruscher, R., Kummer, R. L., Lee, Y. J., Jameson, S. C. & Hogquist, K. A. CD8alphaalpha intraepithelial lymphocytes arise from two main thymic precursors. Nat. Immunol. 18, 771–779 (2017).
Mayans, S. et al. alphabetaT cell receptors expressed by CD4−CD8alphabeta− intraepithelial T cells drive their fate into a unique lineage with unusual MHC reactivities. Immunity 41, 207–218 (2014).
Leishman, A. J. et al. Precursors of functional MHC class I- or class II-restricted CD8alphaalpha+ T cells are positively selected in the thymus by agonist self-peptides. Immunity 16, 355–364 (2002).
Berlin, C. et al. Alpha 4 beta 7 integrin mediates lymphocyte binding to the mucosal vascular addressin MAdCAM-1. Cell 74, 185–195 (1993).
Cepek, K. L. et al. Adhesion between epithelial cells and T lymphocytes mediated by E-cadherin and the alpha E beta 7 integrin. Nature 372, 190–193 (1994).
Wagner, N. et al. Critical role for beta7 integrins in formation of the gut-associated lymphoid tissue. Nature 382, 366–370 (1996).
El-Asady, R. et al. TGF-β-dependent CD103 expression by CD8+ T cells promotes selective destruction of the host intestinal epithelium during graft-versus-host disease. J. Exp. Med 201, 1647–1657 (2005).
Konkel, J. E. et al. Control of the development of CD8alphaalpha+ intestinal intraepithelial lymphocytes by TGF-beta. Nat. Immunol. 12, 312–319 (2011).
Li, Y. et al. Exogenous stimuli maintain intraepithelial lymphocytes via aryl hydrocarbon receptor activation. Cell 147, 629–640 (2011).
Schon, M. P. et al. Mucosal T lymphocyte numbers are selectively reduced in integrin alpha E (CD103)-deficient mice. J. Immunol. 162, 6641–6649 (1999).
Lai, Y. G. et al. IL-15 does not affect IEL development in the thymus but regulates homeostasis of putative precursors and mature CD8 alpha alpha+ IELs in the intestine. J. Immunol. 180, 3757–3765 (2008).
Klose, C. S. et al. The transcription factor T-bet is induced by IL-15 and thymic agonist selection and controls CD8alphaalpha+ intraepithelial lymphocyte development. Immunity 41, 230–243 (2014).
Reis, B. S., Hoytema van Konijnenburg, D. P., Grivennikov, S. I. & Mucida, D. Transcription factor T-bet regulates intraepithelial lymphocyte functional maturation. Immunity 41, 244–256 (2014).
Davies, J. M. et al. Novel BTB/POZ domain zinc-finger protein, LRF, is a potential target of the LAZ-3/BCL-6 oncogene. Oncogene 18, 365–375 (1999).
Ellmeier, W. & Taniuchi, I. The role of BTB-zinc finger transcription factors during T cell development and in the regulation of T cell-mediated immunity. Curr. Top. Microbiol. Immunol. 381, 21–49 (2014).
Maeda, T. Regulation of hematopoietic development by ZBTB transcription factors. Int. J. Hematol. 104, 310–323 (2016).
He, X. et al. The zinc finger transcription factor Th-POK regulates CD4 versus CD8 T-cell lineage commitment. Nature 433, 826–833 (2005).
Sun, G. et al. The zinc finger protein cKrox directs CD4 lineage differentiation during intrathymic T cell positive selection. Nat. Immunol. 6, 373–381 (2005).
Carpenter, A. C. et al. The transcription factors Thpok and LRF are necessary and partly redundant for T helper cell differentiation. Immunity 37, 622–633 (2012).
Vacchio, M. S. et al. A ThPOK-LRF transcriptional node maintains the integrity and effector potential of post-thymic CD4+ T cells. Nat. Immunol. 15, 947–956 (2014).
Maeda, T. et al. Role of the proto-oncogene Pokemon in cellular transformation and ARF repression. Nature 433, 278–285 (2005).
Maeda, T. et al. Regulation of B versus T lymphoid lineage fate decision by the proto-oncogene LRF. Science 316, 860–866 (2007).
Tabung, F. K. et al. Influence of dietary patterns on plasma soluble CD14, a surrogate marker of gut barrier dysfunction. Curr. Dev. Nutr. 1, e001396 (2017). https://doi.org/10.3945/cdn.117.001396
Mucida, D. et al. Transcriptional reprogramming of mature CD4+ helper T cells generates distinct MHC class II-restricted cytotoxic T lymphocytes. Nat. Immunol. 14, 281–289 (2013).
Sujino, T. et al. Tissue adaptation of regulatory and intraepithelial CD4+ T cells controls gut inflammation. Science 352, 1581–1586 (2016).
Lambolez, F., Kronenberg, M. & Cheroutre, H. Thymic differentiation of TCR alpha beta+ CD8 alpha alpha+ IELs. Immunol. Rev. 215, 178–188 (2007).
Yamagata, T., Mathis, D. & Benoist, C. Self-reactivity in thymic double-positive cells commits cells to a CD8 alpha alpha lineage with characteristics of innate immune cells. Nat. Immunol. 5, 597–605 (2004).
Gangadharan, D. et al. Identification of pre- and postselection TCRalphabeta+ intraepithelial lymphocyte precursors in the thymus. Immunity 25, 631–641 (2006).
Ruscher, R. et al. Intestinal CD8alphaalpha IELs derived from two distinct thymic precursors have staggered ontogeny. J. Exp. Med. 217, e20192336 (2020).
Poussier, P., Ning, T., Banerjee, D. & Julius, M. A unique subset of self-specific intraintestinal T cells maintains gut integrity. J. Exp. Med 195, 1491–1497 (2002).
Odumade, O. A., Weinreich, M. A., Jameson, S. C. & Hogquist, K. A. Krüppel-like factor 2 regulates trafficking and homeostasis of γδ T cells. J. Immunol. 184, 6060–6066 (2010).
Xing, Y., Wang, X., Jameson, S. C. & Hogquist, K. A. Late stages of T cell maturation in the thymus involve NF-kappaB and tonic type I interferon signaling. Nat. Immunol. 17, 565–573 (2016).
Chopp, L. B. et al. An integrated epigenomic and transcriptomic map of mouse and human alphabeta T cell development. Immunity 53, 1182–1201.e1188 (2020).
Kovalovsky, D. et al. The BTB-zinc finger transcriptional regulator PLZF controls the development of invariant natural killer T cell effector functions. Nat. Immunol. 9, 1055–1064 (2008).
Savage, A. K. et al. The transcription factor PLZF directs the effector program of the NKT cell lineage. Immunity 29, 391–403 (2008).
Moran, A. E. et al. T cell receptor signal strength in Treg and iNKT cell development demonstrated by a novel fluorescent reporter mouse. J. Exp. Med. 208, 1279–1289 (2011).
Ciucci, T. et al. The emergence and functional fitness of memory CD4+ T cells require the transcription factor Thpok. Immunity 50, 91–105.e104 (2019).
Kamimoto, K., Hoffmann, C. M. & Morris, S. A. CellOracle: dissecting cell identity via network inference and in silico gene perturbation. Preprint at bioRxiv https://doi.org/10.1101/2020.02.17.947416 (2020).
Cervantes-Barragan, L. et al. Lactobacillus reuteri induces gut intraepithelial CD4+CD8alphaalpha+ T cells. Science 357, 806–810 (2017).
Kernfeld, E. M. et al. A single-cell transcriptomic atlas of thymus organogenesis resolves cell types and developmental maturation. Immunity 48, 1258–1270.e1256 (2018).
Hummel, J. F. et al. Single-cell RNA-sequencing identifies the developmental trajectory of C-Myc-dependent NK1.1− T-bet+ intraepithelial lymphocyte precursors. Mucosal Immunol. 13, 257–270 (2020).
Park, J. E. et al. A cell atlas of human thymic development defines T cell repertoire formation. Science 367, eaay3224 (2020).
Le, J. et al. Single-cell RNA-seq mapping of human thymopoiesis reveals lineage specification trajectories and a commitment spectrum in T cell development. Immunity 52, 1105–1118.e1109 (2020).
Egawa, T. & Littman, D. R. ThPOK acts late in specification of the helper T cell lineage and suppresses Runx-mediated commitment to the cytotoxic T cell lineage. Nat. Immunol. 9, 1131–1139 (2008).
Driegen, S. et al. A generic tool for biotinylation of tagged proteins in transgenic mice. Transgenic Res. 14, 477–482 (2005).
Wang, L. et al. The zinc finger transcription factor Zbtb7b represses CD8-lineage gene expression in peripheral CD4+ T cells. Immunity 29, 876–887 (2008).
Lee, P. P. et al. A critical role for Dnmt1 and DNA methylation in T cell development, function, and survival. Immunity 15, 763–774 (2001).
Saitoh, T., Nakano, H., Yamamoto, N. & Yamaoka, S. Lymphotoxin-beta receptor mediates NEMO-independent NF-kappaB activation. FEBS Lett. 532, 45–51 (2002).
Vacchio, M. S. et al. A Thpok-directed transcriptional circuitry promotes Bcl6 and Maf expression to orchestrate T follicular helper differentiation. Immunity 51, 465–478.e466 (2019).
Morita, S., Kojima, T. & Kitamura, T. Plat-E: an efficient and stable system for transient packaging of retroviruses. Gene Ther. 7, 1063–1066 (2000).
Carpenter, A. C., Kim, J. K. & Bosselut, R. Purification of thymocyte and T cell subsets. Methods Mol. Biol. 1323, 87–97 (2016).
Molloy, M. J. et al. Intraluminal containment of commensal outgrowth in the gut during infection-induced dysbiosis. Cell Host Microbe 14, 318–328 (2013).
Fonseca, D. M. et al. Microbiota-dependent sequelae of acute infection compromise tissue-specific immunity. Cell 163, 354–366 (2015).
Kozich, J. J., Westcott, S. L., Baxter, N. T., Highlander, S. K. & Schloss, P. D. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ. Microbiol. 79, 5112–5120 (2013).
Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).
Callahan, B. J., McMurdie, P. J. & Holmes, S. P. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J. 11, 2639–2643 (2017).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Mudge, J. M. & Harrow, J. Creating reference gene annotation for the mouse C57BL6/J genome assembly. Mamm. Genome 26, 366–378 (2015).
Anders, S., Pyl, P. T. & Huber, W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015).
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).
Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888–1902.e1821 (2019).
Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587.e3529 (2021).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Liu, T. Use model-based analysis of ChIP-Seq (MACS) to analyze short reads generated by sequencing protein–DNA interactions in embryonic stem cells. Methods Mol. Biol. 1150, 81–95 (2014).
Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).
Jiang, W. et al. Recognition of gut microbiota by NOD2 is essential for the homeostasis of intestinal intraepithelial lymphocytes. J. Exp. Med. 210, 2465–2476 (2013).
Acknowledgements
We thank P. Subramanian (Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases (NIAID)) for assistance with microbiome analyses, the Center for Cancer Research (CCR) Flow Cytometry Core, the NIH high-performance computing cluster and the NIAID microbiome program for assistance, and W. J. Chen, J. Brenchley and M. S. Vacchio for critical reading of the manuscript. This work was supported by the Intramural Research Program of the NCI, CCR, NIH and the Intramural Research Programs of the NIAID and NINDS. The CCR Single Cell Analysis Facility is funded by the Frederick National Laboratory for Cancer Research (contract no. 75N91019D00024). Sequencing was performed using the CCR Genomics Core.
Author information
Authors and Affiliations
Contributions
J.N. and R.B. conceived the research and designed experiments with contributions from A.C., D.B.M., M.K. and Y.B. J.N. and A.C. performed experiments, with assistance from X.Q. They also analyzed the data. J.N., L.C. and T. Chen performed bioinformatics analyses with contributions from T. Ciucci, J.N. and M.B.-C. R.B. wrote the manuscript with input from other co-authors and supervised the research.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing interests.
Peer review
Peer review information
Nature Immunology thanks the anonymous reviewers for their contribution to the peer review of this work. L. A. Dempsey was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Extended data
Extended Data Fig. 1 Characterization of LRF KO mice.
(a) LRF expression (MFI) of indicated cells in Fig. 1a relative to LRF MFI in LRF-KO CD8+ splenocytes, set to 1. Data summarizes two independent experiments with a total of three mice. (b) (left) CD8α vs. CD4 expression on TCRβ+ cells in thymus, spleen, and mLN from Ctrl and LRF KO mice.(right) Number (bottom) and percentage (among TCRαβ+ cells) of CD4–CD8α+ T cells. Data summarizes five independent experiments with a total of 4 (thymus), 16 (spleen), and 9 (mLN) mice of each genotype. (c) Serum concentration of soluble CD14 (sCD14) in Ctrl (n = 5) and LRF KO (n = 5) mice. Data summarizes two independent experiments. (d) Microbial communities in the small intestine luminal contents and mucosal-associated fraction from Ctrl (n = 5) and LRF KO (n = 5) mice. Data are from one experiment representative of two (the other being shown in Fig. 1d), each column representing one mouse. Color code as in Fig. 1d. (e) Expression of intra-cellular LRF in indicated IEL from Ctrl and LRF KO mice. (f, g) (left) Expression of CD45.2 vs. CD45.1 in TCRβ+ CD4+ CD8α– and CD4+ CD8α+ IEL (f), and CD4–CD8α+ splenocytes (g) from bone marrow chimera analyzed in Fig. 1e. (right) Tester/competitor ratios in indicated subsets, normalized to tester/competitor ratio of B220+ splenocytes. Data summarizes two independent experiments with a total of 6 mice per group. In (f), tester-competitor ratios (average ± SEM) were 0.78 ± 0.082 (Ctrl) and 0.33 ± 0.031 (KO) for CD4+CD8α– IEL, and 0.54 ± 0.043 (Ctrl) and 0.09 ± 0.008 (KO) for CD4+CD8α+ IEL. (h) (left) CD8α vs. CD4 expression on lamina propria TCRβ+ cells from Ctrl and LRF KO mice. (right) Percentage (top) and absolute number (bottom) of CD4+ and CD8+ cells among TCRβ+ cells. Data summarizes four independent experiments with a total of 4 mice per genotype. Error bars indicate standard error of the mean (SEM). P values are from two-tailed unpaired t-test (b, c, d, f, g and h). (a-d, f-h): Each symbol represents one mouse.
Extended Data Fig. 2 Development of LRF KO IELp.
(a) LRF expression in indicated subsets from Cd4cre+ Thpokfl/fl mice (to exclude cross reactive staining of Thpok by the LRF antibody). LRF KO TCRβ+ CD4–CD8+ splenocytes are shown as a control (grey-shaded). Data are from one experiment representative of two with 4 mice total. Graph (right) summarizes LRF expression (MFI) of indicated cells relative to that in wild-type IELp (analyzed as reference in each experiment), set to 1. (b) CD45.2 vs. CD45.1 expression in IELp from bone marrow chimera analyzed in Fig. 1e. Graphs (right) show tester/competitor ratios in IELp normalized to tester/competitor ratio of B220+ splenocytes and summarize two independent experiments totaling 6 mice per group. (c) Overlaid expression of Bim (left) and Bcl2 (right) in gated Ctrl and LRF KO IELp. Graphs (right) show the indicated protein expression (MFI) in IELp relative to that in IELp from wild type mice, set at 100 in each experiment. Data summarizes two independent experiments totaling 3 Ctrl and 4 LRF KO mice. (d) Contour plots show cleaved Caspase3 levels vs. FSC in wild-type CD4+CD8α+ or immature Bim+ CD4+ SP (Bim+ CD4+ CD8– CD69+ MHC-I–) thymocytes, and in Ctrl and LRF KO IELp. Data are from one experiment representative of two with a total of 3 Ctrl mice and 4 LRF KO mice. (e, f) Staining for extra-cellular annexin V and cell viability (L/D) on Ctrl and LRF KO IELp after in vitro culture for 0 h, 2 h or 4 h (e). Graph (f) summarizes the percent of L/D–Annexin V+ cells among IELp, from 4 Ctrl and 5 LRF KO mice analyzed in two independent experiments. (g, h) Total numbers of (g), and CD8α vs. CD8β expression by (h, left), Ctrl and LRF KO IELp after 4−day in vitro culture with the indicated IL-15 concentration. Right graph in (h) shows numbers of CD8αα and CD8αβ cells. Data is from three determinations for each genotype, acquired in two independent experiments Error bars indicate standard error of the mean (SEM). P values are from two-tailed unpaired t-test (b, c) or two-way ANOVA (g, h). (a-c, f-h) Each symbol in graphs represents one mouse.
Extended Data Fig. 3 Impact of LRF on IELp homing.
(a) Graph shows the absolute number of the indicated TCRβ+ tester cells (Ctrl or LRF KO) among IEL or spleen T cells analyzed in Fig. 3ab. Data are from one experiment (5 mice per group) representative of two. (b) CD8α vs. CD8β expression on TCRαβ+ CD8α+ splenocytes from bone marrow chimera analyzed in Fig. 1e. Graph (right) shows the percentage of CD8αα cells among TCRαβ+ CD8α+ splenocytes. Data pooled from two independent experiments with a total of 6 mice per group. Each symbol represents one mouse. (c-e) NSG host mice were adoptively transferred with a 1:1 mixture of CD45.2+ tester (either Ctrl or LRF KO) and CD45.1+CD45.2+ competitor CD8αβ splenocytes, and analyzed one week after transfer. Data are from one experiment (5 Ctrl and 4 KO mice) representative of two. (c) Schematic of the experiment (d, e) Top contour plots show CD45.2 vs. CD45.1 expression in TCRβ+ CD45.2+ splenocytes (d) and IEL (e). Colored boxes define Ctrl (blue) and KO (red) testers populations assessed for CD8α vs. CD8β expression in bottom contour plots. Top right graphs show tester/competitor ratios in each organ. Each symbol represents one mouse. Bottom right panel in (e) shows CD8α vs. CD8β expression on CD8α+ IEL from an unmanipulated C57BL/6 (WT) mouse. Error bars indicate standard error of the mean (SEM). P values (a, b, d, e) are from two-tailed unpaired t-test.
Extended Data Fig. 4 Effect of LRF on thymocyte α4β7 expression.
(a) Histogram overlays show the expression of α4β7 on wild-type IELp and conventional CD8+ SP thymocytes cells. Gray-shaded histogram (Bkgd) shows background of PE fluorochrome signal in IELp from Ctrl mice for which the primary α4β7 antibody was omitted from the staining mix. Right graphs show protein expression (MFI), computed on cells expressing each protein (left plot bracket). (b) Histogram (left) shows the expression of α4β7 on TCRβhiCD8α+ SP thymocytes from Ctrl or LRF KO mice, displayed as in (a). Graph (right) shows the percentage of α4β7+ cells among TCRβhi CD8α+ SP thymocytes. (c) Expression of α4β7 on Ctrl (solid line) and LRF KO (dashed line) TCRβhiCD4+ SP thymocytes, displayed as in (a). (a-c) Data are from one experiment (4 mice per group) representative of two. Each symbol in summary graphs represents one mouse. Error bars indicate standard error of the mean (SEM). P values (a, b) are from two-tailed unpaired t-test.
Extended Data Fig. 5 Control of IELp gene expression by LRF.
(a-b) Population RNAseq of thymic IELp. (a) Scatter plots compare gene expression (Log2 values, full gene set) in Ctrl vs. KO IELp. Genes with two-fold or greater differential expression between genotypes (and FDR < 0.01) are shown in blue or red. (b) RNAseq expression levels (counts per million) of Itgb7 and Itga4 genes in IELp from Ctrl and KO mice. Error bars indicate SEM. P values are from two-tailed unpaired t-test. (c-f) ScRNAseq of thymic IELp from Ctrl and KO mice. (c) UMAP analysis of IELp, performed as in Fig. 5a, displayed separately for each experiment and color-coded by genotype. (d) Bar plots indicate the Ctrl (gray) vs. LRF KO (red) genotype distribution of IELp clusters referred to in Fig. 5a,b. (e) Violin plot shows the expression of Lrf in indicated clusters from Ctrl IELp. (f) Volcano plot showing differentially expressed genes (FDR < 0.05, |Log2FC | >0.25) between Ctrl T4 (mature) and LRF KO T2 (intermediate) IELp clusters. Blue and red symbols indicate genes preferentially expressed in KO and Ctrl IELp, respectively.
Extended Data Fig. 6 Control of IEL gene expression by LRF.
(a-d) scRNAseq of CD8αα IEL from Ctrl and CD8αα splenocytes from KO mice. (a) Top plots show sorting strategy for CD8αα splenocytes and CD8αα IEL purification. Bottom graphs show the purity of indicated sorted subsets used for scRNAseq analyses (Fig. 7c-f). (b) UMAP plot of Ctrl CD8αα IEL and KO CD8αα splenocytes, as in Fig. 7c, displayed separately for each experiment and color-coded by genotype. (c) Bar plots indicate the Ctrl (gray) vs. LRF KO (red) genotype distribution of CD8αα clusters referred to in Fig. 7c-f. (d) Heatmap shows row-standardized expression of selected genes among triplicate RNAseq samples from the indicated populations (color scale at right).
Supplementary information
Supplementary Tables 1–10.
File including ten Supplementary tables. Legends for these tables are included in the combined supplementary pdf file.
Source data
Source Data Fig. 1
Statistical source data.
Source Data Fig. 2
Statistical source data.
Source Data Fig. 3
Statistical source data.
Source Data Fig. 4
Statistical source data.
Source Data Extended Data Fig. 1
Statistical source data.
Source Data Extended Data Fig. 2
Statistical source data.
Source Data Extended Data Fig. 3
Statistical source data.
Source Data Extended Data Fig. 4
Statistical source data.
Source Data Extended Data Fig. 5
Statistical source data.
Rights and permissions
About this article
Cite this article
Nie, J., Carpenter, A.C., Chopp, L.B. et al. The transcription factor LRF promotes integrin β7 expression by and gut homing of CD8αα+ intraepithelial lymphocyte precursors. Nat Immunol 23, 594–604 (2022). https://doi.org/10.1038/s41590-022-01161-x
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/s41590-022-01161-x