The DOI matches its Crossref record; 42 of the 42 references it cites were found in a registry or an index.
Metabolic heterogeneity underlies reciprocal fates of TH17 cell stemness and plasticity
Open accessAbstract
A defining feature of adaptive immunity is the development of long-lived memory T cells to curtail infection. Recent studies have identified a unique stem-like T-cell subset amongst exhausted CD8-positive T cells in chronic infection1–3, but it remains unclear whether CD4-positive T-cell subsets with similar features exist in chronic inflammatory conditions. Amongst helper T cells, TH17 cells have prominent roles in autoimmunity and tissue inflammation and are characterized by inherent plasticity4–7, although how such plasticity is regulated is poorly understood. Here we demonstrate that TH17 cells in a mouse model of autoimmune disease are functionally and metabolically heterogeneous; they contain a subset with stemness-associated features but lower anabolic metabolism, and a reciprocal subset with higher metabolic activity that supports transdifferentiation into TH1-like cells. These two TH17-cell subsets are defined by selective expression of the transcription factors TCF-1 and T-bet, and by discrete levels of CD27 expression. We also identify signalling via the kinase complex mTORC1 as a central regulator of TH17-cell fate decisions by coordinating metabolic and transcriptional programmes. TH17 cells with disrupted mTORC1 signalling or anabolic metabolism fail to induce autoimmune neuroinflammation or to develop into TH1-like cells, but instead upregulate TCF-1 expression and acquire stemness-associated features. Single-cell RNA sequencing and experimental validation reveal heterogeneity in fate-mapped TH17 cells, and a developmental arrest in the TH1 transdifferentiation trajectory upon loss of mTORC1 activity or metabolic perturbation. Our results establish that the dichotomy of stemness and effector function underlies the heterogeneous TH17 responses and autoimmune pathogenesis, and point to previously unappreciated metabolic control of plasticity in helper T cells. Phenotypically, transcriptionally and metabolically diverse subsets of TH17 cells develop in a chronic autoimmune disease: one subset has inferred stemness features and low anabolic metabolism, while a reciprocal subset has higher metabolic activity that supports transdifferentiation into TH1 cells.
Overview
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.
Integrity signals
Registry
Cites
Statistics
Verification
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.
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?
In the citing paper
“the non-pathogenic/homeostatic and pathogenic Th17 cell phenotypes studied in the mouse models may mirror the physiological roles of human Th17 cell subsets that are important for immunity against distinct bacteria and fungi”
From TH17 cell heterogeneity and its role in tissue inflammation (2023) · cites this paper as [64]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625
limma powers differential expression analyses for RNA-sequencing and microarray studies
Ritchie, M. E., Phipson, B., Wu, D., Hu, Y., Law, C. W., Shi, W., & Smyth, G. K. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv007 · Cited by 40,458 · cited 1×
“1) or by fitting a linear model implemented in the R package “limma” 30 .”
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
Model-based Analysis of ChIP-Seq (MACS)
Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386
Robinson, J. T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E. S., Getz, G., & Mesirov, J. P. (2011) · Nature Biotechnology · doi:10.1038/nbt.1754 · Cited by 15,390
MEME SUITE: tools for motif discovery and searching
Bailey, T. L., Boden, M., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., Ren, J., Li, W. W., & Noble, W. S. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp335 · Cited by 10,648
Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets.
Macosko, E. Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., Tirosh, I., Bialas, A. R., Kamitaki, N., Martersteck, E. M., et al. (2015) · Cell · doi:10.1016/j.cell.2015.05.002 · Cited by 7,110 · cited 3×
“The Cell Ranger 1.3 Single-Cell Software Suite (10× Genomics) was implemented to process the raw sequencing data from the Illumina HiSeq run.”
InfluentialBuenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., & Greenleaf, W. J. (2013) · Nature Methods · doi:10.1038/nmeth.2688 · Cited by 6,422 · cited 3×
“After adjustment of Tn5 shift (reads were offset by +4 bp for the sense strand and −5 bp for the antisense strand), we separated reads into nucleosome-free, mononucleosome, dinucleosome, and trinucleosome as described in Buenrostro et al. 15 by fragment size and generated bigwig files by using the center 80 bp of frag…”
voom: precision weights unlock linear model analysis tools for RNA-seq read counts
Law, C. W., Chen, Y., Shi, W., & Smyth, G. K. (2014) · Genome Biology · doi:10.1186/gb-2014-15-2-r29 · Cited by 6,155
Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy
Im, S. J., Hashimoto, M., Gerner, M. Y., Lee, J., Kissick, H. T., Burger, M. C., Shan, Q., Hale, J. S., Lee, J., Nasti, T. H., et al. (2016) · Nature · doi:10.1038/nature19330 · Cited by 2,070
Single-cell mRNA quantification and differential analysis with Census
Qiu, X., Hill, A. J., Packer, J. S., Lin, D., Ma, Y.-A., & Trapnell, C. (2017) · Nature Methods · doi:10.1038/nmeth.4150 · Cited by 1,904 · cited 1×
“…mainly comprised of Raptor-deficient cells were enriched with memory-associated gene signatures 1–3, 13 , while WT-dominant WT-dominant clusters were To reconstruct developmental trajectory, we analyzed our scRNA-Seq data using Monocle 2 for pseudo-temporal ordering of cells (pseudotime) 20 .”
Shi, L. Z., Wang, R., Huang, G., Vogel, P., Neale, G., Green, D. R., & Chi, H. (2011) · Journal of Experimental Medicine · doi:10.1084/jem.20110278 · Cited by 1,803
Self-citationMetabolic Instruction of Immunity
Buck, M. D., Sowell, R., Kaech, S. M., & Pearce, E. L. (2017) · Cell · doi:10.1016/j.cell.2017.04.004 · Cited by 1,270 · cited 2×
“Emerging studies highlight the importance of metabolic reprogramming for T cell activation and differentiation 14 , but metabolic control of cellular plasticity is unclear.”
Combining evidence using p-values: application to sequence homology searches.
Bailey, T. L., & Gribskov, M. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.1.48 · Cited by 1,254
Fate mapping of IL-17-producing T cells in inflammatory responses
Hirota, K., Duarte, J. H., Veldhoen, M., Hornsby, E., Li, Y., Cua, D. J., Ahlfors, H., Wilhelm, C., Tolaini, M., Menzel, U., et al. (2011) · Nature Immunology · doi:10.1038/ni.1993 · Cited by 1,176 · cited 2×
“We therefore determined the effects of blocking mTORC1 activity by deleting the signature component Raptor (encoded by Rptor) via Il17aCre and R26R eYFP system 6 on T H 17 heterogeneity and plasticity.”
Late Developmental Plasticity in the T Helper 17 Lineage
Lee, Y. K., Turner, H., Maynard, C. L., Oliver, J. R., Chen, D., Elson, C. O., & Weaver, C. T. (2009) · Immunity · doi:10.1016/j.immuni.2008.11.005 · Cited by 1,053 · cited 1×
“Mice were observed daily for clinical signs and scored: normal mouse; no overt signs of disease (0), limp tail (1), limp tail + hindlimb weakness (2), total hindlimb paralysis (3), hindlimb paralysis + 75% of body paralysis (forelimb paralysis/ weakness) (4), and moribund (5).”
Th17 cells transdifferentiate into regulatory T cells during resolution of inflammation
Gagliani, N., Vesely, M. C. A., Iseppon, A., Brockmann, L., Xu, H. Y., Palm, N. W., de Zoete, M. R., Licona-Limón, P., Paiva, R., Ching, T. H., et al. (2015) · Nature · doi:10.1038/nature14452 · Cited by 830 · cited 1×
“Mice were observed daily for clinical signs and scored: normal mouse; no overt signs of disease (0), limp tail (1), limp tail + hindlimb weakness (2), total hindlimb paralysis (3), hindlimb paralysis + 75% of body paralysis (forelimb paralysis/ weakness) (4), and moribund (5).”
Bettelli, E., Pagany, M., Weiner, H. L., Linington, C., Sobel, R. A., & Kuchroo, V. K. (2003) · The Journal of Experimental Medicine · doi:10.1084/jem.20021603 · Cited by 828 · cited 1×
“1 + hosts, except that 2D2-transgenic mice (expressing MOG antigen-specific T cell receptors 28 ; crossed onto the Il17aCre (R26R eYFP ) fate-mapping system) were used as donor mice, and CD4 T cell enrichment was performed at the time of analysis, to facilitate flow cytometric detection of the rare…”
mTORC1 couples immune signals and metabolic programming to establish Treg-cell function
Zeng, H., Yang, K., Cloer, C., Neale, G. A. M., Vogel, P., & Chi, H. (2013) · Nature · doi:10.1038/nature12297 · Cited by 806 · cited 1×
“Rptor fl , Myc fl , and Hmgcr fl mice were as described previously 21–23 .”
Self-citationCD27 is required for generation and long-term maintenance of T cell immunity
Hendriks, J., Gravestein, L. A., Tesselaar, K., van Lier, R. A. W., Schumacher, T. N., & Borst, J. G. (2000) · Nature Immunology · doi:10.1038/80877 · Cited by 777
Differentiation and persistence of memory CD8+ T cells depend on T cell factor 1
Zhou, X.-Y., Yu, S.-Y., Zhao, D.-M., Harty, J., Badovinac, V., & Xue, H.-H. (2010) · Immunity · doi:10.1016/j.immuni.2010.08.002 · Cited by 689
Follicular CXCR5-expressing CD8+ T cells curtail chronic viral infection
He, R., Hou, S., Liu, C., Zhang, A.-L., Bai, Q., Han, M., Yang, Y., Wei, G., Shen, T., Yang, X.-X., et al. (2016) · Nature · doi:10.1038/nature19317 · Cited by 643
Self-citationKalia, V., Sarkar, S., Subramaniam, S., Haining, W. N., Smith, K. A., & Ahmed, R. (2010) · Immunity · doi:10.1016/j.immuni.2009.11.010 · Cited by 607
Single-cell genomics unveils critical regulators of Th17 cell pathogenicity
Gaublomme, J. T., Yosef, N., Lee, Y., Gertner, R. S., Yang, L. V., Wu, C., Pandolfi, P. P., Mak, T., Satija, R., Shalek, A. K., et al. (2015) · Cell · doi:10.1016/j.cell.2015.11.009 · Cited by 575 · cited 7×
“With progression of EAE, the CD27 + subset in YFP + T H 17 cells was diminished in proportion initially and then stabilized (Extended Data Fig.”
InfluentialHirota, K., Turner, J.-E., Villa, M., Duarte, J. H., Demengeot, J., Steinmetz, O. M., & Stockinger, B. (2013) · Nature Immunology · doi:10.1038/ni.2552 · Cited by 509
CXCR5+ follicular cytotoxic T cells control viral infection in B cell follicles
Leong, Y. A., Chen, Y., Ong, H. S., Wu, D., Man, K., Deléage, C., Minnich, M., Meckiff, B. J., Wei, Y., Hou, Z., et al. (2016) · Nature Immunology · doi:10.1038/ni.3543 · Cited by 493 · cited 1×
“Clusters mainly comprised of Raptor-deficient cells were enriched with memory-associated gene signatures 1–3, 13 , while WT-dominant WT-dominant clusters were To reconstruct developmental trajectory, we analyzed our scRNA-Seq data using Monocle 2 for pseudo-temporal ordering of cells (pseudotime)…”
Th17 cells are long lived and retain a stem cell-like molecular signature
Muranski, P., Borman, Z. A., Kerkar, S. P., Klebanoff, C. A., Ji, Y., Sanchez-Perez, L., Sukumar, M., Reger, R. N., Yu, Z., Kern, S. J., et al. (2011) · Immunity · doi:10.1016/j.immuni.2011.09.019 · Cited by 443 · cited 1×
“We used published gene sets that are shared between memory and T FH cells (“Memory T FH overlap UP” and “Memory T FH overlap DOWN”) 13 , and early and late CD8 + T cell memory gene sets previously used to show memory features of T H 17 cells (“Early memory” and “Late memory”) 19 .”
Cutting Edge: Increased Expression of Bcl-2 in Antigen-Specific Memory CD8+ T Cells
Grayson, J. M., Zajac, A. J., Altman, J. D., & Ahmed, R. (2000) · The Journal of Immunology · doi:10.4049/jimmunol.164.8.3950 · Cited by 350 · cited 1×
“1f), factors mediating CD8 + T cell memory 10,11 , and showed in vivo persistence upon transfer into Rag1 –/– recipients (Fig.”
Zeng, H., Cohen, S., Guy, C. S., Shrestha, S., Neale, G. A. M., Brown, S. A., Cloer, C., Kishton, R. J., Gao, X., Youngblood, B., et al. (2016) · Immunity · doi:10.1016/j.immuni.2016.08.017 · Cited by 347 · cited 1×
“Rptor fl , Myc fl , and Hmgcr fl mice were as described previously 21–23 .”
Self-citationChoi, Y. S., Gullicksrud, J. A., Xing, S., Zeng, Z., Shan, Q., Li, F., Love, P. E., Peng, W., Xue, H., & Crotty, S. (2015) · Nature Immunology · doi:10.1038/ni.3226 · Cited by 337 · cited 1×
“To identify additional target genes aside from known TCF-1 target genes 16,17 , we computationally identified genes whose genomic regions became more accessible from ATAC-Seq data as a result of Raptor deletion.”
Zhu, J., Jankovic, D., Oler, A. J., Wei, G., Sharma, S., Hu, G., Guo, L., Yagi, R., Yamane, H., Punkosdy, G., et al. (2012) · Immunity · doi:10.1016/j.immuni.2012.09.007 · Cited by 335 · cited 1×
“We generated a Tbx21 (T-bet)-dependent signature (“T-bet targets”) from previously published gene expression changes in cultured T H 1 cells sufficient or deficient for Tbx21 (Log 2 fold change ≥ 3; GSE38808) 42 .”
Pepper, M., Linehan, J. L., Pagán, A. J., Zell, T., Dileepan, T., Cleary, P. P., & Jenkins, M. K. (2009) · Nature Immunology · doi:10.1038/ni.1826 · Cited by 284
Wirth, T. C., Xue, H., Rai, D., Sabel, J. T., Bair, T., Harty, J. T., & Badovinac, V. P. (2010) · Immunity · doi:10.1016/j.immuni.2010.06.014 · Cited by 263
Choi, Y. S., Kotov, J. A., Yusuf, I., Johnston, R. J., Greenbaum, J., Peters, B., & Crotty, S. (2013) · The Journal of Immunology · doi:10.4049/jimmunol.1202963 · Cited by 243 · cited 3×
“For example, genes enriched in cluster 1 compared to other clusters were associated with proliferative events. e , Summary of cluster-specific functional enrichment analysis via Fisher’s exact test using signatures of “T-bet targets”, “late memory”, “memory T FH overlap DOWN”, “HALLMARK_GLYCOLYSIS”, “memory T FH overl…”
Xu, L., Cao, Y., Xie, Z., Huang, Q., Baï, Q., Yang, X., He, R., Hao, Y., Wang, H., Zhao, T., et al. (2015) · Nature Immunology · doi:10.1038/ni.3229 · Cited by 230 · cited 1×
“To identify additional target genes aside from known TCF-1 target genes 16,17 , we computationally identified genes whose genomic regions became more accessible from ATAC-Seq data as a result of Raptor deletion.”
Hippo/Mst signalling couples metabolic state and immune function of CD8α+ dendritic cells
Du, X., Wen, J., Wang, Y., Karmaus, P. W. F., Khatamian, A., Tan, H., Li, Y., Guy, C. S., Nguyen, T.-L. M., Dhungana, Y., et al. (2018) · Nature · doi:10.1038/s41586-018-0177-0 · Cited by 224
Self-citationHomeostatic control of metabolic and functional fitness of Treg cells by LKB1 signalling
Yang, K., Blanco, D. B., Neale, G. A. M., Vogel, P., Ávila-Pacheco, J., Clish, C. B., Wu, C., Shrestha, S., Rankin, S. L., Long, L., et al. (2017) · Nature · doi:10.1038/nature23665 · Cited by 203
Self-citationTranscription of Il17 and Il17f Is Controlled by Conserved Noncoding Sequence 2
Wang, X., Zhang, Y.-B., Yang, X. O., Nurieva, R., Chang, S. H., Ojeda, S. S., Kang, H. S., Schluns, K. S., Gui, J., Jetten, A. M., et al. (2012) · Immunity · doi:10.1016/j.immuni.2011.10.019 · Cited by 127
Epigenetic priors for identifying active transcription factor binding sites
Cuéllar-Partida, G., Buske, F. A., McLeay, R. C., Whitington, T., Noble, W. S., & Bailey, T. L. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr614 · Cited by 122
Metabolic signaling directs the reciprocal lineage decisions of αβ and γδ T cells
Yang, K., Blanco, D. B., Chen, X. '., Dash, P., Neale, G. A. M., Rosencrance, C. D., Easton, J. B., Chen, W., Cheng, C., Dhungana, Y., et al. (2018) · Science Immunology · doi:10.1126/sciimmunol.aas9818 · Cited by 76
Self-citationNagashima, S., Yagyu, H., Ohashi, K., Tazoe, F., Takahashi, M., Ohshiro, T., Tumenbayar, B., Okada, K., Sekiya, M., Osuga, J.-I., et al. (2012) · Arteriosclerosis Thrombosis and Vascular Biology · doi:10.1161/atvbaha.111.240754 · Cited by 52
Flagged first, then by citations
Cited by
Sorted by citations
The pathogenicity of Th17 cells in autoimmune diseases
Yasuda, K., Takeuchi, Y., & Hirota, K. (2019) · Seminars in Immunopathology · doi:10.1007/s00281-019-00733-8 · Cited by 586
Metabolic modeling of single Th17 cells reveals regulators of autoimmunity
Wagner, A., Wang, C., Fessler, J., DeTomaso, D., Avila-Pacheco, J., Kaminski, J., Zaghouani, S., Christian, E., Thakore, P., Schellhaass, B., et al. (2021) · Cell · doi:10.1016/j.cell.2021.05.045 · Cited by 524
Saravia, J., Chapman, N. M., & Chi, H. (2019) · Cellular & Molecular Immunology · doi:10.1038/s41423-019-0220-6 · Cited by 489
Self-citationTargeting REGNASE-1 programs long-lived effector T cells for cancer therapy
Wei, J., Long, L., Zheng, W., Dhungana, Y., Lim, S. A., Guy, C. S., Wang, Y., Wang, Y., Qian, C., Xu, B., et al. (2019) · Nature · doi:10.1038/s41586-019-1821-z · Cited by 447
Self-citationLipid signalling enforces functional specialization of Treg cells in tumours
Lim, S. A., Wei, J., Nguyen, T.-L. M., Shi, H., SU, W. W., Palacios, G. F., Dhungana, Y., Chapman, N. M., Long, L., Saravia, J., et al. (2021) · Nature · doi:10.1038/s41586-021-03235-6 · Cited by 434
Self-citation
Metadata
- Authors
- Karmaus, P. W. F., Chen, X., Lim, S. A., Herrada, A. A., Nguyen, T.-L. M., Xu, B., Dhungana, Y., Rankin, S., Chen, W., Rosencrance, C., Yang, K., Fan, Y., Cheng, Y., Easton, J., Neale, G., Vogel, P., & Chi, H.
- Affiliations
- St. Jude Children's Research Hospital (US)
- Corresponding author
- Chi, Hongbo
- ORCID
- Venue
- Nature
- Published
- 2018-12-19
- Volume
- 565
- Issue
- 7737
- Pages
- 101-105
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC6420879
- OpenAlex
- W2905426112
- Semantic Scholar
- ebe01d7ca54b23c200f359ee77ec3f9d963ffe99
- Cited by
- 215
- References
- 42
- Citations by year
- 2026: 18 · 2025: 30 · 2024: 37 · 2023: 24 · 2022: 21 · 2021: 32 · 2020: 35 · 2019: 17
- FWCI
- 9.02
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- St. Jude Children's Research Hospital
- National Institutes of Health
- National Cancer Institute (R01CA176624, R01CA221290, P30CA021765)
- National Institute of Allergy and Infectious Diseases (R01AI101407, R01AI105887, R01AI140761, R01AI131703, R37AI105887)
- National Institute of Neurological Disorders and Stroke (R01NS064599)
- Topics
- Life Sciences › Immunology and Microbiology › Immunology › T-cell and B-cell Immunology
- Life Sciences › Immunology and Microbiology › Immunology › Psoriasis: Treatment and Pathogenesis
- Life Sciences › Immunology and Microbiology › Immunology › IL-33, ST2, and ILC Pathways
- Keywords
- Th17 cells, T cell stemness, T cell plasticity, mTORC1 signaling, TCF1, T-bet, CD27, anabolic metabolism, autoimmune neuroinflammation, chronic autoimmune disease, single-cell RNA sequencing
- MeSH terms
- Mechanistic Target of Rapamycin Complex 1, Regulatory-Associated Protein of mTOR, T-bet Transcription Factor, Animals, Autoimmune Diseases, Disease Models, Animal, Female, Immunologic Memory, Inflammation, Male, Stem Cells, Signal Transduction, Sequence Analysis, RNA, Tumor Necrosis Factor Receptor Superfamily, Member 7, T-Box Domain Proteins, Mice, T Cell Transcription Factor 1, Cell Transdifferentiation, Th17 Cells, Single-Cell Analysis
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