Lactate modulates RNA splicing to promote CTLA-4 expression in tumor-infiltrating regulatory T cells.
Immunity
RNA splicing is involved in cancer initiation and progression, but how it influences host antitumor immunity in the metabolically abnormal tumor microenvironment (TME) remains unclear. Here, we demonstrate that lactate modulates Foxp3-dependent RNA splicing to maintain the phenotypic and functional status of tumor-infiltrating regulatory T (Treg) cells via CTLA-4. RNA splicing in Treg cells was correlated with the Treg cell signatures in the TME. Ubiquitin-specific peptidase 39 (USP39), a component of the RNA splicing machinery, maintained RNA-splicing-mediated CTLA-4 expression to control Treg cell function. Mechanistically, lactate promoted USP39-mediated RNA splicing to facilitate CTLA-4 expression in a Foxp3-dependent manner. Moreover, the efficiency of CTLA-4 RNA splicing was increased in tumor-infiltrating Treg cells from patients with colorectal cancer. These findings highlight the immunological relevance of RNA splicing in Treg cells and provide important insights into the environmental mechanism governing CTLA-4 expression in Treg cells.
10.1016/j.immuni.2024.01.019
Long noncoding RNA LIRIL2R modulates FOXP3 levels and suppressive function of human CD4 regulatory T cells by regulating IL2RA.
Proceedings of the National Academy of Sciences of the United States of America
Regulatory T cells (Tregs) are central in controlling immune responses, and dysregulation of their function can lead to autoimmune disorders or cancer. Despite extensive studies on Tregs, the basis of epigenetic regulation of human Treg development and function is incompletely understood. Long intergenic noncoding RNAs (lincRNA)s are important for shaping and maintaining the epigenetic landscape in different cell types. In this study, we identified a gene on the chromosome 6p25.3 locus, encoding a lincRNA, that was up-regulated during early differentiation of human Tregs. The lincRNA regulated the expression of interleukin-2 receptor alpha (IL2RA), and we named it the lincRNA regulator of IL2RA (LIRIL2R). Through transcriptomics, epigenomics, and proteomics analysis of LIRIL2R-deficient Tregs, coupled with global profiling of LIRIL2R binding sites using chromatin isolation by RNA purification, followed by sequencing, we identified IL2RA as a target of LIRIL2R. This nuclear lincRNA binds upstream of the locus and regulates its epigenetic landscape and transcription. CRISPR-mediated deletion of the LIRIL2R-bound region at the locus resulted in reduced IL2RA expression. Notably, LIRIL2R deficiency led to reduced expression of Treg-signature genes (e.g., , , and ), upregulation of genes associated with effector T cells (e.g., and ), and loss of Treg-mediated suppression.
10.1073/pnas.2315363121
Immunological synapse formation between T regulatory cells and cancer-associated fibroblasts promotes tumour development.
Nature communications
Cancer-associated fibroblasts (CAFs) have emerged as a dominant non-hematopoietic cell population in the tumour microenvironment, serving diverse functions in tumour progression. However, the mechanisms via which CAFs influence the anti-tumour immunity remain poorly understood. Here, using multiple tumour models and biopsies from cancer patients, we report that α-SMA CAFs can form immunological synapses with Foxp3 regulatory T cells (Tregs) in tumours. Notably, α-SMA CAFs can phagocytose and process tumour antigens and exhibit a tolerogenic phenotype which instructs movement arrest, activation and proliferation in Tregs in an antigen-specific manner. Moreover, α-SMA CAFs display double-membrane structures resembling autophagosomes in their cytoplasm. Single-cell transcriptomic data showed an enrichment in autophagy and antigen processing/presentation pathways in α-SMA-expressing CAF clusters. Conditional knockout of Atg5 in α-SMA CAFs promoted inflammatory re-programming in CAFs, reduced Treg cell infiltration and attenuated tumour development. Overall, our findings reveal an immunosuppressive mechanism entailing the formation of synapses between α-SMA CAFs and Tregs in an autophagy-dependent manner.
10.1038/s41467-024-49282-1
Transcription factor Ikzf1 associates with Foxp3 to repress gene expression in Treg cells and limit autoimmunity and anti-tumor immunity.
Immunity
The master transcription factor of regulatory T (Treg) cells, forkhead box protein P3 (Foxp3), controls Treg cell function by targeting certain genes for activation or repression, but the specific mechanisms by which it mediates this activation or repression under different conditions remain unclear. We found that Ikzf1 associates with Foxp3 via its exon 5 (IkE5) and that IkE5-deficient Treg cells highly expressed genes that would otherwise be repressed by Foxp3 upon T cell receptor stimulation, including Ifng. Treg-specific IkE5-deletion caused interferon-γ (IFN-γ) overproduction, which destabilized Foxp3 expression and impaired Treg suppressive function, leading to systemic autoimmune disease and strong anti-tumor immunity. Pomalidomide, which degrades IKZF1 and IKZF3, induced IFN-γ overproduction in human Treg cells. Mechanistically, the Foxp3-Ikzf1-Ikzf3 complex competed with epigenetic co-activators, such as p300, for binding to target gene loci via chromatin remodeling. Therefore, the Ikzf1 association with Foxp3 is essential for the gene-repressive function of Foxp3 and could be exploited to treat autoimmune disease and cancer.
10.1016/j.immuni.2024.07.010
Lymphotoxin limits Foxp3 regulatory T cell development from Foxp3 precursors via IL-4 signaling.
Nature communications
Regulatory T cells (T) are critical players of immune tolerance that develop in the thymus via two distinct developmental pathways involving CD25Foxp3 and CD25Foxp3 precursors. However, the mechanisms regulating the recently identified Foxp3 precursor pathway remain unclear. Here, we find that the membrane-bound lymphotoxin αβ (LTαβ) heterocomplex is upregulated during T development upon TCR/CD28 and IL-2 stimulation. We show that Lta expression limits the maturational development of T from Foxp3 precursors by regulating their proliferation, survival, and metabolic profile. Transgenic reporter mice and transcriptomic analyses further reveal that medullary thymic epithelial cells (mTEC) constitute an unexpected source of IL-4. We demonstrate that LTαβ-lymphotoxin β receptor-mediated interactions with mTEC limit T development by down-regulating IL-4 expression in mTEC. Collectively, our findings identify the lymphotoxin axis as the first inhibitory checkpoint of thymic T development that fine-tunes the Foxp3 T precursor pathway by limiting IL-4 availability.
10.1038/s41467-024-51164-5
Cancer-associated SF3B1-K700E mutation controls immune responses by regulating T function via aberrant splicing.
Science advances
Recurrent somatic mutations in spliceosome factor 3b subunit 1 (SF3B1) are identified in hematopoietic malignancies, with SF3B1-K700E being the most common one. Here, we show that regulatory T cell (T)-specific expression of SF3B1-K700E () results in spontaneous autoimmune phenotypes. CD4 T cells from mice display defective T differentiation and inhibitory function, which is demonstrated by failed prevention of adoptive transfer colitis by T. Mechanically, SF3B1-K700E induces an aberrant splicing event that results in reduced expression of a cell proliferation regulator due to the insertion of a 231-base pair DNA fragment to the 5' untranslated region. Forced expression of the gene restores the differentiation and ability of T to prevent adoptive transfer colitis. In addition, acute myeloid leukemia grows faster in aged, but not young, mice compared to mice. Our results highlight the impact of cancer-associated mutation on immune responses, which affect cancer development.
10.1126/sciadv.ado4274
Human OX40L-CAR-T target activated antigen-presenting cells and control T cell alloreactivity.
Science translational medicine
Regulatory T cells (T) make major contributions to immune homeostasis. Because T dysfunction can lead to both allo- and autoimmunity, there is interest in correcting these disorders through T adoptive transfer. Two of the central challenges in clinically deploying T cellular therapies are ensuring phenotypic stability and maximizing potency. Here, we describe an approach to address both issues through the creation of OX40 ligand (OX40L)-specific chimeric antigen receptor (CAR)-T under the control of a synthetic forkhead box P3 () promoter. The creation of these CAR-T enabled selective T stimulation by engagement of OX40L, a key activation antigen in alloimmunity, including both graft-versus-host disease and solid organ transplant rejection, and autoimmunity, including rheumatoid arthritis, systemic sclerosis, and systemic lupus erythematosus. We demonstrated that OX40L-CAR-T were robustly activated in the presence of OX40L-expressing cells, leading to up-regulation of T suppressive proteins without induction of proinflammatory cytokine production. Compared with control T, OX40L-CAR-T more potently suppressed alloreactive T cell proliferation in vitro and were directly inhibitory toward activated monocyte-derived dendritic cells (DCs). We identified trogocytosis as one of the central mechanisms by which these CAR-T effectively decrease extracellular display of OX40L, resulting in decreased DC stimulatory capacity. OX40L-CAR-T demonstrated an enhanced ability to control xenogeneic graft-versus-host disease compared with control T without abolishing the graft-versus-leukemia effect. These results suggest that OX40L-CAR-T may have wide applicability as a potent cellular therapy to control both allo- and autoimmune diseases.
10.1126/scitranslmed.adj9331