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1.
Nat Immunol ; 25(8): 1395-1410, 2024 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-39009838

RESUMEN

Interleukin-17 (IL-17)-producing helper T (TH17) cells are heterogenous and consist of nonpathogenic TH17 (npTH17) cells that contribute to tissue homeostasis and pathogenic TH17 (pTH17) cells that mediate tissue inflammation. Here, we characterize regulatory pathways underlying TH17 heterogeneity and discover substantial differences in the chromatin landscape of npTH17 and pTH17 cells both in vitro and in vivo. Compared to other CD4+ T cell subsets, npTH17 cells share accessible chromatin configurations with regulatory T cells, whereas pTH17 cells exhibit features of both npTH17 cells and type 1 helper T (TH1) cells. Integrating single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) and single-cell RNA sequencing (scRNA-seq), we infer self-reinforcing and mutually exclusive regulatory networks controlling different cell states and predicted transcription factors regulating TH17 cell pathogenicity. We validate that BACH2 promotes immunomodulatory npTH17 programs and restrains proinflammatory TH1-like programs in TH17 cells in vitro and in vivo. Furthermore, human genetics implicate BACH2 in multiple sclerosis. Overall, our work identifies regulators of TH17 heterogeneity as potential targets to mitigate autoimmunity.


Asunto(s)
Factores de Transcripción con Cremalleras de Leucina de Carácter Básico , Cromatina , Células Th17 , Animales , Femenino , Humanos , Ratones , Factores de Transcripción con Cremalleras de Leucina de Carácter Básico/metabolismo , Factores de Transcripción con Cremalleras de Leucina de Carácter Básico/genética , Cromatina/metabolismo , Encefalomielitis Autoinmune Experimental/inmunología , Encefalomielitis Autoinmune Experimental/genética , Inflamación/inmunología , Inflamación/genética , Ratones Endogámicos C57BL , Ratones Noqueados , Esclerosis Múltiple/inmunología , Esclerosis Múltiple/genética , Análisis de la Célula Individual , Linfocitos T Reguladores/inmunología , Linfocitos T Reguladores/metabolismo , Células TH1/inmunología , Células Th17/inmunología , Células Th17/metabolismo
2.
Cell ; 184(16): 4168-4185.e21, 2021 08 05.
Artículo en Inglés | MEDLINE | ID: mdl-34216539

RESUMEN

Metabolism is a major regulator of immune cell function, but it remains difficult to study the metabolic status of individual cells. Here, we present Compass, an algorithm to characterize cellular metabolic states based on single-cell RNA sequencing and flux balance analysis. We applied Compass to associate metabolic states with T helper 17 (Th17) functional variability (pathogenic potential) and recovered a metabolic switch between glycolysis and fatty acid oxidation, akin to known Th17/regulatory T cell (Treg) differences, which we validated by metabolic assays. Compass also predicted that Th17 pathogenicity was associated with arginine and downstream polyamine metabolism. Indeed, polyamine-related enzyme expression was enhanced in pathogenic Th17 and suppressed in Treg cells. Chemical and genetic perturbation of polyamine metabolism inhibited Th17 cytokines, promoted Foxp3 expression, and remodeled the transcriptome and epigenome of Th17 cells toward a Treg-like state. In vivo perturbations of the polyamine pathway altered the phenotype of encephalitogenic T cells and attenuated tissue inflammation in CNS autoimmunity.


Asunto(s)
Autoinmunidad/inmunología , Modelos Biológicos , Células Th17/inmunología , Acetiltransferasas/metabolismo , Adenosina Trifosfato/metabolismo , Aerobiosis/efectos de los fármacos , Algoritmos , Animales , Autoinmunidad/efectos de los fármacos , Cromatina/metabolismo , Ciclo del Ácido Cítrico/efectos de los fármacos , Citocinas/metabolismo , Eflornitina/farmacología , Encefalomielitis Autoinmune Experimental/metabolismo , Encefalomielitis Autoinmune Experimental/patología , Epigenoma , Ácidos Grasos/metabolismo , Glucólisis/efectos de los fármacos , Histona Demetilasas con Dominio de Jumonji/metabolismo , Ratones Endogámicos C57BL , Proteínas de Transporte de Membrana Mitocondrial/metabolismo , Oxidación-Reducción/efectos de los fármacos , Putrescina/metabolismo , Análisis de la Célula Individual , Linfocitos T Reguladores/efectos de los fármacos , Linfocitos T Reguladores/inmunología , Células Th17/efectos de los fármacos , Transcriptoma/genética
3.
Cell ; 176(6): 1325-1339.e22, 2019 03 07.
Artículo en Inglés | MEDLINE | ID: mdl-30827679

RESUMEN

Lineage tracing provides key insights into the fate of individual cells in complex organisms. Although effective genetic labeling approaches are available in model systems, in humans, most approaches require detection of nuclear somatic mutations, which have high error rates, limited scale, and do not capture cell state information. Here, we show that somatic mutations in mtDNA can be tracked by single-cell RNA or assay for transposase accessible chromatin (ATAC) sequencing. We leverage somatic mtDNA mutations as natural genetic barcodes and demonstrate their utility as highly accurate clonal markers to infer cellular relationships. We track native human cells both in vitro and in vivo and relate clonal dynamics to gene expression and chromatin accessibility. Our approach should allow clonal tracking at a 1,000-fold greater scale than with nuclear genome sequencing, with simultaneous information on cell state, opening the way to chart cellular dynamics in human health and disease.


Asunto(s)
ADN Mitocondrial/genética , Mitocondrias/genética , Secuencia de Bases , Linaje de la Célula , Cromatina , Neoplasias Colorrectales/genética , Neoplasias Colorrectales/patología , Genómica/métodos , Células HEK293 , Células Madre Hematopoyéticas/fisiología , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Humanos , Mutación , Análisis de la Célula Individual , Transposasas
4.
Immunity ; 55(1): 159-173.e9, 2022 01 11.
Artículo en Inglés | MEDLINE | ID: mdl-34982959

RESUMEN

To accommodate the changing needs of the developing brain, microglia must undergo substantial morphological, phenotypic, and functional reprogramming. Here, we examined whether cellular metabolism regulates microglial function during neurodevelopment. Microglial mitochondria bioenergetics correlated with and were functionally coupled to phagocytic activity in the developing brain. Transcriptional profiling of microglia with diverse metabolic profiles revealed an activation signature wherein the interleukin (IL)-33 signaling axis is associated with phagocytic activity. Genetic perturbation of IL-33 or its receptor ST2 led to microglial dystrophy, impaired synaptic function, and behavioral abnormalities. Conditional deletion of Il33 from astrocytes or Il1rl1, encoding ST2, in microglia increased susceptibility to seizures. Mechanistically, IL-33 promoted mitochondrial activity and phagocytosis in an AKT-dependent manner. Mitochondrial metabolism and AKT activity were temporally regulated in vivo. Thus, a microglia-astrocyte circuit mediated by the IL-33-ST2-AKT signaling axis supports microglial metabolic adaptation and phagocytic function during early development, with implications for neurodevelopmental and neuropsychiatric disorders.


Asunto(s)
Proteína 1 Similar al Receptor de Interleucina-1/metabolismo , Interleucina-33/metabolismo , Microglía/metabolismo , Mitocondrias/metabolismo , Convulsiones/inmunología , Animales , Conducta Animal , Susceptibilidad a Enfermedades , Sinapsis Eléctricas/metabolismo , Metabolismo Energético , Humanos , Proteína 1 Similar al Receptor de Interleucina-1/genética , Interleucina-33/genética , Ratones , Ratones Noqueados , Microglía/patología , Neurogénesis/genética , Proteína Oncogénica v-akt/metabolismo , Fagocitosis , Transducción de Señal
5.
Immunity ; 53(3): 658-671.e6, 2020 09 15.
Artículo en Inglés | MEDLINE | ID: mdl-32937153

RESUMEN

Identifying signals in the tumor microenvironment (TME) that shape CD8+ T cell phenotype can inform novel therapeutic approaches for cancer. Here, we identified a gradient of increasing glucocorticoid receptor (GR) expression and signaling from naïve to dysfunctional CD8+ tumor-infiltrating lymphocytes (TILs). Conditional deletion of the GR in CD8+ TILs improved effector differentiation, reduced expression of the transcription factor TCF-1, and inhibited the dysfunctional phenotype, culminating in tumor growth inhibition. GR signaling transactivated the expression of multiple checkpoint receptors and promoted the induction of dysfunction-associated genes upon T cell activation. In the TME, monocyte-macrophage lineage cells produced glucocorticoids and genetic ablation of steroidogenesis in these cells as well as localized pharmacologic inhibition of glucocorticoid biosynthesis improved tumor growth control. Active glucocorticoid signaling associated with failure to respond to checkpoint blockade in both preclinical models and melanoma patients. Thus, endogenous steroid hormone signaling in CD8+ TILs promotes dysfunction, with important implications for cancer immunotherapy.


Asunto(s)
Linfocitos T CD8-positivos/inmunología , Glucocorticoides/metabolismo , Macrófagos/metabolismo , Melanoma Experimental/patología , Microambiente Tumoral/inmunología , Animales , Linfocitos T CD8-positivos/citología , Línea Celular Tumoral , Hematopoyesis/inmunología , Factor Nuclear 1-alfa del Hepatocito/biosíntesis , Inhibidores de Puntos de Control Inmunológico , Activación de Linfocitos/inmunología , Macrófagos/inmunología , Ratones , Ratones Endogámicos C57BL , Ratones Noqueados , Receptores de Glucocorticoides/genética , Receptores de Glucocorticoides/metabolismo , Transducción de Señal/inmunología
6.
Nature ; 619(7969): 348-356, 2023 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-37344597

RESUMEN

The role of B cells in anti-tumour immunity is still debated and, accordingly, immunotherapies have focused on targeting T and natural killer cells to inhibit tumour growth1,2. Here, using high-throughput flow cytometry as well as bulk and single-cell RNA-sequencing and B-cell-receptor-sequencing analysis of B cells temporally during B16F10 melanoma growth, we identified a subset of B cells that expands specifically in the draining lymph node over time in tumour-bearing mice. The expanding B cell subset expresses the cell surface molecule T cell immunoglobulin and mucin domain 1 (TIM-1, encoded by Havcr1) and a unique transcriptional signature, including multiple co-inhibitory molecules such as PD-1, TIM-3, TIGIT and LAG-3. Although conditional deletion of these co-inhibitory molecules on B cells had little or no effect on tumour burden, selective deletion of Havcr1 in B cells both substantially inhibited tumour growth and enhanced effector T cell responses. Loss of TIM-1 enhanced the type 1 interferon response in B cells, which augmented B cell activation and increased antigen presentation and co-stimulation, resulting in increased expansion of tumour-specific effector T cells. Our results demonstrate that manipulation of TIM-1-expressing B cells enables engagement of the second arm of adaptive immunity to promote anti-tumour immunity and inhibit tumour growth.


Asunto(s)
Linfocitos B , Melanoma , Animales , Ratones , Linfocitos B/citología , Linfocitos B/inmunología , Linfocitos B/metabolismo , Activación de Linfocitos , Melanoma/inmunología , Melanoma/patología , Melanoma/prevención & control , Linfocitos T/citología , Linfocitos T/inmunología , Citometría de Flujo , Melanoma Experimental/inmunología , Melanoma Experimental/patología , Ganglios Linfáticos/citología , Ganglios Linfáticos/inmunología , Presentación de Antígeno , Receptores de Antígenos de Linfocitos B/genética , Análisis de Expresión Génica de una Sola Célula , Carga Tumoral , Interferón Tipo I
7.
Immunity ; 50(1): 181-194.e6, 2019 01 15.
Artículo en Inglés | MEDLINE | ID: mdl-30635236

RESUMEN

An improved understanding of the anti-tumor CD8+ T cell response after checkpoint blockade would enable more informed and effective therapeutic strategies. Here we examined the dynamics of the effector response of CD8+ tumor-infiltrating lymphocytes (TILs) after checkpoint blockade therapy. Bulk and single-cell RNA profiles of CD8+ TILs after combined Tim-3+PD-1 blockade in preclinical models revealed significant changes in the transcriptional profile of PD-1- TILs. These cells could be divided into subsets bearing characterstics of naive-, effector-, and memory-precursor-like cells. Effector- and memory-precursor-like TILs contained tumor-antigen-specific cells, exhibited proliferative and effector capacity, and expanded in response to different checkpoint blockade therapies across different tumor models. The memory-precursor-like subset shared features with CD8+ T cells associated with response to checkpoint blockade in patients and was compromised in the absence of Tcf7. Expression of Tcf7/Tcf1 was requisite for the efficacy of diverse immunotherapies, highlighting the importance of this transcriptional regulator in the development of effective CD8+ T cell responses upon immunotherapy.


Asunto(s)
Anticuerpos Monoclonales/uso terapéutico , Linfocitos T CD8-positivos/inmunología , Linfocitos Infiltrantes de Tumor/inmunología , Neoplasias Experimentales/terapia , Receptor de Muerte Celular Programada 1/antagonistas & inhibidores , Subgrupos de Linfocitos T/inmunología , Animales , Antígenos de Neoplasias/inmunología , Linfocitos T CD8-positivos/efectos de los fármacos , Proliferación Celular , Receptor 2 Celular del Virus de la Hepatitis A/antagonistas & inhibidores , Factor Nuclear 1-alfa del Hepatocito/genética , Factor Nuclear 1-alfa del Hepatocito/metabolismo , Humanos , Memoria Inmunológica/genética , Inmunoterapia , Linfocitos Infiltrantes de Tumor/efectos de los fármacos , Melanoma Experimental , Ratones , Ratones Endogámicos C57BL , Neoplasias Experimentales/inmunología , Transcriptoma
8.
Immunity ; 51(4): 709-723.e6, 2019 10 15.
Artículo en Inglés | MEDLINE | ID: mdl-31604686

RESUMEN

Neuroimmune interactions have emerged as critical modulators of allergic inflammation, and type 2 innate lymphoid cells (ILC2s) are an important cell type for mediating these interactions. Here, we show that ILC2s expressed both the neuropeptide calcitonin gene-related peptide (CGRP) and its receptor. CGRP potently inhibited alarmin-driven type 2 cytokine production and proliferation by lung ILC2s both in vitro and in vivo. CGRP induced marked changes in ILC2 expression programs in vivo and in vitro, attenuating alarmin-driven proliferative and effector responses. A distinct subset of ILCs scored highly for a CGRP-specific gene signature after in vivo alarmin stimulation, suggesting CGRP regulated this response. Finally, we observed increased ILC2 proliferation and type 2 cytokine production as well as exaggerated responses to alarmins in mice lacking the CGRP receptor. Together, these data indicate that endogenous CGRP is a critical negative regulator of ILC2 responses in vivo.


Asunto(s)
Péptido Relacionado con Gen de Calcitonina/metabolismo , Linfocitos/fisiología , Neuropéptidos/metabolismo , Receptores de Péptido Relacionado con el Gen de Calcitonina/metabolismo , Alarminas/metabolismo , Animales , Péptido Relacionado con Gen de Calcitonina/genética , Proliferación Celular , Células Cultivadas , Retroalimentación Fisiológica , Inmunidad Innata , Interleucina-33/metabolismo , Ratones , Ratones Endogámicos C57BL , Ratones Noqueados , Neuroinmunomodulación , Neuropéptidos/genética , Receptores de Péptido Relacionado con el Gen de Calcitonina/genética , Transducción de Señal , Células Th2/inmunología
9.
Immunol Rev ; 326(1): 83-101, 2024 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-39092839

RESUMEN

Food allergy is classically characterized by an inappropriate type-2 immune response to allergenic food antigens. However, how allergens are detected and how that detection leads to the initiation of allergic immunity is poorly understood. In addition to the gastrointestinal tract, the barrier epithelium of the skin may also act as a site of food allergen sensitization. These barrier epithelia are densely innervated by sensory neurons, which respond to diverse physical environmental stimuli. Recent findings suggest that sensory neurons can directly detect a broad array of immunogens, including allergens, triggering sensory responses and the release of neuropeptides that influence immune cell function. Reciprocally, immune mediators modulate the activation or responsiveness of sensory neurons, forming neuroimmune feedback loops that may impact allergic immune responses. By utilizing cutaneous allergen exposure as a model, this review explores the pivotal role of sensory neurons in allergen detection and their dynamic bidirectional communication with the immune system, which ultimately orchestrates the type-2 immune response. Furthermore, it sheds light on how peripheral signals are integrated within the central nervous system to coordinate hallmark features of allergic reactions. Drawing from this emerging evidence, we propose that atopy arises from a dysregulated neuroimmune circuit.


Asunto(s)
Alérgenos , Hipersensibilidad a los Alimentos , Neuroinmunomodulación , Células Receptoras Sensoriales , Humanos , Hipersensibilidad a los Alimentos/inmunología , Animales , Células Receptoras Sensoriales/inmunología , Células Receptoras Sensoriales/metabolismo , Alérgenos/inmunología , Piel/inmunología
10.
Nature ; 592(7852): 128-132, 2021 04.
Artículo en Inglés | MEDLINE | ID: mdl-33536623

RESUMEN

Tissue-resident innate lymphoid cells (ILCs) help sustain barrier function and respond to local signals. ILCs are traditionally classified as ILC1, ILC2 or ILC3 on the basis of their expression of specific transcription factors and cytokines1. In the skin, disease-specific production of ILC3-associated cytokines interleukin (IL)-17 and IL-22 in response to IL-23 signalling contributes to dermal inflammation in psoriasis. However, it is not known whether this response is initiated by pre-committed ILCs or by cell-state transitions. Here we show that the induction of psoriasis in mice by IL-23 or imiquimod reconfigures a spectrum of skin ILCs, which converge on a pathogenic ILC3-like state. Tissue-resident ILCs were necessary and sufficient, in the absence of circulatory ILCs, to drive pathology. Single-cell RNA-sequencing (scRNA-seq) profiles of skin ILCs along a time course of psoriatic inflammation formed a dense transcriptional continuum-even at steady state-reflecting fluid ILC states, including a naive or quiescent-like state and an ILC2 effector state. Upon disease induction, the continuum shifted rapidly to span a mixed, ILC3-like subset also expressing cytokines characteristic of ILC2s, which we inferred as arising through multiple trajectories. We confirmed the transition potential of quiescent-like and ILC2 states using in vitro experiments, single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) and in vivo fate mapping. Our results highlight the range and flexibility of skin ILC responses, suggesting that immune activities primed in healthy tissues dynamically adapt to provocations and, left unchecked, drive pathological remodelling.


Asunto(s)
Inmunidad Innata/inmunología , Linfocitos/inmunología , Linfocitos/patología , Psoriasis/inmunología , Psoriasis/patología , Piel/inmunología , Piel/patología , Animales , Diferenciación Celular , Linaje de la Célula , Cromatina/genética , Modelos Animales de Enfermedad , Femenino , Inflamación/genética , Inflamación/inmunología , Inflamación/patología , Interleucina-23/inmunología , Análisis de Clases Latentes , Linfocitos/clasificación , Masculino , Ratones , Psoriasis/genética , ARN Citoplasmático Pequeño/genética , Reproducibilidad de los Resultados , Factores de Tiempo
11.
J Bacteriol ; 202(22)2020 10 22.
Artículo en Inglés | MEDLINE | ID: mdl-32839177

RESUMEN

The Gram-negative enterobacterium Erwinia amylovora causes fire blight disease in apple and pear trees. Lipopolysaccharides and the exopolysaccharide amylovoran are essential E. amylovora virulence factors. We found that mutations in rfbX disrupted amylovoran production and virulence in apple fruits and tree shoots and that the deletion of yibD suppressed the rfbX mutant phenotype. The level of expression of yibD was about 10-fold higher in the ΔrfbX mutant than the wild type. A forward genetic suppressor screen in the ΔrfbX mutant uncovered multiple mutations in yibD and supported the conclusion that the virulence defect of rfbX mutants is due to reduced amylovoran production. The yibD and rfbX genes are expressed as a two-gene operon, yibD rfbX The rfbX gene encodes a previously uncharacterized putative polysaccharide subunit transporter, while yibD encodes a predicted glycosyltransferase. Mutation of rfbX did not have a detectable effect on lipopolysaccharide patterns; however, the overexpression of yibD in both the wild-type and ΔyibD ΔrfbX genetic backgrounds disrupted both amylovoran and lipopolysaccharide production. Additionally, the overexpression of yibD in the ΔyibD ΔrfbX mutant inhibited bacterial growth in amylovoran-inducing medium. This growth inhibition phenotype was used in a forward genetic suppressor screen and reverse-genetics tests to identify several genes involved in lipopolysaccharide production, which, when mutated, restored the ability of the ΔyibD ΔrfbX mutant overexpressing yibD to grow in amylovoran-inducing medium. Remarkably, all the lipopolysaccharide gene mutants tested were defective in lipopolysaccharide and amylovoran production. These results reveal a genetic connection between amylovoran and lipopolysaccharide production in E. amylovoraIMPORTANCE This study discovered previously unknown genetic connections between exopolysaccharide and lipopolysaccharide production in the fire blight pathogen Erwinia amylovora This represents a step forward in our understanding of the biology underlying the production of these two macromolecules. Fire blight is an economically important disease that impacts the production of apples and pears worldwide. Few fire blight control measures are available, and growers rely heavily on antibiotic applications at bloom time. Both exopolysaccharide and lipopolysaccharide are E. amylovora virulence factors. Our results indicate that the overexpression of the yibD gene in E. amylovora disrupts both lipopolysaccharide production and exopolysaccharide production. This effect could potentially be used as the basis for the development of an antivirulence treatment for the prevention of fire blight disease.


Asunto(s)
Proteínas Bacterianas/metabolismo , Erwinia amylovora/genética , Proteínas de Transporte de Membrana/metabolismo , Enfermedades de las Plantas/microbiología , Polisacáridos Bacterianos/biosíntesis , Proteínas Bacterianas/genética , Erwinia amylovora/metabolismo , Erwinia amylovora/patogenicidad , Regulación Bacteriana de la Expresión Génica , Genes Bacterianos , Malus/microbiología , Proteínas de Transporte de Membrana/genética , Mutación/genética , Operón , Pyrus/microbiología , Virulencia/genética
12.
Nat Biotechnol ; 40(2): 209-217, 2022 02.
Artículo en Inglés | MEDLINE | ID: mdl-34663921

RESUMEN

Tumor-associated epitopes presented on MHC-I that can activate the immune system against cancer cells are typically identified from annotated protein-coding regions of the genome, but whether peptides originating from novel or unannotated open reading frames (nuORFs) can contribute to antitumor immune responses remains unclear. Here we show that peptides originating from nuORFs detected by ribosome profiling of malignant and healthy samples can be displayed on MHC-I of cancer cells, acting as additional sources of cancer antigens. We constructed a high-confidence database of translated nuORFs across tissues (nuORFdb) and used it to detect 3,555 translated nuORFs from MHC-I immunopeptidome mass spectrometry analysis, including peptides that result from somatic mutations in nuORFs of cancer samples as well as tumor-specific nuORFs translated in melanoma, chronic lymphocytic leukemia and glioblastoma. NuORFs are an unexplored pool of MHC-I-presented, tumor-specific peptides with potential as immunotherapy targets.


Asunto(s)
Inmunoterapia , Melanoma , Antígenos de Neoplasias , Antígenos de Histocompatibilidad Clase I/genética , Antígenos de Histocompatibilidad Clase I/metabolismo , Humanos , Inmunoterapia/métodos , Espectrometría de Masas , Melanoma/genética , Péptidos
13.
Sci Adv ; 7(18)2021 04.
Artículo en Inglés | MEDLINE | ID: mdl-33931442

RESUMEN

T cell exhaustion has been associated with poor prognosis in persistent viral infection and cancer. Conversely, in the context of autoimmunity, T cell exhaustion has been favorably correlated with long-term clinical outcome. Understanding the development of exhaustion in autoimmune settings may provide underlying principles that can be exploited to quell autoreactive T cells. Here, we demonstrate that the adaptor molecule Bat3 acts as a molecular checkpoint of T cell exhaustion, with deficiency of Bat3 promoting a profound exhaustion phenotype, suppressing autoreactive T cell-mediated neuroinflammation. Mechanistically, Bat3 acts as a critical mTORC2 inhibitor to suppress Akt function. As a result, Bat3 deficiency leads to increased Akt activity and FoxO1 phosphorylation, indirectly promoting Prdm1 expression. Transcriptional analysis of Bat3 -/- T cells revealed up-regulation of dysfunction-associated genes, concomitant with down-regulation of genes associated with T cell effector function, suggesting that absence of Bat3 can trigger T cell dysfunction even under highly proinflammatory autoimmune conditions.

14.
Nat Biotechnol ; 39(4): 451-461, 2021 04.
Artículo en Inglés | MEDLINE | ID: mdl-32788668

RESUMEN

Natural mitochondrial DNA (mtDNA) mutations enable the inference of clonal relationships among cells. mtDNA can be profiled along with measures of cell state, but has not yet been combined with the massively parallel approaches needed to tackle the complexity of human tissue. Here, we introduce a high-throughput, droplet-based mitochondrial single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq), a method that combines high-confidence mtDNA mutation calling in thousands of single cells with their concomitant high-quality accessible chromatin profile. This enables the inference of mtDNA heteroplasmy, clonal relationships, cell state and accessible chromatin variation in individual cells. We reveal single-cell variation in heteroplasmy of a pathologic mtDNA variant, which we associate with intra-individual chromatin variability and clonal evolution. We clonally trace thousands of cells from cancers, linking epigenomic variability to subclonal evolution, and infer cellular dynamics of differentiating hematopoietic cells in vitro and in vivo. Taken together, our approach enables the study of cellular population dynamics and clonal properties in vivo.


Asunto(s)
ADN Mitocondrial/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Mitocondrias/genética , Neoplasias/genética , Análisis de la Célula Individual/métodos , Anciano de 80 o más Años , Diferenciación Celular , Células Cultivadas , Evolución Clonal , Células Clonales , Epigénesis Genética , Femenino , Técnicas de Genotipaje , Hematopoyesis , Humanos , Mutación , Análisis de Secuencia de ADN
15.
Cell Rep ; 33(8): 108433, 2020 11 24.
Artículo en Inglés | MEDLINE | ID: mdl-33238123

RESUMEN

Interleukin-27 (IL-27) is an immunoregulatory cytokine that suppresses inflammation through multiple mechanisms, including induction of IL-10, but the transcriptional network mediating its diverse functions remains unclear. Combining temporal RNA profiling with computational algorithms, we predict 79 transcription factors induced by IL-27 in T cells. We validate 11 known and discover 5 positive (Cebpb, Fosl2, Tbx21, Hlx, and Atf3) and 2 negative (Irf9 and Irf8) Il10 regulators, generating an experimentally refined regulatory network for Il10. We report two central regulators, Prdm1 and Maf, that cooperatively drive the expression of signature genes induced by IL-27 in type 1 regulatory T cells, mediate IL-10 expression in all T helper cells, and determine the regulatory phenotype of colonic Foxp3+ regulatory T cells. Prdm1/Maf double-knockout mice develop spontaneous colitis, phenocopying ll10-deficient mice. Our work provides insights into IL-27-driven transcriptional networks and identifies two shared Il10 regulators that orchestrate immunoregulatory programs across T helper cell subsets.


Asunto(s)
Redes Reguladoras de Genes/genética , Interleucina-10/metabolismo , Interleucina-27/metabolismo , Células TH1/metabolismo , Animales , Humanos , Ratones , Ratones Noqueados
16.
J Exp Med ; 215(10): 2617-2635, 2018 10 01.
Artículo en Inglés | MEDLINE | ID: mdl-30185635

RESUMEN

A number of autoimmunity-associated MHC class II proteins interact only weakly with the invariant chain-derived class II-associated invariant chain peptide (CLIP). CLIP dissociates rapidly from I-Ag7 even in the absence of DM, and this property is related to the type 1 diabetes-associated ß57 polymorphism. We generated knock-in non-obese diabetic (NOD) mice with a single amino acid change in the CLIP segment of the invariant chain in order to moderately slow CLIP dissociation from I-Ag7 These knock-in mice had a significantly reduced incidence of spontaneous type 1 diabetes and diminished islet infiltration by CD4 T cells, in particular T cells specific for fusion peptides generated by covalent linkage of proteolytic fragments within ß cell secretory granules. Rapid CLIP dissociation enhanced the presentation of such extracellular peptides, thus bypassing the conventional MHC class II antigen-processing pathway. Autoimmunity-associated MHC class II polymorphisms therefore not only modify binding of self-peptides, but also alter the biochemistry of peptide acquisition.


Asunto(s)
Presentación de Antígeno , Antígenos de Diferenciación de Linfocitos B/inmunología , Autoinmunidad , Linfocitos T CD4-Positivos/inmunología , Antígenos de Histocompatibilidad Clase II/inmunología , Animales , Antígenos de Diferenciación de Linfocitos B/genética , Linfocitos T CD4-Positivos/citología , Técnicas de Sustitución del Gen , Antígenos de Histocompatibilidad Clase II/genética , Ratones , Ratones Endogámicos NOD , Ratones Transgénicos
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