RESUMEN
Precise control of gene expression levels is essential for normal cell functions, yet how they are defined and tightly maintained, particularly at intermediate levels, remains elusive. Here, using a series of newly developed sequencing, imaging, and functional assays, we uncover a class of transcription factors with dual roles as activators and repressors, referred to as condensate-forming level-regulating dual-action transcription factors (TFs). They reduce high expression but increase low expression to achieve stable intermediate levels. Dual-action TFs directly exert activating and repressing functions via condensate-forming domains that compartmentalize core transcriptional unit selectively. Clinically relevant mutations in these domains, which are linked to a range of developmental disorders, impair condensate selectivity and dual-action TF activity. These results collectively address a fundamental question in expression regulation and demonstrate the potential of level-regulating dual-action TFs as powerful effectors for engineering controlled expression levels.
Asunto(s)
Factores de Transcripción , Animales , Humanos , Ratones , Regulación de la Expresión Génica , Mutación , Proteínas Represoras/metabolismo , Proteínas Represoras/genética , Factores de Transcripción/metabolismo , Factores de Transcripción/genética , Línea CelularRESUMEN
Through studies in mice and in humans, Stuart Orkin showed that GATA-1 is a master transcriptional regulator of hematopoiesis. He has highlighted the role of BCL11A in the fetal-adult hemoglobin switch. The Gairdner Foundation Award recognizes Orkin's contribution to the development of gene therapy of sickle cell disease.
Asunto(s)
Anemia de Células Falciformes , Distinciones y Premios , Terapia Genética , Anemia de Células Falciformes/genética , Anemia de Células Falciformes/terapia , Animales , Modelos Animales de Enfermedad , Hemoglobina Fetal/genética , Hematopoyesis/genética , Humanos , Ratones , Proteínas Represoras/genéticaRESUMEN
Non-small cell lung cancers (NSCLCs) harboring KEAP1 mutations are often resistant to immunotherapy. Here, we show that KEAP1 targets EMSY for ubiquitin-mediated degradation to regulate homologous recombination repair (HRR) and anti-tumor immunity. Loss of KEAP1 in NSCLC induces stabilization of EMSY, producing a BRCAness phenotype, i.e., HRR defects and sensitivity to PARP inhibitors. Defective HRR contributes to a high tumor mutational burden that, in turn, is expected to prompt an innate immune response. Notably, EMSY accumulation suppresses the type I interferon response and impairs innate immune signaling, fostering cancer immune evasion. Activation of the type I interferon response in the tumor microenvironment using a STING agonist results in the engagement of innate and adaptive immune signaling and impairs the growth of KEAP1-mutant tumors. Our results suggest that targeting PARP and STING pathways, individually or in combination, represents a therapeutic strategy in NSCLC patients harboring alterations in KEAP1.
Asunto(s)
Carcinoma de Pulmón de Células no Pequeñas/inmunología , Interferón Tipo I/metabolismo , Neoplasias Pulmonares/inmunología , Proteínas de Neoplasias/metabolismo , Proteínas Nucleares/metabolismo , Reparación del ADN por Recombinación/genética , Proteínas Represoras/metabolismo , Escape del Tumor/genética , Animales , Carcinoma de Pulmón de Células no Pequeñas/genética , Carcinoma de Pulmón de Células no Pequeñas/metabolismo , Carcinoma de Pulmón de Células no Pequeñas/patología , Línea Celular Tumoral , Femenino , Células HEK293 , Humanos , Inmunidad Innata/genética , Proteína 1 Asociada A ECH Tipo Kelch/genética , Proteína 1 Asociada A ECH Tipo Kelch/metabolismo , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/metabolismo , Neoplasias Pulmonares/patología , Ratones , Ratones Endogámicos C57BL , Ratones Endogámicos NOD , Mutación , Proteínas de Neoplasias/genética , Proteínas Nucleares/genética , Proteínas Represoras/genética , Transducción de Señal/genética , Microambiente Tumoral/genética , Microambiente Tumoral/inmunología , Ensayos Antitumor por Modelo de XenoinjertoRESUMEN
Adaptive immunity relies on specialized effector functions elicited by lymphocytes, yet how antigen recognition activates appropriate effector responses through nonspecific signaling intermediates is unclear. Here we examined the role of chromatin priming in specifying the functional outputs of effector T cells and found that most of the cis-regulatory landscape active in effector T cells was poised early in development before the expression of the T cell antigen receptor. We identified two principal mechanisms underpinning this poised landscape: the recruitment of the nucleosome remodeler mammalian SWItch/Sucrose Non-Fermentable (mSWI/SNF) by the transcription factors RUNX1 and PU.1 to establish chromatin accessibility at T effector loci; and a 'relay' whereby the transcription factor BCL11B succeeded PU.1 to maintain occupancy of the chromatin remodeling complex mSWI/SNF together with RUNX1, after PU.1 silencing during lineage commitment. These mechanisms define modes by which T cells acquire the potential to elicit specialized effector functions early in their ontogeny and underscore the importance of integrating extrinsic cues to the developmentally specified intrinsic program.
Asunto(s)
Subunidad alfa 2 del Factor de Unión al Sitio Principal , Proteínas Proto-Oncogénicas , Proteínas Represoras , Transactivadores , Factores de Transcripción , Proteínas Supresoras de Tumor , Proteínas Proto-Oncogénicas/metabolismo , Animales , Transactivadores/metabolismo , Transactivadores/genética , Ratones , Subunidad alfa 2 del Factor de Unión al Sitio Principal/metabolismo , Subunidad alfa 2 del Factor de Unión al Sitio Principal/genética , Proteínas Represoras/metabolismo , Proteínas Represoras/genética , Factores de Transcripción/metabolismo , Factores de Transcripción/genética , Proteínas Supresoras de Tumor/metabolismo , Proteínas Supresoras de Tumor/genética , Ratones Endogámicos C57BL , Proteínas Cromosómicas no Histona/metabolismo , Linfocitos T/inmunología , Linfocitos T/metabolismo , Ratones Noqueados , Ensamble y Desensamble de Cromatina , Diferenciación Celular/inmunologíaRESUMEN
Group 1 innate lymphoid cells (ILC1s) are cytotoxic and interferon gamma-producing lymphocytes lacking antigen-specific receptors, which include ILC1s and natural killer (NK) cells. In mice, ILC1s differ from NK cells, as they develop independently of the NK-specifying transcription factor EOMES, while requiring the repressor ZFP683 (ZNF683 in humans) for tissue residency. Here we identify highly variable ILC1 subtypes across tissues through investigation of human ILC1 diversity by single-cell RNA sequencing and flow cytometry. The intestinal epithelium contained abundant mature EOMES- ILC1s expressing PRDM1 rather than ZNF683, alongside a few immature TCF7+PRDM1- ILC1s. Other tissues harbored NK cells expressing ZNF683 and EOMES transcripts; however, EOMES protein content was variable. These ZNF683+ NK cells are tissue-imprinted NK cells phenotypically resembling ILC1s. The tissue ILC1-NK spectrum also encompassed conventional NK cells and NK cells distinguished by PTGDS expression. These findings establish a foundation for evaluating phenotypic and functional changes within the NK-ILC1 spectrum in diseases.
Asunto(s)
Inmunidad Innata , Células Asesinas Naturales , Linfocitos , Factor 1 de Unión al Dominio 1 de Regulación Positiva , Proteínas de Dominio T Box , Humanos , Células Asesinas Naturales/inmunología , Células Asesinas Naturales/metabolismo , Proteínas de Dominio T Box/metabolismo , Proteínas de Dominio T Box/genética , Factor 1 de Unión al Dominio 1 de Regulación Positiva/metabolismo , Factor 1 de Unión al Dominio 1 de Regulación Positiva/genética , Linfocitos/inmunología , Linfocitos/metabolismo , Análisis de la Célula Individual , Mucosa Intestinal/inmunología , Mucosa Intestinal/metabolismo , Animales , Ratones , Subgrupos Linfocitarios/inmunología , Subgrupos Linfocitarios/metabolismo , Proteínas Represoras/metabolismo , Proteínas Represoras/genéticaRESUMEN
The striosome compartment within the dorsal striatum has been implicated in reinforcement learning and regulation of motivation, but how striosomal neurons contribute to these functions remains elusive. Here, we show that a genetically identified striosomal population, which expresses the Teashirt family zinc finger 1 (Tshz1) and belongs to the direct pathway, drives negative reinforcement and is essential for aversive learning in mice. Contrasting a "conventional" striosomal direct pathway, the Tshz1 neurons cause aversion, movement suppression, and negative reinforcement once activated, and they receive a distinct set of synaptic inputs. These neurons are predominantly excited by punishment rather than reward and represent the anticipation of punishment or the motivation for avoidance. Furthermore, inhibiting these neurons impairs punishment-based learning without affecting reward learning or movement. These results establish a major role of striosomal neurons in behaviors reinforced by punishment and moreover uncover functions of the direct pathway unaccounted for in classic models.
Asunto(s)
Reacción de Prevención/fisiología , Cuerpo Estriado/fisiología , Proteínas de Homeodominio/genética , Proteínas Represoras/genética , Animales , Ganglios Basales , Femenino , Proteínas de Homeodominio/metabolismo , Aprendizaje/fisiología , Masculino , Ratones , Ratones Endogámicos C57BL , Ratones Noqueados , Motivación , Neuronas/fisiología , Castigo , Refuerzo en Psicología , Proteínas Represoras/metabolismoRESUMEN
To discover regulatory elements driving the specificity of gene expression in different cell types and regions of the developing human brain, we generated an atlas of open chromatin from nine dissected regions of the mid-gestation human telencephalon, as well as microdissected upper and deep layers of the prefrontal cortex. We identified a subset of open chromatin regions (OCRs), termed predicted regulatory elements (pREs), that are likely to function as developmental brain enhancers. pREs showed temporal, regional, and laminar differences in chromatin accessibility and were correlated with gene expression differences across regions and gestational ages. We identified two functional de novo variants in a pRE for autism risk gene SLC6A1, and using CRISPRa, demonstrated that this pRE regulates SCL6A1. Additionally, mouse transgenic experiments validated enhancer activity for pREs proximal to FEZF2 and BCL11A. Thus, this atlas serves as a resource for decoding neurodevelopmental gene regulation in health and disease.
Asunto(s)
Cromatina/genética , Cromatina/metabolismo , Elementos de Facilitación Genéticos , Regulación del Desarrollo de la Expresión Génica/genética , Corteza Prefrontal/embriología , Telencéfalo/embriología , Animales , Trastorno Autístico/genética , Línea Celular , Secuenciación de Inmunoprecipitación de Cromatina , Eucromatina/genética , Proteínas Transportadoras de GABA en la Membrana Plasmática/genética , Ontología de Genes , Predisposición Genética a la Enfermedad , Edad Gestacional , Humanos , Ratones , Ratones Transgénicos , Motivos de Nucleótidos , Mutación Puntual , Corteza Prefrontal/metabolismo , Proteínas Represoras/genética , Proteínas Represoras/metabolismo , Análisis Espacio-Temporal , Telencéfalo/metabolismo , Factores de Transcripción/genética , Factores de Transcripción/metabolismoRESUMEN
The most aggressive B cell lymphomas frequently manifest extranodal distribution and carry somatic mutations in the poorly characterized gene TBL1XR1. Here, we show that TBL1XR1 mutations skew the humoral immune response toward generating abnormal immature memory B cells (MB), while impairing plasma cell differentiation. At the molecular level, TBL1XR1 mutants co-opt SMRT/HDAC3 repressor complexes toward binding the MB cell transcription factor (TF) BACH2 at the expense of the germinal center (GC) TF BCL6, leading to pre-memory transcriptional reprogramming and cell-fate bias. Upon antigen recall, TBL1XR1 mutant MB cells fail to differentiate into plasma cells and instead preferentially reenter new GC reactions, providing evidence for a cyclic reentry lymphomagenesis mechanism. Ultimately, TBL1XR1 alterations lead to a striking extranodal immunoblastic lymphoma phenotype that mimics the human disease. Both human and murine lymphomas feature expanded MB-like cell populations, consistent with a MB-cell origin and delineating an unforeseen pathway for malignant transformation of the immune system.
Asunto(s)
Memoria Inmunológica/fisiología , Linfoma de Células B Grandes Difuso/patología , Proteínas Nucleares/genética , Células Precursoras de Linfocitos B/inmunología , Receptores Citoplasmáticos y Nucleares/genética , Proteínas Represoras/genética , Animales , Factores de Transcripción con Cremalleras de Leucina de Carácter Básico/genética , Factores de Transcripción con Cremalleras de Leucina de Carácter Básico/metabolismo , Cromatina/química , Cromatina/metabolismo , Centro Germinal/citología , Centro Germinal/inmunología , Centro Germinal/metabolismo , Histona Desacetilasas/metabolismo , Humanos , Linfoma de Células B Grandes Difuso/inmunología , Linfoma de Células B Grandes Difuso/metabolismo , Ratones , Ratones Endogámicos C57BL , Ratones Noqueados , Mutagénesis Sitio-Dirigida , Proteínas Nucleares/química , Proteínas Nucleares/metabolismo , Co-Represor 2 de Receptor Nuclear/química , Co-Represor 2 de Receptor Nuclear/metabolismo , Células Precursoras de Linfocitos B/citología , Células Precursoras de Linfocitos B/metabolismo , Unión Proteica , Proteínas Proto-Oncogénicas c-bcl-6/antagonistas & inhibidores , Proteínas Proto-Oncogénicas c-bcl-6/genética , Proteínas Proto-Oncogénicas c-bcl-6/metabolismo , Interferencia de ARN , ARN Interferente Pequeño/metabolismo , Receptores Citoplasmáticos y Nucleares/química , Receptores Citoplasmáticos y Nucleares/metabolismo , Proteínas Represoras/química , Proteínas Represoras/metabolismo , Transcripción GenéticaRESUMEN
Metabolic conditions affect the developmental tempo of animals. Developmental gene regulatory networks (GRNs) must therefore synchronize their dynamics with a variable timescale. We find that layered repression of genes couples GRN output with variable metabolism. When repressors of transcription or mRNA and protein stability are lost, fewer errors in Drosophila development occur when metabolism is lowered. We demonstrate the universality of this phenomenon by eliminating the entire microRNA family of repressors and find that development to maturity can be largely rescued when metabolism is reduced. Using a mathematical model that replicates GRN dynamics, we find that lowering metabolism suppresses the emergence of developmental errors by curtailing the influence of auxiliary repressors on GRN output. We experimentally show that gene expression dynamics are less affected by loss of repressors when metabolism is reduced. Thus, layered repression provides robustness through error suppression and may provide an evolutionary route to a shorter reproductive cycle.
Asunto(s)
Drosophila melanogaster/genética , Drosophila melanogaster/metabolismo , Regulación del Desarrollo de la Expresión Génica , Redes Reguladoras de Genes , Neuronas/metabolismo , Animales , Animales Modificados Genéticamente , Encéfalo/citología , Drosophila melanogaster/crecimiento & desarrollo , Ojo/citología , Femenino , Insulina/metabolismo , Mutación con Pérdida de Función , MicroARNs/metabolismo , Modelos Teóricos , Proteínas Represoras/genética , Proteínas Represoras/metabolismo , Transcripción GenéticaRESUMEN
Roquin and Regnase-1 proteins bind and post-transcriptionally regulate proinflammatory target messenger RNAs to maintain immune homeostasis. Either the sanroque mutation in Roquin-1 or loss of Regnase-1 cause systemic lupus erythematosus-like phenotypes. Analyzing mice with T cells that lack expression of Roquin-1, its paralog Roquin-2 and Regnase-1 proteins, we detect overlapping or unique phenotypes by comparing individual and combined inactivation. These comprised spontaneous activation, metabolic reprogramming and persistence of T cells leading to autoimmunity. Here, we define an interaction surface in Roquin-1 for binding to Regnase-1 that included the sanroque residue. Mutations in Roquin-1 impairing this interaction and cooperative regulation of targets induced T follicular helper cells, germinal center B cells and autoantibody formation. These mutations also improved the functionality of tumor-specific T cells by promoting their accumulation in the tumor and reducing expression of exhaustion markers. Our data reveal the physical interaction of Roquin-1 with Regnase-1 as a hub to control self-reactivity and effector functions in immune cell therapies.
Asunto(s)
Autoinmunidad , Citotoxicidad Inmunológica , Inmunoterapia Adoptiva , Melanoma Experimental/terapia , Proteínas Represoras/metabolismo , Ribonucleasas/metabolismo , Neoplasias Cutáneas/terapia , Linfocitos T/trasplante , Ubiquitina-Proteína Ligasas/metabolismo , Animales , Femenino , Células HEK293 , Células HeLa , Humanos , Inmunidad Humoral , Masculino , Melanoma Experimental/genética , Melanoma Experimental/inmunología , Melanoma Experimental/metabolismo , Ratones Endogámicos C57BL , Ratones Transgénicos , Mutación , Fenotipo , Unión Proteica , Proteínas Represoras/genética , Ribonucleasas/genética , Neoplasias Cutáneas/genética , Neoplasias Cutáneas/inmunología , Neoplasias Cutáneas/metabolismo , Linfocitos T/inmunología , Linfocitos T/metabolismo , Microambiente Tumoral , Ubiquitina-Proteína Ligasas/genéticaRESUMEN
Type 2 innate lymphoid cells (ILC2) contribute to immune homeostasis, protective immunity and tissue repair. Here we demonstrate that functional ILC2 cells can arise in the embryonic thymus from shared T cell precursors, preceding the emergence of CD4+CD8+ (double-positive) T cells. Thymic ILC2 cells migrated to mucosal tissues, with colonization of the intestinal lamina propria. Expression of the transcription factor RORα repressed T cell development while promoting ILC2 development in the thymus. From RNA-seq, assay for transposase-accessible chromatin sequencing (ATAC-seq) and chromatin immunoprecipitation followed by sequencing (ChIP-seq) data, we propose a revised transcriptional circuit to explain the co-development of T cells and ILC2 cells from common progenitors in the thymus. When Notch signaling is present, BCL11B dampens Nfil3 and Id2 expression, permitting E protein-directed T cell commitment. However, concomitant expression of RORα overrides the repression of Nfil3 and Id2 repression, allowing ID2 to repress E proteins and promote ILC2 differentiation. Thus, we demonstrate that RORα expression represents a critical checkpoint at the bifurcation of the T cell and ILC2 lineages in the embryonic thymus.
Asunto(s)
Linfocitos T CD4-Positivos/metabolismo , Linfocitos T CD8-positivos/metabolismo , Diferenciación Celular , Linaje de la Célula , Inmunidad Innata , Miembro 1 del Grupo F de la Subfamilia 1 de Receptores Nucleares/metabolismo , Timocitos/metabolismo , Timo/metabolismo , Animales , Factores de Transcripción con Cremalleras de Leucina de Carácter Básico/genética , Factores de Transcripción con Cremalleras de Leucina de Carácter Básico/metabolismo , Linfocitos T CD4-Positivos/inmunología , Linfocitos T CD8-positivos/inmunología , Movimiento Celular , Células Cultivadas , Técnicas de Cocultivo , Femenino , Regulación del Desarrollo de la Expresión Génica , Proteína 2 Inhibidora de la Diferenciación/genética , Proteína 2 Inhibidora de la Diferenciación/metabolismo , Masculino , Ratones , Ratones Endogámicos C57BL , Ratones Noqueados , Miembro 1 del Grupo F de la Subfamilia 1 de Receptores Nucleares/genética , Técnicas de Cultivo de Órganos , Fenotipo , Proteínas Represoras/genética , Proteínas Represoras/metabolismo , Transducción de Señal , Timocitos/inmunología , Timo/embriología , Timo/inmunología , Proteínas Supresoras de Tumor/genética , Proteínas Supresoras de Tumor/metabolismoRESUMEN
The DNA-binding protein REST forms complexes with histone deacetylases (HDACs) to repress neuronal genes in non-neuronal cells. In differentiating neurons, REST is downregulated predominantly by transcriptional silencing. Here we report that post-transcriptional inactivation of REST by alternative splicing is required for hearing in humans and mice. We show that, in the mechanosensory hair cells of the mouse ear, regulated alternative splicing of a frameshift-causing exon into the Rest mRNA is essential for the derepression of many neuronal genes. Heterozygous deletion of this alternative exon of mouse Rest causes hair cell degeneration and deafness, and the HDAC inhibitor SAHA (Vorinostat) rescues the hearing of these mice. In humans, inhibition of the frameshifting splicing event by a novel REST variant is associated with dominantly inherited deafness. Our data reveal the necessity for alternative splicing-dependent regulation of REST in hair cells, and they identify a potential treatment for a group of hereditary deafness cases.
Asunto(s)
Sordera/genética , Proteínas Represoras/genética , Proteínas Represoras/metabolismo , Empalme Alternativo/genética , Animales , Línea Celular , Exones , Regulación de la Expresión Génica/genética , Células HEK293 , Células Ciliadas Auditivas/fisiología , Audición/genética , Audición/fisiología , Inhibidores de Histona Desacetilasas/metabolismo , Histona Desacetilasas/metabolismo , Humanos , Ratones , Ratones Endogámicos C57BL , Neuronas , Empalme del ARN/genética , Proteínas Represoras/fisiología , Factores de Transcripción , Vorinostat/farmacologíaRESUMEN
The Notch signaling pathway comprises multiple ligands that are used in distinct biological contexts. In principle, different ligands could activate distinct target programs in signal-receiving cells, but it is unclear how such ligand discrimination could occur. Here, we show that cells use dynamics to discriminate signaling by the ligands Dll1 and Dll4 through the Notch1 receptor. Quantitative single-cell imaging revealed that Dll1 activates Notch1 in discrete, frequency-modulated pulses that specifically upregulate the Notch target gene Hes1. By contrast, Dll4 activates Notch1 in a sustained, amplitude-modulated manner that predominantly upregulates Hey1 and HeyL. Ectopic expression of Dll1 or Dll4 in chick neural crest produced opposite effects on myogenic differentiation, showing that ligand discrimination can occur in vivo. Finally, analysis of chimeric ligands suggests that ligand-receptor clustering underlies dynamic encoding of ligand identity. The ability of the pathway to utilize ligands as distinct communication channels has implications for diverse Notch-dependent processes.
Asunto(s)
Péptidos y Proteínas de Señalización Intercelular/metabolismo , Péptidos y Proteínas de Señalización Intracelular/metabolismo , Proteínas de la Membrana/metabolismo , Receptor Notch1/metabolismo , Transducción de Señal , Proteínas Adaptadoras Transductoras de Señales , Animales , Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico/biosíntesis , Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico/genética , Células CHO , Proteínas de Unión al Calcio , Proteínas de Ciclo Celular/biosíntesis , Proteínas de Ciclo Celular/genética , Embrión de Pollo , Cricetulus , Humanos , Péptidos y Proteínas de Señalización Intercelular/genética , Péptidos y Proteínas de Señalización Intracelular/genética , Ligandos , Proteínas de la Membrana/genética , Ratones , Receptor Notch1/genética , Proteínas Represoras/biosíntesis , Proteínas Represoras/genética , Regulación hacia ArribaRESUMEN
As in eukaryotes, bacterial genomes are not randomly folded. Bacterial genetic information is generally carried on a circular chromosome with a single origin of replication from which two replication forks proceed bidirectionally toward the opposite terminus region. Here, we investigate the higher-order architecture of the Escherichia coli genome, showing its partition into two structurally distinct entities by a complex and intertwined network of contacts: the replication terminus (ter) region and the rest of the chromosome. Outside of ter, the condensin MukBEF and the ubiquitous nucleoid-associated protein (NAP) HU promote DNA contacts in the megabase range. Within ter, the MatP protein prevents MukBEF activity, and contacts are restricted to â¼280 kb, creating a domain with distinct structural properties. We also show how other NAPs contribute to nucleoid organization, such as H-NS, which restricts short-range interactions. Combined, these results reveal the contributions of major evolutionarily conserved proteins in a bacterial chromosome organization.
Asunto(s)
Adenosina Trifosfatasas , Cromosomas Bacterianos , Proteínas de Unión al ADN , Escherichia coli K12 , Complejos Multiproteicos , Adenosina Trifosfatasas/genética , Adenosina Trifosfatasas/metabolismo , Adenosina Trifosfatasas/ultraestructura , Proteínas Cromosómicas no Histona/genética , Proteínas Cromosómicas no Histona/metabolismo , Cromosomas Bacterianos/genética , Cromosomas Bacterianos/metabolismo , Cromosomas Bacterianos/ultraestructura , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/metabolismo , Proteínas de Unión al ADN/ultraestructura , Escherichia coli K12/genética , Escherichia coli K12/metabolismo , Escherichia coli K12/ultraestructura , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Complejos Multiproteicos/genética , Complejos Multiproteicos/metabolismo , Complejos Multiproteicos/ultraestructura , Estructura Cuaternaria de Proteína , Proteínas Represoras/genética , Proteínas Represoras/metabolismoRESUMEN
Using integrative genomic analysis of 360 metastatic castration-resistant prostate cancer (mCRPC) samples, we identified a novel subtype of prostate cancer typified by biallelic loss of CDK12 that is mutually exclusive with tumors driven by DNA repair deficiency, ETS fusions, and SPOP mutations. CDK12 loss is enriched in mCRPC relative to clinically localized disease and characterized by focal tandem duplications (FTDs) that lead to increased gene fusions and marked differential gene expression. FTDs associated with CDK12 loss result in highly recurrent gains at loci of genes involved in the cell cycle and DNA replication. CDK12 mutant cases are baseline diploid and do not exhibit DNA mutational signatures linked to defects in homologous recombination. CDK12 mutant cases are associated with elevated neoantigen burden ensuing from fusion-induced chimeric open reading frames and increased tumor T cell infiltration/clonal expansion. CDK12 inactivation thereby defines a distinct class of mCRPC that may benefit from immune checkpoint immunotherapy.
Asunto(s)
Quinasas Ciclina-Dependientes/metabolismo , Neoplasias de la Próstata/patología , Anticuerpos Monoclonales/uso terapéutico , Línea Celular Tumoral , Quimiocina CCL21/genética , Quimiocina CCL21/metabolismo , Quinasas Ciclina-Dependientes/antagonistas & inhibidores , Quinasas Ciclina-Dependientes/genética , Reparación del ADN , Regulación Neoplásica de la Expresión Génica , Inestabilidad Genómica , Humanos , Masculino , Mutación Missense , Estadificación de Neoplasias , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Fenotipo , Receptor de Muerte Celular Programada 1/inmunología , Próstata/diagnóstico por imagen , Neoplasias de la Próstata/tratamiento farmacológico , Neoplasias de la Próstata/inmunología , Interferencia de ARN , ARN Interferente Pequeño/metabolismo , Proteínas Represoras/genética , Proteínas Represoras/metabolismo , Linfocitos T/metabolismo , Linfocitos T/patología , Tomografía Computarizada por Rayos XRESUMEN
Living organisms sense and respond to light, a crucial environmental factor, using photoreceptors, which rely on bound chromophores such as retinal, flavins, or linear tetrapyrroles for light sensing. The discovery of photoreceptors that sense light using 5'-deoxyadenosylcobalamin, a form of vitamin B12 that is best known as an enzyme cofactor, has expanded the number of known photoreceptor families and unveiled a new biological role of this vitamin. The prototype of these B12-dependent photoreceptors, the transcriptional repressor CarH, is widespread in bacteria and mediates light-dependent gene regulation in a photoprotective cellular response. CarH activity as a transcription factor relies on the modulation of its oligomeric state by 5'-deoxyadenosylcobalamin and light. This review surveys current knowledge about these B12-dependent photoreceptors, their distribution and mode of action, and the structural and photochemical basis of how they orchestrate signal transduction and control gene expression.
Asunto(s)
Proteínas Bacterianas/química , Cobamidas/metabolismo , Regulación Bacteriana de la Expresión Génica , Fotorreceptores Microbianos/química , Proteínas Represoras/química , Factores de Transcripción/química , Bacillus megaterium/genética , Bacillus megaterium/metabolismo , Bacillus megaterium/efectos de la radiación , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Cobamidas/química , Luz , Modelos Moleculares , Myxococcus xanthus/genética , Myxococcus xanthus/metabolismo , Myxococcus xanthus/efectos de la radiación , Fotoquímica , Fotorreceptores Microbianos/genética , Fotorreceptores Microbianos/metabolismo , Conformación Proteica , Proteínas Represoras/genética , Proteínas Represoras/metabolismo , Transducción de Señal , Thermus thermophilus/genética , Thermus thermophilus/metabolismo , Thermus thermophilus/efectos de la radiación , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Transcripción Genética , Vitamina B 12/química , Vitamina B 12/metabolismoRESUMEN
Antiviral CD8+ T cell responses are characterized by an initial activation/priming of T lymphocytes followed by a massive proliferation, subset differentiation, population contraction and the development of a stable memory pool. The transcription factor BATF3 has been shown to play a central role in the development of conventional dendritic cells, which in turn are critical for optimal priming of CD8+ T cells. Here we show that BATF3 was expressed transiently within the first days after T cell priming and had long-lasting T cell-intrinsic effects. T cells that lacked Batf3 showed normal expansion and differentiation, yet succumbed to an aggravated contraction and had a diminished memory response. Vice versa, BATF3 overexpression in CD8+ T cells promoted their survival and transition to memory. Mechanistically, BATF3 regulated T cell apoptosis and longevity via the proapoptotic factor BIM. By programing CD8+ T cell survival and memory, BATF3 is a promising molecule to optimize adoptive T cell therapy in patients.
Asunto(s)
Factores de Transcripción con Cremalleras de Leucina de Carácter Básico/genética , Linfocitos T CD8-positivos/inmunología , Linfocitos T CD8-positivos/metabolismo , Reprogramación Celular/genética , Memoria Inmunológica/genética , Proteínas Represoras/genética , Animales , Factores de Transcripción con Cremalleras de Leucina de Carácter Básico/metabolismo , Diferenciación Celular , Supervivencia Celular/genética , Expresión Génica , Humanos , Inmunofenotipificación , Ratones , Ratones Noqueados , Ratones Transgénicos , Proteínas Represoras/metabolismo , Factores de Transcripción/genética , Factores de Transcripción/metabolismoRESUMEN
The development of TCRαß and TCRγδ T cells comprises a step-wise process in which regulatory events control differentiation and lineage outcome. To clarify these mechanisms, we employed RNA-sequencing, ATAC-sequencing and ChIPmentation on well-defined thymocyte subsets that represent the continuum of human T cell development. The chromatin accessibility dynamics show clear stage specificity and reveal that human T cell-lineage commitment is marked by GATA3- and BCL11B-dependent closing of PU.1 sites. A temporary increase in H3K27me3 without open chromatin modifications is unique for ß-selection, whereas emerging γδ T cells, which originate from common precursors of ß-selected cells, show large chromatin accessibility changes due to strong T cell receptor (TCR) signaling. Furthermore, we unravel distinct chromatin landscapes between CD4+ and CD8+ αß-lineage cells that support their effector functions and reveal gene-specific mechanisms that define mature T cells. This resource provides a framework for studying gene regulatory mechanisms that drive normal and malignant human T cell development.
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Receptores de Antígenos de Linfocitos T alfa-beta/metabolismo , Receptores de Antígenos de Linfocitos T gamma-delta/metabolismo , Linfocitos T/fisiología , Timocitos/fisiología , Diferenciación Celular , Linaje de la Célula , Células Cultivadas , Cromatina/metabolismo , Selección Clonal Mediada por Antígenos , Epigénesis Genética , Factor de Transcripción GATA3/genética , Factor de Transcripción GATA3/metabolismo , Regulación Neoplásica de la Expresión Génica , Histonas/metabolismo , Humanos , Activación de Linfocitos , Proteínas Represoras/genética , Proteínas Represoras/metabolismo , Análisis de Secuencia de ARN , Transducción de Señal , Proteínas Supresoras de Tumor/genética , Proteínas Supresoras de Tumor/metabolismoRESUMEN
T follicular helper (TFH) cells are a distinct type of CD4+ T cells that are essential for most antibody and B lymphocyte responses. TFH cell regulation and dysregulation is involved in a range of diseases. Bcl-6 is the lineage-defining transcription factor of TFH cells and its activity is essential for TFH cell differentiation and function. However, how Bcl-6 controls TFH biology has largely remained unclear, at least in part due to the intrinsic challenges of connecting repressors to gene upregulation in complex cell types with multiple possible differentiation fates. Multiple competing models were tested here by a series of experimental approaches to determine that Bcl-6 exhibits negative autoregulation and controls pleiotropic attributes of TFH differentiation and function, including migration, costimulation, inhibitory receptors and cytokines, via multiple repressor-of-repressor gene circuits.
Asunto(s)
Regulación de la Expresión Génica/inmunología , Centro Germinal/inmunología , Proteínas Proto-Oncogénicas c-bcl-6/metabolismo , Proteínas Represoras/genética , Linfocitos T Colaboradores-Inductores/inmunología , Traslado Adoptivo , Animales , Sistemas CRISPR-Cas/genética , Diferenciación Celular/genética , Diferenciación Celular/inmunología , Línea Celular , Movimiento Celular/genética , Movimiento Celular/inmunología , Secuenciación de Inmunoprecipitación de Cromatina , Citocinas/inmunología , Citocinas/metabolismo , Femenino , Redes Reguladoras de Genes , Centro Germinal/citología , Humanos , Masculino , Ratones , Mutación , Regiones Promotoras Genéticas/genética , Proteínas Proto-Oncogénicas c-bcl-6/genética , RNA-Seq , Proteínas Represoras/metabolismo , Transducción de Señal/genética , Transducción de Señal/inmunología , Linfocitos T Colaboradores-Inductores/metabolismoRESUMEN
Although the importance of genome organization for transcriptional regulation of cell-fate decisions and function is clear, the changes in chromatin architecture and how these impact effector and memory CD8+ T cell differentiation remain unknown. Using Hi-C, we studied how genome configuration is integrated with CD8+ T cell differentiation during infection and investigated the role of CTCF, a key chromatin remodeler, in modulating CD8+ T cell fates through CTCF knockdown approaches and perturbation of specific CTCF-binding sites. We observed subset-specific changes in chromatin organization and CTCF binding and revealed that weak-affinity CTCF binding promotes terminal differentiation of CD8+ T cells through the regulation of transcriptional programs. Further, patients with de novo CTCF mutations had reduced expression of the terminal-effector genes in peripheral blood lymphocytes. Therefore, in addition to establishing genome architecture, CTCF regulates effector CD8+ T cell heterogeneity through altering interactions that regulate the transcription factor landscape and transcriptome.