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1.
Cell ; 187(13): 3390-3408.e19, 2024 Jun 20.
Artículo en Inglés | MEDLINE | ID: mdl-38754421

RESUMEN

Clinical trials have identified ARID1A mutations as enriched among patients who respond favorably to immune checkpoint blockade (ICB) in several solid tumor types independent of microsatellite instability. We show that ARID1A loss in murine models is sufficient to induce anti-tumor immune phenotypes observed in ARID1A mutant human cancers, including increased CD8+ T cell infiltration and cytolytic activity. ARID1A-deficient cancers upregulated an interferon (IFN) gene expression signature, the ARID1A-IFN signature, associated with increased R-loops and cytosolic single-stranded DNA (ssDNA). Overexpression of the R-loop resolving enzyme, RNASEH2B, or cytosolic DNase, TREX1, in ARID1A-deficient cells prevented cytosolic ssDNA accumulation and ARID1A-IFN gene upregulation. Further, the ARID1A-IFN signature and anti-tumor immunity were driven by STING-dependent type I IFN signaling, which was required for improved responsiveness of ARID1A mutant tumors to ICB treatment. These findings define a molecular mechanism underlying anti-tumor immunity in ARID1A mutant cancers.


Asunto(s)
Linfocitos T CD8-positivos , Proteínas de Unión al ADN , Interferón Tipo I , Proteínas de la Membrana , Neoplasias , Transducción de Señal , Factores de Transcripción , Animales , Humanos , Ratones , Linfocitos T CD8-positivos/inmunología , Linfocitos T CD8-positivos/metabolismo , Línea Celular Tumoral , Proteínas de Unión al ADN/metabolismo , Exodesoxirribonucleasas/metabolismo , Inhibidores de Puntos de Control Inmunológico/farmacología , Inhibidores de Puntos de Control Inmunológico/uso terapéutico , Interferón Tipo I/metabolismo , Proteínas de la Membrana/metabolismo , Proteínas de la Membrana/genética , Ratones Endogámicos C57BL , Mutación , Neoplasias/inmunología , Neoplasias/genética , Proteínas Nucleares/metabolismo , Fosfoproteínas/metabolismo , Factores de Transcripción/metabolismo , Masculino , Quimiocinas/genética , Quimiocinas/metabolismo
2.
Cell ; 186(22): 4936-4955.e26, 2023 10 26.
Artículo en Inglés | MEDLINE | ID: mdl-37788668

RESUMEN

Intrinsically disordered regions (IDRs) represent a large percentage of overall nuclear protein content. The prevailing dogma is that IDRs engage in non-specific interactions because they are poorly constrained by evolutionary selection. Here, we demonstrate that condensate formation and heterotypic interactions are distinct and separable features of an IDR within the ARID1A/B subunits of the mSWI/SNF chromatin remodeler, cBAF, and establish distinct "sequence grammars" underlying each contribution. Condensation is driven by uniformly distributed tyrosine residues, and partner interactions are mediated by non-random blocks rich in alanine, glycine, and glutamine residues. These features concentrate a specific cBAF protein-protein interaction network and are essential for chromatin localization and activity. Importantly, human disease-associated perturbations in ARID1B IDR sequence grammars disrupt cBAF function in cells. Together, these data identify IDR contributions to chromatin remodeling and explain how phase separation provides a mechanism through which both genomic localization and functional partner recruitment are achieved.


Asunto(s)
Ensamble y Desensamble de Cromatina , Complejos Multiproteicos , Proteínas Nucleares , Humanos , Cromatina , Proteínas de Unión al ADN/química , Proteínas Intrínsecamente Desordenadas/genética , Proteínas Nucleares/metabolismo , Factores de Transcripción/metabolismo , Complejos Multiproteicos/química , Complejos Multiproteicos/metabolismo
3.
Immunity ; 57(8): 1780-1795.e6, 2024 Aug 13.
Artículo en Inglés | MEDLINE | ID: mdl-38843835

RESUMEN

Macrophages elicit immune responses to pathogens through induction of inflammatory genes. Here, we examined the role of three variants of the SWI/SNF nucleosome remodeling complex-cBAF, ncBAF, and PBAF-in the macrophage response to bacterial endotoxin (lipid A). All three SWI/SNF variants were prebound in macrophages and retargeted to genomic sites undergoing changes in chromatin accessibility following stimulation. Cooperative binding of all three variants associated with de novo chromatin opening and latent enhancer activation. Isolated binding of ncBAF and PBAF, in contrast, associated with activation and repression of active enhancers, respectively. Chemical and genetic perturbations of variant-specific subunits revealed pathway-specific regulation in the activation of lipid A response genes, corresponding to requirement for cBAF and ncBAF in inflammatory and interferon-stimulated gene (ISG) activation, respectively, consistent with differential engagement of SWI/SNF variants by signal-responsive transcription factors. Thus, functional diversity among SWI/SNF variants enables increased regulatory control of innate immune transcriptional programs, with potential for specific therapeutic targeting.


Asunto(s)
Ensamble y Desensamble de Cromatina , Proteínas Cromosómicas no Histona , Elementos de Facilitación Genéticos , Inflamación , Macrófagos , Factores de Transcripción , Macrófagos/inmunología , Macrófagos/metabolismo , Animales , Ratones , Factores de Transcripción/metabolismo , Factores de Transcripción/genética , Proteínas Cromosómicas no Histona/metabolismo , Proteínas Cromosómicas no Histona/genética , Inflamación/inmunología , Inflamación/genética , Elementos de Facilitación Genéticos/genética , Cromatina/metabolismo , Regulación de la Expresión Génica , Ratones Endogámicos C57BL , Inmunidad Innata , Humanos
4.
Immunity ; 56(6): 1303-1319.e5, 2023 06 13.
Artículo en Inglés | MEDLINE | ID: mdl-37315534

RESUMEN

CD8+ T cells provide host protection against pathogens by differentiating into distinct effector and memory cell subsets, but how chromatin is site-specifically remodeled during their differentiation is unclear. Due to its critical role in regulating chromatin and enhancer accessibility through its nucleosome remodeling activities, we investigated the role of the canonical BAF (cBAF) chromatin remodeling complex in antiviral CD8+ T cells during infection. ARID1A, a subunit of cBAF, was recruited early after activation and established de novo open chromatin regions (OCRs) at enhancers. Arid1a deficiency impaired the opening of thousands of activation-induced enhancers, leading to loss of TF binding, dysregulated proliferation and gene expression, and failure to undergo terminal effector differentiation. Although Arid1a was dispensable for circulating memory cell formation, tissue-resident memory (Trm) formation was strongly impaired. Thus, cBAF governs the enhancer landscape of activated CD8+ T cells that orchestrates TF recruitment and activity and the acquisition of specific effector and memory differentiation states.


Asunto(s)
Linfocitos T CD8-positivos , Secuencias Reguladoras de Ácidos Nucleicos , Cromatina , Nucleosomas , Antivirales
5.
Annu Rev Microbiol ; 77: 149-171, 2023 09 15.
Artículo en Inglés | MEDLINE | ID: mdl-37068777

RESUMEN

Biological soil crusts are thin, inconspicuous communities along the soil atmosphere ecotone that, until recently, were unrecognized by ecologists and even more so by microbiologists. In its broadest meaning, the term biological soil crust (or biocrust) encompasses a variety of communities that develop on soil surfaces and are powered by photosynthetic primary producers other than higher plants: cyanobacteria, microalgae, and cryptogams like lichens and mosses. Arid land biocrusts are the most studied, but biocrusts also exist in other settings where plant development is constrained. The minimal requirement is that light impinge directly on the soil; this is impeded by the accumulation of plant litter where plants abound. Since scientists started paying attention, much has been learned about their microbial communities, their composition, ecological extent, and biogeochemical roles, about how they alter the physical behavior of soils, and even how they inform an understanding of early life on land. This has opened new avenues for ecological restoration and agriculture.


Asunto(s)
Cianobacterias , Líquenes , Suelo/química , Ecosistema , Microbiología del Suelo
6.
Am J Hum Genet ; 111(10): 2232-2252, 2024 Oct 03.
Artículo en Inglés | MEDLINE | ID: mdl-39226899

RESUMEN

The BAF chromatin remodeler regulates lineage commitment including cranial neural crest cell (CNCC) specification. Variants in BAF subunits cause Coffin-Siris syndrome (CSS), a congenital disorder characterized by coarse craniofacial features and intellectual disability. Approximately 50% of individuals with CSS harbor variants in one of the mutually exclusive BAF subunits, ARID1A/ARID1B. While Arid1a deletion in mouse neural crest causes severe craniofacial phenotypes, little is known about the role of ARID1A in CNCC specification. Using CSS-patient-derived ARID1A+/- induced pluripotent stem cells to model CNCC specification, we discovered that ARID1A-haploinsufficiency impairs epithelial-to-mesenchymal transition (EMT), a process necessary for CNCC delamination and migration from the neural tube. Furthermore, wild-type ARID1A-BAF regulates enhancers associated with EMT genes. ARID1A-BAF binding at these enhancers is impaired in heterozygotes while binding at promoters is unaffected. At the sequence level, these EMT enhancers contain binding motifs for ZIC2, and ZIC2 binding at these sites is ARID1A-dependent. When excluded from EMT enhancers, ZIC2 relocates to neuronal enhancers, triggering aberrant neuronal gene activation. In mice, deletion of Zic2 impairs NCC delamination, while ZIC2 overexpression in chick embryos at post-migratory neural crest stages elicits ectopic delamination from the neural tube. These findings reveal an essential ARID1A-ZIC2 axis essential for EMT and CNCC delamination.


Asunto(s)
Proteínas de Unión al ADN , Transición Epitelial-Mesenquimal , Cara , Deformidades Congénitas de la Mano , Discapacidad Intelectual , Micrognatismo , Cuello , Cresta Neural , Factores de Transcripción , Cresta Neural/metabolismo , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Transición Epitelial-Mesenquimal/genética , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/metabolismo , Humanos , Discapacidad Intelectual/genética , Micrognatismo/genética , Animales , Cara/anomalías , Cara/embriología , Deformidades Congénitas de la Mano/genética , Deformidades Congénitas de la Mano/patología , Cuello/anomalías , Cuello/embriología , Ratones , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Células Madre Pluripotentes Inducidas/metabolismo , Células Madre Pluripotentes Inducidas/citología , Haploinsuficiencia , Elementos de Facilitación Genéticos/genética , Deformidades Congénitas del Pie/genética , Deformidades Congénitas del Pie/patología , Regulación del Desarrollo de la Expresión Génica , Anomalías Múltiples
7.
Trends Immunol ; 45(8): 568-570, 2024 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-39060141

RESUMEN

In a recent article, Maxwell et al. report that loss of tumor cell-specific AT-rich interaction domain 1A (ARID1A), a component of the chromatin remodeling SWI/SNF complex, triggers antitumor immunity via R-loop-mediated upregulation of the type-I interferon (IFN) pathway. These recent findings uncover a molecular mechanism underlying improved responses to immune checkpoint therapy (ICT) seen in patients harboring an ARID1A loss-of-function mutation.


Asunto(s)
Proteínas de Unión al ADN , Proteínas de la Membrana , Neoplasias , Factores de Transcripción , Humanos , Factores de Transcripción/metabolismo , Factores de Transcripción/genética , Proteínas de Unión al ADN/metabolismo , Proteínas de Unión al ADN/genética , Neoplasias/inmunología , Neoplasias/genética , Animales , Proteínas de la Membrana/genética , Proteínas de la Membrana/metabolismo , Mutación , Transducción de Señal , Interferón Tipo I/metabolismo , Interferón Tipo I/inmunología , Ensamble y Desensamble de Cromatina
8.
J Biol Chem ; 300(7): 107457, 2024 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-38866324

RESUMEN

AT-rich interacting domain (ARID)-containing proteins, Arids, are a heterogeneous DNA-binding protein family involved in transcription regulation and chromatin processing. For the member Arid5a, no exact DNA-binding preference has been experimentally defined so far. Additionally, the protein binds to mRNA motifs for transcript stabilization, supposedly through the DNA-binding ARID domain. To date, however, no unbiased RNA motif definition and clear dissection of nucleic acid-binding through the ARID domain have been undertaken. Using NMR-centered biochemistry, we here define the Arid5a DNA preference. Further, high-throughput in vitro binding reveals a consensus RNA-binding motif engaged by the core ARID domain. Finally, transcriptome-wide binding (iCLIP2) reveals that Arid5a has a weak preference for (A)U-rich regions in pre-mRNA transcripts of factors related to RNA processing. We find that the intrinsically disordered regions flanking the ARID domain modulate the specificity and affinity of DNA binding, while they appear crucial for RNA interactions. Ultimately, our data suggest that Arid5a uses its extended ARID domain for bifunctional gene regulation and that the involvement of IDR extensions is a more general feature of Arids in interacting with different nucleic acids at the chromatin-mRNA interface.


Asunto(s)
Proteínas de Unión al ADN , ADN , Factores de Transcripción , Humanos , Proteínas de Unión al ADN/metabolismo , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/química , ADN/metabolismo , ADN/química , ADN/genética , Factores de Transcripción/metabolismo , Factores de Transcripción/genética , Factores de Transcripción/química , Dominios Proteicos , Regulación de la Expresión Génica , Unión Proteica , ARN Mensajero/metabolismo , ARN Mensajero/genética , ARN/metabolismo , ARN/química , ARN/genética
9.
Syst Biol ; 2024 Jul 02.
Artículo en Inglés | MEDLINE | ID: mdl-38953551

RESUMEN

Advances in genomics have greatly enhanced our understanding of mountain biodiversity, providing new insights into the complex and dynamic mechanisms that drive the formation of mountain biotas. These span from broad biogeographic patterns to population dynamics and adaptations to these environments. However, significant challenges remain in integrating large-scale and fine-scale findings to develop a comprehensive understanding of mountain biodiversity. One significant challenge is the lack of genomic data, particularly in historically understudied arid regions where reptiles are a particularly diverse vertebrate group. In the present study, we assembled a de novo genome-wide SNP dataset for the complete endemic reptile fauna of a mountain range (19 described species with more than 600 specimens sequenced), and integrated state-of-the-art biogeographic analyses at the population, species, and community level. Thus, we provide a holistic integration of how a whole endemic reptile community has originated, diversified and dispersed through a mountain system. Our results show that reptiles independently colonized the Hajar Mountains of southeastern Arabia 11 times. After colonization, species delimitation methods suggest high levels of within-mountain diversification, supporting up to 49 deep lineages. This diversity is strongly structured following local topography, with the highest peaks acting as a broad barrier to gene flow among the entire community. Interestingly, orogenic events do not seem key drivers of the biogeographic history of reptiles in this system. Instead, past climatic events seem to have had a major role in this community assemblage. We observe an increase of vicariant events from Late Pliocene onwards, coinciding with an unstable climatic period of rapid shifts between hyper-arid and semiarid conditions that led to the ongoing desertification of Arabia. We conclude that paleoclimate, and particularly extreme aridification, acted as a main driver of diversification in arid mountain systems which is tangled with the generation of highly adapted endemicity. Overall, our study does not only provide a valuable contribution to understanding the evolution of mountain biodiversity, but also offers a flexible and scalable approach that can be reproduced into any taxonomic group and at any discrete environment.

10.
BMC Biol ; 22(1): 132, 2024 Jun 05.
Artículo en Inglés | MEDLINE | ID: mdl-38835016

RESUMEN

BACKGROUND: ARID1A, a subunit of the SWI/SNF chromatin remodeling complex, is thought to play a significant role both in tumor suppression and tumor initiation, which is highly dependent upon context. Previous studies have suggested that ARID1A deficiency may contribute to cancer development. The specific mechanisms of whether ARID1A loss affects tumorigenesis by RNA editing remain unclear. RESULTS: Our findings indicate that the deficiency of ARID1A leads to an increase in RNA editing levels and alterations in RNA editing categories mediated by adenosine deaminases acting on RNA 1 (ADAR1). ADAR1 edits the CDK13 gene at two previously unidentified sites, namely Q113R and K117R. Given the crucial role of CDK13 as a cyclin-dependent kinase, we further observed that ADAR1 deficiency results in changes in the cell cycle. Importantly, the sensitivity of ARID1A-deficient tumor cells to SR-4835, a CDK12/CDK13 inhibitor, suggests a promising therapeutic approach for individuals with ARID1A-mutant tumors. Knockdown of ADAR1 restored the sensitivity of ARID1A deficient cells to SR-4835 treatment. CONCLUSIONS: ARID1A deficiency promotes RNA editing of CDK13 by regulating ADAR1.


Asunto(s)
Adenosina Desaminasa , Quinasas Ciclina-Dependientes , Proteínas de Unión al ADN , Edición de ARN , Proteínas de Unión al ARN , Factores de Transcripción , Adenosina Desaminasa/metabolismo , Adenosina Desaminasa/genética , Proteínas de Unión al ARN/metabolismo , Proteínas de Unión al ARN/genética , Humanos , Factores de Transcripción/metabolismo , Factores de Transcripción/genética , Proteínas de Unión al ADN/metabolismo , Proteínas de Unión al ADN/genética , Quinasas Ciclina-Dependientes/metabolismo , Quinasas Ciclina-Dependientes/genética , Línea Celular Tumoral , Proteína Quinasa CDC2
11.
Genes Dev ; 31(23-24): 2343-2360, 2017 12 01.
Artículo en Inglés | MEDLINE | ID: mdl-29326336

RESUMEN

The oncogenic transcription factor TAL1/SCL induces an aberrant transcriptional program in T-cell acute lymphoblastic leukemia (T-ALL) cells. However, the critical factors that are directly activated by TAL1 and contribute to T-ALL pathogenesis are largely unknown. Here, we identified AT-rich interactive domain 5B (ARID5B) as a collaborating oncogenic factor involved in the transcriptional program in T-ALL. ARID5B expression is down-regulated at the double-negative 2-4 stages in normal thymocytes, while it is induced by the TAL1 complex in human T-ALL cells. The enhancer located 135 kb upstream of the ARID5B gene locus is activated under a superenhancer in T-ALL cells but not in normal T cells. Notably, ARID5B-bound regions are associated predominantly with active transcription. ARID5B and TAL1 frequently co-occupy target genes and coordinately control their expression. ARID5B positively regulates the expression of TAL1 and its regulatory partners. ARID5B also activates the expression of the oncogene MYC Importantly, ARID5B is required for the survival and growth of T-ALL cells, and forced expression of ARID5B in immature thymocytes results in thymus retention, differentiation arrest, radioresistance, and tumor formation in zebrafish. Our results indicate that ARID5B reinforces the oncogenic transcriptional program by positively regulating the TAL1-induced regulatory circuit and MYC in T-ALL, thereby contributing to T-cell leukemogenesis.


Asunto(s)
Carcinogénesis/genética , Proteínas de Unión al ADN/metabolismo , Regulación Neoplásica de la Expresión Génica , Proteína 1 de la Leucemia Linfocítica T Aguda/metabolismo , Factores de Transcripción/metabolismo , Animales , Línea Celular Tumoral , Supervivencia Celular/genética , Proteínas de Unión al ADN/genética , Elementos de Facilitación Genéticos/genética , Perfilación de la Expresión Génica , Genes myc/genética , Células HEK293 , Humanos , Leucemia-Linfoma Linfoblástico de Células T Precursoras , Unión Proteica , Dominios Proteicos/genética , Timocitos/metabolismo , Timo/crecimiento & desarrollo , Factores de Transcripción/genética , Activación Transcripcional/genética , Pez Cebra
12.
Genes Chromosomes Cancer ; 63(1): e23198, 2024 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-37658696

RESUMEN

Composite hemangioendothelioma is a rare, locally aggressive, and rarely metastasizing vascular neoplasm which affects both children and adults. Recently, a number of gene fusions including YAP1::MAML2, PTBP1::MAML2, and EPC1::PHC2 have been detected in a small subset of cases with or without neuroendocrine expression. Herein, we present four additional cases with novel in-frame fusions. The cohort comprises two females and two males with a wide age range at diagnosis (24-80 years). Two tumors were deep involving the right brachial plexus and mediastinum, while the remaining were superficial (right plantar foot and abdominal wall). The size ranged from 1.5 to 4.8 cm in greatest dimension. Morphologically, all tumors had an admixture of at least two architectural patterns including retiform hemangioendothelioma, hemangioma, epithelioid hemangioendothelioma, or angiosarcoma. The tumors were positive for endothelial markers CD31 (3/3), ERG (4/4), and D2-40 (1/4, focal), while SMA was expressed in 2/3 highlighting the surrounding pericytes. Synaptophysin showed immunoreactivity in 2/3 cases. One patient had a local recurrence after 40 months, while two patients had no evidence of disease 4 months post-resection. Targeted RNA sequencing detected novel in-frame fusions in each of the cases: HSPG2::FGFR1, YAP1::FOXR1, ACTB::MAML2, and ARID1B::MAML2. The two cases with neuroendocrine expression occurred as superficial lesions and harbored YAP1::FOXR1 and ARID1B::MAML2 fusions. Our study expands on the molecular spectrum of this enigmatic tumor, further enhancing our current understanding of the disease.


Asunto(s)
Hemangioendotelioma Epitelioide , Hemangioendotelioma , Hemangioma , Adulto , Masculino , Niño , Femenino , Humanos , Adulto Joven , Persona de Mediana Edad , Anciano , Anciano de 80 o más Años , Hemangioendotelioma/patología , Hemangioendotelioma Epitelioide/genética , Secuencia de Bases , Diagnóstico Diferencial , Biomarcadores de Tumor/genética , Biomarcadores de Tumor/metabolismo , Ribonucleoproteínas Nucleares Heterogéneas , Proteína de Unión al Tracto de Polipirimidina
13.
Genes Chromosomes Cancer ; 63(5): e23242, 2024 05.
Artículo en Inglés | MEDLINE | ID: mdl-38738968

RESUMEN

Constitutional polymorphisms in ARID5B are associated with an increased risk of developing high hyperdiploid (HeH; 51-67 chromosomes) pediatric B-cell precursor acute lymphoblastic leukemia (BCP ALL). Here, we investigated constitutional and somatic ARID5B variants in 1335 BCP ALL cases from five different cohorts, with a particular focus on HeH cases. In 353 HeH ALL that were heterozygous for risk alleles and trisomic for chromosome 10, where ARID5B is located, a significantly higher proportion of risk allele duplication was seen for the SNPs rs7090445 (p = 0.009), rs7089424 (p = 0.005), rs7073837 (p = 0.03), and rs10740055 (p = 0.04). Somatic ARID5B deletions were seen in 16/1335 cases (1.2%), being more common in HeH than in other genetic subtypes (2.2% vs. 0.4%; p = 0.002). The expression of ARID5B in HeH cases with genomic deletions was reduced, consistent with a functional role in leukemogenesis. Whole-genome sequencing and RNA-sequencing in HeH revealed additional somatic events involving ARID5B, resulting in a total frequency of 3.6% of HeH cases displaying a somatic ARID5B aberration. Overall, our results show that both constitutional and somatic events in ARID5B are involved in the leukemogenesis of pediatric BCP ALL, particularly in the HeH subtype.


Asunto(s)
Proteínas de Unión al ADN , Leucemia-Linfoma Linfoblástico de Células Precursoras B , Factores de Transcripción , Niño , Preescolar , Femenino , Humanos , Masculino , Proteínas de Unión al ADN/genética , Polimorfismo de Nucleótido Simple , Leucemia-Linfoma Linfoblástico de Células Precursoras B/genética , Factores de Transcripción/genética
14.
J Proteome Res ; 23(8): 2882-2892, 2024 Aug 02.
Artículo en Inglés | MEDLINE | ID: mdl-38231884

RESUMEN

ARID3C is a protein located on human chromosome 9 and expressed at low levels in various organs, yet its biological function has not been elucidated. In this study, we investigated both the cellular localization and function of ARID3C. Employing a combination of LC-MS/MS and deep learning techniques, we identified NPM1 as a binding partner for ARID3C's nuclear shuttling. ARID3C was found to predominantly localize with the nucleus, where it functioned as a transcription factor for genes STAT3, STAT1, and JUNB, thereby facilitating monocyte-to-macrophage differentiation. The precise binding sites between ARID3C and NPM1 were predicted by AlphaFold2. Mutating this binding site prevented ARID3C from interacting with NPM1, resulting in its retention in the cytoplasm instead of translocation to the nucleus. Consequently, ARID3C lost its ability to bind to the promoters of target genes, leading to a loss of monocyte-to-macrophage differentiation. Collectively, our findings indicate that ARID3C forms a complex with NPM1 to translocate to the nucleus, acting as a transcription factor that promotes the expression of the genes involved in monocyte-to-macrophage differentiation.


Asunto(s)
Diferenciación Celular , Núcleo Celular , Macrófagos , Monocitos , Proteínas Nucleares , Nucleofosmina , Humanos , Monocitos/metabolismo , Monocitos/citología , Proteínas Nucleares/metabolismo , Proteínas Nucleares/genética , Macrófagos/metabolismo , Macrófagos/citología , Núcleo Celular/metabolismo , Factores de Transcripción/metabolismo , Factores de Transcripción/genética , Unión Proteica , Sitios de Unión , Factor de Transcripción STAT1/metabolismo , Factor de Transcripción STAT1/genética , Factor de Transcripción STAT3/metabolismo , Factor de Transcripción STAT3/genética , Proteínas de Unión al ADN/metabolismo , Proteínas de Unión al ADN/genética , Regulación de la Expresión Génica , Espectrometría de Masas en Tándem
15.
Ecol Lett ; 27(5): e14434, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38716556

RESUMEN

Anthropogenic habitat modification can indirectly effect reproduction and survival in social species by changing the group structure and social interactions. We assessed the impact of habitat modification on the fitness and life history traits of a cooperative breeder, the Arabian babbler (Argya squamiceps). We collected spatial, reproductive and social data on 572 individuals belonging to 21 social groups over 6 years and combined it with remote sensing to characterize group territories in an arid landscape. In modified resource-rich habitats, groups bred more and had greater productivity, but individuals lived shorter lives than in natural habitats. Habitat modification favoured a faster pace-of-life with lower dispersal and dominance acquisition ages, which might be driven by higher mortality providing opportunities for the dominant breeding positions. Thus, habitat modification might indirectly impact fitness through changes in social structures. This study shows that trade-offs in novel anthropogenic opportunities might offset survival costs by increased productivity.


Asunto(s)
Ecosistema , Rasgos de la Historia de Vida , Animales , Masculino , Femenino , Reproducción , Passeriformes/fisiología , Aptitud Genética , Efectos Antropogénicos
16.
Cancer Sci ; 2024 Nov 03.
Artículo en Inglés | MEDLINE | ID: mdl-39489500

RESUMEN

High tissue density of the mammary gland is considered a pro-tumorigenic factor, hence suppressing the stimuli that induce matrix buildup carries the potential for cancer interception. We found that in non-malignant mammary epithelial cells the combination of the chemopreventive agents bexarotene (Bex) and carvedilol (Carv) suppresses the zymogen granule protein 16B (ZG16B, PAUF) through an interaction of ARID1A with a proximal enhancer. Bex + Carv also reduced ZG16B levels in vivo in normal breast tissue and MDA-MB231 tumor xenografts. The relevance of ZG16B is underscored by ongoing clinical trials targeting ZG16B in pancreatic cancers, but its role in breast cancer development is unclear. In immortalized mammary epithelial cells, secreted recombinant ZG16B stimulated mitogenic kinase phosphorylation, detachment and mesenchymal characteristics, and promoted proliferation, motility and clonogenic growth. Highly concerted induction of specific laminin, collagen and integrin isoforms indicated a shift in matrix properties toward increased density and cell-matrix interactions. Exogenous ZG16B alone blocked Bex + Carv-mediated control of cell growth and migration, and antagonized Bex + Carv-induced gene programs regulating cell adhesion and migration. In breast cancer cells ZG16B induced colony formation and anchorage-independent growth, and stimulated migration in a PI3K/Akt-dependent manner. In contrast, Bex + Carv inhibited colony formation, reduced Ki67 levels, ZG16B expression and glucose uptake in MDA-MB231 xenografts. These data establish ZG16B as a druggable pro-tumorigenic target in breast cell transformation and suggest a key role of the matrisome network in rexinoid-dependent antitumor activity.

17.
Cancer Sci ; 115(3): 905-915, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-38148578

RESUMEN

Chromatin remodelers are commonly altered in human cancer. The mutation of AT-rich interactive domain 1A (ARID1A) in gastric cancer (GC), a component of the SWI/SNF chromatin remodeling complex, was proven associated with treatment response in our previous study. However, ARID1A loss of function was caused not only by mutations but also copy number deletions. The clinicopathologic, genomic, and immunophenotypic correlates of ARID1A loss is largely uncharacterized in GC. Here, 819 patients with clinicopathological information and sequencing data or formalin-fixed paraffin-embedded tissues from four cohorts, Zhongshan Hospital (ZSHS) cohort (n = 375), The Cancer Genome Atlas (TCGA) cohort (n = 371), Samsung Medical Center (SMC) cohort (n = 53), and ZSHS immunotherapy cohort (n = 20), were enrolled. ARID1A loss was defined by genome sequencing or deficient ARID1A expression by immunohistochemistry. We found that ARID1A mutation and copy number deletion were enriched in GC with microsatellite instability (MSI) and chromosomal-instability (CIN), respectively. In the TCGA and ZSHS cohorts, only CIN GC with ARID1A loss could benefit from fluorouracil-based adjuvant chemotherapy. In the SMC and ZSHS immunotherapy cohorts, ARID1A loss exhibited a tendency of superior responsiveness and indicated favorable overall survival after anti-PD-1 immunotherapy. ARID1A-loss tumors demonstrated elevated mutation burden, neoantigen load, and interferon gamma pathway activation. Moreover, in CIN GC, ARID1A loss was correlated with higher homologous recombination deficiency. ARID1A loss defines a distinct subtype of GC characterized by high levels of genome instability, neoantigen formation, and immune activation. These tumors show sensitivity to both chemotherapy and anti-PD-1 immunotherapy. This study provides valuable insights for precision treatment strategies in GC.


Asunto(s)
Proteínas de Unión al ADN , Neoplasias Gástricas , Humanos , Proteínas de Unión al ADN/genética , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Neoplasias Gástricas/tratamiento farmacológico , Neoplasias Gástricas/genética , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Mutación
18.
Cancer Sci ; 115(2): 439-451, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-38100120

RESUMEN

Loss of AT-interacting domain-rich protein 1A (ARID1A) frequently occurs in human malignancies including lung cancer. The biological consequence of ARID1A mutation in lung cancer is not fully understood. This study was designed to determine the effect of ARID1A-depleted lung cancer cells on fibroblast activation. Conditioned media was collected from ARID1A-depleted lung cancer cells and employed to treat lung fibroblasts. The proliferation and migration of lung fibroblasts were investigated. The secretory genes were profiled in lung cancer cells upon ARID1A knockdown. Antibody-based neutralization was utilized to confirm their role in mediating the cross-talk between lung cancer cells and fibroblasts. NOD-SCID-IL2RgammaC-null (NSG) mice received tumor tissues from patients with ARID1A-mutated lung cancer to establish patient-derived xenograft (PDX) models. Notably, ARID1A-depleted lung cancer cells promoted the proliferation and migration of lung fibroblasts. Mechanistically, ARID1A depletion augmented the expression and secretion of prolyl 4-hydroxylase beta (P4HB) in lung cancer cells, which induced the activation of lung fibroblasts through the ß-catenin signaling pathway. P4HB-activated lung fibroblasts promoted the proliferation, invasion, and chemoresistance in lung cancer cells. Neutralizing P4HB hampered the tumor growth and increased cisplatin cytotoxic efficacy in two PDX models. Serum P4HB levels were higher in ARID1A-mutated lung cancer patients than in healthy controls. Moreover, increased serum levels of P4HB were significantly associated with lung cancer metastasis. Together, our work indicates a pivotal role for P4HB in orchestrating the cross-talk between ARID1A-mutated cancer cells and cancer-associated fibroblasts during lung cancer progression. P4HB may represent a promising target for improving lung cancer treatment.


Asunto(s)
Neoplasias Pulmonares , Prolil Hidroxilasas , Proteína Disulfuro Isomerasas , Humanos , Animales , Ratones , Prolil Hidroxilasas/farmacología , Neoplasias Pulmonares/tratamiento farmacológico , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/patología , Resistencia a Antineoplásicos/genética , Línea Celular Tumoral , Proliferación Celular , Ratones Endogámicos NOD , Ratones SCID , Transformación Celular Neoplásica , Pulmón/patología , Fibroblastos/metabolismo , Proteínas de Unión al ADN/genética , Factores de Transcripción/genética , Procolágeno-Prolina Dioxigenasa/metabolismo , Procolágeno-Prolina Dioxigenasa/farmacología
19.
Development ; 148(8)2021 04 15.
Artículo en Inglés | MEDLINE | ID: mdl-33766930

RESUMEN

Stem cells self-renew or give rise to transit-amplifying cells (TACs) that differentiate into specific functional cell types. The fate determination of stem cells to TACs and their transition to fully differentiated progeny is precisely regulated to maintain tissue homeostasis. Arid1a, a core component of the switch/sucrose nonfermentable complex, performs epigenetic regulation of stage- and tissue-specific genes that is indispensable for stem cell homeostasis and differentiation. However, the functional mechanism of Arid1a in the fate commitment of mesenchymal stem cells (MSCs) and their progeny is not clear. Using the continuously growing adult mouse incisor model, we show that Arid1a maintains tissue homeostasis through limiting proliferation, promoting cell cycle exit and differentiation of TACs by inhibiting the Aurka-Cdk1 axis. Loss of Arid1a overactivates the Aurka-Cdk1 axis, leading to expansion of the mitotic TAC population but compromising their differentiation ability. Furthermore, the defective homeostasis after loss of Arid1a ultimately leads to reduction of the MSC population. These findings reveal the functional significance of Arid1a in regulating the fate of TACs and their interaction with MSCs to maintain tissue homeostasis.


Asunto(s)
Aurora Quinasa A/metabolismo , Proteína Quinasa CDC2/metabolismo , Proteínas de Unión al ADN/metabolismo , Incisivo/embriología , Células Madre Mesenquimatosas/metabolismo , Mitosis , Transducción de Señal , Factores de Transcripción/metabolismo , Animales , Aurora Quinasa A/genética , Proteína Quinasa CDC2/genética , Proteínas de Unión al ADN/genética , Ratones , Ratones Transgénicos , Factores de Transcripción/genética
20.
Small ; : e2406803, 2024 Oct 07.
Artículo en Inglés | MEDLINE | ID: mdl-39375961

RESUMEN

The poor ability of covalent organic frameworks (COFs) based adsorbents at low relative humidity (RH) conditions limits their applications for air-water harvesting in arid environments. In the present work, the sulfonated COFs (DAAQ-TFP-SO3H@LiCl) composites are prepared through the functionalization of sulfonic acid and LiCl composite to improve its hydrophilicity. TheDAAQ-TFP-SO3H@LiCl composites exhibit a good adsorption performance, outperforming many other COF adsorbents developed so far. It can absorb 0.22 ± 0.005 g g-1 and 1.01 ± 0.027 g g-1 of water at room temperature under 20% RH and 90% RH, respectively while demonstrating good cyclic stability. Compared with the isotherm of the DAAQ-TFP, the introduction of the sulfonic acid group shifts the inflection point of the water isotherm toward low humidity, indicating that the sulfonic acid group effectively expends the working humidity range of the adsorbent and enables the effective water adsorption in an arid environment. Furthermore, the DAAQ-TFP-SO3H@LiCl composites display rapid kinetics during both the adsorption and desorption processes, reaching saturation within 60 min in the equilibrium adsorption test and completing desorption within 12 min at 50 °C. This innovative approach provides a new method for designing adsorbent materials with low energy input requirements and high daily water consumption capabilities.

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