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1.
Gastroenterology ; 162(1): 209-222, 2022 01.
Artículo en Inglés | MEDLINE | ID: mdl-34571027

RESUMEN

BACKGROUND AND AIMS: Genomic alterations that encourage stem cell activity and hinder proper maturation are central to the development of colorectal cancer (CRC). Key molecular mediators that promote these malignant properties require further elucidation to galvanize translational advances. We therefore aimed to characterize a key factor that blocks intestinal differentiation, define its transcriptional and epigenetic program, and provide preclinical evidence for therapeutic targeting in CRC. METHODS: Intestinal tissue from transgenic mice and patients were analyzed by means of histopathology and immunostaining. Human CRC cells and neoplastic murine organoids were genetically manipulated for functional studies. Gene expression profiling was obtained through RNA sequencing. Histone modifications and transcription factor binding were determined with the use of chromatin immunoprecipitation sequencing. RESULTS: We demonstrate that SRY-box transcription factor 9 (SOX9) promotes CRC by activating a stem cell-like program that hinders intestinal differentiation. Intestinal adenomas and colorectal adenocarcinomas from mouse models and patients demonstrate ectopic and elevated expression of SOX9. Functional experiments indicate a requirement for SOX9 in human CRC cell lines and engineered neoplastic organoids. Disrupting SOX9 activity impairs primary CRC tumor growth by inducing intestinal differentiation. By binding to genome wide enhancers, SOX9 directly activates genes associated with Paneth and stem cell activity, including prominin 1 (PROM1). SOX9 up-regulates PROM1 via a Wnt-responsive intronic enhancer. A pentaspan transmembrane protein, PROM1 uses its first intracellular domain to support stem cell signaling, at least in part through SOX9, reinforcing a PROM1-SOX9 positive feedback loop. CONCLUSIONS: These studies establish SOX9 as a central regulator of an enhancer-driven stem cell-like program and carry important implications for developing therapeutics directed at overcoming differentiation defects in CRC.


Asunto(s)
Diferenciación Celular , Neoplasias Colorrectales/metabolismo , Elementos de Facilitación Genéticos , Células Madre Neoplásicas/metabolismo , Factor de Transcripción SOX9/metabolismo , Antígeno AC133/genética , Antígeno AC133/metabolismo , Animales , Proliferación Celular , Neoplasias Colorrectales/genética , Neoplasias Colorrectales/patología , Regulación Neoplásica de la Expresión Génica , Genes APC , Células HT29 , Humanos , Ratones Transgénicos , Células Madre Neoplásicas/patología , Factor de Transcripción SOX9/genética , Carga Tumoral , Células Tumorales Cultivadas , Vía de Señalización Wnt
2.
Gut ; 71(4): 665-675, 2022 04.
Artículo en Inglés | MEDLINE | ID: mdl-33789967

RESUMEN

OBJECTIVE: Oesophageal squamous cell carcinoma (OSCC), like other squamous carcinomas, harbour highly recurrent cell cycle pathway alterations, especially hyperactivation of the CCND1/CDK4/6 axis, raising the potential for use of existing CDK4/6 inhibitors in these cancers. Although CDK4/6 inhibition has shown striking success when combined with endocrine therapy in oestrogen receptor positive breast cancer, CDK4/6 inhibitor palbociclib monotherapy has not revealed evidence of efficacy to date in OSCC clinical studies. Herein, we sought to elucidate the identification of key dependencies in OSCC as a foundation for the selection of targets whose blockade could be combined with CDK4/6 inhibition. DESIGN: We combined large-scale genomic dependency and pharmaceutical screening datasets with preclinical cell line models, to identified potential combination therapies in squamous cell cancer. RESULTS: We identified sensitivity to inhibitors to the ERBB family of receptor kinases, results clearly extending beyond the previously described minority of tumours with EGFR amplification/dependence, specifically finding a subset of OSCCs with dual dependence on ERBB3 and ERBB2. Subsequently. we demonstrated marked efficacy of combined pan-ERBB and CDK4/6 inhibition in vitro and in vivo. Furthermore, we demonstrated that squamous lineage transcription factor KLF5 facilitated activation of ERBBs in OSCC. CONCLUSION: These results provide clear rationale for development of combined ERBB and CDK4/6 inhibition in these cancers and raises the potential for KLF5 expression as a candidate biomarker to guide the use of these agents. These data suggested that by combining existing Food and Drug Administration (FDA)-approved agents, we have the capacity to improve therapy for OSCC and other squamous cancer.


Asunto(s)
Carcinoma de Células Escamosas , Neoplasias Esofágicas , Carcinoma de Células Escamosas de Esófago , Carcinoma de Células Escamosas/genética , Línea Celular Tumoral , Quinasa 4 Dependiente de la Ciclina , Quinasa 6 Dependiente de la Ciclina , Neoplasias Esofágicas/tratamiento farmacológico , Neoplasias Esofágicas/patología , Carcinoma de Células Escamosas de Esófago/tratamiento farmacológico , Humanos , Inhibidores de Proteínas Quinasas/farmacología , Inhibidores de Proteínas Quinasas/uso terapéutico
3.
J Biol Chem ; 291(10): 5418-27, 2016 Mar 04.
Artículo en Inglés | MEDLINE | ID: mdl-26728459

RESUMEN

Although juvenile hormone (JH) is known to prevent insect larval metamorphosis and stimulate adult reproduction, the molecular mechanisms of JH action in insect reproduction remain largely unknown. Earlier, we reported that the JH-receptor complex, composed of methoprene-tolerant and steroid receptor co-activator, acts on mini-chromosome maintenance (Mcm) genes Mcm4 and Mcm7 to promote DNA replication and polyploidy for the massive vitellogenin (Vg) synthesis required for egg production in the migratory locust (Guo, W., Wu, Z., Song, J., Jiang, F., Wang, Z., Deng, S., Walker, V. K., and Zhou, S. (2014) PLoS Genet. 10, e1004702). In this study we have investigated the involvement of cell-division-cycle 6 (Cdc6) in JH-dependent vitellogenesis and oogenesis, as Cdc6 is essential for the formation of prereplication complex. We demonstrate here that Cdc6 is expressed in response to JH and methoprene-tolerant, and Cdc6 transcription is directly regulated by the JH-receptor complex. Knockdown of Cdc6 inhibits polyploidization of fat body and follicle cells, resulting in the substantial reduction of Vg expression in the fat body as well as severely impaired oocyte maturation and ovarian growth. Our data indicate the involvement of Cdc6 in JH pathway and a pivotal role of Cdc6 in JH-mediated polyploidization, vitellogenesis, and oogenesis.


Asunto(s)
Proteínas de Ciclo Celular/metabolismo , Proteínas de Drosophila/metabolismo , Hormonas Juveniles/metabolismo , Activación Transcripcional , Vitelogénesis , Secuencia de Aminoácidos , Animales , Proteínas de Ciclo Celular/genética , Línea Celular , Proteínas de Drosophila/genética , Drosophila melanogaster/genética , Drosophila melanogaster/metabolismo , Drosophila melanogaster/fisiología , Cuerpo Adiposo/metabolismo , Femenino , Saltamontes/genética , Saltamontes/metabolismo , Saltamontes/fisiología , Datos de Secuencia Molecular , Folículo Ovárico/metabolismo , Poliploidía , Vitelinas/genética , Vitelinas/metabolismo
4.
Glob Chang Biol ; 22(2): 856-74, 2016 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-26279285

RESUMEN

Elevated CO2 and temperature strongly affect crop production, but understanding of the crop response to combined CO2 and temperature increases under field conditions is still limited while data are scarce. We grew wheat (Triticum aestivum L.) and rice (Oryza sativa L.) under two levels of CO2 (ambient and enriched up to 500 µmol mol(-1) ) and two levels of canopy temperature (ambient and increased by 1.5-2.0 °C) in free-air CO2 enrichment (FACE) systems and carried out a detailed growth and yield component analysis during two growing seasons for both crops. An increase in CO2 resulted in higher grain yield, whereas an increase in temperature reduced grain yield, in both crops. An increase in CO2 was unable to compensate for the negative impact of an increase in temperature on biomass and yield of wheat and rice. Yields of wheat and rice were decreased by 10-12% and 17-35%, respectively, under the combination of elevated CO2 and temperature. The number of filled grains per unit area was the most important yield component accounting for the effects of elevated CO2 and temperature in wheat and rice. Our data showed complex treatment effects on the interplay between preheading duration, nitrogen uptake, tillering, leaf area index, and radiation-use efficiency, and thus on yield components and yield. Nitrogen uptake before heading was crucial in minimizing yield loss due to climate change in both crops. For rice, however, a breeding strategy to increase grain number per m(2) and % filled grains (or to reduce spikelet sterility) at high temperature is also required to prevent yield reduction under conditions of global change.


Asunto(s)
Dióxido de Carbono , Oryza/crecimiento & desarrollo , Triticum/crecimiento & desarrollo , Biomasa , Cambio Climático , Nitrógeno/metabolismo , Oryza/metabolismo , Fotosíntesis , Componentes Aéreos de las Plantas/crecimiento & desarrollo , Componentes Aéreos de las Plantas/metabolismo , Temperatura , Triticum/metabolismo
5.
bioRxiv ; 2024 Mar 25.
Artículo en Inglés | MEDLINE | ID: mdl-37333088

RESUMEN

Recent advances in single-cell epigenomic techniques have created a growing demand for scATAC-seq analysis. One key analysis task is to determine cell type identity based on the epigenetic data. We introduce scATAnno, a python package designed to automatically annotate scATAC-seq data using large-scale scATAC-seq reference atlases. This workflow generates the reference atlases from publicly available datasets enabling accurate cell type annotation by integrating query data with reference atlases, without the use of scRNA-seq data. To enhance annotation accuracy, we have incorporated KNN-based and weighted distance-based uncertainty scores to effectively detect cell populations within the query data that are distinct from all cell types in the reference data. We compare and benchmark scATAnno against 7 other published approaches for cell annotation and show superior performance in multiple data sets and metrics. We showcase the utility of scATAnno across multiple datasets, including peripheral blood mononuclear cell (PBMC), Triple Negative Breast Cancer (TNBC), and basal cell carcinoma (BCC), and demonstrate that scATAnno accurately annotates cell types across conditions. Overall, scATAnno is a useful tool for scATAC-seq reference building and cell type annotation in scATAC-seq data and can aid in the interpretation of new scATAC-seq datasets in complex biological systems.

6.
Nat Cell Biol ; 25(9): 1346-1358, 2023 09.
Artículo en Inglés | MEDLINE | ID: mdl-37591951

RESUMEN

Small cell lung cancer (SCLC) exists broadly in four molecular subtypes: ASCL1, NEUROD1, POU2F3 and Inflammatory. Initially, SCLC subtypes were thought to be mutually exclusive, but recent evidence shows intra-tumoural subtype heterogeneity and plasticity between subtypes. Here, using a CRISPR-based autochthonous SCLC genetically engineered mouse model to study the consequences of KDM6A/UTX inactivation, we show that KDM6A inactivation induced plasticity from ASCL1 to NEUROD1 resulting in SCLC tumours that express both ASCL1 and NEUROD1. Mechanistically, KDM6A normally maintains an active chromatin state that favours the ASCL1 subtype with its loss decreasing H3K4me1 and increasing H3K27me3 at enhancers of neuroendocrine genes leading to a cell state that is primed for ASCL1-to-NEUROD1 subtype switching. This work identifies KDM6A as an epigenetic regulator that controls ASCL1 to NEUROD1 subtype plasticity and provides an autochthonous SCLC genetically engineered mouse model to model ASCL1 and NEUROD1 subtype heterogeneity and plasticity, which is found in 35-40% of human SCLCs.


Asunto(s)
Neoplasias Pulmonares , Carcinoma Pulmonar de Células Pequeñas , Humanos , Animales , Ratones , Carcinoma Pulmonar de Células Pequeñas/genética , Histona Demetilasas/genética , Cromatina , Epigenómica , Neoplasias Pulmonares/genética
7.
Cancer Res ; 83(19): 3284-3304, 2023 10 02.
Artículo en Inglés | MEDLINE | ID: mdl-37450351

RESUMEN

Immunotherapies have yet to demonstrate significant efficacy in the treatment of hormone receptor-positive (HR+) breast cancer. Given that endocrine therapy (ET) is the primary approach for treating HR+ breast cancer, we investigated the effects of ET on the tumor immune microenvironment (TME) in HR+ breast cancer. Spatial proteomics of primary HR+ breast cancer samples obtained at baseline and after ET from patients enrolled in a neoadjuvant clinical trial (NCT02764541) indicated that ET upregulated ß2-microglobulin and influenced the TME in a manner that promotes enhanced immunogenicity. To gain a deeper understanding of the underlying mechanisms, the intrinsic effects of ET on cancer cells were explored, which revealed that ET plays a crucial role in facilitating the chromatin binding of RelA, a key component of the NF-κB complex. Consequently, heightened NF-κB signaling enhanced the response to interferon-gamma, leading to the upregulation of ß2-microglobulin and other antigen presentation-related genes. Further, modulation of NF-κB signaling using a SMAC mimetic in conjunction with ET augmented T-cell migration and enhanced MHC-I-specific T-cell-mediated cytotoxicity. Remarkably, the combination of ET and SMAC mimetics, which also blocks prosurvival effects of NF-κB signaling through the degradation of inhibitors of apoptosis proteins, elicited tumor regression through cell autonomous mechanisms, providing additional support for their combined use in HR+ breast cancer. SIGNIFICANCE: Adding SMAC mimetics to endocrine therapy enhances tumor regression in a cell autonomous manner while increasing tumor immunogenicity, indicating that this combination could be an effective treatment for HR+ patients with breast cancer.


Asunto(s)
Neoplasias de la Mama , FN-kappa B , Humanos , Femenino , FN-kappa B/metabolismo , Péptidos y Proteínas de Señalización Intracelular , Neoplasias de la Mama/patología , Presentación de Antígeno , Proteínas Reguladoras de la Apoptosis , Apoptosis , Línea Celular Tumoral , Proteínas Mitocondriales/metabolismo , Microambiente Tumoral
8.
Dev Cell ; 57(2): 212-227.e8, 2022 01 24.
Artículo en Inglés | MEDLINE | ID: mdl-34990589

RESUMEN

The transcriptional co-activator YAP1 oncogene is the downstream effector of the Hippo pathway, which regulates tissue homeostasis, organ size, regeneration, and tumorigenesis. Multiple cancers are dependent on sustained expression of YAP1 for cell proliferation, survival, and tumorigenesis, but the molecular basis of this oncogene dependency is not well understood. To identify genes that can functionally substitute for YAP1, we performed a genome-scale genetic rescue screen in YAP1-dependent colon cancer cells expressing an inducible YAP1-specific shRNA. We found that the transcription factor PRDM14 rescued cell proliferation and tumorigenesis upon YAP1 suppression in YAP1-dependent cells, xenografts, and colon cancer organoids. YAP1 and PRDM14 individually activated the transcription of calmodulin 2 (CALM2) and a glucose transporter SLC2A1 upon YAP1 suppression, and CALM2 or SLC2A1 expression was required for the rescue of YAP1 suppression. Together, these findings implicate PRDM14-mediated transcriptional upregulation of CALM2 and SLC2A1 as key components of oncogenic YAP1 signaling and dependency.


Asunto(s)
Carcinogénesis/genética , Proteínas de Unión al ADN/metabolismo , Proteínas de Unión al ARN/metabolismo , Factores de Transcripción/metabolismo , Proteínas Señalizadoras YAP/metabolismo , Proteínas Adaptadoras Transductoras de Señales/metabolismo , Animales , Calmodulina/genética , Calmodulina/metabolismo , Línea Celular Tumoral , Proliferación Celular/genética , Supervivencia Celular/genética , Neoplasias del Colon/genética , Proteínas de Unión al ADN/genética , Expresión Génica/genética , Regulación Neoplásica de la Expresión Génica/genética , Transportador de Glucosa de Tipo 1/genética , Humanos , Ratones , Ratones Desnudos , Organoides , Fosfoproteínas/metabolismo , Proteínas de Unión al ARN/genética , Transducción de Señal/genética , Factores de Transcripción/genética , Activación Transcripcional , Ensayos Antitumor por Modelo de Xenoinjerto , Proteínas Señalizadoras YAP/genética , Proteínas Señalizadoras YAP/fisiología
9.
Nat Commun ; 13(1): 2559, 2022 05 13.
Artículo en Inglés | MEDLINE | ID: mdl-35562350

RESUMEN

c-MYC (MYC) is a major driver of prostate cancer tumorigenesis and progression. Although MYC is overexpressed in both early and metastatic disease and associated with poor survival, its impact on prostate transcriptional reprogramming remains elusive. We demonstrate that MYC overexpression significantly diminishes the androgen receptor (AR) transcriptional program (the set of genes directly targeted by the AR protein) in luminal prostate cells without altering AR expression. Analyses of clinical specimens reveal that concurrent low AR and high MYC transcriptional programs accelerate prostate cancer progression toward a metastatic, castration-resistant disease. Data integration of single-cell transcriptomics together with ChIP-seq uncover an increase in RNA polymerase II (Pol II) promoter-proximal pausing at AR-dependent genes following MYC overexpression without an accompanying deactivation of AR-bound enhancers. Altogether, our findings suggest that MYC overexpression antagonizes the canonical AR transcriptional program and contributes to prostate tumor initiation and progression by disrupting transcriptional pause release at AR-regulated genes.


Asunto(s)
Neoplasias de la Próstata , Receptores Androgénicos , Línea Celular Tumoral , Transformación Celular Neoplásica/genética , Regulación Neoplásica de la Expresión Génica , Genes myc , Humanos , Masculino , Próstata/patología , Neoplasias de la Próstata/patología , Proteínas Proto-Oncogénicas c-myc , Receptores Androgénicos/genética , Receptores Androgénicos/metabolismo
10.
Blood Cancer Discov ; 3(2): 116-135, 2022 03 01.
Artículo en Inglés | MEDLINE | ID: mdl-35015684

RESUMEN

Polycomb repressive epigenetic complexes are recurrently dysregulated in cancer. Unlike polycomb repressive complex 2 (PRC2), the role of PRC1 in oncogenesis and therapy resistance is not well-defined. Here, we demonstrate that highly recurrent mutations of the PRC1 subunits BCOR and BCORL1 in leukemia disrupt assembly of a noncanonical PRC1.1 complex, thereby selectively unlinking the RING-PCGF enzymatic core from the chromatin-targeting auxiliary subcomplex. As a result, BCOR-mutated PRC1.1 is localized to chromatin but lacks repressive activity, leading to epigenetic reprogramming and transcriptional activation at target loci. We define a set of functional targets that drive aberrant oncogenic signaling programs in PRC1.1-mutated cells and primary patient samples. Activation of these PRC1.1 targets in BCOR-mutated cells confers acquired resistance to treatment while sensitizing to targeted kinase inhibition. Our study thus reveals a novel epigenetic mechanism that explains PRC1.1 tumor-suppressive activity and identifies a therapeutic strategy in PRC1.1-mutated cancer. SIGNIFICANCE: We demonstrate that BCOR and BCORL1 mutations in leukemia unlink PRC1.1 repressive function from target genes, resulting in epigenetic reprogramming and activation of aberrant cell signaling programs that mediate treatment resistance. Our study provides mechanistic insights into the pathogenesis of PRC1.1-mutated leukemia that inform novel therapeutic approaches. This article is highlighted in the In This Issue feature, p. 85.


Asunto(s)
Carcinogénesis , Leucemia , Carcinogénesis/genética , Proteínas de Ciclo Celular/genética , Cromatina , Epigénesis Genética/genética , Humanos , Leucemia/genética , Mutación/genética , Proteínas Proto-Oncogénicas/genética , Proteínas Represoras/genética , Transducción de Señal/genética
11.
Cancer Res ; 82(20): 3673-3686, 2022 10 17.
Artículo en Inglés | MEDLINE | ID: mdl-35950920

RESUMEN

Most invasive lobular breast cancers (ILC) are of the luminal A subtype and are strongly hormone receptor-positive. Yet, ILC is relatively resistant to tamoxifen and associated with inferior long-term outcomes compared with invasive ductal cancers (IDC). In this study, we sought to gain mechanistic insights into these clinical findings that are not explained by the genetic landscape of ILC and to identify strategies to improve patient outcomes. A comprehensive analysis of the epigenome of ILC in preclinical models and clinical samples showed that, compared with IDC, ILC harbored a distinct chromatin state linked to gained recruitment of FOXA1, a lineage-defining pioneer transcription factor. This resulted in an ILC-unique FOXA1-estrogen receptor (ER) axis that promoted the transcription of genes associated with tumor progression and poor outcomes. The ILC-unique FOXA1-ER axis led to retained ER chromatin binding after tamoxifen treatment, which facilitated tamoxifen resistance while remaining strongly dependent on ER signaling. Mechanistically, gained FOXA1 binding was associated with the autoinduction of FOXA1 in ILC through an ILC-unique FOXA1 binding site. Targeted silencing of this regulatory site resulted in the disruption of the feed-forward loop and growth inhibition in ILC. In summary, ILC is characterized by a unique chromatin state and FOXA1-ER axis that is associated with tumor progression, offering a novel mechanism of tamoxifen resistance. These results underscore the importance of conducting clinical trials dedicated to patients with ILC in order to optimize treatments in this breast cancer subtype. SIGNIFICANCE: A unique FOXA1-ER axis in invasive lobular breast cancer promotes disease progression and tamoxifen resistance, highlighting a potential therapeutic avenue for clinical investigations dedicated to this disease. See related commentary by Blawski and Toska, p. 3668.


Asunto(s)
Neoplasias de la Mama , Carcinoma Ductal de Mama , Carcinoma Lobular , Neoplasias de la Mama/tratamiento farmacológico , Neoplasias de la Mama/genética , Neoplasias de la Mama/patología , Carcinoma Ductal de Mama/patología , Carcinoma Lobular/tratamiento farmacológico , Carcinoma Lobular/genética , Carcinoma Lobular/metabolismo , Cromatina/genética , Resistencia a Antineoplásicos/genética , Femenino , Humanos , Pronóstico , Receptores de Estrógenos/metabolismo , Tamoxifeno/farmacología , Tamoxifeno/uso terapéutico
12.
Genomics Proteomics Bioinformatics ; 19(4): 652-661, 2021 08.
Artículo en Inglés | MEDLINE | ID: mdl-34284136

RESUMEN

Chromatin immunoprecipitation sequencing (ChIP-seq) and the Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) have become essential technologies to effectively measure protein-DNA interactions and chromatin accessibility. However, there is a need for a scalable and reproducible pipeline that incorporates proper normalization between samples, correction of copy number variations, and integration of new downstream analysis tools. Here we present Containerized Bioinformatics workflow for Reproducible ChIP/ATAC-seq Analysis (CoBRA), a modularized computational workflow which quantifies ChIP-seq and ATAC-seq peak regions and performs unsupervised and supervised analyses. CoBRA provides a comprehensive state-of-the-art ChIP-seq and ATAC-seq analysis pipeline that can be used by scientists with limited computational experience. This enables researchers to gain rapid insight into protein-DNA interactions and chromatin accessibility through sample clustering, differential peak calling, motif enrichment, comparison of sites to a reference database, and pathway analysis. CoBRA is publicly available online at https://bitbucket.org/cfce/cobra.


Asunto(s)
Secuenciación de Inmunoprecipitación de Cromatina , Biología Computacional , Cromatina/genética , Variaciones en el Número de Copia de ADN , Secuenciación de Nucleótidos de Alto Rendimiento , Análisis de Secuencia de ADN , Flujo de Trabajo
13.
Nat Cell Biol ; 23(11): 1187-1198, 2021 11.
Artículo en Inglés | MEDLINE | ID: mdl-34737445

RESUMEN

How cancer cells adapt to evade the therapeutic effects of drugs targeting oncogenic drivers is poorly understood. Here we report an epigenetic mechanism leading to the adaptive resistance of triple-negative breast cancer (TNBC) to fibroblast growth factor receptor (FGFR) inhibitors. Prolonged FGFR inhibition suppresses the function of BRG1-dependent chromatin remodelling, leading to an epigenetic state that derepresses YAP-associated enhancers. These chromatin changes induce the expression of several amino acid transporters, resulting in increased intracellular levels of specific amino acids that reactivate mTORC1. Consistent with this mechanism, addition of mTORC1 or YAP inhibitors to FGFR blockade synergistically attenuated the growth of TNBC patient-derived xenograft models. Collectively, these findings reveal a feedback loop involving an epigenetic state transition and metabolic reprogramming that leads to adaptive therapeutic resistance and provides potential therapeutic strategies to overcome this mechanism of resistance.


Asunto(s)
Antineoplásicos/farmacología , Proteínas Cromosómicas no Histona/metabolismo , Resistencia a Antineoplásicos , Compuestos de Fenilurea/farmacología , Pirimidinas/farmacología , Receptores de Factores de Crecimiento de Fibroblastos/antagonistas & inhibidores , Factores de Transcripción/metabolismo , Neoplasias de la Mama Triple Negativas/tratamiento farmacológico , Proteínas Señalizadoras YAP/metabolismo , Aminoácidos/metabolismo , Protocolos de Quimioterapia Combinada Antineoplásica/farmacología , Línea Celular Tumoral , Ensamble y Desensamble de Cromatina , Proteínas Cromosómicas no Histona/genética , ADN Helicasas/genética , ADN Helicasas/metabolismo , Resistencia a Antineoplásicos/genética , Sinergismo Farmacológico , Epigénesis Genética , Femenino , Regulación Neoplásica de la Expresión Génica , Humanos , Diana Mecanicista del Complejo 1 de la Rapamicina/antagonistas & inhibidores , Diana Mecanicista del Complejo 1 de la Rapamicina/genética , Diana Mecanicista del Complejo 1 de la Rapamicina/metabolismo , Terapia Molecular Dirigida , Complejos Multiproteicos , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Receptores de Factores de Crecimiento de Fibroblastos/metabolismo , Transducción de Señal , Factores de Transcripción/genética , Neoplasias de la Mama Triple Negativas/genética , Neoplasias de la Mama Triple Negativas/metabolismo , Neoplasias de la Mama Triple Negativas/patología , Ensayos Antitumor por Modelo de Xenoinjerto , Proteínas Señalizadoras YAP/antagonistas & inhibidores , Proteínas Señalizadoras YAP/genética
14.
Nat Genet ; 53(6): 881-894, 2021 06.
Artículo en Inglés | MEDLINE | ID: mdl-33972779

RESUMEN

Esophageal squamous cell carcinomas (ESCCs) harbor recurrent chromosome 3q amplifications that target the transcription factor SOX2. Beyond its role as an oncogene in ESCC, SOX2 acts in development of the squamous esophagus and maintenance of adult esophageal precursor cells. To compare Sox2 activity in normal and malignant tissue, we developed engineered murine esophageal organoids spanning normal esophagus to Sox2-induced squamous cell carcinoma and mapped Sox2 binding and the epigenetic and transcriptional landscape with evolution from normal to cancer. While oncogenic Sox2 largely maintains actions observed in normal tissue, Sox2 overexpression with p53 and p16 inactivation promotes chromatin remodeling and evolution of the Sox2 cistrome. With Klf5, oncogenic Sox2 acquires new binding sites and enhances activity of oncogenes such as Stat3. Moreover, oncogenic Sox2 activates endogenous retroviruses, inducing expression of double-stranded RNA and dependence on the RNA editing enzyme ADAR1. These data reveal SOX2 functions in ESCC, defining targetable vulnerabilities.


Asunto(s)
Adenosina Desaminasa/metabolismo , Epigenoma , Neoplasias Esofágicas/genética , Carcinoma de Células Escamosas de Esófago/genética , Proteínas de Unión al ARN/metabolismo , Factores de Transcripción SOXB1/metabolismo , Regiones no Traducidas 3'/genética , Animales , Secuencia de Bases , Carcinogénesis/genética , Línea Celular Tumoral , Transformación Celular Neoplásica/genética , Inhibidor p16 de la Quinasa Dependiente de Ciclina/metabolismo , Retrovirus Endógenos/genética , Elementos de Facilitación Genéticos/genética , Regulación Neoplásica de la Expresión Génica , Genoma Humano , Humanos , Interferones/metabolismo , Intrones/genética , Factores de Transcripción de Tipo Kruppel/genética , Ratones , Organoides/patología , Unión Proteica , ARN Bicatenario/metabolismo , Factores de Transcripción SOXB1/genética , Proteína p53 Supresora de Tumor/metabolismo
15.
Cancer Discov ; 11(6): 1524-1541, 2021 06.
Artículo en Inglés | MEDLINE | ID: mdl-33589424

RESUMEN

Immune checkpoint blockade (ICB) therapy revolutionized cancer treatment, but many patients with impaired MHC-I expression remain refractory. Here, we combined FACS-based genome-wide CRISPR screens with a data-mining approach to identify drugs that can upregulate MHC-I without inducing PD-L1. CRISPR screening identified TRAF3, a suppressor of the NFκB pathway, as a negative regulator of MHC-I but not PD-L1. The Traf3-knockout gene expression signature is associated with better survival in ICB-naïve patients with cancer and better ICB response. We then screened for drugs with similar transcriptional effects as this signature and identified Second Mitochondria-derived Activator of Caspase (SMAC) mimetics. We experimentally validated that the SMAC mimetic birinapant upregulates MHC-I, sensitizes cancer cells to T cell-dependent killing, and adds to ICB efficacy. Our findings provide preclinical rationale for treating tumors expressing low MHC-I expression with SMAC mimetics to enhance sensitivity to immunotherapy. The approach used in this study can be generalized to identify other drugs that enhance immunotherapy efficacy. SIGNIFICANCE: MHC-I loss or downregulation in cancer cells is a major mechanism of resistance to T cell-based immunotherapies. Our study reveals that birinapant may be used for patients with low baseline MHC-I to enhance ICB response. This represents promising immunotherapy opportunities given the biosafety profile of birinapant from multiple clinical trials.This article is highlighted in the In This Issue feature, p. 1307.


Asunto(s)
Inhibidores de Puntos de Control Inmunológico/uso terapéutico , Neoplasias/tratamiento farmacológico , Antígeno B7-H1/metabolismo , Minería de Datos , Perfilación de la Expresión Génica , Antígenos de Histocompatibilidad Clase I/metabolismo , Humanos , Inhibidores de Puntos de Control Inmunológico/farmacología , Inmunoterapia , Microambiente Tumoral/efectos de los fármacos
16.
Nat Commun ; 12(1): 5775, 2021 10 01.
Artículo en Inglés | MEDLINE | ID: mdl-34599169

RESUMEN

Neuroendocrine carcinomas (NEC) are tumors expressing markers of neuronal differentiation that can arise at different anatomic sites but have strong histological and clinical similarities. Here we report the chromatin landscapes of a range of human NECs and show convergence to the activation of a common epigenetic program. With a particular focus on treatment emergent neuroendocrine prostate cancer (NEPC), we analyze cell lines, patient-derived xenograft (PDX) models and human clinical samples to show the existence of two distinct NEPC subtypes based on the expression of the neuronal transcription factors ASCL1 and NEUROD1. While in cell lines and PDX models these subtypes are mutually exclusive, single-cell analysis of human clinical samples exhibits a more complex tumor structure with subtypes coexisting as separate sub-populations within the same tumor. These tumor sub-populations differ genetically and epigenetically contributing to intra- and inter-tumoral heterogeneity in human metastases. Overall, our results provide a deeper understanding of the shared clinicopathological characteristics shown by NECs. Furthermore, the intratumoral heterogeneity of human NEPCs suggests the requirement of simultaneous targeting of coexisting tumor populations as a therapeutic strategy.


Asunto(s)
Carcinoma Neuroendocrino/genética , Neoplasias de la Próstata/genética , Factores de Transcripción/metabolismo , Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico/genética , Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico/metabolismo , Cromatina/genética , Cromatina/metabolismo , Epigénesis Genética/genética , Regulación Neoplásica de la Expresión Génica/genética , Regulación Neoplásica de la Expresión Génica/fisiología , Humanos , Masculino , Factores de Transcripción/genética
17.
J Exp Med ; 217(7)2020 07 06.
Artículo en Inglés | MEDLINE | ID: mdl-32374402

RESUMEN

Cytotoxic T cells play a key role in adaptive immunity by killing infected or cancerous cells. While the transcriptional control of CD8 T cell differentiation and effector function following T cell activation has been extensively studied, little is known about epigenetic regulation of these processes. Here we show that the histone deacetylase HDAC3 inhibits CD8 T cell cytotoxicity early during activation and is required for persistence of activated CD8 T cells following resolution of an acute infection. Mechanistically, HDAC3 inhibits gene programs associated with cytotoxicity and effector differentiation of CD8 T cells including genes encoding essential cytotoxicity proteins and key transcription factors. These data identify HDAC3 as an epigenetic regulator of the CD8 T cell cytotoxicity program.


Asunto(s)
Linfocitos T CD8-positivos/inmunología , Epigénesis Genética , Histona Desacetilasas/metabolismo , Linfocitos T Citotóxicos , Acetilación/efectos de los fármacos , Acrilamidas/farmacología , Animales , Antígenos/metabolismo , Secuencia de Bases , Linfocitos T CD8-positivos/efectos de los fármacos , Subunidad alfa 3 del Factor de Unión al Sitio Principal/metabolismo , Epigénesis Genética/efectos de los fármacos , Inhibidores de Histona Desacetilasas/farmacología , Histona Desacetilasas/deficiencia , Histonas/metabolismo , Ganglios Linfáticos/efectos de los fármacos , Ganglios Linfáticos/metabolismo , Activación de Linfocitos/efectos de los fármacos , Activación de Linfocitos/inmunología , Virus de la Coriomeningitis Linfocítica/fisiología , Lisina/metabolismo , Ratones Endogámicos C57BL , Ratones Noqueados , Fenotipo , Fenilendiaminas/farmacología , Factor 1 de Unión al Dominio 1 de Regulación Positiva/metabolismo , Linfocitos T Citotóxicos/efectos de los fármacos , Transcripción Genética/efectos de los fármacos
18.
Genome Biol ; 21(1): 198, 2020 08 07.
Artículo en Inglés | MEDLINE | ID: mdl-32767996

RESUMEN

We present Model-based AnalysEs of Transcriptome and RegulOme (MAESTRO), a comprehensive open-source computational workflow ( http://github.com/liulab-dfci/MAESTRO ) for the integrative analyses of single-cell RNA-seq (scRNA-seq) and ATAC-seq (scATAC-seq) data from multiple platforms. MAESTRO provides functions for pre-processing, alignment, quality control, expression and chromatin accessibility quantification, clustering, differential analysis, and annotation. By modeling gene regulatory potential from chromatin accessibilities at the single-cell level, MAESTRO outperforms the existing methods for integrating the cell clusters between scRNA-seq and scATAC-seq. Furthermore, MAESTRO supports automatic cell-type annotation using predefined cell type marker genes and identifies driver regulators from differential scRNA-seq genes and scATAC-seq peaks.


Asunto(s)
Regulación de la Expresión Génica , Modelos Genéticos , Análisis de la Célula Individual , Programas Informáticos , Transcriptoma , Células de la Médula Ósea/metabolismo , Estudios de Casos y Controles , Humanos , Leucemia Linfocítica Crónica de Células B/metabolismo , Análisis de Secuencia de ARN , Microambiente Tumoral
19.
Nat Protoc ; 15(8): 2503-2518, 2020 08.
Artículo en Inglés | MEDLINE | ID: mdl-32591768

RESUMEN

Fixed-tissue ChIP-seq for H3K27 acetylation (H3K27ac) profiling (FiTAc-seq) is an epigenetic method for profiling active enhancers and promoters in formalin-fixed, paraffin-embedded (FFPE) tissues. We previously developed a modified ChIP-seq protocol (FiT-seq) for chromatin profiling in FFPE. FiT-seq produces high-quality chromatin profiles particularly for methylated histone marks but is not optimized for H3K27ac profiling. FiTAc-seq is a modified protocol that replaces the proteinase K digestion applied in FiT-seq with extended heating at 65 °C in a higher concentration of detergent and a minimized sonication step, to produce robust genome-wide H3K27ac maps from clinical samples. FiTAc-seq generates high-quality enhancer landscapes and super-enhancer (SE) annotation in numerous archived FFPE samples from distinct tumor types. This approach will be of great interest for both basic and clinical researchers. The entire protocol from FFPE blocks to sequence-ready library can be accomplished within 4 d.


Asunto(s)
Secuenciación de Inmunoprecipitación de Cromatina/métodos , Histonas/química , Histonas/metabolismo , Lisina/metabolismo , Adhesión en Parafina , Fijación del Tejido , Acetilación , Animales , Hígado/citología , Ratones
20.
Nat Commun ; 11(1): 1406, 2020 03 16.
Artículo en Inglés | MEDLINE | ID: mdl-32179749

RESUMEN

Chromatin organization is a highly orchestrated process that influences gene expression, in part by modulating access of regulatory factors to DNA and nucleosomes. Here, we report that the chromatin accessibility regulator HMGN1, a target of recurrent DNA copy gains in leukemia, controls myeloid differentiation. HMGN1 amplification is associated with increased accessibility, expression, and histone H3K27 acetylation of loci important for hematopoietic stem cells (HSCs) and leukemia, such as HoxA cluster genes. In vivo, HMGN1 overexpression is linked to decreased quiescence and increased HSC activity in bone marrow transplantation. HMGN1 overexpression also cooperates with the AML-ETO9a fusion oncoprotein to impair myeloid differentiation and enhance leukemia stem cell (LSC) activity. Inhibition of histone acetyltransferases CBP/p300 relieves the HMGN1-associated differentiation block. These data nominate factors that modulate chromatin accessibility as regulators of HSCs and LSCs, and suggest that targeting HMGN1 or its downstream effects on histone acetylation could be therapeutically active in AML.


Asunto(s)
Cromatina/metabolismo , Células Madre Hematopoyéticas/metabolismo , Leucemia Mieloide Aguda/metabolismo , Acetilación , Animales , Diferenciación Celular , Supervivencia Celular , Femenino , Proteína HMGN1/genética , Proteína HMGN1/metabolismo , Células Madre Hematopoyéticas/citología , Histonas/genética , Histonas/metabolismo , Humanos , Leucemia Mieloide Aguda/genética , Ratones , Proteínas de Fusión Oncogénica/genética , Proteínas de Fusión Oncogénica/metabolismo
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