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1.
Blood ; 141(4): 391-405, 2023 01 26.
Artículo en Inglés | MEDLINE | ID: mdl-36126301

RESUMEN

Long noncoding RNAs (lncRNAs) can drive tumorigenesis and are susceptible to therapeutic intervention. Here, we used a large-scale CRISPR interference viability screen to interrogate cell-growth dependency to lncRNA genes in multiple myeloma (MM) and identified a prominent role for the miR-17-92 cluster host gene (MIR17HG). We show that an MIR17HG-derived lncRNA, named lnc-17-92, is the main mediator of cell-growth dependency acting in a microRNA- and DROSHA-independent manner. Lnc-17-92 provides a chromatin scaffold for the functional interaction between c-MYC and WDR82, thus promoting the expression of ACACA, which encodes the rate-limiting enzyme of de novo lipogenesis acetyl-coA carboxylase 1. Targeting MIR17HG pre-RNA with clinically applicable antisense molecules disrupts the transcriptional and functional activities of lnc-17-92, causing potent antitumor effects both in vitro and in vivo in 3 preclinical animal models, including a clinically relevant patient-derived xenograft NSG mouse model. This study establishes a novel oncogenic function of MIR17HG and provides potent inhibitors for translation to clinical trials.


Asunto(s)
MicroARNs , Mieloma Múltiple , ARN Largo no Codificante , Humanos , Animales , Ratones , ARN Largo no Codificante/genética , Mieloma Múltiple/genética , Cromatina , MicroARNs/metabolismo , Proliferación Celular , Regulación Neoplásica de la Expresión Génica
2.
Plant J ; 97(3): 530-542, 2019 02.
Artículo en Inglés | MEDLINE | ID: mdl-30375131

RESUMEN

Epicuticular waxes provide a hydrophobic barrier that protects land plants from environmental stresses. To elucidate the molecular functions of maize glossy mutants that reduce the accumulation of epicuticular waxes, eight non-allelic glossy mutants were subjected to transcriptomic comparisons with their respective wild-type siblings. Transcriptomic comparisons identified 2279 differentially expressed (DE) genes. Other glossy genes tended to be down-regulated in glossy mutants; by contrast stress-responsive pathways were induced in mutants. Gene co-expression network (GCN) analysis found that glossy genes were clustered, suggestive of co-regulation. Genes that potentially regulate the accumulation of glossy gene transcripts were identified via a pathway level co-expression analysis. Expression data from diverse organs showed that maize glossy genes are generally active in young leaves, silks, and tassels, while largely inactive in seeds and roots. Through reverse genetics, a DE gene homologous to Arabidopsis CER8 and co-expressed with known glossy genes was confirmed to participate in epicuticular wax accumulation. GCN data-informed forward genetics approach enabled cloning of the gl14 gene, which encodes a putative membrane-associated protein. Our results deepen understanding of the transcriptional regulation of the genes involved in the accumulation of epicuticular wax, and provide two maize glossy genes and a number of candidate genes for further characterization.


Asunto(s)
Regulación de la Expresión Génica de las Plantas/genética , Ceras/metabolismo , Zea mays/genética , Expresión Génica , Epidermis de la Planta/genética , Epidermis de la Planta/metabolismo , Hojas de la Planta/genética , Hojas de la Planta/metabolismo , Raíces de Plantas/genética , Raíces de Plantas/metabolismo , Zea mays/metabolismo
3.
Blood Adv ; 5(23): 4864-4876, 2021 12 14.
Artículo en Inglés | MEDLINE | ID: mdl-34543389

RESUMEN

Somatic mutations are rare in pediatric acute myeloid leukemia (pAML), indicating that alternate strategies are needed to identify targetable dependencies. We performed the first enhancer mapping of pAML in 22 patient samples. Generally, pAML samples were distinct from adult AML samples, and MLL (KMT2A)-rearranged samples were also distinct from non-KMT2A-rearranged samples. Focusing specifically on superenhancers (SEs), we identified SEs associated with many known leukemia regulators. The retinoic acid receptor alpha (RARA) gene was differentially regulated in our cohort, and a RARA-associated SE was detected in 64% of the study cohort across all cytogenetic and molecular subtypes tested. RARA SE+ pAML cell lines and samples exhibited high RARA messenger RNA levels. These samples were specifically sensitive to the synthetic RARA agonist tamibarotene in vitro, with slowed proliferation, apoptosis induction, differentiation, and upregulated retinoid target gene expression, compared with RARA SE- samples. Tamibarotene prolonged survival and suppressed the leukemia burden of an RARA SE+ pAML patient-derived xenograft mouse model compared with a RARA SE- patient-derived xenograft. Our work shows that examining chromatin regulation can identify new, druggable dependencies in pAML and provides a rationale for a pediatric tamibarotene trial in children with RARA-high AML.


Asunto(s)
Leucemia Mieloide Aguda , Animales , Niño , Estudios de Cohortes , Regulación de la Expresión Génica , Humanos , Leucemia Mieloide Aguda/tratamiento farmacológico , Leucemia Mieloide Aguda/genética , Ratones
4.
Cell Rep Med ; 2(1): 100188, 2021 01 19.
Artículo en Inglés | MEDLINE | ID: mdl-33521702

RESUMEN

Chordomas are rare spinal tumors addicted to expression of the developmental transcription factor brachyury. In chordomas, brachyury is super-enhancer associated and preferentially downregulated by pharmacologic transcriptional CDK inhibition, leading to cell death. To understand the underlying basis of this sensitivity, we dissect the brachyury transcription regulatory network and compare the consequences of brachyury degradation with transcriptional CDK inhibition. Brachyury defines the chordoma super-enhancer landscape and autoregulates through binding its super-enhancer, and its locus forms a transcriptional condensate. Transcriptional CDK inhibition and brachyury degradation disrupt brachyury autoregulation, leading to loss of its transcriptional condensate and transcriptional program. Compared with transcriptional CDK inhibition, which globally downregulates transcription, leading to cell death, brachyury degradation is much more selective, inducing senescence and sensitizing cells to anti-apoptotic inhibition. These data suggest that brachyury downregulation is a core tenet of transcriptional CDK inhibition and motivates developing strategies to target brachyury and its autoregulatory feedback loop.


Asunto(s)
Biomarcadores de Tumor/genética , Cordoma/genética , Quinasas Ciclina-Dependientes/genética , Proteínas Fetales/genética , Proteínas de Neoplasias/genética , Neoplasias de la Columna Vertebral/genética , Proteínas de Dominio T Box/genética , Secuencia de Bases , Biomarcadores de Tumor/metabolismo , Línea Celular Tumoral , Supervivencia Celular , Cordoma/metabolismo , Cordoma/patología , Quinasas Ciclina-Dependientes/metabolismo , Proteínas Fetales/metabolismo , Regulación Neoplásica de la Expresión Génica , Redes Reguladoras de Genes , Células HEK293 , Histonas/genética , Histonas/metabolismo , Humanos , Queratina-18/genética , Queratina-18/metabolismo , Proteína 1 de la Secuencia de Leucemia de Células Mieloides/genética , Proteína 1 de la Secuencia de Leucemia de Células Mieloides/metabolismo , Proteínas de Neoplasias/metabolismo , Proteolisis , Transducción de Señal , Neoplasias de la Columna Vertebral/metabolismo , Neoplasias de la Columna Vertebral/patología , Proteínas de Dominio T Box/metabolismo
5.
Biotechniques ; 68(4): 214-218, 2020 04.
Artículo en Inglés | MEDLINE | ID: mdl-31939314

RESUMEN

Artificial miRNA technology enables the generation of siRNAs to regulate the expression of targeted genes. However, the application of siRNAs to alter gene expression is challenging due to their instability and requires a means to efficiently deliver siRNAs into the host. Here, we report that the siRNAs targeted to animal mRNAs can be heterologously expressed and stably produced in lettuce. We have modified rice miRNA precursors to produce siRNAs in lettuce with the potential to target mRNAs of mouse complement 3 (C3) and coagulation factor 7 (CF7). Expression of primary and mature siRNAs in the transgenic lettuce lines was confirmed via Sanger sequencing. Our study demonstrates an applicable tool to alter gene expression in the targeted host and has potential utility in siRNA-based oral therapeutics.


Asunto(s)
Lactuca , MicroARNs , Plantas Modificadas Genéticamente , ARN Interferente Pequeño , Animales , Genes de Plantas/genética , Lactuca/genética , Lactuca/metabolismo , Ratones , MicroARNs/genética , MicroARNs/metabolismo , Oryza/genética , Plantas Modificadas Genéticamente/genética , Plantas Modificadas Genéticamente/metabolismo , ARN Interferente Pequeño/genética , ARN Interferente Pequeño/metabolismo
6.
Cell Chem Biol ; 26(6): 792-803.e10, 2019 06 20.
Artículo en Inglés | MEDLINE | ID: mdl-30905681

RESUMEN

Cyclin-dependent kinase 7 (CDK7) regulates both cell cycle and transcription, but its precise role remains elusive. We previously described THZ1, a CDK7 inhibitor, which dramatically inhibits superenhancer-associated gene expression. However, potent CDK12/13 off-target activity obscured CDK7s contribution to this phenotype. Here, we describe the discovery of a highly selective covalent CDK7 inhibitor. YKL-5-124 causes arrest at the G1/S transition and inhibition of E2F-driven gene expression; these effects are rescued by a CDK7 mutant unable to covalently engage YKL-5-124, demonstrating on-target specificity. Unlike THZ1, treatment with YKL-5-124 resulted in no change to RNA polymerase II C-terminal domain phosphorylation; however, inhibition could be reconstituted by combining YKL-5-124 and THZ531, a selective CDK12/13 inhibitor, revealing potential redundancies in CDK control of gene transcription. These findings highlight the importance of CDK7/12/13 polypharmacology for anti-cancer activity of THZ1 and posit that selective inhibition of CDK7 may be useful for treatment of cancers marked by E2F misregulation.


Asunto(s)
Ciclo Celular/efectos de los fármacos , Quinasas Ciclina-Dependientes/antagonistas & inhibidores , Inhibidores de Proteínas Quinasas/farmacología , Pirazoles/farmacología , Pirroles/farmacología , Ciclo Celular/genética , Línea Celular , Quinasas Ciclina-Dependientes/metabolismo , Humanos , Células Jurkat , Masculino , Fenotipo , Inhibidores de Proteínas Quinasas/síntesis química , Inhibidores de Proteínas Quinasas/química , Pirazoles/química , Pirroles/química , Quinasa Activadora de Quinasas Ciclina-Dependientes
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