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1.
Cell ; 148(1-2): 84-98, 2012 Jan 20.
Artículo en Inglés | MEDLINE | ID: mdl-22265404

RESUMEN

Higher-order chromosomal organization for transcription regulation is poorly understood in eukaryotes. Using genome-wide Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET), we mapped long-range chromatin interactions associated with RNA polymerase II in human cells and uncovered widespread promoter-centered intragenic, extragenic, and intergenic interactions. These interactions further aggregated into higher-order clusters, wherein proximal and distal genes were engaged through promoter-promoter interactions. Most genes with promoter-promoter interactions were active and transcribed cooperatively, and some interacting promoters could influence each other implying combinatorial complexity of transcriptional controls. Comparative analyses of different cell lines showed that cell-specific chromatin interactions could provide structural frameworks for cell-specific transcription, and suggested significant enrichment of enhancer-promoter interactions for cell-specific functions. Furthermore, genetically-identified disease-associated noncoding elements were found to be spatially engaged with corresponding genes through long-range interactions. Overall, our study provides insights into transcription regulation by three-dimensional chromatin interactions for both housekeeping and cell-specific genes in human cells.


Asunto(s)
Cromatina/metabolismo , Regulación de la Expresión Génica , Regiones Promotoras Genéticas , ARN Polimerasa II/metabolismo , Transcripción Genética , Línea Celular Tumoral , Inmunoprecipitación de Cromatina , Elementos de Facilitación Genéticos , Estudio de Asociación del Genoma Completo , Humanos
2.
Genome Res ; 32(4): 629-642, 2022 04.
Artículo en Inglés | MEDLINE | ID: mdl-35115371

RESUMEN

The MYC oncogene encodes for the MYC protein and is frequently dysregulated across multiple cancer cell types, making it an attractive target for cancer therapy. MYC overexpression leads to MYC binding at active enhancers, resulting in a global transcriptional amplification of active genes. Because super-enhancers are frequently dysregulated in cancer, we hypothesized that MYC preferentially invades into super-enhancers and alters the cancer genome organization. To that end, we performed ChIP-seq, RNA-seq, circular chromosome conformation capture (4C-seq), and Spike-in Quantitative Hi-C (SIQHiC) on the U2OS osteosarcoma cell line with tetracycline-inducible MYC MYC overexpression in U2OS cells modulated histone acetylation and increased MYC binding at super-enhancers. SIQHiC analysis revealed increased global chromatin contact frequency, particularly at chromatin interactions connecting MYC binding sites at promoters and enhancers. Immunofluorescence staining showed that MYC molecules formed punctate foci at these transcriptionally active domains after MYC overexpression. These results demonstrate the accumulation of overexpressed MYC at promoter-enhancer hubs and suggest that MYC invades into enhancers through spatial proximity. At the same time, the increased protein-protein interactions may strengthen these chromatin interactions to increase chromatin contact frequency. CTCF siRNA knockdown in MYC-overexpressed U2OS cells demonstrated that removal of architectural proteins can disperse MYC and abrogate the increase in chromatin contacts. By elucidating the chromatin landscape of MYC-driven cancers, we can potentially target MYC-associated chromatin interactions for cancer therapy.


Asunto(s)
Cromatina , Elementos de Facilitación Genéticos , Genes myc , Sitios de Unión , Línea Celular , Cromatina/genética , Regiones Promotoras Genéticas
3.
Blood ; 141(25): 3078-3090, 2023 06 22.
Artículo en Inglés | MEDLINE | ID: mdl-36796022

RESUMEN

Adenosine-to-inosine RNA editing, which is catalyzed by adenosine deaminases acting on RNA (ADAR) family of enzymes, ADAR1 and ADAR2, has been shown to contribute to multiple cancers. However, other than the chronic myeloid leukemia blast crisis, relatively little is known about its role in other types of hematological malignancies. Here, we found that ADAR2, but not ADAR1 and ADAR3, was specifically downregulated in the core-binding factor (CBF) acute myeloid leukemia (AML) with t(8;21) or inv(16) translocations. In t(8;21) AML, RUNX1-driven transcription of ADAR2 was repressed by the RUNX1-ETO additional exon 9a fusion protein in a dominant-negative manner. Further functional studies confirmed that ADAR2 could suppress leukemogenesis specifically in t(8;21) and inv16 AML cells dependent on its RNA editing capability. Expression of 2 exemplary ADAR2-regulated RNA editing targets coatomer subunit α and component of oligomeric Golgi complex 3 inhibits the clonogenic growth of human t(8;21) AML cells. Our findings support a hitherto, unappreciated mechanism leading to ADAR2 dysregulation in CBF AML and highlight the functional relevance of loss of ADAR2-mediated RNA editing to CBF AML.


Asunto(s)
Factores de Unión al Sitio Principal , Leucemia Mieloide Aguda , Humanos , Regulación hacia Abajo , Factores de Unión al Sitio Principal/metabolismo , Subunidad alfa 2 del Factor de Unión al Sitio Principal/genética , Subunidad alfa 2 del Factor de Unión al Sitio Principal/metabolismo , Edición de ARN , Adenosina Desaminasa/genética , Adenosina Desaminasa/metabolismo , Leucemia Mieloide Aguda/genética , Adenosina/metabolismo
4.
Brief Bioinform ; 23(6)2022 11 19.
Artículo en Inglés | MEDLINE | ID: mdl-36094071

RESUMEN

The emerging ligation-free three-dimensional (3D) genome mapping technologies can identify multiplex chromatin interactions with single-molecule precision. These technologies not only offer new insight into high-dimensional chromatin organization and gene regulation, but also introduce new challenges in data visualization and analysis. To overcome these challenges, we developed MCIBox, a toolkit for multi-way chromatin interaction (MCI) analysis, including a visualization tool and a platform for identifying micro-domains with clustered single-molecule chromatin complexes. MCIBox is based on various clustering algorithms integrated with dimensionality reduction methods that can display multiplex chromatin interactions at single-molecule level, allowing users to explore chromatin extrusion patterns and super-enhancers regulation modes in transcription, and to identify single-molecule chromatin complexes that are clustered into micro-domains. Furthermore, MCIBox incorporates a two-dimensional kernel density estimation algorithm to identify micro-domains boundaries automatically. These micro-domains were stratified with distinctive signatures of transcription activity and contained different cell-cycle-associated genes. Taken together, MCIBox represents an invaluable tool for the study of multiple chromatin interactions and inaugurates a previously unappreciated view of 3D genome structure.


Asunto(s)
Cromatina , Secuencias Reguladoras de Ácidos Nucleicos , Cromatina/genética , Genoma , Regulación de la Expresión Génica
5.
Trends Genet ; 35(2): 145-158, 2019 02.
Artículo en Inglés | MEDLINE | ID: mdl-30577989

RESUMEN

Chromatin interactions regulate gene expression by bringing distal regulatory elements, such as super-enhancers, to promoters in close spatial proximity. It has been recognized that in cancer, chromatin interactions can be dysregulated, leading to aberrant oncogene expression. Chromatin interactions may potentially serve as biomarkers, or be modulated via CRISPR therapy and small molecule inhibitors against transcription. However, these methods face challenges that must be resolved and raise questions for further research. Understanding chromatin interactions is essential for safety aspects of anticancer therapies, such as the mechanism of action of epigenetic regulators and transcription factors in cancer, and potential off-target effects arising from targeting super-enhancers and promoters. In this review article, we discuss how chromatin interactions and regulatory elements may become dysregulated in cancer, potential methods to target them for clinical therapy, and outline outstanding questions that require addressing before epigenetic therapies can translate to the clinic safely and effectively.


Asunto(s)
Elementos de Facilitación Genéticos/genética , Epigenómica , Neoplasias/genética , Factores de Transcripción/genética , Cromatina/genética , Humanos , Regiones Promotoras Genéticas
6.
Gastroenterology ; 159(4): 1311-1327.e19, 2020 10.
Artículo en Inglés | MEDLINE | ID: mdl-32619460

RESUMEN

BACKGROUND & AIMS: We investigated the transcriptome of esophageal squamous cell carcinoma (ESCC) cells, activity of gene regulatory (enhancer and promoter regions), and the effects of blocking epigenetic regulatory proteins. METHODS: We performed chromatin immunoprecipitation sequencing with antibodies against H3K4me1, H3K4me3, and H3K27ac and an assay for transposase-accessible chromatin to map the enhancer regions and accessible chromatin in 8 ESCC cell lines. We used the CRC_Mapper algorithm to identify core regulatory circuitry transcription factors in ESCC cell lines, and determined genome occupancy profiles for 3 of these factors. In ESCC cell lines, expression of transcription factors was knocked down with small hairpin RNAs, promoter and enhancer regions were disrupted by CRISPR/Cas9 genome editing, or bromodomains and extraterminal (BET) family proteins and histone deacetylases (HDACs) were inhibited with ARV-771 and romidepsin, respectively. ESCC cell lines were then analyzed by whole-transcriptome sequencing, immunoprecipitation, immunoblots, immunohistochemistry, and viability assays. Interactions between distal enhancers and promoters were identified and verified with circular chromosome conformation capture sequencing. NOD-SCID mice were given injections of modified ESCC cells, some mice where given injections of HDAC or BET inhibitors, and growth of xenograft tumors was measured. RESULTS: We identified super-enhancer-regulated circuits and transcription factors TP63, SOX2, and KLF5 as core regulatory factors in ESCC cells. Super-enhancer regulation of ALDH3A1 mediated by core regulatory factors was required for ESCC viability. We observed direct interactions between the promoter region of TP63 and functional enhancers, mediated by the core regulatory circuitry transcription factors. Deletion of enhancer regions from ESCC cells decreased expression of the core regulatory circuitry transcription factors and reduced cell viability; these same results were observed with knockdown of each core regulatory circuitry transcription factor. Incubation of ESCC cells with BET and HDAC disrupted the core regulatory circuitry program and the epigenetic modifications observed in these cells; mice given injections of HDAC or BET inhibitors developed smaller xenograft tumors from the ESCC cell lines. Xenograft tumors grew more slowly in mice given the combination of ARV-771 and romidepsin than mice given either agent alone. CONCLUSIONS: In epigenetic and transcriptional analyses of ESCC cell lines, we found the transcription factors TP63, SOX2, and KLF5 to be part of a core regulatory network that determines chromatin accessibility, epigenetic modifications, and gene expression patterns in these cells. A combination of epigenetic inhibitors slowed growth of xenograft tumors derived from ESCC cells in mice.


Asunto(s)
Epigénesis Genética , Neoplasias Esofágicas/genética , Carcinoma de Células Escamosas de Esófago/genética , Regulación Neoplásica de la Expresión Génica , Factores de Transcripción de Tipo Kruppel/genética , Factores de Transcripción SOXB1/genética , Factores de Transcripción/genética , Transcripción Genética , Proteínas Supresoras de Tumor/genética , Animales , Antineoplásicos/farmacología , Línea Celular Tumoral , Proliferación Celular , Ensamble y Desensamble de Cromatina , Epigénesis Genética/efectos de los fármacos , Neoplasias Esofágicas/tratamiento farmacológico , Neoplasias Esofágicas/metabolismo , Neoplasias Esofágicas/patología , Carcinoma de Células Escamosas de Esófago/tratamiento farmacológico , Carcinoma de Células Escamosas de Esófago/metabolismo , Carcinoma de Células Escamosas de Esófago/patología , Regulación Neoplásica de la Expresión Génica/efectos de los fármacos , Inhibidores de Histona Desacetilasas/farmacología , Humanos , Factores de Transcripción de Tipo Kruppel/metabolismo , Ratones Endogámicos NOD , Ratones SCID , Proteínas/antagonistas & inhibidores , Proteínas/metabolismo , Factores de Transcripción SOXB1/metabolismo , Factores de Transcripción/metabolismo , Transcripción Genética/efectos de los fármacos , Transcriptoma , Carga Tumoral , Proteínas Supresoras de Tumor/metabolismo , Ensayos Antitumor por Modelo de Xenoinjerto
7.
Blood ; 134(3): 239-251, 2019 07 18.
Artículo en Inglés | MEDLINE | ID: mdl-31076442

RESUMEN

The oncogenic transcription factor TAL1 regulates the transcriptional program in T-ALL. ARID5B is one of the critical downstream targets of TAL1, which further activates the oncogenic regulatory circuit in T-ALL cells. Here, we elucidated the molecular functions of the noncoding RNA, ARID5B-inducing enhancer associated long noncoding RNA (ARIEL), in T-ALL pathogenesis. We demonstrated that ARIEL is specifically activated in TAL1 + T-ALL cases, and its expression is associated with ARID5B enhancer activity. ARIEL recruits mediator proteins to the ARID5B enhancer, promotes enhancer-promoter interactions, and activates the expression of ARID5B, thereby positively regulating the TAL1-induced transcriptional program and the MYC oncogene. The TAL1 complex coordinately regulates the expression of ARIEL Knockdown of ARIEL inhibits cell growth and survival of T-ALL cells in culture and blocks disease progression in a murine xenograft model. Our results indicate that ARIEL plays an oncogenic role as an enhancer RNA in T-ALL.


Asunto(s)
Carcinogénesis/genética , Regulación Leucémica de la Expresión Génica , Leucemia-Linfoma Linfoblástico de Células T Precursoras/genética , ARN Largo no Codificante/genética , Transcripción Genética , Animales , Sitios de Unión , Línea Celular Tumoral , Proliferación Celular , Supervivencia Celular/genética , Secuenciación de Inmunoprecipitación de Cromatina , Proteínas de Unión al ADN/metabolismo , Modelos Animales de Enfermedad , Progresión de la Enfermedad , Elementos de Facilitación Genéticos , Técnicas de Silenciamiento del Gen , Marcación de Gen , Xenoinjertos , Humanos , Ratones , Modelos Biológicos , Complejos Multiproteicos , Oncogenes , Leucemia-Linfoma Linfoblástico de Células T Precursoras/metabolismo , Regiones Promotoras Genéticas , Unión Proteica , Proteína 1 de la Leucemia Linfocítica T Aguda/metabolismo , Factores de Transcripción/metabolismo
8.
Blood ; 132(12): 1304-1317, 2018 09 20.
Artículo en Inglés | MEDLINE | ID: mdl-30061158

RESUMEN

DNA alterations have been extensively reported in multiple myeloma (MM); however, they cannot yet fully explain all the biological and molecular abnormalities in MM, which remains to this day an incurable disease with eventual emergence of refractory disease. Recent years have seen abnormalities at the RNA levels being reported to possess potential biological relevance in cancers. ADAR1-mediated A-to-I editing is an important posttranscriptional mechanism in human physiology, and the biological implication of its abnormality, especially at the global level, is underexplored in MM. In this study, we define the biological implications of A-to-I editing and how it contributes to MM pathogenesis. Here, we identified that the MM transcriptome is aberrantly hyperedited because of the overexpression of ADAR1. These events were associated with patients' survival independent of 1q21 amplifications and could affect patients' responsiveness to different treatment regimes. Our functional assays established ADAR1 to be oncogenic, driving cellular growth and proliferation in an editing-dependent manner. In addition, we identified NEIL1 (base-excision repair gene) as an essential and a ubiquitously edited ADAR1 target in MM. The recoded NEIL1 protein showed defective oxidative damage repair capacity and loss-of-function properties. Collectively, our data demonstrated that ADAR1-mediated A-to-I editing is both clinically and biologically relevant in MM. These data unraveled novel insights into MM molecular pathogenesis at the global RNA level.


Asunto(s)
Adenosina Desaminasa/genética , Regulación Neoplásica de la Expresión Génica , Mieloma Múltiple/genética , Proteínas de Unión al ARN/genética , Transcriptoma , Regulación hacia Arriba , Animales , Línea Celular Tumoral , ADN Glicosilasas/genética , Humanos , Ratones , Ratones SCID , Mieloma Múltiple/diagnóstico , Mieloma Múltiple/patología , Pronóstico , Edición de ARN
9.
Nature ; 489(7414): 101-8, 2012 Sep 06.
Artículo en Inglés | MEDLINE | ID: mdl-22955620

RESUMEN

Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell's regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.


Asunto(s)
ADN/genética , Enciclopedias como Asunto , Genoma Humano/genética , Anotación de Secuencia Molecular , Secuencias Reguladoras de Ácidos Nucleicos/genética , Transcripción Genética/genética , Transcriptoma/genética , Alelos , Línea Celular , ADN Intergénico/genética , Elementos de Facilitación Genéticos , Exones/genética , Perfilación de la Expresión Génica , Genes/genética , Genómica , Humanos , Poliadenilación/genética , Isoformas de Proteínas/genética , ARN/biosíntesis , ARN/genética , Edición de ARN/genética , Empalme del ARN/genética , Secuencias Repetitivas de Ácidos Nucleicos/genética , Análisis de Secuencia de ARN
10.
Nature ; 462(7269): 58-64, 2009 Nov 05.
Artículo en Inglés | MEDLINE | ID: mdl-19890323

RESUMEN

Genomes are organized into high-level three-dimensional structures, and DNA elements separated by long genomic distances can in principle interact functionally. Many transcription factors bind to regulatory DNA elements distant from gene promoters. Although distal binding sites have been shown to regulate transcription by long-range chromatin interactions at a few loci, chromatin interactions and their impact on transcription regulation have not been investigated in a genome-wide manner. Here we describe the development of a new strategy, chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) for the de novo detection of global chromatin interactions, with which we have comprehensively mapped the chromatin interaction network bound by oestrogen receptor alpha (ER-alpha) in the human genome. We found that most high-confidence remote ER-alpha-binding sites are anchored at gene promoters through long-range chromatin interactions, suggesting that ER-alpha functions by extensive chromatin looping to bring genes together for coordinated transcriptional regulation. We propose that chromatin interactions constitute a primary mechanism for regulating transcription in mammalian genomes.


Asunto(s)
Cromatina/genética , Cromatina/metabolismo , Receptor alfa de Estrógeno/metabolismo , Genoma Humano/genética , Sitios de Unión , Línea Celular , Inmunoprecipitación de Cromatina , Reactivos de Enlaces Cruzados , Formaldehído , Humanos , Regiones Promotoras Genéticas/genética , Unión Proteica , Reproducibilidad de los Resultados , Análisis de Secuencia de ADN , Transcripción Genética , Activación Transcripcional
11.
Methods ; 58(3): 289-99, 2012 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-22926262

RESUMEN

Long-range chromatin contacts between specific DNA regulatory elements play a pivotal role in gene expression regulation, and a global characterization of these interactions in the 3-dimensional (3D) chromatin structure is imperative in understanding signaling networks and cell states. Chromatin Interaction Analysis using Paired-End Tag sequencing (ChIA-PET) is a method which converts functional chromatin structure into millions of short tag sequences. Combining Chromatin Immunoprecipitation (ChIP), proximity ligation and high-throughput sequencing, ChIA-PET provides a global and unbiased interrogation of higher-order chromatin structures associated with specific protein factors. Here, we describe the detailed procedures of the ChIA-PET methodology, unraveling transcription-associated chromatin contacts in a model human cell line.


Asunto(s)
Cromatina/genética , Análisis de Secuencia de ADN , Secuencia de Bases , Línea Celular , Cromatina/ultraestructura , Inmunoprecipitación de Cromatina , Mapeo Cromosómico , Reactivos de Enlaces Cruzados/química , ADN/química , ADN/genética , ADN/aislamiento & purificación , Epistasis Genética , Biblioteca de Genes , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Datos de Secuencia Molecular , Reacción en Cadena de la Polimerasa , Sonicación , Succinimidas/química
12.
Research (Wash D C) ; 2022: 9780293, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-36405252

RESUMEN

DNA replication initiation is a complex process involving various genetic and epigenomic signatures. The correct identification of replication origins (ORIs) could provide important clues for the study of a variety of diseases caused by replication. Here, we design a computational approach named iORI-Epi to recognize ORIs by incorporating epigenome-based features, sequence-based features, and 3D genome-based features. The iORI-Epi displays excellent robustness and generalization ability on both training datasets and independent datasets of K562 cell line. Further experiments confirm that iORI-Epi is highly scalable in other cell lines (MCF7 and HCT116). We also analyze and clarify the regulatory role of epigenomic marks, DNA motifs, and chromatin interaction in DNA replication initiation of eukaryotic genomes. Finally, we discuss gene enrichment pathways from the perspective of ORIs in different replication timing states and heuristically dissect the effect of promoters on replication initiation. Our computational methodology is worth extending to ORI identification in other eukaryotic species.

13.
Front Cell Dev Biol ; 10: 1050769, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-36531953

RESUMEN

Chromatin structural domains, or topologically associated domains (TADs), are a general organizing principle in chromatin biology. RNA polymerase II (RNAPII) mediates multiple chromatin interactive loops, tethering together as RNAPII-associated chromatin interaction domains (RAIDs) to offer a framework for gene regulation. RAID and TAD alterations have been found to be associated with diseases. They can be further dissected as micro-domains (micro-TADs and micro-RAIDs) by clustering single-molecule chromatin-interactive complexes from next-generation three-dimensional (3D) genome techniques, such as ChIA-Drop. Currently, there are few tools available for micro-domain boundary identification. In this work, we developed the MCI-frcnn deep learning method to train a Faster Region-based Convolutional Neural Network (Faster R-CNN) for micro-domain boundary detection. At the training phase in MCI-frcnn, 50 images of RAIDs from Drosophila RNAPII ChIA-Drop data, containing 261 micro-RAIDs with ground truth boundaries, were trained for 7 days. Using this well-trained MCI-frcnn, we detected micro-RAID boundaries for the input new images, with a fast speed (5.26 fps), high recognition accuracy (AUROC = 0.85, mAP = 0.69), and high boundary region quantification (genomic IoU = 76%). We further applied MCI-frcnn to detect human micro-TADs boundaries using human GM12878 SPRITE data and obtained a high region quantification score (mean gIoU = 85%). In all, the MCI-frcnn deep learning method which we developed in this work is a general tool for micro-domain boundary detection.

14.
Cancer Res ; 82(3): 406-418, 2022 02 01.
Artículo en Inglés | MEDLINE | ID: mdl-34893510

RESUMEN

Multiple myeloma is an incurable malignancy with marked clinical and genetic heterogeneity. The cytogenetic abnormality t(4;14) (p16.3;q32.3) confers aggressive behavior in multiple myeloma. Recently, essential oncogenic drivers in a wide range of cancers have been shown to be controlled by super-enhancers (SE). We used chromatin immunoprecipitation sequencing of the active enhancer marker histone H3 lysine 27 acetylation (H3K27ac) to profile unique SEs in t(4;14)-translocated multiple myeloma. The histone chaperone HJURP was aberrantly overexpressed in t(4;14)-positive multiple myeloma due to transcriptional activation by a distal SE induced by the histone lysine methyltransferase NSD2. Silencing of HJURP with short hairpin RNA or CRISPR interference of SE function impaired cell viability and led to apoptosis. Conversely, HJURP overexpression promoted cell proliferation and abrogated apoptosis. Mechanistically, the NSD2/BRD4 complex positively coregulated HJURP transcription by binding the promoter and active elements of its SE. In summary, this study introduces SE profiling as an efficient approach to identify new targets and understand molecular pathogenesis in specific subtypes of cancer. Moreover, HJURP could be a valuable therapeutic target in patients with t(4;14)-positive myeloma. SIGNIFICANCE: A super-enhancer screen in t(4;14) multiple myeloma serves to identify genes that promote growth and survival of myeloma cells, which may be evaluated in future studies as therapeutic targets.


Asunto(s)
Proteínas de Unión al ADN/metabolismo , Mieloma Múltiple/genética , Línea Celular Tumoral , Proliferación Celular , Humanos , Mieloma Múltiple/mortalidad , Mieloma Múltiple/patología , Regulación hacia Arriba
15.
Oncogene ; 41(14): 2106-2121, 2022 04.
Artículo en Inglés | MEDLINE | ID: mdl-35190641

RESUMEN

Recurrent cytogenetic abnormalities are the main hallmark of multiple myeloma (MM) and patients having 2 or more high-risk prognostic events are associated with extremely poor outcome. 17p13(del) and 1q21(gain) are critical and independent high-risk cytogenetic markers, however, the biological significance underlying the poor outcome in MM patients having co-occurrence of both these chromosomal aberrations has never been interrogated. Herein, we identified that patients harbouring concomitant 17p13(del) with 1q21(gain) demonstrated the worst prognosis as compared to patients with single- (either 17p13(del) or 1q21(gain)) and with no chromosomal events (WT for both chromosomal loci); and they are highly enriched for genomic instability (GI) signature. We discovered that the GI feature in the patients with concomitant 17p13(del)-1q21(gain) was recapitulating the biological properties of myeloma cells with co-existing p53-deficiency and NEIL1 mRNA-hyper-editing (associated with chromosome 17p and 1q, respectively) that have inherent DNA damage response (DDR) and persistent activation of Chk1 pathway. Importantly, this became a vulnerable point for therapeutic targeting whereby the cells with this co-abnormalities demonstrated hyper-sensitivity to siRNA- and pharmacological-mediated-Chk1 inhibition, as observed at both the in vitro and in vivo levels. Mechanistically, this was attributable to the synthetic lethal relationship between p53-NEIL1-Chk1 abnormalities. The Chk1 inhibitor (AZD7762) tested showed good synergism with standard-of-care myeloma drugs, velcade and melphalan, thus further reinforcing the translational potential of this therapeutic approach. In summary, combination of NEIL1-p53 abnormalities with an ensuing Chk1 activation could serve as an Achilles heel and predispose MM cells with co-existing 1q21(gain) and 17p13(del) to therapeutic vulnerability for Chk1 inhibition.


Asunto(s)
Quinasa 1 Reguladora del Ciclo Celular (Checkpoint 1) , ADN Glicosilasas , Mieloma Múltiple , Proteína p53 Supresora de Tumor , Quinasa 1 Reguladora del Ciclo Celular (Checkpoint 1)/antagonistas & inhibidores , Quinasa 1 Reguladora del Ciclo Celular (Checkpoint 1)/genética , Aberraciones Cromosómicas , Deleción Cromosómica , ADN Glicosilasas/genética , Inestabilidad Genómica , Humanos , Mieloma Múltiple/tratamiento farmacológico , Mieloma Múltiple/genética , Mutaciones Letales Sintéticas , Proteína p53 Supresora de Tumor/genética
16.
Cancer Res ; 82(14): 2538-2551, 2022 07 18.
Artículo en Inglés | MEDLINE | ID: mdl-35583999

RESUMEN

Mutations in the DNA mismatch repair gene MSH2 are causative of microsatellite instability (MSI) in multiple cancers. Here, we discovered that besides its well-established role in DNA repair, MSH2 exerts a novel epigenomic function in gastric cancer. Unbiased CRISPR-based mass spectrometry combined with genome-wide CRISPR functional screening revealed that in early-stage gastric cancer MSH2 genomic binding is not randomly distributed but rather is associated specifically with tumor-associated super-enhancers controlling the expression of cell adhesion genes. At these loci, MSH2 genomic binding was required for chromatin rewiring, de novo enhancer-promoter interactions, maintenance of histone acetylation levels, and regulation of cell adhesion pathway expression. The chromatin function of MSH2 was independent of its DNA repair catalytic activity but required MSH6, another DNA repair gene, and recruitment to gene loci by the SWI/SNF chromatin remodeler SMARCA4/BRG1. Loss of MSH2 in advanced gastric cancers was accompanied by deficient cell adhesion pathway expression, epithelial-mesenchymal transition, and enhanced tumorigenesis in vitro and in vivo. However, MSH2-deficient gastric cancers also displayed addiction to BAZ1B, a bromodomain-containing family member, and consequent synthetic lethality to bromodomain and extraterminal motif (BET) inhibition. Our results reveal a role for MSH2 in gastric cancer epigenomic regulation and identify BET inhibition as a potential therapy in MSH2-deficient gastric malignancies. SIGNIFICANCE: DNA repair protein MSH2 binds and regulates cell adhesion genes by enabling enhancer-promoter interactions, and loss of MSH2 causes deficient cell adhesion and bromodomain and extraterminal motif inhibitor synthetic lethality in gastric cancer.


Asunto(s)
Reparación de la Incompatibilidad de ADN , Neoplasias Gástricas , Adhesión Celular/genética , Cromatina/genética , ADN Helicasas/genética , Reparación de la Incompatibilidad de ADN/genética , Proteínas de Unión al ADN/genética , Mutación de Línea Germinal , Humanos , Homólogo 1 de la Proteína MutL/genética , Proteína 2 Homóloga a MutS/genética , Proteínas Nucleares/genética , Neoplasias Gástricas/tratamiento farmacológico , Neoplasias Gástricas/genética , Factores de Transcripción/genética
17.
Nat Cell Biol ; 24(6): 928-939, 2022 06.
Artículo en Inglés | MEDLINE | ID: mdl-35618746

RESUMEN

Most mammalian genes generate messenger RNAs with variable untranslated regions (UTRs) that are important post-transcriptional regulators. In cancer, shortening at 3' UTR ends via alternative polyadenylation can activate oncogenes. However, internal 3' UTR splicing remains poorly understood as splicing studies have traditionally focused on protein-coding alterations. Here we systematically map the pan-cancer landscape of 3' UTR splicing and present this in SpUR ( http://www.cbrc.kaust.edu.sa/spur/home/ ). 3' UTR splicing is widespread, upregulated in cancers, correlated with poor prognosis and more prevalent in oncogenes. We show that antisense oligonucleotide-mediated inhibition of 3' UTR splicing efficiently reduces oncogene expression and impedes tumour progression. Notably, CTNNB1 3' UTR splicing is the most consistently dysregulated event across cancers. We validate its upregulation in hepatocellular carcinoma and colon adenocarcinoma, and show that the spliced 3' UTR variant is the predominant contributor to its oncogenic functions. Overall, our study highlights the importance of 3' UTR splicing in cancer and may launch new avenues for RNA-based anti-cancer therapeutics.


Asunto(s)
Adenocarcinoma , Neoplasias del Colon , Regiones no Traducidas 3'/genética , Adenocarcinoma/genética , Empalme Alternativo/genética , Animales , Carcinogénesis/genética , Neoplasias del Colon/genética , Mamíferos , Regulación hacia Arriba
18.
Genome Biol ; 22(1): 226, 2021 08 16.
Artículo en Inglés | MEDLINE | ID: mdl-34399797

RESUMEN

Chromatin interactions play important roles in regulating gene expression. However, the availability of genome-wide chromatin interaction data is limited. We develop a computational method, chromatin interaction neural network (ChINN), to predict chromatin interactions between open chromatin regions using only DNA sequences. ChINN predicts CTCF- and RNA polymerase II-associated and Hi-C chromatin interactions. ChINN shows good across-sample performances and captures various sequence features for chromatin interaction prediction. We apply ChINN to 6 chronic lymphocytic leukemia (CLL) patient samples and a published cohort of 84 CLL open chromatin samples. Our results demonstrate extensive heterogeneity in chromatin interactions among CLL patient samples.


Asunto(s)
Cromatina , Aprendizaje Automático , Redes Neurales de la Computación , Secuencia de Bases , Biología Computacional , Genoma , Humanos , Leucemia/genética
19.
Nat Commun ; 12(1): 4362, 2021 07 16.
Artículo en Inglés | MEDLINE | ID: mdl-34272396

RESUMEN

Squamous cell carcinomas (SCCs) comprise one of the most common histologic types of human cancer. Transcriptional dysregulation of SCC cells is orchestrated by tumor protein p63 (TP63), a master transcription factor (TF) and a well-researched SCC-specific oncogene. In the present study, both Gene Set Enrichment Analysis (GSEA) of SCC patient samples and in vitro loss-of-function assays establish fatty-acid metabolism as a key pathway downstream of TP63. Further studies identify sterol regulatory element binding transcription factor 1 (SREBF1) as a central mediator linking TP63 with fatty-acid metabolism, which regulates the biosynthesis of fatty-acids, sphingolipids (SL), and glycerophospholipids (GPL), as revealed by liquid chromatography tandem mass spectrometry (LC-MS/MS)-based lipidomics. Moreover, a feedback co-regulatory loop consisting of SREBF1/TP63/Kruppel like factor 5 (KLF5) is identified, which promotes overexpression of all three TFs in SCCs. Downstream of SREBF1, a non-canonical, SCC-specific function is elucidated: SREBF1 cooperates with TP63/KLF5 to regulate hundreds of cis-regulatory elements across the SCC epigenome, which converge on activating cancer-promoting pathways. Indeed, SREBF1 is essential for SCC viability and migration, and its overexpression is associated with poor survival in SCC patients. Taken together, these data shed light on mechanisms of transcriptional dysregulation in cancer, identify specific epigenetic regulators of lipid metabolism, and uncover SREBF1 as a potential therapeutic target and prognostic marker in SCC.


Asunto(s)
Carcinoma de Células Escamosas/metabolismo , Neoplasias Esofágicas/metabolismo , Neoplasias de Cabeza y Cuello/metabolismo , Factores de Transcripción de Tipo Kruppel/metabolismo , Metabolismo de los Lípidos/genética , Neoplasias Pulmonares/metabolismo , Proteína 1 de Unión a los Elementos Reguladores de Esteroles/metabolismo , Factores de Transcripción/metabolismo , Proteínas Supresoras de Tumor/metabolismo , Acetilación , Carcinoma de Células Escamosas/genética , Línea Celular Tumoral , Movimiento Celular/genética , Proliferación Celular/genética , Secuenciación de Inmunoprecipitación de Cromatina , Cromatografía Liquida , Epigenómica , Receptores ErbB/genética , Receptores ErbB/metabolismo , Neoplasias Esofágicas/genética , Ácidos Grasos/biosíntesis , Ácidos Grasos/metabolismo , Regulación Neoplásica de la Expresión Génica , Neoplasias de Cabeza y Cuello/genética , Histonas/metabolismo , Humanos , Factores de Transcripción de Tipo Kruppel/genética , Neoplasias Pulmonares/genética , Elementos Reguladores de la Transcripción , Transducción de Señal/genética , Esfingolípidos/biosíntesis , Esfingolípidos/metabolismo , Proteína 1 de Unión a los Elementos Reguladores de Esteroles/genética , Serina-Treonina Quinasas TOR/genética , Serina-Treonina Quinasas TOR/metabolismo , Espectrometría de Masas en Tándem , Factores de Transcripción/genética , Transcriptoma/genética , Proteínas Supresoras de Tumor/genética
20.
Nucleic Acids Res ; 36(5): e32, 2008 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-18285362

RESUMEN

Complex libraries for genomic DNA and cDNA sequencing analyses are typically amplified using bacterial propagation. To reduce biases, large numbers of colonies are plated and scraped from solid-surface agar. This process is time consuming, tedious and limits scaling up. At the same time, multiple displacement amplification (MDA) has been recently developed as a method for in vitro amplification of DNA. However, MDA has no selection function for the removal of ligation multimers. We developed a novel method of briefly introducing ligation reactions into bacteria to select single insert DNA clones followed by MDA to amplify. We applied these methods to a Gene Identification Signatures with Paired-End diTags (GIS-PET) library, which is a complex transcriptome library created by pairing short tags from the 5' and 3' ends of cDNA fragments together, and demonstrated that this selection and amplification strategy is unbiased and efficient.


Asunto(s)
Biblioteca de Genes , Técnicas de Amplificación de Ácido Nucleico , Células Cultivadas , Escherichia coli/genética , Vectores Genéticos , Genómica/métodos , Humanos , Técnicas de Amplificación de Ácido Nucleico/normas , Plásmidos/genética , Control de Calidad , Lugares Marcados de Secuencia
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