RESUMO
The control of cell fate is an epigenetic process initiated by transcription factors (TFs) that recognize DNA motifs and recruit activator complexes and transcriptional machineries to chromatin. Lineage specificity is thought to be provided solely by TF-motif pairing, while the recruited activators are passive. Here, we show that INTS13, a subunit of the Integrator complex, operates as monocytic/macrophagic differentiation factor. Integrator is a general activator of transcription at coding genes and is required for eRNA maturation. Here, we show that INTS13 functions as an independent sub-module and targets enhancers through Early Growth Response (EGR1/2) TFs and their co-factor NAB2. INTS13 binds poised monocytic enhancers eliciting chromatin looping and activation. Independent depletion of INTS13, EGR1, or NAB2 impairs monocytic differentiation of cell lines and primary human progenitors. Our data demonstrate that Integrator is not functionally homogeneous and has TF-specific regulatory potential, revealing a new enhancer regulatory axis that controls myeloid differentiation.
Assuntos
Diferenciação Celular , Proteína 1 de Resposta de Crescimento Precoce/metabolismo , Proteína 2 de Resposta de Crescimento Precoce/metabolismo , Elementos Facilitadores Genéticos , Monócitos/metabolismo , Células Progenitoras Mieloides/metabolismo , Proteínas Repressoras/metabolismo , Linhagem Celular , Proteína 1 de Resposta de Crescimento Precoce/genética , Proteína 2 de Resposta de Crescimento Precoce/genética , Humanos , Células Progenitoras Mieloides/citologia , Proteínas Repressoras/genéticaRESUMO
The hippocampus is associated with essential brain functions, such as learning and memory. Human hippocampal volume is significantly greater than expected compared with that of non-human apes, suggesting a recent expansion. Intermediate progenitors, which are able to undergo multiple rounds of proliferative division before a final neurogenic division, may have played a role in evolutionary hippocampal expansion. To investigate the evolution of gene regulatory networks underpinning hippocampal neurogenesis in apes, we leveraged the differentiation of human and chimpanzee induced pluripotent stem cells into TBR2 (or EOMES)-positive hippocampal intermediate progenitor cells (hpIPCs). We found that the gene networks active in hpIPCs are significantly different between humans and chimpanzees, with â¼2500 genes being differentially expressed. We demonstrate that species-specific transposon-derived enhancers contribute to these transcriptomic differences. Young transposons, predominantly endogenous retroviruses and SINE-Vntr-Alus (SVAs), were co-opted as enhancers in a species-specific manner. Human-specific SVAs provided substrates for thousands of novel TBR2-binding sites, and CRISPR-mediated repression of these SVAs attenuated the expression of â¼25% of the genes that are upregulated in human intermediate progenitors relative to the same cell population in the chimpanzee.
Assuntos
Elementos de DNA Transponíveis , Pan troglodytes , Animais , Elementos de DNA Transponíveis/genética , Redes Reguladoras de Genes , Hipocampo , Humanos , Neurogênese , Pan troglodytes/genéticaRESUMO
Domestication of transposable elements (TEs) into functional cis-regulatory elements is a widespread phenomenon. However, the mechanisms behind why some TEs are co-opted as functional enhancers while others are not are underappreciated. SINE-VNTR-Alus (SVAs) are the youngest group of transposons in the human genome, where ~3,700 copies are annotated, nearly half of which are human-specific. Many studies indicate that SVAs are among the most frequently co-opted TEs in human gene regulation, but the mechanisms underlying such processes have not yet been thoroughly investigated. Here, we leveraged CRISPR-interference (CRISPRi), computational and functional genomics to elucidate the genomic features that underlie SVA domestication into human stem-cell gene regulation. We found that ~750 SVAs are co-opted as functional cis-regulatory elements in human induced pluripotent stem cells. These SVAs are significantly closer to genes and harbor more transcription factor binding sites than non-co-opted SVAs. We show that a long DNA motif composed of flanking YY1/2 and OCT4 binding sites is enriched in the co-opted SVAs and that these two transcription factors bind consecutively on the TE sequence. We used CRISPRi to epigenetically repress active SVAs in stem cell-like NCCIT cells. Epigenetic perturbation of active SVAs strongly attenuated YY1/OCT4 binding and influenced neighboring gene expression. Ultimately, SVA repression resulted in ~3,000 differentially expressed genes, 131 of which were the nearest gene to an annotated SVA. In summary, we demonstrated that SVAs modulate human gene expression, and uncovered that location and sequence composition contribute to SVA domestication into gene regulatory networks.
Assuntos
Células-Tronco Pluripotentes Induzidas , Células-Tronco Pluripotentes , Elementos de DNA Transponíveis/genética , Redes Reguladoras de Genes/genética , Genômica , HumanosRESUMO
Within primates, the great apes are outliers both in terms of body size and lifespan, since they include the largest and longest-lived species in the order. Yet, the molecular bases underlying such features are poorly understood. Here, we leveraged an integrated approach to investigate multiple sources of molecular variation across primates, focusing on over 10,000 genes, including approximately 1,500 previously associated with lifespan, and additional approximately 9,000 for which an association with longevity has never been suggested. We analyzed dN/dS rates, positive selection, gene expression (RNA-seq), and gene regulation (ChIP-seq). By analyzing the correlation between dN/dS, maximum lifespan, and body mass, we identified 276 genes whose rate of evolution positively correlates with maximum lifespan in primates. Further, we identified five genes, important for tumor suppression, adaptive immunity, metastasis, and inflammation, under positive selection exclusively in the great ape lineage. RNA-seq data, generated from the liver of six species representing all the primate lineages, revealed that 8% of approximately 1,500 genes previously associated with longevity are differentially expressed in apes relative to other primates. Importantly, by integrating RNA-seq with ChIP-seq for H3K27ac (which marks active enhancers), we show that the differentially expressed longevity genes are significantly more likely than expected to be located near a novel "ape-specific" enhancer. Moreover, these particular ape-specific enhancers are enriched for young transposable elements, and specifically SINE-Vntr-Alus. In summary, we demonstrate that multiple evolutionary forces have contributed to the evolution of lifespan and body size in primates.
Assuntos
Hominidae , Longevidade , Animais , Evolução Molecular , Hominidae/genética , Longevidade/genética , Primatas/genética , Sequências Reguladoras de Ácido NucleicoRESUMO
Microbial symbionts enable many phytophagous insects to specialize on plant-based diets through a range of metabolic services. Pollen comprises one-plant tissue consumed by such herbivores. While rich in lipids and proteins, its nutrient content is often imbalanced and difficult-to-access due to a digestibly recalcitrant cell wall. Pollen quality can be further degraded by harmful allelochemicals. To identify microbes that may aid in palynivory, we performed cDNA-based 16S rRNA metabarcoding on three related pollen beetles (Nitidulidae: Meligethinae) exhibiting different dietary breadths: Brassicogethes aeneus, B. matronalis, and Meligethes atratus. Nine bacterial symbionts (i.e., 97% OTUs) exhibited high metabolic activity during active feeding. Subsequent PCR surveys revealed varying prevalence of those from three Rickettsialles genera-Lariskella, Rickettsia, and Wolbachia-within beetle populations. Our findings lay the groundwork for future studies on the influence of phylogeny and diet on palynivorous insect microbiomes, and roles of symbionts in the use of challenging diets.
Assuntos
Besouros , Animais , RNA Ribossômico 16S/genética , Insetos , Pólen , PlantasRESUMO
Deciphering the impact of genetic variation on gene regulation is fundamental to understanding common, complex human diseases. Although histone modifications are important markers of gene regulatory elements of the genome, any specific histone modification has not been assayed in more than a few individuals in the human liver. As a result, the effects of genetic variation on histone modification states in the liver are poorly understood. Here, we generate the most comprehensive genome-wide dataset of two epigenetic marks, H3K4me3 and H3K27ac, and annotate thousands of putative regulatory elements in the human liver. We integrate these findings with genome-wide gene expression data collected from the same human liver tissues and high-resolution promoter-focused chromatin interaction maps collected from human liver-derived HepG2 cells. We demonstrate widespread functional consequences of natural genetic variation on putative regulatory element activity and gene expression levels. Leveraging these extensive datasets, we fine-map a total of 74 GWAS loci that have been associated with at least one complex phenotype. Our results reveal a repertoire of genes and regulatory mechanisms governing complex disease development and further the basic understanding of genetic and epigenetic regulation of gene expression in the human liver tissue.
Assuntos
Cromatina/genética , Mapeamento Cromossômico/métodos , Epigênese Genética , Fígado/patologia , Herança Multifatorial/genética , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Adolescente , Adulto , Idoso , Criança , Cromatina/metabolismo , Feminino , Estudos de Associação Genética , Células Hep G2 , Histonas/genética , Humanos , Fígado/metabolismo , Masculino , Pessoa de Meia-Idade , Fenótipo , Regiões Promotoras Genéticas , Estudos Prospectivos , Sequências Reguladoras de Ácido Nucleico , Adulto JovemRESUMO
Gene regulation shapes the evolution of phenotypic diversity. We investigated the evolution of liver promoters and enhancers in six primate species using ChIP-seq (H3K27ac and H3K4me1) to profile cis-regulatory elements (CREs) and using RNA-seq to characterize gene expression in the same individuals. To quantify regulatory divergence, we compared CRE activity across species by testing differential ChIP-seq read depths directly measured for orthologous sequences. We show that the primate regulatory landscape is largely conserved across the lineage, with 63% of the tested human liver CREs showing similar activity across species. Conserved CRE function is associated with sequence conservation, proximity to coding genes, cell-type specificity, and transcription factor binding. Newly evolved CREs are enriched in immune response and neurodevelopmental functions. We further demonstrate that conserved CREs bind master regulators, suggesting that while CREs contribute to species adaptation to the environment, core functions remain intact. Newly evolved CREs are enriched in young transposable elements (TEs), including Long-Terminal-Repeats (LTRs) and SINE-VNTR-Alus (SVAs), that significantly affect gene expression. Conversely, only 16% of conserved CREs overlap TEs. We tested the cis-regulatory activity of 69 TE subfamilies by luciferase reporter assays, spanning all major TE classes, and showed that 95.6% of tested TEs can function as either transcriptional activators or repressors. In conclusion, we demonstrated the critical role of TEs in primate gene regulation and illustrated potential mechanisms underlying evolutionary divergence among the primate species through the noncoding genome.
Assuntos
Elementos de DNA Transponíveis , Evolução Molecular , Regulação da Expressão Gênica/genética , Elementos Reguladores de Transcrição , Animais , Callithrix , Humanos , Especificidade da EspécieRESUMO
BACKGROUND: Transposable elements (TE) are an important source of evolutionary novelty in gene regulation. However, the mechanisms by which TEs contribute to gene expression are largely uncharacterized. RESULTS: Here, we leverage Roadmap and GTEx data to investigate the association of TEs with active and repressed chromatin in 24 tissues. We find 112 human TE families enriched in active regions of the genome across tissues. Short Interspersed Nuclear Elements (SINEs) and DNA transposons are the most frequently enriched classes, while Long Terminal Repeat Retrotransposons (LTRs) are often enriched in a tissue-specific manner. We report across-tissue variability in TE enrichment in active regions. Genes with consistent expression across tissues are less likely to be associated with TE insertions. TE presence in repressed regions similarly follows tissue-specific patterns. Moreover, different TE classes correlate with different repressive marks: LTRs and Long Interspersed Nuclear Elements (LINEs) are overrepresented in regions marked by H3K9me3, while the other TEs are more likely to overlap regions with H3K27me3. Young TEs are typically enriched in repressed regions and depleted in active regions. We detect multiple instances of TEs that are enriched in tissue-specific active regulatory regions. Such TEs contain binding sites for transcription factors that are master regulators for the given tissue. These TEs are enriched in intronic enhancers, and their tissue-specific enrichment correlates with tissue-specific variations in the expression of the nearest genes. CONCLUSIONS: We provide an integrated overview of the contribution of TEs to human gene regulation. Expanding previous analyses, we demonstrate that TEs can potentially contribute to the turnover of regulatory sequences in a tissue-specific fashion.
Assuntos
Elementos de DNA Transponíveis , Regulação da Expressão Gênica , Motivos de Nucleotídeos , Sequências Reguladoras de Ácido Nucleico , Fatores de Transcrição/metabolismo , Sítios de Ligação , Humanos , Especificidade de Órgãos , Sequências Repetidas Terminais , Fatores de Transcrição/genéticaRESUMO
Larval instars II and III of Ochthebius (Ochthebius) capicola (Pdringuey 1892) from South Africa are described and illustrated by SEM, including a detailed analysis of their chaetotaxy and porotaxy. Specimens used in this study were collected with adults of the same species in marine rockpools. The larval morphology of O. capicola is compared to that of other members of the same genus occurring in this habitat, contributing to the current taxonomic and phylogenetic debate on the intrageneric taxonomy of Ochthebiinae.
Assuntos
Besouros/anatomia & histologia , Animais , Besouros/crescimento & desenvolvimento , Larva/anatomia & histologia , Larva/crescimento & desenvolvimento , África do SulRESUMO
Hydraena Kugelann represents the largest genus within the water beetle family Hydraenidae, and in particular within Hydraeninae, with about 900 species widely distributed all over the world and several hundreds not yet described. In a recent cladistic analysis, based on morphological characters, Hydraena s. l. was split into two subgenera: Hydraenopsis Janssens (Gondwanian) and Hydraena s. str. (Laurasian). Moreover, within Hydraena s. str., some derived and well-supported monophyletic clades were recognised, and defined as "lineages". Among them, the "Haenydra" lineage, previously considered by many authors as a valid genus/subgenus, includes 89 species distributed exclusively in western Palaearctic, from Portugal to Iran, but absent in North Africa. The main aim of the present paper is to provide a revision of the whole lineage, re-examining taxonomy, ecology, and biogeography of all known species. All species were therefore redescribed, also providing information about diagnostic characters, taxonomic and phylogenetic relationships, ecology and biogeography. A faunistic dataset, including all the known published, and many unpublished, localities for each species, with a series of detailed geographic maps for each species and species complex, was herein supplied. Finally, dichotomous keys are provided for identification of males of all the "Haenydra" species.
Assuntos
Besouros/anatomia & histologia , Besouros/classificação , Animais , Ásia , Demografia , Ecossistema , Europa (Continente) , Feminino , Masculino , Especificidade da EspécieRESUMO
Adult neurogenic decline, inflammation, and neurodegeneration are phenotypic hallmarks of Alzheimer's disease (AD). Mobilization of transposable elements (TEs) in heterochromatic regions was recently reported in AD, but the underlying mechanisms are still underappreciated. Combining functional genomics with the differentiation of familial and sporadic AD patient derived-iPSCs into hippocampal progenitors, CA3 neurons, and cerebral organoids, we found that the upregulation of the AP-1 subunit, c-Jun, triggers decondensation of genomic regions containing TEs. This leads to the cytoplasmic accumulation of HERVK-derived RNA-DNA hybrids, the activation of the cGAS-STING cascade, and increased levels of cleaved caspase-3, suggesting the initiation of programmed cell death in AD progenitors and neurons. Notably, inhibiting c-Jun effectively blocks all these downstream molecular processes and rescues neuronal death and the impaired neurogenesis phenotype in AD progenitors. Our findings open new avenues for identifying therapeutic strategies and biomarkers to counteract disease progression and diagnose AD in the early, pre-symptomatic stages.
Assuntos
Doença de Alzheimer , Humanos , Doença de Alzheimer/metabolismo , Elementos de DNA Transponíveis/genética , Peptídeos beta-Amiloides/metabolismo , Regulação para Cima , Neurogênese/genética , Imunidade Inata , HipocampoRESUMO
Despite treatment with intensive chemotherapy, acute myelogenous leukemia (AML) remains an aggressive malignancy with a dismal outcome in most patients. We found that AML cells exhibit an unusually rapid accumulation of the repressive histone mark H3K27me3 on nascent DNA. In cell lines, primary cells and xenograft mouse models, inhibition of the H3K27 histone methyltransferase EZH2 to decondense the H3K27me3-marked chromatin of AML cells enhanced chromatin accessibility and chemotherapy-induced DNA damage, apoptosis, and leukemia suppression. These effects were further promoted when chromatin decondensation of AML cells was induced upon S-phase entry after release from a transient G1 arrest mediated by CDK4/6 inhibition. In the p53-null KG-1 and THP-1 AML cell lines, EZH2 inhibitor and doxorubicin cotreatment induced transcriptional reprogramming that was, in part, dependent on derepression of H3K27me3-marked gene promoters and led to increased expression of cell death-promoting and growth-inhibitory genes.In conclusion, decondensing H3K27me3-marked chromatin by EZH2 inhibition represents a promising approach to improve the efficacy of DNA-damaging cytotoxic agents in patients with AML. This strategy might allow for a lowering of chemotherapy doses, with a consequent reduction of treatment-related side effects in elderly patients with AML or those with significant comorbidities. SIGNIFICANCE: Pharmacological inhibition of EZH2 renders DNA of AML cells more accessible to cytotoxic agents, facilitating leukemia suppression with reduced doses of chemotherapy.See related commentary by Adema and Colla, p. 359.
Assuntos
Cromatina/metabolismo , Histonas/metabolismo , Leucemia Mieloide Aguda/genética , Animais , Humanos , CamundongosRESUMO
Hydraena is the largest genus within the water beetle family Hydraenidae, with ca. 1000 species distributed worldwide. Within this large genus some monophyletic groups of species are recognised, among them the "Haenydra" lineage, including ca. 90 species distributed in the western Palaearctic from the Iberian peninsula to Iran. Species of "Haenydra" have often very restricted distributions, and are typical of clean small rivers and streams. We obtained ca. 2.5Kb of mitochondrial and nuclear protein-code and ribosomal markers of 101 specimens of 69 species of "Haenydra", and used Bayesian and Maximum Likelihood phylogenetic methods to reconstruct their phylogeny and diversification history. We found a derived phylogenetic position of the "Haenydra" lineage within the genus Hydraena, as sister to the species of the Hydraenabisulcata group. Within "Haenydra" three main lineages were recognised, with poorly resolved relationships among them: the Hydraena iberica, Hydraena gracilis and Hydraena dentipes lineages, the former restricted to the Iberian peninsula but the latter two distributed through the whole north-Mediterranean area. A Bayesian relaxed molecular clock approach using a combined mitochondrial rate of 2% divergence per MY estimated the origin of "Haenydra" in the Tortonian, ca. 8Mya, and the main diversification and the origin of most extant species in the Pliocene and Pleistocene. We did not found evidence of a phylogenetic connection between the western and eastern species that could be traced to the Messinian salinity crisis, with dispersal only at small geographical scales (e.g. the colonisation of Corsica and Sardinia from NW Italy and SW France). The H. gracilis and H. iberica lineages were estimated to have diversified under a pure birth model with a speciation rate of 0.64 and 0.23 species/MY respectively, while the H. dentipes lineage was estimated to have a decreasing diversification rate with time, with an average rate of 0.29 sp/MY.
Assuntos
Besouros/genética , Evolução Molecular , Variação Genética , Filogenia , Animais , Sequência de Bases , DNA Mitocondrial/genética , Geografia , Região do Mediterrâneo , Fatores de TempoRESUMO
Organismal development is a process that requires a fine-tuned control of cell fate and identity, through timely regulation of lineage-specific genes. These processes are mediated by the concerted action of transcription factors and protein complexes that orchestrate the interaction between cis-regulatory elements (enhancers, promoters) and RNA Polymerase II to elicit transcription. A proper understanding of these dynamics is essential to elucidate the mechanisms underlying developmental diseases. Many developmental disorders, such as Coffin-Siris Syndrome, characterized by growth impairment and intellectual disability are associated with mutations in subunits of the SWI/SNF chromatin remodeler complex, which is an essential regulator of transcription. ARID1B and its paralog ARID1A encode for the two largest, mutually exclusive, subunits of the complex. Mutations in ARID1A and, especially, ARID1B are recurrently associated with a very wide array of developmental disorders, suggesting that these two SWI/SNF subunits play an important role in cell fate decision. In this mini-review we therefore discuss the available scientific literature linking ARID1A and ARID1B to cell fate determination, pluripotency maintenance, and organismal development.
RESUMO
Monocytes and monocyte-derived macrophages originate through a multistep differentiation process. First, hematopoietic stem cells generate lineage-restricted progenitors that eventually develop into peripheral, postmitotic monocytes. Second, blood-circulating monocytes undergo differentiation into macrophages, which are specialized phagocytic cells capable of tissue infiltration. While monocytes mediate some level of inflammation and cell toxicity, macrophages boast the widest set of defense mechanisms against pathogens and elicit robust inflammatory responses. Here, we analyze the molecular determinants of monocytic and macrophagic commitment by profiling the EGR1 transcription factor. EGR1 is essential for monopoiesis and binds enhancers that regulate monocytic developmental genes such as CSF1R However, differentiating macrophages present a very different EGR1 binding pattern. We identify novel binding sites of EGR1 at a large set of inflammatory enhancers, even in the absence of its binding motif. We show that EGR1 repressive activity results in suppression of inflammatory genes and is mediated by the NuRD corepressor complex.
Assuntos
Macrófagos , Monócitos , Diferenciação Celular/genética , Proteína 1 de Resposta de Crescimento Precoce/genética , Proteína 1 de Resposta de Crescimento Precoce/metabolismo , Células-Tronco Hematopoéticas , Humanos , Macrófagos/metabolismo , Monócitos/metabolismoRESUMO
Subunit switches in the BAF chromatin remodeler are essential during development. ARID1B and its paralog ARID1A encode for mutually exclusive BAF subunits. De novo ARID1B haploinsufficient mutations cause neurodevelopmental disorders, including Coffin-Siris syndrome, which is characterized by neurological and craniofacial features. Here, we leveraged ARID1B+/- Coffin-Siris patient-derived iPSCs and modeled cranial neural crest cell (CNCC) formation. We discovered that ARID1B is active only during the first stage of this process, coinciding with neuroectoderm specification, where it is part of a lineage-specific BAF configuration (ARID1B-BAF). ARID1B-BAF regulates exit from pluripotency and lineage commitment by attenuating thousands of enhancers and genes of the NANOG and SOX2 networks. In iPSCs, these enhancers are maintained active by ARID1A-containing BAF. At the onset of differentiation, cells transition from ARID1A- to ARID1B-BAF, eliciting attenuation of the NANOG/SOX2 networks and triggering pluripotency exit. Coffin-Siris patient cells fail to perform the ARID1A/ARID1B switch, and maintain ARID1A-BAF at the pluripotency enhancers throughout all stages of CNCC formation. This leads to persistent NANOG/SOX2 activity which impairs CNCC formation. Despite showing the typical neural crest signature (TFAP2A/SOX9-positive), ARID1B-haploinsufficient CNCCs are also aberrantly NANOG-positive. These findings suggest a connection between ARID1B mutations, neuroectoderm specification and a pathogenic mechanism for Coffin-Siris syndrome.
Assuntos
Cromatina/metabolismo , Proteínas de Ligação a DNA/metabolismo , Proteína Homeobox Nanog/metabolismo , Crista Neural/metabolismo , Fatores de Transcrição/metabolismo , Western Blotting , Proteínas de Ligação a DNA/genética , Citometria de Fluxo , Células HEK293 , Humanos , Mutação/genética , Fatores de Transcrição SOXB1/genética , Fatores de Transcrição SOXB1/metabolismo , Fatores de Transcrição/genéticaRESUMO
A comparative analysis of ITS2 sequences and secondary structures in 89 species of pollen beetles of the subfamily Meligethinae (Coleoptera, Nitidulidae) was performed. The ITS2 folding pattern was highly conserved and comparable with the general model proposed for eukaryotes. Simple sequence repeats (SSRs) were responsible for most of the observed nucleotide variability (approximately 1-3%) and length variation (359-459bp). When plotted on secondary structures, SSRs mapped in expansion segments positioned at the apices of three ITS2 helices ('A', 'B' and 'D1') and appeared to have evolved under mechanisms of compensatory slippage. Homologies among SSRs nucleotides could not be unambiguously assigned, and thus were not useful to resolve phylogeny. However, slippage-derived motifs provided some preliminary genetic support for newly proposed taxonomic arrangements of several genera and subgenera of Meligethinae, corroborating existing morphological and ecological datasets.
Assuntos
Besouros/genética , DNA Espaçador Ribossômico/genética , Conformação de Ácido Nucleico , RNA Ribossômico/genética , Animais , Sequência de Bases , Besouros/classificação , Sequência Conservada , Variação Genética , Modelos Genéticos , Dados de Sequência Molecular , Filogenia , Alinhamento de Sequência , Análise de Sequência de DNA , Especificidade da EspécieRESUMO
Pancreatic ductal adenocarcinoma (PDA) has a poor prognosis, and new strategies for prevention and treatment are urgently needed. We previously reported that histone H4 acetylation is elevated in pancreatic acinar cells harboring Kras mutations prior to the appearance of premalignant lesions. Because acetyl-CoA abundance regulates global histone acetylation, we hypothesized that altered acetyl-CoA metabolism might contribute to metabolic or epigenetic alterations that promote tumorigenesis. We found that acetyl-CoA abundance is elevated in KRAS-mutant acinar cells and that its use in the mevalonate pathway supports acinar-to-ductal metaplasia (ADM). Pancreas-specific loss of the acetyl-CoA-producing enzyme ATP-citrate lyase (ACLY) accordingly suppresses ADM and tumor formation. In PDA cells, growth factors promote AKT-ACLY signaling and histone acetylation, and both cell proliferation and tumor growth can be suppressed by concurrent BET inhibition and statin treatment. Thus, KRAS-driven metabolic alterations promote acinar cell plasticity and tumor development, and targeting acetyl-CoA-dependent processes exerts anticancer effects. SIGNIFICANCE: Pancreatic cancer is among the deadliest of human malignancies. We identify a key role for the metabolic enzyme ACLY, which produces acetyl-CoA, in pancreatic carcinogenesis. The data suggest that acetyl-CoA use for histone acetylation and in the mevalonate pathway facilitates cell plasticity and proliferation, suggesting potential to target these pathways.See related commentary by Halbrook et al., p. 326.This article is highlighted in the In This Issue feature, p. 305.
Assuntos
Acetilcoenzima A/metabolismo , Carcinoma Ductal Pancreático/metabolismo , Neoplasias Pancreáticas/metabolismo , Acetilação , Células Acinares/metabolismo , Células Acinares/patologia , Animais , Carcinogênese/genética , Carcinogênese/metabolismo , Carcinogênese/patologia , Carcinoma Ductal Pancreático/genética , Carcinoma Ductal Pancreático/patologia , Proliferação de Células , Feminino , Genes ras , Xenoenxertos , Histonas/metabolismo , Humanos , Masculino , Camundongos Endogâmicos C57BL , Camundongos Knockout , Camundongos Transgênicos , Mutação , Neoplasias Pancreáticas/genética , Neoplasias Pancreáticas/patologia , Processamento de Proteína Pós-Traducional , Transdução de SinaisRESUMO
AT-rich interactive domain-containing proteins 1A and 1B (ARID1A and ARID1B) are mutually exclusive subunits of the chromatin remodeler SWI/SNF. ARID1A is the most frequently mutated chromatin regulator across all cancers, and ovarian clear cell carcinoma (OCCC) carries the highest prevalence of ARID1A mutations (â¼57%). Despite evidence implicating ARID1A in tumorigenesis, the mechanism remains elusive. Here, we demonstrate that ARID1A binds active regulatory elements in OCCC. Depletion of ARID1A represses RNA polymerase II (RNAPII) transcription but results in modest changes to accessibility. Specifically, pausing of RNAPII is severely impaired after loss of ARID1A. Compromised pausing results in transcriptional dysregulation of active genes, which is compensated by upregulation of ARID1B. However, a subset of ARID1A-dependent genes is not rescued by ARID1B, including many p53 and estrogen receptor (ESR1) targets. Our results provide insight into ARID1A-mediated tumorigenesis and unveil functions of SWI/SNF in modulating RNAPII dynamics.
Assuntos
Proteínas Nucleares/metabolismo , RNA Polimerase II/metabolismo , Fatores de Transcrição/metabolismo , Adenocarcinoma de Células Claras/metabolismo , Adenocarcinoma de Células Claras/patologia , Linhagem Celular Tumoral , Proteínas de Ligação a DNA , Elementos Facilitadores Genéticos , Receptor alfa de Estrogênio/metabolismo , Feminino , Humanos , Proteínas Nucleares/antagonistas & inibidores , Proteínas Nucleares/genética , Neoplasias Ovarianas/metabolismo , Neoplasias Ovarianas/patologia , Regiões Promotoras Genéticas , Interferência de RNA , RNA Interferente Pequeno/metabolismo , Fatores de Transcrição/antagonistas & inibidores , Fatores de Transcrição/genética , Transcrição Gênica , Proteína Supressora de Tumor p53/metabolismo , Regulação para CimaRESUMO
Inactivation of the subunits of SWI/SNF complex such as ARID1A is synthetically lethal with inhibition of EZH2 activity. However, mechanisms of de novo resistance to EZH2 inhibitors in cancers with inactivating SWI/SNF mutations are unknown. Here we show that the switch of the SWI/SNF catalytic subunits from SMARCA4 to SMARCA2 drives resistance to EZH2 inhibitors in ARID1A-mutated cells. SMARCA4 loss upregulates anti-apoptotic genes in the EZH2 inhibitor-resistant cells. EZH2 inhibitor-resistant ARID1A-mutated cells are hypersensitive to BCL2 inhibitors such as ABT263. ABT263 is sufficient to overcome resistance to an EZH2 inhibitor. In addition, ABT263 synergizes with an EZH2 inhibitor in vivo in ARID1A-inactivated ovarian tumor mouse models. Together, these data establish that the switch of the SWI/SNF catalytic subunits from SMARCA4 to SMARCA2 underlies the acquired resistance to EZH2 inhibitors. They suggest BCL2 inhibition alone or in combination with EZH2 inhibition represents urgently needed therapeutic strategy for ARID1A-mutated cancers.