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1.
Cell ; 185(20): 3770-3788.e27, 2022 09 29.
Artigo em Inglês | MEDLINE | ID: mdl-36179669

RESUMO

Realizing the full utility of brain organoids to study human development requires understanding whether organoids precisely replicate endogenous cellular and molecular events, particularly since acquisition of cell identity in organoids can be impaired by abnormal metabolic states. We present a comprehensive single-cell transcriptomic, epigenetic, and spatial atlas of human cortical organoid development, comprising over 610,000 cells, from generation of neural progenitors through production of differentiated neuronal and glial subtypes. We show that processes of cellular diversification correlate closely to endogenous ones, irrespective of metabolic state, empowering the use of this atlas to study human fate specification. We define longitudinal molecular trajectories of cortical cell types during organoid development, identify genes with predicted human-specific roles in lineage establishment, and uncover early transcriptional diversity of human callosal neurons. The findings validate this comprehensive atlas of human corticogenesis in vitro as a resource to prime investigation into the mechanisms of human cortical development.


Assuntos
Córtex Cerebral , Organoides , Diferenciação Celular , Córtex Cerebral/metabolismo , Humanos , Neurogênese , Neurônios , Organoides/metabolismo
2.
EMBO J ; 37(6)2018 03 15.
Artigo em Inglês | MEDLINE | ID: mdl-29335281

RESUMO

In the post-genomic era, thousands of putative noncoding regulatory regions have been identified, such as enhancers, promoters, long noncoding RNAs (lncRNAs), and a cadre of small peptides. These ever-growing catalogs require high-throughput assays to test their functionality at scale. Massively parallel reporter assays have greatly enhanced the understanding of noncoding DNA elements en masse Here, we present a massively parallel RNA assay (MPRNA) that can assay 10,000 or more RNA segments for RNA-based functionality. We applied MPRNA to identify RNA-based nuclear localization domains harbored in lncRNAs. We examined a pool of 11,969 oligos densely tiling 38 human lncRNAs that were fused to a cytosolic transcript. After cell fractionation and barcode sequencing, we identified 109 unique RNA regions that significantly enriched this cytosolic transcript in the nucleus including a cytosine-rich motif. These nuclear enrichment sequences are highly conserved and over-represented in global nuclear fractionation sequencing. Importantly, many of these regions were independently validated by single-molecule RNA fluorescence in situ hybridization. Overall, we demonstrate the utility of MPRNA for future investigation of RNA-based functionalities.


Assuntos
RNA Longo não Codificante/genética , Núcleo Celular/genética , Células HeLa , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Hibridização in Situ Fluorescente , Análise de Sequência de RNA
3.
Genome Res ; 29(3): 344-355, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30683753

RESUMO

Transcription initiates at both coding and noncoding genomic elements, including mRNA and long noncoding RNA (lncRNA) core promoters and enhancer RNAs (eRNAs). However, each class has a different expression profile with lncRNAs and eRNAs being the most tissue specific. How these complex differences in expression profiles and tissue specificities are encoded in a single DNA sequence remains unresolved. Here, we address this question using computational approaches and massively parallel reporter assays (MPRA) surveying hundreds of promoters and enhancers. We find that both divergent lncRNA and mRNA core promoters have higher capacities to drive transcription than nondivergent lncRNA and mRNA core promoters, respectively. Conversely, intergenic lncRNAs (lincRNAs) and eRNAs have lower capacities to drive transcription and are more tissue specific than divergent genes. This higher tissue specificity is strongly associated with having less complex transcription factor (TF) motif profiles at the core promoter. We experimentally validated these findings by testing both engineered single-nucleotide deletions and human single-nucleotide polymorphisms (SNPs) in MPRA. In both cases, we observe that single nucleotides associated with many motifs are important drivers of promoter activity. Thus, we suggest that high TF motif density serves as a robust mechanism to increase promoter activity at the expense of tissue specificity. Moreover, we find that 22% of common SNPs in core promoter regions have significant regulatory effects. Collectively, our findings show that high TF motif density provides redundancy and increases promoter activity at the expense of tissue specificity, suggesting that specificity of expression may be regulated by simplicity of motif usage.


Assuntos
Regiões Promotoras Genéticas , RNA Longo não Codificante/genética , Genoma Humano , Humanos , Especificidade de Órgãos , Polimorfismo de Nucleotídeo Único
4.
Genome Res ; 27(1): 27-37, 2017 01.
Artigo em Inglês | MEDLINE | ID: mdl-27927715

RESUMO

While long intergenic noncoding RNAs (lincRNAs) and mRNAs share similar biogenesis pathways, these transcript classes differ in many regards. LincRNAs are less evolutionarily conserved, less abundant, and more tissue-specific, suggesting that their pre- and post-transcriptional regulation is different from that of mRNAs. Here, we perform an in-depth characterization of the features that contribute to lincRNA regulation in multiple human cell lines. We find that lincRNA promoters are depleted of transcription factor (TF) binding sites, yet enriched for some specific factors such as GATA and FOS relative to mRNA promoters. Surprisingly, we find that H3K9me3-a histone modification typically associated with transcriptional repression-is more enriched at the promoters of active lincRNA loci than at those of active mRNAs. Moreover, H3K9me3-marked lincRNA genes are more tissue-specific. The most discriminant differences between lincRNAs and mRNAs involve splicing. LincRNAs are less efficiently spliced, which cannot be explained by differences in U1 binding or the density of exonic splicing enhancers but may be partially attributed to lower U2AF65 binding and weaker splicing-related motifs. Conversely, the stability of lincRNAs and mRNAs is similar, differing only with regard to the location of stabilizing protein binding sites. Finally, we find that certain transcriptional properties are correlated with higher evolutionary conservation in both DNA and RNA motifs and are enriched in lincRNAs that have been functionally characterized.


Assuntos
Cromatina/genética , Evolução Molecular , RNA Longo não Codificante/genética , Fatores de Transcrição/genética , Sítios de Ligação , Sequência Conservada/genética , Éxons/genética , Regulação da Expressão Gênica/genética , Humanos , Motivos de Nucleotídeos/genética , Especificidade de Órgãos/genética , Regiões Promotoras Genéticas , Splicing de RNA/genética , Estabilidade de RNA/genética , RNA Mensageiro/genética , Fator de Processamento U2AF/genética
5.
Am J Pathol ; 187(3): 627-638, 2017 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-28162229

RESUMO

The roles of transforming growth factor (TGF)-ß in extracellular matrix production and vascular remodeling, coupled with increased TGF-ß expression and signaling in diabetes, suggest TGF-ß as an important contributor to the microangiopathy of diabetic retinopathy and nephropathy. To investigate whether increased TGF-ß signaling could be a therapeutic target for preventing retinopathy, we used a pharmacologic approach (SM16, a selective inhibitor of the type 1 TGF-ß receptor activin receptor-like kinase 5, orally active) to inhibit the increased, but not the basal, Tgf-ß signaling in retinal vessels of diabetic rats. At the level of vascular gene expression, 3.5 months' diabetes induced minimal changes. Diabetes + SM16 for 3 weeks caused widespread changes in gene expression poised to enhance vascular inflammation, thrombosis, leakage, and wall instability; these changes were not observed in control rats given SM16. The synergy of diabetes and SM16 in altering gene expression was not observed in the lung. At the level of vascular network morphology, 7 months' diabetes induced no detectable changes. Diabetes + SM16 for 3 weeks caused instead distorted morphology and decreased density. Thus, in diabetes, retinal vessels become dependent on a small increase in TGF-ß signaling via activin receptor-like kinase 5 to maintain early integrity. The increased TGF-ß signaling may protect against rapid retinopathy progression and should not be a target of inhibitory interventions.


Assuntos
Diabetes Mellitus Experimental/metabolismo , Vasos Retinianos/metabolismo , Transdução de Sinais , Fator de Crescimento Transformador beta/metabolismo , Receptores de Ativinas/metabolismo , Animais , Apoptose/efeitos dos fármacos , Compostos Azabicíclicos/farmacologia , Glicemia/metabolismo , Peso Corporal/efeitos dos fármacos , Capilares/efeitos dos fármacos , Capilares/patologia , Quimiocina CCL2/metabolismo , Diabetes Mellitus Experimental/sangue , Diabetes Mellitus Experimental/genética , Diabetes Mellitus Experimental/patologia , Células Endoteliais/efeitos dos fármacos , Células Endoteliais/metabolismo , Regulação da Expressão Gênica/efeitos dos fármacos , Hemoglobinas Glicadas/metabolismo , Masculino , Proteína Quinase 14 Ativada por Mitógeno/metabolismo , Ratos Sprague-Dawley , Reprodutibilidade dos Testes , Vasos Retinianos/efeitos dos fármacos , Vasos Retinianos/patologia , Transdução de Sinais/efeitos dos fármacos , Fatores de Tempo
6.
Proc Natl Acad Sci U S A ; 112(22): 6855-62, 2015 Jun 02.
Artigo em Inglês | MEDLINE | ID: mdl-26034286

RESUMO

Long noncoding RNAs (lncRNAs) have been implicated in numerous cellular processes including brain development. However, the in vivo expression dynamics and molecular pathways regulated by these loci are not well understood. Here, we leveraged a cohort of 13 lncRNAnull mutant mouse models to investigate the spatiotemporal expression of lncRNAs in the developing and adult brain and the transcriptome alterations resulting from the loss of these lncRNA loci. We show that several lncRNAs are differentially expressed both in time and space, with some presenting highly restricted expression in only selected brain regions. We further demonstrate altered regulation of genes for a large variety of cellular pathways and processes upon deletion of the lncRNA loci. Finally, we found that 4 of the 13 lncRNAs significantly affect the expression of several neighboring proteincoding genes in a cis-like manner. By providing insight into the endogenous expression patterns and the transcriptional perturbations caused by deletion of the lncRNA locus in the developing and postnatal mammalian brain, these data provide a resource to facilitate future examination of the specific functional relevance of these genes in neural development, brain function, and disease.


Assuntos
Encéfalo/crescimento & desenvolvimento , Encéfalo/metabolismo , Regulação da Expressão Gênica/fisiologia , RNA Longo não Codificante/metabolismo , Animais , Sequência de Bases , Perfilação da Expressão Gênica , Regulação da Expressão Gênica/genética , Imuno-Histoquímica , Camundongos , Camundongos Knockout , Microscopia Confocal , Dados de Sequência Molecular , RNA Longo não Codificante/genética , Análise de Sequência de DNA , beta-Galactosidase
7.
BMC Genomics ; 17: 707, 2016 09 05.
Artigo em Inglês | MEDLINE | ID: mdl-27595844

RESUMO

BACKGROUND: Ebola virus is the causative agent of a severe syndrome in humans with a fatality rate that can approach 90 %. During infection, the host immune response is thought to become dysregulated, but the mechanisms through which this happens are not entirely understood. In this study, we analyze RNA sequencing data to determine the host response to Ebola virus infection in circulating immune cells. RESULTS: Approximately half of the 100 genes with the strongest early increases in expression were interferon-stimulated genes, such as ISG15, OAS1, IFIT2, HERC5, MX1 and DHX58. Other highly upregulated genes included cytokines CXCL11, CCL7, IL2RA, IL2R1, IL15RA, and CSF2RB, which have not been previously reported to change during Ebola virus infection. Comparing this response in two different models of exposure (intramuscular and aerosol) revealed a similar signature of infection. The strong innate response in the aerosol model was seen not only in circulating cells, but also in primary and secondary target tissues. Conversely, the innate immune response of vaccinated macaques was almost non-existent. This suggests that the innate response is a major aspect of the cellular response to Ebola virus infection in multiple tissues. CONCLUSIONS: Ebola virus causes a severe infection in humans that is associated with high mortality. The host immune response to virus infection is thought to be an important aspect leading to severe pathology, but the components of this overactive response are not well characterized. Here, we analyzed how circulating immune cells respond to the virus and found that there is a strong innate response dependent on active virus replication. This finding is in stark contrast to in vitro evidence showing a suppression of innate immune signaling, and it suggests that the strong innate response we observe in infected animals may be an important contributor to pathogenesis.


Assuntos
Ebolavirus/fisiologia , Doença pelo Vírus Ebola/imunologia , Imunidade Inata , Leucócitos Mononucleares/imunologia , Animais , Ebolavirus/patogenicidade , Perfilação da Expressão Gênica/métodos , Regulação da Expressão Gênica , Redes Reguladoras de Genes , Doença pelo Vírus Ebola/genética , Doença pelo Vírus Ebola/virologia , Leucócitos Mononucleares/metabolismo , Macaca/virologia , Camundongos , Análise de Sequência de RNA/métodos , Replicação Viral
8.
Sci Adv ; 10(29): eadp6039, 2024 Jul 19.
Artigo em Inglês | MEDLINE | ID: mdl-39028813

RESUMO

The adult hippocampus generates new granule cells (aGCs) with functional capabilities that convey unique forms of plasticity to the preexisting circuits. While early differentiation of adult radial glia-like cells (RGLs) has been studied extensively, the molecular mechanisms guiding the maturation of postmitotic neurons remain unknown. Here, we used a precise birthdating strategy to study aGC differentiation using single-nuclei RNA sequencing. Transcriptional profiling revealed a continuous trajectory from RGLs to mature aGCs, with multiple immature stages bearing increasing levels of effector genes supporting growth, excitability, and synaptogenesis. Analysis of differential gene expression, pseudo-time trajectory, and transcription factors (TFs) revealed critical transitions defining four cellular states: quiescent RGLs, proliferative progenitors, immature aGCs, and mature aGCs. Becoming mature aGCs involved a transcriptional switch that shuts down pathways promoting cell growth, such SoxC TFs, to activate programs that likely control neuronal homeostasis. aGCs overexpressing Sox4 or Sox11 remained immature. Our results unveil precise molecular mechanisms driving adult RGLs through the pathway of neuronal differentiation.


Assuntos
Diferenciação Celular , Hipocampo , Neurogênese , Neurônios , Fatores de Transcrição SOXC , Animais , Hipocampo/metabolismo , Hipocampo/citologia , Neurônios/metabolismo , Neurônios/citologia , Fatores de Transcrição SOXC/metabolismo , Fatores de Transcrição SOXC/genética , Diferenciação Celular/genética , Neurogênese/genética , Camundongos , Transcrição Gênica , Perfilação da Expressão Gênica , Fatores de Transcrição/metabolismo , Fatores de Transcrição/genética , Células Ependimogliais/metabolismo , Células Ependimogliais/citologia
9.
bioRxiv ; 2024 Jan 11.
Artigo em Inglês | MEDLINE | ID: mdl-38260428

RESUMO

The adult hippocampus generates new granule cells (aGCs) that exhibit distinct functional capabilities along development, conveying a unique form of plasticity to the preexisting circuits. While early differentiation of adult radial glia-like neural stem cells (RGL) has been studied extensively, the molecular mechanisms guiding the maturation of postmitotic neurons remain unknown. Here, we used a precise birthdating strategy to follow newborn aGCs along differentiation using single-nuclei RNA sequencing (snRNA-seq). Transcriptional profiling revealed a continuous trajectory from RGLs to mature aGCs, with multiple sequential immature stages bearing increasing levels of effector genes supporting growth, excitability and synaptogenesis. Remarkably, four discrete cellular states were defined by the expression of distinct sets of transcription factors (TFs): quiescent neural stem cells, proliferative progenitors, postmitotic immature aGCs, and mature aGCs. The transition from immature to mature aCGs involved a transcriptional switch that shutdown molecular cascades promoting cell growth, such as the SoxC family of TFs, to activate programs controlling neuronal homeostasis. Indeed, aGCs overexpressing Sox4 or Sox11 remained stalled at the immature state. Our results unveil precise molecular mechanisms driving adult neural stem cells through the pathway of neuronal differentiation.

10.
STAR Protoc ; 4(4): 102731, 2023 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-37980569

RESUMO

Association studies describe genetic associations between noncoding variants and disease susceptibility; however, they do not provide functional insight into the underlying molecular mechanisms of these variants. We present a protocol to assay the regulatory potential of thousands of noncoding variants using massively parallel reporter assays. We describe steps for oligo design, generating a plasmid pool, and extracting tag-seq libraries from cells to quantify the tested sequences. For complete details on the use and execution of this protocol, please refer to Oliveros and Delfosse et al.1.


Assuntos
Plasmídeos , Plasmídeos/genética
11.
PLoS One ; 16(11): e0252848, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34731163

RESUMO

Although many long non-coding RNAs (lncRNAs) exhibit lineage-specific expression, the vast majority remain functionally uncharacterized in the context of development. Here, we report the first described human embryonic stem cell (hESC) lines to repress (CRISPRi) or activate (CRISPRa) transcription during differentiation into all three germ layers, facilitating the modulation of lncRNA expression during early development. We performed an unbiased, genome-wide CRISPRi screen targeting thousands of lncRNA loci expressed during endoderm differentiation. While dozens of lncRNA loci were required for proper differentiation, most differentially expressed lncRNAs were not, supporting the necessity for functional screening instead of relying solely on gene expression analyses. In parallel, we developed a clustering approach to infer mechanisms of action of lncRNA hits based on a variety of genomic features. We subsequently identified and validated FOXD3-AS1 as a functional lncRNA essential for pluripotency and differentiation. Taken together, the cell lines and methodology described herein can be adapted to discover and characterize novel regulators of differentiation into any lineage.


Assuntos
Diferenciação Celular/genética , Sistemas CRISPR-Cas , Fatores de Transcrição Forkhead/genética , Humanos , Interferência de RNA , RNA Longo não Codificante
12.
Genome Biol ; 21(1): 210, 2020 08 20.
Artigo em Inglês | MEDLINE | ID: mdl-32819422

RESUMO

BACKGROUND: Gene expression differences between species are driven by both cis and trans effects. Whereas cis effects are caused by genetic variants located on the same DNA molecule as the target gene, trans effects are due to genetic variants that affect diffusible elements. Previous studies have mostly assessed the impact of cis and trans effects at the gene level. However, how cis and trans effects differentially impact regulatory elements such as enhancers and promoters remains poorly understood. Here, we use massively parallel reporter assays to directly measure the transcriptional outputs of thousands of individual regulatory elements in embryonic stem cells and measure cis and trans effects between human and mouse. RESULTS: Our approach reveals that cis effects are widespread across transcribed regulatory elements, and the strongest cis effects are associated with the disruption of motifs recognized by strong transcriptional activators. Conversely, we find that trans effects are rare but stronger in enhancers than promoters and are associated with a subset of transcription factors that are differentially expressed between human and mouse. While we find that cis-trans compensation is common within promoters, we do not see evidence of widespread cis-trans compensation at enhancers. Cis-trans compensation is inversely correlated with enhancer redundancy, suggesting that such compensation may often occur across multiple enhancers. CONCLUSIONS: Our results highlight differences in the mode of evolution between promoters and enhancers in complex mammalian genomes and indicate that studying the evolution of individual regulatory elements is pivotal to understand the tempo and mode of gene expression evolution.


Assuntos
Elementos Facilitadores Genéticos , Evolução Molecular , Regulação da Expressão Gênica no Desenvolvimento , Regiões Promotoras Genéticas , Animais , Sequência Conservada , Genes Reporter , Humanos , Camundongos , Elementos Reguladores de Transcrição , Fatores de Transcrição
13.
EMBO Mol Med ; 12(5): e12112, 2020 05 08.
Artigo em Inglês | MEDLINE | ID: mdl-32239644

RESUMO

Deriving mechanisms of immune-mediated disease from GWAS data remains a formidable challenge, with attempts to identify causal variants being frequently hampered by strong linkage disequilibrium. To determine whether causal variants could be identified from their functional effects, we adapted a massively parallel reporter assay for use in primary CD4 T cells, the cell type whose regulatory DNA is most enriched for immune-mediated disease SNPs. This enabled the effects of candidate SNPs to be examined in a relevant cellular context and generated testable hypotheses into disease mechanisms. To illustrate the power of this approach, we investigated a locus that has been linked to six immune-mediated diseases but cannot be fine-mapped. By studying the lead expression-modulating SNP, we uncovered an NF-κB-driven regulatory circuit which constrains T-cell activation through the dynamic formation of a super-enhancer that upregulates TNFAIP3 (A20), a key NF-κB inhibitor. In activated T cells, this feedback circuit is disrupted-and super-enhancer formation prevented-by the risk variant at the lead SNP, leading to unrestrained T-cell activation via a molecular mechanism that appears to broadly predispose to human autoimmunity.


Assuntos
Linfócitos T CD4-Positivos , NF-kappa B , Autoimunidade , Humanos , Polimorfismo de Nucleotídeo Único
14.
Genome Biol ; 21(1): 237, 2020 09 07.
Artigo em Inglês | MEDLINE | ID: mdl-32894169

RESUMO

BACKGROUND: Several long noncoding RNAs (lncRNAs) have been shown to function as components of molecular machines that play fundamental roles in biology. While the number of annotated lncRNAs in mammalian genomes has greatly expanded, studying lncRNA function has been a challenge due to their diverse biological roles and because lncRNA loci can contain multiple molecular modes that may exert function. RESULTS: We previously generated and characterized a cohort of 20 lncRNA loci knockout mice. Here, we extend this initial study and provide a more detailed analysis of the highly conserved lncRNA locus, taurine-upregulated gene 1 (Tug1). We report that Tug1-knockout male mice are sterile with underlying defects including a low number of sperm and abnormal sperm morphology. Because lncRNA loci can contain multiple modes of action, we wanted to determine which, if any, potential elements contained in the Tug1 genomic region have any activity. Using engineered mouse models and cell-based assays, we provide evidence that the Tug1 locus harbors two distinct noncoding regulatory activities, as a cis-DNA repressor that regulates neighboring genes and as a lncRNA that can regulate genes by a trans-based function. We also show that Tug1 contains an evolutionary conserved open reading frame that when overexpressed produces a stable protein which impacts mitochondrial membrane potential, suggesting a potential third coding function. CONCLUSIONS: Our results reveal an essential role for the Tug1 locus in male fertility and uncover evidence for distinct molecular modes in the Tug1 locus, thus highlighting the complexity present at lncRNA loci.


Assuntos
Fertilidade/genética , RNA Longo não Codificante/genética , Animais , Regulação da Expressão Gênica , Humanos , Masculino , Camundongos , Camundongos Knockout , Fases de Leitura Aberta , Espermatogênese/genética
15.
Elife ; 82019 11 18.
Artigo em Inglês | MEDLINE | ID: mdl-31738164

RESUMO

Recent evidence has determined that the conserved X chromosome mega-structures controlled by the Firre and Dxz4 loci are not required for X chromosome inactivation (XCI) in cell lines. Here, we examined the in vivo contribution of these loci by generating mice carrying a single or double deletion of Firre and Dxz4. We found that these mutants are viable, fertile and show no defect in random or imprinted XCI. However, the lack of these elements results in many dysregulated genes on autosomes in an organ-specific manner. By comparing the dysregulated genes between the single and double deletion, we identified superloop, megadomain, and Firre locus-dependent gene sets. The largest transcriptional effect was observed in all strains lacking the Firre locus, indicating that this locus is the main driver for these autosomal expression signatures. Collectively, these findings suggest that these X-linked loci are involved in autosomal gene regulation rather than XCI biology.


Assuntos
DNA Complementar/genética , Deleção de Genes , Regulação da Expressão Gênica , RNA Longo não Codificante/genética , Animais , Feminino , Masculino , Camundongos , Camundongos Endogâmicos , Camundongos Knockout , Transcriptoma , Inativação do Cromossomo X
16.
Nat Commun ; 10(1): 5137, 2019 11 13.
Artigo em Inglês | MEDLINE | ID: mdl-31723143

RESUMO

RNA has been classically known to play central roles in biology, including maintaining telomeres, protein synthesis, and in sex chromosome compensation. While thousands of long noncoding RNAs (lncRNAs) have been identified, attributing RNA-based roles to lncRNA loci requires assessing whether phenotype(s) could be due to DNA regulatory elements, transcription, or the lncRNA. Here, we use the conserved X chromosome lncRNA locus Firre, as a model to discriminate between DNA- and RNA-mediated effects in vivo. We demonstrate that (i) Firre mutant mice have cell-specific hematopoietic phenotypes, and (ii) upon exposure to lipopolysaccharide, mice overexpressing Firre exhibit increased levels of pro-inflammatory cytokines and impaired survival. (iii) Deletion of Firre does not result in changes in local gene expression, but rather in changes on autosomes that can be rescued by expression of transgenic Firre RNA. Together, our results provide genetic evidence that the Firre locus produces a trans-acting lncRNA that has physiological roles in hematopoiesis.


Assuntos
Loci Gênicos , Hematopoese/genética , RNA Longo não Codificante/genética , Animais , Fertilidade/genética , Regulação da Expressão Gênica no Desenvolvimento , Imunidade Inata/efeitos dos fármacos , Lipopolissacarídeos/farmacologia , Camundongos Knockout , Especificidade de Órgãos/genética , Fenótipo , RNA Longo não Codificante/metabolismo
17.
Oncotarget ; 9(19): 14764-14790, 2018 Mar 13.
Artigo em Inglês | MEDLINE | ID: mdl-29599906

RESUMO

This manuscript follows a single patient with pancreatic adenocarcinoma for a five year period, detailing the clinical record, pathology, the dynamic evolution of molecular and cellular alterations as well as the responses to treatments with chemotherapies, targeted therapies and immunotherapies. DNA and RNA samples from biopsies and blood identified a dynamic set of changes in allelic imbalances and copy number variations in response to therapies. Organoid cultures established from biopsies over time were employed for extensive drug testing to determine if this approach was feasible for treatments. When an unusual drug response was detected, an extensive RNA sequencing analysis was employed to establish novel mechanisms of action of this drug. Organoid cell cultures were employed to identify possible antigens associated with the tumor and the patient's T-cells were expanded against one of these antigens. Similar and identical T-cell receptor sequences were observed in the initial biopsy and the expanded T-cell population. Immunotherapy treatment failed to shrink the tumor, which had undergone an epithelial to mesenchymal transition prior to therapy. A warm autopsy of the metastatic lung tumor permitted an extensive analysis of tumor heterogeneity over five years of treatment and surgery. This detailed analysis of the clinical descriptions, imaging, pathology, molecular and cellular evolution of the tumors, treatments, and responses to chemotherapy, targeted therapies, and immunotherapies, as well as attempts at the development of personalized medical treatments for a single patient should provide a valuable guide to future directions in cancer treatment.

18.
Diabetes ; 55(10): 2757-62, 2006 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-17003340

RESUMO

Previously studied inhibitors of aldose reductase were largely from two chemical classes, spirosuccinamide/hydantoins and carboxylic acids. Each class has its own drawbacks regarding selectivity, in vivo potency, and human safety; as a result, the pathogenic role of aldose reductase in diabetic retinopathy remains controversial. ARI-809 is a recently discovered aldose reductase inhibitor (ARI) of a new structural class, pyridazinones, and has high selectivity for aldose versus aldehyde reductase. To further test the possible pathogenic role of aldose reductase in the development of diabetic retinopathy, we examined the retinal effects of this structurally novel and highly selective ARI in insulinized streptozotocin-induced diabetic rats. ARI-809 treatment was initiated 1 month after diabetes induction and continued for 3 months at a dose that inhibited the polyol pathway in the retina of diabetic rats to a similar extent as sorbinil, a poorly selective hydantoin ARI previously shown to prevent retinopathy in this model. ARI-809 improved survival, inhibited cataract development, normalized retinal sorbitol and fructose, and protected the retina from abnormalities that also occur in human diabetes: neuronal apoptosis, glial reactivity, and complement deposition. Because ARI-809 is a novel chemotype highly selective for aldose reductase, these results support the notion that aldose reductase is the key relay that converts hyperglycemia into glucose toxicity in neural and glial cell types in the retina.


Assuntos
Aldeído Redutase/antagonistas & inibidores , Retinopatia Diabética/prevenção & controle , Inibidores Enzimáticos/uso terapêutico , Piridazinas/uso terapêutico , Retina/metabolismo , Animais , Diabetes Mellitus Experimental/tratamento farmacológico , Diabetes Mellitus Experimental/patologia , Retinopatia Diabética/tratamento farmacológico , Molécula 1 de Adesão Intercelular/biossíntese , Masculino , Polímeros/metabolismo , Ratos , Ratos Sprague-Dawley , Retina/efeitos dos fármacos , Retina/patologia , Regulação para Cima
19.
Diabetes ; 54(12): 3418-26, 2005 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-16306357

RESUMO

The prevention of diabetic retinopathy requires drugs that leverage the benefits of glycemic control without adding the burden of side effects. Aspirin at dosages of 1-1.5 g/day has prevented manifestations of diabetic retinal microangiopathy in a clinical trial as well as in studies with dogs. Because lower and safer doses of aspirin could be used if its beneficial effects on retinopathy were due to antithrombotic effects, we compared the effects of a selective antiplatelet drug (clopidogrel) to those of aspirin in streptozotocin-induced diabetic rats. Clopidogrel did not prevent neuronal apoptosis, glial reactivity, capillary cell apoptosis, or acellular capillaries in the retina of diabetic rats. Aspirin, at doses yielding serum levels (<0.6 mmol/l) well below the anti-inflammatory range for humans, prevented apoptosis of capillary cells and the development of acellular capillaries but did not prevent neuroglial abnormalities. The aldose reductase inhibitor sorbinil, used as the benchmark for the effect of the other drugs, prevented all abnormalities. The diabetic rat retina showed increased expression of the transcription factor CCAAT/enhancer-binding protein-beta, one of the known targets of low-intermediate concentrations of aspirin. Thus we found a spectrum of drug efficacy on the prevention of experimental diabetic retinopathy, ranging from the absent effect of a selective antiplatelet drug to the prevention of all abnormalities by an aldose reductase inhibitor. Aspirin at low-intermediate concentrations selectively prevented microangiopathy. The minimal effective dose of aspirin should now be sought.


Assuntos
Aspirina/uso terapêutico , Diabetes Mellitus Experimental/fisiopatologia , Retinopatia Diabética/tratamento farmacológico , Vasos Retinianos/fisiopatologia , Animais , Anti-Inflamatórios não Esteroides/uso terapêutico , Apoptose/efeitos dos fármacos , Plaquetas/fisiologia , Clopidogrel , Dinoprostona/metabolismo , Humanos , Neurônios/efeitos dos fármacos , Neurônios/patologia , Neurônios/fisiologia , Inibidores da Agregação Plaquetária/uso terapêutico , Ratos , Retina/metabolismo , Vasos Retinianos/efeitos dos fármacos , Ticlopidina/análogos & derivados , Ticlopidina/uso terapêutico
20.
Cell Rep ; 16(8): 2178-2186, 2016 08 23.
Artigo em Inglês | MEDLINE | ID: mdl-27524623

RESUMO

The Linc-p21 locus, encoding a long non-coding RNA, plays an important role in p53 signaling, cell-cycle regulation, and tumor suppression. However, despite extensive study, confusion exists regarding its mechanism of action: is activity driven by the transcript acting in trans, in cis, or by an underlying functional enhancer? Here, using a knockout mouse model and a massively parallel enhancer assay, we delineate the functional elements at this locus. We observe that, even in tissues with no detectable Linc-p21 transcript, deletion of the locus significantly affects local gene expression, including of the cell-cycle regulator Cdkn1a. To characterize this RNA-independent regulatory effect, we systematically interrogated the underlying DNA sequence for enhancer activity at nucleotide resolution and confirmed the existence of multiple enhancer elements. Together, these data suggest that, in vivo, the cis-regulatory effects mediated by Linc-p21, in the presence or absence of transcription, are due to DNA enhancer elements.


Assuntos
Sequência de Bases , Inibidor de Quinase Dependente de Ciclina p21/genética , Elementos Facilitadores Genéticos , RNA Longo não Codificante/genética , Deleção de Sequência , Proteína Supressora de Tumor p53/genética , Animais , Linhagem Celular , Inibidor de Quinase Dependente de Ciclina p21/metabolismo , Regulação da Expressão Gênica , Loci Gênicos , Sequenciamento de Nucleotídeos em Larga Escala , Ensaios de Triagem em Larga Escala , Camundongos , Camundongos Knockout , Mioblastos/citologia , Mioblastos/metabolismo , Regiões Promotoras Genéticas , RNA Longo não Codificante/metabolismo , Transdução de Sinais , Proteína Supressora de Tumor p53/metabolismo
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