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BACKGROUND: Oscillatory genes, with periodic expression at the mRNA and/or protein level, have been shown to play a pivotal role in many biological contexts. However, with the exception of the circadian clock and cell cycle, only a few such genes are known. Detecting oscillatory genes from snapshot single-cell experiments is a challenging task due to the lack of time information. Oscope is a recently proposed method to identify co-oscillatory gene pairs using single-cell RNA-seq data. Although promising, the current implementation of Oscope does not provide a principled statistical criterion for selecting oscillatory genes. RESULTS: We improve the optimisation scheme underlying Oscope and provide a well-calibrated non-parametric hypothesis test to select oscillatory genes at a given FDR threshold. We evaluate performance on synthetic data and three real datasets and show that our approach is more sensitive than the original Oscope formulation, discovering larger sets of known oscillators while avoiding the need for less interpretable thresholds. We also describe how our proposed pseudo-time estimation method is more accurate in recovering the true cell order for each gene cluster while requiring substantially less computation time than the extended nearest insertion approach. CONCLUSIONS: OscoNet is a robust and versatile approach to detect oscillatory gene networks from snapshot single-cell data addressing many of the limitations of the original Oscope method.
Assuntos
Redes Reguladoras de Genes , Software , Ciclo Celular , Relógios Circadianos/genética , Regulação da Expressão Gênica , Células-Tronco Embrionárias Humanas/metabolismo , Humanos , Análise de Sequência com Séries de Oligonucleotídeos , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Estatísticas não Paramétricas , Fatores de TempoRESUMO
The human retina is a specialized tissue involved in light stimulus transduction. Despite its unique biology, an accurate reference transcriptome is still missing. Here, we performed gene expression analysis (RNA-seq) of 50 retinal samples from non-visually impaired post-mortem donors. We identified novel transcripts with high confidence (Observed Transcriptome (ObsT)) and quantified the expression level of known transcripts (Reference Transcriptome (RefT)). The ObsT included 77 623 transcripts (23 960 genes) covering 137 Mb (35 Mb new transcribed genome). Most of the transcripts (92%) were multi-exonic: 81% with known isoforms, 16% with new isoforms and 3% belonging to new genes. The RefT included 13 792 genes across 94 521 known transcripts. Mitochondrial genes were among the most highly expressed, accounting for about 10% of the reads. Of all the protein-coding genes in Gencode, 65% are expressed in the retina. We exploited inter-individual variability in gene expression to infer a gene co-expression network and to identify genes specifically expressed in photoreceptor cells. We experimentally validated the photoreceptors localization of three genes in human retina that had not been previously reported. RNA-seq data and the gene co-expression network are available online (http://retina.tigem.it).
Assuntos
Proteínas do Olho/genética , Redes Reguladoras de Genes , Genoma Humano , Proteínas Mitocondriais/genética , Retina/metabolismo , Transcriptoma , Adulto , Idoso , Processamento Alternativo , Atlas como Assunto , Mapeamento Cromossômico , Éxons , Proteínas do Olho/metabolismo , Feminino , Perfilação da Expressão Gênica , Ontologia Genética , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Masculino , Pessoa de Meia-Idade , Proteínas Mitocondriais/metabolismo , Anotação de Sequência Molecular , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Retina/citologiaRESUMO
SUMMARY: Elucidation of molecular targets of a compound [mode of action (MoA)] and its off-targets is a crucial step in drug development. We developed an online collaborative resource (MANTRA 2.0) that supports this process by exploiting similarities between drug-induced transcriptional profiles. Drugs are organized in a network of nodes (drugs) and edges (similarities) highlighting 'communities' of drugs sharing a similar MoA. A user can upload gene expression profiles before and after drug treatment in one or multiple cell types. An automated processing pipeline transforms the gene expression profiles into a unique drug 'node' embedded in the drug-network. Visual inspection of the neighbouring drugs and communities helps in revealing its MoA and to suggest new applications of known drugs (drug repurposing). MANTRA 2.0 allows storing and sharing user-generated network nodes, thus making MANTRA 2.0 a collaborative ever-growing resource. AVAILABILITY AND IMPLEMENTATION: The web tool is freely available for academic use at http://mantra.tigem.it.
Assuntos
Descoberta de Drogas/métodos , Reposicionamento de Medicamentos/métodos , Perfilação da Expressão Gênica , Software , Comportamento Cooperativo , Internet , Transcriptoma/efeitos dos fármacosRESUMO
Gene expression profiles can be used to infer previously unknown transcriptional regulatory interaction among thousands of genes, via systems biology 'reverse engineering' approaches. We 'reverse engineered' an embryonic stem (ES)-specific transcriptional network from 171 gene expression profiles, measured in ES cells, to identify master regulators of gene expression ('hubs'). We discovered that E130012A19Rik (E13), highly expressed in mouse ES cells as compared with differentiated cells, was a central 'hub' of the network. We demonstrated that E13 is a protein-coding gene implicated in regulating the commitment towards the different neuronal subtypes and glia cells. The overexpression and knock-down of E13 in ES cell lines, undergoing differentiation into neurons and glia cells, caused a strong up-regulation of the glutamatergic neurons marker Vglut2 and a strong down-regulation of the GABAergic neurons marker GAD65 and of the radial glia marker Blbp. We confirmed E13 expression in the cerebral cortex of adult mice and during development. By immuno-based affinity purification, we characterized protein partners of E13, involved in the Polycomb complex. Our results suggest a role of E13 in regulating the division between glutamatergic projection neurons and GABAergic interneurons and glia cells possibly by epigenetic-mediated transcriptional regulation.
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Células-Tronco Embrionárias/metabolismo , Redes Reguladoras de Genes , Proteínas do Tecido Nervoso/fisiologia , Neurogênese/genética , Animais , Encéfalo/embriologia , Encéfalo/metabolismo , Linhagem Celular , Proteínas Cromossômicas não Histona , Perfilação da Expressão Gênica , Camundongos , Proteínas do Tecido Nervoso/genética , Proteínas do Tecido Nervoso/metabolismo , Mapeamento de Interação de Proteínas , Biologia de Sistemas/métodos , Transcriptoma , TransgenesRESUMO
The developmental role of the T-box transcription factor Tbx1 is exquisitely dosage-sensitive. In this study, we performed a microarray-based transcriptome analysis of E9.5 embryo tissues across a previously generated Tbx1 mouse allelic series. This analysis identified several genes whose expression was affected by Tbx1 dosage. Interestingly, we found that the expression of the gene encoding the cardiogenic transcription factor Mef2c was negatively correlated to Tbx1 dosage. In vivo data revealed Mef2c up-regulation in the second heart field (SHF) of Tbx1 null mutant embryos compared with wild-type littermates at E9.5. Conversely, Mef2c expression was decreased in the SHF and in somites of Tbx1 gain-of-function mutants. These results are consistent with the described role of Tbx1 in suppressing cardiac progenitor cell differentiation and indicate also a negative effect of Tbx1 on Mef2c during skeletal muscle differentiation. We show that Tbx1 occupies conserved regulatory regions of the Mef2c locus, suggesting a direct effect on Mef2c transcription. However, we also show that Tbx1 interferes with the Gata4â Mef2c regulatory pathway. Overall, our study uncovered a target of Tbx1 with critical developmental roles, so highlighting the power of the dosage gradient approach that we used.
Assuntos
Fatores de Regulação Miogênica/genética , Proteínas com Domínio T/genética , Alelos , Animais , Diferenciação Celular , Genótipo , Fatores de Transcrição MEF2 , Camundongos , Camundongos Transgênicos , Fatores de Regulação Miogênica/metabolismo , Fenótipo , Proteínas com Domínio T/metabolismo , Transcriptoma , Transfecção , Regulação para CimaRESUMO
We investigated in children with spinal muscular atrophy type 2 the consistency of 4 different equations for predicting resting energy expenditure (REE) compared with measured REE by using indirect calorimetry. In patients with spinal muscular atrophy type 2, measured REE was lower than predicted. We also found a correlation between energy consumption and motor skills.
Assuntos
Metabolismo Basal , Atrofias Musculares Espinais da Infância/metabolismo , Adolescente , Calorimetria Indireta/métodos , Estudos de Casos e Controles , Criança , Pré-Escolar , Feminino , Humanos , Lactente , MasculinoRESUMO
Quiescence, a reversible state of cell-cycle arrest, is an important state during both normal development and cancer progression. For example, in glioblastoma (GBM) quiescent glioblastoma stem cells (GSCs) play an important role in re-establishing the tumour, leading to relapse. While most studies have focused on identifying differentially expressed genes between proliferative and quiescent cells as potential drivers of this transition, recent studies have shown the importance of protein oscillations in controlling the exit from quiescence of neural stem cells. Here, we have undertaken a genome-wide bioinformatic inference approach to identify genes whose expression oscillates and which may be good candidates for controlling the transition to and from the quiescent cell state in GBM. Our analysis identified, among others, a list of important transcription regulators as potential oscillators, including the stemness gene SOX2, which we verified to oscillate in quiescent GSCs. These findings expand on the way we think about gene regulation and introduce new candidate genes as key regulators of quiescence.
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Glioblastoma , Células-Tronco Neurais , Humanos , Glioblastoma/genética , Divisão Celular , Biologia Computacional , Expressão Gênica , Fatores de Transcrição SOXB1/genéticaRESUMO
BACKGROUND: Glioblastoma (GBM) brain tumors lacking IDH1 mutations (IDHwt) have the worst prognosis of all brain neoplasms. Patients receive surgery and chemoradiotherapy but tumors almost always fatally recur. RESULTS: Using RNA sequencing data from 107 pairs of pre- and post-standard treatment locally recurrent IDHwt GBM tumors, we identify two responder subtypes based on longitudinal changes in gene expression. In two thirds of patients, a specific subset of genes is upregulated from primary to recurrence (Up responders), and in one third, the same genes are downregulated (Down responders), specifically in neoplastic cells. Characterization of the responder subtypes indicates subtype-specific adaptive treatment resistance mechanisms that are associated with distinct changes in the tumor microenvironment. In Up responders, recurrent tumors are enriched in quiescent proneural GBM stem cells and differentiated neoplastic cells, with increased interaction with the surrounding normal brain and neurotransmitter signaling, whereas Down responders commonly undergo mesenchymal transition. ChIP-sequencing data from longitudinal GBM tumors suggests that the observed transcriptional reprogramming could be driven by Polycomb-based chromatin remodeling rather than DNA methylation. CONCLUSIONS: We show that the responder subtype is cancer-cell intrinsic, recapitulated in in vitro GBM cell models, and influenced by the presence of the tumor microenvironment. Stratifying GBM tumors by responder subtype may lead to more effective treatment.
Assuntos
Neoplasias Encefálicas , Glioblastoma , Humanos , Glioblastoma/tratamento farmacológico , Glioblastoma/genética , Glioblastoma/patologia , Recidiva Local de Neoplasia/genética , Neoplasias Encefálicas/genética , Neoplasias Encefálicas/patologia , Encéfalo/patologia , Metilação de DNA , Regulação Neoplásica da Expressão Gênica , Microambiente TumoralRESUMO
Vectors derived from adeno-associated virus (AAV) are promising for human gene therapy, including treatment for retinal blindness. One major limitation of AAVs as vectors is that AAV cargo capacity has been considered to be restricted to 4.7 kb. Here we demonstrate that vectors with an AAV5 capsid (i.e., rAAV2/5) incorporated up to 8.9 kb of genome more efficiently than 6 other serotypes tested, independent of the efficiency of the rAAV2/5 production process. Efficient packaging of the large murine Abca4 and human MYO7A and CEP290 genes, which are mutated in common blinding diseases, was obtained, suggesting that this packaging efficiency is independent of the specific sequence packaged. Expression of proteins of the appropriate size and function was observed following transduction with rAAV2/5 carrying large genes. Intraocular administration of rAAV2/5 encoding ABCA4 resulted in protein localization to rod outer segments and significant and stable morphological and functional improvement of the retina in Abca4(-/-) mice. This use of rAAV2/5 may be a promising therapeutic strategy for recessive Stargardt disease, the most common form of inherited macular degeneration. The possibility of packaging large genes in AAV greatly expands the therapeutic potential of this vector system.
Assuntos
Dependovirus , Técnicas de Transferência de Genes , Vetores Genéticos , Retina , Sorotipagem , Transportadores de Cassetes de Ligação de ATP/genética , Transportadores de Cassetes de Ligação de ATP/metabolismo , Animais , Antígenos de Neoplasias/genética , Antígenos de Neoplasias/metabolismo , Proteínas de Ciclo Celular , Proteínas do Citoesqueleto , Dependovirus/genética , Dependovirus/metabolismo , Dineínas/genética , Dineínas/metabolismo , Eletrorretinografia , Terapia Genética , Vetores Genéticos/genética , Vetores Genéticos/metabolismo , Humanos , Camundongos , Camundongos Endogâmicos BALB C , Camundongos Knockout , Dados de Sequência Molecular , Miosina VIIa , Miosinas/genética , Miosinas/metabolismo , Proteínas de Neoplasias/genética , Proteínas de Neoplasias/metabolismo , Retina/citologia , Retina/metabolismoRESUMO
BACKGROUND: Loss of motor neurons in amyotrophic lateral sclerosis (ALS) leads to progressive paralysis and death. Dysregulation of thousands of RNA molecules with roles in multiple cellular pathways hinders the identification of ALS-causing alterations over downstream changes secondary to the neurodegenerative process. How many and which of these pathological gene expression changes require therapeutic normalisation remains a fundamental question. METHODS: Here, we investigated genome-wide RNA changes in C9ORF72-ALS patient-derived neurons and Drosophila, as well as upon neuroprotection taking advantage of our gene therapy approach which specifically inhibits the SRSF1-dependent nuclear export of pathological C9ORF72-repeat transcripts. This is a critical study to evaluate (i) the overall safety and efficacy of the partial depletion of SRSF1, a member of a protein family involved itself in gene expression, and (ii) a unique opportunity to identify neuroprotective RNA changes. RESULTS: Our study shows that manipulation of 362 transcripts out of 2257 pathological changes, in addition to inhibiting the nuclear export of repeat transcripts, is sufficient to confer neuroprotection in C9ORF72-ALS patient-derived neurons. In particular, expression of 90 disease-altered transcripts is fully reverted upon neuroprotection leading to the characterisation of a human C9ORF72-ALS disease-modifying gene expression signature. These findings were further investigated in vivo in diseased and neuroprotected Drosophila transcriptomes, highlighting a list of 21 neuroprotective changes conserved with 16 human orthologues in patient-derived neurons. We also functionally validated the high neuroprotective potential of one of these disease-modifying transcripts, demonstrating that inhibition of ALS-upregulated human KCNN1-3 (Drosophila SK) voltage-gated potassium channel orthologs mitigates degeneration of human motor neurons and Drosophila motor deficits. CONCLUSIONS: Strikingly, the partial depletion of SRSF1 leads to expression changes in only a small proportion of disease-altered transcripts, indicating that not all RNA alterations need normalization and that the gene therapeutic approach is safe in the above preclinical models as it does not disrupt globally gene expression. The efficacy of this intervention is also validated at genome-wide level with transcripts modulated in the vast majority of biological processes affected in C9ORF72-ALS. Finally, the identification of a characteristic signature with key RNA changes modified in both the disease state and upon neuroprotection also provides potential new therapeutic targets and biomarkers.
Assuntos
Transporte Ativo do Núcleo Celular/fisiologia , Esclerose Lateral Amiotrófica/metabolismo , Proteína C9orf72/metabolismo , Neurônios/metabolismo , RNA/metabolismo , Fatores de Processamento de Serina-Arginina/metabolismo , Esclerose Lateral Amiotrófica/patologia , Animais , Drosophila , Humanos , Neurônios/patologia , Neuroproteção/fisiologiaRESUMO
Single-cell RNA-seq (scRNAseq) is a powerful tool to study heterogeneity of cells. Recently, several clustering based methods have been proposed to identify distinct cell populations. These methods are based on different statistical models and usually require to perform several additional steps, such as preprocessing or dimension reduction, before applying the clustering algorithm. Individual steps are often controlled by method-specific parameters, permitting the method to be used in different modes on the same datasets, depending on the user choices. The large number of possibilities that these methods provide can intimidate non-expert users, since the available choices are not always clearly documented. In addition, to date, no large studies have invistigated the role and the impact that these choices can have in different experimental contexts. This work aims to provide new insights into the advantages and drawbacks of scRNAseq clustering methods and describe the ranges of possibilities that are offered to users. In particular, we provide an extensive evaluation of several methods with respect to different modes of usage and parameter settings by applying them to real and simulated datasets that vary in terms of dimensionality, number of cell populations or levels of noise. Remarkably, the results presented here show that great variability in the performance of the models is strongly attributed to the choice of the user-specific parameter settings. We describe several tendencies in the performance attributed to their modes of usage and different types of datasets, and identify which methods are strongly affected by data dimensionality in terms of computational time. Finally, we highlight some open challenges in scRNAseq data clustering, such as those related to the identification of the number of clusters.
RESUMO
BACKGROUND: Gene expression levels in a given cell can be influenced by different factors, namely pharmacological or medical treatments. The response to a given stimulus is usually different for different genes and may depend on time. One of the goals of modern molecular biology is the high-throughput identification of genes associated with a particular treatment or a biological process of interest. From methodological and computational point of view, analyzing high-dimensional time course microarray data requires very specific set of tools which are usually not included in standard software packages. Recently, the authors of this paper developed a fully Bayesian approach which allows one to identify differentially expressed genes in a 'one-sample' time-course microarray experiment, to rank them and to estimate their expression profiles. The method is based on explicit expressions for calculations and, hence, very computationally efficient. RESULTS: The software package BATS (Bayesian Analysis of Time Series) presented here implements the methodology described above. It allows an user to automatically identify and rank differentially expressed genes and to estimate their expression profiles when at least 5-6 time points are available. The package has a user-friendly interface. BATS successfully manages various technical difficulties which arise in time-course microarray experiments, such as a small number of observations, non-uniform sampling intervals and replicated or missing data. CONCLUSION: BATS is a free user-friendly software for the analysis of both simulated and real microarray time course experiments. The software, the user manual and a brief illustrative example are freely available online at the BATS website: http://www.na.iac.cnr.it/bats.
Assuntos
Teorema de Bayes , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Interface Usuário-Computador , Algoritmos , Expressão Gênica , Perfilação da Expressão Gênica/métodos , Humanos , Projetos de Pesquisa , Tamanho da Amostra , Fatores de TempoRESUMO
MicroRNAs act posttranscriptionally to suppress multiple target genes within a cell population. To what extent this multi-target suppression occurs in individual cells and how it impacts transcriptional heterogeneity and gene co-expression remains unknown. Here we used single-cell sequencing combined with introduction of individual microRNAs. miR-294 and let-7c were introduced into otherwise microRNA-deficient Dgcr8 knockout mouse embryonic stem cells. Both microRNAs induce suppression and correlated expression of their respective gene targets. The two microRNAs had opposing effects on transcriptional heterogeneity within the cell population, with let-7c increasing and miR-294 decreasing the heterogeneity between cells. Furthermore, let-7c promotes, whereas miR-294 suppresses, the phasing of cell cycle genes. These results show at the individual cell level how a microRNA simultaneously has impacts on its many targets and how that in turn can influence a population of cells. The findings have important implications in the understanding of how microRNAs influence the co-expression of genes and pathways, and thus ultimately cell fate.
Assuntos
Células-Tronco Embrionárias/metabolismo , MicroRNAs/metabolismo , Animais , Ciclo Celular , Tamanho Celular , Regulação da Expressão Gênica/fisiologia , Camundongos , Camundongos Knockout , MicroRNAs/genética , Análise de Componente Principal , Proteínas de Ligação a RNA/genética , Proteínas de Ligação a RNA/metabolismo , Análise de Célula Única , Transcrição GênicaRESUMO
We propose a comparative dosimetric study of whole-breast hypofractionated radiation therapy using helical tomotherapy (HT) in supine position and 3-D conformal radiotherapy (3D-CRT) in prone position. Twelve patients undergoing breast-conserving therapy were retrospectively selected from October to December 2012. Specific dose-volume parameters were selected for the study. The target coverage was adequate in all patients for both techniques. Significant differences in lung dose distribution were observed: maximum dose (mean value over the 12 plans) was 23.41 Gy in HT plans and 6.65 Gy in 3D-CRT; V20 (i.e. the lung volume receiving 20 Gy) was 0.31% in HT plans and 0.0% in 3D-CRT plans. The mean dose to the heart was 5.57 Gy and 0.93 Gy, respectively. The differences between the two techniques were significant (p<0.05) only for some parameters. We noted better results in the prone position, but with HT, dose constraints were mentioned for the whole set of considered organs.
Assuntos
Neoplasias da Mama/radioterapia , Fracionamento da Dose de Radiação , Imageamento Tridimensional , Radioterapia Conformacional , Radioterapia de Intensidade Modulada , Adulto , Feminino , Seguimentos , Humanos , Pessoa de Meia-Idade , Órgãos em Risco , Prognóstico , Decúbito Ventral , Radiometria , Planejamento da Radioterapia Assistida por Computador , Estudos Retrospectivos , Decúbito DorsalRESUMO
We consider the problem of finding the set of rankings that best represents a given group of orderings on the same collection of elements (preference lists). This problem arises from social choice and voting theory, in which each voter gives a preference on a set of alternatives, and a system outputs a single preference order based on the observed voters' preferences. In this paper, we observe that, if the given set of preference lists is not homogeneous, a unique true underling ranking might not exist. Moreover only the lists that share the highest amount of information should be aggregated, and thus multiple rankings might provide a more feasible solution to the problem. In this light, we propose Network Selection, an algorithm that, given a heterogeneous group of rankings, first discovers the different communities of homogeneous rankings and then combines only the rank orderings belonging to the same community into a single final ordering. Our novel approach is inspired by graph theory; indeed our set of lists can be loosely read as the nodes of a network. As a consequence, only the lists populating the same community in the network would then be aggregated. In order to highlight the strength of our proposal, we show an application both on simulated and on two real datasets, namely a financial and a biological dataset. Experimental results on simulated data show that Network Selection can significantly outperform existing related methods. The other way around, the empirical evidence achieved on real financial data reveals that Network Selection is also able to select the most relevant variables in data mining predictive models, providing a clear superiority in terms of predictive power of the models built. Furthermore, we show the potentiality of our proposal in the bioinformatics field, providing an application to a biological microarray dataset.
Assuntos
Biologia Computacional , Mineração de Dados , Modelos Estatísticos , AlgoritmosRESUMO
MicroRNAs (miRNAs) are small noncoding RNAs that control gene expression by inducing RNA cleavage or translational inhibition. Most human miRNAs are intragenic and are transcribed as part of their hosting transcription units. We hypothesized that the expression profiles of miRNA host genes and of their targets are inversely correlated and devised a novel procedure, HOCTAR (host gene oppositely correlated targets), which ranks predicted miRNA target genes based on their anti-correlated expression behavior relative to their respective miRNA host genes. HOCTAR is the first tool for systematic miRNA target prediction that utilizes the same set of microarray experiments to monitor the expression of both miRNAs (through their host genes) and candidate targets. We applied the procedure to 178 human intragenic miRNAs and found that it performs better than currently available prediction softwares in pinpointing previously validated miRNA targets. The high-scoring HOCTAR predicted targets were enriched in Gene Ontology categories, which were consistent with previously published data, as in the case of miR-106b and miR-93. By means of overexpression and loss-of-function assays, we also demonstrated that HOCTAR is efficient in predicting novel miRNA targets and we identified, by microarray and qRT-PCR procedures, 34 and 28 novel targets for miR-26b and miR-98, respectively. Overall, we believe that the use of HOCTAR significantly reduces the number of candidate miRNA targets to be tested compared to the procedures based solely on target sequence recognition. Finally, our data further confirm that miRNAs have a significant impact on the mRNA levels of most of their targets.
Assuntos
Perfilação da Expressão Gênica , Regulação da Expressão Gênica/fisiologia , MicroRNAs/genética , MicroRNAs/fisiologia , Análise de Sequência com Séries de Oligonucleotídeos , Algoritmos , Previsões/métodos , Perfilação da Expressão Gênica/métodos , Genes , Células HeLa , Humanos , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Análise de Sequência de RNA/métodosRESUMO
BACKGROUND: The BIO14.6 hamster is an excellent animal model for inherited cardiomyopathy, because of its lethal and well-documented course, due to a spontaneous deletion of delta-sarcoglycan gene promoter and first exon. The muscle disease is progressive and average lifespan is 11 months, because heart slowly dilates towards heart failure. METHODOLOGY/PRINCIPAL FINDINGS: Based on the ability of adeno-associated viral (AAV) vectors to transduce heart together with skeletal muscle following systemic administration, we delivered human delta-sarcoglycan cDNA into male BIO14.6 hamsters by testing different ages of injection, routes of administration and AAV serotypes. Body-wide restoration of delta-SG expression was associated with functional reconstitution of the sarcoglycan complex and with significant lowering of centralized nuclei and fibrosis in skeletal muscle. Motor ability and cardiac functions were completely rescued. However, BIO14.6 hamsters having less than 70% of fibers recovering sarcoglycan developed cardiomyopathy, even if the total rescued protein was normal. When we used serotype 2/8 in combination with serotype 2/1, lifespan was extended up to 22 months with sustained heart function improvement. CONCLUSIONS/SIGNIFICANCE: Our data support multiple systemic administrations of AAV as a general therapeutic strategy for clinical trials in cardiomyopathies and muscle disorders.
Assuntos
Cardiomiopatias/terapia , Dependovirus/genética , Terapia Genética/métodos , Distrofias Musculares/terapia , Sarcoglicanas/administração & dosagem , Animais , Cricetinae , DNA Complementar/administração & dosagem , Vetores Genéticos , Humanos , Músculo Esquelético/metabolismo , Miocárdio/metabolismo , Sarcoglicanas/genética , Taxa de Sobrevida , Transdução GenéticaRESUMO
The pathogenesis of pemphigus vulgaris (PV) is still poorly understood. Autoantibodies present in PV patients can promote detrimental effects by triggering altered transduction of signals, which results in a final acantholysis. To investigate mechanisms involved in PV, cultured keratinocytes were treated with PV serum. PV sera were able to promote the cell cycle progression, inducing the accumulation of cyclin-dependent kinase 2 (Cdk2). Microarray analysis on keratinocytes detected that PV serum induced important changes in genes coding for one and the same proteins with known biological functions involved in PV disease (560 differentially expressed genes were identified). Then, we used two different approaches to investigate the role of Cdk2. First, small interfering RNA depletion of Cdk2 prevented cell-cell detachment induced by PV sera. Second, pharmacological inhibition of Cdk2 activity through roscovitine prevented blister formation and acantholysis in the mouse model of the disease. In vivo PV serum was found to alter multiple different pathways by microarray analysis (1463 differentially expressed genes were identified). Major changes in gene expression induced by roscovitine were studied through comparison of effects of PV serum alone and in association with roscovitine. The most significantly enriched pathways were cell communication, gap junction, focal adhesion, adherens junction, and tight junction. Our data indicate that major Cdk2-dependent multiple gene regulatory events are present in PV. This alteration may influence the evolution of PV and its therapy.
Assuntos
Quinase 2 Dependente de Ciclina/metabolismo , Regulação da Expressão Gênica , Pênfigo/enzimologia , Animais , Animais Recém-Nascidos , Ciclo Celular , Células Cultivadas , Quinase 2 Dependente de Ciclina/genética , Modelos Animais de Doenças , Ativação Enzimática , Humanos , Queratinócitos/enzimologia , Camundongos , Camundongos Endogâmicos BALB C , Análise de Sequência com Séries de Oligonucleotídeos , Pênfigo/genética , Pênfigo/patologia , RNA Interferente Pequeno/genéticaRESUMO
Progressive familial intrahepatic cholestasis (PFIC) is a severe cholestatic liver disease of early life often requiring liver transplantation. Organ shortage leads to consider living-related liver transplantation. Because of possible partial metabolic defect in heterozygotes, the use of familial donors might be questionable. We therefore evaluated the safety of this procedure, for both donors and recipients. We compared a series of seven parental-children pairs, having participated in the living related liver transplant program for PFIC between 1994 and 2001, with that of a series of seven parental-children pairs, performed for biliary atresia (BA) during the same period. No primary graft dysfunction was observed. There was no difference in the course of transaminases, gamma-glutamyl transpeptidase and bilirubin levels after transplantation in both donor and recipient series. Thirteen recipients and 14 donors are alive and well 3-10 yr post-surgery. One PFIC recipient died nine months post-orthotopic liver transplantation from sepsis. We conclude that PFIC heterozygote status of the donor does not increase the risk of liver dysfunction in either recipients or donors, with a similar course compared with BA recipients and donors.