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1.
Environ Int ; 134: 105267, 2019 Nov 05.
Artigo em Inglês | MEDLINE | ID: mdl-31704565

RESUMO

The number of anthropogenic chemicals, manufactured, by-products, metabolites and abiotically formed transformation products, counts to hundreds of thousands, at present. Thus, humans and wildlife are exposed to complex mixtures, never one chemical at a time and rarely with only one dominating effect. Hence there is an urgent need to develop strategies on how exposure to multiple hazardous chemicals and the combination of their effects can be assessed. A workshop, "Advancing the Assessment of Chemical Mixtures and their Risks for Human Health and the Environment" was organized in May 2018 together with Joint Research Center in Ispra, EU-funded research projects and Commission Services and relevant EU agencies. This forum for researchers and policy-makers was created to discuss and identify gaps in risk assessment and governance of chemical mixtures as well as to discuss state of the art science and future research needs. Based on the presentations and discussions at this workshop we want to bring forward the following Key Messages.

2.
Stem Cell Reports ; 13(5): 847-861, 2019 Nov 12.
Artigo em Inglês | MEDLINE | ID: mdl-31607568

RESUMO

The regulation of the proliferation and polarity of neural progenitors is crucial for the development of the brain cortex. Animal studies have implicated glycogen synthase kinase 3 (GSK3) as a pivotal regulator of both proliferation and polarity, yet the functional relevance of its signaling for the unique features of human corticogenesis remains to be elucidated. We harnessed human cortical brain organoids to probe the longitudinal impact of GSK3 inhibition through multiple developmental stages. Chronic GSK3 inhibition increased the proliferation of neural progenitors and caused massive derangement of cortical tissue architecture. Single-cell transcriptome profiling revealed a direct impact on early neurogenesis and uncovered a selective role of GSK3 in the regulation of glutamatergic lineages and outer radial glia output. Our dissection of the GSK3-dependent transcriptional network in human corticogenesis underscores the robustness of the programs determining neuronal identity independent of tissue architecture.

3.
HLA ; 94(4): 396-397, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31369198

RESUMO

HLA-DPA1*01:20 differs from HLA-DPA1*01:03:01:01 by one nucleotide substitution in codon 5 in exon 2.

4.
Hum Mol Genet ; 28(R2): R226-R234, 2019 Nov 21.
Artigo em Inglês | MEDLINE | ID: mdl-31411680

RESUMO

A vast portion of intellectual disability and autism spectrum disorders is genetically caused by mutations in chromatin modulators. These proteins play key roles in development and are also highly expressed in the adult brain. Specifically, the pivotal role of chromatin regulation in transcription has placed enhancers at the core of neurodevelopmental disorders (NDDs) studies, ushering in the coining of the term enhanceropathies. The convergence of these disorders is multilayered, spanning from molecular causes to pathophysiological traits, including extensive overlaps between enhanceropathies and neurocristopathies. The reconstruction of epigenetic circuitries wiring development and underlying cognitive functions has gone hand in hand with the development of tools that increase the sensitivity of identifying regulatory regions and linking enhancers to their target genes. The available models, including loop extrusion and phase separation, have been bringing into relief complementary aspects to interpret gene regulation datasets, reinforcing the idea that enhancers are not all the same and that regulatory regions possess shades of enhancer-ness and promoter-ness. The current limits in enhancer definition, within the emerging broader understanding of chromatin dynamics in time and space, are now on the verge of being transformed by the possibility to interrogate developmentally relevant three-dimensional cellular models at single-cell resolution. Here we discuss the contours of how these technological advances, as well as the epistemic limitations they are set to overcome, may well usher in a change of paradigm for NDDs, moving the quest for convergence from enhancers to the four-dimensional (4D) genome.

5.
Orphanet J Rare Dis ; 14(1): 121, 2019 05 31.
Artigo em Inglês | MEDLINE | ID: mdl-31151468

RESUMO

Williams Beuren syndrome (WBS) is a multiple malformations/intellectual disability (ID) syndrome caused by 7q11.23 microdeletion and clinically characterized by a typical neurocognitive profile including excessive talkativeness and social disinhibition, often defined as "overfriendliness" and "hyersociability". WBS is generally considered as the polar opposite phenotype to Autism Spectrum Disorder (ASD). Surprisingly, the prevalence of ASD has been reported to be significantly higher in WBS (12%) than in general population (1%). Our study aims to investigate the molecular basis of the peculiar association of ASD and WBS. We performed chromosomal microarray analysis and whole exome sequencing in six patients presenting with WBS and ASD, in order to evaluate the possible presence of chromosomal or gene variants considered as pathogenic.Our study shows that the presence of ASD in the recruited WBS patients is due to i) neither atypically large deletions; ii) nor the presence of pathogenic variants in genes localized in the non-deleted 7q11.23 allele which would unmask recessive conditions; iii) moreover, we did not identify a second, indisputable independent genetic diagnosis, related to pathogenic Copy Number Variations or rare pathogenic exonic variants in known ID/ASD causing genes, although several variants of unknown significance were found. Finally, imprinting effect does not appear to be the only cause of autism in WBS patients, since the deletions occurred in alleles of both maternal and paternal origin.The social disinhibition observed in WBS does not follow common social norms and symptoms overlapping with ASD, such as restricted interests and repetitive behavior, can be observed in "typical" WBS patients: therefore, the terms "overfriendliness" and "hypersociability" appear to be a misleading oversimplification.The etiology of ASD in WBS is likely to be heterogeneous. Further studies on large series of patients are needed to clarify the observed variability in WBS social communication, ranging from excessive talkativeness and social disinhibition to absence of verbal language and social deficit.

6.
Neurol Sci ; 40(6): 1227-1235, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30874998

RESUMO

BACKGROUND: Pre-existing small vessel disease (SVD) has been associated with poor functional outcomes in patients with acute ischemic stroke treated with intravenous thrombolysis; however, there are scarce data in patients treated with endovascular therapy. We aimed to investigate the associations between SVD and clinical outcomes in patients treated with endovascular therapy. METHODS: We retrospectivel y evaluated patients with acute ischemic stroke in the anterior circulation receiving endovascular treatment. We assessed SVD markers with visual scales using non-contrast computed tomography. Early outcomes included intracerebral hemorrhage and 7-day/discharge stroke severity, and late outcomes included modified Rankin scale (mRS) 90 days after stroke. We used logistic and ordinal regression models adjusted for age, sex, stroke severity, and time-to-groin puncture time. RESULTS: A total of 175 patients were included in the study, mean (±SD) age 72.3 (± 12.4) years, 90 (51%) males. Among SVD features, only brain atrophy was associated with 7-day stroke severity (OR = 2.28; 95% CI = 1.11-4.68) and with worse mRS at 90 days (OR = 2.72; 95% CI = 1.25-5.91). Global SVD burden was associated with worse mRS at 90 days (OR = 1.63; 95% CI = 1.01-2.62) but not with 7-day stroke severity (OR = 1.71; 95% CI = 0.97-3.01). CONCLUSIONS: Pre-existing SVD burden, mainly driven by brain atrophy, negatively affects early and late clinical outcomes in anterior circulation ischemic stroke treated with endovascular therapy. Our results may help prognostic stratification of stroke patients treated with endovascular therapy.


Assuntos
Isquemia Encefálica/complicações , Doenças de Pequenos Vasos Cerebrais/diagnóstico por imagem , Doenças de Pequenos Vasos Cerebrais/cirurgia , Procedimentos Endovasculares , Acidente Vascular Cerebral/complicações , Idoso , Encéfalo/diagnóstico por imagem , Encéfalo/cirurgia , Doenças de Pequenos Vasos Cerebrais/complicações , Feminino , Humanos , Masculino , Estudos Retrospectivos , Fatores de Risco , Tomografia Computadorizada por Raios X , Resultado do Tratamento
7.
Nat Biotechnol ; 37(3): 314-322, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30778230

RESUMO

Reproducibility in research can be compromised by both biological and technical variation, but most of the focus is on removing the latter. Here we investigate the effects of biological variation in HeLa cell lines using a systems-wide approach. We determine the degree of molecular and phenotypic variability across 14 stock HeLa samples from 13 international laboratories. We cultured cells in uniform conditions and profiled genome-wide copy numbers, mRNAs, proteins and protein turnover rates in each cell line. We discovered substantial heterogeneity between HeLa variants, especially between lines of the CCL2 and Kyoto varieties, and observed progressive divergence within a specific cell line over 50 successive passages. Genomic variability has a complex, nonlinear effect on transcriptome, proteome and protein turnover profiles, and proteotype patterns explain the varying phenotypic response of different cell lines to Salmonella infection. These findings have implications for the interpretation and reproducibility of research results obtained from human cultured cells.


Assuntos
Variações do Número de Cópias de DNA/genética , Genoma Humano/genética , Células HeLa , Transcriptoma/genética , Genômica/normas , Humanos , Proteoma/genética , Reprodutibilidade dos Testes
8.
HLA ; 93(6): 484-485, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30784234

RESUMO

The new allele HLA-A*01:289 differs from HLA-A*01:95 by one nucleotide substitution in exon 2.

9.
Cell Rep ; 25(4): 988-1001, 2018 Oct 23.
Artigo em Inglês | MEDLINE | ID: mdl-30355503

RESUMO

Transdifferentiation of fibroblasts into induced neuronal cells (iNs) by the neuron-specific transcription factors Brn2, Myt1l, and Ascl1 is a paradigmatic example of inter-lineage conversion across epigenetically distant cells. Despite tremendous progress regarding the transcriptional hierarchy underlying transdifferentiation, the enablers of the concomitant epigenome resetting remain to be elucidated. Here, we investigated the role of KMT2A and KMT2B, two histone H3 lysine 4 methylases with cardinal roles in development, through individual and combined inactivation. We found that Kmt2b, whose human homolog's mutations cause dystonia, is selectively required for iN conversion through suppression of the alternative myocyte program and induction of neuronal maturation genes. The identification of KMT2B-vulnerable targets allowed us, in turn, to expose, in a cohort of 225 patients, 45 unique variants in 39 KMT2B targets, which represent promising candidates to dissect the molecular bases of dystonia.

10.
Sci Rep ; 8(1): 8811, 2018 Jun 11.
Artigo em Inglês | MEDLINE | ID: mdl-29891904

RESUMO

The characteristic six layers of the mammalian neocortex develop sequentially as neurons are generated by neural progenitors and subsequently migrate past older neurons to their final position in the cortical plate. One of the earliest steps of neuronal differentiation is the formation of an axon. Small GTPases play essential roles during this process by regulating cytoskeletal dynamics and intracellular trafficking. While the function of GTPases has been studied extensively in cultured neurons and in vivo much less is known about their upstream regulators. Here we show that Arhgef7 (also called ßPix or Cool1) is essential for axon formation during cortical development. The loss of Arhgef7 results in an extensive loss of axons in cultured neurons and in the developing cortex. Arhgef7 is a guanine-nucleotide exchange factor (GEF) for Cdc42, a GTPase that has a central role in directing the formation of axons during brain development. However, active Cdc42 was not able to rescue the knockdown of Arhgef7. We show that Arhgef7 interacts with the GTPase TC10 that is closely related to Cdc42. Expression of active TC10 can restore the ability to extend axons in Arhgef7-deficient neurons. Our results identify an essential role of Arhgef7 during neuronal development that promotes axon formation upstream of TC10.

11.
Science ; 360(6388): 496-498, 2018 05 04.
Artigo em Inglês | MEDLINE | ID: mdl-29724945
12.
Oncogene ; 37(26): 3575-3588, 2018 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-29576613

RESUMO

HOXB7 is a homeodomain (HOX) transcription factor involved in regional body patterning of invertebrates and vertebrates. We previously identified HOXB7 within a ten-gene prognostic signature for lung adenocarcinoma, where increased expression of HOXB7 was associated with poor prognosis. This raises the question of how HOXB7 overexpression can influence the metastatic behavior of lung adenocarcinoma. Here, we analyzed publicly available microarray and RNA-seq lung cancer expression datasets and found that HOXB7-overexpressing tumors are enriched in gene signatures characterizing adult and embryonic stem cells (SC), and induced pluripotent stem cells (iPSC). Experimentally, we found that HOXB7 upregulates several canonical SC/iPSC markers and sustains the expansion of a subpopulation of cells with SC characteristics, through modulation of LIN28B, an emerging cancer gene and pluripotency factor, which we discovered to be a direct target of HOXB7. We validated this new circuit by showing that HOXB7 enhances reprogramming to iPSC with comparable efficiency to LIN28B or its target c-MYC, which is a canonical reprogramming factor.

13.
Prog Neuropsychopharmacol Biol Psychiatry ; 84(Pt B): 306-327, 2018 Jun 08.
Artigo em Inglês | MEDLINE | ID: mdl-29309830

RESUMO

The complexity of the human brain emerges from a long and finely tuned developmental process orchestrated by the crosstalk between genome and environment. Vis à vis other species, the human brain displays unique functional and morphological features that result from this extensive developmental process that is, unsurprisingly, highly vulnerable to both genetically and environmentally induced alterations. One of the most striking outcomes of the recent surge of sequencing-based studies on neurodevelopmental disorders (NDDs) is the emergence of chromatin regulation as one of the two domains most affected by causative mutations or Copy Number Variations besides synaptic function, whose involvement had been largely predicted for obvious reasons. These observations place chromatin dysfunction at the top of the molecular pathways hierarchy that ushers in a sizeable proportion of NDDs and that manifest themselves through synaptic dysfunction and recurrent systemic clinical manifestation. Here we undertake a conceptual investigation of chromatin dysfunction in NDDs with the aim of systematizing the available evidence in a new framework: first, we tease out the developmental vulnerabilities in human corticogenesis as a structuring entry point into the causation of NDDs; second, we provide a much needed clarification of the multiple meanings and explanatory frameworks revolving around "epigenetics", highlighting those that are most relevant for the analysis of these disorders; finally we go in-depth into paradigmatic examples of NDD-causing chromatin dysregulation, with a special focus on human experimental models and datasets.

14.
Nat Commun ; 8(1): 1212, 2017 10 31.
Artigo em Inglês | MEDLINE | ID: mdl-29089484

RESUMO

Down syndrome (DS) is mostly caused by a trisomy of the entire Chromosome 21 (Trisomy 21, T21). Here, we use SWATH mass spectrometry to quantify protein abundance and protein turnover in fibroblasts from a monozygotic twin pair discordant for T21, and to profile protein expression in 11 unrelated DS individuals and matched controls. The integration of the steady-state and turnover proteomic data indicates that protein-specific degradation of members of stoichiometric complexes is a major determinant of T21 gene dosage outcome, both within and between individuals. This effect is not apparent from genomic and transcriptomic data. The data also reveal that T21 results in extensive proteome remodeling, affecting proteins encoded by all chromosomes. Finally, we find broad, organelle-specific post-transcriptional effects such as significant downregulation of the mitochondrial proteome contributing to T21 hallmarks. Overall, we provide a valuable proteomic resource to understand the origin of DS phenotypic manifestations.


Assuntos
Fibroblastos/metabolismo , Fibroblastos/patologia , Proteoma/metabolismo , Proteostase , Trissomia/patologia , Bases de Dados de Proteínas , Compensação de Dosagem (Genética) , Regulação da Expressão Gênica , Humanos , Proteínas Mitocondriais/genética , Proteínas Mitocondriais/metabolismo , Organelas/metabolismo , Proteólise , Proteostase/genética , Transdução de Sinais , Trissomia/genética
15.
Stud Hist Philos Biol Biomed Sci ; 64: 75-87, 2017 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-28689133

RESUMO

This paper identifies a common political struggle behind debates on the validity and permissibility of animal experimentation, through an analysis of two recent European case studies: the Italian implementation of the European Directive 2010/63/EC regulating the use of animals in science, and the recent European Citizens' Initiative (ECI) 'Stop Vivisection'. Drawing from a historical parallel with Victorian antivivisectionism, we highlight important threads in our case studies that mark the often neglected specificities of debates on animal experimentation. From the representation of the sadistic scientist in the XIX century, to his/her claimed capture by vested interests and evasion of public scrutiny in the contemporary cases, we show that animals are not simply the focus of the debate, but also a privileged locus at which much broader issues are being raised about science, its authority, accountability and potential misalignment with public interest. By highlighting this common socio-political conflict underlying public controversies around animal experimentation, our work prompts the exploration of modes of authority and argumentation that, in establishing the usefulness of animals in science, avoid reenacting the traditional divide between epistemic and political fora.


Assuntos
Experimentação Animal/história , Experimentação Animal/legislação & jurisprudência , Direitos dos Animais/história , Política , Vivissecção/história , Experimentação Animal/ética , Animais , Europa (Continente) , União Europeia , Feminino , História do Século XIX , História do Século XX , História do Século XXI , Humanos , Itália , Opinião Pública , Reino Unido , Vivissecção/ética
16.
Stem Cell Reports ; 8(6): 1784-1796, 2017 06 06.
Artigo em Inglês | MEDLINE | ID: mdl-28591656

RESUMO

Both the promises and pitfalls of the cell reprogramming research platform rest on human genetic variation, making the measurement of its impact one of the most urgent issues in the field. Harnessing large transcriptomics datasets of induced pluripotent stem cells (iPSC), we investigate the implications of this variability for iPSC-based disease modeling. In particular, we show that the widespread use of more than one clone per individual in combination with current analytical practices is detrimental to the robustness of the findings. We then proceed to identify methods to address this challenge and leverage multiple clones per individual. Finally, we evaluate the specificity and sensitivity of different sample sizes and experimental designs, presenting computational tools for power analysis. These findings and tools reframe the nature of replicates used in disease modeling and provide important resources for the design, analysis, and interpretation of iPSC-based studies.


Assuntos
Variação Genética , Células-Tronco Pluripotentes Induzidas/metabolismo , Projetos de Pesquisa , Perfilação da Expressão Gênica , Humanos , Células-Tronco Pluripotentes Induzidas/citologia , Modelos Biológicos
17.
Am J Hum Genet ; 100(6): 907-925, 2017 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-28575647

RESUMO

Yin and yang 1 (YY1) is a well-known zinc-finger transcription factor with crucial roles in normal development and malignancy. YY1 acts both as a repressor and as an activator of gene expression. We have identified 23 individuals with de novo mutations or deletions of YY1 and phenotypic features that define a syndrome of cognitive impairment, behavioral alterations, intrauterine growth restriction, feeding problems, and various congenital malformations. Our combined clinical and molecular data define "YY1 syndrome" as a haploinsufficiency syndrome. Through immunoprecipitation of YY1-bound chromatin from affected individuals' cells with antibodies recognizing both ends of the protein, we show that YY1 deletions and missense mutations lead to a global loss of YY1 binding with a preferential retention at high-occupancy sites. Finally, we uncover a widespread loss of H3K27 acetylation in particular on the YY1-bound enhancers, underscoring a crucial role for YY1 in enhancer regulation. Collectively, these results define a clinical syndrome caused by haploinsufficiency of YY1 through dysregulation of key transcriptional regulators.


Assuntos
Cromatina/metabolismo , Haploinsuficiência/genética , Deficiência Intelectual/genética , Transcrição Genética , Fator de Transcrição YY1/genética , Acetilação , Adolescente , Sequência de Bases , Pré-Escolar , Imunoprecipitação da Cromatina , Estudos de Coortes , Elementos Facilitadores Genéticos/genética , Feminino , Ontologia Genética , Haplótipos/genética , Hemizigoto , Histonas/metabolismo , Humanos , Linfócitos/metabolismo , Masculino , Metilação , Modelos Moleculares , Mutação de Sentido Incorreto/genética , Ligação Proteica/genética , Domínios Proteicos , Fator de Transcrição YY1/química
19.
J Mater Sci Mater Med ; 28(3): 43, 2017 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-28150116

RESUMO

Mucopolysaccharidosis type I (MPS I) is caused by a deficiency of α-L-iduronidase (IDUA), resulting in accumulation of glycosaminoglycans (GAG) in lysosomes. Microencapsulation of recombinant cells is a promising gene/cell therapy approach that could overcome the limitations of the current available treatments. In the present study we produced alginate-poly-L-lysine-alginate (APA) microcapsules containing recombinant cells overexpressing IDUA, which were implanted in the subcutaneous space of MPS I mice in order to evaluate their potential effect as a treatment for this disease. APA microcapsules enclosing genetically modified Baby Hamster Kidney cells overexpressing IDUA were produced and implanted in the subcutaneous space of 4-month-old MPS I mice (Idua -/-). Treatment was performed using two cell concentrations: 8.3 × 107 and 8.3 × 106 cells/mL. Untreated MPS I and normal mice were used as controls. Microcapsules were retrieved and analyzed after treatment. Increased IDUA in the liver, kidney and heart was detected 24 h postimplantation. After 120 days, higher IDUA activity was detected in the liver, kidney and heart, in both groups, whereas GAG accumulation was reduced only in the high cell concentration group. Microcapsules analysis showed blood vessels around them, as well as inflammatory cells and a fibrotic layer. Microencapsulated cells were able to ameliorate some aspects of the disease, indicating their potential as a treatment. To achieve better performance of the microcapsules, improvements such as the modulation of inflammatory response are suggested.


Assuntos
Composição de Medicamentos , Iduronidase/química , Injeções Subcutâneas , Mucopolissacaridose I/tratamento farmacológico , Alginatos/química , Animais , Cápsulas/química , Linhagem Celular , Cricetinae , Glicosaminoglicanos/química , Sistema Imunitário , Inflamação , Rim/efeitos dos fármacos , Lisossomos/química , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Transgênicos , Polilisina/análogos & derivados , Polilisina/química , Proteínas Recombinantes/química , Distribuição Tecidual
20.
Nat Methods ; 13(9): 777-83, 2016 09.
Artigo em Inglês | MEDLINE | ID: mdl-27479329

RESUMO

Next-generation mass spectrometric (MS) techniques such as SWATH-MS have substantially increased the throughput and reproducibility of proteomic analysis, but ensuring consistent quantification of thousands of peptide analytes across multiple liquid chromatography-tandem MS (LC-MS/MS) runs remains a challenging and laborious manual process. To produce highly consistent and quantitatively accurate proteomics data matrices in an automated fashion, we developed TRIC (http://proteomics.ethz.ch/tric/), a software tool that utilizes fragment-ion data to perform cross-run alignment, consistent peak-picking and quantification for high-throughput targeted proteomics. TRIC reduced the identification error compared to a state-of-the-art SWATH-MS analysis without alignment by more than threefold at constant recall while correcting for highly nonlinear chromatographic effects. On a pulsed-SILAC experiment performed on human induced pluripotent stem cells, TRIC was able to automatically align and quantify thousands of light and heavy isotopic peak groups. Thus, TRIC fills a gap in the pipeline for automated analysis of massively parallel targeted proteomics data sets.


Assuntos
Processamento Eletrônico de Dados/métodos , Peptídeos/análise , Proteômica/métodos , Alinhamento de Sequência/métodos , Análise de Sequência de Proteína/métodos , Software , Algoritmos , Processamento Eletrônico de Dados/instrumentação , Humanos , Espectrometria de Massas , Peptídeos/metabolismo , Células-Tronco Pluripotentes/metabolismo , Precursores de Proteínas/análise , Precursores de Proteínas/metabolismo , Proteólise , Proteômica/instrumentação , Reprodutibilidade dos Testes , Alinhamento de Sequência/instrumentação , Análise de Sequência de Proteína/instrumentação , Streptococcus pyogenes/metabolismo
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