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1.
Cell ; 183(5): 1185-1201.e20, 2020 11 25.
Artigo em Inglês | MEDLINE | ID: mdl-33242417

RESUMO

Spaceflight is known to impose changes on human physiology with unknown molecular etiologies. To reveal these causes, we used a multi-omics, systems biology analytical approach using biomedical profiles from fifty-nine astronauts and data from NASA's GeneLab derived from hundreds of samples flown in space to determine transcriptomic, proteomic, metabolomic, and epigenetic responses to spaceflight. Overall pathway analyses on the multi-omics datasets showed significant enrichment for mitochondrial processes, as well as innate immunity, chronic inflammation, cell cycle, circadian rhythm, and olfactory functions. Importantly, NASA's Twin Study provided a platform to confirm several of our principal findings. Evidence of altered mitochondrial function and DNA damage was also found in the urine and blood metabolic data compiled from the astronaut cohort and NASA Twin Study data, indicating mitochondrial stress as a consistent phenotype of spaceflight.


Assuntos
Genômica , Mitocôndrias/patologia , Voo Espacial , Estresse Fisiológico , Animais , Ritmo Circadiano , Matriz Extracelular/metabolismo , Humanos , Imunidade Inata , Metabolismo dos Lipídeos , Análise do Fluxo Metabólico , Camundongos Endogâmicos BALB C , Camundongos Endogâmicos C57BL , Músculos/imunologia , Especificidade de Órgãos , Olfato/fisiologia
2.
Nature ; 575(7782): 375-379, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31618756

RESUMO

Mitochondrial homeostasis depends on mitophagy, the programmed degradation of mitochondria. Only a few proteins are known to participate in mitophagy. Here we develop a multidimensional CRISPR-Cas9 genetic screen, using multiple mitophagy reporter systems and pro-mitophagy triggers, and identify numerous components of parkin-dependent mitophagy1. Unexpectedly, we find that the adenine nucleotide translocator (ANT) complex is required for mitophagy in several cell types. Whereas pharmacological inhibition of ANT-mediated ADP/ATP exchange promotes mitophagy, genetic ablation of ANT paradoxically suppresses mitophagy. Notably, ANT promotes mitophagy independently of its nucleotide translocase catalytic activity. Instead, the ANT complex is required for inhibition of the presequence translocase TIM23, which leads to stabilization of PINK1, in response to bioenergetic collapse. ANT modulates TIM23 indirectly via interaction with TIM44, which regulates peptide import through TIM232. Mice that lack ANT1 show blunted mitophagy and consequent profound accumulation of aberrant mitochondria. Disease-causing human mutations in ANT1 abrogate binding to TIM44 and TIM23 and inhibit mitophagy. Together, our findings show that ANT is an essential and fundamental mediator of mitophagy in health and disease.


Assuntos
Mitofagia , Animais , Linhagem Celular , Camundongos , Proteínas de Transporte da Membrana Mitocondrial/genética , Proteínas de Transporte da Membrana Mitocondrial/metabolismo , Proteínas do Complexo de Importação de Proteína Precursora Mitocondrial , Nucleotídeos/metabolismo , Ligação Proteica , Proteínas Quinases/genética , Proteínas Quinases/metabolismo
3.
Proc Natl Acad Sci U S A ; 119(18): e2200549119, 2022 05 03.
Artigo em Inglês | MEDLINE | ID: mdl-35482926

RESUMO

Primary mitochondrial diseases (PMDs) are a heterogeneous group of metabolic disorders that can be caused by hundreds of mutations in both mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) genes. Current therapeutic approaches are limited, although one approach has been exercise training. Endurance exercise is known to improve mitochondrial function in heathy subjects and reduce risk for secondary metabolic disorders such as diabetes or neurodegenerative disorders. However, in PMDs the benefit of endurance exercise is unclear, and exercise might be beneficial for some mitochondrial disorders but contraindicated in others. Here we investigate the effect of an endurance exercise regimen in mouse models for PMDs harboring distinct mitochondrial mutations. We show that while an mtDNA ND6 mutation in complex I demonstrated improvement in response to exercise, mice with a CO1 mutation affecting complex IV showed significantly fewer positive effects, and mice with an ND5 complex I mutation did not respond to exercise at all. For mice deficient in the nDNA adenine nucleotide translocase 1 (Ant1), endurance exercise actually worsened the dilated cardiomyopathy. Correlating the gene expression profile of skeletal muscle and heart with the physiologic exercise response identified oxidative phosphorylation, amino acid metabolism, matrisome (extracellular matrix [ECM]) structure, and cell cycle regulation as key pathways in the exercise response. This emphasizes the crucial role of mitochondria in determining the exercise capacity and exercise response. Consequently, the benefit of endurance exercise in PMDs strongly depends on the underlying mutation, although our results suggest a general beneficial effect.


Assuntos
Doenças Mitocondriais , Condicionamento Físico Animal , Animais , Humanos , Camundongos , Mitocôndrias/genética , Mitocôndrias/metabolismo , Doenças Mitocondriais/genética , Doenças Mitocondriais/metabolismo , Mutação , Condicionamento Físico Animal/fisiologia , Resistência Física/genética
4.
Proc Natl Acad Sci U S A ; 119(45): e2212417119, 2022 Nov 08.
Artigo em Inglês | MEDLINE | ID: mdl-36322731

RESUMO

Mitochondrial dysfunction can be associated with a range of clinical manifestations. Here, we report a family with a complex phenotype including combinations of connective tissue, neurological, and metabolic symptoms that were passed on to all surviving children. Analysis of the maternally inherited mtDNA revealed a novel genotype encompassing the haplogroup J - defining mitochondrial DNA (mtDNA) ND5 m.13708G>A (A458T) variant arising on the mtDNA haplogroup H7A background, an extremely rare combination. Analysis of transmitochondrial cybrids with the 13708A-H7 mtDNA revealed a lower mitochondrial respiration, increased reactive oxygen species production (mROS), and dysregulation of connective tissue gene expression. The mitochondrial dysfunction was exacerbated by histamine, explaining why all eight surviving children inherited the dysfunctional histidine decarboxylase allele (W327X) from the father. Thus, certain combinations of common mtDNA variants can cause mitochondrial dysfunction, mitochondrial dysfunction can affect extracellular matrix gene expression, and histamine-activated mROS production can augment the severity of mitochondrial dysfunction. Most important, we have identified a previously unreported genetic cause of mitochondrial disorder arising from the incompatibility of common, nonpathogenic mtDNA variants.


Assuntos
DNA Mitocondrial , Histamina , DNA Mitocondrial/genética , DNA Mitocondrial/metabolismo , Haplótipos , Histamina/metabolismo , Mitocôndrias/genética , Mitocôndrias/metabolismo , Tecido Conjuntivo/metabolismo
5.
Med Res Rev ; 44(1): 66-137, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-37222435

RESUMO

The demand for novel, fast-acting, and effective antimalarial medications is increasing exponentially. Multidrug resistant forms of malarial parasites, which are rapidly spreading, pose a serious threat to global health. Drug resistance has been addressed using a variety of strategies, such as targeted therapies, the hybrid drug idea, the development of advanced analogues of pre-existing drugs, and the hybrid model of resistant strains control mechanisms. Additionally, the demand for discovering new potent drugs grows due to the prolonged life cycle of conventional therapy brought on by the emergence of resistant strains and ongoing changes in existing therapies. The 1,2,4-trioxane ring system in artemisinin (ART) is the most significant endoperoxide structural scaffold and is thought to be the key pharmacophoric moiety required for the pharmacodynamic potential of endoperoxide-based antimalarials. Several derivatives of artemisinin have also been found as potential treatments for multidrug-resistant strain in this area. Many 1,2,4-trioxanes, 1,2,4-trioxolanes, and 1,2,4,5-tetraoxanes derivatives have been synthesised as a result, and many of these have shown promise antimalarial activity both in vivo and in vitro against Plasmodium parasites. As a consequence, efforts to develop a functionally straight-forward, less expensive, and vastly more effective synthetic pathway to trioxanes continue. This study aims to give a thorough examination of the biological properties and mode of action of endoperoxide compounds derived from 1,2,4-trioxane-based functional scaffolds. The present system of 1,2,4-trioxane, 1,2,4-trioxolane, and 1,2,4,5-tetraoxane compounds and dimers with potentially antimalarial activity will be highlighted in this systematic review (January 1963-December 2022).


Assuntos
Antimaláricos , Artemisininas , Tetraoxanos , Humanos , Antimaláricos/química , Artemisininas/farmacologia , Artemisininas/química , Plasmodium falciparum , Revisões Sistemáticas como Assunto , Tetraoxanos/farmacologia , Tetraoxanos/química
6.
Bioorg Med Chem Lett ; 103: 129700, 2024 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-38479483

RESUMO

This study investigates cutting-edge synthetic chemistry approaches for designing and producing innovative antimalarial drugs with improved efficacy and fewer adverse effects. Novel amino (-NH2) and hydroxy (-OH) functionalized 11-azaartemisinins 9, 12, and 14 were synthesized along with their derivatives 11a, 13a-e, and 15a-b through ART and were tested for their AMA (antimalarial activity) against Plasmodium yoelii via intramuscular (i.m.) and oral routes in Swiss mice. Ether derivative 13c was the most active compound by i.m. route, it has shown 100 % protection at the dose of 12 mg/kg × 4 days and showed 100 % clearance of parasitaemia on day 4 at dose of 6 mg/kg. Amine 11a, ether derivatives 13d, 13e and ether 15a also showed promising antimalarial activity. ß-Arteether gave 100 % protection at the dose of 48 mg/kg × 4 days and 20 % protection at 24 mg/kg × 4 days dose by oral route, while it showed 100 % protection at 6 mg/kg × 4 days and no protection at 3 mg/kg × 4 days by i.m. route.


Assuntos
Antimaláricos , Plasmodium yoelii , Animais , Camundongos , Antimaláricos/química , Éter/farmacologia , Relação Estrutura-Atividade , Resistência a Múltiplos Medicamentos , Etil-Éteres/farmacologia , Éteres/farmacologia
7.
Org Biomol Chem ; 22(16): 3287-3298, 2024 Apr 24.
Artigo em Inglês | MEDLINE | ID: mdl-38573240

RESUMO

We report herein a highly efficient and mild approach for synthesizing pharmacologically active bis(indolyl)methanes 3a-z, utilizing ZrO2 nanoparticles as a catalyst. The method involves a condensation reaction between indole and diverse aromatic aldehydes in acetonitrile under mild conditions. The ZrO2 nano-catalyst prepared via a co-precipitation method demonstrates exceptional efficacy, leading to favourable yields of the target bis(indolyl)methanes 3a-z. The versatility of this methodology is highlighted through substrate screening, showcasing its applicability to various aromatic aldehydes.

8.
Bioorg Chem ; 143: 107043, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38134523

RESUMO

The increasing resistance of various malarial parasite strains to drugs has made the production of a new, rapid-acting, and efficient antimalarial drug more necessary, as the demand for such drugs is growing rapidly. As a major global health concern, various methods have been implemented to address the problem of drug resistance, including the hybrid drug concept, combination therapy, the development of analogues of existing medicines, and the use of drug resistance reversal agents. Artemisinin and its derivatives are currently used against multidrug- resistant P. falciparum species. However, due to its natural origin, its use has been limited by its scarcity in natural resources. As a result, finding a substitute becomes more crucial, and the peroxide group in artemisinin, responsible for the drugs biological action in the form of 1,2,4-trioxane, may hold the key to resolving this issue. The literature suggests that 1,2,4-trioxanes have the potential to become an alternative to current malaria drugs, as highlighted in this review. This is why 1,2,4-trioxanes and their derivatives have been synthesized on a large scale worldwide, as they have shown promising antimalarial activity in vivo and in vitro against Plasmodium species. Consequently, the search for a more convenient, environment friendly, sustainable, efficient, and effective synthetic pathway for the synthesis of 1,2,4-trioxanes continues. The aim of this work is to provide a comprehensive analysis of the synthesis and mechanism of action of 1,2,4-trioxanes. This systematic review highlights the most recent summaries of derivatives of 1,2,4-trioxane compounds and dimers with potential antimalarial activity from January 1988 to 2023.


Assuntos
Antimaláricos , Artemisininas , Compostos Heterocíclicos , Artemisininas/farmacologia , Compostos Heterocíclicos/farmacologia , Plasmodium falciparum
9.
Genome Res ; 30(9): 1228-1242, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32796005

RESUMO

Neuroblastoma is a malignancy of the developing sympathetic nervous system that accounts for 12% of childhood cancer deaths. Like many childhood cancers, neuroblastoma shows a relative paucity of somatic single-nucleotide variants (SNVs) and small insertions and deletions (indels) compared to adult cancers. Here, we assessed the contribution of somatic structural variation (SV) in neuroblastoma using a combination of whole-genome sequencing (WGS) of tumor-normal pairs (n = 135) and single-nucleotide polymorphism (SNP) genotyping of primary tumors (n = 914). Our study design allowed for orthogonal validation and replication across platforms. SV frequency, type, and localization varied significantly among high-risk tumors. MYCN nonamplified high-risk tumors harbored an increased SV burden overall, including a significant excess of tandem duplication events across the genome. Genes disrupted by SV breakpoints were enriched in neuronal lineages and associated with phenotypes such as autism spectrum disorder (ASD). The postsynaptic adapter protein-coding gene, SHANK2, located on Chromosome 11q13, was disrupted by SVs in 14% of MYCN nonamplified high-risk tumors based on WGS and 10% in the SNP array cohort. Expression of SHANK2 was low across human-derived neuroblastoma cell lines and high-risk neuroblastoma tumors. Forced expression of SHANK2 in neuroblastoma cells resulted in significant growth inhibition (P = 2.6 × 10-2 to 3.4 × 10-5) and accelerated neuronal differentiation following treatment with all-trans retinoic acid (P = 3.1 × 10-13 to 2.4 × 10-30). These data further define the complex landscape of somatic structural variation in neuroblastoma and suggest that events leading to deregulation of neurodevelopmental processes, such as inactivation of SHANK2, are key mediators of tumorigenesis in this childhood cancer.


Assuntos
Genes Supressores de Tumor , Variação Estrutural do Genoma , Proteínas do Tecido Nervoso/genética , Neuroblastoma/genética , Neurogênese/genética , Linhagem Celular Tumoral , Cromotripsia , Estudos de Coortes , Quebras de DNA , Variações do Número de Cópias de DNA , Feminino , Humanos , Masculino , Proteína Proto-Oncogênica N-Myc/genética , Neuroblastoma/patologia , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , RNA Neoplásico , RNA-Seq , Medição de Risco , Telomerase/genética , Células Tumorais Cultivadas , Sequenciamento Completo do Genoma
10.
Genes Dev ; 28(12): 1363-79, 2014 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-24939938

RESUMO

Long noncoding RNAs (lncRNAs) are thought to play important roles in regulating gene transcription, but few have well-defined expression patterns or known biological functions during mammalian development. Using a conservative pipeline to identify lncRNAs that have important biological functions, we identified 363 lncRNAs in the lung and foregut endoderm. Importantly, we show that these lncRNAs are spatially correlated with transcription factors across the genome. In-depth expression analyses of lncRNAs with genomic loci adjacent to the critical transcription factors Nkx2.1, Gata6, Foxa2 (forkhead box a2), and Foxf1 mimic the expression patterns of their protein-coding neighbor. Loss-of-function analysis demonstrates that two lncRNAs, LL18/NANCI (Nkx2.1-associated noncoding intergenic RNA) and LL34, play distinct roles in endoderm development by controlling expression of critical developmental transcription factors and pathways, including retinoic acid signaling. In particular, we show that LL18/NANCI acts upstream of Nkx2.1 and downstream from Wnt signaling to regulate lung endoderm gene expression. These studies reveal that lncRNAs play an important role in foregut and lung endoderm development by regulating multiple aspects of gene transcription, often through regulation of transcription factor expression.


Assuntos
Regulação da Expressão Gênica no Desenvolvimento , Pulmão/crescimento & desenvolvimento , RNA Longo não Codificante/metabolismo , Fatores de Transcrição/metabolismo , Animais , Diferenciação Celular/genética , Linhagem Celular , Endoderma/citologia , Endoderma/metabolismo , Perfilação da Expressão Gênica , Técnicas de Silenciamento de Genes , Genoma , Células HEK293 , Humanos , Pulmão/embriologia , Camundongos , Proteínas Nucleares/genética , RNA Longo não Codificante/genética , Fator Nuclear 1 de Tireoide , Fatores de Transcrição/genética , Via de Sinalização Wnt
11.
PLoS Comput Biol ; 16(10): e1008263, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-33119584

RESUMO

Medulloblastoma is a highly heterogeneous pediatric brain tumor with five molecular subtypes, Sonic Hedgehog TP53-mutant, Sonic Hedgehog TP53-wildtype, WNT, Group 3, and Group 4, defined by the World Health Organization. The current mechanism for classification into these molecular subtypes is through the use of immunostaining, methylation, and/or genetics. We surveyed the literature and identified a number of RNA-Seq and microarray datasets in order to develop, train, test, and validate a robust classifier to identify medulloblastoma molecular subtypes through the use of transcriptomic profiling data. We have developed a GPL-3 licensed R package and a Shiny Application to enable users to quickly and robustly classify medulloblastoma samples using transcriptomic data. The classifier utilizes a large composite microarray dataset (15 individual datasets), an individual microarray study, and an RNA-Seq dataset, using gene ratios instead of gene expression measures as features for the model. Discriminating features were identified using the limma R package and samples were classified using an unweighted mean of normalized scores. We utilized two training datasets and applied the classifier in 15 separate datasets. We observed a minimum accuracy of 85.71% in the smallest dataset and a maximum of 100% accuracy in four datasets with an overall median accuracy of 97.8% across the 15 datasets, with the majority of misclassification occurring between the heterogeneous Group 3 and Group 4 subtypes. We anticipate this medulloblastoma transcriptomic subtype classifier will be broadly applicable to the cancer research and clinical communities.


Assuntos
Neoplasias Cerebelares , Perfilação da Expressão Gênica/métodos , Meduloblastoma , Software , Transcriptoma/genética , Neoplasias Cerebelares/classificação , Neoplasias Cerebelares/genética , Neoplasias Cerebelares/metabolismo , Bases de Dados Genéticas , Genômica , Humanos , Meduloblastoma/classificação , Meduloblastoma/genética , Meduloblastoma/metabolismo , Análise de Sequência com Séries de Oligonucleotídeos
12.
Nature ; 526(7574): 578-82, 2015 Oct 22.
Artigo em Inglês | MEDLINE | ID: mdl-26436454

RESUMO

Postnatal tissue quiescence is thought to be a default state in the absence of a proliferative stimulus such as injury. Although previous studies have demonstrated that certain embryonic developmental programs are reactivated aberrantly in adult organs to drive repair and regeneration, it is not well understood how quiescence is maintained in organs such as the lung, which displays a remarkably low level of cellular turnover. Here we demonstrate that quiescence in the adult lung is an actively maintained state and is regulated by hedgehog signalling. Epithelial-specific deletion of sonic hedgehog (Shh) during postnatal homeostasis in the murine lung results in a proliferative expansion of the adjacent lung mesenchyme. Hedgehog signalling is initially downregulated during the acute phase of epithelial injury as the mesenchyme proliferates in response, but returns to baseline during injury resolution as quiescence is restored. Activation of hedgehog during acute epithelial injury attenuates the proliferative expansion of the lung mesenchyme, whereas inactivation of hedgehog signalling prevents the restoration of quiescence during injury resolution. Finally, we show that hedgehog also regulates epithelial quiescence and regeneration in response to injury via a mesenchymal feedback mechanism. These results demonstrate that epithelial-mesenchymal interactions coordinated by hedgehog actively maintain postnatal tissue homeostasis, and deregulation of hedgehog during injury leads to aberrant repair and regeneration in the lung.


Assuntos
Proteínas Hedgehog/metabolismo , Lesão Pulmonar/metabolismo , Lesão Pulmonar/patologia , Pulmão/citologia , Pulmão/metabolismo , Regeneração , Cicatrização , Animais , Proliferação de Células , Regulação para Baixo , Células Epiteliais/citologia , Células Epiteliais/metabolismo , Células Epiteliais/patologia , Retroalimentação Fisiológica , Proteínas Hedgehog/deficiência , Proteínas Hedgehog/genética , Homeostase , Pulmão/patologia , Masculino , Mesoderma/citologia , Mesoderma/metabolismo , Camundongos , Comunicação Parácrina
13.
BMC Bioinformatics ; 21(1): 577, 2020 Dec 14.
Artigo em Inglês | MEDLINE | ID: mdl-33317447

RESUMO

BACKGROUND: Gene fusion events are significant sources of somatic variation across adult and pediatric cancers and are some of the most clinically-effective therapeutic targets, yet low consensus of RNA-Seq fusion prediction algorithms makes therapeutic prioritization difficult. In addition, events such as polymerase read-throughs, mis-mapping due to gene homology, and fusions occurring in healthy normal tissue require informed filtering, making it difficult for researchers and clinicians to rapidly discern gene fusions that might be true underlying oncogenic drivers of a tumor and in some cases, appropriate targets for therapy. RESULTS: We developed annoFuse, an R package, and shinyFuse, a companion web application, to annotate, prioritize, and explore biologically-relevant expressed gene fusions, downstream of fusion calling. We validated annoFuse using a random cohort of TCGA RNA-Seq samples (N = 160) and achieved a 96% sensitivity for retention of high-confidence fusions (N = 603). annoFuse uses FusionAnnotator annotations to filter non-oncogenic and/or artifactual fusions. Then, fusions are prioritized if previously reported in TCGA and/or fusions containing gene partners that are known oncogenes, tumor suppressor genes, COSMIC genes, and/or transcription factors. We applied annoFuse to fusion calls from pediatric brain tumor RNA-Seq samples (N = 1028) provided as part of the Open Pediatric Brain Tumor Atlas (OpenPBTA) Project to determine recurrent fusions and recurrently-fused genes within different brain tumor histologies. annoFuse annotates protein domains using the PFAM database, assesses reciprocality, and annotates gene partners for kinase domain retention. As a standard function, reportFuse enables generation of a reproducible R Markdown report to summarize filtered fusions, visualize breakpoints and protein domains by transcript, and plot recurrent fusions within cohorts. Finally, we created shinyFuse for algorithm-agnostic interactive exploration and plotting of gene fusions. CONCLUSIONS: annoFuse provides standardized filtering and annotation for gene fusion calls from STAR-Fusion and Arriba by merging, filtering, and prioritizing putative oncogenic fusions across large cancer datasets, as demonstrated here with data from the OpenPBTA project. We are expanding the package to be widely-applicable to other fusion algorithms and expect annoFuse to provide researchers a method for rapidly evaluating, prioritizing, and translating fusion findings in patient tumors.


Assuntos
Fusão Gênica , Neoplasias/genética , RNA/metabolismo , Software , Algoritmos , Humanos , Neoplasias/patologia , Proteínas de Fusão Oncogênica/genética , Proteínas de Fusão Oncogênica/metabolismo , RNA/genética
14.
Genet Med ; 22(5): 927-936, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-31911672

RESUMO

PURPOSE: Neurodevelopmental disorders represent a frequent indication for clinical exome sequencing. Fifty percent of cases, however, remain undiagnosed even upon exome reanalysis. Here we show RNA sequencing (RNA-seq) on human B-lymphoblastoid cell lines (LCL) is highly suitable for neurodevelopmental Mendelian gene testing and demonstrate the utility of this approach in suspected cases of Cornelia de Lange syndrome (CdLS). METHODS: Genotype-Tissue Expression project transcriptome data for LCL, blood, and brain were assessed for neurodevelopmental Mendelian gene expression. Detection of abnormal splicing and pathogenic variants in these genes was performed with a novel RNA-seq diagnostic pipeline and using a validation CdLS-LCL cohort (n = 10) and test cohort of patients who carry a clinical diagnosis of CdLS but negative genetic testing (n = 5). RESULTS: LCLs share isoform diversity of brain tissue for a large subset of neurodevelopmental genes and express 1.8-fold more of these genes compared with blood (LCL, n = 1706; whole blood, n = 917). This enables testing of more than 1000 genetic syndromes. The RNA-seq pipeline had 90% sensitivity for detecting pathogenic events and revealed novel diagnoses such as abnormal splice products in NIPBL and pathogenic coding variants in BRD4 and ANKRD11. CONCLUSION: The LCL transcriptome enables robust frontline and/or reflexive diagnostic testing for neurodevelopmental disorders.


Assuntos
Síndrome de Cornélia de Lange , Transtornos do Neurodesenvolvimento , Proteínas de Ciclo Celular/genética , Síndrome de Cornélia de Lange/diagnóstico , Síndrome de Cornélia de Lange/genética , Humanos , Transtornos do Neurodesenvolvimento/diagnóstico , Transtornos do Neurodesenvolvimento/genética , Proteínas Nucleares , Fenótipo , Análise de Sequência de RNA , Fatores de Transcrição
15.
Development ; 142(1): 108-17, 2015 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-25516972

RESUMO

The development of the lung epithelium is regulated in a stepwise fashion to generate numerous differentiated and stem cell lineages in the adult lung. How these different lineages are generated in a spatially and temporally restricted fashion remains poorly understood, although epigenetic regulation probably plays an important role. We show that the Polycomb repressive complex 2 component Ezh2 is highly expressed in early lung development but is gradually downregulated by late gestation. Deletion of Ezh2 in early lung endoderm progenitors leads to the ectopic and premature appearance of Trp63+ basal cells that extend the entire length of the airway. Loss of Ezh2 also leads to reduced secretory cell differentiation. In their place, morphologically similar cells develop that express a subset of basal cell genes, including keratin 5, but no longer express high levels of either Trp63 or of standard secretory cell markers. This suggests that Ezh2 regulates the phenotypic switch between basal cells and secretory cells. Together, these findings show that Ezh2 restricts the basal cell lineage during normal lung endoderm development to allow the proper patterning of epithelial lineages during lung formation.


Assuntos
Linhagem da Célula , Endoderma/citologia , Endoderma/embriologia , Pulmão/citologia , Pulmão/embriologia , Complexo Repressor Polycomb 2/metabolismo , Animais , Biomarcadores/metabolismo , Diferenciação Celular/genética , Linhagem da Célula/genética , Proliferação de Células , Proteína Potenciadora do Homólogo 2 de Zeste , Células Epiteliais/citologia , Células Epiteliais/metabolismo , Epitélio/embriologia , Epitélio/metabolismo , Perfilação da Expressão Gênica , Regulação da Expressão Gênica no Desenvolvimento , Ontologia Genética , Células Caliciformes/citologia , Células Caliciformes/metabolismo , Proteínas Hedgehog/metabolismo , Queratina-5/metabolismo , Pulmão/metabolismo , Camundongos , Mutação/genética , Células Neuroendócrinas/citologia , Células Neuroendócrinas/metabolismo , Proteínas Nucleares/metabolismo , Análise de Sequência com Séries de Oligonucleotídeos , Fosfoproteínas/metabolismo , Software , Fator Nuclear 1 de Tireoide , Transativadores/metabolismo , Fatores de Transcrição/metabolismo
16.
Indian J Med Res ; 148(5): 596-611, 2018 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-30666985

RESUMO

Assessment of the status of health and nutrition of a population is imperative to design and implement sound public health policies and programmes. The various extensive national health and nutrition surveys provide national-level information on different domains of health. These provide vital information and statistics for the country, and the data generated are used to identify the prevalence and risk factors for the diseases and health challenges faced by a country. This review describes the various national health and nutrition surveys conducted in India and also compares the information generated by each of these surveys. These include the National Family Health Survey, District Level Household Survey, Annual Health Survey, National Nutrition Monitoring Bureau Survey, Rapid Survey on Children and Comprehensive National Nutrition Survey.


Assuntos
Política de Saúde , Estado Nutricional , Saúde Pública/métodos , Inquéritos Epidemiológicos , Humanos , Índia/epidemiologia , Avaliação Nutricional , Inquéritos Nutricionais
17.
Drug Dev Res ; 75(6): 343-7, 2014 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-25195578

RESUMO

Gene set analysis provides a method to generate statistical inferences across sets of linked genes, primarily using high-throughput expression data. Common gene sets include biological pathways, operons, and targets of transcriptional regulators. In higher eukaryotes, especially when dealing with diseases with strong genetic and epigenetic components such as cancer, copy number loss and gene silencing through promoter methylation can eliminate the possibility that a gene is transcribed. This, in turn, can adversely affect the estimation of transcription factor or pathway activity from a set of target genes, as some of the targets may not be responsive to transcriptional regulation. Here we introduce a simple filtering approach that removes genes from consideration if they show copy number loss or promoter methylation, and demonstrate the improvement in inference of transcription factor activity in a simulated dataset based on the background expression observed in normal head and neck tissue.


Assuntos
Biologia Computacional/métodos , Dosagem de Genes , Neoplasias/genética , Regiões Promotoras Genéticas , Fatores de Transcrição/genética , Metilação de DNA , Epigênese Genética , Regulação Neoplásica da Expressão Gênica , Humanos , Software
18.
bioRxiv ; 2024 Jan 07.
Artigo em Inglês | MEDLINE | ID: mdl-38106022

RESUMO

Cancer immunotherapies have produced remarkable results in B-cell malignancies; however, optimal cell surface targets for many solid cancers remain elusive. Here, we present an integrative proteomic, transcriptomic, and epigenomic analysis of tumor specimens along with normal tissues to identify biologically relevant cell surface proteins that can serve as immunotherapeutic targets for neuroblastoma, an often-fatal childhood cancer of the developing nervous system. We apply this approach to human-derived cell lines (N=9) and cell/patient-derived xenograft (N=12) models of neuroblastoma. Plasma membrane-enriched mass spectrometry identified 1,461 cell surface proteins in cell lines and 1,401 in xenograft models, respectively. Additional proteogenomic analyses revealed 60 high-confidence candidate immunotherapeutic targets and we prioritized Delta-like canonical notch ligand 1 (DLK1) for further study. High expression of DLK1 directly correlated with the presence of a super-enhancer spanning the DLK1 locus. Robust cell surface expression of DLK1 was validated by immunofluorescence, flow cytometry, and immunohistochemistry. Short hairpin RNA mediated silencing of DLK1 in neuroblastoma cells resulted in increased cellular differentiation. ADCT-701, a DLK1-targeting antibody-drug conjugate (ADC), showed potent and specific cytotoxicity in DLK1-expressing neuroblastoma xenograft models. Moreover, DLK1 is highly expressed in several adult cancer types, including adrenocortical carcinoma (ACC), pheochromocytoma/paraganglioma (PCPG), hepatoblastoma, and small cell lung cancer (SCLC), suggesting potential clinical benefit beyond neuroblastoma. Taken together, our study demonstrates the utility of comprehensive cancer surfaceome characterization and credentials DLK1 as an immunotherapeutic target. Highlights: Plasma membrane enriched proteomics defines surfaceome of neuroblastomaMulti-omic data integration prioritizes DLK1 as a candidate immunotherapeutic target in neuroblastoma and other cancersDLK1 expression is driven by a super-enhancer DLK1 silencing in neuroblastoma cells results in cellular differentiation ADCT-701, a DLK1-targeting antibody-drug conjugate, shows potent and specific cytotoxicity in DLK1-expressing neuroblastoma preclinical models.

19.
Cell Genom ; 3(7): 100340, 2023 Jul 12.
Artigo em Inglês | MEDLINE | ID: mdl-37492101

RESUMO

Pediatric brain and spinal cancers are collectively the leading disease-related cause of death in children; thus, we urgently need curative therapeutic strategies for these tumors. To accelerate such discoveries, the Children's Brain Tumor Network (CBTN) and Pacific Pediatric Neuro-Oncology Consortium (PNOC) created a systematic process for tumor biobanking, model generation, and sequencing with immediate access to harmonized data. We leverage these data to establish OpenPBTA, an open collaborative project with over 40 scalable analysis modules that genomically characterize 1,074 pediatric brain tumors. Transcriptomic classification reveals universal TP53 dysregulation in mismatch repair-deficient hypermutant high-grade gliomas and TP53 loss as a significant marker for poor overall survival in ependymomas and H3 K28-mutant diffuse midline gliomas. Already being actively applied to other pediatric cancers and PNOC molecular tumor board decision-making, OpenPBTA is an invaluable resource to the pediatric oncology community.

20.
ACS Omega ; 7(32): 28471-28480, 2022 Aug 16.
Artigo em Inglês | MEDLINE | ID: mdl-35990458

RESUMO

The synthesis and characterization of a new octahedral Zr(IV) complex of oxygen-depleted N,O-type calixarene ligand comprising two distal-functionalized pyrazole rings have been reported. The cone shape and structure of the prepared complex were confirmed univocally by single-crystal X-ray diffraction and NMR studies. The Zr metal lies at 2.091 Å from the plane of the calixarene ring. This complex has been utilized as an efficient catalyst for the synthesis of Biginelli adducts, bis(indolyl)methanes, and coumarins. This complex (Cl2Zr-calixarene) showed superior activity for these multicomponent reactions in comparison to the corresponding Ti(IV) and Zn(II) analogues. Ferrocene-appended bis(indolyl)methane, prepared using this catalyst, was also evaluated for its anticancer activity against the A-172 cell line.

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