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1.
Anticancer Res ; 40(1): 535-543, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31892609

RESUMO

BACKGROUND/AIM: To assess the impact of vitamin D supplementation on genomic and metabolomic profiles and relate them to the individual's responsiveness to varying doses of vitamin D3 Patients and Methods: Healthy adults were given either 600, 4000 or 10,000 IUs vitamin D3/day for 6 months. Circulating parathyroid hormone (PTH), 25-hydroxyvitamin D [25(OH)D], calcium, peripheral white blood cells broad gene expression and urine and serum metabolomic profiles were evaluated. RESULTS: There was a dose-dependent effect of vitamin D supplementation on serum 25(OH)D, PTH and broad gene expression. Serum calcium levels remained normal for all study subjects and no untoward toxicity was observed. The metabolomic profiles were related to the genomic expression analysis. There were significant inter-individual effects on gene expression and metabolomic profile in response to the same dose of vitamin D3 supplementation, despite similar changes in 25(OH)D and PTH concentrations. CONCLUSION: These results may help explain the variability observed in clinical trials regarding vitamin D's non-calcemic health benefits.


Assuntos
Suplementos Nutricionais , Genômica , Metabolômica , Vitamina D/farmacologia , Adulto , Relação Dose-Resposta a Droga , Feminino , Regulação da Expressão Gênica/efeitos dos fármacos , Humanos , Masculino , Hormônio Paratireóideo/sangue , Análise de Componente Principal , Mapas de Interação de Proteínas/efeitos dos fármacos , Vitamina D/análogos & derivados , Vitamina D/sangue
2.
Gut ; 69(1): 177-186, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-30954949

RESUMO

OBJECTIVE: Increased de novo fatty acid (FA) synthesis and cholesterol biosynthesis have been independently described in many tumour types, including hepatocellular carcinoma (HCC). DESIGN: We investigated the functional contribution of fatty acid synthase (Fasn)-mediated de novo FA synthesis in a murine HCC model induced by loss of Pten and overexpression of c-Met (sgPten/c-Met) using liver-specific Fasn knockout mice. Expression arrays and lipidomic analysis were performed to characterise the global gene expression and lipid profiles, respectively, of sgPten/c-Met HCC from wild-type and Fasn knockout mice. Human HCC cell lines were used for in vitro studies. RESULTS: Ablation of Fasn significantly delayed sgPten/c-Met-driven hepatocarcinogenesis in mice. However, eventually, HCC emerged in Fasn knockout mice. Comparative genomic and lipidomic analyses revealed the upregulation of genes involved in cholesterol biosynthesis, as well as decreased triglyceride levels and increased cholesterol esters, in HCC from these mice. Mechanistically, loss of Fasn promoted nuclear localisation and activation of sterol regulatory element binding protein 2 (Srebp2), which triggered cholesterogenesis. Blocking cholesterol synthesis via the dominant negative form of Srebp2 (dnSrebp2) completely prevented sgPten/c-Met-driven hepatocarcinogenesis in Fasn knockout mice. Similarly, silencing of FASN resulted in increased SREBP2 activation and hydroxy-3-methyl-glutaryl-CoA (HMG-CoA) reductase (HMGCR) expression in human HCC cell lines. Concomitant inhibition of FASN-mediated FA synthesis and HMGCR-driven cholesterol production was highly detrimental for HCC cell growth in culture. CONCLUSION: Our study uncovers a novel functional crosstalk between aberrant lipogenesis and cholesterol biosynthesis pathways in hepatocarcinogenesis, whose concomitant inhibition might represent a therapeutic option for HCC.


Assuntos
Carcinoma Hepatocelular/metabolismo , Colesterol/biossíntese , Ácido Graxo Sintase Tipo I/metabolismo , Ácidos Graxos/biossíntese , Neoplasias Hepáticas/metabolismo , Animais , Vias Biossintéticas/efeitos dos fármacos , Vias Biossintéticas/genética , Carcinogênese/genética , Carcinoma Hepatocelular/genética , Linhagem Celular Tumoral , Ácido Graxo Sintase Tipo I/genética , Feminino , Técnicas de Silenciamento de Genes , Inativação Gênica , Genômica , Humanos , Hidroximetilglutaril-CoA Redutases/genética , Hidroximetilglutaril-CoA Redutases/metabolismo , Neoplasias Hepáticas/genética , Masculino , Camundongos , Camundongos Knockout , PTEN Fosfo-Hidrolase/metabolismo , Proteínas Proto-Oncogênicas c-met/metabolismo , Proteína de Ligação a Elemento Regulador de Esterol 2/genética , Proteína de Ligação a Elemento Regulador de Esterol 2/metabolismo , Transcriptoma
3.
J Urol ; 203(1): 115-119, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31502940

RESUMO

PURPOSE: The following is a summary of discussion at a United States FDA (Food and Drug Administration) public workshop reviewing potential trial designs and end points to develop therapies to treat localized prostate cancer. MATERIALS AND METHODS: The workshop focused on the challenge that drug and device development to treat localized prostate cancer has been limited by the large trial sizes and lengthy timelines required to demonstrate an improvement in overall or metastasis-free survival and by the lack of agreed on alternative end points. Additionally, evolving treatment paradigms in the management of localized prostate cancer include the widespread use of active surveillance of patients with low and some intermediate risk prostate cancer, and the availability of advances in imaging and genomics. RESULTS: The workshop addressed issues related to trial design in this setting. Attendees discussed several potential novel end points such as a delay of morbidity due to radiation or prostatectomy and pathological end points such as Gleason Grade Group upgrade. CONCLUSIONS: The workshop provided an open forum for multiple stakeholder engagement to advance the development of effective treatment options for men with localized prostate cancer.


Assuntos
Ensaios Clínicos como Assunto , Neoplasias da Próstata/terapia , Projetos de Pesquisa , United States Food and Drug Administration , Diagnóstico por Imagem , Educação , Determinação de Ponto Final , Genômica , Humanos , Masculino , Vigilância da População , Estados Unidos , Conduta Expectante
6.
BMC Bioinformatics ; 20(Suppl 24): 596, 2019 Dec 22.
Artigo em Inglês | MEDLINE | ID: mdl-31861975

RESUMO

BACKGROUND: Adenosine-to-inosine RNA editing can markedly diversify the transcriptome, leading to a variety of critical molecular and biological processes in mammals. Over the past several years, researchers have developed several new pipelines and software packages to identify RNA editing sites with a focus on downstream statistical analysis and functional interpretation. RESULTS: Here, we developed a user-friendly public webserver named MIRIA that integrates statistics and visualization techniques to facilitate the comprehensive analysis of RNA editing sites data identified by the pipelines and software packages. MIRIA is unique in that provides several analytical functions, including RNA editing type statistics, genomic feature annotations, editing level statistics, genome-wide distribution of RNA editing sites, tissue-specific analysis and conservation analysis. We collected high-throughput RNA sequencing (RNA-seq) data from eight tissues across seven species as the experimental data for MIRIA and constructed an example result page. CONCLUSION: MIRIA provides both visualization and analysis of mammal RNA editing data for experimental biologists who are interested in revealing the functions of RNA editing sites. MIRIA is freely available at https://mammal.deepomics.org.


Assuntos
Mamíferos , Edição de RNA , Análise de Sequência de RNA , Transcriptoma , Animais , Genoma , Genômica , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Mamíferos/genética , RNA/genética , Análise de Sequência de RNA/métodos
7.
Zhongguo Zhong Yao Za Zhi ; 44(19): 4234-4240, 2019 Oct.
Artigo em Chinês | MEDLINE | ID: mdl-31872704

RESUMO

The aim of this paper was to screen out relevant genes of geniposide-induced hepatotoxicity based on genomics,in order to provide a scientific basis for the non-clinical evaluation of drugs containing Gardeniae Fructus and geniposide. Fifty-five SD rats were randomly divided into normal control group,24 h group and 72 h group. The changes of appearance,behavior and weight of rats were observed after administration by gavage for 3 days. The activities of ALT and AST were detected. Molecular mechanism of geniposideinduced hepatotoxicity was investigated by Affymetrix miRNA 4. 0 and Affymetrix Rat Gene 2. 0 to examine the gene expression levels in Sprague-Dawley rat livers at 24 h and 72 h after administration of overdose-geniposide( 300 mg·kg-1 daily),and then verified by Realtime quantitative PCR. Compared with the normal control group,the activities of ALT and AST were markedly increased. In addition,experimental results indicated that 324 genes were differentially expressed,among which 259 were up-regulated and 65 down-regulated.Nine candidate genes were verified by qRT-PCR,including Bcl2,Il1 b,Tpm3,MMP2,Col1α1,Ifit1,Aldob,Nr0 b2,Cyp2 c23. And Bcl2,Col1α1,Aldob,Nr0 b2 and Cyp2 c23 were found to be correlated with geniposide-induced hepatotoxicity. This study provides an important clue for mechanism of geniposide-induced hepatotoxicity.


Assuntos
Doença Hepática Induzida por Substâncias e Drogas , Iridoides/toxicidade , Animais , Biomarcadores/metabolismo , Genômica , Fígado/metabolismo , Ratos , Ratos Sprague-Dawley
8.
J Surg Oncol ; 120(8): 1427-1435, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31729037

RESUMO

BACKGROUND AND OBJECTIVES: Mucinous adenocarcinoma is a distinct subtype of colorectal cancer (CRC) with a worse prognosis when compared with non-mucinous adenocarcinoma. The aim of this study was to compare somatic mutations and copy number alteration (CNA) between mucinous and non-mucinous CRC. METHODS: Data from The Cancer Genome Atlas-colon adenocarcinoma and rectum adenocarcinoma projects were utilized. Mucinous and non-mucinous CRC were compared with regard to microsatellite status, overall mutation rate, the most frequently mutated genes, mutations in genes coding for mismatch repair (MMR) proteins and genes coding for mucin glycoproteins. CNA analysis and pathway analysis was undertaken. RESULTS: Mucinous CRC was more likely to be microsatellite instability-high (MSI-H) and hypermutated. When corrected for microsatellite status the single-nucleotide variation and insertion-deletion rate was similar between the two cohorts. Mucinous adenocarcinoma was more likely to have mutations in genes coding for MMR proteins and mucin glycoproteins. Pathway analysis revealed further differences between the two histological subtypes in the cell cycle, RTK-RAS, transforming growth factor-ß, and TP53 pathways. CONCLUSIONS: Mucinous CRC has some distinct genomic aberrations when compared with non-mucinous adenocarcinoma, many of which are driven by the increased frequency of MSI-H tumors. These genomic aberrations may play an important part in the difference seen in response to treatment and prognosis in mucinous adenocarcinoma.


Assuntos
Adenocarcinoma Mucinoso/genética , Adenocarcinoma/genética , Neoplasias do Colo/genética , Genômica , Neoplasias Retais/genética , Adenocarcinoma/patologia , Adenocarcinoma Mucinoso/patologia , Estudos de Coortes , Neoplasias do Colo/patologia , Variações do Número de Cópias de DNA , Proteínas de Ligação a DNA/genética , Conjuntos de Dados como Assunto , Regulação Neoplásica da Expressão Gênica , Humanos , Mutação INDEL , Instabilidade de Microssatélites , Mucinas/genética , Mutação , Polimorfismo de Nucleotídeo Único , Proteínas Proto-Oncogênicas B-raf/genética , Proteínas Proto-Oncogênicas p21(ras)/genética , Neoplasias Retais/patologia , Proteína Smad4/genética , Fator de Crescimento Transformador beta/genética , Proteína Supressora de Tumor p53/genética
9.
Zootaxa ; 4642(1): zootaxa.4642.1.1, 2019 Jul 22.
Artigo em Inglês | MEDLINE | ID: mdl-31712451

RESUMO

Phylogenetic relationships of snailfishes of the family Liparidae were analyzed on the basis of two sets of molecular sequence data: one from the mitochondrial DNA cytochrome c oxidase subunit one gene (COI) and another from restriction-site associated genome-wide sequences (RADseq). The analysis of COI sequence data from at least 122 species of 18 genera from the Pacific, Atlantic, and Southern oceans resulted in a moderately well-resolved phylogeny among the major clades, albeit with significant polytomy among central clades. Nectoliparis was the sister of all other members of the family, followed by Liparis. Liparis, Careproctus, and Paraliparis were paraphyletic. Liparis was recovered in two closely related clades, with L. fucensis sister of all other liparids except Nectoliparis, and both Careproctus and Paraliparis were each recovered among at least three widely separated clades. The RADseq analysis of 26 species of 11 genera from the eastern North Pacific strongly confirmed the overall results of the COI analysis, with the exception of the paraphyly of Liparis due to the absence of L. fucensis. Our results show that the pelvic disc has been independently lost multiple times and the pectoral-fin girdle has been independently reduced in multiple lineages.


Assuntos
DNA Mitocondrial , Genômica , Perciformes , Animais , Sequência de Bases , Perciformes/genética , Filogenia , Análise de Sequência de DNA
10.
Zootaxa ; 4585(1): zootaxa.4585.1.7, 2019 Apr 11.
Artigo em Inglês | MEDLINE | ID: mdl-31716185

RESUMO

Systematic relationships within the Cirrhitoidei, a suborder of five closely related families, have been uncertain for over a century. This is particularly true in reference to the families Cheilodactylidae and Latridae, which have been revised numerous times over the past several decades. Species that have been included in these two families are found in temperate regions around the world, which has led to regionally-focused studies that have only exacerbated taxonomic confusion. Here we examine systematic relationships within the Cheilodactylidae and the Latridae using ultraconserved genomic elements with near complete taxonomic sampling, and place our results in the context of the Cirrhitoidei. Our results agree with previous findings suggesting that Cheilodactylidae is restricted to two South African species, with the type species of the family, Cheilodactylus fasciatus Lacépède, forming a clade with C. pixi Smith that together is more closely related to the Chironemidae than to other species historically associated with the genus. We also strongly resolve the relationships of species within the Latridae. As a result of our analyses we revise the taxonomy of Latridae, name a new genus, and re-elevate Chirodactylus and Morwong.


Assuntos
Peixes , Genômica , Animais , Filogenia
11.
Zootaxa ; 4668(4): zootaxa.4668.4.2, 2019 Sep 12.
Artigo em Inglês | MEDLINE | ID: mdl-31716605

RESUMO

We obtained and phylogenetically analyzed whole genome shotgun sequences of nearly all species from the tribe Emesidini Seraphim, Freitas Kaminski, 2018 (Riodinidae) and representatives from other Riodinidae tribes. We see that the recently proposed genera Neoapodemia Trujano, 2018 and Plesioarida Trujano García, 2018 are closely allied with Apodemia C. R. Felder, [1865] and are better viewed as its subgenera, new status. Overall, Emesis Fabricius, 1807 and Apodemia (even after inclusion of the two subgenera) are so phylogenetically close that several species have been previously swapped between these two genera. New combinations are: Apodemia (Neoapodemia) zela (Butler, 1870), Apodemia (Neoapodemia) ares (Edwards, 1882), and Apodemia (Neoapodemia) arnacis (Stichel, 1928) (not Emesis); and Emesis phyciodoides (Barnes Benjamin, 1924) (not Apodemia), assigned to each genus by their monophyly in genomic trees with the type species (TS) of the genus. Surprisingly, we find that Emesis emesia Hewitson, 1867 is not grouped with Emesis, but in addition to Apodemia forms a third lineage of similar rank, here named Curvie Grishin, gen. n. (TS: Symmachia emesia Hewitson, 1867). Furthermore, we partition Emesis into 6 subgenera (4 new): Emesis (TS: Hesperia ovidius Fabricius, 1793, a subjective junior synonym of Papilio cereus Linnaeus, 1767), Aphacitis Hübner, [1819] (TS: Papilio dyndima Cramer, [1780], a subjective junior synonym of Papilio lucinda Cramer, [1775]), Poeasia Grishin, subgen. n. (TS: Emesis poeas Godman, [1901]), Mandania Grishin, subgen. n. (TS: Papilio mandana Cramer, [1780]), Brimia Grishin, subgen. n. (TS: Emesis brimo Godman Salvin, 1889), and Tenedia Grishin, subgen. n. (TS: Emesis tenedia C. R. Felder, 1861). Next, genomic comparison of primary type specimens suggests new status for Emesis vimena Schaus, 1928 as a subspecies of Emesis brimo Godman Salvin, 1889, Emesis adelpha Le Cerf, 1958 with E. a. vicaria Le Cerf, 1958 are subspecies of Emesis heteroclita Stichel, 1929, and Emesis tristis Stichel, 1929 is not a synonym of E. brimo vimena but of Emesis lupina Godman Salvin, 1886. A new status of a species is given to the following taxa: Emesis furor A. Butler H. Druce, 1872 (not a subspecies of E. mandana (Cramer, 1780)), Emesis melancholica Stichel, 1916 (not a subspecies of E. lupina Godman Salvin, 1886), Emesis progne (Godman, 1903) (not a subspecies of E. brimo Godman Salvin, 1889), and Emesis opaca Stichel, 1910 (not a synonym of E. lucinda (Cramer, 1775)). Emesis castigata diringeri Gallard 2008 is a subjective junior synonym of E. opaca, new status. Finally, Xanthosa Grishin, gen. n. (TS: Charmona xanthosa Stichel, 1910) is proposed for a sister lineage of Sertania Callaghan Kaminski, 2017 and Befrostia Grishin, gen. n. (TS: Emesis elegia Stichel, 1929) is proposed for a clade without apparent phylogenetic affinities that we place in Befrostiini Grishin, trib. n. In conclusion, genomic data reveal a number of errors in the current classification of Emesidini and allow us to confidently reclassify the tribe partitioning it in three genera: Apodemia, Curvie gen. n. and Emesis.


Assuntos
Borboletas , Anêmonas-do-Mar , Distribuição Animal , Animais , Genômica , Filogenia
12.
Zootaxa ; 4609(3): zootaxa.4609.3.2, 2019 May 24.
Artigo em Inglês | MEDLINE | ID: mdl-31717092

RESUMO

Woodland salamanders of the genus Plethodon are characterized by strong ecological and morphological conservatism. One assemblage, the Wehrle's salamander (Plethodon wehrlei Fowler Dunn) species group, is distributed from New York to Tennessee, USA, and includes several morphological variants, four of which are sufficiently distinct to have been recognized as species in the past. For many years after two of these species were placed in synonymy, only P. wehrlei and P. punctatus Highton were recognized. A recent phylogeographic study using mitochondrial DNA and nuclear DNA uncovered considerable genetic diversity within the group and conservatively resurrected one of the previously synonymized forms (P. dixi Pope Fowler). However, their analysis could not resolve all relationships among remaining populations of P. wehrlei, leaving the taxon paraphyletic. We re-evaluated the evolutionary history of this group using genomic data, recovered strong support for at least five distinct clades, and corroborated previously reported relationships. We also collected morphological data and demonstrated morphological distinctiveness for four of the five clades that we herein recognize as species. We resurrect the synonymized name P. jacksoni Newman to represent the southern clades of P. wehrlei in southwestern Virginia and North Carolina exclusive of P. dixi. In addition, we describe a yellow-spotted form of P. wehrlei endemic to the Cumberland Plateau as a new species. Although our proposed changes rectify the paraphyly of P. wehrlei, our sampling was not sufficient to resolve potential taxonomic issues remaining within the species herein recognized as P. jacksoni.


Assuntos
DNA Mitocondrial , Urodelos , Animais , Genômica , New York , North Carolina , Filogenia , Análise de Sequência de DNA , Tennessee , Virginia
14.
N Engl J Med ; 381(19): 1884, 2019 11 07.
Artigo em Inglês | MEDLINE | ID: mdl-31693825
15.
J Urol ; 202(4): 708, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31766091
16.
J Urol ; 202(4): 708-709, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31766092
17.
Sheng Wu Gong Cheng Xue Bao ; 35(10): 1889-1900, 2019 Oct 25.
Artigo em Chinês | MEDLINE | ID: mdl-31668036

RESUMO

Novel natural products have always been the most important sources for discovery of new drugs. Since the end of the 20th century, advances in genomics technology have contributed to decode and analyze numerous genomes, revealing remarkable potential for production of new natural products in organisms. However, this potential is hampered by laboratory culture conditions. Therefore, the integration of all these new advances is necessary to unveil these treasures, addressing the rise in resistance to antibiotics. In this review, we discuss the strategies of genome mining, inducing the expression of silent biosynthetic gene clusters and construction of biological chassis.


Assuntos
Produtos Biológicos/metabolismo , Vias Biossintéticas/genética , Genômica , Animais , Genoma/genética , Família Multigênica/genética
18.
Sheng Wu Gong Cheng Xue Bao ; 35(10): 1955-1973, 2019 Oct 25.
Artigo em Chinês | MEDLINE | ID: mdl-31668041

RESUMO

In industrial biotechnology, microbial cell factories utilize renewable resources to produce energy, materials and chemicals. Industrial biotechnology plays an increasingly important role in solving the resource, energy and environmental problems. Systems biology has shed new light on industrial biotechnology, deepening our understanding of industrial microbial cell factories and their bioprocess from "Black-box" to "White-box". Systems-wide profiling of genome, transcriptome, proteome, metabolome, and fluxome has proven valuable to better unveil network operation and regulation on the genome scale. System biology has been successfully applied to create microbial cell factories for numerous products and derive attractive industrial processes, which has constantly expedited the development of industrial biotechnology. This review focused on the recent advance and applications of omics and trans-omics in industrial biotechnology, including genomics, transcriptomics, proteomics, metabolomics, fluxomics and genome scale modeling, and so on. Furthermore, this review also discussed the potential and promise of systems biology in industrial biotechnology.


Assuntos
Biotecnologia , Microbiologia Industrial , Biologia de Sistemas , Genômica , Engenharia Metabólica , Metabolômica
19.
Science ; 366(6465): 570-571, 2019 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-31672881
20.
Zhonghua Yu Fang Yi Xue Za Zhi ; 53(11): 1176-1182, 2019 Nov 06.
Artigo em Chinês | MEDLINE | ID: mdl-31683410

RESUMO

Abnormal genomic DNA methylation is an important epigenetic change in malignant tumors. Esophageal squamous cell cancer is one of common malignant tumors in our country. In this paper summarized and discussed the progress of genomic DNA methylation in the esophageal squamouscell cancer, including the level of genomic DNA methylation, frequent abnormally methylated genes, methylation markers and potential targets, etc. This paper might provide candidate biomarkers and targets for further studies on the mechanism of the tumorigenesis and development of the esophagealsquamouscell cancer, as well as for the clinical application of esophageal cancer.


Assuntos
Metilação de DNA , Neoplasias Esofágicas/genética , Neoplasias Esofágicas/patologia , Carcinoma de Células Escamosas do Esôfago/genética , Carcinoma de Células Escamosas do Esôfago/patologia , Biomarcadores Tumorais , Epigênese Genética , Genômica , Humanos , Regiões Promotoras Genéticas
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