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1.
Arch. latinoam. nutr ; 71(2): 138-148, jun. 2021. tab, graf
Article in English | LILACS, LIVECS | ID: biblio-1290912

ABSTRACT

Reflex-ontogeny and intestinal morphometrics were evaluated in Wistar rats whose mothers were fed on a high-fat diet during the perinatal period. Male pups (n=52) formed four experimental groups: NN (pups from mothers with lab chow diet during gestation and lactation); NH (pups from mothers with lab chow diet during pregnancy and high-fat in lactation); HH (pups from mothers with high-fat diet during gestation and lactation); HN (pups from mothers with high-fat diet during pregnancy and lab chow in lactation). The reflex ontogeny, the maturation of physical characteristics and parameters of somatic growth were evaluated during lactation. In addition, the body mass index (BMI), the specific rate of weight gain (SRWG), the Lee index, the weight of the brain and intestinal parameters were analyzed after weaning. High-fat diet during pregnancy (HH and HN groups) delayed the maturation of reflexes and physical characteristics. The high-fat diet affected somatic growth differently, reducing somatic growth parameters in the groups NH and HH and increasing in the HN group. The highest SRWG was found in group HN. SRWG and BMI were reduced in the groups NH and HH. The relative intestinal weight was reduced in the groups NH, HH and HN. The relative length of small intestine was longer in group HN than in group NN. The total height of the mucosa and size of the villous were lower in group HH than in group NN. In conclusion, high-fat diet promoted negative consequences for the development of the nervous and enteric systems of the offspring(AU)


Ontogenia refleja y morfometría intestinal fueron evaluados en crías de ratas Wistar que fueron alimentadas con una dieta alta en grasas durante el período perinatal. Los descendientes machos (n = 52) formaron cuatro grupos experimentales: NN (hijos de madres que utilizaron alimentos de laboratorio durante la gestación y la lactancia); NH (hijos de madres que comieron dieta de laboratorio durante el embarazo y dieta con un alto contenido de grasas en la lactancia); HH (hijos de madres con una dieta alta en grasas durante el embarazo y la lactancia); HN (hijos de madres que comieron una dieta alta en grasas durante el embarazo y comida de laboratorio durante la lactancia). La ontogenia refleja, la maduración de las características físicas y los parámetros de crecimiento somático durante la lactancia fueron evaluados. Además, el índice de masa corporal (IMC), la tasa específica de aumento de peso (SRWG), el índice de Lee, el peso cerebral y los parámetros intestinales fueron analizados después del destete. La dieta alta en grasas durante el embarazo (grupos HH y HN) retrasó la maduración de reflejos y características físicas. La dieta alta en grasas afectó el crecimiento somático de manera diferente, reduciendo los parámetros de crecimiento somático en los grupos NH y HH y aumentando en el grupo HN. El SRWG más grande se encontró en el grupo HN. El SRWG y el IMC se redujeron en los grupos NH y HH. El peso relativo intestinal se redujo en los grupos NH, HH y HN. La longitud relativa del intestino delgado fue mayor en el grupo HN que en el grupo NN. La altura total de la mucosa y el tamaño de las vellosidades fueron menores en el grupo HH que en el grupo NN. En conclusión, la dieta alta en grasas tuvo consecuencias negativas para el desarrollo de los sistemas nervioso y entérico de la prole(AU)


Subject(s)
Rats , Breast Feeding , Dietary Fats , Gene Ontology , Dietary Sugars , Chronic Disease , Obesity
2.
Electron. j. biotechnol ; 51: 8-16, May. 2021. tab, graf, ilus
Article in English | LILACS | ID: biblio-1343314

ABSTRACT

BACKGROUND: Myogenic regulatory factors (MRFs) such as MyoD, Myf6 and Myf5 play a vital role in the growth and development of muscles. Jeju Native Pig (JNP) is the top ranker in Korea amongst the indigenous livestock reared for meat purpose. Few studies covering transcript abundance of the MRFs and related to their co-expression with Pax7 in JNP have been conducted. Despite having better quality pork, JNP does not have a comparative growth rate with respect to western breeds. Therefore, the present study was designed with the objective to study the relative transcript levels of MRFs in the postnatal myogenesis of longissimus dorsi muscles in JNP and Berkshire breeds. RESULTS: Relative transcript levels were analyzed by qRT-PCR and blot expression analysis through Western blotting. Immunocytochemistry was performed to analyze their expressions at cellular levels. ToppCluster aided in the analysis of gene ontology of biological processes. The quantitative transcript levels of MyoD and Pax7 were significantly (P < 0.05) higher in Berkshire than in JNP. Myotube formation was observed under the co-expression of MyoD and Pax7. ToppCluster helped in the understanding of the linking of biological processes of the MRFs with the different signaling pathways. MyBPH had significantly (P < 0.05) high transcript levels during the chosen age groups in JNP than Berkshire. CONCLUSIONS: The current study can be helpful in understanding the genetic basis for myogenesis in postnatal stage. Moreover, it can act as stepping stone for the identification of marker genes related to body growth and meat quality in JNP.


Subject(s)
Animals , Swine , Myogenic Regulatory Factors/metabolism , Muscle Development/genetics , Immunohistochemistry , Genetic Markers , Blotting, Western , Myogenic Regulatory Factors/genetics , PAX7 Transcription Factor/metabolism , Real-Time Polymerase Chain Reaction , Gene Ontology , Pork Meat
3.
Neotrop. ichthyol ; 19(1): e200106, 2021. tab, graf, mapas, ilus
Article in English | ID: biblio-1154968

ABSTRACT

Two new species from the upper rio Tocantins basin are described in Knodus based on the traditional definition of the genus. The new species are distinguished from other congeners by meristic and morphometric characters, such as the number of cusps in the premaxillary and dentary teeth, the number of scale series between dorsal-fin origin and lateral line, the orbital diameter and the body depth. With the two new species, the number of endemic species in the upper rio Tocantins basin upstream of the mouth of the rio Paranã, rises to 53 (89 to the confluence with rio Araguaia). The existence of a meristic character that changes through ontogeny (allomery), viz. the number of scale series between dorsal-fin origin and lateral line, was detected in some species of Knodus through a regression analysis. Additionally, this paper describes an unambiguous, more informative and precise new method for counting vertebrae, which will enhance the efficacy of this trait in species comparisons.(AU)


Duas novas espécies do alto rio Tocantins são descritas em Knodus com base na definição tradicional do gênero. As novas espécies são distinguidas das demais congêneres por caracteres merísticos e morfométricos, tais como o número de cúspides nos dentes do pré-maxilar e do dentário, o número de séries de escamas entre a origem da nadadeira dorsal e a linha lateral, o diâmetro da órbita e a altura do corpo. Com as duas novas espécies, o número de espécies endêmicas na bacia do alto rio Tocantins, acima da barra do rio Paranã, sobe para 53 (89 até a confluência com o rio Araguaia). A existência de um caráter merístico que muda ao longo da ontogenia (alomeria), ou seja, o número de séries de escamas entre a origem da nadadeira dorsal e a linha lateral, foi detectado em algumas espécies de Knodus com uma análise de regressão. Adicionalmente, este artigo descreve um novo método não-ambíguo, mas informativo e mais preciso, para a contagem de vértebras, que aumentará a eficácia deste caráter em comparações entre espécies.(AU)


Subject(s)
Humans , Characidae , Gene Ontology , Gender Identity
4.
Braz. j. med. biol. res ; 54(11): e11372, 2021. tab, graf
Article in English | LILACS | ID: biblio-1339455

ABSTRACT

Immune-mediated inflammation plays a key role in the pathology of abdominal aortic aneurysm (AAA). We aimed to use a computational approach to profile the immune infiltration patterns and related core genes in AAA samples based on the overexpression of gene signatures. The microarray datasets of AAA and normal abdominal tissues were acquired from gene expression omnibus (GEO) database. We evaluated the composition of immune infiltrates through microenvironment cell populations (MCP)-counter. Weighted gene correlation network analysis (WGCNA) was employed to construct the co-expression network and extract gene information in the most relevant module. Functional and pathway enrichment analysis was performed and immune infiltration related core genes were screened. AAA tissues had a higher level of infiltration by cytotoxic lymphocytes, NK cells, T cells, fibroblasts, myeloid dendritic cells, and neutrophils than normal aorta. The red module was strongly correlated with the infiltrating levels of T cells and cytotoxic lymphocytes. Gene ontology (GO) and pathway analyses revealed that genes in the most relevant module were mainly enriched in T cell activation, regulation of lymphocyte activation, cytokine-cytokine receptor interaction, and chemokine signaling pathway, etc. The expression of GZMK, CCL5, GZMA, CD2, and EOMES showed significant correlations with cytotoxic lymphocytes, while CD247, CD2, CD6, RASGRP1, and CD48 expression were positively associated with T cell infiltration. In conclusion, we comprehensively analyzed profiles of infiltrated immune cells in AAA tissues and their associated marker genes. Our data may provide a novel clue to indicate the underlying molecular mechanisms of AAA formation in terms of immune infiltration.


Subject(s)
Humans , Aortic Aneurysm, Abdominal/genetics , Biomarkers , Gene Expression Profiling , Transcriptome , Gene Ontology
6.
Acta toxicol. argent ; 28(1): 5-12, Apr. 2020. graf
Article in English | LILACS | ID: biblio-1248663

ABSTRACT

Abstract In the 1960s, organochlorine compounds were responsible for the decline of birds of prey populations such as Haliaee- tus leucocephalus and Falco peregrinus. Pesticides similar to DDT cause bioaccumulation in birds, affecting their eggshell com- position and compromising their development. Using system biology tools, the goal of this study was to better comprehend how organochlorines act on birds. We performed a literature review, using the STITCH 5.0 platform, searching for the terms DDT and TCDD. The sub-networks were amplified in 100 interactions in STRING 10.5 and joined by the Cytoscape 3.4.0 Merge software, using the experimental animal model Gallus gallus. Clusterization, gene ontology, and centrality were the parameters evaluated in the resulting network. The resulting network had 1,417 interactions and 137 nodes. The clusterization indicated four clusters and the gene ontology pointed to biological processes related to cell signaling and morphological development. The centrality analysis indicated ESR1 and HSP90AB1 as hub/bottleneck proteins involved in the estrogen pathway and calcium transport. Therefore, it is possible that HSP90 proteins have increased expression in birds contaminated with organochlorine pesticides, favoring ESRI-organochlorines interaction and disturbing the calcium availability related to the eggshell formation. The presence or absence of heat shock proteins, such as HSP90, influences several aspects of reproduction in many species. Therefore, the relationship between the HSP90 protein expression and thin-shell syndrome was identified for the first time in this in silico study.


Resumen En los años 60, los organoclorados fueron responsables del declive de aves de rapiña como Haliaeetus leucocephalus y Falco peregrinus. Pesticidas como el DDT, causan biomagnificación en las aves, afectando las cáscaras de los huevos y dañando su desarrollo. El objetivo de este trabajo fue, a través de herramientas de biología de sistemas, comprender cómo los organoclorados actúan en el organismo de las aves. A través de una revisión bibliográfica se incluyeron dos compuestos, DDT y TCDD. Estos fue ron prospectos en la plataforma STITCH 5.0. Las subredes encontradas fueron aumentadas en 100 interacciones en la plataforma STRING 10.5 y unidas por la herramienta Merge del programa Cytoscape 3.4.0, usando el modelo experimental Gallus gallus. En la red resultante se analizaron la clusterización, la ontología génica y la centralidad. La red resultante presentó 137 nudos y 1.417 interacciones. El análisis de clusterización indicó 4 clusters, siendo que el análisis y ontología génica apuntó procesos biológicos ligados a la señalización y al desarrollo morfológico. El estudio de centralidad apuntó a ESR1 y HSP90AB1 como los hubs-bottle- neck proteínas que estaban involucradas en la vía de recepción de estrógeno y en el transporte de calcio. De acuerdo con los resultados podemos inferir que las proteínas HSP90 tienen su expresión aumentada, en aves contaminadas con pesticidas organoclo rados, favoreciendo la interacción entre ESRI y DDT / TCDD. Con ello, la interacción ESRI y la hormona estrógeno se compromete perjudicando el transporte de calcio y consecuentemente la formación de la cáscara del huevo en aves expuestas. La expresión de proteínas de choque térmico ha sido asociada a varios aspectos de la reproducción en muchas especies, sin embargo, una asociación entre HSP90 y el síndrome de la cáscara fina del huevo fue identificada por primera vez en este experimento in silico.


Subject(s)
Animals , Raptors/abnormalities , Egg Shell/abnormalities , Insecticides, Organochlorine/adverse effects , Computer Simulation , Gene Ontology
7.
Chinese Medical Journal ; (24): 2565-2572, 2020.
Article in English | WPRIM | ID: wpr-877822

ABSTRACT

BACKGROUND@#Recent studies have reported circular RNA (circRNA) expression profiles in various tissue types; however, circRNA expression profile in human epicardial adipose tissue (EAT) remains undefined. This work aimed to compare circRNA expression patterns in EAT between the heart failure (HF) and non-HF groups.@*METHODS@#RNA-sequencing was carried out to compare circRNA expression patterns in EAT specimens from coronary artery disease cases between the HF and non-HF groups. Quantitative real-time polymerase chain reaction was performed for validation. Comparisons of patient characteristics between the two groups were using t test, Mann-Whitney U test, and Chi-squared test.@*RESULTS@#A total of 141 circRNAs substantially different between the HF and non-HF groups (P 2) were detected, including 56 up-regulated and 85 down-regulated. Among them, hsa_circ_0005565 stood out, for it had the highest fold change and was significantly increased in HF patients in quantitative real-time polymerase chain reaction validation. The top highly expressed EAT circRNAs corresponded to genes involved in cell proliferation and inflammatory response, including GSE1, RHOBTB3, HIPK3, UBXN7, PCMTD1, N4BP2L2, CFLAR, EPB41L2, FCHO2, FNDC3B, and SPECC1. The top enriched Gene Ontology term and Kyoto Encyclopedia of Genes and Genomes pathway were positive regulation of metabolic processes and insulin resistance, respectively.@*CONCLUSION@#These data indicate EAT circRNAs may contribute to the pathogenesis of metabolic disorders causing HF.


Subject(s)
Adipose Tissue , Gene Ontology , Heart Failure/genetics , Humans , RNA, Circular , Sequence Analysis, RNA
8.
Braz. j. med. biol. res ; 53(9): 0-0, 2020. tab, graf
Article in English | LILACS, ColecionaSUS | ID: biblio-1132553

ABSTRACT

Myocardial ischemia/reperfusion (MI/R) injury is a complex phenomenon that causes severe damage to the myocardium. However, the potential molecular mechanisms of MI/R injury have not been fully clarified. We identified potential molecular mechanisms and therapeutic targets in MI/R injury through analysis of Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were found between MI/R injury and normal samples, and overlapping DEGs were found between GSE61592 and GSE67308. Gene Ontology (GO) and pathway analysis were performed for overlapping DEGs by Database for Annotation, Visualization and Integration Discovery (DAVID). Then, a network of protein-protein interaction (PPI) was constructed through the Search Tool for the Retrieval of Interacting Genes (STRING) database. Potential microRNAs (miRNAs) and therapeutic small molecules were screened out using microRNA.org database and the Comparative Toxicogenomics database (CTD), respectively. Finally, we identified 21 overlapping DEGs related to MI/R injury. These DEGs were significantly enriched in IL-17 signaling pathway, cytosolic DNA-sensing pathway, chemokine signaling, and cytokine-cytokine receptor interaction pathway. According to the degree in the PPI network, CCL2, LCN2, HP, CCL7, HMOX1, CCL4, and S100A8 were found to be hub genes. Furthermore, we identified potential miRNAs (miR-24-3p, miR-26b-5p, miR-2861, miR-217, miR-4251, and miR-124-3p) and therapeutic small molecules like ozone, troglitazone, rosiglitazone, and n-3 polyunsaturated fatty acids for MI/R injury. These results identified hub genes and potential small molecule drugs, which could contribute to the understanding of molecular mechanisms and treatment for MI/R injury.


Subject(s)
Myocardial Reperfusion Injury , MicroRNAs , Computational Biology , Gene Expression Profiling , Gene Regulatory Networks , Protein Interaction Maps , Gene Ontology
9.
Article in English | WPRIM | ID: wpr-827442

ABSTRACT

OBJECTIVE@#To seek potential Chinese herbal medicine (CHM) for the treatment of coronavirus disease 2019 (COVID-19) through the molecular docking of the medicine with SARS-CoV-2 3CL hydrolytic enzyme and the angiotensin converting enzyme II(ACE2) as receptors, using computer virtual screening technique, so as to provide a basis for combination forecasting.@*METHODS@#The molecular docking of CHM with the SARS-Cov-2 3CL hydrolase and the ACE2 converting enzyme, which were taken as the targets, was achieved by the Autodock Vina software. The CHM monomers acting on 3CLpro and ACE2 receptors were retrieved from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform, the active ingredients were selected, and the key CHMs and compounds were speculated. Based on the perspective of network pharmacology, the chemical-target network was constructed, and the functional enrichment analysis of gene ontology and the pathway enrichment analysis of Kyoto encyclopedia of genes and genomes were carried out by DAVID to speculate about the mechanism of action of the core drug pairs.@*RESULTS@#There are 6 small molecule compounds that have the optimal binding energy with the two target proteins. Among 238 potential anti-COVID-19 herbs screened in total, 16 kinds of CHM containing the most active ingredients, and 5 candidate anti-COVID-19 herbs that had been used in high frequency, as well as a core drug pair, namely, Forsythiae Fructus-Lonicerae Japonicae Flos were selected.@*CONCLUSION@#The core drug pair of Forsythiae Fructus-Lonicerae Japonicae Flos containing multiple components and targets is easy to combine with 3CLpro and ACE2, and exerts an anti-COVID-19 pneumonia effect through multi-component and multi-target, and plays the role of anti-COVID-19 pneumonia in multi-pathway.


Subject(s)
Betacoronavirus , Metabolism , Computer Simulation , Coronavirus Infections , Drug Therapy , Drugs, Chinese Herbal , Therapeutic Uses , Gene Ontology , Humans , Molecular Docking Simulation , Pandemics , Peptidyl-Dipeptidase A , Metabolism , Pneumonia, Viral , Drug Therapy , Thermodynamics
10.
Article in English | WPRIM | ID: wpr-811113

ABSTRACT

BACKGROUND: Platelet-rich plasma (PRP) is a plasma component of autologous blood containing a high concentration of platelets. PRP is used to promote healing of damaged tissues. However, there are not many studies on the composition and expression patterns of active proteins in PRP. The purpose of this study was to identify unknown factors that contribute to tissue healing by proteomic analysis of proteins in PRP.METHODS: Three men in their 30s with no basal disease participated in this study. All identified proteins were classified for tissue healing-related functions on the basis of the gene ontology analysis of adhesion molecule with Ig-like domain 2 (AmiGO2). PRP was prepared by using the ACP kit and GPS III kit.RESULTS: We identified a total of 125 proteins related to wound healing, along with three proteins for angiogenesis involved in wound healing, two proteins for fibroblast migration, four proteins for collagen biosynthesis process, two proteins for glycosaminoglycan biosynthesis process, and 13 proteins for glycosaminoglycan binding. So, in addition to the growth factors that have been already known to be involved in tissue healing, 25 new proteins were identified.CONCLUSIONS: We identified the unknown proteins associated with tissue healing in PRP. Our findings may serve as a foundation for the establishment of basic medical evidence for PRP applications.


Subject(s)
Classification , Collagen , Fibroblasts , Gene Ontology , Humans , Intercellular Signaling Peptides and Proteins , Male , Plasma , Platelet-Rich Plasma , Proteome , Wound Healing
11.
Neotrop. ichthyol ; 17(2): e180131, 2019. tab, graf
Article in English | ID: biblio-1012712

ABSTRACT

Previous study suggested that the southern stingray (Hypanus americanus) displays a marked ontogenetic shift in its habitat use in the Fernando de Noronha Archipelago (FNA), an attractive touristic spot in Brazil, that could be associated with changes in its feeding habits and foraging strategies. Here, we conducted underwater visual surveys (~100 h a 3 years' study) at this site to describe the foraging behavior of the same species in details and to assess diel patterns in activity. We observed that H. americanus is capable of several complex and highly plastic behaviors (we described more than 21 of them) while foraging. The foraging events' timing appears to be related to the size (as well as sex) of the stingrays, environment and depth. In addition, our results support a segregation of habitat mediated by the size and sex of the stingrays, but it is able to modulate its foraging repertoire based mainly on environmental stimulus. Finally, we found that H. americanus forage intermittently throughout the day and tidal cycle, yet are less active during non-crepuscular periods and at flood and ebb tides. These results, coupled with the fact that the species uses both reef and beach environments, should be considered by decision makers in management plans.(AU)


Um estudo anterior sugeriu que a raia-prego (Hypanus americanus) apresenta uma marcante mudança ontogenética no seu uso de hábitat no Arquipélago de Fernando de Noronha (FNA), local turístico atraente no Brasil, que pode ser associado a mudanças em seus hábitos alimentares e estratégias de forrageamento. Aqui, nós conduzimos amostragens visuais subaquáticas (~100 h em 3 anos de estudo) nesse local para descrever o comportamento de forrageamento dessa mesma espécie em detalhes e acessar seu padrão de atividade diário. Nós observamos que H. americanus tem capacidade para comportamentos complexos e altamente plásticos (nós descrevemos mais de 21 deles) enquanto forrageia. O tempo dos eventos de forrageamento parece estar relacionado com o tamanho (e também sexo) das raias, ambiente e profundidade. Além disso, nossos resultados apoiam a ideia de uma segregação de hábitat mediada pelo tamanho e sexo das arraias, mas que ela é capaz de modular seu repertório de forrageio baseado principalmente em estímulos ambientais. Finalmente, nós descobrimos que H. americanus forrageia de forma intermitente ao longo do dia e ciclos de marés, mas é menos ativa durante os períodos não-crepusculares e nas enchentes e vazantes das marés. Esses resultados, somado ao fato que a espécie utiliza tanto ambientes recifais quanto praianos, devem ser considerados pelos tomadores de decisão em planos de manejo.(AU)


Subject(s)
Animals , Skates, Fish/genetics , Feeding Behavior , Gene Ontology
12.
Article in Chinese | WPRIM | ID: wpr-781661

ABSTRACT

To explore the molecular mechanism underlying gastric carcinogenesis and progression by using gene expression profiling array together with bioinformatics. Lentivirus short hairpin RNA targeting STIL(ShSTIL)and scrambled sequence RNA(ShCon)were transduced into the gastric cancer cell line SGC-7901.RNA extraction,complementary DNA synthesis,construction of biotin-labelled amplified RNA probes,and hybridization with gene expression profile were consecutively performed.We collected corresponding data and analyzed differentially expressing genes(DEGs),followed by the analysis of gene ontology(GO)and Kyoto encyclopedia of genes and genomes(KEGG)enrichment,transcription factor regulating network,and protein-protein interacting networks. Compared with ShCon,a total of 417 and 87 genes were respectively down-regulated and up-regulated,respectively,in the ShSTIL group(1 or <-1).GO and KEGG enrichment analysis indicated that genes regulated by STIL were localized in cytoplasm,extracellular exosome,Golgi apparatus and various biomembranes,and were implicated in the ubiquitin-mediated proteolysis,P53 signaling pathway,and pathways regulating pluripotency of stem cells.Evaluation on genes enriched in KEGG pathways,regulation of transcription factors,and protein-protein interacting network demonstrated that IGF1R,STUB1,SKP2,and FOXO1 were localized at the centre of the network and played a key role in the development and progression of gastric cancer. Through the protein-protein interactions,STIL may activate E3 ubiquitin ligase STUB1 or SKP2,promote the proteolysis of FOXO1-a transcription factor,regulate the expression of IGF1R,and thus promote gastric carcinogenesis and progression.


Subject(s)
Computational Biology , Gene Expression Profiling , Gene Ontology , Humans , Stomach Neoplasms , Genetics , Transcriptome
13.
Article in Chinese | WPRIM | ID: wpr-776810

ABSTRACT

OBJECTIVE@#To explore the characteristics of differentially methylated genes and gene ontology associated with neural tube defects (NTDs).@*METHODS@#Twelve subjects from 3 NTDs pedigrees were enrolled. Patients with NTDs have served as the case group, while their family members with normal phenotypes have served as the control group. Genomic DNA was extracted from peripheral venous blood samples of the families and used for DNA methylation analysis. Pairwise comparison was carried out primarily for patient-offspring pairs, and co-segregation of methylation pattern with NTDs was analyzed. Pathway related to differentially methylated genes was predicted with DAVID software.@*RESULTS@#Pairwise comparison indicated that VTRNA2-1 was the only gene in which all CpG sites were methylated. Co-segregation of VTRNA2-1 gene methylation with NTDs was found in all pedigrees. Pathways of hypermethylated genes included plasma membrane component, regulation of cellular protein metabolic process, and regulation of actin cytoskeleton organization, while the pathways of hypomethylated genes have included transcription regulator activity, cell adhesion, and neuronal differentiation.@*CONCLUSION@#Methylation of the VTRNA2-1 gene has co-segregated with NTDs in the studied pedigrees. The pathways of differentially methylated genes has involved with mechanism of neural tube development.


Subject(s)
CpG Islands , DNA Methylation , Gene Ontology , Humans , MicroRNAs , Genetics , Neural Tube Defects , Genetics , Pedigree
14.
Article in English | WPRIM | ID: wpr-759594

ABSTRACT

BACKGROUND: Cord blood (CB) is a reliable source of hematopoietic stem cells, and its utilization in stem cell transplantation is increasing continuously. The CD34+ cell count is arguably one of the most important parameters for evaluating the quality of a cord blood unit (CBU), but there is little evidence on the post-genetic modifications that can affect the CD34+ cell counts. In this study, the difference in the miRNA expression profiles between low and high CD34+ CBU was evaluated. METHODS: Paired CB and maternal samples with low (0.9%) were selected for analysis. MicroRNA profiling was performed, and differentially expressed miRNA were identified. In addition, gene ontology analysis was conducted on the miRNA to elucidate the genes that could potentially affect the CD34+ cell count. RESULTS: Ten miRNA were identified to show significantly different expression between the low and high CD34+ groups. Four of the 10 miRNA were hematopoiesis-related (miR-199a-5p, miR-22-5p, miR-140-5p, and miR-181b-5p). From a total of 119 associated genes, nine (CALCA, FARP2, FSHR, ITGAM, MELK, MLF1, PRG4, TREM2 and VCAM1) were associated with two or more of the aforementioned miRNA. CONCLUSION: This is the first study that examined the difference in the miRNA expression profiles between high and low CD34+ CB cells and revealed the relevant genes associated with hematopoiesis. These results provide basic insight into the genetic processes involving hematopoietic stem cell proliferation.


Subject(s)
Cell Count , Fetal Blood , Gene Ontology , Genetic Phenomena , Hematopoiesis , Hematopoietic Stem Cells , MicroRNAs , Stem Cell Transplantation , Stem Cells
15.
Article in English | WPRIM | ID: wpr-763014

ABSTRACT

Melanoma cells have been shown to respond to BRAF inhibitors; however, intrinsic and acquired resistance limits their clinical application. In this study, we performed RNA-Seq analysis with BRAF inhibitor-sensitive (A375P) and


Subject(s)
Antigen Presentation , Biological Phenomena , Cell Adhesion , Cell Line , Cell Movement , Classification , Collagen , Drug Resistance , Extracellular Matrix , Gene Expression , Gene Ontology , Melanoma , Osteoblasts , Proto-Oncogene Proteins c-akt
16.
Article in English | WPRIM | ID: wpr-762153

ABSTRACT

PURPOSE: Chronic rhinosinusitis (CRS) is a complex immunological condition, and novel experimental modalities are required to explore various clinical and pathophysiological endotypes; mere evaluation of nasal polyp (NP) status is inadequate. Therefore, we collected patient nasal secretions on filter paper and characterized the proteomes. METHODS: We performed liquid chromatography-mass spectrometry (MS)/MS in the data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes. Nasal secretions were collected from 10 controls, 10 CRS without NPs (CRSsNP) and 10 CRS with NPs (CRSwNP). We performed Orbitrap MS-based proteomic analysis in the DDA (5 controls, 5 CRSsNP and 5 CRSwNP) and the DIA (5 controls, 5 CRSsNP and 5 CRSwNP) modes, followed by a statistical analysis and a hierarchical clustering to identify differentially expressed proteins in the 3 groups. RESULTS: We identified 2,020 proteins in nasal secretions. Canonical pathway analysis and gene ontology (GO) evaluation revealed that interleukin (IL)-7, IL-9, IL-17A and IL-22 signaling and neutrophil-mediated immune responses like neutrophil degranulation and activation were significantly increased in CRSwNP compared to control. The GO terms related to the iron ion metabolism that may be associated with CRS and NP development. CONCLUSIONS: Collection of nasal secretions on the filter paper is a practical and non-invasive method for in-depth study of nasal proteomics. Our proteomic signatures also support that Asian NPs could be characterized as non-eosinophilic inflammation features. Therefore, the proteomic profiling of nasal secretions from CRS patients may enhance our understanding of CRS endotypes.


Subject(s)
Asian Continental Ancestry Group , Gene Ontology , Humans , Inflammation , Interleukin-17 , Interleukin-9 , Interleukins , Iron , Metabolism , Methods , Nasal Polyps , Neutrophils , Proteome , Proteomics , Sinusitis , Spectrum Analysis
17.
Article in English | WPRIM | ID: wpr-761799

ABSTRACT

Although atopic dermatitis (AD) is known to be a representative skin disorder, it also affects the systemic immune response. In a recent study, myoblasts were shown to be involved in the immune regulation, but the roles of muscle cells in AD are poorly understood. We aimed to identify the relationship between mitochondria and atopy by genome-wide analysis of skeletal muscles in mice. We induced AD-like symptoms using house dust mite (HDM) extract in NC/Nga mice. The transcriptional profiles of the untreated group and HDM-induced AD-like group were analyzed and compared using microarray, differentially expressed gene and functional pathway analyses, and protein interaction network construction. Our microarray analysis demonstrated that immune response-, calcium handling-, and mitochondrial metabolism-related genes were differentially expressed. In the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology pathway analyses, immune response pathways involved in cytokine interaction, nuclear factor-kappa B, and T-cell receptor signaling, calcium handling pathways, and mitochondria metabolism pathways involved in the citrate cycle were significantly upregulated. In protein interaction network analysis, chemokine family-, muscle contraction process-, and immune response-related genes were identified as hub genes with many interactions. In addition, mitochondrial pathways involved in calcium signaling, cardiac muscle contraction, tricarboxylic acid cycle, oxidation-reduction process, and calcium-mediated signaling were significantly stimulated in KEGG and Gene Ontology analyses. Our results provide a comprehensive understanding of the genome-wide transcriptional changes of HDM-induced AD-like symptoms and the indicated genes that could be used as AD clinical biomarkers.


Subject(s)
Animals , Biomarkers , Calcium , Calcium Signaling , Citric Acid , Citric Acid Cycle , Cytokines , Dermatitis, Atopic , Gene Ontology , Genome , Metabolism , Mice , Microarray Analysis , Mitochondria , Muscle Cells , Muscle Contraction , Muscle, Skeletal , Myoblasts , Myocardium , Oxidation-Reduction , Protein Interaction Maps , Pyroglyphidae , Receptors, Antigen, T-Cell , Skin
18.
Article in English | WPRIM | ID: wpr-761777

ABSTRACT

Cystic echinococcosis (CE), a zoonotic disease caused by Echinococcus granulosus at the larval stage, predominantly develops in the liver and lungs of intermediate hosts and eventually results in organ malfunction or even death. The interaction between E. granulosus and human body is incompletely understood. Exosomes are nanosized particles ubiquitously present in human body fluids. Exosomes carry biomolecules that facilitate communication between cells. To the best of our knowledge, the role of exosomes in patients with CE is not reported. Here, we isolated exosomes from the sera of patients with CE (CE-exo) and healthy donors and subjected them to liquid chromatography-tandem mass spectrometry analysis. Proteomic analysis identified 49 proteins specifically expressed in CE-exo, including 4 proteins of parasitic origin. The most valuable parasitic proteins included tubulin alpha-1C chain and histone H4. And 8 proteins were differentially regulated in CE-exo (fold change>1.5), as analyzed with bioinformatic methods such as annotation and functional enrichment analyses. These findings may improve our understanding about the interaction between E. granulosus and human body, and may contribute to the diagnosis and prevention of CE.


Subject(s)
Computational Biology , Diagnosis , Echinococcosis , Echinococcus granulosus , Echinococcus , Exosomes , Gene Ontology , Histones , Human Body , Humans , Liver , Lung , Mass Spectrometry , Tissue Donors , Tubulin , Zoonoses
19.
Journal of Breast Cancer ; : 219-236, 2019.
Article in English | WPRIM | ID: wpr-764267

ABSTRACT

PURPOSE: Breast cancer is the most frequently diagnosed malignancy in women worldwide. MicroRNAs (miRNAs) are thought to serve as potential biomarkers in various cancers, including breast cancer. METHODS: We evaluated the miRNA expression profiles in 1,083 breast cancer samples and 104 normal breast tissues from The Cancer Genome Atlas database. We used the edgeR package of R software to analyze the differentially expressed miRNAs in normal and cancer tissues, and screened survival-related miRNAs by Kaplan-Meier analysis. A receiver operating characteristic curve was generated to evaluate the accuracy of these miRNAs as molecular markers for breast cancer diagnosis. Furthermore, the functional role of these miRNAs was verified using cell experiments. Targets of candidate miRNAs were predicted using 9 online databases, and Gene Ontology (GO) functional annotation and pathway analyses were conducted using Database for Annotation, Visualization and Integrated Discovery online tool. RESULTS: A total of 68 miRNAs showed significantly different expression patterns between the groups (p < 0.001), and 13 of these miRNAs were significantly associated with poor survival (p < 0.05). Three miRNAs with high specificity and sensitivity, namely, miR-148b-3p, miR-190b, and miR-429, were selected. In vitro experiments showed that the overexpression of these 3 miRNAs significantly promoted the proliferation and migration of MDA-MB-468 and T47D cells and reduced the apoptosis of T47D cells. GO and pathway enrichment analyses revealed that the targets of these dysregulated miRNAs were involved in many critical cancer-related biological processes and pathways. CONCLUSION: The miR-148b-3p, miR-190b, and miR-429 may serve as potential diagnostic and prognostic markers for breast cancer. This study demonstrated the roles of these 3 miRNAs in the initiation and progression of breast cancer.


Subject(s)
Apoptosis , Biological Phenomena , Biological Phenomena , Biomarkers , Breast Neoplasms , Breast , Diagnosis , Female , Gene Ontology , Genome , Humans , In Vitro Techniques , Kaplan-Meier Estimate , MicroRNAs , ROC Curve , Sensitivity and Specificity
20.
Article in English | WPRIM | ID: wpr-764074

ABSTRACT

BACKGROUND AND OBJECTIVES: There have been contradictory reports on the pro-cancer or anti-cancer effects of mesenchymal stem cells. In this study, we investigated whether conditioned medium (CM) from hypoxic human umbilical cord-derived mesenchymal stem cells (hUC-MSCs) (H-CM) showed enhanced anti-cancer effects compared with CM from normoxic hUC-MSCs (N-CM). METHODS AND RESULTS: Compared with N-CM, H-CM not only strongly reduced cell viability and increased apoptosis of human cervical cancer cells (HeLa cells), but also increased caspase-3/7 activity, decreased mitochondrial membrane potential (MMP), and induced cell cycle arrest. In contrast, cell viability, apoptosis, MMP, and cell cycle of human dermal fibroblast (hDFs) were not significantly changed by either CM whereas caspase-3/7 activity was decreased by H-CM. Protein antibody array showed that activin A, Beta IG-H3, TIMP-2, RET, and IGFBP-3 were upregulated in H-CM compared with N-CM. Intracellular proteins that were upregulated by H-CM in HeLa cells were represented by apoptosis and cell cycle arrest terms of biological processes of Gene Ontology (GO), and by cell cycle of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. In hDFs, negative regulation of apoptosis in biological process of GO and PI3K-Akt signaling pathway of KEGG pathways were represented. CONCLUSIONS: H-CM showed enhanced anti-cancer effects on HeLa cells but did not influence cell viability or apoptosis of hDFs and these different effects were supported by profiling of secretory proteins in both kinds of CM and intracellular signaling of HeLa cells and hDFs.


Subject(s)
Activins , Hypoxia , Apoptosis , Biological Phenomena , Cell Cycle , Cell Cycle Checkpoints , Cell Survival , Culture Media, Conditioned , Fibroblasts , Gene Ontology , Genome , HeLa Cells , Humans , Insulin-Like Growth Factor Binding Protein 3 , Membrane Potential, Mitochondrial , Mesenchymal Stem Cells , Tissue Inhibitor of Metalloproteinase-2 , Uterine Cervical Neoplasms
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