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1.
São Paulo; s.n; s.n; 2022. 106 p. tab, graf.
Thesis in English | LILACS | ID: biblio-1380458

ABSTRACT

Fruit ripening is a biochemical process that results in flavor, odor, texture, and color suitable for human consumption, in addition to providing access to important nutrients. Although ripening promotes sensory and nutritional increases in fruits, there is also an increased susceptibility to physical damage, as is the case with papaya. These transformations occur due to changes in gene expression patterns at different stages of maturity, whose control and coordination result from the combined action of plant hormones, especially ethylene. As the action of this hormone in the regulation of gene expression is still elusive, this dissertation sought to address the global analysis of the transcriptome in an overview study of molecular processes involved in the ripening of ethylene-treated and non-treated papaya. Transcription factors related to ethylene synthesis and signaling had increased activity towards exogenous-ethylene treatment. Consequently, ethylene-induced enzymes had their coding genes differentially expressed, like genes related to the synthesis of carotenoids, linalool, and vitamins, which increase color, aroma, and antioxidant activity, respectively. Metabolic pathways related to the synthesis of sugars were suppressed while genes encoding the enzyme responsible for sucrose synthesis maintained a basal expression, showing that the accumulation of sugars occurs before the ripening process. The firmness of the peel and pulp of the fruits were strongly influenced by the treatment with ethylene and by the time of the experiment, suffering the action of numerous enzymes related to the degradation of the cell wall. The main enzyme responsible for softening the pulp was polygalacturonase, together with the activity of other pectinases and cellulases. In contrast to the need for the pre-climacteric action of pectate lyase and pectinesterase reported in other fleshy fruits, such as tomatoes and strawberries, papaya did not show a significant difference in their expression. The meta-analysis of several papaya ripening transcriptomes confirmed the expression profile observed in the previous RNA-seq, besides providing statistical enrichment to the biological narratives. Finally, the present study gathered a range of robust information on the gene regulation of the papaya ripening process, which opens possibilities for future approaches to transcriptomic analysis and validates the use of papaya as a model for such studies


O amadurecimento de frutos é um processo bioquímico que resulta em sabor, odor, textura e cor adequados para o consumo humano, além de propiciar o acesso a nutrientes importantes. Apesar do amadurecimento promover incrementos sensoriais e nutricionais nos frutos, ocorre também um aumento da suscetibilidade a danos físicos, como é o caso do mamão. Essas transformações ocorrem devido às alterações nos padrões de expressão gênica nos diferentes estádios de amadurecimento, cujo controle e coordenação decorrem da ação combinada de hormônios vegetais, principalmente do etileno. Como a ação deste hormônio na regulação da expressão gênica ainda é elusiva, a presente dissertação buscou abordar a análise global do transcriptoma em um amplo estudo dos processos moleculares envolvidos no amadurecimento de mamões tratados e não tratados com etileno. Os fatores de transcrição relacionados com a síntese e a sinalização do etileno tiveram sua atividade aumentada perante o tratamento exógeno com etileno. Consequentemente, as enzimas reguladas por esse hormônio tiveram seus genes de codificação expressos diferencialmente, como foi o caso de genes relacionados à síntese de carotenoides, linalool e vitaminas, que atuam no aumento da cor, aroma e atividade antioxidante, respectivamente. Vias metabólicas relacionadas com à síntese de açúcares foram reprimidas enquanto genes codificantes da enzima responsável pela síntese de sacarose mantiveram uma expressão basal, evidenciando que o acúmulo de açúcares ocorre antes do processo de amadurecimento. A firmeza da casca e da polpa dos frutos foram fortemente influenciadas pelo tratamento com etileno e pelo tempo de experimento, sofrendo ação de inúmeras enzimas relacionadas com a degradação da parede celular. A principal enzima responsável pelo amolecimento da polpa foi a poligalacturonase, em conjunto com a atividade de outras pectinases e celulases. Em contraste com a necessidade da ação pré-climatérica da pectato liase e da pectinesterase relatada em outras frutas carnosas, como tomates e morangos, o mamão não apresentou uma diferença significativa na expressão das mesmas. A meta-análise de diversos transcriptomas do amadurecimento do mamão reafirmaram o perfil de expressão observado no RNA-seq, além de prover enriquecimento estatístico às narrativas biológicas. Por fim, o presente estudo reuniu uma gama de informações robustas sobre a regulação gênica do processo de amadurecimento do mamão papaia, o que abrange a possibilidade para futuras abordagens de análise transcriptomica e valida o uso do mamão como modelo para tais estudos


Subject(s)
Carica/anatomy & histology , Systems Biology/instrumentation , Ethylenes/adverse effects , Sucrose , Climacteric , Gene Expression , Lycopersicon esculentum , Transcriptome/genetics , Fruit , Antioxidants/analysis
2.
Article in English | WPRIM | ID: wpr-922572

ABSTRACT

OBJECTIVE@#To explore the mechanisms of Dangua Recipe (DGR) in improving glycolipid metabolism based on transcriptomics.@*METHODS@#Sprague-Dawley rats with normal glucose level were divided into 3 groups according to a random number table, including a conventional diet group (Group A), a DGR group (Group B, high-calorie diet + 20.5 g DGR), and a high-calorie fodder model group (Group C). After 12 weeks of intervention, the liver tissue of rats was taken. Gene sequence and transcriptional analysis were performed to identify the key genes related to glycolipid metabolism reflecting DGR efficacy, and then gene or protein validation of liver tissue were performed. Nicotinamide phosphoribosyl transferase (Nampt) and phosphoenolpyruvate carboxykinase (PEPCK) proteins in liver tissues were detected by enzyme linked immunosorbent assay, fatty acid synthase (FASN) protein was detected by Western blot, and fatty acid binding protein 5 (FABP5)-mRNA was detected by quantitative real-time polymerase chain reaction. Furthermore, the functional verification was performed on the diabetic model rats by Nampt blocker (GEN-617) injected in vivo. Hemoglobin A@*RESULTS@#Totally, 257 differential-dominant genes of Group A vs. Group C and 392 differential-dominant genes of Group B vs. Group C were found. Moreover, 11 Gene Ontology molecular function terms and 7 Kyoto Encyclopedia of Genes and Genomes enrichment pathways owned by both Group A vs. Group C and Group C vs. Group B were confirmed. The liver tissue target validation showed that Nampt, FASN, PEPCK protein and FABP5-mRNA had the same changes consistent with transcriptome. The in vivo functional tests showed that GEN-617 increased body weight, HbA@*CONCLUSION@#Nampt activation was one of the mechanisms about DGR regulating glycolipid metabolism.


Subject(s)
Animals , Diabetes Mellitus, Experimental , Drugs, Chinese Herbal , Glycolipids , Liver , Metabolic Diseases , Rats , Rats, Sprague-Dawley , Transcriptome/genetics
3.
Frontiers of Medicine ; (4): 251-262, 2022.
Article in English | WPRIM | ID: wpr-929198

ABSTRACT

Pathogenic microbes can induce cellular dysfunction, immune response, and cause infectious disease and other diseases including cancers. However, the cellular distributions of pathogens and their impact on host cells remain rarely explored due to the limited methods. Taking advantage of single-cell RNA-sequencing (scRNA-seq) analysis, we can assess the transcriptomic features at the single-cell level. Still, the tools used to interpret pathogens (such as viruses, bacteria, and fungi) at the single-cell level remain to be explored. Here, we introduced PathogenTrack, a python-based computational pipeline that uses unmapped scRNA-seq data to identify intracellular pathogens at the single-cell level. In addition, we established an R package named Yeskit to import, integrate, analyze, and interpret pathogen abundance and transcriptomic features in host cells. Robustness of these tools has been tested on various real and simulated scRNA-seq datasets. PathogenTrack is competitive to the state-of-the-art tools such as Viral-Track, and the first tools for identifying bacteria at the single-cell level. Using the raw data of bronchoalveolar lavage fluid samples (BALF) from COVID-19 patients in the SRA database, we found the SARS-CoV-2 virus exists in multiple cell types including epithelial cells and macrophages. SARS-CoV-2-positive neutrophils showed increased expression of genes related to type I interferon pathway and antigen presenting module. Additionally, we observed the Haemophilus parahaemolyticus in some macrophage and epithelial cells, indicating a co-infection of the bacterium in some severe cases of COVID-19. The PathogenTrack pipeline and the Yeskit package are publicly available at GitHub.


Subject(s)
COVID-19 , Humans , RNA , SARS-CoV-2/genetics , Single-Cell Analysis/methods , Transcriptome
4.
Protein & Cell ; (12): 281-301, 2022.
Article in English | WPRIM | ID: wpr-929175

ABSTRACT

A fundamental challenge that arises in biomedicine is the need to characterize compounds in a relevant cellular context in order to reveal potential on-target or off-target effects. Recently, the fast accumulation of gene transcriptional profiling data provides us an unprecedented opportunity to explore the protein targets of chemical compounds from the perspective of cell transcriptomics and RNA biology. Here, we propose a novel Siamese spectral-based graph convolutional network (SSGCN) model for inferring the protein targets of chemical compounds from gene transcriptional profiles. Although the gene signature of a compound perturbation only provides indirect clues of the interacting targets, and the biological networks under different experiment conditions further complicate the situation, the SSGCN model was successfully trained to learn from known compound-target pairs by uncovering the hidden correlations between compound perturbation profiles and gene knockdown profiles. On a benchmark set and a large time-split validation dataset, the model achieved higher target inference accuracy as compared to previous methods such as Connectivity Map. Further experimental validations of prediction results highlight the practical usefulness of SSGCN in either inferring the interacting targets of compound, or reversely, in finding novel inhibitors of a given target of interest.


Subject(s)
Drug Delivery Systems , Proteins , Transcriptome
5.
Protein & Cell ; (12): 167-179, 2022.
Article in English | WPRIM | ID: wpr-929172

ABSTRACT

Tumors are complex ecosystems in which heterogeneous cancer cells interact with their microenvironment composed of diverse immune, endothelial, and stromal cells. Cancer biology had been studied using bulk genomic and gene expression profiling, which however mask the cellular diversity and average the variability among individual molecular programs. Recent advances in single-cell transcriptomic sequencing have enabled a detailed dissection of tumor ecosystems and promoted our understanding of tumorigenesis at single-cell resolution. In the present review, we discuss the main topics of recent cancer studies that have implemented single-cell RNA sequencing (scRNA-seq). To study cancer cells, scRNA-seq has provided novel insights into the cancer stem-cell model, treatment resistance, and cancer metastasis. To study the tumor microenvironment, scRNA-seq has portrayed the diverse cell types and complex cellular states of both immune and non-immune cells interacting with cancer cells, with the promise to discover novel targets for future immunotherapy.


Subject(s)
Ecosystem , Gene Expression Profiling , Genomics , Humans , Neoplasms/pathology , Sequence Analysis, RNA , Single-Cell Analysis , Transcriptome , Tumor Microenvironment/genetics
6.
Article in Chinese | WPRIM | ID: wpr-929073

ABSTRACT

Objective Circular RNAs (circRNAs) are non-coding RNAs (ncRNA) circularized without a 3' polyadenylation [poly-(A)] tail or a 5' cap, resulting in a covalently closed loop structure. circRNAs were first discovered in RNA viruses in the 1970s, but only a small number of circRNAs were discovered at that time due to limitations in traditional polyadenylated transcriptome analyses. With the development of specific biochemical and computational methods, recent studies have shown the presence of abundant circRNAs in eukaryotic transcriptomes. circRNAs play vital roles in many physiological and pathological processes, such as acting as miRNA sponges, binding to RNA-binding proteins (RBPs), acting as transcriptional regulatory factors, and even serving as translation templates. Current evidence has shown that circRNAs can be potentially used as excellent biomarkers for diagnosis, therapeutic effect evaluation, and prognostic assessment of a variety of diseases, and they may also provide effective therapeutic targets due to their stability and tissue and development-stage specificity. This review focuses on the properties of circRNAs and their immune relationship to disease, and explores the role of circRNAs in immune-related diseases and the directions of future research.


Subject(s)
Biomarkers , MicroRNAs/genetics , RNA, Circular , Transcriptome
7.
Article in English | WPRIM | ID: wpr-929064

ABSTRACT

Pear is one of the main fruits with thousands of years of cultivation history in China. There are more than 2000 varieties of pear cultivars around the world, including more than 1200 varieties or cultivars in China (Legrand et al., 2016). Xinjiang Uygur Autonomous Region is an important pear production region in China with 30 of varieties or cultivars. Pyrus sinkiangensis is the most popular variety, which is mainly distributed in Xinjiang (Zhou et al., 2018). Chlorogenic acid (CGA), p-coumaric acid, and arbutin are the main polyphenols in pear fruit, and their levels show great differences among different varieties (Li et al., 2014). CGA is a potential chemo-preventive agent, which possesses many important bioactivities including antioxidant, diabetes attenuating, and anti-obesity (Wang et al., 2021). Therefore, the specific CGA content of a variety is considered the embodiment of the functional nutritional value of pears.


Subject(s)
Chlorogenic Acid , Fruit , Gene Expression Profiling , Pyrus/genetics , Transcriptome
8.
Article in Chinese | WPRIM | ID: wpr-928715

ABSTRACT

OBJECTIVE@#To establish an immune gene prognostic model of acute myeloid leukemia (AML) and explore its correlation with immune cells in bone marrow microenvironment.@*METHODS@#Gene expression profile and clinical data of TCGA-AML were downloaded from TCGA database. Immune genes were screened by LASSO analysis to construct prognosis prediction model, and prediction accuracy of the model was quantified by receiver operating characteristic curve and area under the curve. Survival analysis was performed by Log-rank test. Enriched pathways in the different immune risk subtypes were evaluated from train cohort. The relationship between immune prediction model and bone marrow immune microenvironment was verified by flow cytometry in the real world.@*RESULTS@#Patients with low-risk score of immune gene model had better prognosis than those with high-risk score. Multivariate analysis showed that the immune gene risk model was an independent prognostic factor. The risk ratio for AML patients in the training concentration was HR=24.594 (95%CI: 6.180-97.878), and the AUC for 1-year, 3-year, and 5-year overall survival rate was 0.811, 0.815, and 0.837, respectively. In addition, enrichment analysis of differential gene sets indicated activation of immune-related pathways such as cytokines and chemokines as well as autoimmune disease-related pathways. At the same time, real world data showed that patients with high immune risk had lower numbers of CD8+T cells and B lymphocytes compared with low immune risk patients.@*CONCLUSION@#We constructed a stable prognostic model for AML, which can not only predict the prognosis of AML, but also reveal the dysregulation of immune microenvironment.


Subject(s)
Humans , Leukemia, Myeloid, Acute/genetics , Prognosis , ROC Curve , Risk Factors , Transcriptome , Tumor Microenvironment/genetics
9.
Article in Chinese | WPRIM | ID: wpr-927948

ABSTRACT

Artemisia Argyi Folium, a traditional Chinese medicine of important medicinal and economic value, sees increasing demand in medicinal and moxibustion product market. Screening stable and reliable reference genes for quantitative real-time PCR(qRT-PCR) is a prerequisite for the analysis of gene expression in Artemisia argyi. In this study, eight commonly used reference genes, Actin, 18s, EF-1α, GAPDH, SAND, PAL, TUA, and TUB, from the transcriptome of A. argyi, were selected as candidate genes. The expression of each gene in different tissues(roots, stems, and leaves) of A. argyi and in leaves of A. argyi after treatment with methyl jasmonate(MeJA) for different time(0, 4, 8, 12 h) was detected by qRT-PCR. Then, geNorm, NormFinder, BestKeeper, ΔCT, and RefFinder were employed to evaluate their expression stability. The results demonstrated that Actin was the most stable reference gene in different tissues and in leaves treated with MeJA, and coming in the second was SAND. Furthermore, the expression of DXS and MCT which are involved in terpenoid backbone biosynthesis was detected in different tissues and after MeJA treatment. The results showed that the expression patterns of DXS and MCT in different tissues and under MeJA treatment calculated with Actin and SAND as internal reference genes were consistent, which validated the screening results. In conclusion, Actin is the most suitable reference gene for the analysis of gene expression in different tissues of A. argyi and after MeJA treatment. This study provides valuable information for gene expression analysis in A. argyi and lays a foundation for further research on molecular mechanism of quality formation of Artemisia Argyi Folium.


Subject(s)
Artemisia/genetics , Gene Expression Profiling , Genes, Plant/genetics , Plant Leaves/genetics , Real-Time Polymerase Chain Reaction , Reference Standards , Transcriptome
10.
Article in Chinese | WPRIM | ID: wpr-927912

ABSTRACT

Dof(DNA binding with one finger), a unique class of transcription factors in plants, play an important role in seed development, tissue differentiation, and metabolic regulation. To identify the number and function of Dof gene family members in Panax ginseng, this study identified the members of Dof gene family in P. ginseng and systematically analyzed their structures, evolution, functional differentiation, expression patterns, and interactions using bioinformatics methods at the transcriptome level. At the same time, the association analysis of Dof genes from P. ginseng with key enzyme genes for ginsenoside synthesis was carried out to screen the candidate PgDof genes involved in the regulation of ginsenoside biosynthesis. The results showed that there were 54 genes belonging to the Dof gene family in P. ginseng from Jilin. All PgDof genes had Zf-Dof conserved motifs, implying that they were evolutionarily conserved and could be divided into five groups. Expression pattern analysis confirmed that the expression of PgDof gene family members in different tissues, different year-old P. ginseng, and different farm varieties varied significantly. Simultaneously, as revealed by "gene-saponin content" and "gene-gene" linkage analysis, an important candidate PgDof14-1 gene involved in the regulation of ginsenoside biosynthesis was obtained. From the established genetic transformation system of this gene in the hairy roots of P. ginseng, a positive hairy root clone was determined. This study has laid a theoretical foundation for the study of Dof gene family in P. ginseng.


Subject(s)
Gene Expression Profiling/methods , Gene Expression Regulation, Plant , Ginsenosides , Panax , Plant Proteins/metabolism , Plant Roots/metabolism , Transcriptome
11.
Chinese Journal of Biotechnology ; (12): 303-327, 2022.
Article in Chinese | WPRIM | ID: wpr-927713

ABSTRACT

Oolong tea is a semi-fermented tea with strong flavor, which is widely favored by consumers because of its floral and fruity aroma as well as fresh and mellow taste. During the processing of oolong tea, withering is the first indispensable process for improving flavor formation. However, the molecular mechanism that affects the flavor formation of oolong tea during withering remains unclear. Transcriptome sequencing was used to analyze the difference among the fresh leaves, indoor-withered leaves and solar-withered leaves of oolong tea. A total of 10 793 differentially expressed genes were identified from the three samples. KEGG enrichment analysis showed that the differentially expressed genes were mainly involved in flavonoid synthesis, terpenoid synthesis, plant hormone signal transduction and spliceosome pathways. Subsequently, twelve differentially expressed genes and four differential splicing genes were identified from the four enrichment pathways for fluorescence quantitative PCR analysis. The results showed that the expression patterns of the selected genes during withering were consistent with the results in the transcriptome datasets. Further analysis revealed that the transcriptional inhibition of flavonoid biosynthesis-related genes, the transcriptional enhancement of terpenoid biosynthesis-related genes, as well as the jasmonic acid signal transduction and the alternative splicing mechanism jointly contributed to the flavor formation of high floral and fruity aroma and low bitterness in solar-withered leaves. The results may facilitate better understanding the molecular mechanisms of solar-withering treatment in flavor formation of oolong tea.


Subject(s)
Camellia sinensis/genetics , Gene Expression Profiling , Plant Leaves , Plant Proteins/metabolism , Taste , Tea , Transcriptome/genetics
12.
Chinese Journal of Biotechnology ; (12): 287-302, 2022.
Article in Chinese | WPRIM | ID: wpr-927712

ABSTRACT

As a non-essential metal, cadmium (Cd) pollution poses severe threats to plant growth, environment, and human health. Phytoextraction using nursery stocks prior to their transplantation is a potential useful approach for bioremediation of Cd contaminated soil. A greenhouse pot experiment was performed to investigate the growth, Cd accumulation, profiles of transcriptome as well as root-associated microbiomes of Photinia frase in Cd-added soil, upon inoculation of two types of arbuscular mycorrhizal fungi (AMF) Sieverdingia tortuosa and Funneliformis mosseae. Compared with the control, inoculation of F. mosseae increased Cd concentrations in root, stem and leaf by 57.2%, 44.1% and 71.1%, respectively, contributing to a total Cd content of 182 μg/plant. KEGG pathway analysis revealed that hundreds of genes involved in 'Mitogen-activated protein kinase (MAPK) signaling pathway', 'plant hormone signal transduction', 'biosynthesis of secondary metabolites' and 'glycolysis/gluconeogenesis' were enriched upon inoculation of F. mosseae. The relative abundance of Acidobacteria was increased upon inoculation of S. tortuosa, while Chloroflexi and Patescibacteria were increased upon inoculation of F. mosseae, and the abundance of Glomerales increased from 23.0% to above 70%. Correlation analysis indicated that ethylene-responsive transcription factor, alpha-aminoadipic semialdehyde synthase, isoamylase and agmatine deiminase related genes were negatively associated with the relative abundance of Glomerales operational taxonomic units (OTUs) upon inoculation of F. mosseae. In addition, plant cysteine oxidase, heat shock protein, cinnamoyl-CoA reductase and abscisic acid receptor related genes were positively associated with the relative abundance of Patescibacteria OTUs upon inoculation of F. mosseae. These finding suggested that AMF can enhance P. frase Cd uptake by modulating plant gene expression and altering the structure of the soil microbial community. This study provides a theoretical basis for better understanding the relationship between root-associated microbiomes and root transcriptomes of P. frase, from which a cost-effective and environment-friendly strategy for phytoextraction of Cd in Cd-polluted soil might be developed.


Subject(s)
Cadmium , Humans , Microbiota , Mycorrhizae , Photinia , Soil Pollutants , Transcriptome
13.
Acta Physiologica Sinica ; (6): 246-254, 2022.
Article in Chinese | WPRIM | ID: wpr-927600

ABSTRACT

Steroid receptor coactivators (SRCs) significantly increase the transcriptional activity of various steroid hormone receptors, and play an important regulatory role in a variety of physiological functions such as food intake, sleep, stress response and reproduction. Previous studies have found that pregnant mice carrying fetuses with SRC1/2 double-knockout (dKO) manifested delayed labor, partly due to the hypoplasia of fetal lungs and the decreased secretion of pulmonary surfactant protein-A (SP-A) and platelet activating factor (PAF). However, there is still a lack of systematic analysis of the changes in gene expression at the whole transcriptome level in the fetal lungs of SRC1/2 dKO mice. In this study, the SRC1KO, SRC2KO, SRC1/2 dKO and wild-type (WT) mouse fetal lung samples were collected at 18.5 days post coitus. The Illumina platform was employed for transcriptome mRNA sequencing, and then the differentially expressed genes (DEGs) were annotated and analyzed by GO and KEGG analysis. The results showed that the proportion of quality score of the sequencing data above Q30 in all samples was more than 92% and passed the quality control. Compared with WT fetal lungs, SRC1KO and SRC2KO fetal lungs had 61 and 32 DEGs, respectively; SRC1/2 dKO fetal lungs had 480, 11 and 901 DEGs compared with WT, SRC1KO and SRC2KO fetal lungs, respectively. Among these genes, Aspg, Crispld2, Eln, Ntsr2, Slc10a6 and Vgll3 were the unique DEGs of SRC1/2 dKO fetal lungs compared with other genotype mice. Real-time PCR and Western blotting verified the reliability of transcriptome sequencing results. The GO analysis of the DEGs between SRC1/2 dKO and WT mouse fetal lungs showed that the DEGs were significantly enriched in the extracellular space, extracellular region, and extracellular matrix in terms of cellular component. In the biological process, they were significantly enriched in the term of development of multiple organs. KEGG pathway analysis showed that the DEGs were mainly enriched in signaling pathways such as the complement system, extracellular matrix-receptor interactions, and protein digestion and absorption. In summary, this study comprehensively revealed the changes of gene expression in the fetal lungs of SRC1/2 dKO mice at the transcriptome level, which provides a new theoretical basis for the study of the developmental regulatory mechanism of the fetal lung during pregnancy, and the fetus-derived signals that affect the initiation of labor.


Subject(s)
Animals , Female , Gene Expression Profiling , Lung/physiology , Mice , Mice, Knockout , Pregnancy , Reproducibility of Results , Transcriptome
14.
Electron. j. biotechnol ; 51: 40-49, May. 2021. tab, ilus, graf
Article in English | LILACS | ID: biblio-1343322

ABSTRACT

BACKGROUND: Scavenger receptor class B (SRB) is a multifunctional protein in animals that participates in physiological processes, including recognition of a wide range of ligands. Astaxanthin is a major carotenoid found in shrimp. However, the molecular mechanism of astaxanthin and SRB protein binding has not been reported. RESULTS: In the present study, a member of the SRB subfamily, named PmSRB, was identified from the transcriptome of black tiger shrimp (Penaeus monodon). The open reading frame of PmSRB was 1557 bp in length and encoded 518 amino acids. The structure of PmSRB included a putative transmembrane structure at the N-terminal region and a CD36 domain. Multiple sequence alignment indicated that the CD36 domain were conserved. Phylogenetic analysis showed four separate branches (SRA, SRB, SRC, and croquemort) in the phylogenetic tree and that PmSRB was clustered with SRB of Eriocheir sinensis. Quantitative real-time polymerase chain reaction showed that the PmSRB gene was widely expressed in all tissues tested, with the highest expression level observed in the lymphoid organ and brain. Subcellular localization analysis revealed that PmSRB-GFP (green fluorescent protein) fusion proteins were predominantly localized in the cell membrane. The recombinant proteins of PmSRB showed binding activities against astaxanthin in vitro. CONCLUSIONS: PmSRB was identified and characterized in this study. It is firstly reported that PmSRB may take as an important mediator of astaxanthin uptake in shrimp.


Subject(s)
Animals , Penaeidae , Receptors, Scavenger/metabolism , In Vitro Techniques , Blotting, Western , Chromatography, High Pressure Liquid , Sequence Alignment , Xanthophylls , Receptors, Scavenger/isolation & purification , Receptors, Scavenger/genetics , Real-Time Polymerase Chain Reaction/methods , Transcriptome
15.
Electron. j. biotechnol ; 50: 59-67, Mar. 2021. ilus, graf, tab
Article in English | LILACS | ID: biblio-1292412

ABSTRACT

BACKGROUND: Cross talk of tumor­immune cells at the gene expression level has been an area of intense research. However, it is largely unknown at the alternative splicing level which has been found to play important roles in the tumor­immune microenvironment. RESULTS: Here, we re-exploited one transcriptomic dataset to gain insight into tumor­immune interactions from the point of AS level. Our results showed that the AS profiles of triple-negative breast cancer cells co-cultured with activated T cells were significantly changed but not Estrogen receptor positive cells. We further suggested that the alteration in AS profiles in triple-negative breast cancer cells was largely caused by activated T cells rather than paracrine factors from activated T cells. Biological pathway analyses showed that translation initiation and tRNA aminoacylation pathways were most disturbed with T cell treatment. We also established an approach largely based on the AS factor­AS events associations and identified LSM7, an alternative splicing factor, may be responsible for the major altered events. CONCLUSIONS: Our study reveals the notable differences of response to T cells among breast cancer types which may facilitate the development or improvement of tumor immunotherapy.


Subject(s)
T-Lymphocytes , Triple Negative Breast Neoplasms , Peptide Chain Initiation, Translational , Gene Expression , Alternative Splicing , Cell Culture Techniques , Receptor Cross-Talk , Transfer RNA Aminoacylation , Transcriptome , Immunotherapy
16.
Electron. j. biotechnol ; 50: 68-76, Mar. 2021. ilus, tab, graf
Article in English | LILACS | ID: biblio-1292417

ABSTRACT

BACKGROUND: Jasmonic acid (JA) is a signal transducer molecule that plays an important role in plant development and stress response; it can also efficiently stimulate secondary metabolism in plant cells. RESULTS: RNA-Seq technology was applied to identify differentially expressed genes and study the time course of gene expression in Rhazya stricta in response to JA. Of more than 288 million total reads, approximately 27% were mapped to genes in the reference genome. Genes involved during the secondary metabolite pathways were up- or downregulated when treated with JA in R. stricta. Functional annotation and pathway analysis of all up- and downregulated genes identified many biological processes and molecular functions. Jasmonic acid biosynthetic, cell wall organization, and chlorophyll metabolic processes were upregulated at days 2, 6, and 12, respectively. Similarly, the molecular functions of calcium-transporting ATPase activity, ADP binding, and protein kinase activity were also upregulated at days 2, 6, and 12, respectively. Time-dependent transcriptional gene expression analysis showed that JA can induce signaling in the phenylpropanoid and aromatic acid pathways. These pathways are responsible for the production of secondary metabolites, which are essential for the development and environmental defense mechanism of R. stricta during stress conditions. CONCLUSIONS: Our results suggested that genes involved in flavonoid biosynthesis and aromatic acid synthesis pathways were upregulated during JA stress. However, monoterpenoid indole alkaloid (MIA) was unaffected by JA treatment. Hence, we can postulate that JA plays an important role in R. stricta during plant development and environmental stress conditions.


Subject(s)
Cyclopentanes/metabolism , Apocynaceae/genetics , Oxylipins/metabolism , Plant Growth Regulators/metabolism , Stress, Physiological , Flavonoids/biosynthesis , Base Sequence , Gene Expression , Environment , Transcriptome
17.
Braz. j. med. biol. res ; 54(3): e9571, 2021. tab, graf
Article in English | LILACS | ID: biblio-1153526

ABSTRACT

Cancer cell lines are widely used as in vitro models of tumorigenesis, facilitating fundamental discoveries in cancer biology and translational medicine. Currently, there are few options for glioblastoma (GBM) treatment and limited in vitro models with accurate genomic and transcriptomic characterization. Here, a detailed characterization of a new GBM cell line, namely AHOL1, was conducted in order to fully characterize its molecular composition based on its karyotype, copy number alteration (CNA), and transcriptome profiling, followed by the validation of key elements associated with GBM tumorigenesis. Large numbers of CNAs and differentially expressed genes (DEGs) were identified. CNAs were distributed throughout the genome, including gains at Xq11.1-q28, Xp22.33-p11.1, Xq21.1-q21.33, 4p15.1-p14, 8q23.2-q23.3 and losses at Yq11.21-q12, Yp11.31-p11.2, and 15q11.1-q11.2 positions. Nine druggable genes were identified, including HCRTR2, ETV1, PTPRD, PRKX, STS, RPS6KA6, ZFY, USP9Y, and KDM5D. By integrating DEGs and CNAs, we identified 57 overlapping genes enriched in fourteen pathways. Altered expression of several cancer-related candidates found in the DEGs-CNA dataset was confirmed by RT-qPCR. Taken together, this first comprehensive genomic and transcriptomic landscape of AHOL1 provides unique resources for further studies and identifies several druggable targets that may be useful for therapeutics and biologic and molecular investigation of GBM.


Subject(s)
Humans , Glioblastoma/genetics , Gene Expression Regulation, Neoplastic , Minor Histocompatibility Antigens , Genome , Genomics , Cell Line, Tumor , Histone Demethylases , Transcriptome
18.
Braz. j. med. biol. res ; 54(3): e10152, 2021. tab, graf
Article in English | LILACS | ID: biblio-1153522

ABSTRACT

The goal of this study was to identify potential transcriptomic markers in pediatric septic shock prognosis by an integrative analysis of multiple public microarray datasets. Using the R software and bioconductor packages, we performed a statistical analysis to identify differentially expressed (DE) genes in pediatric septic shock non-survivors, and further performed functional interpretation (enrichment analysis and co-expression network construction) and classification quality evaluation of the DE genes identified. Four microarray datasets (3 training datasets and 1 testing dataset, 252 pediatric patients with septic shock in total) were collected for the integrative analysis. A total of 32 DE genes (18 upregulated genes; 14 downregulated genes) were identified in pediatric septic shock non-survivors. Enrichment analysis revealed that those DE genes were strongly associated with acute inflammatory response to antigenic stimulus, response to yeast, and defense response to bacterium. A support vector machine classifier (non-survivors vs survivors) was also trained based on DE genes. In conclusion, the DE genes identified in this study are suggested as candidate transcriptomic markers for pediatric septic shock prognosis and provide novel insights into the progression of pediatric septic shock.


Subject(s)
Humans , Child , Shock, Septic/diagnosis , Shock, Septic/genetics , Transcriptome , Biomarkers , Computational Biology , Gene Expression Profiling , Microarray Analysis
19.
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
20.
Braz. j. med. biol. res ; 54(11): e11069, 2021. tab, graf
Article in English | LILACS | ID: biblio-1339448

ABSTRACT

This study aimed to explore gene expression profiles that drive malignancy from low- to high-grade head and neck carcinomas (HNC), as well as to analyze their correlations with survival. Gene expressions and clinical data of HNC were downloaded from the Gene Expression Omnibus (GEO) repository. The significantly differential genes (SDGs) between low- and high-grade HNC were screened. Cox regressions were performed to identify prognostic SDGs of progression-free survival (PFS) and disease-specific survival (DSS). The genes were experimentally validated by RT-PCR in clinical tissue specimens. Thirty-five SDGs were identified in 47 low-grade and 30 high-grade HNC samples. Cox regression analyses showed that CXCL14, SLC44A1, and UBD were significantly associated with DSS, and PPP2R2C and SLC44A1 were associated with PFS. Patients were grouped into high-risk or low-risk groups for prognosis based on gene signatures. High-risk patients had significantly shorter DSS and PFS than low-risk patients (P=0.033 and P=0.010, respectively). Multivariate Cox regression showed HPV (P=0.033), lymph node status (P=0.032), and residual status (P<0.044) were independent risk factors for PFS. ROC curves showed the risk score had better efficacy to predict survival both for DSS and PFS (AUC=0.858 and AUC=0.901, respectively). The results showed CXCL14 and SLC44A1 were significantly overexpressed in the low-grade HNC tissues and the UBD were overexpressed in the high-grade HNC tissues. Our results suggested that SDGs had different expression profiles between the low-grade and high-grade HNC, and these genes may serve as prognostic biomarkers to predict survival.


Subject(s)
Humans , Biomarkers, Tumor/genetics , Head and Neck Neoplasms/genetics , Antigens, CD , Organic Cation Transport Proteins , Transcriptome
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