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1.
BMC Plant Biol ; 22(1): 144, 2022 Mar 25.
Artigo em Inglês | MEDLINE | ID: mdl-35337273

RESUMO

Sophora davidii is an important plant resource in the karst region of Southwest China, but S. davidii plant-height mutants are rarely reported. Therefore, we performed phenotypic, anatomic structural, transcriptomic and metabolomic analyses to study the mechanisms responsible for S. davidii plant-height mutants. Phenotypic and anatomical observations showed that compared to the wild type, the dwarf mutant displayed a significant decrease in plant height, while the tall mutant displayed a significant increase in plant height. The dwarf mutant cells were smaller and more densely arranged, while those of the wild type and the tall mutant were larger and loosely arranged. Transcriptomic analysis revealed that differentially expressed genes (DEGs) involved in cell wall biosynthesis, expansion, phytohormone biosynthesis, signal transduction pathways, flavonoid biosynthesis and phenylpropanoid biosynthesis were significantly enriched in the S. davidii plant-height mutants. Metabolomic analysis revealed 57 significantly differential metabolites screened from both the dwarf and tall mutants. A total of 8 significantly different flavonoid compounds were annotated to LIPID MAPS, and three metabolites (chlorogenic acid, kaempferol and scopoletin) were involved in phenylpropanoid biosynthesis and flavonoid biosynthesis. These results shed light on the molecular mechanisms of plant height in S. davidii mutants and provide insight for further molecular breeding programs.


Assuntos
Sophora , Transcriptoma , Perfilação da Expressão Gênica , Metabolômica , Reguladores de Crescimento de Plantas/metabolismo , Sophora/genética , Sophora/metabolismo
2.
Gigascience ; 112022 03 24.
Artigo em Inglês | MEDLINE | ID: mdl-35333302

RESUMO

BACKGROUND: Cassava (Manihot esculenta) is an important clonally propagated food crop in tropical and subtropical regions worldwide. Genetic gain by molecular breeding has been limited, partially because cassava is a highly heterozygous crop with a repetitive and difficult-to-assemble genome. FINDINGS: Here we demonstrate that Pacific Biosciences high-fidelity (HiFi) sequencing reads, in combination with the assembler hifiasm, produced genome assemblies at near complete haplotype resolution with higher continuity and accuracy compared to conventional long sequencing reads. We present 2 chromosome-scale haploid genomes phased with Hi-C technology for the diploid African cassava variety TME204. With consensus accuracy >QV46, contig N50 >18 Mb, BUSCO completeness of 99%, and 35k phased gene loci, it is the most accurate, continuous, complete, and haplotype-resolved cassava genome assembly so far. Ab initio gene prediction with RNA-seq data and Iso-Seq transcripts identified abundant novel gene loci, with enriched functionality related to chromatin organization, meristem development, and cell responses. During tissue development, differentially expressed transcripts of different haplotype origins were enriched for different functionality. In each tissue, 20-30% of transcripts showed allele-specific expression (ASE) differences. ASE bias was often tissue specific and inconsistent across different tissues. Direction-shifting was observed in <2% of the ASE transcripts. Despite high gene synteny, the HiFi genome assembly revealed extensive chromosome rearrangements and abundant intra-genomic and inter-genomic divergent sequences, with large structural variations mostly related to LTR retrotransposons. We use the reference-quality assemblies to build a cassava pan-genome and demonstrate its importance in representing the genetic diversity of cassava for downstream reference-guided omics analysis and breeding. CONCLUSIONS: The phased and annotated chromosome pairs allow a systematic view of the heterozygous diploid genome organization in cassava with improved accuracy, completeness, and haplotype resolution. They will be a valuable resource for cassava breeding and research. Our study may also provide insights into developing cost-effective and efficient strategies for resolving complex genomes with high resolution, accuracy, and continuity.


Assuntos
Manihot , Alelos , Cromossomos , Diploide , Haplótipos , Manihot/genética , Melhoramento Vegetal , Análise de Sequência de DNA , Transcriptoma
4.
Genome Med ; 14(1): 59, 2022 06 03.
Artigo em Inglês | MEDLINE | ID: mdl-35655252

RESUMO

BACKGROUND: Three-quarters of bladder cancer patients present with early-stage disease (non-muscle-invasive bladder cancer, NMIBC, UICC TNM stages Ta, T1 and Tis); however, most next-generation sequencing studies to date have concentrated on later-stage disease (muscle-invasive BC, stages T2+). We used exome and transcriptome sequencing to comprehensively characterise NMIBCs of all grades and stages to identify prognostic genes and pathways that could facilitate treatment decisions. Tumour grading is based upon microscopy and cellular appearances (grade 1 BCs are less aggressive, and grade 3 BCs are most aggressive), and we chose to also focus on the most clinically complex NMIBC subgroup, those patients with grade 3 pathological stage T1 (G3 pT1) disease. METHODS: Whole-exome and RNA sequencing were performed in total on 96 primary NMIBCs including 22 G1 pTa, 14 G3 pTa and 53 G3 pT1s, with both exome and RNA sequencing data generated from 75 of these individual samples. Associations between genomic alterations, expression profiles and progression-free survival (PFS) were investigated. RESULTS: NMIBCs clustered into 3 expression subtypes with different somatic alteration characteristics. Amplifications of ARNT and ERBB2 were significant indicators of worse PFS across all NMIBCs. High APOBEC mutagenesis and high tumour mutation burden were both potential indicators of better PFS in G3pT1 NMIBCs. The expression of individual genes was not prognostic in BCG-treated G3pT1 NMIBCs; however, downregulated interferon-alpha and gamma response pathways were significantly associated with worse PFS (adjusted p-value < 0.005). CONCLUSIONS: Multi-omic data may facilitate better prognostication and selection of therapeutic interventions in patients with G3pT1 NMIBC. These findings demonstrate the potential for improving the management of high-risk NMIBC patients and warrant further prospective validation.


Assuntos
Neoplasias da Bexiga Urinária , Progressão da Doença , Exoma , Genômica , Humanos , Transcriptoma , Neoplasias da Bexiga Urinária/genética , Neoplasias da Bexiga Urinária/patologia
5.
Sci Total Environ ; 838(Pt 3): 156420, 2022 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-35660445

RESUMO

Nannochloropsis oculata can accumulate large amounts of lipids under rare earth element (REE) conditions. However, the lipid accumulation mechanism responsible for REE stress has not been elucidated. In this study, the effects of cerium (the most abundant REE) on the growth and lipid accumulation of N. oculata were investigated. The de novo transcriptome data of N. oculata under cerium conditions were subsequently collected and analyzed. The results showed that N. oculata exhibited good cerium-resistance ability, showed slightly decrease in biomass but significantly increase in lipid content (55.8 % dry cell weight) under 6.0 mg/L cerium condition. Meanwhile, about 83.4 % cerium was biological fixated. Through transcriptome analysis, we found that the inhibited photosynthesis and carbon fixation pathways coupled with the stress-sensitive expression of ribosome biogenesis genes acclimatized the cells to REE stress. The active glycolysis pathway accelerated carbon flux to pyruvate and acetyl-CoA, and the upregulation of glycerol kinase and phosphatidate cytidylyltransferase genes further induced lipid accumulation. In addition, cerium downregulated the acyl-CoA oxidase and triacylglycerol lipase genes, which inhibited the degradation of lipids. Therefore, different responses to cerium demonstrate how N. oculata cells adapt to REE stress, and this knowledge may be used to extend our understanding of triacylglycerol (TAG) and the synthesis of other important metabolites.


Assuntos
Cério , Microalgas , Estramenópilas , Cério/metabolismo , Perfilação da Expressão Gênica , Metabolismo dos Lipídeos/fisiologia , Microalgas/metabolismo , Estramenópilas/metabolismo , Transcriptoma , Triglicerídeos/metabolismo
6.
Biol Open ; 11(6)2022 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-35665803

RESUMO

Despite the remarkable progress in probing tumor transcriptomic heterogeneity by single-cell RNA sequencing (sc-RNAseq) data, several gaps exist in prior studies. Tumor heterogeneity is frequently mentioned but not quantified. Clustering analyses typically target cells rather than genes, and differential levels of transcriptomic heterogeneity of gene clusters are not characterized. Relations between gene clusters inferred from multiple datasets remain less explored. We provided a series of quantitative methods to analyze cancer sc-RNAseq data. First, we proposed two quantitative measures to assess intra-tumoral heterogeneity/homogeneity. Second, we established a hierarchy of gene clusters from sc-RNAseq data, devised an algorithm to reduce the gene cluster hierarchy to a compact structure, and characterized the gene clusters with functional enrichment and heterogeneity. Third, we developed an algorithm to align the gene cluster hierarchies from multiple datasets to a small number of meta gene clusters. By applying these methods to nine cancer sc-RNAseq datasets, we discovered that cancer cell transcriptomes were more homogeneous within tumors than the accompanying normal cells. Furthermore, many gene clusters from the nine datasets were aligned to two large meta gene clusters, which had high and low heterogeneity and were enriched with distinct functions. Finally, we found the homogeneous meta gene cluster retained stronger expression coherence and associations with survival times in bulk level RNAseq data than the heterogeneous meta gene cluster, yet the combinatorial expression patterns of breast cancer subtypes in bulk level data were not preserved in single-cell data. The inference outcomes derived from nine cancer sc-RNAseq datasets provide insights about the contributing factors for transcriptomic heterogeneity of cancer cells and complex relations between bulk level and single-cell RNAseq data. They demonstrate the utility of our methods to enable a comprehensive characterization of co-expressed gene clusters in a wide range of sc-RNAseq data in cancers and beyond.


Assuntos
Neoplasias da Mama , Transcriptoma , Algoritmos , Neoplasias da Mama/genética , Análise por Conglomerados , Feminino , Humanos , Família Multigênica
7.
Comput Biol Med ; 146: 105688, 2022 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-35680454

RESUMO

Colorectal cancer (CRC) is the most common malignancy of digestive system with significant mortality rate. CRC patients with comparable clinical symptoms or at similar stages of the disease have different outcomes. This underlying clinical result is almost inevitably due to genetic heterogeneity. Therefore, the current study aimed to highlight gene signatures during CRC and unveil their potential mechanisms through bioinformatic analysis. The gene expression profiles (GSE28000, GSE33113, GSE44861, and GSE37182) were downloaded from the Gene Expression Omnibus database, and the differential expressed genes (DEGs) were identified in normal tissues and tumor tissue samples of CRC patients. In total, 8931 DEGs were identified in CRC, including 411 up-regulated genes and 166 down-regulated genes. Further, a protein-protein interaction network was constructed and the highly related genes were clustered using the Molecular Complex Detection algorithm (MCODE) to retrieve the core interaction in different genes' crosstalk. The screened hub genes were subjected to functional enrichment analysis. GO analysis results showed that up-regulated DEGs were significantly enriched in biological processes (BP), including cell division, cell cycle, and cell proliferation; the down-regulated DEGs were significantly enriched in BP, including cellular homeostasis, detoxification, defense response, intracellular signaling cascade. Additionally, KEGG pathway analysis displayed the up-regulated DEGs were enriched in the cell cycle, TNF signaling, chemokine signaling pathway, while the down-regulated DEGs were enriched in NF-kB signaling, mineral reabsorption. Furthermore, the overall survival and expression levels of hub genes were detected by the UALCAN database and were further validated using Human Protein Atlas database. Taken together the identified DEGs (MT2A, CCNB1, DLGAP5, CCNA2, CXCL2, and RACGAP1) enhance our understanding of the molecular pathways that underpin CRC pathogenesis and could be exploited as molecular targets and diagnostic biomarkers for CRC therapy.


Assuntos
Neoplasias Colorretais , Biologia Computacional , Biomarcadores Tumorais/genética , Biomarcadores Tumorais/metabolismo , Neoplasias Colorretais/diagnóstico , Neoplasias Colorretais/genética , Neoplasias Colorretais/metabolismo , Biologia Computacional/métodos , Perfilação da Expressão Gênica/métodos , Regulação Neoplásica da Expressão Gênica , Ontologia Genética , Humanos , Mapas de Interação de Proteínas/genética , Transcriptoma
8.
Microb Pathog ; 168: 105611, 2022 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-35660509

RESUMO

As a potential anti-Helicobacter pylori agent, zinc causes impairment of Helicobacter pylori growth, and this property of zinc is of broad interest to biological investigators. However, little is known about the molecular mechanisms by which zinc inhibits the growth of Helicobacter pylori. Here, an in vitro experiment revealed that zinc at specific concentrations inhibits Helicobacter pylori growth. Furthermore, an RNA sequencing-based investigation of the global regulatory response to zinc revealed that exposure to zinc altered the Helicobacter pylori transcriptional profile in numerous ways. A high concentration of zinc induced the upregulation of genes related to ribosomal subunit, ribosome biosynthesis, chaperone and adhesins. However, flagellar assembly genes and some type IV secretion system genes were repressed. In addition, the expression levels of some genes that encode transporters of metal ions and that play key roles in Helicobacter pylori pathogenicity were altered under conditions of zinc-induced stress. In summary, high concentrations of zinc initiated antimicrobial activity to Helicobacter pylori under the combined effect of multiple repressed or altered pathogenetic genes and metabolic pathways associated with bacteria growth. This result has significant implications for understanding not only the antimicrobial activity mechanism of zinc but also the role of zinc-mediated homeostasis in Helicobacter pylori.


Assuntos
Anti-Infecciosos , Infecções por Helicobacter , Helicobacter pylori , Anti-Infecciosos/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Perfilação da Expressão Gênica , Regulação Bacteriana da Expressão Gênica , Infecções por Helicobacter/microbiologia , Helicobacter pylori/efeitos dos fármacos , Transcriptoma , Zinco/farmacologia
9.
Aging (Albany NY) ; 14(11): 4786-4818, 2022 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-35675043

RESUMO

Accumulated evidence shows that tumor microenvironment plays crucial roles in predicting clinical outcomes of lung adenocarcinoma (LUAD). The current study aimed to identify some potentially prognostic signatures by systematically revealing the transcriptome characteristics in LUADs with differing immune phenotypes. LUAD gene expression data were retrieved from the public TCGA and GEO databases, and the transcriptome characteristics were systematically revealed using a comprehensive bioinformatics method including single-sample gene set enrichment analysis, differentially expressed gene (DEG) analysis, protein and protein interaction (PPI) network construction, competitive endogenous RNA (ceRNA) network construction, weighted gene coexpression network analysis and prognostic model establishment. Finally, 1169 key DEGs associated with LUAD immune phenotype, including 88 immune DEGs, were excavated. Five essential and eight immune essential DEGs were separately identified by constructing two PPI networks based on the above DEGs. Totals of 1085 key DElncRNAs and 45 key DEmiRNAs were excavated and one ceRNA network consisting of 26 DEmRNAs, 3 DEmiRNAs and 57 DElncRNAs were established. The most significant gene coexpression module (cor=0.63 and p=3e-55) associated with LUAD immune phenotypes and three genes (FGR, BTK, SPI1) related to the immune cell infiltration were identified. Three robust prognostic signatures including a 9-lncRNA, an 8-lncRNA and an 8-mRNA were established. The areas under the curves of 5-year correlated with overall survival rate were separately 0.7319, 0.7228 and 0.713 in the receiver operating characteristic curve. The findings provide novel insights into the immunological mechanism in LUAD biology and in predicting the prognosis of LUAD patients.


Assuntos
Adenocarcinoma , Neoplasias Pulmonares , RNA Longo não Codificante , Adenocarcinoma/genética , Biomarcadores Tumorais/genética , Regulação Neoplásica da Expressão Gênica , Humanos , Pulmão/patologia , Neoplasias Pulmonares/patologia , Fenótipo , Prognóstico , RNA Longo não Codificante/genética , Transcriptoma , Microambiente Tumoral/genética
10.
Mol Biol Evol ; 39(6)2022 Jun 02.
Artigo em Inglês | MEDLINE | ID: mdl-35642306

RESUMO

As the best adapted high altitude population, Tibetans feature a relatively high offspring survival rate. Genome-wide studies have identified hundreds of candidate SNPs related to high altitude adaptation of Tibetans, although most of them have unknown functional relevance. To explore the mechanisms behind successful reproduction at high altitudes, we compared the placental transcriptomes of Tibetans, sea level Hans (SLHan), and Han immigrants (ImHan). Among the three populations, placentas from ImHan showed a hyperactive gene expression pattern. Their increased activation demonstrates a hypoxic stress response similar to sea level individuals experiencing hypoxic conditions. Unlike ImHan, Tibetan placentas were characterized by the significant up-regulation of placenta-specific genes, and the activation of autophagy and the tricarboxylic acid (TCA) cycle. Certain conserved hypoxia response functions, including the antioxidant system and angiogenesis, were activated in both ImHan and Tibetans, but mediated by different genes. The coherence of specific transcriptome features linked to possible genetic contribution was observed in Tibetans. Furthermore, we identified a novel Tibetan-specific EPAS1 isoform with a partial deletion at exon six, which may be involved in the adaption to hypoxia through the EPAS1-centred gene network in the placenta. Overall, our results show that the placenta grants successful pregnancies in Tibetans by strengthening the natural functions of the placenta itself. On the other hand, the placenta of ImHan was in an inhabiting time-dependent acclimatization process representing a common hypoxic stress response pattern.


Assuntos
Altitude , Transcriptoma , Aclimatação/genética , Feminino , Hemoglobinas/genética , Humanos , Hipóxia/metabolismo , Placenta/metabolismo , Gravidez , Reprodução , Tibet
11.
Antimicrob Agents Chemother ; 66(6): e0227621, 2022 Jun 21.
Artigo em Inglês | MEDLINE | ID: mdl-35652307

RESUMO

Candida auris is an emerging multidrug-resistant human fungal pathogen often refractory to treatment by all classes of antifungal drugs. Amphotericin B (AmB) is a fungicidal drug that, despite its toxic side effects, remains a drug of choice for the treatment of drug-resistant fungal infections, including those caused by C. auris. However, the molecular mechanisms underlying AmB resistance are poorly understood. In this study, we present data that suggests membrane lipid alterations and chromatin modifications are critical processes that may contribute to or cause adaptive AmB resistance in clinical C. auris isolates. To determine the plausible cause of increased AmB resistance, we performed RNA-seq of AmB-resistant and sensitive C. auris isolates. Remarkably, AmB-resistant strains show a pronounced enrichment of genes involved in lipid and ergosterol biosynthesis, adhesion, drug transport as well as chromatin remodeling. The transcriptomics data confirm increased adhesion and reduced lipid membrane permeability of AmB-resistant strains compared to the sensitive isolates. The AmB-resistant strains also display hyper-resistance to cell wall perturbing agents, including Congo red, calcofluor white and caffeine. Additionally, we noticed an increased phosphorylation of Mkc1 cell integrity MAP kinase upon AmB treatment. Collectively, these data identify differences in the transcriptional landscapes of AmB-resistant versus AmB-sensitive isolates and provide a framework for the mechanistic understanding of AmB resistance in C. auris.


Assuntos
Anfotericina B , Candidíase , Anfotericina B/farmacologia , Anfotericina B/uso terapêutico , Antifúngicos/farmacologia , Antifúngicos/uso terapêutico , Candida , Candidíase/tratamento farmacológico , Farmacorresistência Fúngica/genética , Humanos , Lipídeos , Testes de Sensibilidade Microbiana , Transcriptoma/genética
12.
Environ Pollut ; 307: 119562, 2022 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-35659910

RESUMO

Dinotefuran is a third-generation neonicotinoid pesticide and is increasingly used in agricultural production, which has adverse effects on nontarget organisms. However, the research on the impact of dinotefuran on nontarget organisms is still limited. Here the toxic effects of dinotefuran on an important economic species and a model lepidopteran insect, Bombyx mori, were investigated. Exposure to different doses of dinotefuran caused physiological disorders or death. Cytochrome P450, glutathione S-transferase, carboxylesterase, and UDP glycosyl-transferase activities were induced in the fat body at early stages after dinotefuran exposure. By contrast, only glutathione S-transferase activity was increased in the midgut. To overcome the lack of sensitivity of the biological assays at the individual organism level, RNA sequencing was performed to measure differential expressions of mRNA from silkworm larvae after dinotefuran exposure. Differential gene expression profiling revealed that various detoxification enzyme genes were significantly increased after dinotefuran exposure, which was consistent with the upregulation of the detoxifying enzyme. The global transcriptional pattern showed that the physiological responses induced by dinotefuran toxicity involved multiple cellular processes, including energy metabolism, oxidative stress, detoxification, and other fundamental physiological processes. Many metabolism processes, such as carbon metabolism, fatty acid biosynthesis, pyruvate metabolism, and the citrate cycle, were partially repressed in the midgut or fat body. Furthermore, dinotefuran significantly activated the MAPK/CREB, CncC/Keap1, PI3K/Akt, and Toll/IMD pathways. The links between physiological, biochemical toxicity and comparative transcriptomic analysis facilitated the systematic understanding of the integrated biological toxicity of dinotefuran. This study provides a holistic view of the toxicity and detoxification metabolism of dinotefuran in silkworm and other organisms.


Assuntos
Bombyx , Animais , Bombyx/genética , Glutationa Transferase/metabolismo , Guanidinas , Proteína 1 Associada a ECH Semelhante a Kelch/genética , Proteína 1 Associada a ECH Semelhante a Kelch/metabolismo , Fator 2 Relacionado a NF-E2/metabolismo , Neonicotinoides/metabolismo , Neonicotinoides/toxicidade , Nitrocompostos , Fosfatidilinositol 3-Quinases/metabolismo , Transcriptoma
13.
PLoS Genet ; 18(6): e1010221, 2022 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-35675353

RESUMO

Despite advances in understanding the pathophysiology of Fragile X syndrome (FXS), its molecular basis is still poorly understood. Whole brain tissue expression profiles have proved surprisingly uninformative, therefore we applied single cell RNA sequencing to profile an FMRP deficient mouse model with higher resolution. We found that the absence of FMRP results in highly cell type specific gene expression changes that are strongest among specific neuronal types, where FMRP-bound mRNAs were prominently downregulated. Metabolic pathways including translation and respiration are significantly upregulated across most cell types with the notable exception of excitatory neurons. These effects point to a potential difference in the activity of mTOR pathways, and together with other dysregulated pathways, suggest an excitatory-inhibitory imbalance in the Fmr1-knock out cortex that is exacerbated by astrocytes. Our data demonstrate that FMRP loss affects abundance of key cellular communication genes that potentially affect neuronal synapses and provide a resource for interrogating the biological basis of this disorder.


Assuntos
Síndrome do Cromossomo X Frágil , Animais , Proteína do X Frágil de Retardo Mental/genética , Proteína do X Frágil de Retardo Mental/metabolismo , Síndrome do Cromossomo X Frágil/genética , Camundongos , Camundongos Knockout , Neurônios/metabolismo , Sinapses/metabolismo , Transcriptoma/genética
14.
BMC Genom Data ; 23(1): 39, 2022 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-35641933

RESUMO

BACKGROUND: The influence of environmental factors, especially temperature, on sex ratio is of great significance to elucidate the mechanism of sex determination. However, the molecular mechanisms by which temperature affects sex determination remains unclear, although a few candidate genes have been found to play a role in the process. In this study, we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. RESULTS: Totals of 1171, 1022 and 2921 differentially expressed genes (DEGs) between high temperature and normal temperature were identified at 35, 45 and 60 days post-fertilization (dpf) respectively, revealing that heat shock proteins (HSPs) and DNA methyltransferases (DNMTs) were involved in the heat-exposed sex reversal. The Gene Ontology (GO) terms and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway that were enriched in individuals after heat treatment included Fanconi anemia (FA) pathway, cell cycle, oocyte meiosis and homologous recombination. CONCLUSIONS: Our study provides the results of comparative transcriptome analyses between high temperature and normal temperature, and reveals that the molecular mechanism of heat-induced masculinization in zebrafish is strongly related to the expression of HSPs and DNMTs and FA pathway during gonad differentiation.


Assuntos
Anemia de Fanconi , Peixe-Zebra , Animais , Anemia de Fanconi/metabolismo , Perfilação da Expressão Gênica/métodos , Ontologia Genética , Gônadas/metabolismo , Transcriptoma/genética , Peixe-Zebra/genética
15.
J Transl Med ; 20(1): 249, 2022 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-35641998

RESUMO

The availability of immune-checkpoint inhibitors (ICI) in the last decade has resulted in a paradigm shift in certain areas of oncology. Patients can be treated either by a monotherapy of anti-CTLA-4 (tremelimumab or ipilimumab), anti-PD-1 (nivolumab or pembrolizumab), or anti-PD-L1 (avelumab or atezolizumab or durvalumab) or as combination therapy of anti-CTLA-4 and anti-PD-1. To maximize the clinical treatment benefit of cancer immunotherapy, the prediction of the actual immune response by the identification and application of clinically useful biomarkers will be required. Whole transcriptomic datasets of patients with ICI treatment could provide the basis for large-scale discovery and ranking of such potential biomarker candidates. In this review, we summarize currently available transcriptomic data from different biological sources (whole blood, fresh-frozen tissue, FFPE) obtained by different methods (microarray, RNA-Seq, RT-qPCR). We directly include only results from clinical trials and other investigations where an ICI treatment was administered. The available datasets are grouped based on the administered treatment and we also summarize the most important results in the individual cohorts. We discuss the limitations and shortcomings of the available datasets. Finally, a subset of animal studies is reviewed to provide an overview of potential in vivo ICI investigations. Our review can provide a swift reference for researchers aiming to find the most suitable study for their investigation, thus saving a significant amount of time.


Assuntos
Inibidores de Checkpoint Imunológico , Neoplasias , Animais , Humanos , Inibidores de Checkpoint Imunológico/farmacologia , Inibidores de Checkpoint Imunológico/uso terapêutico , Imunoterapia/efeitos adversos , Neoplasias/tratamento farmacológico , Neoplasias/genética , Nivolumabe , Transcriptoma/genética
16.
Skelet Muscle ; 12(1): 11, 2022 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-35642060

RESUMO

BACKGROUND: As the interest in manned spaceflight increases, so does the requirement to understand the transcriptomic mechanisms that underlay the detrimental physiological adaptations of skeletal muscle to microgravity. While microgravity-induced differential gene expression (DGE) has been extensively investigated, the contribution of differential alternative splicing (DAS) to the plasticity and functional status of the skeletal muscle transcriptome has not been studied in an animal model. Therefore, by evaluating both DGE and DAS across spaceflight, we set out to provide the first comprehensive characterization of the transcriptomic landscape of skeletal muscle during exposure to microgravity. METHODS: RNA-sequencing, immunohistochemistry, and morphological analyses were conducted utilizing total RNA and tissue sections isolated from the gastrocnemius and quadriceps muscles of 30-week-old female BALB/c mice exposed to microgravity or ground control conditions for 9 weeks. RESULTS: In response to microgravity, the skeletal muscle transcriptome was remodeled via both DGE and DAS. Importantly, while DGE showed variable gene network enrichment, DAS was enriched in structural and functional gene networks of skeletal muscle, resulting in the expression of alternatively spliced transcript isoforms that have been associated with the physiological changes to skeletal muscle in microgravity, including muscle atrophy and altered fiber type function. Finally, RNA-binding proteins, which are required for regulation of pre-mRNA splicing, were themselves differentially spliced but not differentially expressed, an upstream event that is speculated to account for the downstream splicing changes identified in target skeletal muscle genes. CONCLUSIONS: Our work serves as the first investigation of coordinate changes in DGE and DAS in large limb muscles across spaceflight. It opens up a new opportunity to understand (i) the molecular mechanisms by which splice variants of skeletal muscle genes regulate the physiological adaptations of skeletal muscle to microgravity and (ii) how small molecule splicing regulator therapies might thwart muscle atrophy and alterations to fiber type function during prolonged spaceflight.


Assuntos
Voo Espacial , Transcriptoma , Processamento Alternativo , Animais , Feminino , Camundongos , Músculo Esquelético/metabolismo , Atrofia Muscular/genética , Atrofia Muscular/metabolismo , RNA/metabolismo
17.
Toxicol Lett ; 363: 55-66, 2022 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-35643291

RESUMO

GQDs show great potential in drug carriers, bioimaging, biosensors, theranostics, and are recently reported as promising therapeutic agents to treat amyloid-related diseases such as Parkinson's disease and inflammations such as colitis. However, current toxicity data about GQDs based on in vivo toxicity assessments remain scarce. In the study, we examined the mRNA expression changes of zebrafish embryos exposed to four types of GQDs, including raw graphene quantum dots (R-GQDs), graphene oxide quantum dots (GOQDs), carboxyl GQDs (C-GQDs), and aminated GQDs (A-GQDs). Firstly, we treated embryos with the four GQDs at three concentrations (50, 100, and 200 µg/mL), and found that only A-GQDs caused embryonic developmental arrest at 100 and 200 µg/mL with significantly decreased survival rates and heartbeat rates, as well as the elevated malformation rates. Next, we analyzed the mRNA sequencing data acquired from zebrafish embryos exposed to the four GQDs for 7 days at 100 µg/mL, and found that all GQDs can act on potassium (K+) and calcium (Ca2+) channels, and spliceosomes with varying degrees of regulatory effects. Compared to other GQDs, A-GQDs can strongly perturb the anticoagulant protein C (PC) pathway via activating most genes associated with complement and coagulation system, cell adhesion molecules (CAMs), and MAPK. In conclusion, this study provided substantial transcriptomic data underlying the common signaling pathways induced by various types of GQDs and pointed out the specific toxicity of A-GQDs on hemostatic system.


Assuntos
Grafite , Pontos Quânticos , Animais , Grafite/toxicidade , Pontos Quânticos/toxicidade , RNA Mensageiro/genética , Transcriptoma , Peixe-Zebra/genética
18.
RNA Biol ; 19(1): 774-780, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-35653374

RESUMO

High-throughput RNA sequencing offers a comprehensive analysis of transcriptome complexity originated from regulatory events, such as differential gene expression, alternative polyadenylation and others, and allows the increase in diagnostic capacity and precision. For gene expression profiling applications that do not specifically require information on alternative splicing events, the mRNA 3' termini counting approach is a cost-effective alternative to whole transcriptome sequencing. Here, we report MTAS-seq (mRNA sequencing via terminator-assisted synthesis) - a novel RNA-seq library preparation method directed towards mRNA 3' termini. We demonstrate the specific enrichment for 3'-terminal regions by simple and quick single-tube protocol with built-in molecular barcoding to enable accurate estimation of transcript abundance. To achieve that, we synthesized oligonucleotide-modified dideoxynucleotides which enable the generation of cDNA libraries at the reverse transcription step. We validated the performance of MTAS-seq on well-characterized reference bulk RNA and further tested it with eukaryotic cell lysates.


Assuntos
Oligonucleotídeos , Transcriptoma , DNA Complementar/genética , Oligonucleotídeos/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Análise de Sequência de RNA/métodos
19.
Phytomedicine ; 102: 154207, 2022 Jul 20.
Artigo em Inglês | MEDLINE | ID: mdl-35660351

RESUMO

BACKGROUND: Pulmonary fibrosis (PF) is a serious lung disease with unknown etiology and irreversible course. Jiegeng decoction (JGD), a traditional prescription, is widely used to treat lung diseases due to its anti-inflammatory and expectorant effects. PURPOSE: To explore the effect of JGD on mice with PF and its underlying mechanism. For this purpose, we established a mouse model with PF by bleomycin (BLM) and then administered JGD and pirfenidone at different concentrations. RESULTS: In vivo, JGD was found to reduce lung inflammation, improve lung function and decrease collagen deposition to alleviate bleomycin-induced PF in mice. The mouse lung tissue was analyzed using lipidomics and transcriptomics. We found phosphatidylinositol was decreased after JGD treatment in lipidomics results, while transcriptomics results showed the critical roles of PI3K/Akt signaling pathway in JGD treatment group. Then, Western Blot and Immunohistochemistry were used to validate that JGD may regulate the expression of Bax, Caspase3, Caspase8, Caspase9 and Bcl-2 apoptosis-related proteins via PI3K/Akt signaling pathway. TUNEL staining revealed that apoptosis mainly occurs on AEC IIs. CONCLUSION: Our results showed that JGD inhibits apoptosis through the PI3K/Akt signaling pathway, thereby protecting against BLM-induced PF. Hence, JGD is expected to be a potential drug candidate for the treatment of PF.


Assuntos
Fibrose Pulmonar , Animais , Bleomicina , Lipidômica , Camundongos , Fosfatidilinositol 3-Quinases/metabolismo , Proteínas Proto-Oncogênicas c-akt/metabolismo , Fibrose Pulmonar/induzido quimicamente , Fibrose Pulmonar/tratamento farmacológico , Transdução de Sinais , Transcriptoma
20.
Molecules ; 27(11)2022 May 27.
Artigo em Inglês | MEDLINE | ID: mdl-35684411

RESUMO

Colorectal cancer is one of the leading causes of cancer-related deaths worldwide. The gemini nanoparticle formulation of polyphenolic curcumin significantly inhibits the viability of cancer cells. However, the molecular mechanisms and pathways underlying its toxicity in colon cancer are unclear. Here, we aimed to uncover the possible novel targets of gemini curcumin (Gemini-Cur) on colorectal cancer and related cellular pathways. After confirming the cytotoxic effect of Gemini-Cur by MTT and apoptotic assays, RNA sequencing was employed to identify differentially expressed genes (DEGs) in HCT-116 cells. On a total of 3892 DEGs (padj < 0.01), 442 genes showed a log2 FC >|2| (including 244 upregulated and 198 downregulated). Gene ontology (GO) enrichment analysis was performed. Protein-protein interaction (PPI) and gene-pathway networks were constructed by using STRING and Cytoscape. The pathway analysis showed that Gemini-Cur predominantly modulates pathways related to the cell cycle. The gene network analysis revealed five central genes, namely GADD45G, ATF3, BUB1B, CCNA2 and CDK1. Real-time PCR and Western blotting analysis confirmed the significant modulation of these genes in Gemini-Cur-treated compared to non-treated cells. In conclusion, RNA sequencing revealed novel potential targets of curcumin on cancer cells. Further studies are required to elucidate the molecular mechanism of action of Gemini-Cur regarding the modulation of the expression of hub genes.


Assuntos
Neoplasias do Colo , Curcumina , Biologia Computacional , Curcumina/farmacologia , Perfilação da Expressão Gênica , Regulação Neoplásica da Expressão Gênica , Células HCT116 , Humanos , Polifenóis/farmacologia , Mapas de Interação de Proteínas , Análise de Sequência de RNA , Transcriptoma
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