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Frontiers in Oncology 2024Exosomes are a subclass of extracellular vesicles shown to promote the cancer growth and support metastatic progression. The proteomic analysis of neuroblastoma-derived... (Review)
Review
Exosomes are a subclass of extracellular vesicles shown to promote the cancer growth and support metastatic progression. The proteomic analysis of neuroblastoma-derived exosomes has revealed proteins involved in cell migration, proliferation, metastasis, and in the modulation of tumor microenvironment - thus contributing to the tumor development and an aggressive metastatic phenotype. This review gives an overview of the current understanding of the exosomal proteins in neuroblastoma and of their potential as diagnostic/prognostic biomarker of disease and therapeutics.
PubMed: 38962276
DOI: 10.3389/fonc.2024.1414063 -
Frontiers in Oncology 2024Hepatitis B infection is substantially associated with the development of liver cancer globally, with the prevalence of hepatocellular carcinoma (HCC) cases exceeding... (Review)
Review
Hepatitis B infection is substantially associated with the development of liver cancer globally, with the prevalence of hepatocellular carcinoma (HCC) cases exceeding 50%. Hepatitis B virus (HBV) encodes the Hepatitis B virus X (HBx) protein, a pleiotropic regulatory protein necessary for the transcription of the HBV covalently closed circular DNA (cccDNA) microchromosome. In previous studies, HBV-associated HCC was revealed to be affected by HBx in multiple signaling pathways, resulting in genetic mutations and epigenetic modifications in proto-oncogenes and tumor suppressor genes. In addition, transforming growth factor-β (TGF-β) has dichotomous potentials at various phases of malignancy as it is a crucial signaling pathway that regulates multiple cellular and physiological processes. In early HCC, TGF-β has a significant antitumor effect, whereas in advanced HCC, it promotes malignant progression. TGF-β interacts with the HBx protein in HCC, regulating the pathogenesis of HCC. This review summarizes the respective and combined functions of HBx and TGB-β in HCC occurrence and development.
PubMed: 38962270
DOI: 10.3389/fonc.2024.1407434 -
Frontiers in Oncology 2024The escape from T cell-mediated immune surveillance is an important cause of death for patients with acute myeloid leukemia (AML). This study aims to identify clonal...
OBJECTIVE
The escape from T cell-mediated immune surveillance is an important cause of death for patients with acute myeloid leukemia (AML). This study aims to identify clonal heterogeneity in leukemia progenitor cells and explore molecular or signaling pathways associated with AML immune escape.
METHODS
Single-cell RNA sequencing (scRNA-seq) was performed to identified AML-related cellular subsets, and intercellular communication was analyzed to investigate molecular mechanisms associated with AML immune escape. Bulk RNA sequencing (RNA-seq) was performed to screen differentially expressed genes (DEGs) related to hematopoietic stem cell progenitors (HSC-Prog) in AML, and critical ore signaling pathways and hub genes were found by Gene Set Enrichment Analysis (GSEA), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The mRNA level of the hub gene was verified using quantitative real-time PCR (qRT-PCR) and the protein level of human leukocyte antigen A (HLA-A) using enzyme-linked immuno sorbent assay (ELISA).
RESULTS
scRNA-seq analysis revealed a large heterogeneity of HSC-Prog across samples, and the intercellular communication analysis indicated a strong association between HSC-Prog and CD8-T cells, and HSC-Prog also had an association with HLA-A. Transcriptome analysis identified 1748 DEGs, enrichment analysis results showed that non-classical wnt signaling pathway was associated with AML, and 4 pathway-related genes (RHOA, RYK, CSNK1D, NLK) were obtained. After qRT-PCR and ELISA validation, hub genes and HLA-A were found to be down-regulated in AML and up-regulated after activation of the non-classical Wnt signaling pathway.
CONCLUSION
In this study, clonal heterogeneity of HSC-Prog cells in AML was identified, non-classical wnt signaling pathways associated with AML were identified, and it was verified that HLA-A could be upregulated by activation of non-classical wnt signaling, thereby increasing antigen presentation.
PubMed: 38962268
DOI: 10.3389/fonc.2024.1336106 -
NAR Genomics and Bioinformatics Sep 2024Protein language models have been tested and proved to be reliable when used on curated datasets but have not yet been applied to full proteomes. Accordingly, we tested...
Protein language models have been tested and proved to be reliable when used on curated datasets but have not yet been applied to full proteomes. Accordingly, we tested how two different machine learning-based methods performed when decoding functional information from the proteomes of selected model organisms. We found that protein language models are more precise and informative than deep learning methods for all the species tested and across the three gene ontologies studied, and that they better recover functional information from transcriptomic experiments. The results obtained indicate that these language models are likely to be suitable for large-scale annotation and downstream analyses, and we recommend a guide for their use.
PubMed: 38962255
DOI: 10.1093/nargab/lqae078 -
Frontiers in Plant Science 2024The green alga can grow photoautotrophically utilizing light and CO, and heterotrophically utilizing acetate. The physiological and biochemical responses of autotrophy...
BACKGROUND
The green alga can grow photoautotrophically utilizing light and CO, and heterotrophically utilizing acetate. The physiological and biochemical responses of autotrophy and heterotrophy are different in . However, there is no complete understanding of the molecular physiology between autotrophy and heterotrophy. Therefore, we performed biochemical, molecular and transcriptome analysis of between autotrophy and heterotrophy.
RESULTS
The cell growth characterization demonstrated that heterotrophic cell had enhanced growth rates, and autotrophic cell accumulated more chlorophyll. The transcriptome data showed that a total of 2,970 differentially expressed genes (DEGs) were identified from photoautotrophy 12h (P12h) to heterotrophy 12h (H12h). The DEGs were involved in photosynthesis, the tricarboxylic acid cycle (TCA), pyruvate and oxidative phosphorylation metabolisms. Moreover, the results of qRT-PCR revealed that the relative expression levels of malate dehydrogenase (MDH), succinate dehydrogenase (SDH), ATP synthase (ATPase), and starch synthase (SSS) were increased significantly from P12h and H12h. The protein activity of NAD-malate dehydrogenase (NAD-MDH) and succinate dehydrogenase (SDH) were significantly higher in the H12h group.
CONCLUSION
The above results indicated that the high growth rate observed in heterotrophic cell may be the effects of environmental or genetic regulation of photosynthesis. Therefore, the identification of novel candidate genes in heterotrophy will contribute to the development of microalga strains with higher growth capacity and better performance for biomass production.
PubMed: 38962244
DOI: 10.3389/fpls.2024.1407915 -
Frontiers in Plant Science 2024Bulk commodity row crop production in the United States is frequently subject to narrow profit margins, often complicated by weather, supply chains, trade, and other...
Bulk commodity row crop production in the United States is frequently subject to narrow profit margins, often complicated by weather, supply chains, trade, and other factors. Farmers seeking to increase profits and hedge against market volatility often seek to diversify their operations, including producing more lucrative or productive crop varieties. Recombinant plants producing animal or other non-native proteins (commonly referred to as plant molecular farming) present a value-added opportunity for row crop farmers. However, these crops must be produced under robust identity preserved systems to prevent comingling with bulk commodities to maintain the value for farmers, mitigate against market disruptions, and minimize any potential food, feed, or environmental risks.
PubMed: 38962242
DOI: 10.3389/fpls.2024.1434778 -
Data in Brief Jun 2024The bacterium YSY-1.2 was recently isolated from soil collected from Yok Don National Park in Vietnam. Previous experiments showed this bacterium possesses high...
The bacterium YSY-1.2 was recently isolated from soil collected from Yok Don National Park in Vietnam. Previous experiments showed this bacterium possesses high chitin-degrading activity, plant-growth promotion, and biocontrol capacity. Here, we report the draft genome sequence of strain YSY-1.2 for further characterizations related to crop production. The genome sequencing was performed using the DNBSeq-G99 with the Illumina platform. The draft genome of YSY-1.2 has 8,240,519 bp in length and comprises 135 contigs. It has an N50 of 315,408 bp and a GC% of 52.8%. The genome contains 7498 protein-coding genes, 87 tRNA genes, and 1 rRNA gene. Among the protein-coding sequences, 6610 were assigned by COG, while 3230 were assigned by KEGG. The genome possesses at least 61 genes involved in environmental adaptation and plant growth promotion. Additionally; there are 258 carbohydrate-active enzymes deduced from the genome; among them, at least 14 may contribute to the biocontrol capacity. The chitin-degrading system of strain YSY-1.2 contains 16 chitinolytic enzymes, comprising 10 chitinases, 4 β--acetylhexosaminidases, and 2 auxiliary activities. Furthermore, 32 gene clusters encoding antimicrobial metabolites were identified from the genome, with 17 showing no sequence similarities to reported clusters. Data provide an insight into the genomic information of strain YSY-1.2 and could lead to valuable further explorations and applications in crop production. This is the first report describing the genome sequence of isolated from Vietnam.
PubMed: 38962208
DOI: 10.1016/j.dib.2024.110285 -
Data in Brief Jun 2024Genomes of Halomonas species have been studied using the BV-BRC Bioinformatics tool for the presence of CDS, non-CDS, AMR genes, VF genes, transporters, drug targets, GC...
Genomes of Halomonas species have been studied using the BV-BRC Bioinformatics tool for the presence of CDS, non-CDS, AMR genes, VF genes, transporters, drug targets, GC content, and GC skew from outside to the center of the circular view, followed by phylogenetic analysis of unique 1, 4, 5, 6-Tetrahydro-2-methyl-4-pyrimidinecarboxylic acid (THMP) gene clusters for relatedness within the genus Halomonas. Protein structure and chemical structure of 1, 4, 5, 6-Tetrahydro-2-methyl-4-pyrimidinecarboxylic acid (THMP) encoded by the UspA gene in Halomonas strains and amino acid sequence of the novel UspA gene have been predicted by computational method.
PubMed: 38962192
DOI: 10.1016/j.dib.2024.110272 -
Data in Brief Jun 2024Here, we present, for the first time, the Ion Torrent next-generation sequencing (NGS) data for five houndsharks (Chondrichthyes: Triakidae), which include (number of...
Here, we present, for the first time, the Ion Torrent next-generation sequencing (NGS) data for five houndsharks (Chondrichthyes: Triakidae), which include (number of bases pairs (bp) 17,487; GenBank accession number ON652874), (16,708; ON652873), (16,755; ON075077), (16,708; ON075076), and (16,746; ON075075). All assembled mitogenomes encode 13 protein-coding genes (PCGs), two ribosomal (r)RNA genes, and 22 transfer (t)RNA genes ( and are duplicated), except for which contains 23 tRNA genes where is duplicated. The data presented in this paper can assist other researchers in further elucidating the diversification of triakid species and the phylogenetic relationships within Carcharhiniformes (groundsharks) as mitogenomes accumulate in public repositories.
PubMed: 38962188
DOI: 10.1016/j.dib.2024.110280 -
Oxidative Medicine and Cellular... 2024Approximately 70% of all strokes occur in patients over 65 years old, and stroke increases the risk of developing dementia. The circle of Willis (CoW), the ring of...
Approximately 70% of all strokes occur in patients over 65 years old, and stroke increases the risk of developing dementia. The circle of Willis (CoW), the ring of arteries at the base of the brain, links the intracerebral arteries to one another to maintain adequate cerebral perfusion. The CoW proteome is affected in cerebrovascular and neurodegenerative diseases, but changes related to aging have not been described. Here, we report on a quantitative proteomics analysis comparing the CoW from five young (2-3-month-old) and five aged male (18-20-month-old) mice using gene ontology (GO) enrichment, ingenuity pathway analysis (IPA), and iPathwayGuide tools. This revealed 242 proteins that were significantly dysregulated with aging, among which 189 were upregulated and 53 downregulated. GO enrichment-based analysis identified blood coagulation as the top biological function that changed with age and integrin binding and extracellular matrix constituents as the top molecular functions. Consistent with these findings, iPathwayGuide-based impact analysis revealed associations between aging and the complement and coagulation, platelet activation, ECM-receptor interaction, and metabolic process pathways. Furthermore, IPA analysis revealed the enrichment of 97 canonical pathways that contribute to inflammatory responses, as well as 59 inflammation-associated upstream regulators including 39 transcription factors and 20 cytokines. Thus, aging-associated changes in the CoW proteome in male mice demonstrate increases in metabolic, thrombotic, and inflammatory processes.
Topics: Animals; Circle of Willis; Aging; Male; Proteome; Mice; Vascular Diseases; Mice, Inbred C57BL; Proteomics
PubMed: 38962180
DOI: 10.1155/2024/4887877