Comparative Analysis of Comprehensive Genomic Profile in Thymomas and Recurrent Thymomas Reveals Potentially Actionable Mutations for Target Therapies.

Molecular profiles of thymomas and recurrent thymomas are far from being defined. Herein, we report an analysis of a comprehensive genetic profile (CGP) in a highly selected cohort of recurrent thymomas. Among a cohort of 426 thymomas, the tissue was available in 23 recurrent tumors for matching the biomolecular results obtained from primary and relapse samples. A control group composed of non-recurrent thymoma patients was selected through a propensity score match analysis. CGP was performed using the NGS Tru-SightOncology assay to evaluate TMB, MSI, and molecular alterations in 523 genes. CGP does not differ when comparing initial tumor with tumor relapse. A significantly higher frequency of cell cycle control genes alterations (100.0% vs. 57.1%, p = 0.022) is detected in patients with early recurrence (<32 months) compared to late recurrent cases. The CGPs were similar in recurrent thymomas and non-recurrent thymomas. Finally, based on NGS results, an off-label treatment or clinical trial could be potentially proposed in >50% of cases (oncogenic Tier-IIC variants). In conclusion, CGPs do not substantially differ between initial tumor vs. tumor recurrence and recurrent thymomas vs. non-recurrent thymomas. Cell cycle control gene alterations are associated with an early recurrence after thymectomy. Multiple target therapies are potentially available by performing a comprehensive CGP, suggesting that a precision medicine approach on these patients could be further explored.

Development of a Folding Paper System To Enable the Analysis of Gene Profile of Short- and Long-Distance Cancer Cell Migration.

In cancer metastasis, where mortality rates remain high despite advancements in medical treatments, understanding the molecular pathways and cellular dynamics underlying tumor spread is critical for devising more effective therapeutic strategies. Here, a folding paper system was proposed and developed to mimic native tumor microenvironment. This system, composed of 7 stacked layers of paper enclosed in a holder, allows for the culture of cancer cells under conditions mimicking those found in solid tumors, including limited oxygen and nutrients. Because of the migratory capabilities of cancer cells, the cells in the center layer could migrated to outer layers of the paper stack, enabling the differentiation of cells based on their migratory potential. Subsequent gene expression analysis, conducted through RT-PCR and RNA sequencing, revealed significant correlations between cancer cell migration distance and the expression of genes associated with hypoxia, metabolism, ATP production, and cellular process. Moreover, our study identified cells with aggressive phenotypic traits from the outer layers of the paper stack, highlighting the potential of this system for enabling the study of aggressive cancer cell characteristics. Validation of the folding paper system against clinical carcinoma tissue demonstrated its ability to faithfully mimic the native tumor microenvironment. Overall, our findings underscore the utility of the folding paper system as a valuable tool for investigating and identifying critical molecular pathways involved in cancer metastasis.

The Dysregulation of the Monocyte-Dendritic Cell Interplay Is Associated with In-Hospital Mortality in COVID-19 Pneumonia.

Background: The monocyte-phagocyte system (MPS), including monocytes/macrophages and dendritic cells (DCs), plays a key role in anti-viral immunity. We aimed to analyze the prognostic value of the MPS components on in-hospital mortality in a cohort of 58 patients (M/F; mean age ± SD years) with COVID-19 pneumonia and 22 age- and sex-matched healthy controls. Methods: We measured frequencies and absolute numbers of peripheral blood CD169+ monocytes, conventional CD1c+ and CD141+ (namely cDC2 and cDC1), and plasmacytoid CD303+ DCs by means of multi-parametric flow cytometry. A gene profile analysis of 770 immune-inflammatory-related human genes and 20 SARS-CoV-2 genes was also performed. Results: Median frequencies and absolute counts of CD169-expressing monocytes were significantly higher in COVID-19 patients than in controls (p 0.04 and p 0.01, respectively). Conversely, percentages and absolute numbers of all DC subsets were markedly depleted in patients (p < 0.0001). COVID-19 cases with absolute counts of CD169+ monocytes above the median value of 114.68/µL had significantly higher in-hospital mortality (HR 4.96; 95% CI: 1.42-17.27; p = 0.02). Interleukin (IL)-6 concentrations were significantly increased in COVID-19 patients (p < 0.0001 vs. controls), and negatively correlated with the absolute counts of circulating CD1c+ cDC2 (r = -0.29, p = 0.034) and CD303+ pDC (r = -0.29, p = 0.036) subsets. Viral genes were upregulated in patients with worse outcomes along with inflammatory mediators such as interleukin (IL)-1 beta, tumor necrosis-α (TNF-α) and the anticoagulant protein (PROS1). Conversely, surviving patients had upregulated genes related to inflammatory and anti-viral-related pathways along with the T cell membrane molecule CD4. Conclusions: Our results suggest that the dysregulated interplay between the different components of the MPS along with the imbalance between viral gene expression and host anti-viral immunity negatively impacts COVID-19 outcomes. Although the clinical scenario of COVID-19 has changed over time, a deepening of its pathogenesis remains a priority in clinical and experimental research.

Intermittent fasting, exercise, and dietary modification induce unique transcriptomic signatures of multiple tissues governing metabolic homeostasis during weight loss and rebound weight gain.

Obesity and its related metabolic diseases bring great challenges to public health. In-depth understanding on the efficacy of weight-loss interventions is critical for long-term weight control. Our study demonstrated the comparable efficacy of exercise (EX), intermittent fasting (IF), or the change of daily diet from an unhealthy to a normal chow (DR) for weight reduction, but largely divergently affected metabolic status and transcriptome of subcutaneous fat, scapular brown fat, skeletal muscles and liver in high-fat-high-fructose diet (HFHF) induced obese mice. EX and IF reduced systematic inflammation, improved glucose and lipid metabolism in liver and muscle, and amino acid metabolism and thermogenesis in adipose tissues. EX exhibited broad regulatory effects on TCA cycle, carbon metabolism, thermogenesis, propanoate-, fatty acid and amino acid metabolism across multiple tissues. IF prominently affected genes involved in mitophagy and autophagy in adipose tissues and core genes involved in butanoate metabolism in liver. DR, however, failed to improve metabolic homeostasis and biological dysfunctions in obese mice. Notably, by exploring potential inter-organ communication, we identified an obesity-resistant-like gene profile that were strongly correlated with HFHF induced metabolic derangements and could predict the degree of weight regain induced by the follow-up HFHF diet. Among them, 12 genes (e.g., Gdf15, Tfrc, Cdv3, Map2k4, and Nqo1) were causally associated with human metabolic traits, i.e., BMI, body fat mass, HbA1C, fasting glucose, and cholesterol. Our findings provide critical groundwork for improved understanding of the impacts of weight-loss interventions on host metabolism. The identified genes predicting weight regain may be considered regulatory targets for improving long-term weight control.

Exploring miRNA­target gene profiles associated with drug resistance in patients with breast cancer receiving neoadjuvant chemotherapy.

Exosomal microRNAs (miRNAs) are closely related to drug resistance in patients with breast cancer (BC); however, only a few roles of the exosomal miRNA-target gene networks have been clinically implicated in drug resistance in BC. Therefore, the present study aimed to identify the differential expression of exosomal miRNAs associated with drug resistance and their target mRNAs. In vitro microarray analysis was used to verify differentially expressed miRNAs (DEMs) in drug-resistant BC. Next, tumor-derived exosomes (TDEs) were isolated. Furthermore, it was determined whether the candidate drug-resistant miRNAs were also significant in TDEs, and then putative miRNAs in TDEs were validated in plasma samples from 35 patients with BC (20 patients with BC showing no response and 15 patients with BC showing a complete response). It was confirmed that the combination of five exosomal miRNAs, including miR-125b-5p, miR-146a-5p, miR-484, miR-1246-5p and miR-1260b, was effective for predicting therapeutic response to neoadjuvant chemotherapy, with an area under the curve value of 0.95, sensitivity of 75%, and specificity of 95%. Public datasets were analyzed to identify differentially expressed genes (DEGs) related to drug resistance and it was revealed that BAK1, NOVA1, PTGER4, RTKN2, AGO1, CAP1, and ETS1 were the target genes of exosomal miRNAs. Networks between DEMs and DEGs were highly correlated with mitosis, metabolism, drug transport, and immune responses. Consequently, these targets could be used as predictive markers and therapeutic targets for clinical applications to enhance treatment outcomes for patients with BC.

Differential gene expression patterns in ST-elevation Myocardial Infarction and Non-ST-elevation Myocardial Infarction.

The ST-elevation Myocardial Infarction (STEMI) and Non-ST-elevation Myocardial Infarction (NSTEMI) might occur because of coronary artery stenosis. The gene biomarkers apply to the clinical diagnosis and therapeutic decisions in Myocardial Infarction. The aim of this study was to introduce, enrich and estimate timely the blood gene profiles based on the high-throughput data for the molecular distinction of STEMI and NSTEMI. The text mining data (50 genes) annotated with DisGeNET data (144 genes) were merged with the GEO gene expression data (5 datasets) using R software. Then, the STEMI and NSTEMI networks were primarily created using the STRING server, and improved using the Cytoscape software. The high-score genes were enriched using the KEGG signaling pathways and Gene Ontology (GO). Furthermore, the genes were categorized to determine the NSTEMI and STEMI gene profiles. The time cut-off points were identified statistically by monitoring the gene profiles up to 30 days after Myocardial Infarction (MI). The gene heatmaps were clearly created for the STEMI (high-fold genes 69, low-fold genes 45) and NSTEMI (high-fold genes 68, low-fold genes 36). The STEMI and NSTEMI networks suggested the high-score gene profiles. Furthermore, the gene enrichment suggested the different biological conditions for STEMI and NSTEMI. The time cut-off points for the NSTEMI (4 genes) and STEMI (13 genes) gene profiles were established up to three days after Myocardial Infarction. The study showed the different pathophysiologic conditions for STEMI and NSTEMI. Furthermore, the high-score gene profiles are suggested to measure up to 3 days after MI to distinguish the STEMI and NSTEMI.

Bacterial diversity, community structure and function in association of potato scabby tubers during storage in northern Thailand.

Potato scab is a common potato tuber disease that affects quality and cost in the marketplace, shortening storage, and increasing the chance for secondary infection. The tubers with disease severity of 1 to 4 are accepted and stored in potato storage for cheap selling in Thailand. However, there are few studies of the bacterial community of the scabby tuber during storage. Thus, we aim to elucidate the diversity, structure, and function of the bacterial community of 30-day storage potato scabby tubers stored in different temperatures using 16S amplicon metagenomic sequencing. Bacterial communities of storage potato scabby tubers (Spunta cultivar) collected from different storage temperatures, 4 °C (MEP1) and 6 °C (MEP2), were characterized using 16S rRNA amplicon metagenomic sequencing. The alpha-diversity abundance in the bacteriome of the scabby tubers stored at 6 °C was higher than in those stored at 4 °C. Actinobacteria (34.7%) was a dominant phylum in MEP1, while Proteobacteria (39.9%) was predominant in MEP2. The top 10 genera of both communities were Rhizobium group, Streptomyces, Pectobacterium, Ruminococcus, Cellulomonas, Promicromonospora, Prevotella, Enterobacter, Pedobacter, and Paenarthrobacter. Moreover, functional profile prediction of both communities reveals essential genes in the pathosystem: nos, bglA, and cebEFG-msiK for potato scab disease and phc and peh operons for rot disease. Our findings are the first study to explore details of the bacteriome of the accepted potato scabby tubers for selling during storage in Thailand and strongly indicate that although potatoes were stored at low temperatures, diseases still occur by secondary pathogens.

Characterisation of changes in global genes expression in the lung of ICR mice in response to the inflammation and fibrosis induced by polystyrene nanoplastics inhalation.

This study characterised the changes in global gene expression in the lung of ICR mice in response to the inflammation and fibrosis induced by the inhalation of 0.5 µm polystyrene (PS)-nanoplastics (NPs) at various concentrations (4, 8, and 16 µg/mL) for 2 weeks. The total RNA extracted from the lung tissue of NPs-inhaled mice was hybridised into oligonucleotide microarrays. Significant upregulation was detected in several inflammatory responses, including the number of immune cells in bronchoalveolar lavage fluid (BALF), the expression level of inflammatory cytokines, mucin secretion, and histopathological changes, while they accumulated average of 13.38 ± 1.0 µg/g in the lungs of the inhaled ICR mice. Similar responses were observed regarding the levels of fibrosis-related factors in the NPs-inhaled lung of ICR mice, such as pulmonary parenchymal area, expression of pro-fibrotic marker genes, and TGF-ß1 downstream signalling without any significant hepatotoxicity and nephrotoxicity. In microarray analyses, 60 genes were upregulated, and 55 genes were downregulated in the lung of ICR mice during inflammation and fibrosis induced by NPs inhalation compared to the Vehicle-inhaled mice. Among these genes, many were categorised into several ontology categories, including the anatomical structure, binding, membrane, and metabolic process. Furthermore, the major genes in the upregulated categories included Igkv14-126000, Egr1, Scel, Lamb3, and Upk3b. In contrast, the major genes in the down-regulated categories were Olfr417, Olfr519, Rps16, Rap2b, and Vmn1r193. These results suggest several gene functional groups and individual genes as specific biomarkers respond to inflammation and fibrosis induced by PS-NPs inhalation in ICR mice. Supplementary Information: The online version contains supplementary material available at 10.1007/s43188-023-00188-y.

Differential priority effects impact taxonomy and functionality of host-associated microbiomes.

Most multicellular eukaryotes host complex communities of microorganisms, but the factors that govern their assembly are poorly understood. The settlement of specific microorganisms may have a lasting impact on community composition, a phenomenon known as the priority effect. Priority effects of individual bacterial strains on a host's microbiome are, however, rarely studied and their impact on microbiome functionality remains unknown. We experimentally tested the effect of two bacterial strains (Pseudoalteromonas tunicata D2 and Pseudovibrio sp. D323) on the assembly and succession of the microbial communities associated with the green macroalga Ulva australis. Using 16S rRNA gene sequencing and qPCR, we found that both strains exert a priority effect, with strain D2 causing initially strong but temporary taxonomic changes and strain D323 causing weaker but consistent changes. Consistent changes were predominately facilitatory and included taxa that may benefit the algal host. Metagenome analyses revealed that the strains elicited both shared (e.g., depletion of type III secretion system genes) and unique (e.g., enrichment of antibiotic resistance genes) effects on the predicted microbiome functionality. These findings indicate strong idiosyncratic effects of colonizing bacteria on the structure and function of host-associated microbial communities. Understanding the idiosyncrasies in priority effects is key for the development of novel probiotics to improve host condition.

Genetic Diversity of Actinobacillus pleuropneumoniae Serovars in Hungary.

A total of 114 Actinobacillus pleuropneumoniae isolates from porcine hemorrhagic necrotic pleuropneumonia were characterized by the examination of biotype, serovar, antibiotic resistance genes, and genes of toxin production. Pulsed-field gel electrophoresis was used to analyze their genetic relationship, which identified 16 clusters. Serovar 2 (50 isolates), serovar 13 (25 isolates), serovar 9 (11 isolates), and serovar 16 (7 isolates) were the most frequent serovars. Serovar 2 formed nine distinguishable clusters; serovar 13 and serovar 16 were less diverse, exhibiting two potentially related subclusters; serovar 9 was represented by a single cluster. Remarkably small differences were seen in the core genome when nine representative isolates of serovar 13 were subjected to whole-genome sequencing. Tetracycline resistance was relatively frequent in the two clusters of serovar 13; one of them was also frequently resistant against beta-lactams. Resistance in other serovars was sporadic. All isolates carried the apxIV gene. The toxin profiles of serovar 2 were characterized by the production of ApxII and ApxIII toxins, except for a small cluster of three isolates: serovar 9 and serovar 16 isolates produced ApxI and ApxII toxins. Serovar 13 carried apxII and apxIBD genes, indicating the production of the ApxII toxin, but not of ApxI or ApxIII. The unusually high frequency and low diversity of serovar 13 are not explained by its virulence properties, but the high frequency of resistance to beta-lactams and tetracyclines may have played a role in its spread. The emergence of serovar 16 may be facilitated by its high virulence, also explaining its high clonality.

Exploring the taxonomic and functional diversity of marine benthic micro-Eukaryotes along the Red Sea coast of Jeddah city.

Backgrounds: Diverse marine habitats along Jeddah's Red Sea coast support rich biodiversity. Few studies have been done on its diverse communities, especially its microbial counterparts. Metagenomic analysis of marine benthic micro-eukaryotic communities was performed for the first time on the Red Sea coast of Jeddah. This research looks into their community structure and metabolic potential. Methods: Next-generation sequencing was used to examine the micro-eukaryotic communities of seven sedimentary soil samples from four Jeddah coast locations. After isolating DNA from seven benthic sedimentary soil samples, the 18S rDNA V4 regions were amplified and sequenced on the Illumina MiSeq. It was also verified using an Agilent Technologies 2100 Bioanalyzer with a DNA 1000 chip (Agilent Technologies, Fisher Scientific). A standard curve of fluorescence readings generated by qPCR quantification using the Illumina library was achieved using the GS FLX library. Metagenomic data analysis was used to evaluate the microbial communities' biochemical and enzymatic allocations in studied samples. Results: Blast analysis showed that the top ten phyla were Annelida, Eukaryota, Diatomea, Porifera, Phragmoplastophyta, Arthropoda, Dinoflagellata, Xenacoelomorpha Nematoda, and uncultured. Annelida was also found in the highest percentage (93%), in the sample M followed by Porifera (64%), the most abundant in the control sample then Eukaryotes (61%), Phragmatoplastophyta (55%), Arthropoda, and Diatomea (the least common) (32%). community diversity analysis: using Shannon and inverse Simpson indices showed sediment composition to be effective. Also, PICRUST2 indicated that the most abundant pathways were pyruvate fermentation to isobutanol, pyrimidine deoxyribonucleotide phosphorylation, adenosine ribonucleotide de novo biosynthesis, guanosine ribonucleotide de novo biosynthesis, NAD salvage pathway I, the super pathway of glyoxylate bypass and aerobic respiration I (cytochrome c). Conclusion: Results showed that high throughput metagenomics could reveal species diversity and estimate gene profiles. Environmental factors appear to be more important than geographic variation in determining the structure of these microbial communities. This study provides the first report of marine benthic micro-eukaryotic communities found on the Red Sea coast of Jeddah and will serve as a good platform for future research.

Role of Ape1 in Impaired DNA Repair Capacity in Battery Recycling Plant Workers Exposed to Lead.

Exposure to lead in environmental and occupational settings continues to be a serious public health problem. At environmentally relevant doses, two mechanisms may underlie lead exposition-induced genotoxicity, disruption of the redox balance and an interference with DNA repair systems. The aim of the study was to evaluate the ability of lead exposition to induce impaired function of Ape1 and its impact on DNA repair capacity of workers chronically exposed to lead in a battery recycling plant. Our study included 53 participants, 37 lead exposed workers and 16 non-lead exposed workers. Lead intoxication was characterized by high blood lead concentration, high lipid peroxidation and low activity of delta-aminolevulinic acid dehydratase (δ-ALAD). Relevantly, we found a loss of DNA repair capacity related with down-regulation of a set of specific DNA repair genes, showing specifically, for the first time, the role of Ape1 down regulation at transcriptional and protein levels in workers exposed to lead. Additionally, using a functional assay we found an impaired function of Ape1 that correlates with high blood lead concentration and lipid peroxidation. Taken together, these data suggest that occupational exposure to lead could decrease DNA repair capacity, inhibiting the function of Ape1, as well other repair genes through the regulation of the ZF-transcription factor, promoting the genomic instability.

massiveGST: A Mann-Whitney-Wilcoxon Gene-Set Test Tool That Gives Meaning to Gene-Set Enrichment Analysis.

Gene-set enrichment analysis is the key methodology for obtaining biological information from transcriptomic space's statistical result. Since its introduction, Gene-set Enrichment analysis methods have obtained more reliable results and a wider range of application. Great attention has been devoted to global tests, in contrast to competitive methods that have been largely ignored, although they appear more flexible because they are independent from the source of gene-profiles. We analyzed the properties of the Mann-Whitney-Wilcoxon test, a competitive method, and adapted its interpretation in the context of enrichment analysis by introducing a Normalized Enrichment Score that summarize two interpretations: a probability estimate and a location index. Two implementations are presented and compared with relevant literature methods: an R package and an online web tool. Both allow for obtaining tabular and graphical results with attention to reproducible research.

Clostridioides (Clostridium) difficile in children with diarrhoea in Vietnam.

BACKGROUND: Clostridioides (Clostridium) difficile commonly causes hospital-acquired infection which can range from mild diarrhoea to life-threatening toxic megacolon and even death. Reports on C. difficile infection (CDI) in Vietnam are limited, so this study was designed to evaluate the prevalence, molecular epidemiology and antimicrobial susceptibility of C. difficile isolated from children with diarrhoea in Vietnam. Infants are often colonised with C. difficile and it was hypothesised that those colonising strains would represent strains of C. difficile circulating in the hospital/region at the time, however, this was not an attempt to determine if C. difficile was the cause of the diarrhoea. METHODS: Diarrhoeal stool samples collected at two children's hospitals in northern Vietnam from October 1, 2020 to February 28, 2021 were transported to Perth, Western Australia, for culture of C. difficile and further investigations on isolates; PCR ribotyping, toxin gene profiling and antimicrobial susceptibility testing. RESULTS: From these hospitals, 370 diarrhoeal stool samples were collected, most from children aged 1-15 months (71.9%; 266/370). The overall prevalence of C. difficile in stool samples from children aged ≤16 years was 37.8% (140/370) and the highest prevalence was in the 2-12 months age group (52.9%; 74/140). In total, 151 isolates of C. difficile were recovered; the proportion of toxigenic isolates was 16.6% (25/151). Of the 25 toxigenic C. difficile isolates, the toxin gene profiles A+B+CDT- and A-B+CDT- comprised 72% and 28%, respectively. The four most prevalent C. difficile ribotypes (RTs) were QX 011 (25/151), RT 010 (25/151), QX 107 (12/151) and RT 012 (11/151). All isolates were susceptible to vancomycin, metronidazole and fidaxomicin, while there was significant resistance to clindamycin (90.1%), and some to moxifloxacin (6.6%) and rifaximin (3.3%). CONCLUSION: The prevalence of C. difficile in children with diarrhoea was high (37.8%) although the proportion of toxigenic strains was comparatively low. The clinical significance of any isolate needs to be determined.

Effects of hot water spray and sub-zero saline chilling on bacterial decontamination of broiler carcasses.

Reduction of Salmonella on poultry carcasses is one way to prevent salmonellosis. The purpose of this research was to evaluate the effects of subzero saline chilling (SSC) with/without hot water spray (HWS) on broiler carcasses prior to chilling for bacterial reduction. Eviscerated broiler carcasses were subjected to water immersion chilling (WIC, 0% NaCl/0.5°C) or SSC (4% NaCl/-2.41°C) with/without prior HWS at 71°C for 1 min. Broiler carcasses in SSC were chilled faster than those in WIC, regardless of HWS. The combination of HWS and SSC resulted in the best reduction of mesophilic aerobic bacteria, Escherichia coli, and total coliforms on the carcasses over the WIC, SSC, and HWS/WIC. No Salmonella was detected on the carcasses in SSC and HWS/SSC while Salmonella positive was observed on the carcasses chilled in WIC and HWS/WIC. A trace of Gram-negative genus was detected on carcasses in HWS/SSC while many other microbiomes were observed on those in WIC, SSC, and HWS/WIC when quantitative microbiota profiles of 16S rRNA gene sequences were evaluated. Based on these results, chilling of broiler carcasses in 4% NaCl/-2.41°C after HWS at 71°C for 1 min significantly reduced carcass chilling time and bacterial contamination over the control chilling.

Establishment of a prognostic ferroptosis-related gene profile in acute myeloid leukaemia.

Acute myeloid leukaemia (AML) is a heterogeneous disease with a difficult to predict prognosis. Ferroptosis, an iron-induced programmed cell death, is a promising target for cancer therapy. Nevertheless, not much is known about the relationship between ferroptosis-related genes and AML prognosis. Herein, we retrieved RNA profile and corresponding clinical data of AML patients from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. Univariate Cox analysis was employed to identify ferroptosis-related genes significantly associated with AML prognosis. Next, the least absolute shrinkage and selection operator (LASSO) regression was employed to establish a prognostic ferroptosis-related gene profile. 12 ferroptosis-related genes were screened to generate a prognostic model, which stratified patients into a low- (LR) or high-risk (HR) group. Using Kaplan-Meier analysis, we demonstrated that the LR patients exhibited better prognosis than HR patients. Moreover, receiver operating characteristic (ROC) curve analysis confirmed that the prognostic model showed good predictability. Functional enrichment analysis indicated that the infiltration of regulatory T cells (Treg) differed vastly between the LR and HR groups. Our prognostic model can offer guidance into the accurate prediction of AML prognosis and selection of personalized therapy in clinical practice.

Discerning the Antimicrobial Resistance, Virulence, and Phylogenetic Relatedness of Salmonella Isolates Across the Human, Poultry, and Food Materials Sources in Malaysia.

Salmonella enterica subspecies enterica serovar Enteritidis is one of the major foodborne zoonotic pathogens globally. It has significantly impacted human health and global trade. In this investigation, whole-genome sequencing was employed to determine the antimicrobial resistance (AMR) pattern of a collection of Salmonella Enteritidis isolated from humans, poultry, and food sources. The study also investigated the virulence genes profile of the isolates as well as the phylogenetic relationships among strains. Illumina NextSeq technology was used to sequence the genome of 82 Salmonella Enteritidis strains isolated over 3 years (2016-2018) in Peninsular Malaysia. The pattern of resistance showed that tetracycline had the highest frequency (37/82, 45.12%), and isolates from food samples showed the highest rate of 9/18 (50.00%), followed by human 17/35 (48.57%) and then poultry 11/29 (37.93%). The second drug with the highest resistance rate is ampicillin with 5/29 (17.24%) for poultry, 4/35 (11.43%) for human, and 0/18 (0.00%) for food isolates respectively. Similarly, a total of 19 antimicrobial resistance (AMR) genes corresponding to the nine drugs used in the disc diffusion assay were evaluated from the whole genome sequence data. The aminoglycoside resistance gene aac(6')-ly was detected in 79 of the 82 isolates (96.34%). While the phylogenetic analysis revealed distinct lineages isolated, the three sources indicating possible cross-contamination. In conclusion, the results showed that the genomic profile of Salmonella Enteritidis isolated from humans, poultry, and food samples share genetic traits, hence the need to institute measures at controlling the continuous spread of these resistant pathogens.

Robust innate responses to SARS-CoV-2 in children resolve faster than in adults without compromising adaptive immunity.

SARS-CoV-2 infection in children is less severe than it is in adults. We perform a longitudinal analysis of the early innate responses in children and adults with mild infection within household clusters. Children display fewer symptoms than adults do, despite similar initial viral load, and mount a robust anti-viral immune signature typical of the SARS-CoV-2 infection and characterized by early interferon gene responses; increases in cytokines, such as CXCL10 and GM-CSF; and changes in blood cell numbers. When compared with adults, the antiviral response resolves faster (within a week of symptoms), monocytes and dendritic cells are more transiently activated, and genes associated with B cell activation appear earlier in children. Nonetheless, these differences do not have major effects on the quality of SARS-CoV-2-specific antibody responses. Our findings reveal that better early control of inflammation as observed in children may be key for rapidly controlling infection and limiting the disease course.

Cytotoxic T lymphocyte antigen-4 regulates development of xenogenic graft versus host disease in mice via modulation of host immune responses induced by changes in human T cell engraftment and gene expression.

Graft versus host disease (GvHD) is a major clinical problem with a significant unmet medical need. We examined the role of cytotoxic T lymphocyte antigen-4 (CTLA-4) in a xenogenic GvHD (xeno-GvHD) model induced by injection of human peripheral mononuclear cells (hPBMC) into irradiated non-obese diabetic (NOD) SCID gamma (NSG) mice. Targeting the CTLA-4 pathway by treatment with CTLA-4 immunoglobulin (Ig) prevented xeno-GvHD, while anti-CTLA-4 antibody treatment exacerbated the lethality and morbidity associated with GvHD. Xeno-GvHD is associated with infiltration of hPBMCs into the lungs, spleen, stomach, liver and colon and an increase in human proinflammatory cytokines, including interferon (IFN)-γ, tumor necrosis factor (TNF)-α and interleukin (IL)-5. Infiltration of donor cells and increases in cytokines were attenuated by treatment with CTLA-4 Ig, but remained either unaffected or enhanced by anti-CTLA-4 antibody. Further, splenic human T cell phenotyping showed that CTLA-4 Ig treatment prevented the engraftment of human CD45+ cells, while anti-CTLA-4 antibody enhanced donor T cell expansion, particularly CD4+ (CD45RO+ ) subsets, including T box transcription factor TBX21 (Tbet)+ CXCR3+ and CD25+ forkhead box protein 3 (FoxP3) cells. Comprehensive analysis of transcriptional profiling of human cells isolated from mouse spleen identified a set of 417 differentially expressed genes (DEGs) by CTLA-4 Ig treatment and 13 DEGs by anti-CTLA-4 antibody treatment. The CTLA-4 Ig regulated DEGs mapped to down-regulated apoptosis, inflammasome, T helper type 17 (Th17) and regulatory T cell (Treg ) pathways and enhanced Toll-like receptor (TLR) receptor signaling, TNF family signaling, complement system and epigenetic and transcriptional regulation, whereas anti-CTLA-4 antibody produced minimal to no impact on these gene pathways. Our results show an important role of co-inhibitory CTLA-4 signaling in xeno-GvHD and suggest the therapeutic utility of other immune checkpoint co-inhibitory pathways in the treatment of immune-mediated diseases driven by hyperactive T cells.

High-Throughput Gene and Protein Analysis Revealed the Response of Disc Cells to Vitamin D, Depending on the VDR FokI Variants.

Vitamin D showed a protective effect on intervertebral disc degeneration (IDD) although conflicting evidence is reported. An explanation could be due to the presence of the FokI functional variant in the vitamin D receptor (VDR), observed as associated with spine pathologies. The present study was aimed at investigating-through high-throughput gene and protein analysis-the response of human disc cells to vitamin D, depending on the VDR FokI variants. The presence of FokI VDR polymorphism was determined in disc cells from patients with discopathy. 1,25(OH)2D3 was administered to the cells with or without interleukin 1 beta (IL-1ß). Microarray, protein arrays, and multiplex protein analysis were performed. In both FokI genotypes (FF and Ff), vitamin D upregulated metabolic genes of collagen. In FF cells, the hormone promoted the matrix proteins synthesis and a downregulation of enzymes involved in matrix catabolism, whereas Ff cells behaved oppositely. In FF cells, inflammation seems to hamper the synthetic activity mediated by vitamin D. Angiogenic markers were upregulated in FF cells, along with hypertrophic markers, some of them upregulated also in Ff cells after vitamin D treatment. Higher inflammatory protein modulation after vitamin D treatment was observed in inflammatory condition. These findings would help to clarify the clinical potential of vitamin D supplementation in patients affected by IDD.