System-related Genes Research Articles

Pathogenicity assessment of Shiga toxin-producing Escherichia coli strains isolated from wild birds in a major agricultural region in California.

Shiga toxin-producing Escherichia coli (STEC) consists of diverse strains differing in genetic make-up and virulence potential. To better understand the pathogenicity potential of STEC carried by the wildlife, three STEC and one E. coli strains isolated from wild birds near a major agricultural region in California were selected for comparative pathogenomic analyses. Three American crow (Corvus brachyrhynchos) strains, RM9088, RM9513, and RM10410, belonging to phylogroup A with serotypes O109:H48, O9:H30, and O113:H4, respectively, and a red-winged blackbird (Agelaius phoeniceus) strain RM14516 in phylogroup D with serotype O17:H18, were examined. Shiga toxin genes were identified in RM9088 (stx1a), RM10410 (stx1a + stx2d), and RM14516 (stx2a). Unlike STEC O157:H7 strain EDL933, none of the avian STEC strains harbored the pathogenicity islands OI-122, OI-57, and the locus of enterocyte effacement, therefore the type III secretion system biogenesis genes and related effector genes were absent in the three avian STEC genomes. Interestingly, all avian STEC strains exhibited greater (RM9088 and RM14516) or comparable (RM10410) cytotoxicity levels compared with EDL933. Comparative pathogenomic analyses revealed that RM9088 harbored numerous genes encoding toxins, toxins delivery systems, and adherence factors, including heat-labile enterotoxin, serine protease autotransporter toxin Pic, type VI secretion systems, protein adhesin Paa, fimbrial adhesin K88, and colonization factor antigen I. RM9088 also harbored a 36-Kb high pathogenicity island, which is related to iron acquisition and pathogenicity in Yersinia spp. Strain RM14516 carried an acid fitness island like the one in EDL933, containing a nine gene cluster involved in iron acquisition. Genes encoding extracellular serine protease EspP, subtilase cytotoxin, F1C fimbriae, and inverse autotransporter adhesin IatC were only detected in RM14516, and genes encoding serine protease autotransporter EspI and P fimbriae were only identified in RM10410. Although all curli genes were present in avian STEC strains, production of curli fimbriae was only detected for RM9088 and RM14516. Consistently, strong, moderate, and little biofilms were observed for RM9088, RM14516, and RM10410, respectively. Our study revealed novel combinations of virulence factors in two avian strains, which exhibited high level of cytotoxicity and strong biofilm formation. Comparative pathogenomics is powerful in assessing pathogenicity and health risk of STEC strains.

Comparative genomic analysis reveals differential genomic characteristics and featured genes between rapid- and slow-growing non-tuberculous mycobacteria.

Non-tuberculous mycobacteria (NTM) is a major category of environmental bacteria in nature that can be divided into rapidly growing mycobacteria (RGM) and slowly growing mycobacteria (SGM) based on their distinct growth rates. To explore differential molecular mechanisms between RGM and SGM is crucial to understand their survival state, environmental/host adaptation and pathogenicity. Comparative genomic analysis provides a powerful tool for deeply investigating differential molecular mechanisms between them. However, large-scale comparative genomic analysis between RGM and SGM is still uncovered. In this study, we screened 335 high-quality, non-redundant NTM genome sequences covering 187 species from 3,478 online NTM genomes, and then performed a comprehensive comparative genomic analysis to identify differential genomic characteristics and featured genes/protein domains between RGM and SGM. Our findings reveal that RGM has a larger genome size, more genes, lower GC content, and more featured genes/protein domains in metabolism of some main substances (e.g. carbohydrates, amino acids, nucleotides, ions, and coenzymes), energy metabolism, signal transduction, replication, transcription, and translation processes, which are essential for its rapid growth requirements. On the other hand, SGM has a smaller genome size, fewer genes, higher GC content, and more featured genes/protein domains in lipid and secondary metabolite metabolisms and cellular defense mechanisms, which help enhance its genome stability and environmental adaptability. Additionally, orthogroup analysis revealed the important roles of bacterial division and bacteriophage associated genes in RGM and secretion system related genes for better environmental adaptation in SGM. Notably, PCoA analysis of the top 20 genes/protein domains showed precision classification between RGM and SGM, indicating the credibility of our screening/classification strategies. Overall, our findings shed light on differential underlying molecular mechanisms in survival state, adaptation and pathogenicity between RGM and SGM, show the potential for our comparative genomic pipeline to investigate differential genes/protein domains at whole genomic level across different bacterial species on a large scale, and provide an important reference and improved understanding of NTM.

Polyphosphate promotes oxidation resistance of ppk-expressing transgenic rice in low phosphorus culture

Phosphorus (P) plays a crucial role in plant growth. Insufficient availability of inorganic phosphate (Pi) can significantly impact crop yields. To address this, we previously developed transgenic rice expressing the low polyphosphate kinase gene (ppk) - known as ETRS - to enhance the efficiency of P resource utilization. Previous studies have shown that ETRS thrives and presents high yields in the low P culture. ETRS and wild-type rice (WT) were cultivated to the heading stage at 15 μM of P in the low P (LP) culture and 300 μM of P in the normal culture (CK) to identify the molecular pathways behind low P tolerance. Our findings revealed that polyphosphate (polyP) significantly enhanced the growth performance of ETRS in the LP culture. This enhanced tolerance can be attributed to polyP's capacity to mitigate oxidative damage induced by LP. This was evidenced by the reduction in levels of superoxide radicals, hydrogen peroxide, and malondialdehyde. PolyP also improved the antioxidant capacity of ETRS under LP stress by regulating enzymatic antioxidants viz., superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), as well as non-enzymatic antioxidants such as ascorbate (AsA) and glutathione (GSH). In addition, transcriptomics analysis suggested that polyP synthesis positively promoted the expressions of SOD, POD, and CAT related genes and played an active role in regulating the expression of AsA-GSH cycle system related genes in ETRS in the LP culture. These results strongly support the notion that polyP within ETRS mitigates oxidative damage through enhancement of the antioxidant system, ultimately bolstering tolerance to LP conditions.

Ocular and neural genes jointly regulate the visuospatial working memory in ADHD children

ObjectiveWorking memory (WM) deficits have frequently been linked to attention deficit hyperactivity disorder (ADHD). Despite previous studies suggested its high heritability, its genetic basis, especially in ADHD, remains unclear. The current study aimed to comprehensively explore the genetic basis of visual-spatial working memory (VSWM) in ADHD using wide-ranging genetic analyses.MethodsThe current study recruited a cohort consisted of 802 ADHD individuals, all met DSM-IV ADHD diagnostic criteria. VSWM was assessed by Rey-Osterrieth complex figure test (RCFT), which is a widely used psychological test include four memory indexes: detail delayed (DD), structure delayed (SD), structure immediate (SI), detail immediate (DI). Genetic analyses were conducted at the single nucleotide polymorphism (SNP), gene, pathway, polygenic and protein network levels. Polygenic Risk Scores (PRS) were based on summary statistics of various psychiatric disorders, including ADHD, autism spectrum disorder (ASD), major depressive disorder (MDD), schizophrenia (SCZ), obsessive compulsive disorders (OCD), and substance use disorder (SUD).ResultsAnalyses at the single-marker level did not yield significant results (5E−08). However, the potential signals with P values less than E−05 and their mapped genes suggested the regulation of VSWM involved both ocular and neural system related genes, moreover, ADHD-related genes were also involved. The gene-based analysis found RAB11FIP1, whose encoded protein modulates several neurodevelopment processes and visual system, as significantly associated with DD scores (P = 1.96E−06, Padj = 0.036). Candidate pathway enrichment analyses (N = 53) found that forebrain neuron fate commitment significantly enriched in DD (P = 4.78E−04, Padj = 0.025), and dopamine transport enriched in SD (P = 5.90E-04, Padj = 0.031). We also observed a significant negative relationship between DD scores and ADHD PRS scores (P = 0.0025, Empirical P = 0.048).ConclusionsOur results emphasized the joint contribution of ocular and neural genes in regulating VSWM. The study reveals a shared genetic basis between ADHD and VSWM, with GWAS indicating the involvement of ADHD-related genes in VSWM. Additionally, the PRS analysis identifies a significant relationship between ADHD-PRS and DD scores. Overall, our findings shed light on the genetic basis of VSWM deficits in ADHD, and may have important implications for future research and clinical practice.

Abstract 040: Evidence Of Increased Glycolysis In Renal Cortex Of High Salt Fed Sprague Dawley Rats

To determine whole kidney O 2 and substance metabolism in an unanesthetized state, arterial (A), renal venous (Vr) blood and urine (U) were analyzed together with measurements of renal blood flow (RBF), blood pressure (BP) and GFR in conscious freely moving male SD rats. RBF and BP were measured continuously (24/7) via chronically implanted ultrasonic flow probe and A-line respectively. A and Vr blood through chronically implanted catheters and urine (U) were sampled intermittently when rats were fed a 0.4% NaCl (LS) diet and on days 7, 14, and 21 after switching to a 4.0% NaCl (HS) diet (HS7, HS14, HS21). A and Vr O 2 contents were determined by radiometer and a global metabolomic analysis was performed at the JAX Laboratory (LC-MS-MS). GFR was determined in another group of rats by transcutaneous detection of the attenuation of i.v. injected FITC sinistrin. Cortical (Cx) and outer medullary (OM) tissues were obtained from the other group of rats and underwent metabolomic and mRNAseq analyses (Novogene). From another group of rats, glomeruli (Glo), proximal tubules (PT) and non-PT were isolated for RT-PCR. BP and RBF slightly increased by HS3 (P<0.05) and were sustained at these levels. O 2 extraction rose progressively from 0.10 ± 0.01 at LS to 0.14 ± 0.01 at HS21 (P<0.05). GFR increased from 0.64 to 0.83 mL/min/100 g (P<0.05) at HS7 and sustained. Na + reabsorption and O 2 consumption were positively correlated. Clear distinctions were observed in a sparse partial least squares discriminant analysis of tissue metabolomics among LS, HS14, and HS21. The mRNAseq analysis found that the HS diet resulted in the activation of immune system-related genes in both Cx and OM and the downregulation of genes related to the TCA cycle and metabolism of amino acids and fatty acids in Cx only. In contrast, glycolysis-related genes including hexokinase ( Hk ) and pyruvate kinase ( Pkm ) were upregulated in Cx. Metabolic fluxes (A-Vr-U) showed the increased release of lactate and pyruvate from the kidney when fed HS. Increased mRNA expression of Hk and Pkm in HS21 was observed only in PT but not in Glo and non-PT. In summary, SD rats fed a HS diet underwent changes in RBF, O 2 extraction, and utilization of substrates with evidence of increased glycolysis.

Genetic screening in a Brazilian cohort with inborn errors of immunity

BackgroundInherited genetic defects in immune system-related genes can result in Inborn Errors of Immunity (IEI), also known as Primary Immunodeficiencies (PID). Diagnosis of IEI disorders is challenging due to overlapping clinical manifestations. Accurate identification of disease-causing germline variants is crucial for appropriate treatment, prognosis, and genetic counseling. However, genetic sequencing is challenging in low-income countries like Brazil. This study aimed to perform genetic screening on patients treated within Brazil's public Unified Health System to identify candidate genetic variants associated with the patient’s phenotype.MethodsThirteen singleton unrelated patients from three hospitals in Rio de Janeiro were enrolled in this study. Genomic DNA was extracted from the peripheral blood lymphocytes of each patient, and whole exome sequencing (WES) analyses were conducted using Illumina NextSeq. Germline genetic variants in IEI-related genes were prioritized using a computational framework considering their molecular consequence in coding regions; minor allele frequency ≤ 0.01; pathogenicity classification based on American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) guidelines gathered from the VarSome clinical database; and IEI-related phenotype using the Franklin tool. The genes classification into IEI categories follows internationally recognized guidelines informed by the International Union of Immunological Societies Expert Committee. Additional methods for confirmation of the variant included Sanger sequencing, phasing analysis, and splice site prediction.ResultsA total of 16 disease-causing variants in nine genes, encompassing six different IEI categories, were identified. X-Linked Agammaglobulinemia, caused by BTK variations, emerged as the most prevalent IEI disorder in the cohort. However, pathogenic and likely pathogenic variants were also reported in other known IEI-related genes, namely CD40LG, CARD11, WAS, CYBB, C6, and LRBA. Interestingly, two patients with suspected IEI exhibited pathogenic variants in non-IEI-related genes, ABCA12 and SLC25A13, potentially explaining their phenotypes.ConclusionsGenetic screening through WES enabled the detection of potentially harmful variants associated with IEI disorders. These findings contribute to a better understanding of patients' clinical manifestations by elucidating the genetic basis underlying their phenotypes.

Unraveling the Molecular Mechanisms of Tomatoes' Defense against Botrytis cinerea: Insights from Transcriptome Analysis of Micro-Tom and Regular Tomato Varieties.

Botrytis cinerea is a devastating fungal pathogen that causes severe economic losses in global tomato cultivation. Understanding the molecular mechanisms driving tomatoes' response to this pathogen is crucial for developing effective strategies to counter it. Although the Micro-Tom (MT) cultivar has been used as a model, its stage-specific response to B. cinerea remains poorly understood. In this study, we examined the response of the MT and Ailsa Craig (AC) cultivars to B. cinerea at different time points (12-48 h post-infection (hpi)). Our results indicated that MT exhibited a stronger resistant phenotype at 18-24 hpi but became more susceptible to B. cinerea later (26-48 hpi) compared to AC. Transcriptome analysis revealed differential gene expression between MT at 24 hpi and AC at 22 hpi, with MT showing a greater number of differentially expressed genes (DEGs). Pathway and functional annotation analysis revealed significant differential gene expression in processes related to metabolism, biological regulation, detoxification, photosynthesis, and carbon metabolism, as well as some immune system-related genes. MT demonstrated an increased reliance on Ca2+ pathway-related proteins, such as CNGCs, CDPKs, and CaMCMLs, to resist B. cinerea invasion. B. cinerea infection induced the activation of PTI, ETI, and SA signaling pathways, involving the modulation of various genes such as FLS2, BAK1, CERK1, RPM, SGT1, and EDS1. Furthermore, transcription factors such as WRKY, MYB, NAC, and AUX/IAA families played crucial regulatory roles in tomatoes' defense against B. cinerea. These findings provide valuable insights into the molecular mechanisms underlying tomatoes' defense against B. cinerea and offer potential strategies to enhance plant resistance.

Simultaneous antibiotic removal and mitigation of resistance induction by manganese bio-oxidation process

Microbial degradation to remove residual antibiotics in wastewater is of growing interest. However, biological treatment of antibiotics may cause resistance dissemination by mutations and horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). In this study, a Mn(Ⅱ)-oxidizing bacterium (MnOB), Pseudomonas aeruginosa MQ2, simultaneously degraded antibiotics, decreased HGT, and mitigated antibiotic resistance mutation. Intracellular Mn(II) levels increased during manganese oxidation, and biogenic manganese oxides (BioMnOx, including Mn(II), Mn(III) and Mn(IV)) tightly coated the cell surface. Mn(II) bio-oxidation mitigated antibiotic resistance acquisition from an E. coli ARG donor and mitigated antibiotic resistance inducement by decreasing conjugative transfer and mutation, respectively. BioMnOx also oxidized ciprofloxacin (1 mg/L) and tetracycline (5 mg/L), respectively removing 93% and 96% within 24 h. Transcriptomic analysis revealed that two new multicopper oxidase and one peroxidase genes are involved in Mn(II) oxidation. Downregulation of SOS response, multidrug resistance and type Ⅳ secretion system related genes explained that Mn(II) and BioMnOx decreased HGT and mitigated resistance mutation by alleviating oxidative stress, which makes recipient cells more vulnerable to ARG acquisition and mutation. A manganese bio-oxidation based reactor was constructed and completely removed tetracycline with environmental concentration within 4-hour hydraulic retention time. Overall, this study suggests that Mn (II) bio-oxidation process could be exploited to control antibiotic contamination and mitigate resistance propagation during water treatment.

Molecular biology of serotonergic systems in avian brains.

Serotonin (5-hydroxytryptamine, 5-HT) is a phylogenetically conserved neurotransmitter and modulator. Neurons utilizing serotonin have been identified in the central nervous systems of all vertebrates. In the central serotonergic system of vertebrate species examined so far, serotonergic neurons have been confirmed to exist in clusters in the brainstem. Although many serotonin-regulated cognitive, behavioral, and emotional functions have been elucidated in mammals, equivalents remain poorly understood in non-mammalian vertebrates. The purpose of this review is to summarize current knowledge of the anatomical organization and molecular features of the avian central serotonergic system. In addition, selected key functions of serotonin are briefly reviewed. Gene association studies between serotonergic system related genes and behaviors in birds have elucidated that the serotonergic system is involved in the regulation of behavior in birds similar to that observed in mammals. The widespread distribution of serotonergic modulation in the central nervous system and the evolutionary conservation of the serotonergic system provide a strong foundation for understanding and comparing the evolutionary continuity of neural circuits controlling corresponding brain functions within vertebrates. The main focus of this review is the chicken brain, with this type of poultry used as a model bird. The chicken is widely used not only as a model for answering questions in developmental biology and as a model for agriculturally useful breeding, but also in research relating to cognitive, behavioral, and emotional processes. In addition to a wealth of prior research on the projection relationships of avian brain regions, detailed subdivision similarities between avian and mammalian brains have recently been identified. Therefore, identifying the neural circuits modulated by the serotonergic system in avian brains may provide an interesting opportunity for detailed comparative studies of the function of serotonergic systems in mammals.

Sphk1 deficiency induces apoptosis and developmental defects and premature death in zebrafish.

The sphk1 gene plays a crucial role in cell growth and signal transduction. However, the developmental functions of the sphk1 gene during early vertebrate zebrafish embryo remain not completely understood. In this study, we constructed zebrafish sphk1 mutants through CRISPR/Cas9 to investigate its role in zebrafish embryonic development. Knockout of the sphk1 gene was found to cause abnormal development in zebrafish embryos, such as darkening and atrophy of the head, trunk deformities, pericardial edema, retarded yolk sac development, reduced heart rate, and premature death. The acetylcholinesterase activity was significantly increased after the knockout of sphk1, and some of the neurodevelopmental genes and neurotransmission system-related genes were expressed abnormally. The deletion of sphk1 led to abnormal expression of immune genes, as well as a significant decrease in the number of hematopoietic stem cells and neutrophils. The mRNA levels of cardiac development-related genes were significantly decreased. In addition, cell apoptosis increases in the sphk1 mutants, and the proliferation of head cells decreases. Therefore, our study has shown that the sphk1 is a key gene for zebrafish embryonic survival and regulation of organ development. It deepened our understanding of its physiological function. Our study lays the foundation for investigating the mechanism of the sphk1 gene in early zebrafish embryonic development.

Flagellar gene fliP contributes to the virulence of Pseudomonas plecoglossicida by regulating its motility

As an opportunistic causative pathogen of “Visceral White Spot Disease” in several kinds of teleost, Pseudomonas plecoglossicida has caused huge economic losses to aquaculture. Flagella is the motility organ of bacteria as well as a vital virulence factor. The protein encoded by the fliP gene is involved in the formation of the flagellar type III secretion export apparatus, which plays a crucial role in flagellar assembly. In this study, the ΔfliP and C-ΔfliP strains of P. plecoglossicida were constructed to explore the biological profiles mediated by the fliP gene and its effects on the virulence of this organism. Compared to the wild type strain (NZBD9) of P. plecoglossicida, the deletion strain ΔfliP exhibited a significant impairment in swimming motility, chemotaxis, adhesion, and biofilm formation abilities. The transcriptomic analysis of the NZBD9, ΔfliP and C-ΔfliP strains revealed that the fliP gene may affect the biological profiles of P. plecoglossicida by down-regulating the expression of flagellar assembly, type 6 secretion system and bacterial chemotaxis related genes. Furthermore, the results of artificial infection showed that the virulence of ΔfliP strain to hybrid grouper (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂) was attenuated, with a LD50 value of 2.5 × 104 CFU/fish. These findings demonstrate that the fliP gene contributes to the virulence of P. plecoglossicida by regulating its motility.

Evaluatin of Association of rs4986790 and rs4986791 Single-Nucleotide Polymorphisms in TLR4 with Febrile Neutropenia in Childhood Acute Lymphoblastic Leukemia

Background: Infections cause significant complications and, in severe cases, death in patients with childhood Acute Lymphoid Leukemia (ALL). Toll-like receptors (TLRs) play a crucial role in initiating innate immune responses. Previous studies indicate the role of TLR4 gene polymorphisms in the increased risk of infection in adults and children. This study investigated the potential association between Asp299Gly (rs4986790) and Thr399Ile (rs4986791) polymorphisms in the TLR4 gene with febrile neutropenia, as a hallmark of infection, in children with ALL.
 Material and Methods: This cross-sectional study was performed on 51 ALL child patients, with age (mean±s.d.) 5.2 ± 3.4 years. Genotype analysis of rs4986790 and rs4986791 polymorphisms in the TLR4 gene was evaluated by ARMS- PCR and PCR-RFLP, respectively. Statistical analysis was performed using SPSS software. P-values <0.05 were considered significant.
 Results: The rs4986790 and rs4986791 polymorphisms were detected in 5.8% and 7.8% of ALL patients, respectively. The mean of recurrence of febrile neutropenia in patients without TLR4 rs4986790 and TLR4 rs4986791 polymorphisms was 3.1 ±2 and 3 ±1.9, respectively, while in patients with TLR4 rs4986790 and TLR4 rs4986791 polymorphisms, they were 4.6 ± 3 and 5.2 ±2.8, respectively (P = 0.09). No association was found between TLR4 rs4986790 and rs4986791 polymorphisms and the number of febrile neutropenia recurrences (P = 0.4).
 Conclusion: Although rs4986790 and rs4986791 polymorphisms were detected in ALL patients, these polymorphisms were not associated with febrile neutropenia. It is suggested to investigate other polymorphisms in immune system-related genes and their role in febrile neutropenia.

A heterozygous mutation in UBE2H in a patient with developmental delay leads to an aberrant brain development in zebrafish

BackgroundUbiquitin-related rare diseases are generally characterized by developmental delays and mental retardation, but the exact incidence or prevalence is not yet fully understood. The clinical application of next-generation sequencing for pediatric seizures and developmental delay of unknown causes has become common in studies aimed at identification of a causal gene in patients with ubiquitin-related rare diseases that cannot be diagnosed using conventional fluorescence in situ hybridization or chromosome microarray tests. Our study aimed to investigate the effects of ubiquitin–proteasome system on ultra-rare neurodevelopmental diseases, through functional identification of candidate genes and variants.MethodsIn our present work, we carried out genome analysis of a patient with clinical phenotypes of developmental delay and intractable convulsion, to identify causal mutations. Further characterization of the candidate gene was performed using zebrafish, through gene knockdown approaches. Transcriptomic analysis using whole embryos of zebrafish knockdown morphants and additional functional studies identified downstream pathways of the candidate gene affecting neurogenesis.ResultsThrough trio-based whole-genome sequencing analysis, we identified a de novo missense variant of the ubiquitin system-related gene UBE2H (c.449C>T; p.Thr150Met) in the proband. Using zebrafish, we found that Ube2h is required for normal brain development. Differential gene expression analysis revealed activation of the ATM-p53 signaling pathway in the absence of Ube2h. Moreover, depletion of ube2h led to induction of apoptosis, specifically in the differentiated neural cells. Finally, we found that a missense mutation in zebrafish, ube2h (c.449C>T; p.Thr150Met), which mimics a variant identified in a patient with neurodevelopmental defects, causes aberrant Ube2h function in zebrafish embryos.ConclusionA de novo heterozygous variant in the UBE2H c.449C>T (p.Thr150Met) has been identified in a pediatric patient with global developmental delay and UBE2H is essential for normal neurogenesis in the brain.

Apigenin-7-Glucoside Attenuates Hydrogen Peroxide-Induced Oxidative Stress and Neuronal Death in SH-SY5Y Cells Via Activation of Antioxidant Enzymes System and Inhibition of Caspases Genes Expression

Aims: In this study, it was aimed to investigate the possible neuroprotective effect of Apigenin-7-Glycoside (AP7Glu), a natural product with known anticancer and anti-inflammatory activity, against hydrogen proxide (H2O2)-induced oxidative stress in SH-SY5Y cells. Methods: The effect of H2O2 and AP7Glu on cell viability was determined by XTT analysis. SOD and catalase analyzes were performed to determine antioxidant enzyme activities. Expression levels of antioxidant defense system related genes and caspase genes were evaluated by qRT-PCR analysis. Results: After treatment of 300 µM H2O2 to SH-SY5Y cells for 24 hours, cell viability was determined as 63.18% and this dose was used to induce oxidative stress. H2O2 treatment in the presence of different concentrations of AP7Glu increased cell viability compared to H2O2-treated cells. And, H2O2 decreased SOD and catalase enzyme activities compared to control group. With the treatment of H2O2 in the presence of AP7Glu, an increase was observed in these enzymes activities compared to H2O2-treated cells. In addition, H2O2 decreased the expression levels of genes associated with antioxidant defense system and increased expression levels of Caspase genes. And, H2O2 treatment in the presence of AP7Glu increased the expression levels of genes associated with antioxidant defense system and decreased CASP8 expression compared to H2O2-treated cells. Conclusion: AP7Glu has a neuroprotective effect against H2O2-induced oxidative stress and neuronal cell death.

Peripheral myeloid cells control resolution of painful Chemotherapy-Induced Peripheral Neuropathy (CIPN) (S23.001)

<h3>Objective:</h3> The objective of this study is to identify endogenous mediators controlling CIPN pain resolution. <h3>Background:</h3> Chemotherapies contribute to decreased cancer mortality but are associated with severe side effects including Chemotherapy-Induced Peripheral Neuropathy (CIPN). CIPN presents as a distal symmetric polyneuropathy causing numbness, tingling, and in a subset of patients, pain. Painful CIPN is a main cause for chemotherapy dose reduction, treatment cessation and reduced quality of life. A subset of painful CIPN patients will have pain resolution while others maintain pain persistency, however the mechanisms that mediate pain resolution are unknown and constitute a large gap of knowledge. <h3>Design/Methods:</h3> We developed painful CIPN models in mice using the chemotherapeutic paclitaxel, where mice treated with specific injection protocols develop resolving or persistent mechanical hypersensitivity measured via von Frey. Using these models, we performed bulk RNA sequencing on hind paw, whole dorsal root ganglion (DRG), DRG sensory neurons and spinal cord at initiation, pre-resolution, post-resolution, and persistency time points. DEGs were selected (P-adj &lt;0.05, FC &gt; 2, RPKM &gt; 1) and PANTHER analysis was performed to identify biological processes. To investigate the contribution of particular cell types in these tissues, we used the inducible diphtheria toxin receptor ablation model. <h3>Results:</h3> PANTHER analysis identified upregulation of immune system related genes in the hind paw during resolution of Model-1 not seen in Model-2. As myeloid cells are known to contribute to immune system related genes in the periphery, we ablated myeloid cells. We identified that CD11b+ peripheral, but not IBA1+ central, myeloid cells are critical for painful CIPN resolution. Further RNA sequencing analysis identified pro-inflammatory pathways correlated with painful CIPN resolution. <h3>Conclusions:</h3> These studies provide mechanistic insights for CIPN pain resolution and identify a unique therapeutic strategy for permanent treatment of painful CIPN. Future studies will delineate the myeloid cell sub-type and factors required for CIPN pain resolution. <b>Disclosure:</b> Mr. Naratadam has nothing to disclose. Prof. Akopian has nothing to disclose.

Mouse CCL9 Chemokine Acts as Tumor Suppressor in a Murine Model of Colon Cancer.

Colorectal cancer is the third most frequently diagnosed cancer in the world. Despite extensive studies and apparent progress in modern strategies for disease control, the treatment options are still not sufficient and effective, mostly due to frequently encountered resistance to immunotherapy of colon cancer patients in common clinical practice. In our study, we aimed to uncover the CCL9 chemokine action employing the murine model of colon cancer to seek new, potential molecular targets that could be promising in the development of colon cancer therapy. Mouse CT26.CL25 colon cancer cell line was used for introducing lentivirus-mediated CCL9 overexpression. The blank control cell line contained an empty vector, while the cell line marked as CCL9+ carried the CCL9-overexpressing vector. Next, cancer cells with empty vector (control) or CCL9-overexpressing cells were injected subcutaneously, and the growing tumors were measured within 2 weeks. Surprisingly, CCL9 contributed to a decline in tumor growth in vivo but had no effect on CT26.CL25 cell proliferation or migration in vitro. Microarray analysis of the collected tumor tissues revealed upregulation of the immune system-related genes in the CCL9 group. Obtained results suggest that CCL9 reveals its anti-proliferative functions by interplay with host immune cells and mediators that were absent in the isolated, in vitro system. Under specific study conditions, we determined unknown features of the murine CCL9 that have so far bee reported to be predominantly pro-oncogenic.

The natural product, echinatin, protects mice from methicillin-resistant Staphylococcus aureus pneumonia by inhibition of alpha-hemolysin expression.

Antimicrobial resistance (AMR) is a global, multifaceted crisis that poses significant challenges to the successful eradication of devastating pathogens, particularly methicillin-resistant Staphylococcus aureus (MRSA), a persistent superbug that causes devastating infections. The scarcity of new antibacterial drugs is obvious, and antivirulence strategies that reduce the pathogenicity of bacteria by weakening their virulence have become the subject of intense investigation. Alpha-hemolysin (Hla), a cytolytic pore-forming toxin, has a pivotal role in S. aureus pathogenesis. Here, we demonstrated that echinatin, a natural compound isolated from licorice, effectively inhibited the hemolytic activity of MRSA at 32 μg/mL. In addition, echinatin did not interfere with bacterial growth and had no significant cytotoxicity at the inhibitory concentration of S. aureus hemolysis. Heptamer formation tightly correlated with Hla-mediated cell invasion, whereas echinatin did not affect deoxycholic acid-induced oligomerization of Hla. Echinatin affected hemolytic activity through indirect binding to Hla as confirmed by the neutralization assay and cellular thermal shift assay (CETSA). Furthermore, qRT-PCR and western blot analyses revealed that echinatin suppressed Hla expression at both the mRNA and protein levels as well as the transcript levels of Agr quorum-sensing system-related genes. Additionally, when echinatin was added to a coculture system of A549 cells and S. aureus, it significantly reduced cell damage. Importantly, echinatin exhibited a significant therapeutic effect in an MRSA-induced mouse pneumonia model. In conclusion, the present findings demonstrated that echinatin significantly inhibits the hemolysin effect and may be a potential candidate compound for combating drug-resistant MRSA infections.

Identification and validation of chemokine system-related genes in idiopathic pulmonary fibrosis.

Idiopathic pulmonary fibrosis (IPF) is a chronic progressive interstitial lung disease with limited therapeutic options. Recent studies have demonstrated that chemokines play a vital role in IPF pathogenesis. In the present study, we explored whether the gene signature associated with chemokines could be used as a reliable biological marker for patients with IPF. Chemokine-related differentially expressed genes (CR-DEGs) in IPF and control lung tissue samples were identified using data from the Gene Expression Omnibus database. A chemokine-related signature of the diagnostic model was established using the LASSO-Cox regression. In addition, unsupervised cluster analysis was conducted using consensus-clustering algorithms. The CIBERSORT algorithm was used to calculate immune cell infiltration across patient subgroups. Finally, we established a mouse model of bleomycin-induced pulmonary fibrosis and a model of fibroblasts treated with TGFβ1. Expression levels of chemokine-related signature genes were determined using real-time quantitative polymerase chain reaction (RT-qPCR). We established a chemokine-related eleven-gene signature of a diagnostic model consisting of CXCL2, CCRL2, ARRB1, XCL1, GRK5, PPBP, CCL19, CCL13, CCL11, CXCL6, and CXCL13, which could easily distinguish between IPF patients and controls. Additionally, we identified two subtypes of IPF samples based on chemokine-related gene expression. Pulmonary function parameters and stromal scores were significantly higher in subtype 1 than in subtype 2. Several immune cell types, especially plasma cells and macrophages, differ significantly between the two subtypes. RT-qPCR results showed that the expression levels of Cxcl2 and Ccl2 increased considerably in bleomycin-induced mice. Meanwhile, Arrb1, Ccrl2, Grk5, and Ppbp expression was significantly reduced. Furthermore, multiple chemokine-related genes were altered in TGFβ1 or TNFα-induced fibroblast cells. A novel chemokine-related eleven-signature of diagnostic model was developed. These genes are potential biomarkers of IPF and may play essential roles in its pathogenesis.

Nervous system-related gene regulatory networks and functional evolution of ETS proteins across species

The ETS domain transcription factor family is one of the major transcription factor superfamilies that play regulatory roles in development, cell growth, and cancer progression. Although different functions of ETS member proteins in the nervous system have been demonstrated in various studies, their role in neuronal cell differentiation and the evolutionary conservation of its target genes have not yet been extensively studied. In this study, we focused on the regulatory role of ETS transcription factors in neuronal differentiation and their functional evolution by comparative transcriptomics. In order to investigate the regulatory role of ETS transcription factors in neuronal differentiation across species, transcriptional profiles of ETS members and their target genes were investigated by comparing differentially expressed genes and gene regulatory networks, which were analyzed using human, gorilla, mouse, fruit fly and worm transcriptomics datasets. Bioinformatics approaches to examine the evolutionary conservation of ETS transcription factors during neuronal differentiation have shown that ETS member proteins regulate genes associated with neuronal differentiation, nervous system development, axon, and synaptic regulation in different organisms. This study is a comparative transcriptomic study of ETS transcription factors in terms of neuronal differentiation using a gene regulatory network inference algorithm. Overall, a comparison of gene regulation networks revealed that ETS members are indeed evolutionarily conserved in the regulation of neuronal differentiation. Nonetheless, ETS, PEA3, and ELF subfamilies were found to be relatively more active transcription factors in the transcriptional regulation of neuronal differentiation.

Nonsteroidal anti-inflammatory drug diclofenac accelerates the emergence of antibiotic resistance via mutagenesis

Overuse of antimicrobial agents are generally considered to be a key factor in the occurrence of antibiotic resistance bacteria (ARB). Nevertheless, it is unclear whether ARB can be induced by non-antibiotic chemicals such as nonsteroidal anti-inflammatory drug (NSAID). Thus, the objective of this study is to investigate whether NSAID diclofenac (DCF) promote the emergence of antibiotic resistance in Escherichia coli K12 MG1655. Our results suggested that DCF induced the occurrence of ARB which showed hereditary stability of resistance. Meanwhile, gene variation was identified on chromosome of the ARB, and DCF can cause bacterial oxidative stress and SOS response. Subsequently, transcriptional levels of antioxidant (soxS, sodA, sodC, gor, katG, ahpF) and SOS (recA, lexA, uvrA, uvrB, ruvA, ruvB, dinB, umuC, polB) system-related genes were enhanced. However, the expression of related genes cannot be increased in high-dosage treatment compared with low-dosage samples because of cytotoxicity and cellular damage. Simultaneously, high-dosage DCF decreased the mutation frequency but enhanced the resistance of mutants. Our findings expand our knowledge of the promoting effect on the emergence of ARB caused by DCF. More attention and regulations should be given to these potential ecological and health risks for widespread DCF.