Regulation Of Chemotaxis Research Articles

Identification of target genes and prognostic evaluation for colorectal cancer using integrated bioinformatics analysis

The underlying molecular mechanisms of colorectal cancer (CRC) has attracted great attention from the scholarly community. The aim of our study is to identify pivotal genes related to the pathogenesis and prognosis of CRC. We integrated five microarray datasets from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were analyzed with the limma package. DAVID and OmicShare tools were used for Gene Ontology (GO) and KEGG enrichment analysis. The protein–protein interaction (PPI) network of DEGs was constructed. The prognostic analysis of hub genes was performed through Kaplan Meier-plotter. Finally, potential drugs were predicted in the CMap database. Through five microarray datasets, a total of 90 DEGs were detected including 54 up-regulated and 36 down-regulated genes. Biological process analysis showed DEGs were mainly enriched in positive regulation of neutrophil chemotaxis, chemokine-mediated signaling pathway, and bicarbonate transport. Signaling pathway analysis indicated that DEGs played a vital in proximal tubule bicarbonate reclamation, cell cycle and progesterone-mediated oocyte maturation. The GEPIA database confirmed that overexpression levels of hub genes were significantly associated with better survival of patients. Finally, the 20 most significant small molecules were obtained based on the CMap database. Our study has identified novel candidate biomarkers, pathways, and kinases associated with CRC prognosis.

Ag NCs as a potent antibiofilm agent against pathogenic Pseudomonas aeruginosa and Acinetobacter baumannii and drug-resistant Bacillus subtilis by affecting chemotaxis and flagellar assembly pathway genes.

Biofilm infections are highly resistant to commercial antibiotics. Therefore, developing a potent agent against such drug-resistant bacterial infections is highly desirable. Here, we synthesized positively charged silver nanoclusters (Ag NCs) with a diameter of <2 nm, which were found to be very effective antibacterial and antibiofilm agents against tetracycline-resistant Bacillus subtilis and most importantly multidrug-resistant pathogenic strains of Pseudomonas aeruginosa and Acinetobacter baumannii. Ag NCs were able to both prevent and eradicate the biofilm formation very effectively. The antibiofilm activity can be significantly increased with α-amylase and/or DNase which degrade the structural components of biofilms. The antibiofilm activity of antibiotics gets considerably lowered due to poor penetration and the acidic microenvironment of biofilms. However, the potency of antibiotics gets significantly increased when applied with Ag NCs. Finally, RNA seq-based analysis has demonstrated that the biofilm degradation was likely due to the regulation of bacterial chemotaxis and flagellar assembly pathway genes by Ag NCs.

The anti-inflammatory peptide Catestatin blocks chemotaxis.

Increased levels of the anti‐inflammatory peptide Catestatin (CST), a cleavage product of the pro‐hormone chromogranin A, correlate with less severe outcomes in hypertension, colitis, and diabetes. However, it is unknown how CST reduces the infiltration of monocytes and macrophages (Mϕs) in inflamed tissues. Here, it is reported that CST blocks leukocyte migration toward inflammatory chemokines. By in vitro and in vivo migration assays, it is shown that although CST itself is chemotactic, it blocks migration of monocytes and neutrophils to inflammatory attracting factor CC‐chemokine ligand 2 (CCL2) and C‐X‐C motif chemokine ligand 2 (CXCL2). Moreover, it directs CX3CR1+ Mϕs away from pancreatic islets. These findings suggest that the anti‐inflammatory actions of CST are partly caused by its regulation of chemotaxis.

Spatial transcriptomics of human middle temporal gyrus reveals layer‐specific gene expression in early Alzheimer’s disease

In many neurodegenerative diseases including Alzheimer's disease (AD), specific subpopulations of cells and brain regions are more sensitive to dysfunction and degeneration than others. For example, excitatory neurons in the layer 2/3 of middle temporal gyrus (MTG) is particularly vulnerable to degeneration in early AD. The mechanisms underpinning this selective cellular and regional vulnerability, however, are unclear. Recently, the spatially resolved transcriptomics has been used in AD-like mouse models to identify genes altered in the vicinity of amyloid plaques and genes differentially expressed in those vulnerable regions in AD. Here we report that spatial transcriptomics of human postmortem MTG reveals differential gene expression in layer 2/3 of early AD compared to non-AD cases. Human MTG frozen sections from 2 non-AD and 2 early AD cases were mounted over the capture areas with poly T probes on the 10x Visium Gene Expression slide. The cDNA libraries were generated by following the 10x Visium Spatial Gene Expression Reagent Kits user guide. Then cDNA libraries from 4 samples were pooled in a NovaSeq6000 SP v1.0 flowcell and paired end sequencing were performed on an Illumina NovaSeq6000 sequencer. The sequence data were analyzed via 10x Genomics software (Space Ranger v 4.0.0 and Loupe Browser v 4.1.0) and Seurat (v 3.2.2). Uniform Manifold Approximation and Projection (UMAP) analysis of spatial transcriptomics data generated seven cell clusters, which correspond to the cortical layers 1-6 and the white matter in MTG. In the identified differentially expressed genes (DEGs) in layer 2/3, we found many signatures associated with AD including plaque-induced genes, disease associated microglia genes, oligodendrocyte response genes, A1 astrocyte genes, as well as tangle-associated genes. GO enrichment analysis of these DEGs revealed important functional pathways that may be implicated in the pathogenesis of AD, such as synapse structure or activity, protein folding and stability, neuronal apoptosis, autophagy, ER stress, oxidative stress, response to amyloid-beta, microglial activation, neuroinflammatory response, regulation of chemotaxis, and myelination. Taken together, we demonstrate that the genome-wide the spatially resolved transcriptomics provide an unprecedented and unbiased approach to untangle the selective cellular and regional vulnerability in early AD.

Causal effects of microglia-mediated innate immune responses in the pathogenesis of c9orf72 frontotemporal dementia and amyotrophic lateral sclerosis.

The most common monogenic cause of frontotemporal dementia and amyotrophic lateral sclerosis (FTD/ALS) are G4 C2 repeat expansions in the c9orf72 gene. Aggregations of dipeptide repeat proteins (DPR) produced by these expansions have toxic effects on cellular homeostasis, coinciding with neuroinflammation and cell death. Glycine-Arginine (GR) aggregates are significantly present in regions of the brain impacted by FTD/ALS. Here, we demonstrate the causal role of microglia mediated innate immune responses in the pathogenesis of FTD/ALS and identify the NLRP3 inflammasome as a therapeutic target for FTD/ALS. Wild-type C57BL6/J and Nlrp3 deficient (Nlrp3 -/- ) mice were transfected via intracerebroventricular injection with either AAV9-GFP or AAV9-GFP(GR)100 . At 14 weeks, animals were tested for motor function and memory. Cortical tissue (CTX) was dissected for analysis. Microglia density and activation were assessed in vivo by immunofluorescence for Iba1 and Sholl analysis. ELISA for IL-1β was performed and levels of active caspase-1 was measured via western blot. To investigate a mechanism by which neurons could induce activation of microglia, primary neurons were transfected with GFP-(GR)100 and CXCL10, a regulator of chemotaxis and inducer of proinflammatory phenotypes of microglia was measured via ELISA. Wild-type GFP-(GR)100 mice exhibited significant motor impairment and memory deficits, leading to mortality. Microglia were increased in GFP-(GR)100 and found to be in an activated state. IL-1β was elevated in the cortex and accompanied by an increase in active caspase-1. Primary neurons transfected with GFP-(GR)100 exhibited a significant increase in CXCL10. Genetic ablation of Nlrp3 in GFP-(GR)100 mice conferred protection in motor function and memory, leading to a significant reduction in mortality. Furthermore, Nlrp3-/- GFP-(GR)100 mice did not exhibit increases in IL-1β or active caspase-1. Microglia mediated neuroinflammation is present in FTD/ALS. In vivo, significant neuroinflammation was noted by increased microglia density and activation, with elevated IL-1β and active caspase-1. In vitro studies indicated a mechanism by which neurons can induce proliferation and activation of microglia in response to FTD/ALS neuropathologies. Genetic ablation of Nlrp3 resulted in significant attenuation of FTD/ALS neuropathologies, leading to improvements in behavior and survival. These data implicate microglia mediated innate immune responses as a potent target for treatment of FTD/ALS.

Mass Cytometric Analysis Revealed Dynamic Alteration of the Tumor Immune Environment in Bone Marrow from Children with Recurrent B Cell Precursor Acute Lymphoblastic Leukemia

IntroductionDue to the considerable success of cancer immunotherapy for leukemia, the tumor immune environment (TIE) has become a focus of intense research; however, there are few reports on the dynamics of the TIE in leukemia, especially in bone marrow (BM), the primary site of leukemia. Mass cytometry, which allows high-dimensional analysis with single-cell resolution, is a powerful tool for the characterization of the TIE, and enables us to examine pediatric BM samples containing only a few numbers of immune cells.MethodsPrimary and recurrent BM samples were collected serially from pediatric patients with BCP-ALL at Kyoto University Hospital from 2006 to 2013. Mononuclear cells were isolated by density centrifugation and viably preserved until they were used. We examined the TIE of pediatric B cell precursor acute lymphoblastic leukemia (BCP-ALL) by analyzing serial BM samples from patients in primary and recurrent disease phases by mass cytometry, using 39 immunophenotype markers, and transcriptome analysis.Results and DiscussionThe proportion of BCP-ALL cells in the samples was 87.3-97.8% (mean: 94.0%) at onset, and 81.3-98.8% (mean: 92.2%) at relapse. High-dimensional single-cell analysis by mass cytometry elucidated a dynamic shift of T cells from naïve to effector subsets, and clarified that the TIE during relapse comprised a T helper 1 (Th1)-polarized immune profile, together with the increase of effector regulatory T cells (Tregs). Th1 cells are typically known as supporters of cytotoxic T lymphocytes which would eliminate leukemia cells and work against relapse, but recently, it is reported that Th1 cells directly support ALL proliferation in vitro (Traxel et al. Oncogene. 2019; 38:2420-2431), and that the concentrations of pro-inflammatory cytokines and Th1 cytokines (IFN-γ and IL-12) were elevated in patients with ALL, which could create favorable conditions for ALL (Perez-Figueroa et al. Oncol Rep. 2016; 35: 2699-2706, Vilchis-Ordonez et al. Biomed Res Int. 2015; 2015: 386165). Therefore, there is a possibility that the Th1-polarized immune profile would work in favor of leukemia survival for relapse.Furthermore, Gene set enrichment analysis based on RNA expression identified the enrichment of six immune-related pathways were enriched at the time of relapse; chemokine activity, chemokine production, complement activation, positive regulation of cytokine production involved in immune response, positive regulation of lymphocyte chemotaxis, and positive regulation of lymphocyte migration. These expression signatures suggest that BCP-ALL cells attract lymphocytes, and upregulate immune activities at relapse.ConclusionIn summary, a TIE characterized by a Th1-polarized immune profile, with the increase of effector Tregs, may be involved in the pathophysiology of recurrent ALL, and BCP-ALL cells at relapse were enriched with gene expressions related to lymphocyte attraction and activities. This information could contribute to the development of effective immunotherapeutic approaches against BCP-ALL relapse. DisclosuresOgawa: Eisai Co., Ltd.: Research Funding; Kan Research Laboratory, Inc.: Consultancy, Research Funding; Ashahi Genomics: Current holder of individual stocks in a privately-held company; Dainippon-Sumitomo Pharmaceutical, Inc.: Research Funding; Otsuka Pharmaceutical Co., Ltd.: Research Funding; ChordiaTherapeutics, Inc.: Consultancy, Research Funding.

A novel class of oxazepine-based anti-cancer agents induces cell death in primary human CLL cells and efficiently reduces tumor growth in Eμ-TCL1 mice through the JNK/STAT4/p66Shc axis

Survival and expansion of malignant B cells in chronic lymphocytic leukemia (CLL) are highly dependent both on intrinsic defects in the apoptotic machinery and on the interactions with cells and soluble factors in the lymphoid microenvironment. The adaptor protein p66Shc is a negative regulator of antigen receptor signaling, chemotaxis and apoptosis whose loss in CLL B cells contributes to their extended survival and poor prognosis. Hence, the identification of compounds that restore p66Shc expression and function in malignant B cells may pave the way to a new therapeutic approach for CLL. Here we show that a novel oxazepine-based compound (OBC-1) restores p66Shc expression in primary human CLL cells by promoting JNK-dependent STAT4 activation without affecting normal B cells. Moreover, we demonstrate that the potent pro-apoptotic activity of OBC-1 in human leukemic cells directly correlates with p66Shc expression levels and is abrogated when p66Shc is genetically deleted. Preclinical testing of OBC-1 and the novel analogue OBC-2 in Eμ-TCL1 tumor-bearing mice resulted in a significantly longer overall survival and a reduction of the tumor burden in the spleen and peritoneum. Interestingly, OBCs promote leukemic cell mobilization from the spleen to the blood, which correlates with upregulation of sphingosine-1-phosphate receptor expression. In summary, our work identifies OBCs as a promising class of compounds that, by boosting p66Shc expression through the activation of the JNK/STAT4 pathway, display dual therapeutic effects for CLL intervention, namely the ability to mobilize cells from secondary lymphoid organs and a potent pro-apoptotic activity against circulating leukemic cells.

CXCR4 is a Novel Biomarker Correlated With Malignant Transformation and Immune Infiltrates in Gastric Precancerous Lesions.

Background: As early gastric cancer (EGC) has a far better prognosis than advanced gastric cancer (GC), early diagnosis and treatment are essential. However, understanding the mechanism of the process from gastric precancerous lesion (GPL) becoming EGC has made little advances. Besides, biomarkers that can monitor the progression of GPL-to-GC are still much insufficient. Methods: Key gene modules associated with GPL progression to EGC were identified by integrating two GPL-related data sets, GSE55696 and GSE130823, using the WGCNA method. Combining with the TCGA-STAD cohort, hub genes were identified. Immunofluorescence was conducted to validate the expression. To explore the implication of hub genes in GPL malignant transformation, a correlation test was conducted to identify their co-expression genes, co-expression cytokines, and co-expression immune cells. Least absolute shrinkage and selection operator (LASSO) Cox regression was applied to shrink CXCR4-related predictors and construct a prognostic model. Functional enrichment was applied for exploring the potential mechanism. Results: The green module in GSE55696 and the yellow module in GSE130823 were regarded as key gene modules associated with GPL progression to EGC, and 219 intersection genes from them were mainly enriched in critical immune biological processes. Combining with the TCGA-STAD cohort, CXCR4 was identified as a novel biomarker correlated with the malignant transformation of GPL, the positive rate of which was increased with GPL progression according to immunofluorescence. CXCR4 co-expression genes were found mainly involved in regulation of actin. CXCR4 co-expression cytokines were enriched in regulation of chemotaxis, cell chemotaxis, mononuclear cell migration, leukocyte chemotaxis, etc. As for co-expression immune cells, the expression level of CXCR4 was positively correlated with the abundance of macrophages but negatively correlated with that of effector memory T cells and NKT cells during GPL malignant transformation. In addition, the CXCR4-related prognostic model was able to predict the prognosis of GC and serve as an independent predictor for overall survival (OS). Conclusions: CXCR4 was a novel biomarker correlated with malignant transformation of GPL and played a vital role in the control of tumor immunity. CXCR4 is possible to serve as a therapeutic target for malignant transformation of GPL.

Pharmacogenetics and Pharmacokinetic of Azithromycin Eyedrops in Meibomian Gland Dysfunction Treatment

Meibomian gland dysfunction (MGD) is the leading cause of ocular surface disease throughout the world, which has a prevalence that varied widely from 3.5 to 70% according to age, sex, and ethnicity. Azithromycin (AZM) is the first azalidic antibiotic, a class of macrolide antibiotics, which has derived from erythromycin. It is widely used in clinical practice, not only for respiratory diseases and sexually transmitted infections but also for ocular diseases. azithromycin suppressed zymosan-induced mRNA expression and protein production of proinflammatory cytokines (tumor necrosis factor α and IL-1β), chemokines (IL-6 and RANTES), and MMPs (MMP-1, MMP-3, and MMP-9) by human corneal epithelial cells and suggested the potential for using azithromycin to treat ocular surface It controls the initiation and resolution of inflammatory responses through the regulation of chemotaxis, activation, and survival of lymphocytes. The anti-inflammatory role of TGF-β1 has been recognized in different cell types by inhibiting proinflammatory cytokines including tumor necrosis factor α, IL-1, and interferon γ.The combination of a topical AZM solution 1.0% with corticosteroid (DEX 0.1%) was found superior in the comprehensive treatment of MGD after 2 weeks. AZM is a one of the safest antibiotics, well tolerated, and has special pharmacokinetic properties. Moreover, it has a broad antimicrobial spectrum. AZM is efficacious for the treatment of a lot of ocular diseases and may be included as monotherapy or in combination therapy in new treatment protocols for more ocular infections.

Rho signaling inhibition mitigates lung injury via targeting neutrophil recruitment and selectin-AKT signaling

Neutrophils, the early responders of the immune system, eliminate intruders, but their over-activation can also instigate tissue damage leading to various autoimmune and inflammatory disease conditions. As approaches causing neutropenia are associated with immunodeficiency, targeting aberrant neutrophil infiltration offers an attractive strategy in neutrophil-centered diseases including acute lung injury. Rho GTPase family proteins Rho, Rac and Cdc42 play important role as regulators of chemotaxis in diverse systems. Rho inhibitors protected against lung injuries, while genetic Rho-deficiency exhibited neutrophil hyperactivity and exacerbated lung injury. These differential outcomes might be due to distinct effects on different cell types or activation/ inhibition of specific signaling pathways responsible for neutrophil polarity, migration and functions. In this study, we explored neutrophil centric effects of Rho signaling mitigation. Consistent with previous reports, Rho signaling inhibitor Y-27632 provided protection against acute lung injury, but without regulating LPS mediated systemic increase of neutrophils in the circulation. Interestingly, the adoptive transfer approach identified a specific defect in neutrophil migration capacity after Rho signaling mitigation. These defects were associated with loss of polarity and altered actin dynamics identified using time-lapse in vitro studies. Further analysis revealed a rescue of stimulation-dependent L-selectin shedding on neutrophils with Rho signaling inhibitor. Surprisingly, functional blocking of L-selectin (CD62L) led to defective recruitment of neutrophils into inflamed lungs. Further, single-cell level analyses identified MAPK signaling as downstream mechanism of Rho signaling and L-selectin mediated effects. p-AKT levels were diminished in detergent resistance membrane-associated signalosome upon Rho signaling inhibition and blockade of selectin. Moreover, inhibition of AKT signaling as well as selectin blocking led to defects in neutrophil polarity. Together, this study identified Rho-dependent distinct L-selectin and AKT signaling mediated regulation of neutrophil recruitment to inflamed lung tissue.

Prognostic Significance of ROR2 Expression in Patients with Urothelial Carcinoma.

We investigated the association of receptor tyrosine kinase-like orphan receptor 2 (ROR2) expression with clinicopathological features and oncologic outcomes in large urothelial carcinoma (UC) of the upper tract (UTUC) and urinary bladder (UBUC) cohorts. Through transcriptomic profiling of a published dataset (GSE31684), ROR2 was discovered to be the most upregulated gene during UC progression, focusing on the JNK cascade (GO:0007254). Initially, the evaluation of ROR2 mRNA expression in 50 frozen UBUCs showed significantly upregulated levels in high-stage UC. Moreover, high ROR2 immunoexpression significantly correlated with high tumor stage, high tumor grade, lymph node metastasis, and vascular invasion (all p < 0.05). In multivariate analysis, after adjusting for standard clinicopathological features, ROR2 expression status was an independent prognosticator of cancer-specific survival and metastasis-free survival in UTUC and UBUC (all p < 0.01). In the subgroup analysis, it also significantly predicted bladder tumor recurrence in non-muscle invasive UBUC. Furthermore, the GO enrichment analysis showed that fatty acid, monocarboxylic acid, carboxylic acid metabolic processes, negative regulation of neutrophil migration, and negative regulation of granulocyte and neutrophil chemotaxis were significantly enriched by ROR2 dysregulation. In conclusion, high ROR2 immunoexpression was associated with aggressive pathological characteristics in UC and independently predicted worse prognosis, suggesting it could play roles in clinical risk stratification and therapy decisions.

The Effect of tonB Gene on the Virulence of Pseudomonas plecoglossicida and the Immune Response of Epinephelus coioides.

Pseudomonas plecoglossicida is the causative agent of “visceral white spot disease” in cultured fish and has resulted in serious economic losses. tonB gene plays a crucial role in the uptake of nutrients from the outer membranes in Gram-negative bacteria. The previous results of our lab showed that the expression of tonB gene of P. plecoglossicida was significantly upregulated in the spleens of infected Epinephelus coioides. To explore the effect of tonB gene on the virulence of P. plecoglossicida and the immune response of E. coioides, tonB gene of P. plecoglossicida was knocked down by RNAi; and the differences between the wild-type strain and the tonB-RNAi strain of P. plecoglossicida were investigated. The results showed that all of the four mutants of P. plecoglossicida exhibited significant decreases in mRNA of tonB gene, and the best knockdown efficiency was 94.0%; the survival rate of E. coioides infected with the tonB-RNAi strain was 20% higher than of the counterpart infected with the wild strain of P. plecoglossicida. Meanwhile, the E. coioides infected with the tonB-RNAi strain of P. plecoglossicida carried less pathogens in the spleen and less white spots on the surface of the spleen; compared with the wild-type strain, the motility, chemotaxis, adhesion, and biofilm formation of the tonB-RNAi strain were significantly attenuated; the transcriptome data of E. coioides infected with the tonB-RNAi strain were different from the counterpart infected with the wild strain of P. plecoglossicida; the antigen processing and presentation pathway and the complement and coagulation cascade pathway were the most enriched immune pathways. The results indicated that tonB was a virulence gene of P. plecoglossicida; tonB gene was involved in the regulation of motility, chemotaxis, adhesion, and biofilm formation; tonB gene affected the immune response of E. coioides to P. plecoglossicida infection.

Annotation of chemotaxis gene clusters and proteins involved in chemotaxis of Bacillus subtilis strain MB378 capable of biodecolorizing different dyes.

This study explores the chemotactic potential of Bacillus subtilis MB378 against industrial dyes. Initial screening with swim plate assay showed significant movement of Bacillus subtilis MB378 towards test compounds. According to quantitative capillary assay, B. subtilis MB378 exhibited high chemotaxis potential towards Acid Orange 52 (CI: 9.52), followed by Direct Red 28 (CI: 8.39) and Basic Green 4 (CI: 5.21) in glucose-supplemented medium. Sequencing and gene annotation results evidently showed presence of chemotaxis genes and flagellar motor proteins in Bacillus subtilis draft genome. Methyl-accepting proteins (involved in chemotaxis regulation) belonged to pfam00672, pfam00072, and pfam00015 protein families. Annotated chemotaxis machinery of MB378 comprised 8 Che genes, 5 chemoreceptor genes, associated flagellar proteins, and rotary motors. Chemotaxis genes of B. subtilis MB378 were compared with genes of closely related Bacillus strains (168, WK1, and HTA426), depicting highly conserved regions showing evolutionary relation between them. Considering results of present study, it can be speculated that test compounds triggered chemotactic genes, which made these compounds bioavailable to the bacterium. Hence, the bacterium recognized and approached these compounds and facilitated biodegradation and detoxification of these compounds.

MAPK10 Expression as a Prognostic Marker of the Immunosuppressive Tumor Microenvironment in Human Hepatocellular Carcinoma.

Hepatocellular carcinoma (HCC) remains a devastating malignancy worldwide due to lack of effective therapy. The immune-rich contexture of HCC tumor microenvironment (TME) makes this tumor an appealing target for immune-based therapies; however, the immunosuppressive TME is still a major challenge for more efficient immunotherapy in HCC. Using bioinformatics analysis based on the TCGA database, here we found that MAPK10 is frequently down-regulated in HCC tumors and significantly correlates with poor survival of HCC patients. HCC patients with low MAPK10 expression have lower expression scores of tumor infiltration lymphocytes (TILs) and stromal cells in the TME and increased scores of tumor cells than those with high MAPK10 expression. Further transcriptomic analyses revealed that the immune activity in the TME of HCC was markedly reduced in the low-MAPK10 group of HCC patients compared to the high-MAPK10 group. Additionally, we identified 495 differentially expressed immune-associated genes (DIGs), with 482 genes down-regulated and 13 genes up-regulated in parallel with the decrease of MAPK10 expression. GO enrichment and KEGG pathway analyses indicated that the biological functions of these DIGs included cell chemotaxis, leukocyte migration and positive regulation of the response to cytokine–cytokine receptor interaction, T cell receptor activation and MAPK signaling pathway. Protein–protein interaction (PPI) analyses of the 495 DIGs revealed five potential downstream hub genes of MAPK10, including SYK, CBL, VAV1, LCK, and CD3G. Several hub genes such as SYK, LCK, and VAV1 could respond to the immunological costimulatory signaling mediated by the transmembrane protein ICAM1, which was identified as a down-regulated DIG associated with low-MAPK10 expression. Moreover, ectopic overexpression or knock-down of MAPK10 could up-regulate or down-regulate ICAM1 expression via phosphorylation of c-jun at Ser63 in HCC cell lines, respectively. Collectively, our results demonstrated that MAPK10 down-regulation likely contributes to the immunosuppressive TME of HCC, and this gene might serve as a potential immunotherapeutic target and a prognostic factor for HCC patients.

FOXE1-Dependent Regulation of Macrophage Chemotaxis by Thyroid Cells In Vitro and In Vivo.

Forkhead box E1 (FOXE1) is a lineage-restricted transcription factor involved in thyroid cancer susceptibility. Cancer-associated polymorphisms map in regulatory regions, thus affecting the extent of gene expression. We have recently shown that genetic reduction of FOXE1 dosage modifies multiple thyroid cancer phenotypes. To identify relevant effectors playing roles in thyroid cancer development, here we analyse FOXE1-induced transcriptional alterations in thyroid cells that do not express endogenous FOXE1. Expression of FOXE1 elicits cell migration, while transcriptome analysis reveals that several immune cells-related categories are highly enriched in differentially expressed genes, including several upregulated chemokines involved in macrophage recruitment. Accordingly, FOXE1-expressing cells induce chemotaxis of co-cultured monocytes. We then asked if FOXE1 was able to regulate macrophage infiltration in thyroid cancers in vivo by using a mouse model of cancer, either wild type or with only one functional FOXE1 allele. Expression of the same set of chemokines directly correlates with FOXE1 dosage, and pro-tumourigenic M2 macrophage infiltration is decreased in tumours with reduced FOXE1. These data establish a novel link between FOXE1 and macrophages recruitment in the thyroid cancer microenvironment, highlighting an unsuspected function of this gene in the crosstalk between neoplastic and immune cells that shape tumour development and progression.

Mechanisms and heterogeneity of in situ mineral processing by the marine nitrogen fixer Trichodesmium revealed by single-colony metaproteomics

The keystone marine nitrogen fixer Trichodesmium thrives in high-dust environments. While laboratory investigations have observed that Trichodesmium colonies can access the essential nutrient iron from dust particles, less clear are the biochemical strategies underlying particle–colony interactions in nature. Here we demonstrate that Trichodesmium colonies engage with mineral particles in the wild with distinct molecular responses. We encountered particle-laden Trichodesmium colonies at a sampling location in the Southern Caribbean Sea; microscopy and synchrotron-based imaging then demonstrated heterogeneous associations with iron oxide and iron-silicate minerals. Metaproteomic analysis of individual colonies by a new low-biomass approach revealed responses in biogeochemically relevant proteins including photosynthesis proteins and metalloproteins containing iron, nickel, copper, and zinc. The iron-storage protein ferritin was particularly enriched implying accumulation of mineral-derived iron, and multiple iron acquisition pathways including Fe(II), Fe(III), and Fe-siderophore transporters were engaged. While the particles provided key trace metals such as iron and nickel, there was also evidence that Trichodesmium was altering its strategy to confront increased superoxide production and metal exposure. Chemotaxis regulators also responded to mineral presence suggesting involvement in particle entrainment. These molecular responses are fundamental to Trichodesmium’s ecological success and global biogeochemical impact, and may contribute to the leaching of particulate trace metals with implications for global iron and carbon cycling.

Assessment of changes in genetic transcriptome in nasal epithelial cells exposed to ozone-aged black carbon and pollen allergen by high-throughput transcriptomics

BackgroundAir pollution may be associated with increased airway responsiveness to allergens in allergic rhinitis (AR). Ozone-aged environmental black carbon (O3BC) is an important constituent of atmospheric particulate matter (PM), for which the mechanisms underlying its effects have not been fully elucidated in AR. The objective of the present study was to determine the O3BC and pollen-induced alterations in the transcriptome in human nasal epithelial cells (hNECs) in vitro.MethodshNECs from nasal epithelial mucosal samples of healthy individuals undergoing nasal surgery (turbinoplasty or septoplasty) were established as air–liquid interface (ALI) cultures and exposed to O3BC, pollen, or a combination of O3BC+ pollen. Changes in cell viability were analyzed by fluorescence and changes in the transcriptome by high-throughput RNA sequencing (RNA-seq). Several differentially expressed genes were verified by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Enrichment analysis, based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database, was performed to determine major biological functions and pathways involved.ResultsExposure to ≥ 50 μg/ml O3BC or 25 μg/ml O3BC+ 200 μg /ml pollen significantly decreased cell viability of the hNECs compared to control (p < 0.05) or 25 μg/ml O3BC alone (p < 0.05); whereas exposure to pollen alone did not alter cell viability at any concentration investigated. High-throughput RNA sequencing analysis indicated that there was significant difference in gene expression between pollen or O3BC alone and O3BC+ pollen exposed cells. Exposure to 200 μg/ml O3BC was associated with hypoxia stress response GO terms, whereas exposure to 25 μg/ml O3BC+ 200 μg/ml pollen was associated with inflammatory response GO terms; including regulation of neutrophil migration and chemotaxis, macrophage differentiation and chemotaxis, mast cell activation, and phagocytosis. KEGG pathway analysis indicated the top 10 upstream regulators to be IL1B, CSF1, CCL2, TLR2, LPL, IGF8, SPP1, CXCL8, FCER1G and IL1RN; of which expressions of inflammation-related genes IL1B, CSF1 and FCER1G were significantly increased.ConclusionO3BC and pollen allergen combined exposure may induce innate immune and allergic inflammation in hNECs, and therefore potentially exacerbate the symptoms of AR in affected individuals.

M2 Macrophage Co-Expression Factors Correlate With Immune Phenotype and Predict Prognosis of Bladder Cancer.

PurposeTherapeutic targets of tumor-associated macrophages have been discovered and used clinically as immunotherapy. M2 macrophages are tumor-associated macrophages that promote cancer progression. This article explores the related factors and the effects of type M2 macrophages.MethodWe obtained bladder cancer (BC) sequencing data from TCGA and GSE31189. We used the CIBERSORT algorithm calculate M2 macrophage proportions among 22 type immune cells. The Estimate package was used to measure BC purity. M2 macrophage-related genes were selected using WGCNA. Receiver operating characteristic curves and Kaplan–Meier analyses were performed to determine the risk score, conducted for M2 macrophage-related factors. The Pearson test was used to determine the correlation among M2 macrophage-related genes, clinical phenotype, immune phenotype and tumor mutation burden (TMB). The TIMER database was used to calculate correlations among M2 macrophages and other cancers.ResultsExpression of four M2 macrophages co-expressed genes (CD163, CD209, CSF1, MMD) positively correlated with infiltration of M2 macrophages, which were enriched in the negative regulation of immune system process and the positive regulation of tumor necrosis factor production. M2 macrophage-related factors are robust biomarkers for predicting the BC and immune phenotypes. The Cox regression model built on these four co-expression factors showed a close correlation with outcome (AUC = 0.64). The four co-expression factors negatively correlated outcome and TMB.ConclusionFour co-expressed genes promote high levels of infiltration of type M2 macrophages in the negative regulation of immune system processes and the positive regulation of tumor necrosis factor production processes. These co-expressed genes and the biological process they involve might suggest new strategies for regulation of chemotaxis in M2 macrophages.

Comprehensive genomic and immunophenotypic analysis of CD4 T cell infiltrating human triple-negative breast cancer

The aim of this study is to investigate the gene expression module of tumor-infiltrating CD4+T cells and its potential roles in modulating immune cell functions in triple-negative breast cancer. Differentially expressed genes were identified by comparison of the expression profile in CD4+T cells isolated from tumor tissues and peripheral blood of TNBC patients respectively. The differential expression analysis was conducted using R, and then the functional and pathway enrichment of the DEGs were analyzed using GSEA, followed by integrated regulatory network construction and genetic analysis of tumor-infiltrating immune cells based on a scientific deconvolution algorithm. As a result, abundant Treg and exhausted lymphocytes were detected, accompanied by largely decreased of effector/memory and cytotoxic T cells. Immune-related gene correlation analysis showed that the extent of follicular helper T cells gene expression signatures were inversely associated with those of CD4+ naive T cells and CD4+ memory resting T cells, but positively correlated with that of CD4+ memory activated T cells. In addition, we found five core genes including IFNG, CTLA4, FAS, CXCR6, and JUN were significantly over expressed in CD4+ TILs which may contribute to exhaustion of lymphocytes and participate in biological processes associated with regulation of chemotaxis. Study provides a comprehensive understanding of the roles of DEGs associated with the chemotactic and exhausted immunophenotypes of CD4+ TILs that are a valuable resource from which future investigation may be carried out to better understand the mechanisms that promote TNBC progression.

Genome-wide identification of Azospirillum brasilense Sp245 small RNAs responsive to nitrogen starvation and likely involvement in plant-microbe interactions

BackgroundSmall RNAs (sRNAs) are non-coding RNAs known to regulate various biological functions such as stress adaptation, metabolism, virulence as well as pathogenicity across a wide range of bacteria, mainly by controlling mRNA stabilization or regulating translation. Identification and functional characterization of sRNAs has been carried out in various plant growth-promoting bacteria and they have been shown to help the cells cope up with environmental stress. No study has been carried out to uncover these regulatory molecules in the diazotrophic alpha-proteobacterium Azospirillum brasilense Sp245 to date.ResultsExpression-based sRNA identification (RNA-seq) revealed the first list of ~ 468 sRNA candidate genes in A. brasilense Sp245 that were differentially expressed in nitrogen starvation versus non-starved conditions. In parallel, in silico tools also identified 2 of the above as candidate sRNAs. Altogether, putative candidates were stringently curated from RNA-seq data based on known sRNA parameters (size, location, secondary structure, and abundance). In total, ~ 59 significantly expressed sRNAs were identified in this study of which 53 are potentially novel sRNAs as they have no Rfam and BSRD homologs. Sixteen sRNAs were randomly selected and validated for differential expression, which largely was found to be in congruence with the RNA-seq data.ConclusionsDifferential expression of 468 A. brasilense sRNAs was indicated by RNA-seq data, a subset of which was confirmed by expression analysis. Four of the significantly expressed sRNAs were not observed in nitrogen starvation while 16 sRNAs were found to be exclusively expressed in nitrogen depletion. Putative candidate sRNAs identified have potential mRNA targets primarily involved in stress (abiotic and biotic) adaptability; regulation of bacterial cellular, biological and molecular pathways such as nitrogen fixation, polyhydroxybutyrate synthesis, chemotaxis, biofilm formation and transcriptional regulation. In addition to directly influencing bacteria, some of these sRNAs also have targets influencing plant-microbe interactions through adhesion of bacteria to plant roots directly, suppressing host response, inducing plant defence and signalling.