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Objective: Screening of feature genes involved in cytokine release syndrome (CRS) from the coronavirus disease 19 (COVID-19). Methods: The data sets related to COVID-19 were retrieved using Gene Expression Omnibus (GEO) database, the differentially expressed genes (DEGs) related to CRS were analyzed with R software and Venn diagram, and the biological processes and signaling pathways involved in DEGs were analyzed with GO and KEGG enrichment. Core genes were screened using Betweenness and MCC algorithms. GSE164805 and GSE171110 dataset were used to verify the expression level of core genes. Immunoinfiltration analysis was performed by ssGSEA algorithm in the GSVA package. The DrugBank database was used to analyze the feature genes for potential therapeutic drugs. Results: This study obtained 6950 DEGs, of which 971 corresponded with CRS disease genes (common genes). GO and KEGG enrichment showed that multiple biological processes and signaling pathways associated with common genes were closely related to the inflammatory response. Furthermore, the analysis revealed that transcription factors that regulate these common genes are also involved in inflammatory response. Betweenness and MCC algorithms were used for common gene screening, yielding seven key genes. GSE164805 and GSE171110 dataset validation revealed significant differences between the COVID-19 and normal controls in four core genes (feature genes), namely IL6R, TLR4, TLR2, and IFNG. The upregulated IL6R, TLR4, and TLR2 genes were mainly involved in the Toll-like receptor signaling pathway of the inflammatory pathway, while the downregulated IFNG genes primarily participated in the necroptosis and JAK-STAT signaling pathways. Moreover, immune infiltration analysis indicated that higher expression of these genes was associated with immune cell infiltration that mediates inflammatory response. In addition, potential therapeutic drugs for these four feature genes were identified via the DrugBank database. Conclusion: IL6R, TLR4, TLR2, and IFNG may be potential pathogenic genes and therapeutic targets for the CRS associated with COVID-19. [ABSTRACT FROM AUTHOR]

Selecting suitable promoters to drive gene overexpression can provide significant insight into the development of engineered bacteria. In this study, we analyzed the transcriptome data of Burkholderia pyrrocinia JK-SH007 and identified 54 highly expressed genes. The promoter sequences were located using genome-wide data and scored using the prokaryotic promoter prediction software BPROM to further screen out 18 promoter sequences. We also developed a promoter trap system based on two reporter proteins adapted for promoter optimization in B. pyrrocinia JK-SH007: firefly luciferase encoded by the luciferase gene set (Luc) and trimethoprim (TP)-resistant dihydrofolate reductase (TPr). Ultimately, eight constitutive promoters were successfully inserted into the probe vector and transformed into B. pyrrocinia JK-SH007. The transformants were successfully grown on Tp antibiotic plates, and firefly luciferase expression was determined by measuring the relative light unit (RLU). Five of the promoters (P4, P9, P10, P14, and P19) showed 1.01–2.51-fold higher activity than the control promoter λ phage transcriptional promoter (PRPL). The promoter activity was further validated via qPCR analysis, indicating that promoters P14 and P19 showed stable high transcription levels at all time points. Then, GFP and RFP proteins were overexpressed in JK-SH007. In addition, promoters P14 and P19 were successfully used to drive gene expression in Burkholderia multivorans WS-FJ9 and Escherichia coli S17-1. The two constitutive promoters can be used not only in B. pyrrocinia JK-SH007 itself to gene overexpression but also to expand the scope of application. [ABSTRACT FROM AUTHOR]

Motivation Clustered regularly interspaced short palindromic repeats (CRISPR)-based genetic perturbation screen is a powerful tool to probe gene function. However, experimental noises, especially for the lowly expressed genes, need to be accounted for to maintain proper control of false positive rate. Methods We develop a statistical method, named CRISPR screen with Expression Data Analysis (CEDA), to integrate gene expression profiles and CRISPR screen data for identifying essential genes. CEDA stratifies genes based on expression level and adopts a three-component mixture model for the log-fold change of single-guide RNAs (sgRNAs). Empirical Bayesian prior and expectation–maximization algorithm are used for parameter estimation and false discovery rate inference. Results Taking advantage of gene expression data, CEDA identifies essential genes with higher expression. Compared to existing methods, CEDA shows comparable reliability but higher sensitivity in detecting essential genes with moderate sgRNA fold change. Therefore, using the same CRISPR data, CEDA generates an additional hit gene list. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Background: Tumour immune microenvironment heterogeneity is prevalent in numerous cancers and can negatively impact immunotherapy response. Immune heterogeneity and evolution in gastroesophageal adenocarcinoma (GEA) have not been studied in the past. Methods: Together with a multi-region sampling of normal, primary and metastatic tissues, we performed whole exome sequencing, TCR sequencing as well as immune cell infiltration estimation through deconvolution of gene expression signals. Results: We discovered high TCR repertoire and immune cell infiltration heterogeneity among metastatic sites, while they were homogeneous among primary and normal samples. Metastatic sites shared high levels of abundant TCR clonotypes with blood, indicating immune surveillance via blood. Metastatic sites also had low levels of tumour-eliminating immune cells and were undergoing heavy immunomodulation compared to normal and primary tumour tissues. There was co-evolution of neo-antigen and TCR repertoire, but only in patients with late diverging mutational evolution. Co-evolution of TCR repertoire and immune cell infiltration was seen in all except one patient. Conclusions: Our findings revealed immune heterogeneity and co-evolution in GEA, which may inform immunotherapy decision-making. [ABSTRACT FROM AUTHOR]

Simple Summary: Bladder cancer ranks fourth among the most prevalent cancers in men and is the most expensive cancer to treat on a per-patient basis. The muscle-invasive form of bladder cancer is one of the deadliest cancers, with a 5-year survival rate of only 6% in patients with distant metastasis. Effective therapeutic options remain few and far between. SNHG1 is a long non-coding RNA that is over-expressed in 95% of muscle-invasive bladder cancers. However, very little information is available about the role and mechanisms of SNHG1 in bladder tumor formation and progression. Here, we provide experimental evidence establishing that SNHG1 drives bladder cancer cell invasion and stem-cell-like behaviors through a specific signaling pathway. Our results reveal novel biomarkers predictive of the progression of muscle-invasive bladder cancer and potential new targets for therapeutic intervention. The stem-cell-like behavior of cancer cells plays a central role in tumor heterogeneity and invasion and correlates closely with drug resistance and unfavorable clinical outcomes. However, the molecular underpinnings of cancer cell stemness remain incompletely defined. Here, we show that SNHG1, a long non-coding RNA that is over-expressed in ~95% of human muscle-invasive bladder cancers (MIBCs), induces stem-cell-like sphere formation and the invasion of cultured bladder cancer cells by upregulating Rho GTPase, Rac1. We further show that SNHG1 binds to DNA methylation transferase 3A protein (DNMT3A), and tethers DNMT3A to the promoter of miR-129-2, thus hyper-methylating and repressing miR-129-2-5p transcription. The reduced binding of miR-129-2 to the 3′-UTR of Rac1 mRNA leads to the stabilization of Rac1 mRNA and increased levels of Rac1 protein, which then stimulates MIBC cell sphere formation and invasion. Analysis of the Human Protein Atlas shows that a high expression of Rac1 is strongly associated with poor survival in patients with MIBC. Our data strongly suggest that the SNHG1/DNMT3A/miR-129-2-5p/Rac1 effector pathway drives stem-cell-like and invasive behaviors in MIBC, a deadly form of bladder cancer. Targeting this pathway, alone or in combination with platinum-based therapy, may reduce chemoresistance and improve longer-term outcomes in MIBC patients. [ABSTRACT FROM AUTHOR]

Cancer is a complex disease with usually multiple disease mechanisms. Target combination is a better strategy than a single target in developing cancer therapies. However, target combinations are generally more difficult to be predicted. Current CRISPR-cas9 technology enables genome-wide screening for potential targets, but only a handful of genes have been screend as target combinations. Thus, an effective computational approach for selecting candidate target combinations is highly desirable. Selected target combinations also need to be translational between cell lines and cancer patients. We have therefore developed DSCN (double-targetselection guided byCRISPR screening andnetwork), a method that matches expression levels in patients and gene essentialities in cell lines through spectral-clustered protein-protein interaction (PPI) network. In DSCN, a sub-sampling approach is developed to model first-target knockdown and its impact on the PPI network, and it also facilitates the selection of a second target. Our analysis first demonstrated a high correlation of the DSCN sub-sampling-based gene knockdown model and its predicted differential gene expressions using observed gene expression in 22 pancreatic cell lines before and after MAP2K1 and MAP2K2 inhibition (R2 = 0.75). In DSCN algorithm, various scoring schemes were evaluated. The 'diffusion-path' method showed the most significant statistical power of differentialting known synthetic lethal (SL) versus non-SL gene pairs (P = 0.001) in pancreatic cancer. The superior performance of DSCN over existing network-based algorithms, such as OptiCon and VIPER, in the selection of target combinations is attributable to its ability to calculate combinations for any gene pairs, whereas other approaches focus on the combinations among optimized regulators in the network. DSCN's computational speed is also at least ten times fast than that of other methods. Finally, in applying DSCN to predict target combinations and drug combinations for individual samples (DSCNi), DSCNi showed high correlation between target combinations predicted and real synergistic combinations (P = 1e-5) in pancreatic cell lines. In summary, DSCN is a highly effective computational method for the selection of target combinations. Author summary: Cancer therapies require targets to function. Compared to a single target, a target combination is a better strategy for developing cancer therapies. However, predicting target combination is more complicated than predicting a single target. Current CRISPR technology enables whole-genome screening of potential targets. But most of the experiments have been conducted on a single target (gene) level. To facilitate the discovery of novel target (combinations), we developed DSCN (double-targetselection guided byCRISPR screening andnetwork) that utilize single target-level CRISPR screening data and expression profiles for predicting target combinations by connecting cell-line omics-data with tissue omics-data. DSCN showed great accuracy on different cancer types and superior performance compared to existing network-based prediction tools. We also introduced DSCNi derived from DSCN and designed specifically for predicting target combinations for single-tient patient. Our results showed synergistic target combinations predicted by DSCNi accurately reflected synergies on drug combination levels. Thus, DSCN and DSCNi have the potential to be further applied in the clinical personalized medicine practice. [ABSTRACT FROM AUTHOR]

Bacterial intestinal inflammation is a common disease of aquatic animal in high-density aquaculture. This study aims to construct a model of intestinal inflammation in northern snakehead, and analyze the intestinal transcriptome after Aeromonas hydrophila (A. hydrophila) infection by high-throughput sequencing technologies (RNA-seq), in order to obtain candidate genes and regulatory pathways that may participate in inflammatory response. Northern snakehead [(13.05 ± 2.39) g] were infected through anal for 24 h with different concentrations of A. hydrophila (1.0 × 10−4, 1.0 × 10−5, 1.0 × 10−6, 1.0 × 10−7 and 1.0 × 10−8 CFU/mL). Intestinal histology observation showed that infection with A. hydrophila caused obvious inflammatory responses in intestine, especially in hindgut. The results also indicated that intestinal permeability related parameters (D-LA and Na+-K+-ATP), immune-related parameters (C3, LZM, AKP, MPO, IL-1β and TNF-α) and immune-related gene expression (il-1β and tnf-α) were significantly changed compared to the CK group. In this process, high concentration of A. hydrophila infection caused the death of snakehead. On the basis of the above evaluation, we successfully constructed a model of intestinal inflammation induced by A. hydrophila in northern snakehead, and the optimal dosage of A. hydrophila was 1.0 × 10−6 CFU/mL. Subsequently, the constructed model was analyzed on the Illumina Genome Analyser II platform for intestinal transcriptome. Results showed that a total of 370,492,420 clean reads, 145,236 transcripts and 89,431 unigenes were obtained. Moreover, a total of 7566 differentially expressed genes (DEGs) were found, including 4486 upregulated genes and 3080 downregulated genes. Notably, the key pathways [Toll-like receptors (TLRs) and NOD-like receptors (NLRs)] and genes [ tlr1 , tlr2 , tlr5 , nf-κb , tnf-α , il-1β , il-10 , nod1 ] related to inflammation were discovered. These results revealed the response of northern snakehead to A. hydrophila at the transcriptional level, which provide insights for the regulatory mechanisms of intestinal inflammation in northern snakehead. • A model of intestinal inflammation in northern snakehead was constructed by Aeromonas hydrophila. • The optimal dosage of Aeromonas hydrophila for inducing intestinal inflammation in northern snakehead was 1.0 × 10−6 CFU/mL. • The key pathways and genes related to inflammation were discovered by high-throughput sequencing technologies. [ABSTRACT FROM AUTHOR]

Background: Cryptosporidium is an important zoonotic pathogen responsible for severe enteric diseases in humans and animals. However, the molecular mechanisms underlying host and Cryptosporidium interactions are still not clear. Methods: To study the roles of circRNAs in host cells during Cryptosporidium infection, the expression profiles of circRNAs in HCT-8 cells infected with C. parvum were investigated using a microarray assay, and the regulatory role of a significantly upregulated circRNA, ciRS-7, was investigated during C. parvum infection. Results: C. parvum infection caused notable alterations in the expression profiles of circRNAs in HCT-8 cells, and a total of 178 (including 128 up- and 50 downregulated) circRNAs were significantly differentially expressed following C. parvum infection. Among them, ciRS-7 was significantly upregulated and regulated the NF-κB signaling pathway by sponging miR-1270 during C. parvum infection. Furthermore, the ciRS-7/miR-1270/relA axis markedly affected the propagation of C. parvum in HCT-8 cells. Conclusions: Our results revealed that ciRS-7 would promote C. parvum propagation by regulating the miR-1270/relA axis and affecting the NF-κB pathway. To the best of our knowledge, this is the first study to investigate the role of circRNA during Cryptosporidium infection, and the findings provide a novel view for implementing control strategies against Cryptosporidium infection. [ABSTRACT FROM AUTHOR]

Goblet cell adenocarcinoma (GCA) is a rare amphicrine tumor and difficult to diagnose. GCA is traditionally found in the appendix, but extra-appendiceal GCA may be underestimated. Intestinal adenocarcinoma with signet ring cell component is also very rare, and some signet ring cell carcinomas are well cohesive, having some similar morphological features to GCAs. It is necessary to differentiate GCA from intestinal adenocarcinomas with cohesive signet ring cell component (IACSRCC). The goal of this study is to find occurrence of extra-appendiceal GCA and characterize the histological, immunohistochemical, transcriptional, and immune landscape of GCA. We collected 12 cases of GCAs and 10 IACSRCCs and reviewed the clinicopathologic characters of these cases. Immunohistochemical stains were performed with synaptophysin, chromogranin A, CD56, somatostatin receptor (SSTR) 2, and Ki-67. Whole transcriptome RNA-sequencing was performed, and data were used to analyze differential gene expression and predict immune cell infiltration levels in GCA and IACSRCC. RNA-sequencing data for colorectal adenocarcinoma were gathered from TCGA data portal. Of the 12 patients with GCA, there were 4 women and 8 men. There were three appendiceal cases and nine extra-appendiceal cases. GCAs were immunohistochemically different from IACSRCC. GCA also had different levels of B-cell and CD8+ T-cell infiltration compared to both colorectal adenocarcinoma and cohesive IACSRCCs. Differential gene expression analysis showed distinct gene expression patterns in GCA compared to colorectal adenocarcinoma, with a number of cancer-related differentially expressed genes, including upregulation of TMEM14A, GOLT1A, DSCC1, and HSD17B8, and downregulation of KCNQ1OT1 and MXRA5. GCA also had several differentially expressed genes compared to IACSRCCs, including upregulation of PRSS21, EPPIN, RPRM, TNFRSF12A, and BZRAP1, and downregulation of HIST1H2BE, TCN1, AC069363.1, RP11-538I12.2, and REG4. In summary, the number of extra-appendiceal GCA was underestimated in Chinese patients. GCA can be seen as a distinct morphological, immunohistochemical, transcriptomic, and immunological entity. The classic low-grade component of GCA and the immunoreactivity for neuroendocrine markers are the key points to diagnosing GCA. [ABSTRACT FROM AUTHOR]

• −337 to −159 bp and −704 to −556 bp of GRIN1 contain transcription repression regions. • −556 to −337 bp of GRIN1 enhanced gene expression in neuronal cell lines. • The proximal promoter region of GRIN1 may related to neuropsychiatric diseases. Abnormal expression of ionotropic glutamate receptor NMDA type subunit 1, the key subunit of the NMDA receptor, may be related to many neuropsychiatric disorders. In this study, we explored the functional sequence of the 5′ regulatory region of the human GRIN1 gene and discussed the transcription factors that may regulate gene expression. Twelve recombinant pGL3 vectors with gradually truncated fragment lengths were constructed, transfected into HEK-293, U87, and SK-N-SH cell lines, and analyzed through the luciferase reporter gene assay. JASPAR database is used to predict transcription factors. In SK-N-SH and U87 cell lines, regions from −337 to −159 bp, −704 to −556 bp inhibited gene expression, while −556 to −337 bp upregulated gene expression. In HEK-293 and U87 cell lines, the expression of fragment −1703 to + 188 bp was significantly increased compared to adjacent fragments −1539 to + 188 bp and −1843 to + 188 bp. The protein expressions of fragments −2162 to + 188 bp and −2025 to + 188 bp, −1539 to + 188 bp and −1215 to + 188 bp, −1215 to + 188 bp and −1066 to + 188 bp were significantly different in HEK-293 and SK-N-SH cells. According to the predictions of the JASPAR database, the transcription factors REST, EGR1, and CREB1/HIC2 may bind the DNA sequences of GRIN1 gene from the −337 to −159, −556 to −337, and −704 to −556, respectively. In addition, zinc finger transcription factors may regulate the expression of other differentially expressed fragments. Abnormal transcription regulation in the proximal promoter region of GRIN1 (-704 to + 188 bp) may be involved in the course of neuropsychiatric diseases. [ABSTRACT FROM AUTHOR]

The limited cardiomyocyte proliferation is insufficient for repair of the myocardium. Therefore, activating cardiomyocyte proliferation might be a reasonable option for myocardial regeneration. Here, we investigated effect of retinoic acid (RA) on inducing adult cardiomyocyte proliferation and assessed efficacy of self-assembling peptide (SAP)-released RA in activating regeneration of the infarcted myocardium. Effect of RA on inducing cardiomyocyte proliferation was examined with the isolated cardiomyocytes. Expression of the cell cycle-associated genes and paracrine factors in the infarcted myocardium was examined at one week after treatment with SAP-carried RA. Cardiomyocyte proliferation, myocardial regeneration and improvement of cardiac function were assessed at four weeks after treatment. In the adult rat myocardium, expression of RA synthetase gene Raldh2 and RA concentration were decreased significantly. After treatment with RA, the proliferated cardiomyocytes were increased. The formulated SAP could sustainedly release RA. After treatment with SAP-carried RA, expression of the pro-proliferative genes in cell cycle and paracrine factors in the infarcted myocardium were up-regulated. Myocardial regeneration was enhanced, and cardiac function was improved significantly. These results demonstrate that RA can induce adult cardiomyocytes to proliferate effectively. The sustained release of RA with SAP is a promise strategy to enhance repair of the infarcted myocardium. [Display omitted] • Synthesis of retinoic acid in adult myocardium is decreased. • Retinoic acid can induce proliferation of adult cardiomyocytes. • Sustained release of retinoic acid is effective for repair of the infarcted myocardium. [ABSTRACT FROM AUTHOR]