Identification of the Resveratrol Potential Targets in the Treatment of Osteoarthritis

Objectives. Osteoarthritis (OA) is a chronic joint degenerative disease and has become an important health problem for the elderly. However, there is still a lack of effective drugs for the treatment of OA. Our research combines bioinformatics and experimental strategies to determine the target of resveratrol for OA treatment. Methods. First, the differentially expressed genes (DEGs) of OA joint tissues were obtained from the related microarray gene expression data. Second, resveratrol, a natural polyphenol compound, was used to screen the drug treatment target genes. Third, the drug-disease network was established, and the resveratrol target genes for OA treatment were obtained and verified through experimental verification. Results. A total of 300 differentially expressed genes with 246 upregulated and 54 downregulated were found in OA joint tissues, and 310 resveratrol potential target genes were obtained. Finally, six genes, namely, CXCL1, HIF1A, IL-6, MMP3, NOX4, and PTGS2, were selected to validate the treatment effects of the resveratrol. The results showed that all six genes in human OA chondrocytes were significantly increased. In addition, in these chondrocytes, CXCL1, HIF1A, IL-6, MMP3, NOX4, and PTGS2 were reduced considerably, but HIF1A was significantly increased after resveratrol treatment. Conclusions. Our data indicates that CXCL1, HIF1A, IL-6, MMP3, NOX4, and PTGS2 are all targets of resveratrol therapy. Our findings may provide valuable information for the mechanism and therapeutic of OA.

Development and Validation of a Six-Gene Prognostic Signature for Bladder Cancer

Human bladder cancer (BCa) is the most common urogenital system malignancy. Patients with BCa have limited treatment efficacy in clinical practice. Novel biomarkers could provide more crucial information conferring to cancer diagnosis, treatment, and prognosis. Here, we aimed to explore and identify novel biomarkers associated with cancer-specific survival of patients with BCa to build a prognostic signature. Based on univariate Cox regression, Lasso regression, and multivariate Cox regression analysis, we conducted an integrated analysis in the training set (GSE32894) and established a six-gene signature to predict the cancer-specific survival for human BCa. The six genes were Cyclin Dependent Kinase 4 (CDK4), E2F Transcription Factor 7 (E2F7), Collagen Type XI Alpha 1 Chain (COL11A1), Bradykinin Receptor B2 (BDKRB2), Yip1 Interacting Factor Homolog B (YIF1B), and Zinc Finger Protein 415 (ZNF415). Then, we validated the prognostic value of the model by using two other datasets (GSE13507 and TCGA). Also, we conducted univariate and multivariate Cox regression analyses, and results indicated that the six-gene signature was an independent prognostic factor of cancer-specific survival of patients with BCa. Functional analysis was performed based on the differentially expressed genes of low- and high-risk patients, and we found that they were enriched in lipid metabolic and cell division-related biological processes. Meanwhile, the gene set enrichment analysis (GSEA) revealed that high-risk samples were enriched in cell cycle and cancer-related pathways [G2/M checkpoint, E2F targets, mitotic spindle, mTOR signaling, spermatogenesis, epithelial–mesenchymal transition (EMT), DNA repair, PI3K/AKT/mTOR signaling, unfolded protein response (UPR), and MYC targets V2]. Lastly, we detected the relative expression of each signature in BCa cell lines by quantitative real-time PCR (qRT-PCR). As far as we know, currently, the present study is the first research that developed and validated a cancer-specific survival prognostic index based on three independent cohorts. The results revealed that this six-gene signature has a predictive ability for cancer-specific prognosis. Moreover, we also verified the relative expression of these six signatures between the bladder cell line and four BCa cell lines by qRT-PCR. Nevertheless, experiments to further explore the function of six genes are lacking.

Biomarker Expression in Multifocal Vulvar High-Grade Squamous Intraepithelial Lesions

In patients with high-grade squamous intraepithelial lesion (HSIL) of the vulva, the presence of multiple lesions, called multifocal HSIL, is common. The aim of this exploratory study was to investigate biomarker expression profiles in multifocal HSIL. In total, 27 lesions from 12 patients with high-risk human papillomavirus (HPV)-positive multifocal HSIL were tested for HPV genotype, expression of p16INK4a and Ki-67, and DNA methylation of six genes. HPV16 was found most commonly in 21 (77.8%) HSILs. In two (16.4%) patients, HPV genotype differed between the lesions. All lesions demonstrated diffuse p16INK4a staining, of which three (11.1%) were combined with patchy staining. One patient (8.3%) demonstrated markedly different DNA methylation levels between lesions. Generally, heterogeneity in methylation profiles was observed between different patients, even when other biomarkers showed similar expression. In conclusion, this study is the first to demonstrate heterogeneity of individual lesions in patients with multifocal HSIL. The studied biomarkers have the potential to refine prognostic and predictive diagnostics. Future prospective, longitudinal studies are needed to further explore the potential of a biomarker profile for management of patients with multifocal HSIL.

Bioinformatics and Transcriptome Analysis of CFEM Proteins in Fusarium graminearum

Fusarium blight of wheat is usually caused by Fusarium graminearum, and the pathogenic fungi will secrete effectors into the host plant tissue to affect its normal physiological process, so as to make it pathogenic. The CFEM (Common in Fungal Extracellular Membrane) protein domain is unique to fungi, but it is not found in all fungi. The CFEM protein contained in F. graminearum may be closely related to pathogenicity. In this study, 23 FgCFEM proteins were identified from the F. graminearum genome. Then, features of these proteins, such as signal peptide, subcellular localization, and transmembrane domains, etc., were analyzed and candidate effectors were screened out. Sequence alignment results revealed that each FgCFEM protein contains one CFEM domain. The amino acids of the CFEM domain are highly conserved and contain eight spaced cysteines, with the exception that FgCFEM8, 9, and 15 lack two cysteines and three cysteines were missed in FgCFEM18 and FgCFEM22. A recently identified CFEM_DR motif was detected in 11 FgCFEMs, and importantly we identified two new conserved motifs containing about 29 and 18 amino acids (CFEM_WR and CFEM_KF), respectively, in some of FgCFEM proteins. Transcriptome analysis of the genes encoding CFEM proteins indicated that all the CFEM-containing genes were expressed during wheat infection, with seven and six genes significantly up- and down-regulated, respectively, compared with in planta and in vitro. Based on the above analysis, FgCFEM11 and FgCFEM23 were predicted to be F. graminearum effectors. This study provides the basis for future functional analyses of CFEM proteins in F. graminearum.

Identification of Methylation-Driven Genes Prognosis Signature and Immune Microenvironment in Epithelial Ovarian Cancer

Background Aberrant gene methylation has been implicated in the development and progression of tumors. We aimed to identity methylation driven genes involved in EOC to establish a prognostic signature for patients with EOC. Methods The methylation, RNA expression and clinical data of EOC patients were downloaded from UCSC Xena website. The “MethylMix” R package was employed to identify the methylation driven genes (MDGs), GO and KEGG analyses were performed to identify the biological functions of the identified genes, univariate, LASSO, and multivariate analyses were carried out to reveal key prognostic genes. Combined with clinical parameters, a prognostic risk nomogram model was established, and its predictive value was internally evaluated using AUC curves and externally verified in the GEO database. Results 111 differentially expressed MDGs were identified, among which six (SLC9A1, MARVELD1, PI3, MFAP4, MSX1, IL18BP) were selected to establish a prognostic risk scoring model. Results of univariate and multivariate analyses indicated that the risk score model was an independent risk factor for EOC. Combined with clinical parameters, a nomogram was constructed, which showed good predictive performance as evidenced by AUC values. The risk scores and the nomogram were externally verified using GSE26193 and GSE53963 datasets. Analysis of mRNA levels of the six genes in OVCAR3 before and after DAC treatment revealed that DAC inhibited the methylation of six genes, thereby increasing mRNA levels of the six genes. GSEA analysis show that associated with the 6 MDGs in the two risk score model groups signaling pathways are closely related to tumor invasion and metastasis. There are significant differences between the two risk score model groups in terms of immune function, check point and TMB. Conclusions We identified and verified 6 MDGs that are closely related to the prognosis of ovarian cancer. A prognostic risk score model and nomogram for predicting the prognosis of EOC were constructed based on the six MDGs. It can also effectively reflect the immune environment and immunotherapy response of EOC. These MDGs have great significance to the implementation of individualized treatment and disease monitoring of EOC patients.

Systematic position of Bombyx incomposita (Lepidoptera: Bombycidae), with notes on its immature biology and hostplant association

The immature stages, morphology, and systematic position of Bombyx incomposita (van Eecke, 1929) are reported. The morphology of larva was investigated using scanning electron microscopy, and the phylogeny was inferred using six genes (COI, CAD, EF-1α, GAPDH, RpS5, and wgl). The molecular phylogeny strongly supported that B. incomposita is sister to B. huttoni Westwood, 1847. The divergence of the COI barcode, phylogenetic reconstruction, and difference in immature stages support the current classification, in which the species incomposita belongs to the genus Bombyx. We give illustrations of male and female genitalia and briefly discuss the utility of the chaetotaxy of the first instar larvae on taxonomy of silkmoths. The SV group bears six setae in B. mandarina, but eight in B. incomposita. The L1 bears three setae in Rotunda, but just single seta in Bombyx.

Germline mutations among Polish patients with acute myeloid leukemia

Background A small but important proportion of patients (4–10 %) with AML have germline mutations. They can cause the development of AML at an earlier age, confer a higher risk of relapse or predispose to secondary leukemias, including therapy-related leukemias. The analysis of germline mutations in a patient and his/her family is also critical for the selection of suitable family donors if the patient is a candidate for hematopoietic stem cell transplantation (HSCT). Methods 103 unrelated consecutive patients with de novo AML were enrolled in the study. Control group consisted of 103 persons from the general population. We performed NGS sequencing of bone marrow cells and buccal swabs DNA of six genes: CEBPA, DDX41, ETV6, TERT, GATA2, and IDH2 to detect germline pathogenic mutations. Results In the investigated group, 49 variants were detected in six genes. 26 of them were somatic and 23 germline. Germline variants were detected in all six tested genes. Eight pathogenic germline mutations were detected in 7 AML patients, in three genes: CEBPA, ETV6, and IDH2. One patient had two pathogenic germinal mutations, one in ETV6 and one in CEBPA gene. We identified one novel pathogenic germline mutation in CEBPA gene. The difference in frequency of all pathogenic germline mutations between the tested (7.77 %) and control groups (0.97 %) was statistically significant (p = 0.046). In the tested group, the median age at AML diagnosis was 11 years lower in patients with pathogenic germline mutations than in patients without them (p = 0.028). Conclusions We showed higher frequency of CEBPA, ETV6, and IDH2 germline mutations in AML patients than in control group, which confirms the role of these mutations in the development of AML. We also showed that the median age at the onset of AML in patients with pathogenic germline mutations is significantly lower than in patients without them.

SARS-CoV-2 suppresses IFNβ production mediated by NSP1, 5, 6, 15, ORF6 and ORF7b but does not suppress the effects of added interferon

Type I Interferons (IFN-Is) are a family of cytokines which play a major role in inhibiting viral infection. Resultantly, many viruses have evolved mechanisms in which to evade the IFN-I response. Here we tested the impact of expression of 27 different SARS-CoV-2 genes in relation to their effect on IFN production and activity using three independent experimental methods. We identified six gene products; NSP6, ORF6, ORF7b, NSP1, NSP5 and NSP15, which strongly (>10-fold) blocked MAVS-induced (but not TRIF-induced) IFNβ production. Expression of the first three of these SARS-CoV-2 genes specifically blocked MAVS-induced IFNβ-promoter activity, whereas all six genes induced a collapse in IFNβ mRNA levels, corresponding with suppressed IFNβ protein secretion. Five of these six genes furthermore suppressed MAVS-induced activation of IFNλs, however with no effect on IFNα or IFNγ production. In sharp contrast, SARS-CoV-2 infected cells remained extremely sensitive to anti-viral activity exerted by added IFN-Is. None of the SARS-CoV-2 genes were able to block IFN-I signaling, as demonstrated by robust activation of Interferon Stimulated Genes (ISGs) by added interferon. This, despite the reduced levels of STAT1 and phospho-STAT1, was likely caused by broad translation inhibition mediated by NSP1. Finally, we found that a truncated ORF7b variant that has arisen from a mutant SARS-CoV-2 strain harboring a 382-nucleotide deletion associating with mild disease (Δ382 strain identified in Singapore & Taiwan in 2020) lost its ability to suppress type I and type III IFN production. In summary, our findings support a multi-gene process in which SARS-CoV-2 blocks IFN-production, with ORF7b as a major player, presumably facilitating evasion of host detection during early infection. However, SARS-CoV-2 fails to suppress IFN-I signaling thus providing an opportunity to exploit IFN-Is as potential therapeutic antiviral drugs.

Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights into the Origin and Distribution of Nitrogen Fixation across Bacteria and Archaea

The phylogeny of nitrogenase has only been analyzed using the structural proteins NifHDK. As nifHDKENB has been established as the minimum number of genes necessary for in silico prediction of diazotrophy, we present an updated phylogeny of diazotrophs using both structural (NifHDK) and cofactor assembly proteins (NifENB). Annotated Nif sequences were obtained from InterPro from 963 culture-derived genomes. Nif sequences were aligned individually and concatenated to form one NifHDKENB sequence. Phylogenies obtained using PhyML, FastTree, RapidNJ, and ASTRAL from individuals and concatenated protein sequences were compared and analyzed. All six genes were found across the Actinobacteria, Aquificae, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Deferribacteres, Firmicutes, Fusobacteria, Nitrospira, Proteobacteria, PVC group, and Spirochaetes, as well as the Euryarchaeota. The phylogenies of individual Nif proteins were very similar to the overall NifHDKENB phylogeny, indicating the assembly proteins have evolved together. Our higher resolution database upheld the three cluster phylogeny, but revealed undocumented horizontal gene transfers across phyla. Only 48% of the 325 genera containing all six nif genes are currently supported by biochemical evidence of diazotrophy. In addition, this work provides reference for any inter-phyla comparison of Nif sequences and a quality database of Nif proteins that can be used for identifying new Nif sequences.