MNNMDA: Predicting human microbe-disease association via a method to minimize matrix nuclear norm.

Identifying the potential associations between microbes and diseases is the first step for revealing the pathological mechanisms of microbe-associated diseases. However, traditional culture-based microbial experiments are expensive and time-consuming. Thus, it is critical to prioritize disease-associated microbes by computational methods for further experimental validation. In this study, we proposed a novel method called MNNMDA, to predict microbe-disease associations (MDAs) by applying a Matrix Nuclear Norm method into known microbe and disease data. Specifically, we first calculated Gaussian interaction profile kernel similarity and functional similarity for diseases and microbes. Then we constructed a heterogeneous information network by combining the integrated disease similarity network, the integrated microbe similarity network and the known microbe-disease bipartite network. Finally, we formulated the microbe-disease association prediction problem as a low-rank matrix completion problem, which was solved by minimizing the nuclear norm of a matrix with a few regularization terms. We tested the performances of MNNMDA in three datasets including HMDAD, Disbiome, and Combined Data with small, medium and large sizes respectively. We also compared MNNMDA with 5 state-of-the-art methods including KATZHMDA, LRLSHMDA, NTSHMDA, GATMDA, and KGNMDA, respectively. MNNMDA achieved area under the ROC curves (AUROC) of 0.9536 and 0.9364 respectively on HDMAD and Disbiome, better than the AUCs of compared methods under the 5-fold cross-validation for all microbe-disease associations. It also obtained a relatively good performance with AUROC 0.8858 in the combined data. In addition, MNNMDA was also better than other methods in area under precision and recall curve (AUPR) under the 5-fold cross-validation for all associations, and in both AUROC and AUPR under the 5-fold cross-validation for diseases and the 5-fold cross-validation for microbes. Finally, the case studies on colon cancer and inflammatory bowel disease (IBD) also validated the effectiveness of MNNMDA. In conclusion, MNNMDA is an effective method in predicting microbe-disease associations. Availability: The codes and data for this paper are freely available at Github https://github.com/Haiyan-Liu666/MNNMDA.

Whole Exome Sequencing Identified Two Single Nucleotide Polymorphisms of Human Leukocyte Antigen-DRB5 in Familial Sarcoidosis in China.

BACKGROUND: Sarcoidosis is a multisystem granulomatous disorder whose etiology is related to genetic and immunological factors. Familial aggregation and ethnic prevalence suggest a genetic predisposition and inherited susceptibility to sarcoidosis. OBJECTIVE: This study aimed to identify suspected risk loci for familial sarcoidosis patients. METHODS: We conducted whole exome sequencing on two sarcoidosis patients and five healthy family members in a Chinese family for a case-control study. The two sarcoidosis patients were siblings who showed chronic disease. RESULTS: The Gene Ontology results showed single nucleotide polymorphisms in three genes, including human leukocyte antigen (HLA)-DRB1, HLA-DRB5, and KIR2DL4, associated with both 'antigen processing and presentation' and 'regulation of immune response.' Sanger sequencing verified two nonsynonymous mutations in HLA-DRB5 (rs696318 and rs115817940) located on 6p21.3 in the major histocompatibility complex (MHC) class II beta 1 region. The structural model simulated on Prot- Param protein analysis by the Expert Protein Analysis System predicted that the hydropathy index changed at two mutation sites (rs696318: p.F96L, -1.844 to -1.656 and rs115817940: p.T106N, -0.322 to -0.633), which indicated the probability of changes in peptide-binding selectivity. CONCLUSION: Our results indicated that two nonsynonymous mutations of HLA-DRB5 have been identified in two sarcoidosis siblings, while their healthy family members do not have the mutations. The two HLA-DRB5 alleles may influence genetic susceptibility and chronic disease progression through peptide mutations on the MHC class II molecule among the two affected family members.

Exome Sequencing Reveals Genetic Variability and Identifies Chronic Prognostic Loci in Chinese Sarcoidosis Patients.

Background: Sarcoidosis is an inflammatory disease characterized by non-caseating granuloma formation in various organs, with several recognized genetic and environmental risk factors. Despite substantial progress, the genetic determinants associated with its prognosis remain largely unknown. Objectives: This study aimed to identify the genetic changes involved in sarcoidosis and evaluate their clinical relevance. Methods: We performed whole-exome sequencing (WES) in 116 sporadic sarcoidosis patients (acute sarcoidosis patients, n=58; chronic sarcoidosis patients, n=58). In addition, 208 healthy controls were selected from 1000 G East Asian population data. To identify genes enriched in sarcoidosis, Fisher exact tests were performed. The identified genes were included for further pathway analysis using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Additionally, we used the STRING database to construct a protein network of rare variants and Cytoscape to identify hub genes of signaling pathways. Results: WES and Fisher's exact test identified 1,311 variants in 439 protein-coding genes. A total of 135 single nucleotide polymorphisms (SNPs) on 30 protein-coding genes involved in the immunological process based on the GO and KEGG enrichment analysis. Pathway enrichment analysis showed osteoclast differentiation and cytokine-cytokine receptor interactions. Three missense mutations (rs76740888, rs149664918, and rs78251590) in two genes (PRSS3 and CNN2) of immune-related genes showed significantly different mutation frequencies between the disease group and healthy controls. The correlation of genetic abnormalities with clinical outcomes using multivariate analysis of the clinical features and mutation loci showed that the missense variant (rs76740888, Chr9:33796673 G>A) of PRSS3 [p=0.04, odds ratio (OR) = 2.49] was significantly associated with chronic disease prognosis. Additionally, the top two hub genes were CCL4 and CXCR4 based on protein-protein interaction (PPI) network analysis. Conclusion: Our study provides new insights into the molecular pathogenesis of sarcoidosis and identifies novel genetic alterations in this disease, especially PRSS3, which may be promising targets for future therapeutic strategies for chronic sarcoidosis.

Percutaneous dilatational tracheostomy versus fibre optic bronchoscopy-guided percutaneous dilatational tracheostomy in critically ill patients: a randomised controlled trial.

BACKGROUND: To determine whether fibre optic bronchoscopy-guided percutaneous dilatational tracheostomy (FOB-PDT) is a better option in critically ill patients, we compared the efficacy and incidence of procedure complications between PDT with and without FOB. METHODS: We included 90 patients with oral intubation and mechanical ventilation who received PDT with (n = 45, FOB-PDT group) and without (n = 45, PDT group) FOB. For all patients, a simplification of the Griggs technique was used in this study with a central venous catheter set and dilating forceps. Demographic data, body mass index (BMI), Sequential Organ Failure Assessment (SOFA) score, Acute Physiology and Chronic Health Evaluation II (APACHE II) score, rate of first-time success, complication rate and time of procedure were evaluated in both groups. PDT was performed guided by FOB only in the FOB-PDT group. RESULTS: The rate of major complications, including minor or major haemorrhage requiring intervention and subcutaneous emphysema in the neck or pneumothorax, was significantly higher in the PDT group than in the PDT-FOB group (40% vs. 20%, P < 0.05). Significant differences were observed between the two groups with respect to the rate of first-time success (64.4% vs. 93.3%, P < 0.05); the rate of first-time success puncture with the puncture needle in the PDT-FOB group was higher than that in the PDT group (93.3% vs. 75.6%, P < 0.05). The mean procedure duration was significantly longer in the PDT group than in the PDT-FOB group (12.9 ± 1.1 vs. 9.8 ± 1.2 min, P < 0 .05). CONCLUSIONS: PDT with FOB offers the advantages of a high rate of first-time success, a low complication rate and short-procedure duration. Thus, FOB-PDT is a better option in critically ill patients.

Modulatory Potential of Curcumin and Resveratrol on p53 Post-Translational Modifications during Gastric Cancer.

The combination approach is now a well-established treatment for cancer. The present study evaluated the potential of curcumin and resveratrol on p53 post-translational modifications during gastric cancer. We segregated rats into five groups that included normal controls, dimethylhydrazine (DMH) treated, DMH + curcumin treated, DMH + resveratrol treated, and DMH + curcumin + resveratrol treated. Morphological analyses of tumor nodules confirmed carcinogenesis in rats after 25 weeks of DMH administration. The DMH treatment significantly induced carcinogenesis, as evidenced by high tumor burden in DMH-treated rats compared with controls. Moreover, DMH treatment caused a significant increase in the protein expressions of p53 as well as p53 phosphorylation in the DMH-treated rats. In addition, a significant rise was observed in 14C glucose uptake and 3H-thymidin uptakes in DMH-treated rats. Furthermore, enzyme activities of lactate dehydrogenase and alkaline phosphatase also showed a significant rise. On the contrary, significant decline was noticed in the p53 acetylation at residue 382 of DMH-treated rats. Conversely, combined treatment with curcumin and resveratrol to DMH-treated rats resulted in significant moderation in the tumor burden. In addition, a significant rise in p53 acetylation was at residue 382 of DMH-treated rats after treatment with phytochemicals. Supplementation with phytochemicals significantly modulated other biophysical and biochemical indices to near normal levels. Therefore, we conclude that curcumin and resveratrol significantly modulated p53 post-translational modifications during gastric cancer.

Mapping native disulfide bonds at a proteome scale.

We developed a high-throughput mass spectrometry method, pLink-SS (http://pfind.ict.ac.cn/software/pLink/2014/pLink-SS.html), for precise identification of disulfide-linked peptides. Using pLink-SS, we mapped all native disulfide bonds of a monoclonal antibody and ten standard proteins. We performed disulfide proteome analyses and identified 199 disulfide bonds in Escherichia coli and 568 in proteins secreted by human endothelial cells. We discovered many regulatory disulfide bonds involving catalytic or metal-binding cysteine residues.

Characterization and proteomic analysis of ovarian cancer-derived exosomes.

Ovarian cancer is the most lethal type of cancer among all frequent gynecologic malignancies, because most patients present with advanced disease at diagnosis. Exosomes are important intercellular communication vehicles, released by various cell types. Here we presented firstly the protein profile of highly purified exosomes derived from two ovarian cancer cell lines, OVCAR-3 and IGROV1. The exosomes derived from ovarian cancer cell lines were round and mostly 30-100 nm in diameter when viewed under an electron microscope. The exosomal marker proteins TSG101 and Alix were detected in exosome preparations. The range of density was between 1.09 g/ml and 1.15 g/ml. A total of 2230 proteins were identified from two ovarian cell-derived exosomes. Among them, 1017 proteins were identified in both exosomes including all of the major exosomal protein markers. There were 380 proteins that are not reported in the ExoCarta database. In addition to common proteins from exosomes of various origins, our results showed that ovarian cancer-derived exosomes also carried tissue specific proteins associated with tumorigenesis and metastasis, especially in ovarian carcinoma. Based on the known roles of exosomes in cellular communication, these data indicate that exosomes released by ovarian cancer cells may play important roles in ovarian cancer progression and provide a potential source of blood-based protein biomarkers.