Multiplex-Heterogeneous Network-Based Capturing Potential SNP "Switches" of Pathways Associating With Diverse Disease Characteristics of Asthma.

Asthma is a complex heterogeneous respiratory disorder. In recent years nubbly regions of the role of genetic variants and transcriptome including mRNAs, microRNAs, and long non-coding RNAs in the pathogenesis of asthma have been separately excavated and reported. However, how to systematically integrate and decode this scattered information remains unclear. Further exploration would improve understanding of the internal communication of asthma. To excavate new insights into the pathogenesis of asthma, we ascertained three asthma characteristics according to reviews, airway inflammation, airway hyperresponsiveness, and airway remodeling. We manually created a contemporary catalog of corresponding risk transcriptome, including mRNAs, miRNAs, and lncRNAs. MIMP is a multiplex-heterogeneous networks-based approach, measuring the relevance of disease characteristics to the pathway by examining the similarity between the determined vectors of risk transcriptome and pathways in the same low-dimensional vector space. It was developed to enable a more concentrated and in-depth exploration of potential pathways. We integrated experimentally validated competing endogenous RNA regulatory information and the SNPs with significant pathways into the ceRNA-mediated SNP switching pathway network (CSSPN) to analyze ceRNA regulation of pathways and the role of SNP in these dysfunctions. We discovered 11 crucial ceRNA regulations concerning asthma disease feature pathway and propose a potential mechanism of ceRNA regulatory SNP → gene → pathway → disease feature effecting asthma pathogenesis, especially for MALAT1 (rs765499057/rs764699354/rs189435941) → hsa-miR-155 → IL13 (rs201185816/rs1000978586/rs202101165) → Interleukin-4 and Interleukin-13 signaling → inflammation/airway remodeling and MALAT1 (rs765499057/rs764699354/rs189435941) → hsa-miR-155 → IL17RB (rs948046241) → Interleukin-17 signaling (airway remodeling)/Cytokine-cytokine receptor interaction (inflammation). This study showed a systematic and propagable workflow for capturing the potential SNP "switch" of asthma through text and database mining and provides further information on the pathogenesis of asthma.

Predictive Score of Risk Associated with Progression of Patients with COVID-19 Pneumonia in Wuhan, China: the ALA Score.

Background The Coronavirus Disease 2019 (COVID-19) had become a Public Health Emergency of International Concern with more than 90 million confirmed cases worldwide. Therefore, this study aims to establish a predictive score model of progression to severe type in patients with COVID-19. Methods This is a retrospective cohort study of 151 patients with COVID-19 diagnosed by nucleic acid test or specific serum antibodies from February 13, 2020, to March 14, 2020, hospitalized in a COVID-19-designed hospital in Wuhan, China. Results Of the 151 patients with average age of 63 years, 64 patients were male (42.4%), and 29 patients (19.2%) were classified as severe group. Multivariate analysis showed that age > 65 years (odds ratio [OR] = 9.72, 95%CI: 2.92-32.31, P < 0.001), lymphocyte count ≤ 1.1 × 109/L (OR = 3.42, 95%CI: 1.24-9.41, P = 0.017) and AST > 35 U/L (OR = 3.19, 95%CI: 1.11-9.19, P = 0.032) were independent risk factors for the disease severity. The area under curve (AUC) of receiver operating characteristic curve of the probabilities of the composite continuous variable (age + lymphocyte + AST) is 0.796. Finally, a predictive score model called ALA was established, and its AUC was 0.83 (95%CI: 0.75-0.92). Using a cutoff value of 9.5 points, the positive and negative predictive values were 54.1% (38-70.1%) and 92.1% (87.2-97.1%), respectively. Conclusion The ALA score model can quickly identify severe patients with COVID-19, so as to help clinicians to better choose accurate management strategy.

Factors Associated with a Positive Severe Acute Respiratory Syndrome Coronavirus 2 Testing in Suspected Cases Presenting with Pneumonia: A Retrospective Cohort Study in a Single Medical Center.

BACKGROUND: Coronavirus disease 2019 (COVID-19) has become a global emerging infectious disease. OBJECTIVES: To analyze the initial clinical characteristics of COVID-19 suspected and confirmed patients on admission in order to find out which kinds may be more likely to get positive nucleic acid testing results, and to explore the risk factors associated with all-cause death. METHODS: Medical records from 309 highly suspected cases with pneumonia were collected from February 13, 2020, to March 14, 2020, in a COVID-19-designated hospital of Wuhan. The majority of the clinical data were collected on the first day of hospital admission. RESULTS: Of 309 patients with median age 64 years (interquartile ranges [IQR], 53-72 years), 111 patients (35.9%) were confirmed by nucleic acid testing (median age 64 years, IQR: 56-71 years; 48 males). Of those 111 patients, 13 (11.7%) patients died. In multivariate analysis, factors associated with positive testing included fatigue (odds ratios [OR] = 3.14; 95% confidence interval [CI]: 1.88-5.24, p < 0.001), cough (OR = 0.55; 95% CI: 0.32-0.95, p = 0.032), no less than 1 comorbidity (OR = 1.77; 95% CI: 1.06-2.98, p = 0.030), and severe pneumonia (OR = 2.67; 95% CI: 1.20-5.97, p = 0.016). Furthermore, age, dyspnea, noneffective antibiotic treatment, white blood cell, lymphocyte, platelets, and organ dysfunction (e.g., higher lactate dehydrogenase) were significantly associated with all-cause in-hospital death in patients with COVID-19. CONCLUSION: Patients with severe forms of this disease were more likely to get positive results. Age and organ dysfunction were associated with a greater risk of death.

Ratios of neutrophil-to-lymphocyte and platelet-to-lymphocyte predict all-cause mortality in inpatients with coronavirus disease 2019 (COVID-19): a retrospective cohort study in a single medical centre.

The Coronavirus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a public health emergency of international concern. The current study aims to explore whether the neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) are associated with the development of death in patients with COVID-19. A total of 131 patients diagnosed with COVID-19 from 13 February 2020 to 14 March 2020 in a hospital in Wuhan designated for treating COVID-19 were enrolled in the current study. These 131 patients had a median age of 64 years old (interquartile range: 56-71 years old). Furthermore, among these patients, 111 (91.8%) patients were discharged and 12 (9.2%) patients died in the hospital. The pooled analysis revealed that the NLR at admission was significantly elevated for non-survivors, when compared to survivors (P < 0.001). The NLR of 3.338 was associated with all-cause mortality, with a sensitivity of 100.0% and a specificity of 84.0% (area under the curve (AUC): 0.963, 95% confidence interval (CI) 0.911-1.000; P < 0.001). In view of the small number of deaths (n = 12) in the current study, NLR of 2.306 might have potential value for helping clinicians to identify patients with severe COVID-19, with a sensitivity of 100.0% and a specificity of 56.7% (AUC: 0.729, 95% CI 0.563-0.892; P = 0.063). The NLR was significantly associated with the development of death in patients with COVID-19. Hence, NLR is a useful biomarker to predict the all-cause mortality of COVID-19.

Circular RNA hsa_circ_0014130 Inhibits Apoptosis in Non-Small Cell Lung Cancer by Sponging miR-136-5p and Upregulating BCL2.

Previous studies indicated that circular RNAs (circRNA) played vital roles in the development of non-small cell lung cancer (NSCLC). Although hsa_circ_0014130 might be a potential NSCLC biomarker, its function in NSCLC remains unknown. Thus, this study aimed to investigate the role of hsa_circ_0014130 in the progression of NSCLC. The levels of hsa_circ_0014130 in NSCLC tissues and adjacent normal tissues were determined by qRT-PCR. In addition, the expressions of Bcl-2 and cleaved caspase-3 in A549 cells were detected with Western blot analysis. Meanwhile, the dual luciferase reporter system assay was used to determine the interaction of hsa_circ_0014130 and miR-136-5p or Bcl-2 and miR-136-5p in NSCLC, respectively. The level of hsa_circ_0014130 was significantly upregulated in NSCLC tissues. Downregulation of hsa_circ_0014130 markedly inhibited the proliferation and invasion of A549 cells via inducing apoptosis. In addition, downregulation of hsa_circ_0014130 inhibited the tumorigenesis of subcutaneous A549 xenograft in mice in vivo. Meanwhile, mechanistic analysis indicated that downregulation of hsa_circ_0014130 decreased the expression of miR-136-5p-targeted gene Bcl-2 via acting as a competitive "sponge" of miR-136-5p. In this study, we found that hsa_circ_0014130 was upregulated in NSCLC tissues. In addition, hsa_circ_0014130 functions as a tumor promoter in NSCLC to promote tumor growth through upregulating Bcl-2 partially via "sponging" miR-136-5p. IMPLICATIONS: In conclusion, hsa_circ_0014130 might function as a prognostic factor for patients with NSCLC and might be a therapeutic target for the treatment of NSCLC in future.

Construction of asthma related competing endogenous RNA network revealed novel long non-coding RNAs and potential new drugs.

BACKGROUND: Asthma is a heterogeneous disease characterized by chronic airway inflammation. Long non-coding RNA can act as competing endogenous RNA to mRNA, and play significant role in many diseases. However, there is little known about the profiles of long non-coding RNA and the long non-coding RNA related competing endogenous RNA network in asthma. In current study, we aimed to explore the long non-coding RNA-microRNA-mRNA competing endogenous RNA network in asthma and their potential implications for therapy and prognosis. METHODS: Asthma-related gene expression profiles were downloaded from the Gene Expression Omnibus database, re-annotated with these genes and identified for asthma-associated differentially expressed mRNAs and long non-coding RNAs. The long non-coding RNA-miRNA interaction data and mRNA-miRNA interaction data were downloaded using the starBase database to construct a long non-coding RNA-miRNA-mRNA global competing endogenous RNA network and extract asthma-related differentially expressed competing endogenous RNA network. Finally, functional enrichment analysis and drug repositioning of asthma-associated differentially expressed competing endogenous RNA networks were performed to further identify key long non-coding RNAs and potential therapeutics associated with asthma. RESULTS: This study constructed an asthma-associated competing endogenous RNA network, determined 5 key long non-coding RNAs (MALAT1, MIR17HG, CASC2, MAGI2-AS3, DAPK1-IT1) and identified 8 potential new drugs (Tamoxifen, Ruxolitinib, Tretinoin, Quercetin, Dasatinib, Levocarnitine, Niflumic Acid, Glyburide). CONCLUSIONS: The results suggested that long non-coding RNA played an important role in asthma, and these novel long non-coding RNAs could be potential therapeutic target and prognostic biomarkers. At the same time, potential new drugs for asthma treatment have been discovered through drug repositioning techniques, providing a new direction for the treatment of asthma.

Corticosteroid therapy in pneumonia from swine-origin influenza A (H1N1) in China.

The first three cases of confirmed infection with the virus in China were documented between May 10 and May 15, 2009. Although the clinical characteristics of the H1N1 pneumonia were described in clinical reports, the therapy has few been described. Therefore, we report our experiences of 53 cases of the H1N1 pneumonia with treatment. We describe clinical characteristic of 53 patients who were hospitalized for laboratory-confirmed H1N1 pneumonia at the 2nd Clinical College of Harbin Medical University. In addition, we measure the role of corticosteroid, mechanical ventilation, and non-corticosteroid antiviral therapy in the management of pneumonia patients with novel H1N1 infection. Real-time reverse-transcriptase-polymerase chain (RT-PCR) testing was used to confirm infection. The outcome of therapy was compared in scores of PaO2 and CT. The data was statistical analyzed by the Shapiro-Wilk, anova, Student-Newman-Keuls Test, and Kruskal-Wallis Test. The most common symptoms were dyspnea. In moderate ill patients, the changes in the increased PaO2 were lower in the non-corticosteroid antiviral therapy group than in the combination of corticosteroid and non-corticosteroid antiviral therapy after 5 days' therapy. The therapy protocol of non-corticosteriod + mechanical ventilation played important role in the recovery of severe ill patients.

Identification of crucial microRNAs and genes in hypoxia-induced human lung adenocarcinoma cells.

BACKGROUND: Variations of microRNA (miRNA) expression profile in hypoxic lung cancer cells have not been studied so far. Therefore, using miRNA microarray technology, this study aimed to study the miRNA expression profile and investigate the potential crucial miRNAs and their target genes in hypoxia-induced human lung adenocarcinoma cells. MATERIALS AND METHODS: Based on miRNA microarray, miRNA expression profiling of hypoxia-induced lung adenocarcinoma A549 cells was obtained. After identification of differentially expressed miRNAs (DE-miRNAs) in hypoxic cells, target genes of DE-miRNAs were predicted, and functional enrichment analysis of targets was conducted. Furthermore, the expression levels of DE-miRNAs and their target genes were validated by real-time quantitative polymerase chain reaction. In addition, using miRNA mimics, the effect of overexpressed DE-miRNAs on A549 cell behaviors (cell proliferation, cell cycle, and apoptosis) was evaluated. RESULTS: In total, 14 DE-miRNAs (nine upregulated miRNAs and five downregulated miRNAs) were identified in hypoxic cells, compared with normoxic cells. Target genes of both upregulated and downregulated miRNAs were enriched in the functions such as chromatin modification, and pathways such as Wnt signaling pathway and transforming growth factor (TGF)-ß signaling pathway. The expression levels of several miRNAs and their target genes were confirmed, including hsa-miR-301b/FOXF2, hsa-miR-148b-3p/WNT10B, hsa-miR-769-5p/(SMAD2, ARID1A), and hsa-miR-622. Among them, hsa-miR-301b was verified to regulate FOXF2, and hsa-miR-769-5p was verified to modulate ARID1A. In addition, the overexpression of hsa-miR-301b and hsa-miR-769-5p significantly affected the cell cycle of A549 cells, but not cell proliferation and apoptosis. CONCLUSION: miRNA expression profile was changed in hypoxia-induced lung cancer cells. Those validated miRNAs and genes may play crucial roles in the response of lung cancer cells to hypoxia.

MicroRNA-29b promotes the adipogenic differentiation of human adipose tissue-derived stromal cells.

OBJECTIVE: Obesity is primarily characterized by the accumulation of large amounts of fat in adipose tissue. Within the adipose tissue, adipocytes are derived from adipose tissue-derived stromal cells (ADSCs) via a specialized cell lineage differentiation process, and ADSCs play a key role in the generation and metabolism of adipose tissue. This study investigated whether microRNAs (miRNAs) play a role in adipocyte differentiation. METHODS: Using luciferase reporter and ChIP assays, the relationship between miR-29b, SP1, and TNF-α was examined. RESULTS: During the normal adipogenic differentiation of ADSCs, up-regulation of miR-29b promoted adipogenesis by enhancing SP1-mediated inhibition of TNF-α. CONCLUSIONS: This study investigated the regulatory role of miR-29b during the adipogenic differentiation of ADSCs and found that miR-29b is an effective positive regulator of adipogenesis.

Genistein-induced differentiation of breast cancer stem/progenitor cells through a paracrine mechanism.

It is believed that breast cancer stem cells (BCSCs), like normal stem cell counterparts, have the capacity of self-renewal and differentiation. Simultaneously, estrogen receptor (ER)-negative (-) BCSCs are affected by surrounding differentiated ER-positive (+) tumor cells by virtue of paracrine signaling within the tumor micro-environment. Genistein (GEN), as a sort of phytoestrogen, can act on ER+ breast cancer cells but the role of GEN in the differentiation of neighboring ER- BCSCs has not been defined. Transwell co-culture system was utilized so as to elaborate the interaction between well-differentiated ER+ breast cancer cells (MCF-7) and ER- breast cancer stem/progenitor cells (mammospheres derived from MDA-MB-231 cells). GEN-induced differentiation of BCSCs was analyzed by mammospheres formation assay, flow cytometry and RT-PCR after a 3 day solo-culture or co-culture. We find that GEN sized 2 µM, and 40 nM, effectively promotes morphological alteration of mammospheres, reduces the ratio of subset of CD44+/CD24-/ESA+ cells and upregulates the expression of differentiated cell markers of mammospheres in co-culture system, but not in solo-culture condition. Besides, we demonstrate that the differentiation-inducing effect of GEN on mammospheres is associated with PI3K/Akt and MEK/ERK signaling pathways which are activated by amphiregulin released from ER+ cancer cells. These results indicate that GEN was able to induce the differentiation of breast cancer stem/progenitor cells through interaction with ER+ cancer cells by a paracrine mechanism.

Pneumonia in novel swine-origin influenza A (H1N1) virus infection: high-resolution CT findings.

OBJECTIVE: The purpose of our study was to review the initial high-resolution CT (HRCT) findings in pneumonia patients with presumed/laboratory-confirmed novel swine-origin influenza A (H1N1) virus (S-OIV) infection and detect pneumonia earlier. MATERIALS AND METHODS: High-resolution CT (HRCT) findings of 106 patients with presumed/laboratory-confirmed novel S-OIV (H1N1) infection were reviewed. The 106 patients were divided into two groups according to the serious condition of the diseases. The pattern (consolidation, ground-glass, nodules, and reticulation), distribution, and extent of abnormality on the HRCT were evaluated in both groups. The dates of the onset of symptoms of the patients were recorded. RESULTS: The predominant CT findings in the patients at presentation were unilateral or bilateral multifocal asymmetric ground-glass opacities alone (n=29, 27.4%), with unilateral or bilateral consolidation (n=50, 47.2%). The consolidation had peribronchovascular and subpleural predominance. The areas of consolidation were found mainly in the posterior, middle and lower regions of the lungs. Reticular opacities were found in 6 cases of the initial MDCT scan. The extent of disease was greater in group 1 patients requiring advanced mechanical ventilation, with diffuse involvement in 19 patients (63.3%) of group 1 patients, and only 15/76 (19.7%) of group 2 patients (p<0.01, χ2 test). 20 cases (19%) of the 106 patients had small bilateral or unilateral pleural effusions. None had evidence of hilar or mediastinal lymph node enlargement on CT performed at admission or later. CONCLUSIONS: The most common radiographic and CT findings in patients with S-OIV infection are unilateral or bilateral ground-glass opacities with or without associated focal or multifocal areas of consolidation. On HRCT, the ground-glass opacities had a predominant peribronchovascular and subpleural distribution. CT plays an important role in the early recognition of severe S-OIV (H1N1).

Association of ADAM33 gene with susceptibility to COPD in Tibetan population of China.

Chronic obstructive pulmonary disease (COPD) is a common, complex disorder associated with substantial morbidity and mortality, influenced by both environmental factor and genetic factor. ADAM33 gene was found to be associated with asthma, declined lung function and COPD. The purpose of the study was to test whether SNPs in ADAM33 were associated with COPD in Tibetan population of China. Polymerase chain reaction-restriction fragment length polymorphism was carried out to genotype the eight SNPs (V4, T2, T1, S2, S1, Q-1 and F + 1) of ADAM33 on 240 COPD patients and 221 healthy individuals. Four SNPs (V4, T2, T1 and S1) and four haplotypes (H2 CGAAGAGC, H5 GAGAGAGC, H9 GAAAGAGC and H6 CGGGGAGC of ADAM33 gene were associated with COPD significantly (defined as P < 0.05). The results indicate that there is an association between ADAM33 polymorphisms and COPD in Tibetan population of China.

RA induces the neural-like cells generated from epigenetic modified NIH/3T3 cells.

Recently, differentiated somatic cells had been reprogrammed to pluripotential state in vitro, and various tissue cells had been elicited from those cells. Epigenetic modifications allow differentiated cells to perpetuate the molecular memory needed for the cells to retain their identity. DNA methylation and histone deacetylation are important patterns involved in epigenetic modification, which take critical roles in regulating DNA expression. In this study, we dedifferentiated NIH/3T3 fibroblasts by 5-aza-2-deoxycytidine (5-aza-dC) and Trichstatin A (TSA) combination, and detected gene expression pattern, DNA methylation level, and differentiation potential of reprogrammed cells. As the results, embryonic marker Sox2, klf4, c-Myc and Oct4 were expressed in reprogrammed NIH/3T3 fibroblasts. Total DNA methylation level was significant decreased after the treatment. Moreover, exposure of the reprogrammed cells to all trans-retinoic acid (RA) medium elicited the generation of neuronal class IIIbeta-tubulin-positive, neuron-specific enolase (NSE)-positive, nestin-positive, and neurofilament light chain (NF-L)-positive neural-like cells.

Association of ADAM33 gene polymorphisms with adult concomitant allergic rhinitis and asthma in Chinese Han population.

Allergic Rhinitis (AR) and allergic asthma (AS) are very common diseases involving genetic and environmental factors. Most patients with asthma also have rhinitis, which suggests the concept of 'one airway, one disease'. A disintegrin and metalloproteinase 33 (ADAM33) was discovered as the first asthma-susceptible gene by positional cloning. To evaluate the potential influences of ADAM33 gene polymorphisms on concomitant allergic rhinitis and asthma (ARA), a case-control study was conducted in Han population of Northeast China. Six polymorphic sites (V4, T + 1, T2, T1, S1 and Q - 1) were genotyped in 135 ARA patients and 151 controls (CTR). Genotypes were determined by the polymerase chain restriction fragment length polymorphism (PCR-RFLP) method. Data was analyzed using the Chisquaretest and Haploview software. The SNPs (V4 G/C, T2 A/G, T1 G/A, and Q - 1A/G) of the ADAM33 gene may be the causal variants in ARA disease.

Association of ADAM33 gene polymorphisms with adult allergic asthma and rhinitis in a Chinese Han population.

BACKGROUND: Rhinitis and asthma are very common diseases involving genetic and environmental factors. Most patients with asthma also have rhinitis, which suggests the concept of 'one airway, one disease.' A disintegrin and metalloproteinase 33 (ADAM33) is the first asthma-susceptible gene to be discovered by positional cloning. To evaluate the potential influence of ADAM33 gene polymorphisms on allergic rhinitis (AR) and allergic asthma (AS), a case-control study was conducted on the Han population of northeast China. METHODS: Six polymorphic sites (V4, T+1, T2, T1, S1, and Q-1) were genotyped in 128 patients with AR, 181 patients with AS, and 151 healthy controls (CTR). Genotypes were determined by the polymerase chain restriction fragment length polymorphism (PCR-RFLP) method. Data were analyzed using the chi-square test with Haploview software. RESULTS: The single nucleotide polymorphisms (SNPs), V4 G/C, T+1 A/G, and T1 G/A, of the ADAM33 gene may be the causal variants in AR, whereas ADAM33 V4 G/C, T2 A/G, T1 G/A, and Q-1A/G may participate in the susceptibility of AS. CONCLUSION: These results suggest that polymorphisms of the ADAM33 gene may modify individual susceptibility to AR and AS in a Chinese Han population.