Identifying lncRNAs and mRNAs related to survival of NSCLC based on bioinformatic analysis and machine learning.

Non-small cell lung cancer (NSCLC) is the most common histopathological type, and it is purposeful for screening potential prognostic biomarkers for NSCLC. This study aims to identify the lncRNAs and mRNAs related to survival of non-small cell lung cancer (NSCLC). The expression profile data of lung adenocarcinoma and lung squamous cell carcinoma were downloaded in The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) dataset. A total of eight survival related long non-coding RNAs (lncRNAs) and 262 survival related mRNAs were filtered. By gene set enrichment analysis, 17 significantly correlated Gene Ontology signal pathways and 14 Kyoto Encyclopedia of Genes and Genomes signal pathways were screened. Based on the clinical survival and prognosis information of the samples, we screened eight lncRNAs and 193 mRNAs by single factor Cox regression analysis. Further single and multifactor Cox regression analysis were performed, 30 independent prognostication-related mRNAs were obtained. The PPI network was further constructed. We then performed the machine learning algorithms (Least absolute shrinkage and selection operator, Recursive feature elimination, and Random forest) to screen the optimized DEGs combination, and a total of 17 overlapping mRNAs were obtained. Based on the 17 characteristic mRNAs obtained, we firstly built a Nomogram prediction model, and the ROC values of training set and testing set were 0.835 and 0.767, respectively. By overlapping the 17 characteristic mRNAs and PPI network hub genes, three genes were obtained: CDC6, CEP55, TYMS, which were considered as key factors associated with survival of NSCLC. The in vitro experiments were performed to examine the effect of CDC6, CEP55, and TYMS on NSCLC cells. Finally, the lncRNAs-mRNAs networks were constructed.

Lung ultrasound score as a tool to predict severity of bronchopulmonary dysplasia in neonates born ≤25 weeks of gestational age.

OBJECTIVE: The primary aim was to evaluate whether the addition of the posterior lung aided in diagnostic accuracy of predicting bronchopulmonary dysplasia (BPD) vs moderate-severe BPD (msBPD); the secondary aim was to explore the diagnostic accuracy of two protocols for BPD vs msBPD. STUDY DESIGN: This was a single-center prospective observational study. Preterm infants with a gestational age ≤ 25 weeks were included. Two LUS score protocols were evaluated on the 14th day of life (DOL): (A) evaluating the anterolateral (LUS score-al) lung and (B) the anterolateral combined with posterior (LUS score-alp) lung. The LUS score range for the two protocols was 0-32 and 0-48, respectively. RESULTS: A total of eighty-nine infants were enrolled. Both the LUS score-al and LUS score-alp were higher in neonates developing BPD and msBPD than in the rest of the cohort (LUS score-al 24 (23,26) vs 22 (20,23); LUS score-alp 36 (34,39) vs 28 (25,32)) (LUS score-al 25 (24,26) vs 23 (21,24); LUS score-alp 40 (39,40) vs 34 (28,36)). The LUS score-al on the 14th DOL showed a moderate diagnostic accuracy to predict BPD and msBPD (AUC 95% CI: 0.797 [0.697-0.896]; 0.811[0.713-0.909]), while the LUS score-alp significantly improved diagnostic accuracy of BPD and msBPD (AUC 95% CI: 0.902 [0.834-0.970]; 0.922 [0.848-0.996]). A cutoff of 25 points in the LUS score-al provided a sensitivity, specificity, positive likelihood ratio, and negative likelihood ratio of 76.9%, 79.4%, 3.7, and 0.3 respectively to predict msBPD. Meanwhile, that of 39 points in the LUS score-alp provided a sensitivity, specificity, positive likelihood ratio, and negative likelihood ratio of 81%, 98.4%, 50.5 and 0.19 to predict msBPD, respectively. CONCLUSIONS: The LUS score on the 14th DOL can predict BPD and msBPD with moderate diagnostic accuracy. Apart from that, scanning posterior enhanced diagnostic accuracy.

Lung ultrasound score predicts patent ductus arteriosus ligation among neonates ≤25 weeks.

BACKGROUND: This prospective study aimed to investigate whether lung ultrasound score (LUSs) can predict the patent ductus arteriosus (PDA) ligation. METHODS: Preterm infants ≤25 weeks of gestational age (GA) were enrolled. A lung ultrasound was performed on the 14th day of life. Each lung zone was given a score between 0 and 4. A receiver-operating characteristic (ROC) curve was constructed to evaluate the ability of the LUSs for predicting ligation. RESULTS: A total of 81 infants were eligible with a median GA and birth weight (BW) of 25 weeks (24.1-25.2) and 710 g (645-770), respectively. The median time from birth to ligation was 35 days (32-51). Those who underwent ligation had a longer time of mechanical ventilation (34 [26-39] vs. 19 [12-30], p < 0.001), shorter time of noninvasive respiratory support (39 [32-51] vs. 50 [41.5-57], p < 0.01), higher incidence of the bronchopulmonary dysplasia (BPD) (p < 0.01), and severe BPD (p < 0.001). The LUSs had an area under the ROC of 0.96 (95% confidence interval: 0.93-0.99) for the prediction of ligation. A LUSs cutoff of 36 has a sensitivity and specificity of 96% and 86% and positive and negative predictive values of 82% and 98%, respectively. CONCLUSIONS: LUSs at an early stage of life can predict PDA ligation in extremely preterm infants. It would be helpful to reduce morbidity by reducing the duration and magnitude of respiratory support.

Risk factors of acute cerebral infarction in patients with primary hypertension.

OBJECTIVE: To explore the risk factors of acute cerebral infarction (ACI) in patients with primary hypertension. METHODS: Patients diagnosed with primary hypertension and ACI and confirmed by MRI, who were admitted to Honghuagang District people's Hospital, Zunyi City, from January 2020 to December 2020, were selected. Concurrent patients with primary hypertension were selected as the control group. The risk factor including sex, age, smoking, drinking, laboratory examination, and other complications was analyzed. RESULTS: Three hundred patients with hypertensive ACI and 117 cases with hypertension were included. The laboratory examination comparison between the two groups showed that patients in the ACI group had higher glycosylated hemoglobin, D-dimer and FDPs then patients of the control group (P < 0.05). There was significant association between diabetes mellitus and acute cerebral infarction in patients with primary hypertension (OR = 1.452, P = 0.004). CONCLUSION: Poor control of blood glucose in pre-morbid diabetes mellitus may be related to the occurrence of ACI. Diabetes mellitus is an independent risk factor in ACI patients with primary hypertension.

The Value of Lung Ultrasound Score in Neonatology.

Point-of-care lung ultrasound (LUS) is increasingly applied in the neonatal intensive care unit (NICU). Diagnostic applications for LUS in the NICU contain the diagnosis of many common neonatal pulmonary diseases (such as Respiratory distress syndrome, Transient tachypnea of the newborn, Meconium aspiration syndrome, Pneumonia, Pneumothorax, and Pleural effusion) which have been validated. In addition to being employed as a diagnostic tool in the classical sense of the term, recent studies have shown that the number and type of artifacts are associated with lung aeration. Based on this theory, over the last few years, LUS has also been used as a semi-quantitative method or as a "functional" tool. Scores have been proposed to monitor the progress of neonatal lung diseases and to decide whether or not to perform a specific treatment. The semi-quantitative LUS scores (LUSs) have been developed to predict the demand for surfactant therapy, the need of respiratory support and the progress of bronchopulmonary dysplasia. Given their ease of use, accuracy and lack of invasiveness, the use of LUSs is increasing in clinical practice. Therefore, this manuscript will review the application of LUSs in neonatal lung diseases.

Protective effects of Ligularia fischeri root extracts against ulcerative colitis in mice through activation of Bcl-2/Bax signalings.

BACKGROUND: Ulcerative colitis (UC) is a chronic inflammatory bowel disease characterized by high levels of proinflammatory cytokines and epithelial barrier dysfunction. The root of Ligularia fischeri (Ledeb.) Turcz. is a traditional Chinese medicinal herb with diverse therapeutic properties, which has been successfully used to treat inflammation-related diseases. However, little is known about its effect and mechanism against UC. PURPOSE: To investigate the efficacy and mechanism of L. fischeri root extracts against UC. METHODS: L. fischeri root samples were prepared using the alcohol extraction method and liquid-liquid extraction method. A dextran sodium sulfate-induced UC mouse model and a lipopolysaccharide (LPS)-induced inflammatory cell model were employed in the present study. Cell apoptosis was detected by TUNEL staining, and an enzyme-linked immunosorbent assay was used to quantify the abundance of inflammatory factors in tissues. Hematoxylin and eosin staining and Masson staining were employed to analyze drug toxicity to the liver and kidney. A myeloperoxidase (MPO) assay kit was used to detect neutrophil infiltration in colon tissues. RT-qPCR was then employed to quantify the transcriptional levels of proinflammatory and apoptotic-related genes, while tight junction and apoptosis-related proteins were quantified via western blotting. Gas Chromatography/Mass Spectrometry analysis was then performed to identify the natural compounds in L. fischeri root extracts. RESULTS: The water decoction extract, methanol extract, and especially the chloroform extract (CE) exerted potent therapeutic effects in UC mice. Similar to the positive control group (5-aminosalicylic acid), oral administration of CE (30, 60, and 90 mg/kg/d) elicited distinct therapeutic effects on UC mice in the medium- and high-dose groups. CE decreased disease activity index, histopathological score, and MPO level significantly, and effectively retained the colon length. Furthermore, CE significantly reduced the levels of proinflammatory cytokines, including interleukin (IL)-1ß, IL-6, and tumor necrosis factor-α and enhanced the expression of tight junction proteins, such as zonula occludens (ZO)-1, ZO-2, claudin-1, and occludin, as well as the transcriptional levels of mucins, such as MUC-1 and MUC-2, in UC mice. Notably, CE prevented apoptosis of colonic epithelial cells by up-regulating Bcl-2 and down-regulating Bax. Also, CE inhibited the secretion of pro-inflammatory cytokines and apoptosis in LPS-induced RAW264.7 macrophages via the activation of Bcl-2/Bax signals. CONCLUSIONS: Collectively, L. fischeri root extracts, especially CE, have obvious therapeutic effects against UC. CE reduces inflammation and protects the intestinal epithelial cells and intestinal epithelial barrier via activation of the Bcl-2/Bax signaling pathway, and may be a promising therapeutic agent for UC treatment.

Chromosomal genome and population genetic analyses to reveal genetic architecture, breeding history and genes related to cadmium accumulation in Lentinula edodes.

BACKGROUND: Lentinula edodes (Berk.) is the second most productive mushroom in the world. It contains compounds effective for antiviral, antitumor, antioxidant and immune regulation. Although genomes have previously been reported for this species, a high-quality chromosome-level reference for L. edodes is unavailable. This hinders detailed investigation of population genetics, breeding history of strains and genes related to environmental stress responses. RESULTS: A high-quality chromosome-level genome was constructed. We separated a monokaryon from protoplasts of the commercial L. edodes strain L808 and assembled the genome of L. edodes using PacBio long-read and Illumina short-read sequencing, along with the high-throughput chromatin conformation capture (Hi-C) technique. We assembled a 45.87 Mb genome, and 99% of the sequences were anchored onto 10 chromosomes. The contig and scaffold N50 length were 2.17 and 4.94 Mb, respectively. Over 96% of the complete Benchmarking Universal Single-Copy Orthologs (BUSCO) were identified, and 9853 protein-coding genes were predicted. We performed population genome resequencing using 34 wild strains and 65 commercial cultivars of L. edodes originating from China, Japan, the United States and Australia. Based on whole-genome variants, we showed substantial differences in the Chinese wild population, which divided into different branches according to the main areas of their geographical distribution. We also determined the breeding history of L. edodes at the molecular level, and demonstrated that the cultivated strains in China mainly originated from wild strains from China and Northeast Asia. Phenotypic analysis showed that 99 strains exhibited differences on the Cd accumulation. Three significant loci in the of L. edodes genome were identified using the genome-wide association study (GWAS) of Cd accumulation traits. Functional genes associated with Cd accumulation traits were related to DNA ligase and aminoacyl tRNA synthetase, indicating that DNA damage repair and in vivo protein translation may be responses to Cd stress. CONCLUSIONS: A high-quality chromosome-level genome and population genetic data of L. edodes provide genetic resources for functional genomic, evolutionary and artificial breeding studies for L. edodes.

Structural characterisation and antitumor activity against non-small cell lung cancer of polysaccharides from Sanghuangporus vaninii.

The medicinal fungus Sanghuangporus vaninii can be cultivated in large scale and has outstanding antitumour activity. In this study, water-soluble S. vaninii polysaccharides (SVPs) were extracted from fruiting bodies. Four polysaccharide sub-fractions (SVP-W, SVP-1, SVP-2 and SVP-3) were isolated, with molecular weights from 90.50 kDa to 261.70 kDa, and all inhibited the proliferation of non-small cell lung cancer cell lines A549, 95-D and NCI-H460, especially the acidic SVP-1. SVP-1 affected cell morphology and colony formation in NCI-H460 cells. It also promoted cell apoptosis following nuclear fluorescence staining and flow cytometry. Methylation and nuclear magnetic resonance analyses revealed that SVP-1 is a heteroglycan with the main chain →4)-ß-D-Glcp-(1 â†’ 6)-ß-D-Glcp-(1 â†’ 6)-α-D-Galp-(1 â†’ 6)-ß-D-Glcp-(1→, and the branched chain α-D-Manp-(1 â†’ 2)-α-D-Manp-(1 â†’ 3)-ß-D-Glcp-(1 â†’ 3,6)-ß-D-Glcp-(1→. The findings indicate that this natural acidic polysaccharide has potential for non-small cell lung cancer therapy.

Panax Notoginseng Saponins Protect H9c2 Cells From Hypoxia-reoxygenation Injury Through the Forkhead Box O3a Hypoxia-inducible Factor-1 Alpha Cell Signaling Pathway.

ABSTRACT: Panax notoginseng saponins (PNS) are commonly used in the treatment of cardiovascular diseases. Whether PNS can protect myocardial ischemia-reperfusion injury by regulating the forkhead box O3a hypoxia-inducible factor-1 alpha (FOXO3a/HIF-1α) cell signaling pathway remains unclear. The purpose of this study was to investigate the protective effect of PNS on H9c2 cardiomyocytes through the FOXO3a/HIF-1α cell signaling pathway. Hypoxia and reoxygenation of H9C2 cells were used to mimic MIRI in vitro, and the cells were treated with PNS, 2-methoxyestradiol (2ME2), and LY294002." Cell proliferation, lactate dehydrogenase, and malonaldehyde were used to evaluate the degree of cell injury. The level of reactive oxygen species was detected with a fluorescence microscope. The apoptosis rate was detected by flow cytometry. The expression of autophagy-related proteins and apoptosis-related proteins was detected by western blot assay. PNS could reduce H9c2 hypoxia-reoxygenation injury by promoting autophagy and inhibiting apoptosis through the HIF-1α/FOXO3a cell signaling pathway. Furthermore, the protective effects of PNS were abolished by HIF-1α inhibitor 2ME2 and PI3K/Akt inhibitor LY294002. PNS could reduce H9c2 hypoxia-reoxygenation injury by promoting autophagy and inhibiting apoptosis through the HIF-1α/FOXO3a cell signaling pathway.

Genome Sequencing of Paecilomyces Penicillatus Provides Insights into Its Phylogenetic Placement and Mycoparasitism Mechanisms on Morel Mushrooms.

Morels (Morchella spp.) are popular edible fungi with significant economic and scientific value. However, white mold disease, caused by Paecilomyces penicillatus, can reduce morel yield by up to 80% in the main cultivation area in China. Paecilomyces is a polyphyletic genus and the exact phylogenetic placement of P. penicillatus is currently still unclear. Here, we obtained the first high-quality genome sequence of P. penicillatus generated through the single-molecule real-time (SMRT) sequencing platform. The assembled draft genome of P. penicillatus was 40.2 Mb, had an N50 value of 2.6 Mb and encoded 9454 genes. Phylogenetic analysis of single-copy orthologous genes revealed that P. penicillatus is in Hypocreales and closely related to Hypocreaceae, which includes several genera exhibiting a mycoparasitic lifestyle. CAZymes analysis demonstrated that P. penicillatus encodes a large number of fungal cell wall degradation enzymes. We identified many gene clusters involved in the production of secondary metabolites known to exhibit antifungal, antibacterial, or insecticidal activities. We further demonstrated through dual culture assays that P. penicillatus secretes certain soluble compounds that are inhibitory to the mycelial growth of Morchella sextelata. This study provides insights into the correct phylogenetic placement of P. penicillatus and the molecular mechanisms that underlie P. penicillatus pathogenesis.

Panax Notoginseng Saponins Attenuate Myocardial Ischemia-Reperfusion Injury Through the HIF-1α/BNIP3 Pathway of Autophagy.

BACKGROUND AND OBJECTIVE: Panax Notoginseng Saponins (PNS) is a formula of Chinese medicine commonly used for treating ischemia myocardial in China. However, its mechanism of action is yet unclear. This study investigated the effect and the mechanism of PNS on myocardial ischemia-reperfusion injury (MIRI) through the hypoxia-inducible factor 1α (HIF-1α)/bcl-2/adenovirus E1B19kDa-interacting protein3 (BNIP3) pathway of autophagy. METHODS: We constructed a rat model of myocardial injury and compared among 4 groups (n = 10, each): the sham-operated group (Sham), the ischemia-reperfusion group (IR), the PNS low-dose group, and the PNS high-dose group were pretreated with PNS (30 and 60 mg/kg, respectively). Serum creatine kinase, malonaldehyde (MDA), lactate dehydrogenase, myocardial tissue superoxide dismutase, and reactive oxygen species were detected in rats with myocardial ischemia-reperfusion after the intervention of PNS. The rat myocardial tissue was examined using hematoxylin and eosin (H&E) staining, and the mitochondria of myocardial cells were observed using transmission electron microscopy. The expressions of microtubule-associated protein light chain 3 (LC3), HIF-1α, BNIP3, Beclin-1, and autophagy-related gene-5 (Atg5) in rat myocardial tissue were detected using Western blotting. RESULTS: The results showed that PNS was significantly protected against MIRI, as evidenced by the decreasing in the concentration of serum CK, MDA, lactate dehydrogenase, and myocardial tissue superoxide dismutase, reactive oxygen species, the attenuation of myocardial tissue histopathological changes and the mitochondrial damages of myocardial cells, and the increase of mitochondria autophagosome in myocardial cells. In addition, PNS significantly increased the expression of LC3 and the ratio of LC3II/LC3I in rat myocardial tissue. Moreover, PNS significantly increased the expression of HIF-1α, BNIP3, Atg5, and Beclin-1 in rat myocardial tissue. CONCLUSIONS: The protective effect of PNS on MIRI was mainly due to its ability to enhance the mitochondrial autophagy of myocardial tissue through the HIF-1α/BNIP3 pathway.

Enzymatic gene expression by Pleurotus tuoliensis (Bailinggu): differential regulation under low temperature induction conditions.

Pleurotus tuoliensis is a valuable, rare and edible mushroom that is been commercially cultivated and is rapidly developing in China markets. Low temperatures are required to induces primordia initiation for the successful production of fruiting bodies (basidiomes) during commercial cultivation. In this work, we investigated the enzymatic activities and performed transcription profiling analysis of enzymatic genes under different low temperature conditions. The results suggest that the enzymatic activities and transcription levels decrease or increase significantly at 4 and 13 °C. Lacc10 and mnp6 seems to play a dominant role during nutrition growth. Furthermore, the expression of laccase and peroxidase genes was highly correlated to the detected extracellular enzymatic activity. Cold stress genes expression profiles were upregulated under 4 °C/13 °C (3 days), while only the Hsp70 gene was downregulated (at the stage of fruiting bodies production) at 13 °C (12 days). Our results showed that the transcriptional regulation of laccase and ligninolytic peroxidase genes plays an important role in the fruiting bodies of Bailinggu under low temperature induction (4 °C). Induction at low temperatures was a highly important cultivation condition in Bailinggu.

Functional Variant of C-689T in the Peroxisome Proliferator-Activated Receptor-γ2 Promoter is Associated with Coronary Heart Disease in Chinese Nondiabetic Han People.

Objective To investigate the association between the polymorphism of C-689T in the peroxisome proliferator-activated receptor-γ2 (PPARγ2) promoter and coronary heart disease (CHD). Methods This case-controlled study was conducted in nondiabetic Chinese Han people, which enrolled 455 patients with CHD (cases) and 693 subjects without CHD (controls). Data of clinical indexes were collected, including height, body weight, waist circumstance, systolic blood pressure (SBP), diastolic blood pressure (DBP), smoking, drinking, physical activity, as well as body mass index (BMI). Fasting blood glucose (FBG), plasma total cholesterol (TC) and triglyceride (TG) levels were measured. Polymerase chain reaction-restricted fragments length polymorphism (PCR-RFLP) was used to determine the PPARγ2 promoter C-689→T substitution. The genotype distribution of PPARγ2 promoter C-689T, allelic frequency, clinical indexes, and laboratorial measurements were compared between the two groups. The effect of genotype on the risk of CHD was assessed using univariate and multivariate regression model. Results The genotype frequencies of CC, CT and TT in PPARγ2 promoter C-689T were 89.7%, 9.9% and 0.4% in the case group, and 93.1%, 6.6% and 0.3% in the control group, respectively (CC vs. CT+TT, χ2= 6.243, P=0.041). Carriers of -689T allele (n=95) had significantly higher TC level than non-carriers (n=1053) (5.12±1.26 vs. 4.76±1.22 mmol/L, P=0.001). Male carriers of -689T allele (n=51) were significantly higher in waist circumference, body weight, TC and TG than male non-carriers (n=656) (all P<0.05). In subjects whose BMI was over 25 kg/m2, carriers of -689T allele (n=82) had significantly higher levels of waist circumference, BMI, SBP and TC than non-carriers (n=231) (all p<0.05). The -689T allele was an independent risk factor for CHD (OR=1.668, 95%CI: 1.031-2.705, P=0.037) after adjusting for age, gender, waist circumference, body weight, BMI, smoking, physical activities, SBP, DBP, FBG, TC and TG level. Conclusion These data support the hypothesis that the -689T allele is associated with an increased risk of CHD, in Chinese Han people and correlates significantly with the profiles of CHD-related risk factors.

[Cloning and functional analysis of SCTF-1 encoding a C2H2-type Zinc finger protein from soybean].

The zinc finger protein is one of the proteins with finger-like domain. Some of them are transcription factors which play important role in plant growth and plant resistance to abiotic stresses. In this paper, a novel C2H2-type zinc finger protein gene SCTF-1 (GenBank accession number JQ692081) was isolated from soybean (Glycine max (L.) Merr.) This gene has a 699 bp ORF (open reading frame) with no intron and encodes a 24.9 kDa protein with 233 amino acids. Its isoelectric point (pI) is 8.33. The SCTF-1 protein contains two typical C2H2-type zinc finger domains. Both of them have highly conserved amino acid sequence-QALGGH which is a particular characteristic of plant. Transient expression of the GFP-SCTF-1 protein in onion epidermal cell showed that SCTF-1 was localized in cell nuclei. RT-PCR results showed that SCTF-1 gene was expressed with high levels in flowers and leaves in soybean, but low in roots and stems. The expression of SCTF-1 gene was strongly induced by low temperature in the soybean seedlings. Overexpression of SCTF-1 enhanced cold tolerance of transgenic tobacco (Nicotiana tabacum L.) compared to the control.