Identification of Costimulatory Molecule-Related lncRNAs Associated With Gastric Carcinoma Progression: Evidence From Bioinformatics Analysis and Cell Experiments.

Costimulatory molecules (CMGs) play essential roles in multiple cancers. However, lncRNAs regulating costimulatory molecules have not been fully explored in gastric cancer (GC). Public data of GC patients were obtained from The Cancer Genome Atlas database. R software v4.1.1, SPSS v13.0, and GraphPad Prism 8 were used to perform all the analyses. The Limma package was used for differential expression analysis. The survival package was used for patient prognosis analysis. The gene set enrichment analysis (GSEA), gene ontology (GO), and the Kyoto encyclopedia of genes and genomes (KEGG) analysis were used for pathway enrichment analysis. qRT-PCR was used to detect the RNA level of target lncRNA. CCK-8 and colony formation assay were used to assess the proliferation ability of GC cells. The transwell assay was used to evaluate the invasion and migration ability of GC cells. We first identified CMG-related lncRNAs (CMLs) through co-expression analysis. Then, an eight-CML-based signature was constructed to predict patient overall survival (OS), which showed satisfactory predictive efficiency (the training cohort: 1-year AUC = 0.764, 3-year AUC = 0.810, 5-year AUC = 0.840; the validation cohort: 1-year AUC = 0.661, 3-year AUC = 0.718, 5-year AUC = 0.822). The patients in the high-risk group tend to have a worse prognosis. GSEA showed that epithelial-mesenchymal transition, KRAS signaling, and angiogenesis were aberrantly activated in high-risk patients. GO and KEGG analyses indicated that the biological difference between high- and low-risk patients was mainly enriched in the extracellular matrix. Immune infiltration analysis showed that macrophages (M1 and M2), dendritic cells, monocytes, Tregs, and T regulatory cells were positively correlated with the risk scores, partly responsible for the worsening OS of high-risk patients. Finally, lncRNA AP000695.2 was selected for further experiments. The result showed that AP000695.2 was upregulated in GC cell lines and could facilitate the proliferation, invasion, and migration of GC cells. In summary, this study established an effective prognosis model based on eight CMLs, which would be helpful for further therapy options for cancer. Also, we found that AP000695.2 could promote GC cell malignant phenotype, making it an underlying therapy target in GC.

The Prevalence, Popular Trends, and Associated and Predictive Factors of Non-Obese Fatty Liver Disease.

Background and Aims: There are few studies on non-obese fatty liver disease, the aims of this study was to analyze its prevalence, popular trends, and associated and predictive factors, so as to provide reference for its prevention and treatment. Methods: Individuals with complete data of body mass index, sex, age, and abdominal ultrasound in Karamay Central Hospital from 2009 to 2016 were selected to analyze the prevalence and popular trends of non-obese fatty liver disease (body mass index <24 kg/m2), and associated and predictive factors. Results: Between 2009 and 2016, a total of 191,555 medical check-ups were included. The prevalence of non-obese fatty liver disease increased from 1.9% to 5.1% among general medical examinants (P<0.001), increased from 4.6% to 11.7% in non-obese individuals (P<0.001). Compared with the non-obese control group, the levels of age, body mass index, blood pressure, fasting blood glucose, triglycerides, total cholesterol and uric acid in the non-obese fatty liver group were higher (P<0. 05). Even among non-obese subjects, elevated body mass index was associated with a 0.63-fold increased risk for non-obese fatty liver disease (P<0.001, odds ratio=1.63, 95% confidence interval 1.54-1.72) for every one-unit increase in body mass index. The most common abnormal indicator of non-obese fatty liver disease was elevated triglycerides (44.2%), which was also the best predictor of non-obese fatty liver disease (area under the curve =0.795) in non-obese physical examinators. Conclusions: The prevalence of non-obese fatty liver disease was high and increasing rapidly in Karamay. Triglycerides is the best predictor of non-obese fatty liver in non-obese physical examinators.

Chromatin 3D structure reconstruction with consideration of adjacency relationship among genomic loci.

BACKGROUND: Chromatin 3D conformation plays important roles in regulating gene or protein functions. High-throughout chromosome conformation capture (3C)-based technologies, such as Hi-C, have been exploited to acquire the contact frequencies among genomic loci at genome-scale. Various computational tools have been proposed to recover the underlying chromatin 3D structures from in situ Hi-C contact map data. As connected residuals in a polymer, neighboring genomic loci have intrinsic mutual dependencies in building a 3D conformation. However, current methods seldom take this feature into account. RESULTS: We present a method called ShNeigh, which combines the classical MDS technique with local dependence of neighboring loci modeled by a Gaussian formula, to infer the best 3D structure from noisy and incomplete contact frequency matrices. We validated ShNeigh by comparing it to two typical distance-based algorithms, ShRec3D and ChromSDE. The comparison results on simulated Hi-C dataset showed that, while keeping the high-speed nature of classical MDS, ShNeigh can recover the true structure better than ShRec3D and ChromSDE. Meanwhile, ShNeigh is more robust to data noise. On the publicly available human GM06990 Hi-C data, we demonstrated that the structures reconstructed by ShNeigh are more reproducible between different restriction enzymes than by ShRec3D and ChromSDE, especially at high resolutions manifested by sparse contact maps, which means ShNeigh is more robust to signal coverage. CONCLUSIONS: Our method can recover stable structures in high noise and sparse signal settings. It can also reconstruct similar structures from Hi-C data obtained using different restriction enzymes. Therefore, our method provides a new direction for enhancing the reconstruction quality of chromatin 3D structures.

Altered interhemispheric resting-state functional connectivity in young male smokers.

With the help of advanced neuroimaging approaches, previous studies revealed structural and functional brain changes in smokers compared with healthy non-smokers. Homotopic resting-state functional connectivity between the corresponding regions in cerebral hemispheres may help us to deduce the changes of functional coordination in the whole brain of young male smokers. Functional homotopy reflects an essential aspect of brain function and communication between the left and right cerebral hemispheres, which is important for the integrity of brain function. However, few studies used voxel mirrored homotopic connectivity (VMHC) method to investigate the changes of homotopic connectivity in young male smokers. Twenty-seven young male smokers and 27 matched healthy male non-smokers were recruited in our study. Compared with healthy male non-smokers, young male smokers showed decreased VMHC values in the insula and putamen, and increased VMHC values in the prefrontal cortex. Correlation analysis demonstrated that there were significant positive correlations between the average VMHC values of the prefrontal cortex and pack-years in young male smokers. In addition, significant negative correlation was found between the average VMHC values in the insula and pack-years. Our results revealed the disrupted homotopic resting-state functional connectivity in young male smokers. The novel findings may extend our understanding of smoking.

Functional Connectivity Abnormalities of Brain Regions with Structural Deficits in Young Adult Male Smokers.

Smoking is one of the most prevalent dependence disorders. Previous studies have detected structural and functional deficits in smokers. However, few studies focused on the changes of resting state functional connectivity (RSFC) of the brain regions with structural deficits in young adult smokers. Twenty-six young adult smokers and 26 well-matched healthy non-smokers participated in our study. Voxel-based morphometry (VBM) and RSFC were employed to investigate the structural and functional changes in young adult smokers. Compared with healthy non-smokers, young smokers showed increased gray matter (GM) volume in the left putamen and decreased GM volume in the left anterior cingulate cortex (ACC). Moreover, GM volume in the left ACC has a negative correlation trend with pack-years and GM volume in the left putamen was positively correlated with pack-years. The left ACC and putamen with abnormal volumes were chosen as the regions of interest (ROIs) for the RSFC analysis. We found that smokers showed increased RSFC between the left ACC and right amygdala and between the left putamen and right anterior insula. We revealed structural and functional deficits within the frontostriatal circuits in young smokers, which may shed new insights into the neural mechanisms of smoking.

Electrophysiological mechanisms of biased response to smoking-related cues in young smokers.

Cigarette smoking during young adult may result in serious health issues in later life. Hence, it is extremely necessary to study the smoking neurophysiological mechanisms in this critical transitional period. However, few studies revealed the electrophysiological mechanisms of cognitive processing biases in young adult smokers. In present study, nineteen young smokers with 12h abstinent and 19 matched nonsmokers were recruited. By employing event-related potentials (ERP) measurements during a smoking cue induced craving task, electrophysiological brain responses were compared between the young adult smokers and nonsmokers. The Slow Positive Wave (SPW) amplitude of smoking-related cues was enhanced in young adult smokers compared with nonsmokers. In addition, increased P300/SPW component of smoking-related cues relative to neutral cues were found in young adult smokers. Meanwhile, a positive correlation between Cigarette Per Day (CPD) and the amplitude of ERPs wave (P300/SPW) at anterior (Fz), central (Cz) were observed in young adult smokers. Our findings provided direct electrophysiological evidence for the cognitive processing bias of smoking cue and may shed new insights into the smoking behavior in young adult smokers.

[Influence of human mesenchymal stem cells on cell proliferation and chemo-sensitivity of K562 cells].

This study was aimed to compare K562 cell proliferation, chemo-sensitivity and alteration of MDR1 before and after adhesive culture with MSC, so as to evaluate the relationship between chemodrug-resistance of leukemia cells and hemopoietic microenvironment. K562 cell cultivated in suspension and adhesively cultivated with MSC were collected respectively and cell proliferation curves were drawn; the cell cycle was determined by flow cytometry; the effect of chemotherapy on cellular viability and apoptosis of K562 cell was investigated, the MDR1 gene expression was determined by RT-PCR. The results showed that K562 cells adhesively cultivated with MSC were inhibited and cells in G0/G1 increased (P < 0.05), cells in S phase decreased (P < 0.05) and those in G0/G1 increased (P < 0.01), compared with that cultivated in suspension. In process of daunomycin-inducing apoptosis, K562 cell apoptosis in the adhesive culture with MSC was inhibited (P < 0.05). MDR1 gene expression in K562 cells was not induced or altered by adhesive co-cultivation. It is concluded that by co-culture of cell-cell contact with MSC, growth suppression and induction of chemo-resistance of K562 cells take place. The mechanism, however, seems not relevant with MDR1.