A Study of Sperm DNA Damage Mechanism Based on miRNA Sequencing.

Objective To analyze differentially expressed proteins in A375 melanoma cells before and after short hairpin RNA (shRNA) -mediated Cbl-b gene silencing. Methods The label-free quantitative proteomics approach was performed to identify differentially expressed proteins between A375 cells transfected with lentiviral vectors containing Cbl-b shRNA (Cbl-b shRNA group) and those with control lentiviral vectors (control group) . Then, the properties of differentially expressed proteins were analyzed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) enrichment analysis. Western blot analysis was conducted to determine the expression of differential proteins (EphA2 and GSK3β) and phosphorylated protein kinase (p-AKT) after shRNA-mediated Cbl-b gene silencing. Statistical analysis was carried out by t test of two independent-samples for comparison of protein expression abundance between the two groups with SPSS 23.0 software. Additionally, the results of GO and KEGG enrichment analysis were analyzed by Fisher′s exact test. Results A total of 3 449 proteins were identified and quantified, and 74 of them were differentially expressed between the Cbl-b shRNA group and control group. Compared with the control group, 52 proteins were up-regulated and 22 were down-regulated in the Cbl-b shRNA group. GO enrichment analysis of differential proteins revealed that the top five significantly enriched biological processes were integrin-mediated cell adhesion, single-organism metabolic process, regulation of integrin-mediated cell adhesion, regulation of protein-targeting mitochondria and nucleic acid metabolic process. The top five significantly enriched molecular functions included DNA binding, 2-iron, 2-sulfur cluster binding, signaling receptor activity, cadherin binding and cell adhesion molecule binding. The top five significantly enriched cell components included nucleosome, DNA packaging complex, photoreceptor connecting cilium, DNA-protein complex and extracellular region part. KEGG enrichment analysis demonstrated that the top five significantly enriched melanoma-related signaling pathways were folate biosynthesis, axon guidance, extracellular matrix-receptor interaction, adherens junction and Wnt signaling pathways. As Western blot analysis revealed, the Cbl-b shRNA group showed lower protein expression of EphA2 (0.369) , but higher protein expression of GSK3β (3.524) compared with the control group (1) , which were consistent with the results of proteomics analysis. Additionally, the protein expression of p-AKT was down-regulated in Cbl-b shRNA group (0.453) compared with the control group (1) . Conclusion Cbl-b may be involved in the occurrence of melanoma through a variety of biological pathways, and the EphA2/PI3K/AKT signaling pathway may be one important pathway. Key words: Melanoma; Ubiquitin-protein ligases; Proto-oncogene proteins cbl-b; RNA, small interfering; Proteomics

Investigation of the mechanisms leading to human sperm DNA damage based on transcriptome analysis by RNA-seq techniques

Previous studies have shown that asthma is a risk factor for lung cancer, while the mechanisms involved remain unclear. We attempted to further explore the association between asthma and non-small cell lung cancer (NSCLC) via bioinformatics analysis. We obtained GSE143303 and GSE18842 from the GEO database. Lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) groups were downloaded from the TCGA database. Based on the results of differentially expressed genes (DEGs) between asthma and NSCLC, we determined common DEGs by constructing a Venn diagram. Enrichment analysis was used to explore the common pathways of asthma and NSCLC. A protein-protein interaction (PPI) network was constructed to screen hub genes. KM survival analysis was performed to screen prognostic genes in the LUAD and LUSC groups. A Cox model was constructed based on hub genes and validated internally and externally. Tumor Immune Estimation Resource (TIMER) was used to evaluate the association of prognostic gene models with the tumor microenvironment (TME) and immune cell infiltration. Nomogram model was constructed by combining prognostic genes and clinical features. 114 common DEGs were obtained based on asthma and NSCLC data, and enrichment analysis showed that significant enrichment pathways mainly focused on inflammatory pathways. Screening of 5 hub genes as a key prognostic gene model for asthma progression to LUAD, and internal and external validation led to consistent conclusions. In addition, the risk score of the 5 hub genes could be used as a tool to assess the TME and immune cell infiltration. The nomogram model constructed by combining the 5 hub genes with clinical features was accurate for LUAD. Five-hub genes enrich our understanding of the potential mechanisms by which asthma contributes to the increased risk of lung cancer.

To construct and analyze the differential expression profiles of microRNAs (miRNA) and mRNA in oral squamous cell carcinoma (OSCC). To explore the miRNA and mRNA of OSCC development and progression. The differential expression profiles of miRNA and mRNA were built by high-throughput deep sequencing technology. Using Gene Ontology (GO) enrichment analysis, the roles of differentially expressed miRNA and mRNA in cell cycle, cell proliferation, cell differentiation and cell apoptosis were analyzed. Seventy-seven differentially expressed miRNA and 1 298 differentially expressed mRNAs were identified in OSCC. GO analysis showed that 73 miRNA had found target mRNA in cell cycle, cell proliferation, cell differentiation and cell apoptosis of OSCC. Moreover, a miRNA could regulate multiple mRNA. The differential expression profiles of miRNA and mRNA have close relationship with the development and progression of OSCC.

Increased oxidative deoxyribonucleic acid damage in the spermatozoa of infertile male patients

Objective: To analyze the types and functions of CD34+ cells in full-thickness skin defect wounds of normal mice and diabetic mice by single-cell RNA sequencing. Methods: This study was an experimental study. The CD34+ cell lineage tracing mouse was produced, and the visualization of CD34+ cells under the fluorescent condition was realized. Six male CD34+ cell lineage tracing mice aged 7-8 weeks (designated as diabetic group) were intraperitoneally injected with streptozotocin to establish a diabetic model, and full-thickness skin defect wounds were prepared on their backs when they reached 13 weeks old. Another 6 male CD34+ cell lineage tracing mice aged 13 weeks (designated as control group) were also subjected to full-thickness skin defect wounds on their backs. On post-injury day (PID) 4, wound tissue was collected from 3 mice in control group and 2 mice in diabetic group, and digested to prepare single-cell suspensions. CD34+ cells were screened using fluorescence-activated cell sorting, followed by single-cell RNA sequencing. The Seurat 4.0.2 program in the R programming language was utilized for dimensionality reduction, visualization, and cell clustering analysis of CD34+ cell types, and to screen and annotate the marker genes for each CD34+ cell subpopulation. Kyoto encyclopedia of genes and genomes (KEGG) and gene ontology (GO) enrichment analysis was performed to analyze the differentially expressed genes (DEGs) of CD34+ fibroblasts (Fbs), smooth muscle cells (SMCs), keratinocytes (KCs), and chondrocyte-like cells (CLCs) in the wound tissue of two groups of mice for exploring cellular functions. Results: On PID 4, CD34+ cells in the wound tissue of both groups of mice were consisted of 7 cell types, specifically endothelial cells, Fbs, KCs, macrophages, T cells, SMCs, and CLCs. Among these, Fbs were further classified into 5 subpopulations. Compared with those in control group, the proportions of CD34+ endothelial cells, Fbs subpopulation 1, Fbs subpopulation 4, KCs, and CLCs in the wound tissue of mice were increased in diabetic group, while the proportions of CD34+ Fbs subpopulation 2, Fbs subpopulation 3, and SMCs were decreased. The marker genes for annotating CD34+ CLCs, endothelial cells, Fbs subpopulation 1, Fbs subpopulation 2, Fbs subpopulation 3, Fbs subpopulation 4, Fbs subpopulation 5, KCs, macrophages, SMCs, and T cells were respectively metastasis-associated lung adenocarcinoma transcript 1, fatty acid binding protein 4, Gremlin 1, complement component 4B, H19 imprinted maternally expressed transcript, Dickkopf Wnt signaling pathway inhibitor 2, fibromodulin, keratin 5, CD74 molecule, regulator of G protein signaling 5, and inducible T-cell co-stimulator molecule. KEGG and GO enrichment analysis revealed that, compared with those in control group, DEGs with significant differential expression (SDE) in CD34+ Fbs from the wound tissue of mice in diabetic group on PID 4 were significantly enriched in terms related to inflammatory response, extracellular matrix (ECM) organization, regulation of cell proliferation, and aging (with Pvalues all <0.05), DEGs with SDE in CD34+ SMCs were significantly enriched in terms related to cell migration, apoptotic process, positive regulation of transcription, and phagosome (with P values all <0.05), DEGs with SDE in CD34+ KCs were significantly enriched in terms related to mitochondrial function, transcription, and neurodegenerative diseases (with P values all <0.05), and DEGs with SDE in CD34+ CLCs were significantly enriched in terms related to rhythm regulation, ECM, and viral infection (with P values all <0.05). Conclusions: CD34+ cells display high heterogeneity in the healing process of full-thickness skin defect wounds in both normal mice and diabetic mice. The significantly enriched functions of DEGs with SDE in CD34+ cell subpopulations in the wound tissue of the two mouse groups are closely related to the wound healing process.

To study the differential gene expression and clinical significance in human immunodeficiency virus-infected individuals (HIVIIs) with penile squamous cell carcinoma. At our hospital from 2019 to 2020, we selected six samples of HIV-related penile squamous cell carcinoma for the experimental group and six samples of non-HIV-related penile squamous cell carcinoma for the control group. Transcriptome sequencing of sample mRNAs was performed by high-throughput sequencing. Differential gene expression analysis, differential Gene Ontology (GO) enrichment analysis and differential Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were carried out, and the reads per kilobase per million reads (RPKM) value was used as a measure of gene expression. A total of 2418 differentially expressed genes were obtained, of which 663 were upregulated and 1755 were downregulated (absolute value of logFC >1 and p value <.05). On the basis of the significance of the GO enrichment analysis, we found that the tumor protein p63 (TP63) gene was significantly upregulated and that the LIM domain only 4 (LMO4) gene was significantly downregulated in the experimental group compared with the control group. KEGG pathway analysis of the differentially expressed genes revealed that DNA replication was the most significant pathway associated with the upregulated genes and cell adhesion molecule (CAM) metabolism was the most significant pathway associated with the downregulated genes. The gene expression profiles of HIV-related penile squamous cell carcinoma and non-HIV-related penile squamous cell carcinoma are significantly different and involve significant GO enrichment and KEGG metabolic pathways, and this is very meaningful for the study of non-AIDS-defining cancers (NADCs). Differential expression of genes may be an important target for the prevention of penile squamous cell carcinoma in HIVIIs.

Identification of Hub genes associated with infection of three lung cell lines by SARS-CoV-2 with integrated bioinformatics analysis.

This study aimed to explore critical genes as potential biomarkers for the diagnosis and prognosis of colorectal cancer (CRC) for clinical utility. To identify and screen candidate genes involved in CRC carcinogenesis and disease progression, we downloaded microarray datasets GSE89076, GSE73360, and GSE32323 from the GEO database identified differentially expressed genes (DEGs), and performed a functional enrichment analysis. A protein-protein interaction network was constructed, and correlated module analysis was performed using STRING and Cytoscape. The Kaplan-Meier survival curve shows the survival of the hub genes. The expression of cyclin-dependent kinase (CDK1), cyclin B1 (CCNB1), and PCNA in tissues and changes in tumor grade were analyzed. A total of 329 DEGs were identified, including 264 upregulated and 65 downregulated genes. The functions and pathways of DEGs include the mitotic cell cycle, poly(A) RNA binding replication, ATP binding, DNA replication, ribosome biogenesis in eukaryotes, and RNA transport. Forty-seven Hub genes were identified, and biological process analysis showed that these genes were mainly enriched in cell cycle and DNA replication. Patients with mutations in CDK1, PCNA, and CCNB1 had poorer survival rates. CDK1, PCNA, and CCNB1 were significantly overexpressed in the tumor tissues. The expression of CDK1 and CCNB1 gradually decreased with increasing tumor grade. CDK1, CCNB1, and PCNA can be used as potential markers for the diagnosis and prognosis of CRC. These genes are overexpressed in colon cancer tissues and are associated with low survival rates in CRC patients.

Pancreatic cancer is the eighth-leading cause of cancer-associated mortality worldwide. To date, the cellular and molecular mechanisms associated with the invasion and metastasis of pancreatic cancer remain unclear. To examine these mechanisms, a microRNA (miRNA/miR) microarray with 1,965 genes was hybridized with labeled miRNA probes from invasive PC-1.0 and non-invasive PC-1 cells for molecular profiling analysis. In addition, reverse transcription quantitative-polymerase chain reaction (RT-qPCR) was utilized to validate the microarray results. Online miRNA target prediction algorithms online were used to predict the target genes of the differentially expressed miRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) term enrichment analysis were performed for the potential targets of the differentially expressed miRNAs. The results demonstrated that 54 miRNAs were differentially expressed, of which 33 were upregulated and 21 were downregulated in the PC-1.0 cell line compared with the PC-1 cell line. A total of 6 upregulated miRNAs (miR-31, -34a, -181a, -181b, -193a-3p, and -193b) and 4 downregulated miRNAs (miR-221, -222, -484, and -502-3p) were selected from these 54 miRNAs and validated by RT-qPCR. The differentially expressed miRNAs were further validated by RT-qPCR in the human pancreatic cancer cell lines AsPC-1 (highly invasive) and CAPAN-2 (less invasive). The results revealed that 2 upregulated miRNAs (miR-34a and -193a-3p) and 4 downregulated miRNAs (miR-221, -222, -484, and -502-3p) exhibited a consistent expression pattern between the PC-1.0/PC-1 and AsPC-1/CAPAN-2 pancreatic cancer cells. The GO and KEGG enrichment analysis indicated that the mRNAs potentially targeted by miRNAs were involved in a range of biological functions. These results suggest that different miRNA expression profiles occur between highly and weakly invasive and metastatic pancreatic cancer cell lines, and may affect a variety of biological functions in pancreatic cancer.

There are clinical reports of nerve injury caused by ropivacaine. The mechanism for nerve injury induced by ropivacaine has not been fully clarified. This study aims to investigate the changes of pain threshold and L3 spinal cord genomics at 6 h and 24 h after intrathecal injection of 0.5% and 1.0% ropivacaine, and to explore the underlying mechanisms for nerve injury caused by ropivacaine. A total of 30 male Sprague Dawley rats weighing 220-260 g were successfully implanted with microspinal catheter. The rats were randomly divided into 5 groups (each n=6): a control group (given saline), a ropivacaine group 1 and a ropivacaine group 2 (both given 1% ropivacaine), a ropivacaine group 3 and a ropivacaine group 4 (both given 0.5% ropivacaine). The rats received continuous intrathecal injection of corresponding drugs at 8.3 μL/h for 24 h via an implanted intrathecal catheter followed by 24 h-pause of injection for the ropivacaine group 2, the ropivacaine group 4 and the control group, 6 h-pause of injection for the ropivacaine group 1 and the ropivacaine group 3. For each group, the observation of behavioral change and the paw withdrawal mechanical threshold (PWMT) was conducted immediately after the injection and again after the pause of injection. After the PWMT observation, the rats were dissected to acquire L3 spinal cords. Illumina sequencing was applied to construct gene libraries. Then the statistical methods were used to find out differentially expressed genes between the groups. Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway analysis were conducted for those genes. Real-time RT-PCR was used to determine different expressions of some of those genes. Compared with control group, the PWMT got higher in the ropivacaine group 1-4 and was positively correlated with concentration, negatively correlated with discontinuation duration. Compared with control group, the ropivacaine group 1 had 488 differentially expressed genes, of which 456 were up-regulated and 32 were down-regulated; the ropivacaine group 2 had 1 194 differentially expressed genes, of which 1 092 were up-regulated and 102 were down-regulated; the ropivacaine group 3 had 518 differentially expressed genes, of which 384 were up-regulated and 134 were down-regulated; and the ropivacaine group 4 had 68 differentially expressed genes, of which 46 were up-regulated and 22 were down-regulated. GO enrichment analysis and KEGG signaling pathway analysis showed that most of these differentially expressed genes were related to signaling pathways of inflammatory response. After intrathecal injection of 0.5% ropivacaine and 1.0% ropivacaine for 24 h, the differentially expressed genes in L3 spinal cord of rats are mainly related to signaling pathways of inflammatory response.

Osteosarcoma (OS) is a cancerous tumor in a bone. We aimed to identify the critical genes involved in OS progression, and then try to elucidate the molecular mechanisms of this disease. The microarray data of GSE32395 was used for the present study. We analyzed differentially expressed genes (DEGs) in OS cells compared with control group by Student’s t-test. The significant enriched gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathways were analyzed for upregulated genes and downregulated genes, respectively. In addition, a protein-protein interaction (PPI) network was constructed. GO and KEGG enrichment analyses were conducted for genes in the PPI network. In total, 183 DEGs, including 100 upregulated DEGs and 83 downregulated DEGs were screened. The upregulated DEGs were significantly enriched in 2 KEGG pathways, such as “Glycosaminoglycan biosynthesis-chondroitin sulfate” and the downregulated DEGs were significantly enriched in 12 pathways, including “cell adhesion molecules,” “pentose phosphate pathway” and “allograft rejection.” GO enrichment analysis indicated that the upregulated DEGs were significantly involved in biological process, such as “multicellular organismal metabolic process” and “limb morphogenesis,” while the downregulated DEGs were significantly enriched in biological process, such as “Positive regulation of pathway-restricted SMAD protein phosphorylation.” The PPI network included 84 interactions and 51 nodes. The “glycosaminoglycan biosynthesis-chondroitin sulfate pathway,” “microtubule motor activityfunction,” and “regulation of mitosis process” were significantly enriched by genes in PPI network. In particular, CENPE, PRC1, TTK, and PLK4 had higher degrees in the PPI network. The interactions between TTK and PLK4 as well as CENPE and PRC1 may involve in the OS development. These 4 genes might be possible biomarkers for the treatment and diagnosis of OS.

The morbidity and mortality rates for gastric cancer (GC) rank second among all cancers, indicating the serious threat it poses to human health, as well as human life. This study aims to identify the pathways and genes as well as investigate the molecular mechanisms of tumor-related genes in gastric cancer (GC). We compared differentially expressed genes (DEGs) and differentially methylated genes (DMGs) in gastric cancer and normal tissue samples using The Cancer Genome Atlas (TCGA) data. The Kyoto Encyclopedia of Gene and Genome (KEGG) and the Gene Ontology (GO) enrichment analysis' pathway annotations were conducted on DMGs and DEGs using a clusterProfiler R package to identify the important functions, as well as the biological processes and pathways involved. The intersection of the two was chosen and defined as differentially methylated and expressed genes (DMEGs). For DMEGs, we used the principal component analysis (PCA) to differentiate gastric cancer from adjacent samples. The linear discriminant analysis method was applied to categorize the samples using DMEGs methylation data and DMEGs expression profiles data and was validated using the leave-one-out cross-validation (LOOCV) method. We plotted the ROC curve for the classification and calculated the AUC (area under the ROC curve) value for a more intuitive view of the classification effect. We also used the NetworkAnalyst 3.0 tool to analyze DMEGs, using DrugBank to acquire information on protein-drug interactions and generate a network map of gene-drug interactions. We identified a total of 971 DMGs in 188 PD-1 negative and 187 PD-1 positive gastric cancer samples obtained from TCGA. The KEGG and GO enrichment analysis showed the involvement of the regulation of ion transmembrane transport, collagen-containing extracellular matrix, cell-cell junction, and peptidase regulator activity. We simultaneously obtained 1,189 DEGs, out of which 986 were downregulated, while 203 were upregulated in tumors. The enriched analysis of the GO's and KEGG's pathways indicated that the most significant pathways included an intestinal immune network for IgA production, Staphylococcus aureus infection, cytokine-cytokine receptor interaction, and viral protein interaction with cytokine and cytokine receptor, which have previously been linked with gastric cancer. The compound DB01830 can bind well to the active site of the LCK protein and shows good stability, thus making it a potential inhibitor of the LCK protein. To observe the relationship between DMEGs' expression and prognosis, we observed 10 genes, among which were TRIM29, TSPAN8, EOMES, PPP1R16B, SELL, PCED1B, IYD, JPH1, CEACAM5, and RP11-44K6.2. Their high expressions were related to high risks. Besides, those genes were validated in different internal and external validation sets. These results may provide potential molecular biological therapy for PD-1 negative gastric cancer.

Objective: To analyze target genes of human platelet-rich plasma (PRP) in regulating and controlling human epidermal stem cells (ESCs). Methods: (1) The discarded foreskin tissues were collected from 6 male patients of the First Affiliated Hospital of Army Medical University after urological surgery. The patients aged 5 to 25 years with good health and without urinary system infection. Human ESCs were cultivated using quick attachment method, and were subjected to morphological observation and identification. Venous blood sample in the volume of 40 mL was collected from a female healthy volunteer (aged 29 years) of General Hospital of Southern Theater Command of PLA, and PRP was extracted by second centrifugation method. (2) The successfully cultured primary human ESCs were divided into control group and PRP group according to the random number table, with 3 wells in each group. The cells in control group were not specially treated. In PRP group, PRP was added to the ESC medium to achieve final volume fraction of 2.5% after the cells were adhered for 12 hours. RNA was extracted, and transcriptome sequencing and data analysis of human ESCs of two groups were performed using RNA sequencing technology. Using the false discovery rate less than 0.05 and the fold change more than or equal to 4 as the standard, the differentially expressed genes were screened by Dr. Tom data mining system. Gene ontology (GO) enrichment analysis was performed on the obtained differentially expressed genes to find out the GO entries with significant enrichment. Then Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation analysis was used to further analyze the biological processes or metabolic pathways in which differentially expressed genes might be involved. Finally, the genes related to re-epithelialization and significantly differentially expressed were selected, and the differential expression of genes was verified by real-time fluorescent quantitative reverse transcription polymerase chain reaction (RT-PCR). Data were statistically analyzed with independent-samples t test. Results: (1) The cultured cells were cloned with a paving stone-like shape and positive rate of CD49f of 95.132% and CD71 of 0.006%, which proved that the primary culture of ESCs was successful. (2) The quality control data analysis showed that the selected samples had better quality and higher sequence alignment rate, which met the requirements of sequencing. (3) Sequencing data showed that there were a total of 449 differentially expressed genes between the two groups, including 354 up-regulated genes and 95 down-regulated genes. Further cluster analysis determined that there were 18 significantly up-regulated genes and 5 significantly down-regulated genes between the two groups. GO enrichment analysis and KEGG pathway annotation analysis showed that the significantly differentially expressed genes were mainly enriched in the epidermis construction and keratinization process, which also might be related to interleukin 17 signaling pathway. (4) Keratin 19, keratin 10, and S100A7 genes which were related to the process of re-epithelialization and significantly differentially expressed were selected for verification. Real-time fluorescent quantitative RT-PCR showed that compared with those of control group, the mRNA expressions of keratin 19 and S100A7 of cells in PRP group were significantly increased (t=10.270, 5.690, P<0.01), while the mRNA expression of keratin 10 was significantly decreased (t=7.306, P<0.01), which was consistent with the result of sequencing data. Conclusions: PRP regulates function of human ESCs and promotes wound re-epithelialization involving transcriptional regulation of multiple genes, including keratin 19, keratin 10, and S100A7. In-depth exploration of the possible regulatory network of PRP affecting human ESCs will provide the basis for its subsequent clinical application.

P094 Transcriptomic and small RNA sequencing profile in ileal resections from complicated Crohn′s Disease patients