Corrigendum to "System Analysis of ROS-Related Genes in the Prognosis, Immune Infiltration, and Drug Sensitivity in Hepatocellular Carcinoma".

[This corrects the article DOI: 10.1155/2021/6485871.].

System Analysis of ROS-Related Genes in the Prognosis, Immune Infiltration, and Drug Sensitivity in Hepatocellular Carcinoma.

Hepatocellular carcinoma (HCC) is an aggressive malignant tumor with a poor prognosis. Reactive oxygen species (ROS) play an important role in tumors; however, the role of ROS-related genes is still unclear in HCC. Therefore, we analyzed the role of ROS-related genes in HCC via bioinformatics methods. Firstly, a prognosis model was constructed using LASSO Cox regression and multivariate analyses. We also investigated the potential function of the ROS-related genes and the correlation with immune infiltration, tumor stemness, and drug sensitivity. ICGC database was used for validation. Secondly, we further analyzed the role of 11 ROS-related genes in HCC. As a member of ROS gene family, the role of STK25 has remained unclear in HCC. We explored the biological function of STK25 using in vitro experiments. The present study was the first to construct a ROS-related prognostic model in HCC. The correlation of ROS-related genes with immune infiltration, tumor stemness, and drug sensitivity was dissected. Furthermore, we demonstrated that STK25 knockdown could increase the proliferation, migration, and invasion capacity of HCC cells.

ADAM15 correlates with prognosis, immune infiltration and apoptosis in hepatocellular carcinoma.

ADAM15 is highly expressed in malignant tumors and is correlated with tumor progression. However, the role of ADAM15 in hepatocellular carcinoma (HCC) remains unclear. In the study, our results indicated that ADAM15 was highly expressed in HCC tissues and cells compared with corresponding tissues and liver cells. Overexpression of ADAM15 was linked to poor prognosis, and was an independent risk factor for HCC prognosis. Besides, analysis of immune infiltration indicated that ADAM15 expression was related to tumor infiltrating lymphocytes based on the TIMER, TISIDB and GEPIA databases. Many immune checkpoint gene expression was associated with ADAM15 expression. Functional enrichment analyses indicated that apoptosis, cell adhesion was enriched. ADAM15 knockdown promoted apoptosis and suppressed proliferation, migration and invasion of liver cancer cells. The findings of western blot showed that ADAM15 knockdown reduced the expression of Bcl-2, Vimentin, N-Cadherin and Snail, and elevated the expression of Bax, E-cadherin and ZO-1. However, overexpression of ADAM15 had the opposite results. Collectively, our findings demonstrated that ADAM15 was connected with poor prognosis of HCC patients, and could be considered as a potential biomarker for the diagnosis and treatment of HCC.

Identification of circRNA-miRNA-mRNA regulatory network in gastric cancer by analysis of microarray data.

BACKGROUND: Evidence is increasingly indicating that circular RNAs (circRNAs) are closely involved in tumorigenesis and cancer progression. However, the function of circRNAs in gastric cancer (GC) are still unknown. Here, we aimed to determine the regulatory mechanism of circRNAs in GC. METHODS: Expression profiles of circRNAs were downloaded from four Gene Expression Omnibus (GEO) microarray datasets. Expression profiles of miRNAs and mRNAs were collected from The Cancer Genome Atlas (TCGA) database. We used the robust rank aggregation method to identify differentially expressed circRNAs (DEcircRNAs) and a ceRNA network was constructed based on circRNA-miRNA pairs and miRNA-mRNA pairs. Functional and pathway enrichment analyses were performed and interactions between proteins were predicted using Cytoscape. Aa subnetwork regulatory module was built using the MCODE plugin. RESULTS: A total of eight DEcircRNAs, 240 DEmiRNAs, and 4578 DEmRNAs were identified. The circRNA-miRNA-mRNA network was constructed based on seven circRNAs, 33 miRNAs, 69 mRNAs in GC. GO and KEGG pathway analysis indicated DEmRNAs might be associated with GC onset and progression. A PPI network was established and four hub genes (MCM4, KIF23, MCM8, and NCAPD2) were determined from the network. Then a circRNA-miRNA-hub gene subnetwork was constructed based on the four DEcircRNAs, three DEmiRNAs, and four DEmRNAs. CONCLUSIONS: Our findings provide a deeper understanding the circRNA-related competing endogenous RNA regulatory mechanism in GC pathogenesis.

Development and validation of prognostic nomograms for medullary thyroid cancer.

BACKGROUND: This aim of study was to develop and validate clinical nomograms to predict the survival of patients with medullary thyroid cancer. PATIENTS AND METHODS: Patient data were collected from the Surveillance, Epidemiology, and End Results database between 2004 and 2013. All included patients were randomly assigned into the training and validation sets. Multivariate analysis using Cox proportional hazards regression was performed, and nomograms were constructed. Model performance was evaluated by discrimination and calibration plots. RESULTS: A total of 1,657 patients were retrospectively analyzed. The multivariate Cox model identified age, tumor size, extrathyroidal extension, N stage, and M stage as independent covariates associated with overall survival (OS) and cancer-specific survival (CSS). Nomograms predicting OS and CSS were constructed based on these covariates. The nomograms predicting both OS and CSS exhibited superior discrimination power to that of TNM staging system in the training and validation sets. Calibration plots indicated that both the nomograms in OS and CSS exhibited high correlation to actual observed results. CONCLUSION: The nomograms established in this study provided an alternative tool for prognostic prediction, which may thereby improve individualized assessment of survival risks and lead to the creation of additional clinical therapies.

Nomograms for estimating survival in patients with liver-only colorectal metastases: A retrospective study.

BACKGROUND: The aim of this study was to develop and validate nomograms for individual risk prediction in patients with liver-only colorectal metastases (CRLM). METHODS: Histologically confirmed CRLM diagnosed between 2010 and 2015 were analysed from the Surveillance, Epidemiology, and End Results (SEER) database. Univariate and multivariate analyses were used to obtain independent prognostic factors to build nomograms for predicting 1- and 3-year overall survival (OS) and cancer-specific survival (CSS). The predictive accuracy of the nomogram was determined by concordance index (C-index) and calibration plots. RESULTS: A total of 9615 patients with CRLM were included in the study. A nomogram predicting OS was constructed according to 9 independent clinicopathological factors. A nomogram predicting CSS was constructed based on the same 9 factors. The C-indexes of the nomograms were significantly better than the TNM staging system (7th edition) in both sets for predicting both OS and CSS. The calibration plots displayed an optimal agreement between the predictive results and the actual observed outcomes. CONCLUSIONS: The proposed nomograms can help clinicians calculate the probability in patients with CRLM.

A five-variable signature predicts radioresistance and prognosis in nasopharyngeal carcinoma patients receiving radical radiotherapy.

Radioresistance poses a major challenge in nasopharyngeal carcinoma (NPC) treatment. Clinical tumor-node-metastasis (TNM) staging has limited accuracy in predicting NPC radioresponse and determining its therapeutic regimens. To construct a risk score model for predicting NPC radioresistance, immunohistochemistry was used to assess the expression of four proteins (14-3-3σ, Maspin, RKIP, and GRP78) in 149 NPC samples with different radiosensitivity. Sequentially, a logistic regression analysis was performed to identify independent predictors of NPC radioresistance and establish a risk score model. As a result, a risk score model, Z = -3.189 - 1.478 (14-3-3σ) - 1.082 (Maspin) - 1.666 (RKIP) + 2.499 (GRP78) + 2.597 (TNM stage), was constructed, and a patient's risk score was estimated by the formula: e (Z)/(e (Z) + 1) × 100, where "e" is the base of natural logarithm. High-risk score was closely associated with NPC radioresistance, and was observed more frequently in the radioresistant patients than that in the radiosensitive patients. The sensitivity, specificity, and accuracy of the risk score model for predicting NPC radioresistance was 88.00, 86.48, and 87.25 %, respectively, which was clearly superior to each individual protein and TNM stage. Furthermore, Kaplan-Meier survival analysis showed that high-risk score correlated with the markedly reduced overall survival (OS) and disease-free survival (DFS) of the patients, and Cox regression analysis showed that the risk score model was an independent predictor for OS and DFS. This study constructs a risk score model for predicting NPC radioresistance and patient survival, and it may serve as a complement to current radioresistance risk stratification approaches.

[Identification of Env-specific monoclonal antibodies from Chinese HIV-1 infected person by B cell activation and RT-PCR cloning].

To obtain protective human monoclonal antibody from HIV-1 infected person, we adapted a technology for isolating antigen specific monoclonal antibody from human memory B cells through in vitro B cell activation coupled with RT-PCT and expression cloning. Human B cells were purified by negative sorting from PBMCs of HIV-1 infected individuals and memory B cells were further enriched using anti-CD27 microbeads. Two hundred memory B cells per well were cultured in 96-well round-bottom plates Env-specific antibodies in supernatants were with feeder cells in medium containing EBV and CpG. screened by ELISA after 1-2 weeks' culture. Cells from positive wells of Env-specific antibody were harvested and total RNA was isolated. Human VH and Vkappa or Vlambda genes were amplified by RT-PCR and cloned into IgG1 and kappa or lambda expressing vectors. Functional VH and Vkappa or Vlambda were identified by cotransfecting 293T cells with individual heavy chain and light chain clones followed by analysis of culture supernatants by ELISA for Env-specific antibodies. Finally, corresponding mAb was produced by transient transfection of 293T cells with the identified VH and Vkappa/lambda pair and purified by protein A affinity chromatography. Purified monocolonal antibodies were used for HIV-1 specific antibody-dependent cell-mediated cytotoxicity (ADCC) and neutralizing activity assay. Four monocolonal Env-specific antibodies were isolated from one HIV-1 subtype B' infected individual. Two of them showed strong ADCC activity and one showed weak neutralizing activity against HIV-1. Its further studies on their application in therapeutic or prophylactic vaccines against HIV-1 should be grounded.

Identification of the amyloid ß-protein precursor and cystatin C as novel epidermal growth factor receptor regulated secretory proteins in nasopharyngeal carcinoma by proteomics.

The epidermal growth factor receptor (EGFR) is usually overexpressed in nasopharyngeal carcinoma (NPC) and is associated with pathogenesis of NPC. However, while EGFR-modulated intracellular proteins have been extensively studied, little is known concerning their extracellular counterparts. To identify EGFR-regulated secreted proteins in NPC, we compared the secretome profiles of TGF-α-stimulated and unstimulated NPC cell line CNE-2. CNE-2 cells were cultured in the absence or presence of TGF-α for 24 h, and secreted proteins were obtained from conditioned serum-free media and enriched by ultrafiltration centrifugation. Using 2-DE and subsequent mass spectrometry, we identified 16 differential secreted proteins, among which the amyloid ß-protein precursor (APP) was up-regulated and cystatin C was down-regulated after TGF-α stimulation. We further showed that the secretory changes of APP and cystatin C in CNE-2 after TGF-α stimulation could be abrogated by pretreatment of EGFR tyrosine kinase inhibitor PD153035 and PI3 kinase inhibitor Wortmannin, validating that APP and cystatin C are EGFR-regulated secreted proteins in NPC cells. Immunohistochemistry showed that the expression level of EGFR was positively correlated with the expression level of APP and negatively correlated with the expression level of cystatin C in NPC tissues, indicating that EGFR also regulates expression of APP and cystatin C in clinical NPC tissues. Furthermore, functional analysis showed that the growth and migration of CNE-2 cells decreased after neutralization of secretory APP in the medium using the anti-APP antibody. Our data provide substantial evidence that APP and cystatin C are target secreted proteins of EGFR in NPC, and upregulation of secretory APP by EGFR may be involved in the pathogenesis of NPC.

[Clinical significance of parameters of prostate volume measured by transabdominal ultrasonography in evaluating bladder outlet obstruction].

OBJECTIVE: To explore the correlation between the parameters of prostate volume (PV) measured by transabdominal ultrasonography and urodynamic results in diagnosing bladder outlet obstruction (BOO). METHODS: 112 BPH patients aged 45-85 underwent transabdominal ultrasonography to measure the superior-inferior diameter (R1) anterior-posterior diameter (R2), and left-right diameter (R3). Urodynamic examination was conducted to record the maximum flow rate (Qmax), detrusor pressure at maximum urinary flow rate (Pdet. Qmax), and detrusor pressure at minimum urinary flow rate (Pdet. Qmin), Schafer grading and international prostate symptom score (IPSS) scores were calculated. Correlation analysis was performed. RESULTS: The PV, R1, R2, and R3 were (48 +/- 29) ml, (4.3 +/- 1.0) cm, (3.7 +/- 0.9) cm, and (5.2 +/- 0.8) cm respectively. The Qmax, Pdet. Qmax, Schafer score, and IPSS score were (6.2 +/- 3.2) ml/s, (56 +/- 41) cm H2O, 3.1 +/- 1.8 (0-6) and 23 +/- 2 (15-31) respectively. Logistic regression analysis showed that R1 (OR = 22.662, P = 0.000), PV (OR = 0.946, P = 0.008) , and Qmax (OR = 0.760, P = 0.013) were positively correlated with Schafer grading value. CONCLUSION: The parameters of PV measured by transabdominal ultrasonography are reliable to diagnose BOO due to BPH.

[Effect of bizhongxiao decoction on the expression of 2-dimensional polyacrylamide gel electrophoresis protein in the synovial tissue with collagen-induced arthritis in rats].

OBJECTIVE: To explore the effect of bizhongxiao decoction (BZXD) on the protein maps of BZXD-treated synovitis of collagen-induced arthritis (CIA) in rats in 2-dimensional gel electrophoresis (2-DE), and to provide new clues for illuminating the active mechanism of BZXD in treating the rheumatoid arthritis (RA). METHODS: Seventy SD rats were randomly divided into nor- mal group, model group and BZXD group. The experimental arthritis rat model was established by subcutaneouly injecting Type II collagen and complete Freunds adjuvant. The total proteins of synovial tissue of rat joints in the normal group, model group and BZXD group were seperated by 2-DE respectively. The gels of the 3 groups were stained by Coomassie brilliant blue. Electron pictures were obtained by scanning the gels, and then the differential proteins among the normal group, model group and BZXD group were examined by comparing the spots density volume in the gels. The electrophoregrams of the gels were analyzed in Pdquest software. RESULTS: The incidence of arthritis in the rats was approximately 88%. The 2-DE maps of rat synovial tissue in the normal group, model group and BZXD group were well duplicated. The average protein spots in the normal group, model group and BZXD group were 947 +/- 39, 994 +/- 41, and 1031 +/- 52, and the match rates were 92%, 91%, and 94.2% respectively. The average deviations of spot position were (0.896 +/- 0.217) mm in isoelectric focusing (IEF) and (1.102 +/- 0.104) mm in sodiumdo-decylsufate-polyacrylamide gel electrophoresis (SDS-PAGE), respectively. Three hundred twenty-eight differential proteins were observed between the model group and BZXD group, of which 174 were up-regulated, 147 were down-regulated in the BZXD group, and 7 proteins were expressed only in the model group. One hundred ninty-three differential proteins were displayed between the model group and the normal group, of which 123 proteins were up-regulated and 70 were down-regulated in the model group. CONCLUSION: 2-DE protein expression profiles of synovial tissue in CIA rats are established, and many differential proteins are discovered. Further analysis on the differential proteins may serve as a new method to study the moleculer mechanism of BZXD in treating the rheumatoid arthritis.

[Effect of HLCDG1 gene transfection on growth of lung carcinoma cells].

BACKGROUND & OBJECTIVE: HLCDG1, which locates in chromosome 5q33 (between D5S436 and D5S470),is a novel gene that our laboratory has cloned recently. The expression of HLCDG1 gene was significantly down-regulated or deleted in the primary lung carcinoma. This study was designed to observe if HLCDG1 has the potential to suppress growth of lung carcinoma cells. METHODS: The recombinant plasmid, pcDNA3.1(+)/HLCDG1, was constructed and subsequently transfected into A549 cells through liposome transfection. The A549 cells stably expressing HLCDG1 gene were established by G418 selection. RT-PCR was used to demonstrate the expression of HLCDG1 gene. Furthermore, the cell proliferation assay, the soft agar assay, and the tumorigenesis assay were used to analyze the malignant phenotype of the HLCDG1-transfected cells. RESULTS: The HLCDG1-transfected cells exhibited the expression of HLCDG1 mRNA by RT-PCR. The population double time (PDT) of HLCDG1-transfected group, vector-transfected group, and nontransfected group were 70.0 hours, 43.3 hours, and 39.5 hours, respectively; the difference between HLCDG1-transfected group and the other two groups was significant (P< 0.05). The colony formation rates of HLCDG1-transfected group, the vector-transfected group, and nontransfected group were 8.5%, 29.0%, and 35.0%, respectively. The rate of HLCDG1-transfected cells was markedly lower than those of the other two groups (P< 0.05). Moreover, these clones were injected into athymic nude mice. After 43 days, they were killed, and their tumors were isolated. These tumors weighed 0.120g, 0.612g, and 0.924g, respectively. CONCLUSION: The expression of HLCDG1 in A549 cells may have the potential to suppress tumor cell growth and the tumorigenesis of A549 cells transplanted in nude mice. These results suggested that HLCDG1 gene might be a good candidate of tumor suppressor gene correlated with lung carcinoma.

[Cloning and expression analysis of lung carcinoma related gene HLCDG1].

BACKGROUND & OBJECTIVE: High frequent loss of hetero- zygosity (LOH) of 3p, 5q, 6q, 9p, 10q, 11p, 13q, 17p, and 19p in lung carcinoma was detected by comparative genomic hybridization (CGH) and genomic-wide scan for analysis of genetic alteration with microsatellite allelotying. It was indicated that there might be some other unknown tumor susceptible genes or suppressor genes likely to be involved in lung carcinoma development and progression. The aim of this study was to clone the full-length cDNA of LXDD1,an expressed sequence tag(EST) isolated by mRNA differential display, which is significantly down-regulated in lung carcinoma and represents a novel gene. METHODS: Differential expression of LXDD1 in lung carcinoma was confirmed by Northern blot analysis, the expression of the LXDD1 in human normal tissues and the size of the transcription of the LXDD1-representative gene were also determined using MTN (Multiple Tissues Northern Blots). The putative full-length cDNA of the EST-representative gene was cloned and analyzed by bioinformatics. In addition, differential reverse transcription polymerase chain reaction (RT-PCR) was used to detect the expression of the novel gene in various cancer cell lines, primary lung carcinomas, and matched normal lung tissues. RESULTS: The full length cDNA with no homology to any reported genes in the database of GenBank was successfully cloned and named HLCDG1 (Human lung carcinoma deleted gene 1, GenBank accession number AF447582). A transmembrane protein with 166 amino acids was deduced to come from the open reading frame of the 3113 bp full-length cDNA, HLCDG1 gene was confirmed to be located at chromosome band 5q33 by alignment of electric polymerase chain reaction (e-PCR). CONCLUSION: HLCDG1 is a novel gene down-regulated in lung carcinoma, which may be involved in the development of lung carcinoma.

[Identification of down-regulated expressed sequence tag at chromosome 3p21 in nasopharyngeal carcinoma].

BACKGROUND & OBJECTIVE: It was reported that a locus of high frequency loss of heterozygosity was found at 3p14-25 of nasopharyngeal carcinoma (NPC) cells. This study was designed to identify the expressed sequence tags (ESTs) associated with NPC at chromosome 3p21 in order to clone new candidate NPC-associated genes at the locus. METHODS: The expression of relative ESTs at 3p21 was determined in nasopharyngeal carcinoma tissues and normal nasopharyngeal epithelia using ESTs homology analysis with bioinformatics in computer network combined with reverse transcription-polymerase chain reaction (RT-PCR). The expression of EST was detected in other normal tissues and tumor cell lines using Northern blot analysis. RESULTS: Comparing with expression of normal nasopharyngeal epithelia, EST (N31985) was down-regulated in 60.00% (3/5) nasopharyngeal carcinoma cell lines and 47.06% (16/34) nasopharyngeal carcinoma tissues (P < 0.05). CONCLUSION: N31985 is down-regulated in NPC, suggesting it may play a role in NPC carcinogenesis.

[Isolation and identification of cDNA sequence differentially expressed in human lung carcinoma].

BACKGROUND & OBJECTIVE: The molecular mechanism of the pathogenesis of lung carcinoma is unclear; because key genes related to lung carcinoma have not been identified. This study was designed to isolate and identify differentially expressed cDNA sequences in human lung carcinoma for cloning lung carcinoma-related genes. METHOD: Using mRNA differential display method combined with cloning and reserve Northern dot blot and sequencing and RT-PCR, differentially expressed cDNA sequences were isolated between two lung cancer cell lines, two adult lung carcinoma tissue and paired normal tissue of trachea epithelia. RESULT: Sixteen differentially expressed cDNA fragments were isolated, subsequent cloning of sixteen differentially expressed cDNA fragments were confirmed by reverse Northern dot blot and sequencing and BLAST analysis. Two of these were shown to be novel gene sequences that had not been reported. Eight of the remaining cDNA sequences homologize to known genes; additionally two differentially expressed cDNA sequences were confirmed by RT-PCR. CONCLUSION: Using mRNA differentially display, The authors had successfully isolated ten differentially expressed cDNA sequences from human lung carcinoma, these cDNA sequences might be involved in the pathogenesis of lung carcinoma.

[Differential proteomic analysis of human lung adenocarcinoma cell line A-549 and of normal cell line HBE].

To explore the differential proteomic expressions between human lung adenocarcinoma cell line A-549 and normal cell line HBE, a series of methods, including immobilized pH gradient-two dimensional polyacrylamide gel electrophoresis, silver staining, PDQuest 2-DE software analysis, peptide mass fingerprinting based on matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) and SWISS-PROT database searching, were used to separate and identify the differential proteomic expressions between A-549 and HBE. The results showed that the good 2-DE pattern including high resolution and reproducibility was obtained. After silver staining, the 2-DE image analysis by PDQuest 2-DE software detected average (890 +/- 38) spots in A-549, and (757 +/- 27) spots in HBE. The average positional deviation of the matched spots between A-549 and HBE 2-DE maps was (2.85 +/- 0.48) mm in IEF direction, and (2.69 +/- 0.37) mm in SDS-PAGE direction. The differential proteomic expression analysis found that there were 535 matched spots between A-549 and HBE 2-DE maps, 355 spots that were not matched in A-549, 222 spots that were not matched in HBE. 18 differential spots (8 spots in A-549 and 10 spots in HBE) were cut off from silver staining gel at random, digested in gel with TPCK-trypsin, measured with MALDI-TOF-MS and searched in the SWISS-PROT database with PeptIdent software. 18 protein were preliminarily identified. These proteins were related to cell signal transduction, cell metabolism, proliferation and differentiation etc. There was a significant difference at protein level between human lung adenocarcinoma cell line A-549 and normal cell line HBE. It suggests that the differential expression analysis of proteomes may be useful to further study of the related proteins and the molecular markers of lung adenocarcinoma.

Isolation and Identification of cDNA Sequences Differentially Expressed in Laryngeal Carcinoma.

The isolation of the genes related to laryngeal carcinoma(LC) is necessary for revealing mechanisms of carcinogenesis and genetic predisposition to LC. The mRNA differential display method was used to compare and analyze mRNAs prepared from two adult laryngeal carcinoma tissues and paired tumor-adjacent normal tissues. A total of twenty-two differential display experiments was performed and thirty-five cDNA fragments differentially expressed in normal or malignant laryngeal epithelial tissues were identified. Differential expression of six of these thirty-five cDNA fragmens was confirmed by reverse northern dot blot. Subsequent cloning of six differentially expressed cDNA fragments and sequencing and BLASTn analysis resulted in the identification of twelve distinct cDNA sequences. Four of these were shown to be novel gene sequences that have not been reported. Eight of the remaining cDNA sequences showed sequence homology to those previously reported. The differential expression of these twelve cDNA sequences in the carcinoma or normal tissue of the larynx were confirmed by fixing the twelve cDNA sequences on the membrane, followed by the hybridization with the total cDNA probes from laryngeal carcinoma or normal tumor-adjacent tissues and by differential RT-PCR. These results suggest that these cDNA sequences might be involved in carcinogenesis of laryngeal carcinoma.