An immune subtype-related prognostic signature of hepatocellular carcinoma based on single-cell sequencing analysis

Prognostic model development and molecular subtypes identification in bladder urothelial cancer by oxidative stress signatures

BACKGROUND

Mounting studies indicate that oxidative stress (OS) significantly contributes to tumor progression. Our study focused on bladder urothelial cancer (BLCA), an escalating malignancy worldwide that is growing rapidly. Our objective was to verify the predictive precision of genes associated with overall survival (OS) by constructing a model that forecasts outcomes for bladder cancer and evaluates the prognostic importance of these genetic markers.

METHODS

Transcriptomic data were obtained from TCGA-BLCA and GSE31684, which are components of the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), respectively. To delineate distinct molecular subtypes, we employed the non-negative matrix factorization (NMF)method. The significance of OS-associated genes in predicting outcomes was assessed using lasso regression, multivariate Cox analysis, and univariate Cox regression analysis. For external validation, we employed the GSE31684 dataset. CIBERSORT was utilized to examine the tumor immune microenvironment (TIME). A nomogram was created and verified using calibration and receiver operating characteristic (ROC) curves, which are based on risk signatures. We examined variations in clinical characteristics and tumor mutational burden (TMB) among groups classified as high-risk and low-risk. To evaluate the potential of immunotherapy, the immune phenomenon score (IPS) was computed based on the risk score. In the end, the pRRophetic algorithm was employed to forecast the IC50 values of chemotherapy medications.

RESULTS

In our research, we examined the expression of 275 genes associated with OS in 19 healthy and 414 cancerous tissues of the bladder obtained from the TCGA database. As a result, a new risk signature was created that includes 4 genes associated with OS (RBPMS, CRYAB, P4HB, and PDGFRA). We found two separate groups, C1 and C2, that showed notable variations in immune cells and stromal score. According to the Kaplan-Meier analysis, patients classified as high-risk experienced a considerably reduced overall survival in comparison to those categorized as low-risk (P<0.001). The predictive capability of the model was indicated by the area under the curve (AUC) of the receiver operating characteristic (ROC) curve surpassing 0.6. Our model showed consistent distribution of samples from both the GEO database and TCGA data. Both the univariate and multivariate Cox regression analyses validated the importance of the risk score in relation to overall survival (P < 0.001). According to our research, patients with a lower risk profile may experience greater advantages from using a CTLA4 inhibitor, whereas patients with a higher risk profile demonstrated a higher level of responsiveness to Paclitaxel and Cisplatin. In addition, methotrexate exhibited a more positive outcome in patients with low risk compared to those with high risk.

CONCLUSIONS

Our research introduces a novel model associated with OS gene signature in bladder cancer, which uncovers unique survival results. This model can assist in tailoring personalized treatment approaches and enhancing patient therapeutic effect in the management of bladder cancer.

Identification and validation of methylation-CpG prognostic signature for prognosis of hepatocellular carcinoma

Epigenetic biomarkers help predict the prognosis of cancer patients and evaluating the clinical outcome of immunization therapy. In this study, we present a personalized gene methylation-CpG signature to enhance the accuracy of survival prediction for individuals with hepatocellular carcinoma (HCC). Utilizing RNA sequencing and methylation datasets from GEO as well as TCGA, we conducted single sample GSEA (ssGSEA), WGCNA, as well as Cox regression. Through these analyses, we identified 175 oxidative stress and immune-related genes along with 4 CpG loci that are associated with the prognosis of HCC. Subsequently, we constructed a prognostic signature for HCC utilizing these 4 CpG sites, referred to as the HCC Prognostic Signature of Methylation-CpG sites (HPSM). Further investigation revealed an enrichment of immune-related signal pathways in the HPSM-low group, which demonstrated a positive correlation with better survival among HCC patients. Moreover, the methylation of the CpG sites in HPSM was found to be closely linked to drug sensitivity. In vitro experiments tentatively confirmed that promoter methylation regulated the expression of BMPER, one of the CpG sites within HPSM. The expression of BMPER was significantly correlated with cell death in the oxidative stress pathway, and overexpression of BMPER effectively inhibited HCC cell proliferation. Consequently, our findings suggest that HPSM is an independent predictive factor and holds promise for accurately predicting the prognosis of HCC patients.

Prognostic Significance of Glycolysis-Related Genes in Lung Squamous Cell Carcinoma

Lung squamous cell carcinoma (LUSC) is one of the most common malignancies. There is growing evidence that glycolysis-related genes play a critical role in tumor development, maintenance, and therapeutic response by altering tumor metabolism and thereby influencing the tumor immune microenvironment. However, the overall impact of glycolysis-related genes on the prognostic significance, tumor microenvironment characteristics, and treatment outcome of patients with LUSC has not been fully elucidated. We used The Cancer Genome Atlas (TCGA) dataset to screen glycolysis-related genes with prognostic effects in LUSC and constructed signature and nomogram models using Lasso and Cox regression, respectively. In addition, we analyzed the immune infiltration and tumor mutation load of the genes in the models. We finally obtained a total of glycolysis-associated DEGs. The signature model and nomogram model had good prognostic power for LUSC. Gene expression in the models was highly correlated with multiple immune cells in LUSC. Through this analysis, we have identified and validated for the first time that glycolysis-related genes are highly associated with the development of LUSC. In addition, we constructed the signature model and nomogram model for clinical decision-making.

The Prognostic and Therapeutic Roles of ARL-6 Gene in Hepatocellular Carcinoma

Background: Hepatocellular carcinoma (HCC) is one of the most prevalent human cancers. ARL-6, a member of the ADP ribosylation factor (like) (ARF) protein family, has gained attention as a potential therapeutic target in various malignancies and a prognostic biomarker. However, its specific roles in HCC, both prognostically and biochemically, remain largely unclear. Methods: To examine the functional relevance of ARL-6 in HCC, we acquired data from GEPIA, UALCAN, TIMER, TCGA, GeneMANIA, and Metascape databases. Then, we conducted immunohistochemistry on a replication sample comprising 26 HCC specimens to assess the efficacy of the ARL-6 gene. To unravel the mechanistic intricacies, we employed diverse assays such as the cell counting kit 8 (CCK8), flow cytometry, and transwell invasion assessment. Results: Our findings demonstrated the mRNA expression of ARL-6 was significantly upregulated in HCC compared to normal tissue, as evidenced by comprehensive database analysis. Immunohistochemistry further revealed that ARL-6 expression was remarkably higher in HCC than in para-carcinoma tissues. Moreover, ARL-6 expression exhibited noteworthy variations across diverse LIHC characteristics, including sample type, histological subtype, TP53 mutation status, nodal metastatic status, and cancer stage. In addition, high transcriptional levels of ARL-6 were correlated with diminished overall survival (OS) and disease-free survival (DFS) in HCC patients. Furthermore, our study indicated positive correlations between ARL-6 expression levels and the activities of tumor-infiltrating immune cells such as B cells, myeloid dendritic cells, macrophages, neutrophils, CD8+T cells, and CD4+T cells. Substantiating our findings, database analysis uncovered additional evidence of ARL-6 gene co-expression and its functional significance in HCC cases. Finally, we demonstrated the involvement of the ARL-6 gene in HCC cell invasion, proliferation, and apoptosis. Conclusions: In conclusion, our investigation sheds light on the pivotal role of ARL-6 in influencing HCC prognosis and treatment by modulating the biological activities of tumor cells. These discoveries hold promise for the development of predictive biomarkers and novel therapeutic avenues for affected patients.

A novel metabolism-related gene signature in patients with hepatocellular carcinoma

Hepatocellular carcinoma (HCC) remains a global challenge as it is the sixth most common neoplasm worldwide and the third leading cause of cancer-related death. A key feature of HCC is abnormal metabolism, which promotes cancer cell proliferation, survival, invasion, and metastasis. However, the significance of metabolism-related genes (MRGs) in HCC remains to be elucidated. Here, we aim to establish a novel metabolism-related prognostic signature for the prediction of patient outcomes and to investigate the value of MRG expression in the prognostic prediction of HCC. In our research, a Metabolism-Related Risk Score (MRRS) model was constructed using 14 MRGs (DLAT, SEPHS1, ACADS, UCK2, GOT2, ADH4, LDHA, ME1, TXNRD1, B4GALT2, AK2, PTDSS2, CSAD, and AMD1). The Kaplan-Meier curve confirmed that the MRRS has a high accuracy in predicting the prognosis of HCC patients (p < 0.001). According to the MRRS model, the area under the curve (AUC) values for predicting the prognosis of patients with hepatocellular carcinoma at 1, 3, and 5 years reached 0.829, 0.760, and 0.739, respectively. Functional analyses revealed that signaling pathways associated with the cell cycle were largely enriched by differential genes between high and low-risk groups. In addition, dendritic cells (DCs) (p < 0.001), CD4+ T cells (p < 0.01), CD8+ T cells (p < 0.001), B cells (p < 0.001), neutrophils (p < 0.001), macrophages (p < 0.001) had a higher proportion of infiltrates in high-risk populations. Low GOT2 expression is associated with poor prognosis in patients with hepatocellular carcinoma. Knockdown of GOT2 significantly increased the migration capacity of the Huh7 and MHCC97H hepatocellular carcinoma lines. Our research reveals that GOT2 is negatively related to the survival of patients with hepatocellular carcinoma and GOT2 may contribute to tumor progression by inhibiting the ability of tumor cells to migrate.

MCF2L-AS1 promotes the biological behaviors of hepatocellular carcinoma cells by regulating the miR-33a-5p/FGF2 axis

Long noncoding RNA MCF2L-AS1 functions in the development of cancers like lung cancer, ovarian cancer, and colorectal cancer. Notwithstanding, its function in hepatocellular carcinoma (HCC) stays obscure. Our research probes its role in MHCC97H and HCCLM3 cell proliferation, migration, and invasion. qRT-PCR gauged MCF2L-AS1 and miR-33a-5p expressions in HCC tissues. CCK8, colony formation, Transwell, and EdU assays detected HCC cell proliferation, invasion, and migration, respectively. The xenograft tumor model was built to confirm the MCF2L-AS1-mediated role in HCC cell growth. Western blot and immunohistochemistry detected FGF2 expression in HCC tissues. Bioinformatics analysis predicted the targeted relationships between MCF2L-AS1 or FGF2 and miR-33a-5p, which were further examined through dual-luciferase reporter gene and pull-down assays. MCF2L-AS1 was expressed highly in HCC tissues and cells. MCF2L-AS1 upregulation enhanced HCC cells' proliferation, growth, migration, and invasion and reduced apoptosis. miR-33a-5p was demonstrated as an underlying target of MCF2L-AS1. miR-33a-5p impeded HCC cells' malignant behaviors. MCF2L-AS1 overexpression reversed miR-33a-5p-mediated effects. MCF2L-AS1 knockdown enhanced miR-33a-5p and negatively regulated FGF2 protein. miR-33a-5p targeted and inhibited FGF2. miR-33a-5p overexpression or FGF2 knockdown inhibited MCF2L-AS1-mediated oncologic effects in MHCC97H. By modulating miR-33a-5p/FGF2, MCF2L-AS1 exerts a tumor-promotive function in HCC. The MCF2L-AS1-miR-33a-5p-FGF2 axis may provide new therapeutic targets for HCC treatment.

Signature construction and molecular subtype identification based on immune-related genes for better prediction of prognosis in hepatocellular carcinoma

OBJECTIVE

Hepatocellular carcinoma (HCC) immunotherapy is a focus of current research. We established a model that can effectively predict the prognosis and efficacy of HCC immunotherapy by analyzing the immune genes of HCC.

METHODS

Through the data mining of hepatocellular carcinoma in The Cancer Genome Atlas (TCGA), the immune genes with differences in tumor and normal tissues are screened, and then the univariate regression analysis is carried out to screen the immune genes with differences related to prognosis. The prognosis model of immune related genes is constructed by using the minimum absolute contraction and selection operator (lasso) Cox regression model in the TCGA training set data, The risk score of each sample was calculated, and the survival was compared with the Kaplan Meier curve and the receiver operating characteristic (ROC) curve to evaluate the predictive ability. Data sets from ICGC and TCGA were used to verify the reliability of signatures. The correlation between clinicopathological features, immune infiltration, immune escape and risk score was analyzed.

RESULTS

Seven immune genes were finally determined as the prognostic model of liver cancer. According to these 7 genes, the samples were divided into the high and low risk groups, and the results suggested that the high-risk group had a poorer prognosis, lower risk of immune escape, and better immunotherapy effect. In addition, the expression of TP53 and MSI was positively correlated in the high-risk group. Consensus clustering was performed to identify two main molecular subtypes (named clusters 1 and 2) based on the signature. It was found that compared with cluster 1, better survival outcome was observed in cluster 2.

CONCLUSION

Signature construction and molecular subtype identification of immune-related genes could be used to predict the prognosis of HCC, which may provide a specific reference for the development of novel biomarkers for HCC immunotherapy.

Costimulatory molecule-related lncRNA model as a potential prognostic biomarker in non-small cell lung cancer

OBJECTIVE

Costimulatory molecules have been demonstrated to exert essential roles in multiple cancers. However, their role in lung cancer remains elusive. Here, we sought to identify costimulatory molecule-related lncRNAs in non-small cell lung cancer (NSCLC) and establish a prognostic signature to predict the prognosis of patients with NSCLC.

METHODS

A total of 535 lung adenocarcinoma (LUAD) and 502 lung squamous cell carcinoma (LUSC) patients from the cancer genome atlas (TCGA) database were recruited. A novel costimulatory molecule-based lncRNA prognostic model was constructed using the least absolute shrinkage and selection operator (LASSO) algorithm to predict the overall survival. The Homo_sapiens.GRCh38 data set was set as a reference file for probe annotation.

RESULTS

A total of 593 costimulatory molecule-related lncRNAs were extracted. After analysis, six costimulatory molecule-related lncRNAs (AC084859.1, AC079949.2, HSPC324, LINC01150, LINC01150, and AC090617.5) were screened. A prognostic model based on the six lncRNAs was established using systematic bioinformatics analyses. The prognostic model had a prognostic value in NSCLC patients. Furthermore, a prognostic nomogram was established based on clinical parameters and a risk-score model. Patients with different risk scores had considerably different tumor-infiltrating immune cells, somatic mutational loading, clinical outcomes, signaling pathways, and immunotherapy efficacy. In addition, LINC01137 was associated with unfavorable disease outcomes and fueled tumor progression in NSCLC.

CONCLUSION

Taken together, our study demonstrated that a costimulatory molecule-related lncRNA model could be a potential prognostic biomarker in NSCLC. Moreover, LINC01137 could facilitate the proliferation and invasion of lung cancer.

Identification of m6A regulator-mediated RNA methylation modification patterns and key immune-related genes involved in atrial fibrillation

The role of m6A in the regulation of the immune microenvironment in atrial fibrillation (AF) remains unclear. This study systematically evaluated the RNA modification patterns mediated by differential m6A regulators in 62 AF samples, identified the pattern of immune cell infiltration in AF and identified several immune-related genes associated with AF. A total of six key differential m6A regulators between healthy subjects and AF patients were identified by the random forest classifier. Three distinct RNA modification patterns (m6A cluster-A, -B and -C) among AF samples were identified based on the expression of 6 key m6A regulators. Differential infiltrating immune cells and HALLMARKS signaling pathways between normal and AF samples as well as among samples with three distinct m6A modification patterns were identified. A total of 16 overlapping key genes were identified by weighted gene coexpression network analysis (WGCNA) combined with two machine learning methods. The expression levels of the NCF2 and HCST genes were different between controls and AF patient samples as well as among samples with the distinct m6A modification patterns. RT-qPCR also proved that the expression of NCF2 and HCST was significantly increased in AF patients compared with control participants. These results suggested that m6A modification plays a key role in the complexity and diversity of the immune microenvironment of AF. Immunotyping of patients with AF will help to develop more accurate immunotherapy strategies for those with a significant immune response. The NCF2 and HCST genes may be novel biomarkers for the accurate diagnosis and immunotherapy of AF.

Development and validation of a novel risk model in newly diagnosed de novo bone metastatic prostate cancer (M1b): a retrospective study

Background

Previous studies suggested that bone metastasis has a significant effect on the time of progression to metastatic castration-resistant prostate cancer (CRPC) for newly diagnosed de novo bone metastatic hormone-sensitive prostate cancer (mHSPC). Nevertheless, the effect of different bone metastasis sites was not fully evaluated. This study aimed to develop and validate a novel bone metastatic risk model.

Methods

We enrolled 122 patients who were newly diagnosed with de novo bone metastatic prostate cancer following primary androgen deprivation based therapy at our institution from January 2008 to June 2021. The metastatic bone sites were classified into six sites: skull; cervical, thoracic, and lumbar vertebrae; chest (ribs and sternum); pelvis; upper limbs; and lower limbs. We calculated the bone metastatic score (BMS) for each site: 0 points were assigned for non-metastasis and 1 point was assigned for metastasis. The X-tile was adopted to acquire optimal cutoff points of BMS. We defined high-risk group (HRG) as BMS ≥ 3 and low-risk group (LRG) as BMS < 3. The new bone risk stratification was validated by calculating the area under the receiver operating characteristic curve (AUC). Subsequently, the relevant clinical prognostic variables were added to construct a predictive nomogram for predicting CRPC.

Results

The median patient age was 73 years. Most patients had Gleason score ≤8 (93 cases, 76.2%). The median follow-up duration was 11.5 months (range: 2-92 months). Eighty-six patients progressed to CRPC during the follow-up. The most common bone metastatic site was the pelvis (90.2%). The median BMS was 4. Seventy-six patients had HRG, while forty-six had LRG. The 1-, 2-, and 3-year AUCs for H/LRG were 0.620, 0.754, and 0.793, respectively. The HRG was associated with earlier time to CRPC. A nomogram based on four parameters (Gleason score, H/LRG, prostate-specific antigen [PSA] nadir, and time to PSA nadir) was developed to predict CRPC. Internal validation using bootstrapping demonstrated good accuracy for predicting the CRPC (C-index: 0.727). The calibration analysis demonstrated that the model performed well.

Conclusion

We established a novel H/LRG risk model for newly diagnosed de novo bone metastatic prostate cancer, which provided evidence to support clinical decision-making.

Identification of the ageing-related prognostic gene signature, and the associated regulation axis in skin cutaneous melanoma

Skin cutaneous melanoma (SKCM) has substantial malignancy and a poor prognosis. The function of ageing-related genes (ARGs) in SKCM is unknown. In this study, a prognostic risk-scoring model for ARG was constructed based on SKCM RNA-seq, mutation, and clinical data in The Cancer Genome Atlas. Our novel prognostic model, which included four ARGs (IRS2, PDGFRA, TFAP2A, and SOD2), could distinguish between low-risk and high-risk groups. Low-risk patients benefited more from immunotherapy and commonly used targeted and chemotherapy drugs than high-risk patients. There were also considerable differences in immunocyte infiltration and tumour microenvironment between the two groups. Furthermore, multivariate Cox regression analysis revealed that age, pT_stage, pM_stage, body mass index, tumour mutation burden, and risk score were independent factors influencing the prognosis of patients with SKCM; therefore, we devised a prognosis nomogram. Last, a long non-coding (lncRNA) NEAT1/miR-33a-5p/IRS2 regulatory axis of the competing endogenous RNA network was built to investigate the mechanisms of SKCM metastasis progression. Grouping based on the scoring system could predict the prognosis of SKCM and predict the sensitivity of patients to immunotherapy, targeted therapy, and chemotherapy. This could facilitate the formulation of individualised treatment strategies and help drug research and development. These findings highlight the regulatory axis of the lncRNA NEAT1/miR-33a-5p/IRS2, which may play a role in SKCM metastasis.

FBXO43 increases CCND1 stability to promote hepatocellular carcinoma cell proliferation and migration

Background and Aims

Abnormal expression of E3 ubiquitin ligase plays an important role in the development and progression of hepatocellular carcinoma (HCC), although the mechanism has remained elusive. This study aimed to investigate the biological function and potential mechanism of FBXO43 in HCC.

Methods

FBXO43 expression in tissues and cells were detected by quantitative real-time PCR (qRT-PCR), Western blot, and immunohistochemistry (IHC). The Kaplan-Meier method and Cox regression analysis were used to explore the correlation between the expression level of FBXO43 and the clinical survival. MTT assay, EdU incorporation, colony formation, Transwell, and wound healing assays were performed to evaluate the function of FBXO43 in cell proliferation and migration in vitro. The interaction between FBXO43 and cyclin D1 (CCND1) was assessed by co-immunoprecipitation (Co-IP) assay and in vivo ubiquitination assay.

Results

We found that FBXO43 was upregulated in HCC patient tissues and positively associated with poor clinicopathological features. Meanwhile, HCC patients with high expression of FBXO43 had shorter overall survival (OS) and disease-free survival (DFS). Furthermore, knockdown of FBXO43 inhibited HCC cell proliferation, migration and epithelial-mesenchymal transition (EMT) in HCC cells. Mechanistically, FBXO43 interacted with CCND1 and promoted its stability by polyubiquitination, leading to HCC cell proliferation, migration and EMT. Functional rescue experiments demonstrated that knockdown of CCND1 blocks FBXO43-mediated cell proliferation and metastasis.

Conclusions

FBXO43, as an independent prognostic biomarker, promotes HCC cell proliferation, metastasis and EMT by stability of CCND1, which provides a new potential strategy for HCC treatment by targeting FBXO43-CCND1 axis.

Identification of immune-related and autophagy-related genes for the prediction of survival in bladder cancer

Background

Bladder cancer has the characteristics of high morbidity and mortality, and the prevalence of bladder cancer has been increasing in recent years. Immune and autophagy related genes play important roles in cancer, but there are few studies on their effects on the prognosis of bladder cancer patients.

Methods

Using gene expression data from the TCGA-BLCA database, we clustered bladder cancer samples into 6 immune-related and autophagy-related molecular subtypes with different prognostic outcomes based on 2208 immune-related and autophagy-related genes. Six subtypes were divided into two groups which had significantly different prognosis. Differential expression analysis was used to explore genes closely related to the progression of bladder cancer. Then we used Cox stepwise regression to define a combination of gene expression levels and immune infiltration indexes to construct the risk model. Finally, we built a Nomogram which consist of risk score and several other prognosis-related clinical indicators.

Results

The risk model suggested that high expression of C5AR2, CSF3R, FBXW10, FCAR, GHR, OLR1, PGLYRP3, RASGRP4, S100A12 was associated with poor prognosis, while high expression level of CD96, IL10, MEFV pointed to a better prognosis. Validation by internal and external dataset suggested that our risk model had a high ability to discriminate between the outcomes of patients with bladder cancer. The immunohistochemical results basically confirmed our results. The C-Index value and Calibration curves verified the robustness of Nomogram.

Conclusions

Our study constructed a model that included a risk score for patients with bladder cancer, which provided a lot of helps to predict the prognosis of patients with bladder cancer.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12863-022-01073-7.

A pan-cancer analysis of the oncogenic role of ribonucleotide reductase subunit M2 in human tumors

Background

Recent studies have identified ribonucleotide reductase subunit M2 (RRM2) as a putative promoter of tumors. However, no systematic analysis of its carcinogenicity has been conducted.

Methods

The potential functions of RRM2 in various tumor types were investigated using data from the Genotype-Tissue Expression (GTEx), the Clinical Proteomic Tumor Analysis Consortium (CPTAC), the Cancer Genome Atlas (TCGA), the Human Protein Atlas (HPA), cBioPortal, GEPIA, String, and Gene Set Enrichment Analysis (GSEA). We analyzed the difference in mRNA and protein expression, pathological stage, survival, mutation, tumor microenvironment (TME), and immune cell infiltration in relation to RRM2. Meanwhile, using TCGA and the Tumor Immune Estimation Resource 2 (TIMER 2), the associations between RRM2 expression, immune infiltration, and immune-related genes were assessed. Additionally, CCK-8, Edu and RT-PCR assays were used to validate that RRM2 acts as an oncogene in liver cancer cells and its association with HBx. A cohort of liver hepatocellular carcinoma (LIHC) patients (n=154) from Huashan Hospital was analyzed for the expression of RRM2 and the association between RRM2 and immune infiltration.

Results

Using the GTEx and TCGA databases, we discovered that 28 tumors expressed RRM2 at significantly higher levels than the corresponding normal tissues. Increased RRM2 expression may be predictive of a poor overall survival (OS) in patients with seven different cancers. GO, KEGG, and GSEA analyses revealed that the biological process of RRM2 was associated with the regulation of carcinogenic processes and immune pathways in a variety of tumor types. The expression of RRM2 was highly correlated with maker genes involved in immune activation and immunosuppression, immune checkpoints, DNA mismatch repair system (MMR), and the infiltration levels of Tregs and macrophages (TAMs), suggesting that the carcinogenic effect of RRM2 may be achieved by regulating immune related genes. Moreover, as demonstrated by CCK-8 and Edu assays, RRM2 was an oncogene in liver cancer cells. We confirmed for the first time that RRM2 was significantly upregulated by HBx, suggesting that RRM2 may be a key regulator of LIHC induced by HBV. IHC analysis validated the upregulated expression of RRM2 protein and its correlation with immune infiltration makers in a LIHC patient cohort.

Conclusion

RRM2 may be a valuable molecular biomarker for predicting prognosis and immunotherapeutic efficacy in pan-cancer, particularly in LIHC.

Identification and validation of core genes as promising diagnostic signature in hepatocellular carcinoma based on integrated bioinformatics approach

The primary objective of this investigation was to determine the hub genes of hepatocellular carcinoma (HCC) through an in silico approach. In the current context of the increased incidence of liver cancers, this approach could be a useful prognostic biomarker and HCC prevention target. This study aimed to examine hub genes for immune cell infiltration and their good prognostic characteristics for HCC research. Human genes selected from databases (Gene Cards and DisGeNET) were used to identify the HCC markers. Further, classification of the hub genes from communicating genes was performed using data derived from the targets' protein-protein interaction (PPI) platform. The expression as well as survival studies of all these selected genes were validated by utilizing databases such as GEPIA2, HPA, and immune cell infiltration. Based on the studies, five hub genes (TP53, ESR1, AKT1, CASP3, and JUN) were identified, which have been linked to HCC. They may be an important prognostic biomarker and preventative target of HCC. In silico analysis revealed that out of five hub genes, the TP53 and ESR1 hub genes potentially act as key targets for HCC prevention and treatment.

MicroRNA-21 as a potential biomarker for detecting esophageal carcinoma in Asian populations: a meta-analysis

Background

MicroRNA-21 (miR-21) is significantly expressed in a variety of cancers and could be used as a tumor biomarker. However, the results are varied, and no studies on the diagnostic usefulness of miR-21 in Asian esophageal cancer (EC) patients have been published. This meta-analysis was aimed at exploring whether miR-21 can be used as a diagnostic marker and assessing its effectiveness.

Methods

The relevant literature was identified in six main databases: Ovid MEDLINE, PsycINFO, PubMed MEDLINE, Embase, Web of Science, and the Cochrane Library. Two researchers independently selected the literature based on the inclusion and exclusion criteria, extracted data, and evaluated the risk of bias. The meta-analysis was carried out using Review Manager 5.4, Meta-Disc 1.4 and STATA 15.1 software. In the end, 987 patients from 12 different studies were included. Quality evaluation of diagnostic accuracy studies 2 (QUADAS-2) was used to examine the risk of bias.

Results

The pooled sensitivity (SEN) was 0.72 (95% CI [0.69-0.75]), the pooled specificity (SPE) was 0.78 (95% CI [0.75-0.81]), the pooled positive likelihood ratio (PLR) was 2.87 (95% CI [2.28-3.59]), the pooled negative likelihood ratio (NLR) was 0.36 (95% CI [0.31-0.43]), the pooled diagnostic odds ratio (DOR) was 10.00 (95% CI [7.73-12.95]), and the area under the curve 0.82 (95% CI [0.79-0.85]). A Deeks' funnel plot shows that there was no publication bias (P = 0.99).

Conclusion

Our findings suggest miR-21 might be the potential biomarker for detecting EC in Asian populations, with a good diagnostic value.

An insight into the invasion of breast ductal carcinoma in situ based on clinical, pathological and hematological data

Background

Ductal carcinoma in situ (DCIS) has become a non-negligible part of breast cancers owing to the greatly increased incidence. While its natural history was not fully elucidated, which is the reason for current controversies in clinical treatment. Exploration of this issue from a clinical perspective is meaningful.

Methods

Medical records of 389 patients diagnosed with DCIS or DCIS with invasive ductal carcinoma (IDC) were reviewed. All of them received appropriate medical care in our center. All 324 patients in training cohort were divided into invasion and non-invasion groups based on pathology. Differences in DCIS immunohistochemical markers and hematological indicators between them were analyzed. In the invasion group, differences between DCIS and matched IDC were compared to explore changes in the tumor heterogeneity during invasion. Conclusions are validated in the validation cohort of 65 patients.

Results

Patients in invasion and non-invasion groups were balanced in baseline characteristics and no statistically significant differences were noticed for DCIS immunohistochemical markers. For hematological indicators, high expression of platelet >291.50) (odds ratio, 2.46; CI [1.35-4.46]; p = 0.003) and SII (>347.20) (odds ratio, 2.54; CI [1.56-4.12]; p < 0.001) were established as independent predictors for invasion by logistic analysis and were validated in the validation cohort. Ki-67 of IDC was significantly higher than that of matched DCIS (p < 0.001). HER2 expression and histological grade of DCIS were separately linearly related to those of IDC.

Conclusion

The change in hematological indicators is an independent predictor for invasion and can be incorporated into the treatment decision-making process for DCIS. Invasion tumor cells exhibit a stronger proliferative capacity compared with the in-situ ones. There are linear relationships in HER2 expression and histological grades between DCIS and matched IDC. DCIS subclones with different histological grades will develop into invasive carcinomas separately.

An integrative analysis to reveal that CLEC2B and ferroptosis may bridge the gap between psoriatic arthritis and cancer development

Patients with cutaneous psoriasis (PsC) and psoriatic arthritis (PsA) are reported with increased cancer risk, but the underlying mechanism is less clear, especially the association between the presence of PsA and cancer risk. Motivated by the role of ferroptosis in the progression of cancers as well as inflammation response in psoriasis, this experiment attempts to investigate the relationship between ferroptosis regulators and hub genes in PsA by bioinformatic analysis. The findings revealed an exclusive correlation between CISD1 (ferroptosis regulator) and CLEC2B (hub gene) in PsA group as well as multiple cancer types. Furthermore, CLEC2B was discovered differentially expressed in a variety of cancers and is closely associated with immune cell infiltration as well as immune checkpoints. These results indicate that ferroptosis may act as a bridge between psoriatic arthritis and the onset of certain malignancies.

The Predictive Value of Changes in the Absolute Counts of Peripheral Lymphocyte Subsets for Progression and Prognosis in Breast Cancer Patients

Background

As the number and proportion of lymphocyte subsets are an important indicator of the immune function, an in depth understanding of the immune function of patients with malignant tumor has important clinical values for the treatment, prognosis, and evaluation of the disease. This retrospective study was to evaluate the clinical value of the absolute counts of lymphocyte subsets as potential blood biomarkers for progression and prognosis in breast cancer patients.

Methods

A total of 237 BC patients and 55 age-matched female normal healthy donors were included in this study. Flow cytometry was used to determine the absolute counts and the percentages of CD3⁺, CD4⁺, CD8⁺, B, and NK cells. The receiver operating characteristic curve (ROC) was used to evaluate the accuracy of absolute count of lymphocyte subsets in the curative efficacy assessment. The clinicopathological parameters influencing the disease progression were determined by Cox proportional hazards regression. Progression-free survival (PFS) was estimated using the Kaplan–Meier method with the log-rank test. Results: Compared with the healthy donors, the absolute counts of lymphocyte subsets in patients decreased significantly. ROC analysis showed that the area under the curve of the CD4⁺ absolute count was 90% (95% confidence interval 0.859–0.940), and the sensitivity and specificity were 80.9% and 85.3%, respectively. The analysis of Cox regression showed that the cutoff value of the CD4⁺ absolute count ≥451 cells/μL might be a favorable prognostic factor. Multivariate analysis of prognostic factors of PFS showed that the CD4⁺ and CD8⁺ absolute count were independent factors for predicting PFS.

Conclusions

The remarkably impaired absolute counts of the CD3⁺, CD4⁺, CD8⁺, B, and NK cells in patients with breast cancer can be used as potential susceptible biomarkers to evaluate the patient's immune status. The higher level of CD4⁺ and CD8⁺ absolute counts probably contributed to the longer PFS and favorable outcome of BC patients.

Clinical Value of Coagulation Index Changes in Early Diagnosis and Nursing Intervention for PICC-Related Venous Thrombosis in Tumor Patients

Purpose

To explore the clinical value of coagulation index changes in early diagnosis and nursing intervention for PICC-related venous thrombosis in tumor patients. Patients and Methods. A total of 170 tumor patients hospitalized for the first time with catheterization were enrolled from February 2018 to June 2022. According to the diagnostic criteria of venous thromboembolism, high-risk patients with venous thrombosis within 13 days after catheterization were enrolled in the observation group, and those without thromboembolism were enrolled in the control group. Venous blood was taken from all patients on days 1, 5, 9, and 13 after catheterization to measure the change trend of coagulation indexes of patients and to compare the difference of coagulation indexes between the observation group and the control group.

Results

PT values of all patients were within the normal reference range at days 1, 5, 9, and 13 after catheterization. Compared with the control group, the observation group was significantly reduced on days 5, 9, and 13 after catheterization (P < 0.05), and continued to decrease with the prolonging of time(P < 0.05). After catheterization, the values of all patients at each time point were lower than the normal reference range. Compared with the control group, the values of tumor patients in the observation group were significantly decreased on days 5, 9, and 13 (P < 0.05) and continued to decrease at each time point (P < 0.05). DD values in the observation group were all higher than the normal reference range on days 1, 5, 9, and 13 after catheterization. Compared with the control group, DD values in the observation group were significantly higher on days 1, 5, 9, and 13 after catheterization (P < 0.05).

Conclusion

PT and APTT continued to decrease after catheterization, and DD kept fluctuating at a high level, highly suggesting the possibility of venous thrombosis. The nursing staff should keep high vigilance and give appropriate nursing intervention.

Association of Cytokine Gene Polymorphisms with Prostate Cancer Risk from a Study in Central China

Our study intended to investigate five cytokine gene single nucleotide polymorphisms (SNPs) and their associations with prostate cancer risk. Genotypes of five cytokine gene SNPs were detected by MassARRAY for blood samples from a group of patients with prostate cancer (n = 90) and a control group (n = 140) in central China. The differences in tumor clinical stages, Gleason scores, and PSA values in patients with prostate cancer were also investigated. The frequencies of the five cytokine gene SNPs (L-1β rs16944, IL-4 rs2070874, IL-4rs2227284, IL-16 rs7175701, and IL-16 rs11556218) genotypes were not found to be significantly mutated in prostate cancer patients compared with the control group. In addition, for five cytokine gene SNPs genotypic comparisons, patients with different Gleason scores, clinical stages, and PSA values were grouped into two subgroups. There was also no statistically significant association in all these subgroups. Our study suggests that cytokine gene polymorphisms may not be a risk factor for prostate cancer in a central Chinese population. Nevertheless, more large-scale studies on the Chinese population are necessary to examine our conclusions. The discovery of cytokine gene polymorphisms related to prostate cancer could update our understanding of the etiology and improve our knowledge of the early detection, diagnosis, and treatment of prostate cancer.

Identification of Potential Biomarkers of Platelet RNA in Glioblastoma by Bioinformatics Analysis

Objective

Glioblastoma is one of the most common and fatal malignancies in adults. Current treatment is still not optimistic. Glioblastoma (GBM) transports RNA to platelets in the blood system via microvesicles, suggesting that platelet RNA can be a potential diagnostic and therapeutic target. The roles of specific platelet RNAs in treatment of GBM are not well understood.

Methods

Platelet RNA profiling of 8 GBM and 12 normal samples were downloaded from the GEO database. Differentially expressed genes (DEGs) were identified between tumors and normal samples. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to elucidate the functions of up- and downregulated genes. miRNA was predicted by miRTarBase, TargetScan, and miRDB databases. circBase and circBank were used for circRNA prediction. ceRNA (circRNA-mRNA-miRNA) network was constructed to investigate the potential interactions.

Results

22 genes were upregulated and 9 genes were downregulated. There are only two genes (CCR7 and FAM102A) that connect to miRNAs (hsa-let-7a-5p, hsa-miR-1-3p). We assessed the overall survival rates by Kaplan-Meier plotter, and relative expression of GBM and subtypes for overlapped mRNA (CCR7 and FAM102A) were evaluated, and further, we obtained circRNAs (has-circ-0015164, hsa-circ-0003243) by circBank and circBase and bind sites through the CSCD database. Finally, a ceRNA network (circRNA-mRNA-miRNA) was constructed based on 2 miRNAs, 2 mRNAs, and 2 circRNAs by Cytoscape. This study focused on potential mRNA and ceRNA biomarkers to targeted treatment of GBM and provided ideas for clinical treatment through the combination of hematology and oncology.

Conclusion

The findings of this study contribute to better understand the relationship between GBM and the blood system (platelets) and might lay a solid foundation for improving GBM molecule and gene diagnosis and prognosis.

Application of Visual Artificial Airway in Patients with ARDS Assisted by Pulmonary Ultrasound

Objective

To explore the application of pulmonary ultrasound in visual nursing of artificial airway in patients with acute respiratory distress syndrome (ARDS).

Methods

Seventy-eight ARDS patients with mechanical ventilation admitted from February 2021 to January 2022 were included and divided into the intervention group and the control group. The control group was given routine airway nursing, and the intervention group was given visual airway nursing management through lung ultrasound. The arterial blood gas analysis indexes, mechanical ventilation time, ICU treatment time, total hospitalization time, aspiration, and the incidence of ventilator-associated pneumonia (VAP) were compared between the two groups.

Results

After treatment, PaO2, PaCO2, SPO2, and oxygenation indexes were significantly improved compared with those before treatment, and the indexes in the intervention group were better than those in the control group after treatment, and the differences were statistically significant (P < 0.05). The mechanical ventilation time (5.39 ± 0.68 vs. 7.92 ± 0.59 days), ICU treatment time (8.05 ± 1.14 vs. 10.71 ± 1.16 days), and total hospitalization time (12.05 ± 2.20 vs. 15.68 ± 2.18 days) in the intervention group were significantly shorter than those in the control group (P < 0.05). The incidences of aspiration (2.56% vs. 15.38%) and VAP (5.13% vs. 20.51%) in the intervention group was significantly lower than that in the control group (P < 0.05).

Conclusion

The application of visual artificial airway management assisted by lung ultrasound in ARDS patients can shorten the treatment time and hospitalization time of mechanical ventilation, reduce the incidence of aspiration and VAP, and improve the prognosis of patients.

Regulatory Roles of Noncoding RNAs in the Progression of Gastrointestinal Cancers and Health Disparities

Annually, more than a million individuals are diagnosed with gastrointestinal (GI) cancers worldwide. With the advancements in radio- and chemotherapy and surgery, the survival rates for GI cancer patients have improved in recent years. However, the prognosis for advanced-stage GI cancers remains poor. Site-specific GI cancers share a few common risk factors; however, they are largely distinct in their etiologies and descriptive epidemiologic profiles. A large number of mutations or copy number changes associated with carcinogenesis are commonly found in noncoding DNA regions, which transcribe several noncoding RNAs (ncRNAs) that are implicated to regulate cancer initiation, metastasis, and drug resistance. In this review, we summarize the regulatory functions of ncRNAs in GI cancer development, progression, chemoresistance, and health disparities. We also highlight the potential roles of ncRNAs as therapeutic targets and biomarkers, mainly focusing on their ethnicity-/race-specific prognostic value, and discuss the prospects of genome-wide association studies (GWAS) to investigate the contribution of ncRNAs in GI tumorigenesis.

PD-L1 rs2890658 Polymorphism Increases Risk for Non-Small-Cell Lung Cancer in Northern China Population Based on Experimental Data and Meta-Analysis

Purpose

To dig the PD-L1 rs2890658 polymorphism with susceptibility of non-small-cell lung cancer (NSCLC) in northern China.

Patients and Methods

There were 600 NSCLC patients and 600 age and sex matched controls from the same ethnic origin recruited in the present research. Polymerase chain reaction-restriction fragment length polymorphism method genotyped PD-L1 rs2890658 polymorphism. PubMed and Embase were searched to get eligible literature for meta-analysis. The association between PD-L1 rs2890658 polymorphism and NSCLC risk was calculated with odds ratio and 95% confidence interval.

Results

It is more likely that individuals who have CC genotype and C allele are 2.15 and 1.41 times to develop NSCLC compared with individuals with AA genotype and A allele, respectively. Meta-analysis showed that the individuals who have C allele and CA genotype increased the risk of suffering from NSCLC.

Conclusion

PD-L1 rs2890658 polymorphism increased NSCLC risk in northern China population and it might predict the occurrence of NSCLC.

Diagnostic Value of Prostate-Specific Antigen Combined with Plasma miRNA-149 Expression in Patients with Prostate Cancer Based on Experimental Data and Bioinformatics

Purpose

The aim of this study is to explore the diagnostic value of prostate-specific antigen (PSA) combined with serum miRNA-149 expression in prostate cancer (PCa) by conducting experiments and bioinformatics analysis. Patients and Methods. 50 PCa patients were enrolled on the experimental group from January 2020 to December 2021. 56 patients with benign prostatic hyperplasia (BPH) were selected as the control group at the same time. Real-time fluorescent quantitative PCR was applied to investigate the miRNA-149 expression. PSA was detected by using a chemiluminescence meter using Abbott i4000. Applying bioinformatics analysis, we explored the expression of hsa-miR-149 in PCa in The Cancer Genome Atlas (TCGA) database. Kaplan–Meier analyses were used to evaluate the prognostic value, and the ROC curve was applied.

Results

The expression level of miRNA-149 in the PCa group was significantly higher than that in the BPH group (P < 0.05). The PSA level in the PCa group was also significantly higher than that in the BPH group (P < 0.05). TCGA data analysis revealed that PCa tissues had significantly increased hsa-miR-149 expression. The results of survival analysis showed that patients with high expression of hsa-miR-149 had better prognosis. Additionally, the pathological N stage of PCa correlates with the hsa-miR-149 expression level (P = 0.002). According to ROC curve analysis, the region under the curve was 0.653, 95% CI: 0.576–0.730.

Conclusion

High expression of serum miRNA-149 is associated with PCa patients. Although combined PSA did not improve the diagnostic efficacy, miRNA-149 has high specificity in the diagnosis of PCa. miRNA-149 might be a novel marker for early diagnosis and prognosis assessment for PCa.

Genetic Polymorphism of E2F1 Influences Susceptibility to Ovarian Cancer in a Chinese Population

Purpose

The present study is aimed at exploring whether rs3213172, rs3213173, and rs3213176 polymorphisms of the E2F1 gene confer risk for ovarian cancer.

Methods

A total of 80 patients with ovarian cancer were selected from the first affiliated hospital of Soochow University in Jiangsu Province from January 2016 to June 2021, including 48 cases that were premenopausal and 32 cases that were menopausal. 130 healthy women who participated in normal physical examinations during the same period were selected as the control group. The rs3213172, rs3213173, and rs3213176 polymorphisms of the E2F1 gene were detected by the fluorescent probe method.

Results

For rs3213173 and rs3213176 loci, there were no statistical significances in genotype distribution frequency between the ovarian cancer group and the control group (P > 0.05). For rs3213172 loci, a significant difference was observed in CT genotype between the ovarian cancer group and the control group (P=0.024).

Conclusion

E2F1 gene rs3213173 and rs3213176 polymorphisms confer no risk to ovarian cancer risk. The CT genotype of E2F1 gene rs3213172 polymorphism is associated with an increased risk of ovarian cancer, and E2F1 gene rs3213172 polymorphism may be a novel marker for the risk prediction of ovarian cancer.

Clinical value of serum miR-92 and miR-122 expression level combined with pulmonary ultrasound score in the prognosis of neonatal acute respiratory distress syndrome

Purpose

To explore the value of the expression of serum miR‐92 and miR‐122 combined with lung ultrasound score (LUS) in the prognosis of neonatal acute respiratory distress syndrome (ARDS).

Patients and methods

This study involved 148 neonatal ARDS cases from January 2018 to October 2021, of which 77 children were discharged from hospital and 31 died. The children with ARDS were classified according to disease severity based on X‐ray examination as mild (n = 69 cases) and severe (n = 39 cases). The expression of serum miR‐92 and miR‐122 was detected by real‐time fluorescence quantitative PCR and the LUS score was recorded. The data were subjected to ROC curve analysis and Pearson correlation analysis.

Results

The expression of serum miR‐92, miR‐122, and LUS score in the patients that died were significantly higher than in those who survived (p < 0.05). These indicators were also significantly higher in the severe disease group compared to the mild disease group (p < 0.05). ROC curve showed that serum miR‐92 and miR‐122 combined with the LUS score had the largest area under the curve (0.920, 95% CI: 0.860–0.977) for predicting death, with a sensitivity and specificity of 92.0% and 87.0%, respectively. Pearson correlation analysis showed that the expression levels of serum miR‐92 and miR‐122 were positively correlated with the LUS score (all p < 0.01).

Conclusions

The increased expression of serum miR‐92 and miR‐122 is related to the severity and prognosis of children with ARDS, combined with the LUS score are of value to predict the prognosis of children with ARDS.