High SEC61G expression predicts poor prognosis in patients with Head and Neck Squamous Cell Carcinomas

Retinol-binding protein type 1 expression predicts poor prognosis in head and neck squamous cell carcinoma

BACKGROUND

Head and neck squamous cell carcinoma (HNSCC) is the sixth most prevalent malignancy worldwide, with high incidence and poor survival rates. RBP1 is highly expressed in several kinds of cancer and plays a potential prognostic factor. However, the relationship between RBP1 and HNSCC were analyzed based on The Cancer Genome Atlas (TCGA) database.

MATERIALS AND METHODS

RBP1 expression and clinical information were obtained from the Cancer Genome Atlas (TCGA) database. Tumor tissue and adjacent normal tissue of 6 HNSCC patients were collected to analyze the RBP1 mRNA expression level by quantitative PCR. Cox regression analysis was used to evaluate the prognostic values of RBP1 and clinical data in HNSCC. A nomogram was also established to predict the impact of RBP1 on prognosis based on Cox multivariate results. The methylation level of RBP1 in HNSC and its prognosis were analyzed in UALACN and MethSurv. Finally, the potential biological functions of RBP1 were investigated using gene set enrichment analysis (GSEA) and single sample GSEA (ssGSEA).

RESULTS

The mRNA expression levels of RBP1 were highly expressed in HNSCC tissue. The Cox analyses demonstrate that highly-expressed RBP1 is an independent prognosis marker(P < 0.05). ROC curve analysis showed that performances of RBP1 (area under the ROC curve: 0.887, sensitivity: 84.1%, specificity: 79.9%). The methylation was increased in HNSCC patients compared with normal subjects(P < 0.05) and was associated with better prognosis at sites cg06208339, cg12298268, cg12497564, cg15288618, cg20532370, cg23448348. Additionally, RBP1 expression is mildly associated with immune cell infiltration and immunological checkpoints.

CONCLUSION

RBP1 is overexpressed and associated with poor patient prognosis in head and neck squamous cell carcinoma.

Identification of SEC61G as a Diagnostic and Prognostic Biomarker in Oral Squamous Cell Carcinoma

Oral squamous cell carcinoma (OSCC) is a heterogeneous malignancy originating from the oral mucosal epithelium. Detecting novel biomarkers can offer crucial information on disease aggressiveness and expected clinical outcomes for individual patients. SEC61G, an aberrantly expressed gene in various cancers, has been associated with negative clinical outcomes. However, its expression and clinical significance in OSCC is still unclear. In the present study, we investigated the SEC61G expression level in OSCC using bioinformatic and immunohistochemical analyses. Additionally, our findings revealed a significant correlation between SEC61G expression and clinicopathological characteristics, as well as a worse prognosis in OSCC patients. Notably, flow cytometry analysis on patient samples revealed that SEC61G expression was also linked to decreased immune infiltration in OSCC patients. In conclusion, our study provides evidence supporting SEC61G's role as a potential diagnostic, prognostic, and therapeutic marker in OSCC.

Effect of PTGES3 on the Prognosis and Immune Regulation in Lung Adenocarcinoma

Background

PTGES3 is upregulated in multiple cancer types and promotes tumorigenesis and progression. However, the clinical outcome and immune regulation of PTGES3 in lung adenocarcinoma (LUAD) are not fully understood. This study aimed to explore the expression level and prognostic value of PTGES3 and its correlation with potential immunotherapy in LUAD.

Methods

All data were obtained from several databases, including the Cancer Genome Atlas database. Firstly, gene and protein expression of PTGES3 were analyzed using Tumor Immune Estimation Resource (TIMER), R software, Clinical Proteomic Tumor Analysis Consortium (CPTAC), and Human Protein Atlas (HPA). Thereafter, survival analysis was conducted using the R software, Gene Expression Profiling Interactive Analysis 2 (GEPIA2), and Kaplan-Meier Plotter. In addition, gene alteration and mutation analyses were conducted using the cBio Cancer Genomics Portal (cBioPortal) and Catalog of Somatic Mutations in Cancer (COSMIC) databases. The molecular mechanisms associated with PTGES3 were assessed via Search Tool for the Retrieval of Interacting Genes/Proteins (STRING), GeneMANIA, GEPIA2, and R software. Lastly, the role of PTGES3 in immune regulation in LUAD was investigated using TIMER, Tumor-Immune System Interaction Database (TISIDB), and SangerBox.

Results

The gene and protein expression of PTGES3 were elevated in LUAD tissues and compared to the normal tissues, and the high expression of PTGES3 was correlated with cancer stage and tumor grade. Survival analysis revealed that overexpression of PTGES3 was associated with poor prognosis of LUAD patients. Moreover, gene alteration and mutation analysis revealed the occurrence of several types of PTGES3 gene alterations in LUAD. Moreover, co-expression analysis and cross-analysis revealed that three genes, including CACYBP, HNRNPC, and TCP1, were correlated and interacted with PTGES3. Functional analysis of these genes revealed that PTGES3 was primarily enriched in oocyte meiosis, progesterone-mediated oocyte maturation, and arachidonic acid metabolism pathways. Furthermore, we found that PTGES3 participated in a complex immune regulation network in LUAD.

Conclusion

The current study indicated the crucial role of PTGES3 in LUAD prognosis and immune regulation. Altogether, our results suggested that PTGES3 could serve as a promising therapeutic and prognosis biomarker for the LUAD.

Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single-cell resolution

Synthetic glucocorticoids, such as dexamethasone, have been used as a treatment for many immune conditions, such as asthma and, more recently, severe COVID-19. Single-cell data can capture more fine-grained details on transcriptional variability and dynamics to gain a better understanding of the molecular underpinnings of inter-individual variation in drug response. Here, we used single-cell RNA-seq to study the dynamics of the transcriptional response to glucocorticoids in activated peripheral blood mononuclear cells from 96 African American children. We used novel statistical approaches to calculate a mean-independent measure of gene expression variability and a measure of transcriptional response pseudotime. Using these approaches, we showed that glucocorticoids reverse the effects of immune stimulation on both gene expression mean and variability. Our novel measure of gene expression response dynamics, based on the diagonal linear discriminant analysis, separated individual cells by response status on the basis of their transcriptional profiles and allowed us to identify different dynamic patterns of gene expression along the response pseudotime. We identified genetic variants regulating gene expression mean and variability, including treatment-specific effects, and showed widespread genetic regulation of the transcriptional dynamics of the gene expression response.

Increased response to TPF chemotherapy promotes immune escape in hypopharyngeal squamous cell carcinoma

Background: There is an urgent need to identify which patients would benefit from TPF chemotherapy in hypopharyngeal squamous cell carcinoma (HPSCC) and to explore new combinations to improve the treatment effect. Materials and methods: Gene-expression profiles in 15 TPF-sensitive patients were compared to 13 resistant patients. Immunohistochemistry (IHC) was performed to detect CD8⁺ T cells in 28 samples. Patient-Derived Tumor Xenograft (PDX) model and IHC were used to verify markers that optimize treatment for HPSCC. Results: Through RNA sequencing 188 genes were up-regulated in TPF chemotherapy-resistant (CR) tissues were involved in T cell activation, while 60 down-regulated genes were involved in glycolysis. Gene set enrichment analysis (GSEA) showed that chemotherapy-sensitive (CS) group upregulation of the pathways of glycolysis, while immune response was downregulated. CIBERSORT, MCP-counter, and IHC proved that most immune cells including CD8⁺ T cells in the CR significantly higher than that in CS group. Among the 16 up-regulated genes in CS had close associations, the most significant negative correlation between the gene level and CD8⁺ T cells existed in SEC61G. SEC61G was related to glycolysis, which was transcriptionally regulated by E2F1, and participated in antigen degradation through ubiquitin-dependent protein catabolic process. Palbociclib, combined with Cetuximab decreased the tumor burden and significantly suppressed the expression of E2F1 and SEC61G while activating MHC-I in PDX model. Conclusion: Enhanced glycolysis promoted immune escape, but increased response to TPF chemotherapy. SEC61G was the center of the molecular network and targeting the E2F1/SEC61G pathway increased the expression level of MHC-I.

NUTF2 as a Prognostic Indicator and Potential Therapeutic Target in Head and Neck Squamous Cell Carcinoma

Aim: To identify genes associated with the prognosis of head and neck squamous cell carcinoma (HNSC) and potential molecular targets for therapy. Materials and Methods: Gene Expression Profiling Interactive Analysis, Human Protein Atlas, University of ALabama at Birmingham CANcer, LinkedOmics, cBioPortal, Cell Counting Kit 8, and polymerase chain reaction were used in this study. Results: The expression level of nuclear transport factor 2 (NUTF2) was elevated in HNSC tissues and was associated with poor prognosis in HNSC patients. NUTF2-targeted intervention inhibited the proliferation of HNSC cells. SEC61G, which was positively correlated with NUTF2, was decreased in HNSC cells with NUTF2 suppression. Conclusions: NUTF2 may be correlated with the prognosis and development of HNSC, laying the foundation for future studies on the potential role of NUTF2 in HNSC.

Comprehensive Analysis of the Role of SLC2A3 on Prognosis and Immune Infiltration in Head and Neck Squamous Cell Carcinoma

Background. SLC2A3 is upregulated in various cancer types and promotes proliferation, invasion, and metabolism. However, its role in the prognosis and immune regulation of head and neck squamous cell carcinoma (HNSCC) is still obscure. This study is aimed at exploring the prognostic and immunotherapeutic potential of SLC2A3 in HNSCC. Methods. All data were downloaded from TCGA database and integrated via R software. SLC2A3 expression was evaluated using R software, TIMER, CPTAC, and HPA databases. The association between SLC2A3 expression and clinicopathologic characteristics was assessed by R software. The effect of SLC2A3 on survival was analyzed by R software and Kaplan-Meier Plotter. Genomic alterations in SLC2A3 were investigated using the cBioPortal database. Coexpression of SLC2A3 was studied using LinkedOmics and STRING, and enrichment analyses were performed with R software. The relationship between SLC2A3 expression and immune infiltration was determined using TIMER and TISIDB databases. Immune checkpoints and ESTIMATE score were analyzed via the SangerBox database. Results. SLC2A3 expression was upregulated in HNSCC tissues compared to normal tissues. It was significantly related to TNM stage, histological grade, and alcohol history. High SLC2A3 expression was associated with poor prognosis in HNSCC. Coexpression analysis indicated that SLC2A3 mostly participated in the HIF-1 signaling pathway and glycolysis. Furthermore, SLC2A3 expression strongly correlated with tumor-infiltrating lymphocytes in HNSCC. Conclusion. SLC2A3 could serve as a potential prognostic biomarker for tumor immune infiltration in HNSCC.

DDX59-AS1 is a prognostic biomarker and correlated with immune infiltrates in OSCC

Background: lncRNAs play a critical role in multiple steps of gene regulation associated with tumor progression. However, the engagement of DDX59-AS1, a lncRNA, remains equivocal, particularly in oral squamous cell carcinoma (OSCC). In this study, the expression of DDX59-AS1 and its association with immune infiltration were investigated, and its prognostic value in OSSC was evaluated.

Methods: OSCC patients were collected from The Cancer Genome Atlas (TCGA) database. The expression of DDX59-AS1 in OSCC and healthy tissue was compared using Wilcoxon rank sum test. The relationship between DDX59-AS1 and clinicopathological features was analyzed using Logistic regression. Gene ontology (GO) terminology analysis, gene set enrichment analysis (GSEA), and single sample GSEA (ssGSEA) were utilized to interpret the enrichment pathway and functionality and to quantify the immune cell infiltration of DDX59-AS1. The correlation between survival and DDA59-AS1 was evaluated by Kaplan-Meier analysis and Cox regression. The prognostic impact of DDX59-AS1 was predicted by the nomogram based on Cox multivariate analysis.

Results: High expression of DDX59-AS1 was significantly correlated with T stage, clinical stage, race, and age (p < 0.05). Multivariate survival analysis demonstrated that the high expression of DDX59-AS1 was associated with lower overall and specific survival rates. The prognosis prediction was validated by the nomogram and calibration curves. The expression of DDX59-AS1 was negatively correlated with Mast cells, Tfh, T cells, Treg, and B cells, and positively related with the Tgd infiltration level.

Conclusion: DDX59-AS1 played a crucial role in the progression and prognosis of OSCC and was potentially a predictive biomarker for OSCC.

DCBLD1 Overexpression Is Associated With a Poor Prognosis in Head and Neck Squamous Cell Carcinoma

Background

DCBLD1 is highly expressed in several kinds of cancer and plays a potential prognostic factor. However, the prognostic value and immune infiltration in head and neck squamous cell carcinoma remain unclear and need further research.

Materials and Methods

DCBLD1 expression and clinical information were obtained from the Cancer Genome Atlas (TCGA) database. The mRNA level in cell lines (SCC25 and CAL27) and gingival fibroblasts were detected using quantitative PCR. Cox regression analysis was used to evaluate the prognostic values of DCBLD1 and clinical data in HNSCC. A nomogram was also established to predict the impact of DCBLD1 on prognosis based on Cox multivariate results. The methylation level of DCBLD1 in HNSC and its prognosis were analyzed in UALACN and MethSurv. Finally, the potential biological functions of DCBLD1 were investigated using gene set enrichment analysis (GSEA) and single-sample GSEA (ssGSEA).

Results

The mRNA and protein expression levels of DCBLD1 were highly expressed in HNSCC tissue and cell lines. The Cox analyses demonstrate that highly expressed DCBLD1 is an independent prognosis marker (p < 0.05). ROC curve analysis showed the performance of DCBLD1 (area under the ROC curve: 0.948, sensitivity: 93.2%, specificity: 84.7%). The methylation was increased in HNSCC patients compared with normal subjects (p < 0.05) and was associated with poor prognosis at sites cg27642470 and cg21104965. Additionally, DCBLD1 expression is poorly associated with immune cell infiltration and immunological checkpoints PD-L1 and TIM-3.

Conclusion

In head and neck squamous cell carcinoma, DCBLD1 is overexpressed, associated with poor patient prognosis. The detailed underlying mechanism merits further research.

SEC61G participates in endoplasmic reticulum stress by interacting with CREB3 to promote the malignant progression of lung adenocarcinoma

As the most common type of lung cancer, lung adenocarcinoma (LUAD) poses a great threat to human health worldwide and severely compromises the quality of life of the patients. The present study aimed to explore the potential pathogenesis of LUAD. Reverse transcription-quantitative PCR and western blotting were applied to measure the expression levels of SEC61 translocon subunit γ (SEC61G) and cyclic AMP-responsive element-binding protein 3 (CREB3). Western blotting was also used to determine the expression of endoplasmic reticulum (ER) stress-, apoptosis- and migration-related proteins. Cell Counting Kit-8, colony formation, TUNEL, wound healing and Transwell assays were used, respectively, to determine the viability, proliferation, apoptosis, migration and invasion of LUAD A549 cells. The association between SEC61G and CREB3 was verified by co-immunoprecipitation assay. The results revealed that SEC61G was upregulated in A549 cells and its downregulation could activate ER stress. It was also found that silencing SEC61G inhibited the malignant development of LUAD through ER stress. In addition, SEC61G was verified to participate in ER stress in LUAD via CREB3 and silencing SEC61G exerted inhibitory effects on the malignant progression of LUAD by regulating CREB3. In summary, SEC61G participated in ER stress and its knockdown exerted inhibitory effects on A549 cells via regulating CREB3, which suggests that SEC61G may be a potential therapy for patients with LUAD.

Salivary Metabolomics for Prognosis of Oral Squamous Cell Carcinoma

This study aimed to identify salivary metabolomic biomarkers for predicting the prognosis of oral squamous cell carcinoma (OSCC) based on comprehensive metabolomic analyses. Quantified metabolomics data of unstimulated saliva samples collected from patients with OSCC (n = 72) were randomly divided into the training (n = 35) and validation groups (n = 37). The training data were used to develop a Cox proportional hazards regression model for identifying significant metabolites as prognostic factors for overall survival (OS) and disease-free survival. Moreover, the validation group was used to develop another Cox proportional hazards regression model using the previously identified metabolites. There were no significant between-group differences in the participants’ characteristics, including age, sex, and the median follow-up periods (55 months [range: 3–100] vs. 43 months [range: 0–97]). The concentrations of 5-hydroxylysine (p = 0.009) and 3-methylhistidine (p = 0.012) were identified as significant prognostic factors for OS in the training group. Among them, the concentration of 3-methylhistidine was a significant prognostic factor for OS in the validation group (p = 0.048). Our findings revealed that salivary 3-methylhistidine is a prognostic factor for OS in patients with OSCC.

Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single cell resolution.. [PMID: 35313584 PMCID: PMC8936121 DOI: 10.1101/2021.09.30.462672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Synthetic glucocorticoids, such as dexamethasone, have been used as treatment for many immune conditions, such as asthma and more recently severe COVID-19. Single cell data can capture more fine-grained details on transcriptional variability and dynamics to gain a better understanding of the molecular underpinnings of inter-individual variation in drug response. Here, we used single cell RNA-seq to study the dynamics of the transcriptional response to glucocorticoids in activated Peripheral Blood Mononuclear Cells from 96 African American children. We employed novel statistical approaches to calculate a mean-independent measure of gene expression variability and a measure of transcriptional response pseudotime. Using these approaches, we demonstrated that glucocorticoids reverse the effects of immune stimulation on both gene expression mean and variability. Our novel measure of gene expression response dynamics, based on the diagonal linear discriminant analysis, separated individual cells by response status on the basis of their transcriptional profiles and allowed us to identify different dynamic patterns of gene expression along the response pseudotime. We identified genetic variants regulating gene expression mean and variability, including treatment-specific effects, and demonstrated widespread genetic regulation of the transcriptional dynamics of the gene expression response.