Decreased Interferon Alpha/Beta Signature Associated with Human Lung Tumorigenesis

FAM65A promotes the progression and growth of lung squamous cell carcinoma in vivo and vitro

BACKGROUNDS

Currently, family with sequence similarity 65 member A (FAM65A) is reported as a pivotal regulator in various cancers. However, the effect of FAM65A in lung squamous cell carcinoma (LSCC) is still unclear, the prime objective of this research is to explore the role of FAM65A in LSCC.

METHODS

Gene expression data and correlated clinical information were downloaded from the public database and the expression of FAM65A was detected. The expression of FAM65A was also detected in our collected clinical samples and LSCC cell lines. Survival package of R language was used to determine the survival significance of FAM65A. Proteins expression level was determined via western blot assay. Cell function experiments and in vivo experiments were performed to explore the effect of FAM65A on LSCC cell biological behaviors.

RESULTS

FAM65A expression was significantly increased in LSCC clinical samples and cell lines. High FAM65A expression predicted poor prognosis in LSCC patients. After silencing FAM65A, the ability of LSCC cell proliferation, invasion and migration was decreased, and LSCC cell cycle was blocked. Moreover, in vivo experiments revealed that silencing FAM65A could inhibit LSCC cell proliferation.

CONCLUSIONS

High FAM65A expression could enhance proliferative, invasive and migratory abilities of LSCC. FAM65A might be a novel biomarker of LSCC.

Therapeutic Targeting of EZH2 and BET BRD4 in Pediatric Rhabdoid Tumors

Aberrant activity of the H3K27 modifiers EZH2 and BRD4 is an important oncogenic driver for atypical teratoid/rhabdoid tumor (AT/RT), and each is potentially a possible therapeutic target for treating AT/RT. We, therefore, determined whether targeting distinct histone modifier activities was an effective approach for treating AT/RT. The effects of EZH2 and BRD4 inhibition on histone modification, cell proliferation, and cell invasion were analyzed by immunoblotting, MTS assay, colony formation assay, and cell invasion assay. RNA- and chromatin immunoprecipitation-sequencing were used to determine transcriptional and epigenetic changes in AT/RT cells treated with EZH2 and BRD4 inhibitors. We treated mice bearing human AT/RT xenografts with EZH2 and BRD4 inhibitors. Intracranial tumor growth was monitored by bioluminescence imaging, and the therapeutic response was evaluated by animal survival. AT/RT cells showed elevated levels of H3K27 trimethylation (H3K27me3) and H3K27 acetylation (H3K27ac), with expression of EZH2 and BRD4, and lack of SMARCB1 proteins. Targeted inhibition of EZH2 and BRD4 activities reduced cell proliferation and invasiveness of AT/RT in association with decreasing H3K27me3 and H3K27ac. Differential genomic occupancy of H3K27me3 and H3K27ac regulated specific gene expression in response to EZH2 and BRD4 inhibitions. A combination of EZH2 and BRD4 inhibition increased the therapeutic benefit in vitro and in vivo, outperforming either monotherapy. Overall, histones H3K27me3 and H3K27ac were elevated in AT/RT cells and distributed in distinct chromatin regions to regulate specific gene expression and to promote AT/RT growth. Targeting EZH2 and BRD4 activity is, therefore, a potential combination therapy for AT/RT.

Increased PPARD Expression May Play a Protective Role in Human Lung Adenocarcinoma and Squamous Cell Carcinoma

Peroxisome proliferator-activated receptor-δ, encoded by gene PPARD, is overexpressed in a majority of human lung cancer subtypes, but its role in the tumor progression remains poorly understood. We have analyzed the expression of PPARD in lung adenocarcinoma (LA) and squamous cell carcinoma (LSCC) datasets. The potential roles of PPARD in the pathological development of LA and LSCC were explored through literature-based pathway analysis and pathway enrichment analysis. In all LA datasets ( $N=11$ ) and in seven out of nine LSCC studies, the levels of PPARD were increased as compared to control tissues (log-fold changes were $0.37\pm 0.20$ and $0.10\pm 0.37$ for LA and LSCC, respectively). On average, the expression levels of PPARD in LA were higher than those in LSCC ( $p=0.036$ ). Pathway analysis showed that the overexpression of PPARD might play both positive and negative roles in the development of both LA and LSCC. Specifically, PPARD inhibits seven LSCC promoters and seven LA promoters and activates one LSCC inhibitor and another LA inhibitor. However, PPARD also activates six and one promoters of LA and LSCC, respectively, which would facilitate the development of LA/LSCC. Our results suggested a mixed role of PPARD in LA/LSCC, which may add new insights into the understanding of the PPARD-lung cancer relationship.

Identification of Immune Subtypes of Lung Squamous Cell Carcinoma by Integrative Genome-Scale Analysis

Background

Characterization of the tumor microenvironment is helpful to understand the tumor immune environment of lung cancer and help predict the prognosis.

Methods

First, immune subtypes were identified by consensus subtype among lung squamous carcinoma (LUSC) patients. Immune cell infiltration was evaluated by CIBERSORT and ESTIMATE analyses. Then, based on differentially expressed genes (DEGs) identified, a risk score model was constructed. Finally, gene FPR1 was validated by using YTMLC-90.

Findings

LUSC samples were divided into four heterogeneous immune subtypes, with significantly different prognoses with subtype 4 having the poorest overall survival (OS). The immune infiltration score showed that subtype 4 was characterized as immune enriched and fibrotic, while subtype 3 was tumor enriched. DEG analysis showed that upregulated genes in subtype 4 were enriched of neutrophil and exhausted T cell-related biological processes. Based on a univariate Cox regression model, prognostic 7 immune-related genes were combined to construct a risk score model and able to predict OS rates in the validation datasets. Wound healing and transwell assay were conducted to evaluate the invasion property after activating the gene FPR1.

Interpretation

The analysis of tumor immune microenvironments among LUSC subtypes may provide new insights into the strategy of immunotherapy.

The bioinformatics analysis of RIOX2 gene in lung adenocarcinoma and squamous cell carcinoma

Lung cancer is characterized by high morbidity and mortality rates, and it has become an important public health issue worldwide. The occurrence and development of tumors is a multi-gene and multi-stage complex process. As an oncogene, ribosomal oxygenase 2 (RIOX2) has been associated with a variety of cancers. In this article, we analyzed the correlation between RIOX2 expression and methylation in lung cancer based on the databases including the cancer genome atlas (TCGA) (https://portal.gdc.cancer.gov/) and the gene expression omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/). It was found that RIOX2 is highly expressed in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) tissues, whose expression is negatively correlated with its methylation level. In this regard, methylation at cg09716038, cg14773523, cg14941179, and cg22299097 had a significant negative correlation with RIOX2 expression in LUAD, whereas in LUSC, methylation at cg09716038, cg14773523, cg14941179, cg22299097, cg05451573, cg10779801, and cg23629183 is negatively correlated with RIOX2 expression. According to the analysis based on the databases, RIOX2 gene could not be considered as the independent prognostic biomarker in lung adenocarcinoma or squamous cell lung cancer. However, the molecular mechanism of RIOX2 gene in the development of lung cancer may be helpful in improving lung cancer therapy.

Association of Cigarette Smoking, COPD, and Lung Cancer With Expression of SARS-CoV-2 Entry Genes in Human Airway Epithelial Cells

SARS-CoV-2 enters into human airway epithelial cells via membrane fusion or endocytosis, and this process is dependent on ACE2, TMPRSS2, and cathepsin L. In this study, we examined the expression profiles of the three SARS-CoV-2 entry genes in primary human airway epithelial cells isolated from smokers, non-smokers, patients with chronic obstructive pulmonary disease or lung cancer. An exhaustive search of the GEO database was performed to identify eligible data on 1st June 2020. In total, 46 GEO datasets comprising transcriptomic data of 3,053 samples were identified as eligible data for further analysis. All meta-analysis were performed using RStudio. Standardized mean difference was utilized to assess the effect size of a factor on the expression of targeted genes and 95% confidence intervals (CIs) were calculated. This study revealed that (i) cigarette smoking is associated with an increased expression of ACE2 and TMPRSS2 and a decreased expression of cathepsin L; (ii) significant alternations in expression of ACE2, TMPRSS2, and cathepsin L were observed between current smokers and former smokers, but not between former smokers and never smokers; (iii) when compared with healthy controls with identical smoking status, patients with COPD or lung cancer showed negligible changes in expression of ACE2, TMPRSS2, and cathepsin L. Therefore, this study implicates cigarette smoking might contribute to the development of COVID-19 by affecting the expression of SARS-CoV-2 entry genes, while smoking cessation could be effective to reduce the potential risk.

Analyses of multi-omics differences between patients with high and low PD1/PDL1 expression in lung squamous cell carcinoma

BACKGROUND

Immunotherapy has achieved excellent results in patients with lung squamous cell carcinoma. However, in which population it can exert the greatest effect is still unknown. Some studies have suggested that its effect is related to the expression level of PD1. Analyzing the relationship between PD1 expression level and genetic differences in lung squamous cell carcinoma patients will be helpful in understanding the underlying causes of this immunotherapy effect and provide a reference for clinical practice.

METHODS

In this study, we used RNA-seq, miRNA-seq, methylation array, mutation profiles, and copy number variation data from the TCGA database and RNA-seq data from the GEO database to analyze the distinctive genomic patterns associated with PD1 and PDL1 expression. RNA-seq data from 44 LUSC patients who underwent surgery at Zhongshan Hospital were also included in the study.

RESULTS

After grouping LUSC patients according to the expression levels of PD1 and PDL1, we found no significant difference in survival between the two groups. However, 178 genes, including IL-21, KLRC3, and KLRC4, were significantly upregulated in both the TCGA and GEO databases in the high expression group, and there was a precise correlation between gene expression and epigenetic changes in the two groups. At the same time, the overall level of somatic mutations was not significantly different between the two groups. It is worth noting that the gene enrichment results showed that the differential pathways were mainly enriched in immune regulation, especially T cell-related immune activities.

CONCLUSION

We found that the differences in gene expression between the two groups were related to immunity, which may affect the effectiveness of immunotherapy. We hope our results can provide a reference for further research and help in finding other targets to improve the efficacy of immunotherapy.

Villi development core-related gene expression associated with lung squamous cancer prognosis

Similarities between embryonic development and tumorigenesis are reflected in biological behavior and gene expression. Although the gene signature during development and the clinical phenotype of different cancers show certain correlation pattern, the correlation between early embryo development and cancer remains largely unexplored. To compare the gene expression profile between development and cancer, our study analyzed the gene expression of chorionic villi samples at different gestational ages (6, 7, 8, 9, 10, 40 weeks) obtained from gene expression omnibus (GEO) datasets using correlation test. Then the villi development-related genes that gradually showed a positive correlation (upregulated) (n = 394) or negative correlation (downregulated) (n = 325) with time were used to construct protein-protein interaction (PPI) networks. Three subnetworks among the gradually upregulated genes and 3 subnetworks among the downregulated genes were identified using the molecular complex detection (MCODE) plugin in Cytoscape software. The most significant GO terms for villi-correlated genes were immune, inflammatory response and cell division. These gene clusters were also dysregulated in lung squamous cell carcinoma (SCC). Moreover the prognostic value of the gene clusters was then analyzed with TCGA lung SCC data, which showed 4 clusters that were associated with prognosis. Our results demonstrate the gene expression similarity between development and lung SCC and identified development-associated gene clusters that could contain prognostic information for lung SCC patients.

Clinical Significance of Serum Type III Interferons in Patients with Gastric Cancer

Type III interferon (IFN) is a newly established IFN that shows roles different from those of type I and II IFNs. However, the effect of type III IFN on the prognosis of patients with gastric cancer (GC) is controversial. This study aimed to investigate the effects of serum IFN-α, IFN-β, IFN-γ, IFN-λ1, and IFN-λ2/3 levels on the survival of patients with GC. LEGENDplex bead-based immunoassays were used to analyze the serum IFN-α, IFN-β, IFN-γ, IFN-λ1, and IFN-λ2/3 levels in patients with GC and healthy volunteers. Flow cytometry was used to test the IFN concentrations. Compared with the healthy controls, the patients with GC had significantly decreased serum IFN-α, IFN-γ, and IFN-λ1 levels, but significantly increased serum IFN-λ2/3 level. Analysis of the serum IFN concentrations and clinical parameters of the patients with GC showed significant correlations of serum IFN-α, IFN-β, IFN-γ, and IFN-λ2/3 levels with clinical stages. Serum IFN-λ1 levels significantly correlated with tumor location, histopathology, and lymph node involvement. Serum IFN-λ2/3 levels significantly correlated with lymph node involvement and distant metastasis. In addition, serum IFN-α, IFN-β, and IFN-γ levels significantly correlated with clinical stage and lymph node metastasis. Serum IFN-β and IFN-γ levels also significantly correlated with Lauren classification. Furthermore, the patients with stage IV GC exhibited significantly lower IFN-λ2/3 levels and higher IFN-α, IFN-β, and IFN-γ levels than the patients with stage I-III GC. The univariate analysis revealed that tumor sizes of >5 cm, higher clinical stage, and high IFN-λ2/3 level were significantly associated with poor prognosis. This study shows the relationship between serum IFN level and GC progression. High serum IFN-λ2/3 levels were associated with poor prognosis and could be a novel biomarker for evaluating GC progression and predicting the outcomes of nonmetastatic GC.

Proliferation genes in lung development associated with the prognosis of lung adenocarcinoma but not squamous cell carcinoma

There are many similarities between embryonic development and tumorigenesis, and gene expression profiles show that certain correlations exist between the gene signature during development and the clinical phenotypes of different cancers. Our group previously reported the gene expression profiles of human lung development, and the expression of one group of proliferation-related genes (PTN1 genes) steadily decreased during lung development. Here, we examined the prognostic value of PTN1 genes in 5 independent lung adenocarcinoma (ADC) and 5 lung independent squamous cell carcinoma (SCC) microarray datasets and found that the expression levels of PTN1 genes were associated with survival in lung ADC but not lung SCC. All of the lung ADC datasets contained a set of highly correlated genes from PTN1 genes, but the lung SCC datasets had no similar set of genes. We identified 63 unique core genes from the PTN1 genes in the 5 lung ADC datasets: 17 of these core genes appeared in at least 4 of the lung ADC datasets, and the 17 corresponding proteins clearly interacted more strongly with each other in lung ADC than in lung SCC. Moreover, 16 of the 17 core genes play major roles in the G₂ /M phase of the cell cycle. These data indicate that proliferation-related genes in lung development have a significant prognostic value for lung ADC; the synergistic effects of the 17 core genes play an important role in lung ADC prognosis. These genes may have significant clinical implications for the treatment and prognosis of lung ADC.