SPOCK2 Serves as a Potential Prognostic Marker and Correlates With Immune Infiltration in Lung Adenocarcinoma

The novel prognostic marker SPOCK2 regulates tumour progression in melanoma

Secreted protein acidic and cysteine rich/osteonectin, cwcv and kazal-like domain proteoglycan 2 (SPOCK2) is a protein that regulates cell differentiation and growth. Recent studies have reported that SPOCK2 plays important roles in the progression of various human cancers; however, the role of SPOCK2 in melanoma remains unknown. Therefore, this study investigated the roles of SPOCK2 and the related mechanisms in melanoma progression. To evaluate the clinical significance of SPOCK2 expression in patients with melanoma, we analysed the association between SPOCK2 expression and its prognostic value for patients with melanoma using systematic multiomic analysis. Subsequently, to investigate the roles of Spock2 in melanoma progression in vitro and in vivo, we knocked down Spock2 in the B16F10 melanoma cell line. High SPOCK2 levels were positively associated with good prognosis and long survival rate of patients with melanoma. Spock2 knockdown promoted melanoma cell proliferation by inducing the cell cycle and inhibiting apoptosis. Moreover, Spock2 downregulation significantly increased cell migration and invasion by upregulating MMP2 and MT1-MMP. The increased cell proliferation and migration were inhibited by MAPK inhibitor, and ERK phosphorylation was considerably enhanced in Spock2 knockdown cells. Therefore, Spock2 could function as a tumour suppressor gene to regulate melanoma progression by regulating the MAPK/ERK signalling pathway. Additionally, Spock2 knockdown cell injection induced considerable tumour growth and lung metastasis in C57BL6 mice compared to that in the control group. Our findings suggest that SPOCK2 plays crucial roles in malignant progression of melanoma and functions as a novel therapeutic target of melanoma.

SPOCK2 modulates neuropathic pain by interacting with MT1-MMP to regulate astrocytic MMP-2 activation in rats with chronic constriction injury

BACKGROUND

Neuropathic pain (NP) is a kind of intractable pain. The pathogenesis of NP remains a complicated issue for pain management practitioners. SPARC/osteonectin, CWCV, and Kazal-like domains proteoglycan 2 (SPOCK2) are members of the SPOCK family that play a significant role in the development of the central nervous system. In this study, we investigated the role of SPOCK2 in the development of NP in a rat model of chronic constriction injury (CCI).

METHODS

Sprague-Dawley rats were randomly grouped to establish CCI models. We examined the effects of SPOCK2 on pain hpersensitivity and spinal astrocyte activation after CCI-induced NP. Paw withdrawal threshold (PWT) and paw withdrawal latency (PWL) were used to reflects the pain behavioral degree. Molecular mechanisms involved in SPOCK2-mediated NP in vivo were examined by western blot analysis, immunofluorescence, immunohistochemistry, and co-immunoprecipitation. In addition, we examined the SPOCK2-mediated potential protein-protein interaction (PPI) in vitro coimmunoprecipitation (Co-IP) experiments.

RESULTS

We founded the expression level of SPOCK2 in rat spinal cord was markedly increased after CCI-induced NP, while SPOCK2 downregulation could partially relieve pain caused by CCI. Our research showed that SPOCK2 expressed significantly increase in spinal astrocytes when CCI-induced NP. In addition, SPOCK2 could act as an upstream signaling molecule to regulate the activation of matrix metalloproteinase-2 (MMP-2), thus affecting astrocytic ERK1/2 activation and interleukin (IL)-1β production in the development of NP. Moreover, in vitro coimmunoprecipitation (Co-IP) experiments showed that SPOCK2 could interact with membrane-type 1 matrix metalloproteinase (MT1-MMP/MMP14) to regulate MMP-2 activation by the SPARC extracellular (SPARC_EC) domain.

CONCLUSIONS

Research shows that SPOCK2 can interact with MT1-MMP to regulate MMP-2 activation, thus affecting astrocytic ERK1/2 activation and IL-1β production to achieve positive promotion of NP.

Pan-cancer analysis of PLAU indicates its potential prognostic value and correlation with neutrophil infiltration in BLCA

BACKGROUND

PLAU is known as a selected serine protease converting plasminogen to plasmin. The role of PLAU in the development of pan-cancer, especially bladder urothelial carcinoma (BLCA) remains unclear.

METHOD

A variety of online tools and cancer databases, including TCGA, GETx, HPA database, GSCALite, UALCAN, ESTIMATE, CIBERSORT, ssGSEA algorithms and SangerBox website, were applied to investigate the associations between PLAU expression and prognosis, genetic alterations, pathway activation, and tumor immunity in pan-cancer. Through cBioPortal and STITCH platforms, the oncogenic role of PLAU and related targeting medicines in BLCA were also explored. We verified the expression of PLAU in pan-cancer cells and its function in bladder cancer cell lines using wet-lab experiments.

RESULTS

PLAU expression levels were significantly higher in most cancer tissues. PLAU had a certain accuracy in the diagnosis of various types of cancers (90 % AUC > 0.700). In BLCA, PLAU has abundant methylated sites and showed statistical differences in clinical features. PLAU was involved in tumor immune infiltration, and especially positively correlated with neutrophil infiltration. High-expressed PLAU indicated poorer prognosis in the BLCA patients receiving Atezolizumab. A high mRNA and protein expression levels of PLAU were observed in pan-cancer cell lines, especially BLCA cells. Knockdown of PLAU inhibited the invasive, proliferative, and aggressive phenotypes of bladder cancer cells. Immunohistochemical staining validated PLAU's higher expression in BLCA tissues than in adjacent non-cancerous tissues. And overexpression of PLAU was associated with more advanced TNM stage, and high infiltrating depth.

CONCLUSION

Our study revealed that PLAU can serve as a potential therapeutic target and prognostic marker for various malignancies, especially BLCA.

Identification of BANF1 as a novel prognostic biomarker in gastric cancer and validation via in-vitro and in-vivo experiments

Gastric cancer (GC) is a widespread malignancy characterized by a notably high incidence rate and an unfavorable prognosis. We conducted a meticulous analysis of GC high-throughput sequencing data downloaded from the Gene Expression Omnibus (GEO) repository to pinpoint distinctive genes associated with GC. Our investigation successfully identified three signature genes implicated in GC, with a specific focus on the barrier to autointegration factor 1 (BANF1), which exhibits elevated expression across various cancer types, including GC. Bioinformatic analysis has highlighted BANF1 as a prognostic indicator for patients with GC, with direct implications for immune cell infiltration. To gain a more comprehensive understanding of the significance of BANF1 in GC, we performed a series of in vitro experiments to confirm its high expression in GC tissues and cellular components. Intriguingly, the induction of BANF1 knockdown resulted in a marked attenuation of proliferation, migratory capacity, and invasive potential in GC cells. Moreover, our in vivo experiments using nude mouse models revealed a notable impediment in tumor growth following BANF1 knockdown. These insights underscore the feasibility of BANF1 as a novel therapeutic target for GC.

Dickkopf-related protein 1 as a biomarker of local immune status and worse prognosis of Oral squamous cell carcinoma

BACKGROUND

Oral squamous cell carcinoma (OSCC) is an infiltrative malignancy characterized by a significantly elevated recurrence rate. Dickkopf-related protein 1 (DKK1), which plays an oncogene role in many cancers, acts as an inhibitor of the Wingless protein (Wnt) signaling pathway. Currently, there is a lack of consensus regarding the role of DKK1 in OSCC or its clinical significance.

OBJECTIVE

To examine the role and effect of DKK1 in OSCC.

METHODS

The identification of differentially expressed genes (DEGs) in OSCC was conducted by utilizing databases such as The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). A comprehensive analysis of gene expression profile interactions (GEPIA) and Kaplan-Meier curve were conducted to investigate the associations among DEGs, patient survival and prognosis in individuals with OSCC. The biological function of DKK1 in OSCC was investigated by using molecular biology approaches.

RESULTS

The expression of DKK1 was found to be upregulated in OSCC tissues at various stages. High levels of DKK1 expression exhibited a positive correlation with the overall survival (OS) and progression-free survival (PFS) rates among OSCC patients. DKK1 knockdown suppressed the proliferation and induced apoptotic response in OSCC cells. Moreover, DKK1 exerted a positive regulatory effect on HMGA2 expression, thereby modulating cell growth and apoptosis in OSCC. The expression of DKK1 was found to be positively correlated with the infiltration of immune cells in patients with OSCC. Additionally, higher levels of CD4 + T cells were associated with improved 5-year survival rates.

CONCLUSION

DKK1 is a prognostic biomarker for patients with OSCC.

Bioinformatics-based analysis of the roles of basement membrane-related gene AGRN in systemic lupus erythematosus and pan-cancer development

Introduction

Systemic lupus erythematosus (SLE) is an autoimmune disease involving many systems and organs, and individuals with SLE exhibit unique cancer risk characteristics. The significance of the basement membrane (BM) in the occurrence and progression of human autoimmune diseases and tumors has been established through research. However, the roles of BM-related genes and their protein expression mechanisms in the pathogenesis of SLE and pan-cancer development has not been elucidated.

Methods

In this study, we applied bioinformatics methods to perform differential expression analysis of BM-related genes in datasets from SLE patients. We utilized LASSO logistic regression, SVM-RFE, and RandomForest to screen for feature genes and construct a diagnosis model for SLE. In order to attain a comprehensive comprehension of the biological functionalities of the feature genes, we conducted GSEA analysis, ROC analysis, and computed levels of immune cell infiltration. Finally, we sourced pan-cancer expression profiles from the TCGA and GTEx databases and performed pan-cancer analysis.

Results

We screened six feature genes (AGRN, PHF13, SPOCK2, TGFBI, COL4A3, and COLQ) to construct an SLE diagnostic model. Immune infiltration analysis showed a significant correlation between AGRN and immune cell functions such as parainflammation and type I IFN response. After further gene expression validation, we finally selected AGRN for pan-cancer analysis. The results showed that AGRN's expression level varied according to distinct tumor types and was closely correlated with some tumor patients' prognosis, immune cell infiltration, and other indicators.

Discussion

In conclusion, BM-related genes play a pivotal role in the pathogenesis of SLE, and AGRN shows immense promise as a target in SLE and the progression of multiple tumors.

Proteogenomic data and resources for pan-cancer analysis

The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigates tumors from a proteogenomic perspective, creating rich multi-omics datasets connecting genomic aberrations to cancer phenotypes. To facilitate pan-cancer investigations, we have generated harmonized genomic, transcriptomic, proteomic, and clinical data for >1000 tumors in 10 cohorts to create a cohesive and powerful dataset for scientific discovery. We outline efforts by the CPTAC pan-cancer working group in data harmonization, data dissemination, and computational resources for aiding biological discoveries. We also discuss challenges for multi-omics data integration and analysis, specifically the unique challenges of working with both nucleotide sequencing and mass spectrometry proteomics data.

SPOCK2 gene expression is downregulated in pancreatic ductal adenocarcinoma cells and correlates with prognosis of patients with pancreatic cancer

OBJECTIVES

Pancreatic ductal adenocarcinoma (PDAC) represents a widespread form of malignant pancreatic neoplasms and a leading oncologic cause of death in Europe and the USA. Despite advances in understanding its molecular biology, the 5-year survival rate remains low at 10%. The extracellular matrix in PDAC contains proteins, including SPOCK2, which are essential for tumorigenicity and drug resistance. The present study aims to explore the possible role of SPOCK2 in the pathogenesis of PDAC.

MATERIALS AND METHODS

Expression of SPOCK2 was evaluated in 7 PDAC cell lines and 1 normal pancreatic cell line using quantitative RT-PCR. Demethylation of the gene was carried out using 5-aza-2'-deoxycytidine (5-aza-dC) treatment with subsequent validation Western Blot analysis. In vitro downregulation of SPOCK2 gene was performed using siRNA transfection. MTT and transwell assays were employed to evaluate the impact of the SPOK2 demethylation on the proliferation and migration of PDAC cells. KM Plotter was applied to analyze a correlation between SPOCK2 mRNA expression and the survival of PDAC patients.

RESULTS

In contrast to the normal pancreatic cell line, SPOCK2 expression was significantly downregulated in PDAC cell lines. Treatment with 5-aza-dC, led to increase in SPOCK2 expression in the cell lines tested. Importantly, compared with control cells, transfected with SPOCK2 siRNA cells exhibited increased growth rates and more migration ability. Finally, we demonstrated that a high SPOCK2 expression level correlated with longer overall survival of patients with PDAC.

CONCLUSION

The expression of SPOCK2 is downregulated in PDAC as a result of hypermethylation of its corresponding gene. SPOCK2 expression as well as the demethylation of its gene could be a potential marker for PDAC.

SPOCK2 and SPRED1 function downstream of EZH2 to impede the malignant progression of lung adenocarcinoma in vitro and in vivo

Enhancer of zeste homolog 2 (EZH2) is an important epigenetic regulator, and is associated with the malignant progression of lung cancer. However, the mechanisms of EZH2 on lung adenocarcinoma (LUAD) remain unclear. The relationship between EZH2 and SPOCK2 or SPRED1 was confirmed by dual-luciferase reporter assay. The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were analyzed to examine the expression of SPOCK2 and SPRED1 and their prognostic values of LUAD. The effects of SPOCK2 and SPRED1 on the biological characters of LUAD cells were identified on functional assays in vitro and in vivo. Our results showed that EZH2 suppressed the expression and transcriptional activity of SPOCK2 and SPRED1, and these effects were reversed by the EZH2 inhibitor, Tazemetostat. SPOCK2 and SPRED1 were expressed at low levels in LUAD patients, and a high expression level of SPOCK2 or SPRED1 predicted better survival. Moreover, overexpression of SPOCK2 or SPRED1 could inhibit tumoral proliferation, migration ratio, and invasion activity in vitro as well as retard tumor growth in vivo. However, EZH2 elevation could rescue these impacts and accelerate LUAD progression. Our findings reveal that SPOCK2 and SPRED1 are epigenetically suppressed by EZH2 and may act as novel regulators to inhibit the proliferation, migration, and invasion of LUAD cells.

SPOCK2 Promotes the Malignant Behavior of Ovarian Cancer via Regulation of the Wnt/β-Catenin Signaling Pathway

Background

Ovarian cancer (OC) is a common clinical gynecological disease, which seriously threatens women's health and life. We investigated the roles of SPOCK2 in OC and its associated molecular mechanism in the current study.

Methods

The expressions and prognostic value of SPOCK2 in OC were identified using the clinical data and data from the GEPIA database. Then, SPOCK2 silence was implemented to search functions of SPOCK2 in OC cells. CCK-8 was used to examine cell proliferation. Cell apoptosis was detected by flow cytometry. The OC cell invasion and migration were evaluated by transwell assays.

Results

Overexpressed SPOCK2 was identified in OC, which was correlated with poor prognosis and a shorter survival rate. SPOCK2 downregulation significantly suppressed OC cell proliferation, migration, and invasion, and cell apoptosis was markedly promoted by SPOCK2 silence. Meanwhile, SPOCK2 knockdown could effectively suppress Wnt/β-catenin.

Conclusion

SPOCK2 exerted crucial functions in OC progression and could serve as a promising candidate for OC targeted therapy.

A feature selection-based framework to identify biomarkers for cancer diagnosis: A focus on lung adenocarcinoma

Lung cancer (LC) represents most of the cancer incidences in the world. There are many types of LC, but Lung Adenocarcinoma (LUAD) is the most common type. Although RNA-seq and microarray data provide a vast amount of gene expression data, most of the genes are insignificant to clinical diagnosis. Feature selection (FS) techniques overcome the high dimensionality and sparsity issues of the large-scale data. We propose a framework that applies an ensemble of feature selection techniques to identify genes highly correlated to LUAD. Utilizing LUAD RNA-seq data from the Cancer Genome Atlas (TCGA), we employed mutual information (MI) and recursive feature elimination (RFE) feature selection techniques along with support vector machine (SVM) classification model. We have also utilized Random Forest (RF) as an embedded FS technique. The results were integrated and candidate biomarker genes across all techniques were identified. The proposed framework has identified 12 potential biomarkers that are highly correlated with different LC types, especially LUAD. A predictive model has been trained utilizing the identified biomarker expression profiling and performance of 97.99% was achieved. In addition, upon performing differential gene expression analysis, we could find that all 12 genes were significantly differentially expressed between normal and LUAD tissues, and strongly correlated with LUAD according to previous reports. We here propose that using multiple feature selection methods effectively reduces the number of identified biomarkers and directly affects their biological relevance.

A Microarray Study on the Expression of ANKRD49 in Lung Squamous Cell Carcinoma and Its Clinicopathologic Significance

Lung squamous cell carcinoma (LUSC) is associated with poor clinical outcomes and identifying novel biomarkers that are involved in the progression of LUSC is important for prognosis and targeted treatment. Herein, ankyrin repeat domain 49 (ANKRD49) protein in LUSC versus paired noncancerous lung tissues was tested and its clinical significance was evaluated through χ 2 test, log-rank test, and Cox proportional hazards model. The results showed the ANKRD49 protein in LUSC was elevated and correlated with the tumor-node-metastasis stage, lymph node metastasis, distal metastasis, and differentiation. Patients with higher ANKRD49 had lower overall survival rate and higher ANKRD49 expression in lung tissues may be used as an independent prognostic marker for LUSC patients.

A Pan-Cancer Analysis Revealing the Dual Roles of Lysine (K)-Specific Demethylase 6B in Tumorigenesis and Immunity

Introduction: Epigenetic-targeted therapy has been increasingly applied in the treatment of cancers. Lysine (K)-specific demethylase 6B (KDM6B) is an epigenetic enzyme involved in the coordinated control between cellular intrinsic regulators and the tissue microenvironment whereas the pan-cancer analysis of KDM6B remains unavailable.

Methods: The dual role of KDM6B in 33 cancers was investigated based on the GEO (Gene Expression Omnibus) and TCGA (The Cancer Genome Atlas) databases. TIMER2 and GEPIA2 were applied to investigate the KDM6B levels in different subtypes or stages of tumors. Besides, the Human Protein Atlas database allowed us to conduct a pan-cancer study of the KDM6B protein levels. GEPIA2 and Kaplan–Meier plotter were used for the prognosis analysis in different cancers. Characterization of genetic modifications of the KDM6B gene was analyzed by the cBioPortal. DNA methylation levels of different KDM6B probes in different TCGA tumors were analyzed by MEXPRESS. TIMER2 was applied to determine the association of the KDM6B expression and immune infiltration and DNA methyltransferases. Spearman correlation analysis was used to assess the association of the KDM6B expression with TMB (tumor mutation burden) and MSI (microsatellite instability). The KEGG (Kyoto encyclopedia of genes and genomes) pathway analysis and GO (Gene ontology) enrichment analysis were used to further investigate the potential mechanism of KDM6B in tumor pathophysiology.

Results: KDM6B was downregulated in 11 cancer types and upregulated across five types. In KIRC (kidney renal clear cell carcinoma) and OV (ovarian serous cystadenocarcinoma), the KDM6B level was significantly associated with the pathological stage. A high level of KDM6B was related to poor OS (overall survival) outcomes for THCA (thyroid carcinoma), while a low level was correlated with poor OS and DFS (disease-free survival) prognosis of KIRC. The KDM6B expression level was associated with TMB, MSI, and immune cell infiltration, particularly cancer-associated fibroblasts, across various cancer types with different correlations. Furthermore, the enrichment analysis revealed the relationship between H3K4 and H3K27 methylation and KDM6B function.

Conclusion: Dysregulation of the DNA methyltransferase activity and methylation levels of H3K4 and H3K27 may involve in the dual role of KDM6B in tumorigenesis and development. Our study offered a relatively comprehensive understanding of KDM6B’s dual role in cancer development and response to immunotherapy.

DNA methylation of ARHGAP30 is negatively associated with ARHGAP30 expression in lung adenocarcinoma, which reduces tumor immunity and is detrimental to patient survival

Rho-GTPase activating protein 30 (ARHGAP30) can enhance the intrinsic hydrolysis of GTP and regulates Rho-GTPase negatively. The relationship between ARHGAP30 expression and lung adenocarcinoma is unclear. Therefore, the present study aimed to assess the differences in expression of ARHGAP30 between lung adenocarcinoma tissues and normal tissues and the relationship between DNA methylation and ARHGAP30 expression in lung adenocarcinoma. To determine the role of ARHGAP30 expression in the prognosis and survival of patients with lung adenocarcinoma, gene set enrichment analysis of ARHGAP30 was performed, comprising analyses of Kyoto Encyclopedia of Genes and Genomes pathways, Panther pathways, Reactome pathways, Wikipathways, Gene Ontology, Kinase Target Network, Transcription Factor Network, and a protein-protein interaction network. The association of ARHGAP30 expression with tumor-infiltrating lymphocytes, immunostimulators, major histocompatibility complex molecules, chemokines, and chemokine receptors in lung adenocarcinoma tissues was also analyzed. DNA methylation of ARHGAP30 correlated negatively with ARHGAP30 expression. Patients with lung adenocarcinoma with high DNA methylation of ARHGAP30 had poor prognosis. The prognosis of patients with lung adenocarcinoma with low ARHGAP30 expression was also poor. ARHGAP30 expression in lung adenocarcinoma correlated positively, whereas methylation of ARHGAP30 correlated negatively, with levels of tumor infiltrating lymphocytes. Gene set enrichment analysis revealed that many pathways associated with ARHGAP30 should be studied to improve the diagnosis, treatment, and prognosis of lung adenocarcinoma. We speculated that DNA methylation of ARHGAP30 suppresses ARHGAP30 expression, which reduces tumor immunity, leading to poor prognosis for patients with lung adenocarcinoma.

Prognostic Analysis of Lung Adenocarcinoma Based on DNA Methylation Regulatory Factor Clustering

There is a known link between DNA methylation and cancer immunity/immunotherapy; however, the effect of DNA methylation on immunotherapy in lung adenocarcinoma (LUAD) remains to be elucidated. In the current study, we aimed to screen key markers for prognostic analysis of LUAD based on DNA methylation regulatory factor clustering. We classified LUAD using the NMF clustering method, and as a result, we obtained 20 DNA methylation regulatory genes. These 20 regulatory genes were used to determine the pattern of DNA methylation regulation, and patients were grouped for further analysis. The risk score model was analyzed in the TCGA dataset and an external validation set, and the correlation between the risk score and DNA methylation regulatory gene expression was explored. We analyzed the correlation between the prognostic model and immune infiltration and checkpoints. Finally, we analyzed the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes functions of the prognosis model and established the nomogram model and decision tree model. The survival analyses of ClusterA and ClusterB were significantly different. Survival analysis showed that patients with a high risk score had a poor prognosis. Survival models (tobacco, T, N, M, stage, sex, age, status, and risk score) were abnormally correlated with T cells and macrophages. The higher the risk score associated with smoking was and the higher the stage was, the more severe the LUAD and the more maladjusted the immune system were. Immune infiltration and abnormal expression of immune checkpoint genes in the prognostic model of LUAD were associated with the risk score. The prognostic models were mainly enriched in the cell cycle and DNA replication. Characterization of DNA methylation regulatory patterns is helpful to improve our understanding of the immune microenvironment in LUAD and to guide the development of a more personalized immunotherapy strategy in the future.

Identification of Prognostic miRNAs Associated With Immune Cell Tumor Infiltration Predictive of Clinical Outcomes in Patients With Non-Small Cell Lung Cancer

Background

A detailed means of prognostic stratification in patients with non-small cell lung cancer (NSCLC) is urgently needed to support individualized treatment plans. Recently, microRNAs (miRNAs) have been used as biomarkers due to their previously reported prognostic roles in cancer. This study aimed to construct an immune-related miRNA signature that effectively predicts NSCLC patient prognosis.

Methods

The miRNAs and mRNA expression and mutation data of NSCLC was obtained from The Cancer Genome Atlas (TCGA). Immune-associated miRNAs were identified using immune scores calculated by the ESTIMATE algorithm. LASSO-penalized multivariate survival models were using for development of a tumor immune-related miRNA signature (TIM-Sig), which was evaluated in several public cohorts from the Gene Expression Omnibus (GEO) and the CellMiner database. The miRTarBase was used for constructing the miRNA-target interactions.

Results

The TIM-Sig, including 10 immune-related miRNAs, was constructed and successfully predicted overall survival (OS) in the validation cohorts. TIM-Sig score negatively correlated with CD8+ T cell infiltration, IFN-γ expression, CYT activity, and tumor mutation burden. The correlation between TIM-Sig score and genomic mutation and cancer chemotherapeutics was also evaluated. A miRNA-target network of 10 miRNAs in TIM-Sig was constructed. Further analysis revealed that these target genes showed prognostic value in both lung squamous cell carcinoma and adenocarcinoma.

Conclusions

We concluded that the immune-related miRNAs demonstrated a potential value in clinical prognosis.

Investigation on Potential Correlation Between Small Nuclear Ribonucleoprotein Polypeptide A and Lung Cancer

SNRPA (small nuclear ribonucleoprotein polypeptide A) gene is essential for the pre-mRNA splicing process. Using the available datasets of TCGA or GEO, we aimed at exploring the potential association between the SNRPA gene and lung cancer by several online tools (such as GEIPA2, MEXPRESS, Oncomine) and bioinformatics analysis software (R or GSEA). SNRPA was highly expressed in the tissues of lung adenocarcinoma (LUAD) and lung squamous cell carcinoma tissue (LUSC), compared with control tissues. The high SNRPA expression was associated with a poor survival prognosis of LUAD cases, while the genetic alteration within SNRPA was linked to the overall survival prognosis of LUSC cases. There was a potential correlation between promoter methylation and the expression of SNRPA for LUAD. Compared with normal tissues, we observed a higher phosphorylation level at the S115 site of SNRPA protein (NP_004587.1) (p = 0.002) in the primary LUAD tissues. The potential ATR kinase of the S115 site was predicted. Besides, SNRPA expression in lung cancer was negatively correlated with the infiltration level of M2 macrophage but positively correlated with that of Follicular B helper T cells, in both LUAD and LUSC. The enrichment analysis of SNRPA-correlated genes showed that cell cycle and ubiquitin mechanism-related issues were mainly observed for LUAD; however, RNA splicing-related cellular issues were mainly for LUSC. In summary, the SNRPA gene was identified as a potential prognosis biomarker of lung cancer, especially lung adenocarcinoma, which sheds new light on the association between the spliceosomal complex component and tumorigenesis.