Interleukins as new prognostic genetic biomarkers in non-small cell lung cancer

Immunomodulatory gene polymorphisms in non-small cell lung carcinoma susceptibility and survival

Lung cancer is the leading cause of cancer-associated mortality and non-small cell lung carcinoma (NSCLC) constitutes 85 % of all lung cancer cases. This malignancy is characterized by multifactorial risk factors, poor prognosis, and deplorable clinical outcome. Considerable evidence indicates that there is inter-individual variability in the lung cancer predisposition and survival due to genetic variations introduced by genetic polymorphisms between individuals, indirectly affecting the lung cancer susceptibility and the patient survival. In the past decades, immune landscape in the tumour environment and host immune response are constantly implicated as determining factor in NSCLC development and patients' survival. With the change of paradigm in NSCLC treatment to immunotherapy and increasing recognition of the role of the immune system in cancer development and survival, the inspection of single nucleotide polymorphisms (SNPs) in immunomodulated markers associated with the risk and prognosis for NSCLC is crucial. Despite extensive studies reported the implication of SNPs in predicting the risk and survival of NSCLC. SNPs in the genes that modulate immune response in NSCLC have not been reviewed before. Hence, this review uncovers the evidence on the genetic polymorphisms of immunomodulatory markers which include immune checkpoints, immune checkpoint inhibitors, chemokines, interleukins, human leukocyte antigen and its receptors, and antigen presenting machinery genes, and their significance in the susceptibility, prognosis and survival in NSCLC. The identification of genetic factors associated with NSCLC risk and survival provides invaluable information for a greater comprehension of the pathogenesis and progression of the disease, also to refine prognosis and personalize clinical care in early and advanced-stages disease.

Identification of Prognostic Genes and Immune Landscape Signatures Based on Tumor Microenvironment in Lung Adenocarcinoma

Background

Lung adenocarcinoma is the most common lung cancer subtype and accounts for the highest proportion of cancer-related deaths. The tumor microenvironment influences prognostic outcomes in lung adenocarcinoma (LUAD).

Materials and Methods

We used the ESTIMATE algorithm (Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data) to investigate the role of microenvironment-related genes and stromal cells in lung adenocarcinoma prognosis. This analysis was done on lung adenocarcinoma cases from The Cancer Genome Atlas (TCGA). The cases were divided into high and low groups on the basis of immune and stromal scores, respectively.

Results

There were close correlations between immune scores with prognosis and disease stage. There were 367 differentially expressed genes. Combining the Gene Expression Omnibus (GEO) database, we found 14 prognosis-related genes.

Results

There were close correlations between immune scores with prognosis and disease stage. There were 367 differentially expressed genes. Combining the Gene Expression Omnibus (GEO) database, we found 14 prognosis-related genes. Results. Based on the enrichment levels of the immune cell types, we clustered LUAD into Immunity_H and Immunity_L subtypes. Most of these genes were upregulated in Immunity_H subtype. Finally, using the Human Protein Atlas (HPA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC) databases, most of the proteins corresponding to prognostic genes were verified to be differentially expressed between the tumor and normal groups.

Conclusions

The key genes identified in this study are involved in molecular mechanisms of LUAD.

IL-1β in breast cancer bone metastasis

Bone is the most common site for advanced breast cancer to metastasise. The proinflammatory cytokine, interleukin-1β (IL-1β) plays a complex and contradictory role in this process. Recent studies have demonstrated that breast cancer patients whose primary tumours express IL-1β are more likely to experience relapse in bone or other organs. Importantly, IL-1β affects different stages of the metastatic process including growth of the primary tumour, epithelial to mesenchymal transition (EMT), dissemination of tumour cells into the blood stream, tumour cell homing to the bone microenvironment and, once in bone, this cytokine participates in the interaction between cancer cells and bone cells, promoting metastatic outgrowth at this site. Interestingly, although inhibition of IL-1β signalling has been shown to have potent anti-metastatic effects, inhibition of the activity of this cytokine has contradictory effects on primary tumours, sometimes reducing but often promoting their growth. In this review, we focus on the complex roles of IL-1β on breast cancer bone metastasis: specifically, we discuss the distinct effects of IL-1β derived from tumour cells and/or microenvironment on inhibition/induction of primary breast tumour growth, induction of the metastatic process through the EMT, promotion of tumour cell dissemination into the bone metastatic niche and formation of overt metastases.

Impact of Genetic Polymorphisms on the Metabolic Pathway of Vitamin D and Survival in Non-Small Cell Lung Cancer

Vitamin D has been associated with risk, development, and progression of cancer. However, the genes involved in its metabolism are highly polymorphic, compromising its activity. The aim of this study is to evaluate the association between the gene polymorphisms involved in the metabolic pathway of vitamin D and survival in patients with non-small-cell lung cancer (NSCLC). The study was designed as an observational cohort which included 194 Caucasians patients from southern Spain with NSCLC. Real-time polymerase chain reaction was used to analyze the following polymorphisms: CYP27B1 rs4646536, rs3782130, and rs10877012; CYP24A1 rs6068816 and rs4809957; GC rs7041; CYP2R1 rs10741657; VDR rs1544410 (BsmI), rs11568820 (Cdx-2), rs2228570 (FokI), rs7975232 (ApaI), and rs731236 (TaqI). Progression-free survival (PFS) and overall survival were assessed. Cox regression showed that rs4646536 was associated with PFS in the general population (p = 0.0233) and in the non-resected NSCLC subgroup (p = 0.0233). In the resected NSCLC subgroup, rs11568820 was associated with OS (p = 0.0129) and rs7041 with PFS (p = 0.0447). In the non-resected NSCLC subgroup, rs6068816 was associated with PFS (p = 0.0048) and OS (p = 0.0089) and rs731236 and rs7975232 were associated with OS (p = 0.0005) and PFS (p = 0.0002), respectively. The other polymorphisms showed no effect on the results. The rs4646536, rs6068816, rs7041, rs11568820, rs731236, and rs7975232 polymorphisms are associated with survival in NSCLC and may have a substantial role as prognostic markers of the disease.

Survival Rates of Patients with Non-Small Cell Lung Cancer Depending on Lymph Node Metastasis: A Focus on Saliva

The aim of this study was to compare overall survival (OS) rates at different pN stages of NSCLC depending on tumor characteristics and to assess the applicability of saliva biochemical markers as prognostic signs. The study included 239 patients with NSCLC (pN₀-120, pN₁-51, pN₂-68). Saliva was analyzed for 34 biochemical indicators before the start of treatment. For pN₀, the tumor size does not have a prognostic effect, but the histological type should be taken into account. For pN₁ and pN₂, long-term results are significantly worse in squamous cell cancer with a large tumor size. A larger volume of surgical treatment reduces the differences between OS. The statistically significant factors of an unfavorable prognosis at pN₀ are the lactate dehydrogenase activity <1294 U/L and the level of diene conjugates >3.97 c.u. (HR = 3.48, 95% CI 1.21-9.85, p = 0.01541); at pN₁, the content of imidazole compounds >0.296 mmol/L (HR = 6.75, 95% CI 1.28-34.57, p = 0.00822); at pN₂ levels of protein <0.583 g/L and Schiff bases >0.602 c.u., as well as protein >0.583 g/L and Schiff bases <0.602 c.u. (HR = 2.07, 95% CI 1.47-8.93, p = 0.04351). Using salivary biochemical indicators, it is possible to carry out stratification into prognostic groups depending on the lymph node metastasis.

Establishment of a Novel Risk Score System of Immune Genes Associated With Prognosis in Esophageal Carcinoma

Background

Few studies have addressed the role of immune-related genes in the survival and prognosis of different esophageal cancer (EC) sub-types. We established two new prognostic model indexes by bioinformatics analysis to select patients with esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC) who may benefit from immunotherapy.

Methods

Based on TCGA and ImmPort data sets, we screened immune genes differentially expressed between tumor and normal tissues in ESCC and EAC and analyzed the relationship between these genes and patient survival outcomes. We established the risk score models of immune-related genes in ESCC and EAC by multivariate COX regression analysis.

Results

We identified 12 and 11 immune-related differentially expressed genes associated with the clinical prognosis of ESCC and EAC respectively, based on which two prognostic risk score models of the two EC sub-types were constructed. It was found that the survival probability of patients with high scores was significantly lower than that of patients with low scores (p < 0.001). BMP1, EGFR, S100A12, HLA-B, TNFSF18, IL1B, MAPT and OXTR were significantly related to sex, TNM stage or survival outcomes of ESCC or EAC patients (p < 0.05). In addition, the risk score of ESCC was significantly correlated with the level of B cell infiltration in immune cells (p < 0.05).

Conclusions

The prognosis-related immune gene model indexes described herein prove to be useful prognostic biomarkers of the two EC sub-types in that they may provide a reference direction for looking for the beneficiaries of immunotherapy for EC patients.

Significant Association of Interleukin-16 Genetic Variations to Taiwanese Lung Cancer

BACKGROUND/AIM

Interleukin-16 has been reported to exhibit tumoricidal effects, however, the contribution of IL-16 genotypes to lung cancer is still largely unrevealed. This study aimed at investigating whether IL-16 genotypes contribute to lung cancer susceptibility.

MATERIALS AND METHODS

IL-16 rs4778889, rs11556218, and rs4072111 genotypic characteristics were determined among 358 lung cancer patients and 716 controls via the polymerase chain reaction-based restriction fragment length polymorphism (PCR-RFLP) methodology.

RESULTS

The highlight finding is that the distributions of genotypic (p=8.6E-10) and allelic (p=0.0001) frequencies of IL-16 rs11556218 was significantly different between cases and controls. In detail, the frequencies of IL-16 rs11556218 heterozygous variant TG and homozygous variant GG were 36.6 and 7.3% among the lung cancer patients, significantly higher than those among the controls (22.5% and 2.6%). On the other way, no difference was observed regarding IL-16 rs4778889 or IL-16 rs4072111.

CONCLUSION

The present study indicates IL-16 rs11556218 G allele is significantly associated with increased Taiwan lung cancer risk.

Identification of 10 Hub genes related to the progression of colorectal cancer by co-expression analysis

Background

Colorectal cancer (CRC) is the third most common cancer in the world. The present study is aimed at identifying hub genes associated with the progression of CRC.

Method

The data of the patients with CRC were obtained from the Gene Expression Omnibus (GEO) database and assessed by weighted gene co-expression network analysis (WGCNA), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses performed in R by WGCNA, several hub genes that regulate the mechanism of tumorigenesis in CRC were identified. Differentially expressed genes in the data sets GSE28000 and GSE42284 were used to construct a co-expression network for WGCNA. The yellow, black and blue modules associated with CRC level were filtered. Combining the co-expression network and the PPI network, 15 candidate hub genes were screened.

Results

After validation using the TCGA-COAD dataset, a total of 10 hub genes (MT1X, MT1G, MT2A, CXCL8, IL1B, CXCL5, CXCL11, IL10RA, GZMB, KIT) closely related to the progression of CRC were identified. The expressions of MT1G, CXCL8, IL1B, CXCL5, CXCL11 and GZMB in CRC tissues were higher than normal tissues (p-value < 0.05). The expressions of MT1X, MT2A, IL10RA and KIT in CRC tissues were lower than normal tissues (p-value < 0.05).

Conclusions

By combinating with a series of methods including GO enrichment analysis, KEGG pathway analysis, PPI network analysis and gene co-expression network analysis, we identified 10 hub genes that were associated with the progression of CRC.

Development and Validation of a Novel 8 Immune Gene Prognostic Signature Based on the Immune Expression Profile for Hepatocellular Carcinoma

Background

The immune microenvironment plays a vital role in the development of hepatocellular carcinoma (HCC). This study explored novel immune-related biomarkers to predict the prognosis of patients with HCC.

Methods

RNA-Seq data were downloaded from The Cancer Genome Atlas (TCGA). Univariate Cox regression was used to identify prognosis-related genes; the Lasso method was used to construct the prognosis risk model. Validation was performed on the International Cancer Genome Consortium (ICGC) cohort, and the C-index was calculated to evaluate its overall predictive performance. Western blots were conducted to evaluate the expression of genes.

Results

There were 320 immune-related genes, 40 of which were significantly related to prognosis. Eight immune gene signatures (CKLF, IL12A, CCL20, PRELID1, GLMN, ACVR2A, CD7, and FYN) were established by Lasso Cox regression analysis. This immune signature performed well in different cohorts and can be an independent risk factor for prognosis. In addition, the overall predictive performance of this model was higher than the other models reported previously.

Conclusion

The predictive immune model will enable patients with HCC to be more accurately managed in immunotherapy.

IL-1B rs2853550 polymorphism contributes to esophageal cancer susceptibility in Chinese Han population of Northwest China

BACKGROUND

Esophageal cancer (EC) is one of the most common human cancers, with a particularly aggressive behavior and increased incidence worldwide. The aim of this study was to assess the associations of single-nucleotide polymorphisms (SNPs) in IL-1B with the risk of EC in a northwest Chinese Han population.

METHODS

In order to evaluate the correlations between IL-1B polymorphisms and EC risk, an Agena MassARRAY platform was used to determine the genotype of the candidate SNPs among 384 EC patients and 499 controls. The associations between IL-1B variants and EC risk were examined using logistic regression analysis with adjustment for gender and age. Haplotype construction and analysis were performed to detect the potential associations between haplotypes within IL-1B and EC susceptibility. Additionally, bioinformatics databases were used for gene expression analysis and SNP functional prediction.

RESULTS

A significant relationship was found between IL-1B rs2853550 and an increased risk of EC in the allele model [odds ratio (OR) = 1.38, 95% confidence interval (95% CI): 1.01-1.89, p = 0.041), the codominant model (A/G, OR = 1.63, 95% CI: 1.10-2.42, p = 0.011), and the dominant model (OR = 1.49, 95% CI: 1.02-2.18, p = 0.041). Functional analysis revealed the potential effects of rs2853550, which further reinforced its influence on EC susceptibility. However, there were no statistically significant differences for other SNPs or haplotypes between EC cases and healthy controls. Expression analysis conducted with dataset indicated that the expression level of IL-1B was higher in EC cases than that in normal samples.

CONCLUSIONS

This study demonstrated that rs2853550 in IL-1B might increase EC susceptibility in the Chinese Han population of Northwest China.

Association between IL1B gene and cervical cancer susceptibility in Chinese Uygur Population: A Case-Control study

BACKGROUND

Interleukin-1β (IL-1B) has been recognized as a pro-inflammatory cytokine and associated with tumorigenesis. We aimed to evaluate the contribution of IL-1B polymorphisms to the susceptibility of cervical cancer in Chinese Uygur population.

METHODS

Seven variants were genotyped by Agena MassARRAY platform in 267 cervical cancer patients and 302 healthy controls. Allelic, genotypic, and haplotypic association analyses adjusted for age were investigated using odds ratios (OR) and 95% confidence intervals (CI). GEPIA and UALCAN databases were used to evaluate expression and prognostic of IL-1B gene in cervical cancer.

RESULTS

Our result revealed IL-1B rs1143627-AA (OR = 1.98, p = 0.029) and rs16944-GG (OR = 2.01, p = 0.025) was associated with an increased risk of cervical cancer. Besides, we also found two protective single nucleotide polymorphisms (SNPs) rs3136558 (OR = 0.63, p = 0.011) and rs1143630 (OR = 0.63, p = 0.019). Haplotype ″TGA″ in the block (rs1143630, rs1143627, and rs16944) significantly decreased the susceptibility of cervical cancer (OR = 0.53, p = 0.0007). IL-1B mRNA level was up-regulated in the cervical cancer patients, which was related with poor prognosis in silico.

CONCLUSIONS

For the first time, our results provide evidence on polymorphism of IL-1B gene associated with cervical cancer risk in Chinese Uygur population.

Pharmacogenomic analyses of sunitinib in patients with pancreatic neuroendocrine tumors

Aim: Evaluate associations between clinical outcomes and SNPs in patients with well-differentiated pancreatic neuroendocrine tumors receiving sunitinib. Patients & methods: Kaplan–Meier and Cox proportional hazards models were used to analyze the association between SNPs and survival outcomes using data from a sunitinib Phase IV (genotyped, n = 56) study. Fisher’s exact test was used to analyze objective response rate and genotype associations. Results: After multiplicity adjustment, progression-free and overall survivals were not significantly correlated with SNPs; however, a higher objective response rate was significantly associated with IL1B rs16944 G/A versus G/G (46.4 vs 4.5%; p = 0.001). Conclusion: IL1B SNPs may predict treatment response in patients with pancreatic neuroendocrine tumors. VEGF pathway SNPs are potentially associated with survival outcomes.

The Correlation between IL-1β-C31T Gene Polymorphism and Susceptibility to Breast Cancer

Purpose

Interleukin-1 beta (IL-1β), a pro-inflammatory cytokine, has been shown to influence breast cancer susceptibility. The relationship between its risk of breast cancer and IL-1β-C31T polymorphism has been demonstrated, but the results remain controversial. Therefore, our study aimed to investigate the correlation between the IL-1β-C31T gene polymorphism and susceptibility to breast cancer.

Methods

The genotype frequencies of IL-1β-C31T polymorphism were compared between 204 breast cancer cases and 210 controls using polymerase chain reaction and restriction fragment length polymorphism techinques. Further multivariate binary logistic regression analyses were used to assess the association between IL-1β-C31T polymorphism and breast cancer risk.

Results

The frequency of the T allele of IL-1β-C31T polymorphism in breast cancer cases was significantly higher than that in the controls (56.1% vs. 47.9%). The frequencies of genotypes CC, CT, and TT in the cases were 22.1%, 43.6%, and 34.3%, respectively, while in the control group they were 24.3%, 55.7%, and 20.0%, respectively. There was a significant difference between the prevalence of TT genotype in the 2 groups (adjusted odds ratio [OR], 2.06; 95% confidence interval [CI], 1.16–3.66; p  =  0.014). Breast cancer risk increased in women with TT genotype, body mass index (BMI) ≥ 25 kg/m² (OR, 2.19; 95% CI, 1.09–4.36), late age at first birth (OR, 2.43; 95% CI, 1.29–4.56), postmenopausal status (OR, 3.15; 95% CI, 1.39–7.16), and negative smoking history (OR, 2.52; 95% CI, 1.32–4.82). Furthermore, increase in breast cancer risk among women diagnosed with invasive ductal carcinoma was associated with CT/TT genotypes (OR, 2.82; 95% CI, 1.38–5.76).

Conclusion

The IL-1β-C31T polymorphism affects breast cancer susceptibility, especially in women with late age at first birth, high BMI, postmenopausal status, negative smoking history, and invasive ductal carcinoma. Our study adds to the evidence about the importance of IL-1β-C31T polymorphism in breast cancer susceptibility.

Integrated Analysis of Transcriptome and Prognosis Data Identifies FGF22 as a Prognostic Marker of Lung Adenocarcinoma

Lung adenocarcinoma is one of the most common cancers worldwide. However, the molecular mechanisms of lung adenocarcinoma development are still unclear. This study aimed to investigate the expression profiles of anti-lung cancer target genes in different cancer stages and to explore their functions in tumor development. Lung adenocarcinoma transcriptome and clinical data were downloaded from Genomic Data Commons Data Portal, and the anti-lung cancer target genes were retrieved from the Thomson Reuters Integrity database. The results showed that 16 anti-lung target genes were deregulated in all stages. Among these target genes, fibroblast growth factor 22 showed the most important role in transcription regulatory networks. Further analysis revealed that APC, BRIP1, and PTTG1 may regulate fibroblast growth factor 22 and subsequently influence MAPK signaling pathway, Rap1 signaling pathways, and other tumorigenic processes in all stages. Moreover, high fibroblast growth factor 22 expression leads to poor overall survival (hazard ratio = 1.55, P = .019). These findings provide valuable information for the pathological research and treatment of lung adenocarcinoma. Future studies are needed to verify these results.

Systematic assessment of the clinicopathological prognostic significance of tissue cytokine expression for lung adenocarcinoma based on integrative analysis of TCGA data

Dysregulated intratumoral immune reactions are shaped by complex networks of cytokines, which coordinate with tumor cells to determine tumor progression and aggressiveness. In lung adenocarcinoma (LUAD), the role of intratumoral cytokine gene expression for stratifying prognosis has not been systematically investigated. Using high-dimensional datasets of cancer specimens from clinical patients in The Cancer Genome Atlas (TCGA), we explored the transcript abundance and prognostic impact of 27 clinically evaluable cytokines in 500 LUAD tumor samples according to clinicopathological features and two common driver mutations (EGFR and KRAS). We found that reduced expression of IL12B presented as the single prognostic factor for both poor overall survival (OS) and recurrence free survival (RFS) with high hazard ratios. Moreover, we identified that elevated expression of IL6, CXCL8 and CSF3 were additional independent predictors of poor RFS in LUAD patients. Their prognostic significance was further strengthened by their ability to stratify within clinicopathological factors. Notably, we prioritized high risk cytokines for patients with or without mutations in EGFR and KRAS. Our results provide integrative associations of cytokine gene expression with patient survival and tumor recurrence and demonstrate the necessity and validity of relating clinicopathological and genetic disposition factors for precise and personalized disease prognosis.