Multi-marker analysis of genomic annotation on gastric cancer GWAS data from Chinese populations

Exploring the genetic components and multi-omics sources of inflammatory bowel disease from the perspective of autoimmune disorders

BACKGROUND

Inflammatory bowel disease (IBD) and autoimmune disorders result from immune system dysregulation. However, the genetic overlap between them remains unclear. Our study aimed to investigate the genetic mechanisms and structure of IBD from the perspective of autoimmune disorders.

METHODS

The genetic correlation (rg) between traits can provide valuable information about the shared underlying biological mechanisms. Utilizing summary statistics from genome-wide association studies, we delved into the genetic correlation, shared inheritance, and potential causality of IBD (N = 34,652) with autoimmune disorders (N = 1,755,610). We performed transcriptomics at the gene level, multi-marker analyses of genome annotations, and enrichment analyses of biological pathways to highlight shared and diverse perspectives.

RESULTS

There were significant genetic correlations between IBD and ankylosing spondylitis (rg = 0.327), rheumatoid arthritis (rg = 0.242), type 1 diabetes (rg = - 0.061), psoriasis (rg = 0.246), and ankylosing spondylitis (rg = 0.308). We identified 110 unique regions (including 5p33.3, 10q25.3, and 22q13.31) after a consistent study at the gene levels. By implementing transcriptomics techniques, we discovered potential common biological mechanisms in several tissues, including blood, spleen, thyroid, and pancreas, revealing potential common biological mechanisms involving lincRNA, protein-coding, and pseudogenes.

CONCLUSION

Our study demonstrated hypothesized pleiotropic genomic regions that provide important clues to delve into the genetic basis of IBD and autoimmune disorders on the basis of multi-omics. Moreover, we have identified shared pathogenic processes and potential common therapeutic targets among these diseases. Key Points • The finding provides a new perspective on the genetic basis of inflammatory bowel disease and autoimmune disease across multi-omics platforms. • Fine mapping of functional summary-based imputation and causal genomes has identified hypothesized pleiotropic genomic regions. • The identified genes and pathways may offer innovative targets for the prevention of immune-related diseases.

BRD4 expression and its regulatory interaction with miR-26a-3p, DLG5-AS1, and JMJD1C-AS1 lncRNAs in gastric cancer progression

Gastric cancer remains a significant health challenge despite advancements in diagnosis and treatment. Early detection is critical to reducing mortality, necessitating the investigation of molecular mechanisms underlying gastric cancer progression. This study focuses on BRD4 expression and its correlation with miR-26a-3p, DLG5-AS1, and JMJD1C-AS1 lncRNAs in gastric cancer. Analysis of The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets revealed significant upregulation of BRD4 in gastric cancer tissues compared to normal tissues, correlating negatively with miR-26a-3p and positively with DLG5-AS1 and JMJD1C-AS1 lncRNAs. Quantitative RT-PCR confirmed these findings in 25 gastric cancer tissue samples and 25 normal samples. BRD4's overexpression was associated with reduced survival rates and older patient age. MiR-26a-3p, a known tumor suppressor, showed decreased expression in gastric cancer tissues, with ROC analysis suggesting it, alongside BRD4, as a potential diagnostic biomarker. Additionally, bioinformatics predicted miR-26a-3p's interaction with BRD4 mRNA. Upregulated lncRNAs DLG5-AS1 and JMJD1C-AS1 likely act as competing endogenous RNAs, sponging miR-26a-3p, thus promoting BRD4 dysregulation. These lncRNAs have not been previously studied in gastric cancer. The findings propose a novel BRD4/lncRNA/miRNA regulatory axis in gastric cancer, highlighting the potential of BRD4, DLG5-AS1, and JMJD1C-AS1 as biomarkers for early diagnosis. Further studies with larger sample sizes and in vivo and in vitro experiments are needed to elucidate this regulatory mechanism's role in gastric cancer progression.

Alternative Splicing Factor Heterogeneous Nuclear Ribonucleoprotein U as a Promising Biomarker for Gastric Cancer Risk and Prognosis with Tumor-Promoting Properties

Gastric cancer (GC) is a major global health concern with poor outcomes. Heterogeneous nuclear ribonucleoprotein U (HNRNPU) is a multifunctional protein that participates in pre-mRNA packaging, alternative splicing regulation, and chromatin remodeling. Its potential role in GC remains unclear. In this study, the expression characteristics of HNRNPU were analyzed by The Cancer Genome Atlas data, Gene Expression Omnibus data, and then further identified by real-time quantitative PCR and immunohistochemistry using tissue specimens. From superficial gastritis, atrophic gastritis, and hyperplasia to GC, the in situ expression of HNRNPU protein gradually increased, and the areas under the curve for diagnosis of GC and its precancerous lesions were 0.911 and 0.847, respectively. A nomogram integrating HNRNPU expression, lymph node metastasis, and other prognostic indicators exhibited an area under the curve of 0.785 for predicting survival risk. Knockdown of HNRNPU significantly inhibited GC cell proliferation, migration, and invasion and promoted apoptosis in vitro. In addition, RNA-sequencing analysis showed that HNRNPU could affect alternative splicing events in GC cells, with functional enrichment analysis revealing that HNRNPU may exert malignant biological function in GC progression through alternative splicing regulation. In summary, the increased expression of HNRNPU was significantly associated with the development of GC, with a good performance in diagnosing and predicting the prognostic risk of GC. Functionally, HNRNPU may play an oncogenic role in GC by regulating alternative splicing.

Genomic analysis and clinical implications of immune cell infiltration in gastric cancer

The immune infiltration of patients with gastric cancer (GC) is closely associated with clinical prognosis. However, previous studies failed to explain the different subsets of immune cells involved in immune responses and diverse functions. The present study aimed to uncover the differences in immunophenotypes in a tumor microenvironment (TME) between adjacent and tumor tissues and to explore their therapeutic targets. In our study, the relative proportion of immune cells in 229 GC tumor samples and 22 paired matched tissues was evaluated with a Cell type Identification By Estimating Relative Subsets Of known RNA Transcripts (CIBERSORT) algorithm. The correlation between immune cell infiltration and clinical information was analyzed. The proportion of 22 immune cell subsets was assessed to determine the correlation between each immune cell type and clinical features. Three molecular subtypes were identified with ‘CancerSubtypes’ R-package. Functional enrichment was analyzed in each subtype. The profiles of immune infiltration in the GC cohort from The Cancer Genome Atlas (TCGA) varied significantly between the 22 paired tissues. TNM stage was associated with M1 macrophages and eosinophils. Follicular helper T cells were activated at the late stage. Monocytes were associated with radiation therapy. Three clustering processes were obtained via the ‘CancerSubtypes’ R-package. Each cancer subtype had a specific molecular classification and subtype-specific characterization. These findings showed that the CIBERSOFT algorithm could be used to detect differences in the composition of immune-infiltrating cells in GC samples, and these differences might be an important driver of GC progression and treatment response.

Interleukin (IL)-7 Signaling in the Tumor Microenvironment

Interleukin (IL)-7 plays an important immunoregulatory role in different types of cells. Therefore, it attracts researcher's attention, but despite the fact, many aspects of its modulatory action, as well as other functionalities, are still poorly understood. The review summarizes current knowledge on the interleukin-7 and its signaling cascade in context of cancer development. Moreover, it provides a cancer-type focused description of the involvement of IL-7 in solid tumors, as well as hematological malignancies.The interleukin has been discovered as a growth factor crucial for the early lymphocyte development and supporting the growth of malignant cells in certain leukemias and lymphomas. Therefore, its targeting has been explored as a treatment modality in hematological malignancies, while the unique ability to expand lymphocyte populations selectively and without hyperinflammation has been used in experimental immunotherapies in patients with lymphopenia. Ever since the early research demonstrated a reduced growth of solid tumors in the presence of IL-7, the interleukin application in boosting up the anticancer immunity has been investigated. However, a growing body of evidence indicative of IL-7 upregulation in carcinomas, facilitating tumor growth and metastasis and aiding drug-resistance, is accumulating. It therefore becomes increasingly apparent that the response to the IL-7 stimulus strongly depends on cell type, their developmental stage, and microenvironmental context. The interleukin exerts its regulatory action mainly through phosphorylation events in JAK/STAT and PI3K/Akt pathways, while the significance of MAPK pathway seems to be limited to solid tumors. Given the unwavering interest in IL-7 application in immunotherapy, a better understanding of interleukin role, source in tumor microenvironment, and signaling pathways, as well as the identification of cells that are likely to respond should be a research priority.

Interaction between regulatory T cells and mast cells via IL-9 and TGF-β production

Research on the immunosuppression of cancer cells has attracted much attention in recent years. The present study sought to provide a new strategy for tumor immunotherapy targeting mast cells by studying the mechanisms underlying mast cell function in cancer immunosuppression. Between January 2015 and December 2017, the tumor tissues of 40 patients with gastric cancer (GC) were collected and grouped in Lihuili Hospital of Ningbo City, China. Pathological sections were prepared and an immunofluorescence assay was performed to analyze the expression of forkhead Box Protein P3 (FOXP3), tryptase, TGFβ1, TGF-βR, IL-9, IL-9R and Oxford 40 ligand (OX40L). Then, the correlations between FOXP3 and tryptase, TGFβ1 and tryptase expression, and the expression of OX40L in patients with GC with different stages were analyzed. The results revealed that high levels of mast cells were present in patients GC, and tryptase and FOXP3 expressions were positively correlated. Mast cells regulate T regulatory (reg) cells in the gastric tumor microenvironment by secreting TGFβ1. Tregs, in turn, promote the survival of mast cells in the tumor microenvironment by producing IL-9. Furthermore, OX40L expression in mast cells was significantly associated with Tumor-Node-Metastasis staging of GC. Overall, the present study reported a positive feedback system that functions through TGFβ1 and IL-9 to allow cross-talk between Tregs and mast cells. Moreover, OX40L may be a potential target for the diagnosis and treatment of GC. These results may provide a new strategy for tumor immunotherapy targeting mast cells.

Genetic variants of the peroxisome proliferator-activated receptor (PPAR) signaling pathway genes and risk of pancreatic cancer

Because the peroxisome proliferator-activated receptor (PPAR) signaling pathway is involved in development and progression of pancreatic cancer, we investigated associations between genetic variants of the PPAR pathway genes and pancreatic cancer risk by using three published genome-wide association study datasets including 8477 cases and 6946 controls of European ancestry. Expression quantitative trait loci (eQTL) analysis was also performed for correlations between genotypes of the identified genetic variants and messenger RNA (mRNA) expression levels of their genes by using available databases of the 1000 Genomes, TCGA, and GTEx projects. In the single-locus logistic regression analysis, we identified 1141 out of 17 532 significant single-nucleotide polymorphisms (SNPs) in 112 PPAR pathway genes. Further multivariate logistic regression analysis identified three independent, potentially functional loci (rs12947620 in MED1, rs11079651 in PRKCA, and rs34367566 in PRKCB) for pancreatic cancer risk (odds ratio [OR] = 1.11, 95% confidence interval [CI], [1.06-1.17], P = 5.46 × 10-5 ; OR = 1.10, 95% CI, [1.04-1.15], P = 1.99 × 10-4 ; and OR = 1.09, 95% CI, [1.04-1.14], P = 3.16 × 10-4 , respectively) among 65 SNPs that passed multiple comparison correction by false discovery rate (< 0.2). When risk genotypes of these three SNPs were combined, carriers with 2 to 3 unfavorable genotypes (NUGs) had a higher risk of pancreatic cancer than those with 0 to 1 NUGs. The eQTL analysis showed that rs34367566 A>AG was associated with decreased expression levels of PRKCB mRNA in 373 lymphoblastoid cell lines. Our findings indicate that genetic variants of the PPAR pathway genes, particularly MED1, PRKCA, and PRKCB, may contribute to susceptibility to pancreatic cancer.

CLDN4 silencing promotes proliferation and reduces chemotherapy sensitivity of gastric cancer cells through activation of the PI3K/Akt signalling pathway

NEW FINDINGS

What is the central question of this study? What is the influence of the interaction between the matrix protein CLDN4 and the PI3K/Akt signalling pathway on tumour progression and chemotherapy sensitivity in gastric cancer? What is the main finding and its importance? Silencing of CLDN4 can promote the growth and proliferation of gastric cancer cells by activating the PI3K/Akt signalling pathway, and thus reduce the sensitivity of gastric cancer cells to chemotherapy.

ABSTRACT

Gastric cancer (GC) is one of the most common cancers worldwide and has a high mortality rate, accompanied by metastasis. Claudins (CLDNs) are major tight-junction proteins that mediate cellular polarity and differentiation. In the present study, we investigated the role of claudin 4 (CLDN4) in modulating cell proliferation and chemotherapeutic sensitivity in GC. Immunohistochemistry and RT-qPCR were initially used to detect the expression of CLDN4 in cancer tissues and adjacent normal tissues collected from GC patients. GC cell lines with the highest and the lowest CLDN4 expression were selected for subsequent experiments. The effects of CLDN4 on GC cell chemosensitivity, proliferation, invasion, migration, apoptosis and tumourigenic capacity were evaluated by conducting gain- and loss-of-function studies of CLDN4. Expression of CLDN4 was significantly decreased in GC tissues and cell lines compared to adjacent normal tissues or gastric epithelial cells. Silencing of CLDN4 increased the extent of PI3K and Akt phosphorylation, and also the proliferation, migration, invasion and tumourigenesis of GC cells; at the same time apoptosis and the sensitivity of GC cells to chemotherapy were reduced. In conclusion, CLDN4 may play a pivotal role in attenuating GC cell proliferation and enhancing sensitivity of GC cells to chemotherapy by inactivating the PI3K/Akt signalling pathway.

Contribution of interaction between genetic variants of interleukin-11 and Helicobacter pylori infection to the susceptibility of gastric cancer

Background

Gastric cancer (GC) ranks the second leading cause of cancer-related mortality worldwide. We aimed to clarify the relevance of genetic variants of IL-11, a hub of various carcinogenic pathways, as well as their interactions with Helicobacter pylori (H. pylori) infection in the development of GC.

Methods

A case-control study with 880 GC cases and 900 healthy controls was conducted in a Chinese population. Six tagSNPs were detected by Taqman Allelic Discrimination assay, while H. pylori status was detected by Typing Detection Kit for Antibody to H. pylori and serum IL-11 level was measured using ELISA method.

Results

We found that rs1126760 (C vs T: OR=1.39, 95% CIs=1.13-1.70, P=0.002) and rs1126757 (C vs T: OR=0.82, 95% CIs=0.72-0.93, P=0.002) were significantly associated with susceptibility of GC. Even adjusted for Bonferroni correction, the results were still significant (P=0.002×6=0.012). IL-11 rs1126760 was significantly associated with higher serum and expression level of IL-11, while rs1126757 was significantly associated with lower serum IL-11 level (P<0.001). Significant interaction with H. pylori infection was identified for rs1126760 (P for interaction =0.005). Higher expression of the IL-11 gene was significant with development and poor prognosis of GC.

Conclusion

Our study provides strong evidence that genetic variants of the IL-11 gene may interact with H. pylori infection and contribute to the development of GC. Further studies with larger sample size and functional experiments are needed to validate our findings.