Gastric cancer biomarkers; A systems biology approach

A systems biology approach to pathogenesis of gastric cancer: gene network modeling and pathway analysis

BACKGROUND

Gastric cancer (GC) ranks among the most common malignancies worldwide. This study aimed to find critical genes/pathways in GC pathogenesis.

METHODS

Gene interactions were analyzed, and the protein-protein interaction network was drawn. Then enrichment analysis of the hub genes was performed and network cluster analysis and promoter analysis of the hub genes were done. Age/sex analysis was done on the identified genes.

RESULTS

Eleven hub genes in GC were identified in the current study (ATP5A1, ATP5B, ATP5D, MT-ATP8, COX7A2, COX6C, ND4, ND6, NDUFS3, RPL8, and RPS16), mostly involved in mitochondrial functions. There was no report on the ATP5D, ND6, NDUFS3, RPL8, and RPS16 in GC. Our results showed that the most affected processes in GC are the metabolic processes, and the oxidative phosphorylation pathway was considerably enriched which showed the significance of mitochondria in GC pathogenesis. Most of the affected pathways in GC were also involved in neurodegenerative diseases. Promoter analysis showed that negative regulation of signal transduction might play an important role in GC pathogenesis. In the analysis of the basal expression pattern of the selected genes whose basal expression presented a change during the age, we found that a change in age may be an indicator of changes in disease insurgence and/or progression at different ages.

CONCLUSIONS

These results might open up new insights into GC pathogenesis. The identified genes might be novel diagnostic/prognostic biomarkers or potential therapeutic targets for GC. This work, being based on bioinformatics analysis act as a hypothesis generator that requires further clinical validation.

Expression of hepatocyte nuclear factor 4 alpha, wingless-related integration site, and β-catenin in clinical gastric cancer

BACKGROUND

Gastric cancer (GC) is the second most common cause of cancer-related deaths worldwide. Hepatocyte nuclear factor 4 alpha (HNF4α) that belongs to the nuclear hormone receptor superfamily, is overexpressed in GC tissues, and might be involved in the development of GC by regulating its downstream wingless-related integration site (WNT)/β-catenin signaling.

AIM

To clarify the expression of HNF4α/WNT5a/β-catenin signaling proteins in clinical GC tissues.

METHODS

We immunohistochemically stained pathological blocks of GC and matched para-cancerous tissues. The intensity of HNF4α, WNT5a and β-catenin staining in the tumor cells was determined according to cell rates and staining intensity. The correlations between GC and HNF4α, WNT5a, and β-catenin expression using chi-square and paired chi-square tests. Relationships between double-positive HNF4α and WNT5a expression and types of gastric tumor tissues were assessed using regression analysis. Correlations between HNF4α and WNT5a expression at the RNA level in GC tissues found in the TCGA database were analyzed using Pearson correlation coefficients.

RESULTS

We found more abundant HNF4α and WNT5a proteins in GC, especially in mucinous adenocarcinoma and mixed GC than in adjacent tissues (P < 0.001). Low and high levels of cytoplasmic β-catenin respectively expressed in GC and adjacent tissues (P < 0.001) were not significantly associated with pathological parameters.

CONCLUSION

The expressions of HNF4α and WNT5a could serve as early diagnostic biomarkers for GC.

Telomere Attrition With Concomitant hTERT Overexpression Involved in the Progression of Gastric Cancer May Have Prognostic and Clinical Implications in High-Risk Population Group From North India

Genetic instabilities exacerbated by the dysfunction of telomeres can lead to the development of cancer. Nearly 90% of all human malignancies are linked with telomere dysregulation and overexpression of telomerase, an enzyme that catalyzes the synthesis of telomeric DNA repeats at the ends of chromosomes. The burden of gastric cancer continues to inflict a deterring impact on the global health scenario, accounting for over one million new cases in 2020. The disease is asymptomatic in its early stages of progression, which is attributed to the poor prognosis and overall surge in mortality rate worldwide. Exploiting telomere physiology can provide extensive mechanistic insight into telomere-associated gastric cancer progression and its use as a target in a variety of therapeutic interventions. In this study, we aimed to evaluate the clinical implications of c-Myc, human telomerase reverse transcriptase (hTERT) expression, and telomere length in patients with gastric cancer. A total of 57 gastric cancer cases and adjacent controls were included in the study. RT-PCR and immunohistochemistry were used to assess the expression levels of c-Myc and hTERT. The relative telomere length was measured by MMQPCR using the Cawthon method. Our results indicated that the shorter telomere and increased hTERT expression were associated with gastric cancer progression. The study also highlighted the role of short telomeres and increased expression of hTERT in gastric cancer progression and its association with various etiological risk factors, transcriptional activators, and overall survival among the ethnic Kashmiri population of North India.

Identification of circRNA Biomarker for Gastric Cancer through Integrated Analysis

Gastric cancer (GC) is one of the most common malignant tumors and ranks third in cancer mortality globally. Although, a lot of advancements have been made in diagnosis and treatment of gastric cancer, there is still lack of ideal biomarker for the diagnosis and treatment of gastric cancer. Due to the poor prognosis, the survival rate is not improved much. Circular RNAs (circRNAs) are single-stranded RNAs with a covalently closed loop structure that don't have the 5'-3' polarity and a 3' polyA tail. Because of their circular structure, circRNAs are more stable than linear RNAs. Previous studies have found that circRNAs are involved in several biological processes like cell cycle, proliferation, apoptosis, autophagy, migration and invasion in different cancers, and participate in some molecular mechanisms including sponging microRNAs (miRNAs), protein translation and binding to RNA-binding proteins. Several studies have reported that circRNAs play crucial role in the occurrence and development of different types of cancers. Although, some studies have reported several circRNAs in gastric cancer, more studies are needed in searching new biomarkers for gastric cancer diagnosis and treatment. Here, we investigated potential circRNA biomarkers for GC using next-generation sequencing (NGS) data collected from 5 paired GC samples. A total of 45,783 circRNAs were identified in all samples and among them 478 were differentially expressed (DE). The gene ontology (GO) analysis of the host genes of the DE circRNAs showed that some genes were enriched in several important biological processes, molecular functions and cellular components. The Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis revealed that some host genes were enriched in several GC related pathways. The circRNA-miRNA-gene interaction network analysis showed that two circRNAs circCEACAM5 and circCOL1A1 were interacted with gastric cancer related miRNAs, and their host genes were also the important therapeutic and prognostic biomarkers for GC. The experimental results also validated that these two circRNAs were DE in GC compared to adjacent normal tissues. Overall, our findings suggest that these two circRNAs circCEACAM5 and circCOL1A1 might be the potential biomarkers for the diagnosis and treatment of GC.

Silencing of long non-coding RNA XIST represses gastric cancer progression through blocking NFκB pathway via inhibiting HNF4A-mediated transcription of EPHA1

Gastric cancer (GC) is a common cancer and a leading cause of cancer-related deaths worldwide. Recent studies have supported the important role of long non-coding RNAs (lncRNAs) in GC progression. This study identified functional significance of X inactive specific transcript (XIST) in GC. The expression of XIST and EPHA1 in GC tissues and cells was measured. Then, dual luciferase reporter gene assay, RNA immunoprecipitation (RIP) assay and Chromatin Immunoprecipitation (ChIP) assay were performed to explore the interaction among XIST, EPHA1 and HNF4A. The effects of XIST on GG progression were evaluated by determining expression of proliferation- and invasion-related proteins (Ki67, PCNA, MMP-2, and MMP-9). Further, the functional role of XIST in GC with the involvement of NFκB pathway was also analyzed. Subsequently, the tumor growth in nude mice was evaluated. High expression of XIST and EPHA1 was observed in GC. XIST elevated EPHA1 expression by recruiting HNF4A. In addition, silencing of XIST inhibited GC progression in vitro and in vivo. Overexpressed XIST and EPHA1 yielded a reversed effect on cell proliferation and invasion. SN50 treatment (inhibitor of NFκB pathway) counteracted the promotive effect on GC cell proliferation and invasion mediated by XIST. The present study unveils that XIST increases the enrichment of HNF4A in the promoter region of EPHA1, thus promoting the deterioration of GC.

Systems Biology of Gastric Cancer: Perspectives on the Omics-Based Diagnosis and Treatment

Gastric cancer is the fifth most diagnosed cancer in the world, affecting more than a million people and causing nearly 783,000 deaths each year. The prognosis of advanced gastric cancer remains extremely poor despite the use of surgery and adjuvant therapy. Therefore, understanding the mechanism of gastric cancer development, and the discovery of novel diagnostic biomarkers and therapeutics are major goals in gastric cancer research. Here, we review recent progress in application of omics technologies in gastric cancer research, with special focus on the utilization of systems biology approaches to integrate multi-omics data. In addition, the association between gastrointestinal microbiota and gastric cancer are discussed, which may offer insights in exploring the novel microbiota-targeted therapeutics. Finally, the application of data-driven systems biology and machine learning approaches could provide a predictive understanding of gastric cancer, and pave the way to the development of novel biomarkers and rational design of cancer therapeutics.

Knockdown of LINC00511 promotes radiosensitivity of thyroid carcinoma cells via suppressing JAK2/STAT3 signaling pathway

Thyroid carcinoma is the most widespread malignancy in endocrine system with the increasing incidence. Despite of the advanced approaches to the management of thyroid carcinoma, the therapeutic effects remain unpleasant largely due to the radiosensitivity of thyroid carcinoma cells. LncRNAs play important part in the tumorigenesis and development, especially in the radiosensitivity of tumor cells. However, their roles in thyroid carcinoma still needed to be explored deeply. The purpose of our research is to inspect the possible biological role and regulation mechanism of LINC00511 desirable for therapies of thyroid carcinoma patients. In the present study, LINC00511 was significantly overexpressed in thyroid carcinoma and its silencing boosted radiosensitivity of thyroid carcinoma cells. Then we unveiled that LINC00511 regulated JAK2/STAT3 signaling pathway which was resistant to radiation treatment. Besides, TAF1 modulated JAK2 at transcriptional level. Moreover, LINC00511 bound to TAF1 and further promoted JAK2 expression. In conclusion, rescue experiments verified that the radiosensitivity of thyroid carcinoma cells was attributed to LINC00511/TAF1/JAK2/STAT3 axis. The current paper investigated the underlying mechanism of LINC00511 and set a new therapeutic direction for the therapy of thyroid carcinoma.

The Role of Systems Biologic Approach in Cell Signaling and Drug Development Responses-A Mini Review

The immune system is an integral aspect of the human defense system and is primarily responsible for and involved in the communication between the immune cells. It also plays an important role in the protection of the organism from foreign invaders. Recent studies in the literature have described its role in the process of hematopoiesis, lymphocyte recruitment, T cell subset differentiation and inflammation. However, the specific molecular mechanisms underlying these observations remain elusive, impeding the elaborate manipulation of cytokine sequential delivery in tissue repair. Previously, the discovery of new drugs and systems biology went hand in hand; although Systems biology as a term has only originated in the last century. Various new chemicals were tested on the human body, and studied through observation. Animal models replaced humans for initial trials, but the interactions, response, dose and effect between animals and humans could not be directly correlated. Therefore, there is a need to form disease models outside of human subjects to check the effectiveness and response of the newer natural or synthetic chemicals. These emulate human disease conditions wherein the behavior of the chemicals would be similar in the disease model and humans.