Revealing potential immunotherapy targets through analysis of a ceRNA network in human colon adenocarcinoma

Identification of Key Genes and Drug Recommendations in Diffuse Large B-Cell Lymphoma Based on Analysis of Glutathione-Related Genes

BACKGROUND

Various malignancies can be efficiently combated by focusing on glutathione. It is unclear how glutathione-related genes link to diffuse large B-cell lymphoma (DLBCL).

METHODS

Clinical information was gathered from DLBCL patients, and differences in glutathione-related differentially expressed genes (DEGs) between DLBCL and healthy groups were found. Enrichment analysis was run on the DEGs associated with glutathione. We discovered hub genes in glutathione, confirmed hub genes' capacity for diagnosis and function prediction, and estimated drug sensitivity. Immune microenvironmental variations between healthy and DLBCL people were assessed, and hub genes for transcription factor (TF) targeting and miRNAs were found.

RESULTS

The glutathione-related DEGs were linked to biological processes such as response to oxidative stress and response to xenobiotic stimulus, according to enrichment analysis. Out of DEGs associated with glutathione, six hub genes were chosen. In the DLBCL population, there was a notable upregulation of the six hub genes. All the genes' AUC values in the diagnostic ability category were more than 0.7, showing strong hub gene diagnostic capacity. The DLBCL population had a high level of T-cell infiltration, according to immune infiltration analysis techniques. Similar activities, such as the cell cycle G2/M phase transition and the negative control of organelle formation, are demonstrated by gene function prediction for hub. According to drug sensitivity prediction, there was a favorable link between KPNA2 with pracinostat, BRCA1 with B-7100, and LEE-011. The gene KPNA2 was shown to be concurrently targeted by many miRNAs and TFs, according to the miRNA-gene-TF interaction network.

CONCLUSION

The relationship between DLBCL and glutathione-related genes was uncovered by our research, and six glutathione genes were linked to DLBCL. These genes might be used as diagnostic biomarkers or targets for treatment for DLBCL patients.

Sodium Butyrate Inhibits the Malignant Proliferation of Colon Cancer Cells via the miR-183/DNAJB4 Axis

Colorectal carcinoma (CRC) is one of the most common malignant tumors in the digestive tract. It was found that butyric acid could inhibit the expression of miR-183 to slow down malignant progression of CRC in the early stage. However, its regulatory mechanism remains unclear. This study screened the IC50 value of butyrate on inhibition of CRC cells malignant progression. Its inhibitory effects were detected by MTT assay, colony formation experiment, Transwell migration experiment, and apoptosis evaluation by flow cytometry. Next, the expressions of miR-183 and DNAJB4 were, respectively, determined in butyrate treated and miR-183 analog or si-DNAJB4-transfected CRC cells to further detect the role of upregulated miR-183 or silencing DNAJB4 in CRC cells malignant progression. Subsequently, the targeted regulatory relationship between miR-183 and si-DNAJB4 was confirmed by bioinformatic prediction tools and double luciferase report genes analysis method. The regulatory mechanism of butyrate on miR-183/DNAJB4 axis signal pathway was evaluated in molecular level, and verified in nude mouse xerograft tumor model and immunohistochemical analysis tests of Ki67 positive rates. The results displayed that butyrate with increased concentration can hinder the proliferation and improve apoptosis of CRC cells by decreasing the expression of miR-183. Thus, butyrate reduces miR-183 expression and increases DNAJB4 expression via the miR-183/DNAJB4 axis, ultimately inhibiting the malignant progression and increasing apoptosis of CRC. While over expression of miR-183 downregulate the expression of DNAJB4, which can reverse the inhibitory effect of butyrate.

Expression of long noncoding RNA MEG3 and microRNA-302b-3p in colon cancer: Correlation with clinical stage and value in predicing prognosis after surgical treatment

BACKGROUND

More and more long non-coding RNAs and microRNAs have been found to have significant changes in expression levels during the occurrence and development of tumors, which can affect the expression of tumor suppressor genes or oncogenes and play an important role in the proliferation and metastasis of cancer cells.

AIM

To investigate the correlation between the expression of long non-coding RNA maternal imprinted gene 3 (LncRNA MEG3) and microRNA (miR)-302b-3p in colon cancer and clinical stage and analyze their value in predicting the prognosis after surgical treatment.

METHODS

A total of 97 patients with colon cancer treated at Jinhua Hospital of TCM from January 2017 to March 2022 were selected to compare the expression of LncRNA MEG3 and miR-302b-3p in different tissues, analyze the correlation between the expression of LncRNA MEG3 and miR-302b-3p and clinical pathological characteristics, compare the recurrence in patients with different LncRNA MEG3 and miR-302b-3p expression, analyze the factors affecting the recurrence of colon cancer after surgery, and analyze the impact of the interaction between LncRNA MEG3 and miR-302b-3p on the recurrence of colon cancer. The predictive value of LncRNA MEG3 and miR-302b-3p expression for the recurrence of colon cancer after surgery was evaluated.

RESULTS

The expression of LncRNA MEG3 and miR-302b-3p in colon cancer tissues was lower than that in tumor-adjacent tissues (P < 0.05). The expression of LncRNA MEG3 and miR-302b-3p in colon cancer tissues was not correlated with sex, age, or tumor size (P > 0.05), but was correlated with tumor differentiation, clinical stage, and lymph node metastasis (P < 0.05). In colon cancer tissues, the recurrence rate in patients with high LncRNA MEG3 and miR-302b-3p expression was lower than that of patients with lower LncRNA MEG3 and miR-302b-3p expression (P < 0.05). Tumor differentiation degree, clinical stage, and lymph node metastasis were all identified to be risk factors for colon cancer recurrence, and LncRNA MEG3 and miR-302b-3p expression were protective factors for colon cancer recurrence (P < 0.05). The interaction analysis showed that the synergistic effect of simultaneous exposure to LncRNA MEG3 and miR-302b-3p was 15.888 times greater than the effect of exposure to either LncRNA MEG3 or miR-302b-3p alone, and when simultaneously exposing to both, 56.98% of the risk of colon cancer recurrence was attributed to their synergistic effect. The area under the curve (AUC) (95% confidence interval [CI]) of LncRNA MEG3 and miR-302b-3p in predicting the prognosis of colon cancer patients was 0.720 (0.620-0.807) and 0.767 (0.670-0.847), respectively, and that of the combined prediction was 0.892 (0.813-0.946), with a sensitivity and specificity of 92.31% and 83.33%, respectively, which were significantly higher than those of either LncRNA MEG3 or miR-302b-3p alone.

CONCLUSION

The down-regulated expression of LncRNA MEG3 and miR-302b-3p in colon cancer is related to clinical stage. Clinical detection of their expression can be used to determine the malignant degree of tumor and predict the prognosis of surgical treatment, thus providing reference for adjustment of clinical treatment plan.

Network analysis reveals miRNA crosstalk between periodontitis and oral squamous cell carcinoma

BACKGROUND

Oral squamous cell carcinoma (OSCC) is one of the malignant tumors with a poor prognosis. Periodontitis (PD is considered a high-risk factor for OSCC, but the genetic mechanism is rarely studied. This study aims to link OSCC and PD by identifying common differentially expressed miRNAs (Co-DEmiRNAs), their related genes (Hub genes), transcription factors (TFs), signaling pathways, enrichment functions, and compounds, and searching for genetic commonalities.

METHODS

The miRNAs expression datasets of OSCC and PD were searched from the GEO database. The miRNA and related crosstalk mechanism between OSCC and PD was obtained through a series of analyses.

RESULTS

hsa-mir-497, hsa-mir-224, hsa-mir-210, hsa-mir-29c, hsa-mir-486-5p, and hsa-mir-31are the top miRNA nodes in Co-DEmiRNA-Target networks. The most significant candidate miRNA dysregulation genes are ZNF460, FBN1, CDK6, BTG2, and CBX6, while the most important dysregulation TF includes HIF1A, TP53, E2F1, MYCN, and JUN. 5-fluorouracil, Ginsenoside, Rh2, and Formaldehyde are the most correlated compounds. Enrichment analysis revealed cancer-related pathways and so on.

CONCLUSIONS

The comprehensive analysis reveals the interacting genetic and molecular mechanism between OSCC and PD, linking both and providing a foundation for future basic and clinical research.