LncRNA SENCR promotes cell proliferation and progression in non-small-cell lung cancer cells via sponging miR-1-3p

ncRNAs-mediated TIMELESS overexpression in lung adenocarcinoma correlates with reduced tumor immune cell infiltration and poor prognosis

Lung adenocarcinoma (LUAD) has a poor prognosis. Circadian genes such as TIMELESS have been associated with several pathologies, including cancer. The expression of TIMELESS and the relationship between TIMELESS, infiltration of tumors and prognosis in LUAD requires further investigation. In this study, we investigated the expression of TIMELESS and its association with survival across several types of human cancer using data from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression Program. Noncoding RNAs (ncRNAs) regulating overexpression of TIMELESS in lung adenocarcinoma (LUAD) were explored with expression, correlation, and survival analyses. Immune cell infiltration and biomarkers were analyzed between different TIMELESS expression levels. The relationship between TIMELESS expression and immunophenoscores, which were used to predict response to immunotherapy, was evaluated. TIMELESS was identified as a potential oncogene in LUAD. NcRNA analysis showed MIR4435-2HG/hsa-miR-1-3p may interact with TIMELESS in a competitive endogenous RNA network in LUAD tumor tissues. Most immune cells were significantly decreased in TCGA LUAD tumor tissues with high TIMELESS expression except for CD4+T cells and Th2 cells. TIMELESS expression in LUAD tumor tissues was significantly negatively correlated with neutrophil biomarkers, dendritic cell biomarkers (HLA-DPB1, HLA-DQB1, HLA-DRA, HLA-DPA1, CD1C) and an immunophenoscore that predicted outcomes associated with the use of immune checkpoint inhibitors. These findings imply that ncRNAs-mediated TIMELESS overexpression in LUAD tumor tissues correlated with poor prognosis, reduced immune cell infiltration in the tumor microenvironment, and poor response to immune checkpoint inhibitors.

DNA methylation-related lncRNAs predict prognosis and immunotherapy response in gastric cancer

BACKGROUND

LncRNAs and DNA methylation are both key regulators of tumorigenesis and immune regulation. However, the interaction between lncRNA and DNA methylation, their regulation and their clinical and immune relevance in gastric cancer (GC) remain unclear.

METHODS

In this study, we identified DNA methylation regulator-related lncRNAs through Pearson correlation analysis in The Cancer Genome Atlas datasets. Univariate Cox regression was used to screen DNA methylationrelated prognostic lncRNAs. Further, through least absolute shrinkage and selection operator Cox regression, a prognostic model based on 13 lncRNAs was established. Survival analysis and receiver operating characteristic curve analysis verified the accuracy of the model in predicting the survival of GC patients. Univariate and multivariate analyses also confirmed that the risk score obtained from the risk model could be applied as an independent prognostic factor for patients with GC. Furthermore, based on the risk score and other clinicopathological characteristics that can be used as independent prognostic factors, we constructed a nomogram that could accurately determine the survival time of each patient. In addition, a lncRNA score was constructed using a principal component analysis algorithm to quantify the DNA methylation-related lncRNA expression patterns of individual tumors.

RESULTS

We found that a higher lncRNA score indicated a worse the prognosis and was associated with a reduced tumor mutation burden and immunosuppression. A low lncRNA score was related to an increase in neoantigen load and an increase in the anti-PDL1/CTLA4 immunotherapy response. Additionally, a low lncRNA score was related to a significant therapeutic advantage and clinical benefit.

CONCLUSIONS

This study describes a DNA methylation regulator-related lncRNA signature model, which provides a new approach for predicting therapeutic response and patient stratification in GC. Assessing lncRNA expression patterns in individual tumors will contribute to enhancing our understanding of tumor microenvironment infiltration and guide more effective immunotherapy strategies.

Long noncoding RNA SENCR facilitates the progression of acute myeloid leukemia through the miR-4731-5p/IRF2 pathway

BACKGROUND

Acute myeloid leukemia (AML) is a type of hematological tumor caused by malignant clone hematopoietic stem cells. The relationship between lncRNAs and tumor occurrence and progression has been gaining attention. Research has shown that Smooth muscle and endothelial cell-enriched migration/differentiation-associated lncRNA (SENCR) is abnormally expressed in various diseases, whereas its role in AML is still poorly understood.

METHODS

The expression of SENCR, microRNA-4731-5p (miR-4731-5p) and Interferon regulatory factor 2 (IRF2) were measured using qRT-PCR. The proliferation, cycle and apoptosis of AML cells with or without knockdown of SENCR were detected by CCK-8 assay, EdU assay, flow cytometry, western blotting and TUNEL assay, respectively. Consistently, SENCR knockdown was impaired the AML progression in immunodeficient mice. In addition, the binding of miR-4731-5p to SENCR or IRF2 was confirmed by luciferase reporter genes assay. Finally, rescue experiments were conducted to confirm the role of SENCR/miR-4731-5p/IRF2 axis in AML.

RESULTS

SENCR is highly expressed in AML patients and cell lines. The patients with high SENCR expression had poorer prognosis compared with those with low SENCR expression. Interestingly, knockdown of SENCR inhibits the growth of AML cells. Further results demonstrated that the reduction of SENCR slows the progression of AML in vivo. SENCR could function as a competing endogenous RNA (ceRNA) to negatively regulate miR-4731-5p in AML cells. Furthermore, IRF2 was validated as a direct target gene of miR-4731-5p in AML cells.

CONCLUSIONS

Our findings underscore the important role of SENCR in regulating the malignant phenotype of AML cells by targeting the miR-4731-5p/IRF2 axis.

A review on the role of cyclin dependent kinases in cancers

The Cyclin-dependent kinase (CDK) class of serine/threonine kinases has crucial roles in the regulation of cell cycle transition and is mainly involved in the pathogenesis of cancers. The expression of CDKs is controlled by a complex regulatory network comprised of genetic and epigenetic mechanisms, which are dysregulated during the progression of cancer. The abnormal activation of CDKs results in uncontrolled cancer cell proliferation and the induction of cancer stem cell characteristics. The levels of CDKs can be utilized to predict the prognosis and treatment response of cancer patients, and further understanding of the function and underlying mechanisms of CDKs in human tumors would pave the way for future cancer therapies that effectively target CDKs. Defects in the regulation of cell cycle and mutations in the genes coding cell-cycle regulatory proteins lead to unrestrained proliferation of cells leading to formation of tumors. A number of treatment modalities have been designed to combat dysregulation of cell cycle through affecting expression or activity of CDKs. However, effective application of these methods in the clinical settings requires recognition of the role of CDKs in the progression of each type of cancer, their partners, their interactions with signaling pathways and the effects of suppression of these kinases on malignant features. Thus, we designed this literature search to summarize these findings at cellular level, as well as in vivo and clinical levels.

Identification of pyroptosis-related genes and long non-coding RNAs signatures in osteosarcoma

Osteosarcoma is a highly malignant tumor, with very high disability and fatality rates. However, the overall prognosis is not optimistic. Pyroptosis is a newly discovered cell death modality accompanied by inflammation, which is closely related to varieties of cancers. In this study, the RNA-seq data were downloaded from public databases, the differences in the expression of the pyroptosis-related genes (PRGs) were identified, and the six PRGs signature was established through the univariate and LASSO Cox analysis. The patients were grouped according to the PRGs signature, and the prognosis between the two groups was further compared. In addition, a ten pyroptosis-related lncRNAs (PRLs) prognostic signature was also constructed. Through functional analysis of the differentially expressed genes (DEGs), the immune-related pathways were found to be enriched. The Pearson correlation analysis showed a strong correlation between the pyroptosis-related biomarkers. Finally, we identified a promising biomarker, CHMP4C, which is highly expressed in osteosarcoma. Overexpression of CHMP4C promoted the proliferation, migration and invasion of the osteosarcoma cell. Our results thus provide new evidence for exploring prognostic biomarkers and therapeutic targets of osteosarcoma.

Identification of cuproptosis-associated IncRNAs signature and establishment of a novel nomogram for prognosis of stomach adenocarcinoma

Purpose: Stomach adenocarcinoma (STAD) is one of the common cancers globally. Cuproptosis is a newly identified cell death pattern. The role of cuproptosis-associated lncRNAs in STAD is unknown.

Methods: STAD patient data from TCGA were used to identify prognostic lncRNAs by Cox regression and LASSO. A nomogram was constructed to predict patient survival. The biological profiles were evaluated through GO and KEGG.

Results: We identified 298 cuproptosis-related lncRNAs and 13 survival-related lncRNAs. Patients could be categorized into either high risk group or low risk group with 9-lncRNA risk model with significantly different survival time (p < 0.001). ROC curve and nomogram confirmed the 9-lncRNA risk mode had good prediction capability. Patients in the lower risk score had high gene mutation burden. We also found that patients in the two groups might respond differently to immune checkpoint inhibitors and some anti-tumor compounds.

Conclusion: The nomogram with 9-lncRNA may help guide treatment of STAD. Future clinical studies are necessary to verify the nomogram.

Effect of lncRNA00511 on Non-Small Cell Lung Cancer by Regulating miR-29b-3p

This study assessed the effect of LINC00511 on NSCLC cells through regulating miR-29b-3p/DRAM1 axis. LINC00511 expression in NSCLC tissue and para-carcinoma tissue was analyzed and its correlation with TNM stage was assessed. Lung carcinoma cells as A549 cells were cultivated in vitro and transfected with LINC00511 siRNA or plasmid with DRAM1 overexpression followed by analysis of LINC00511 and miR-184 expression by RT-PCR, cell proliferation and invasion, Bcl-2, Bax and DRAM1 expression by Western Blot. LINC00511 was significantly upregulated in NSCLC tissue and positively correlated with the TNM staging. However, miR-29b-3p was significantly downregulated in NSCLC tissue. The miR-29b-3p was a target of LINC00511. The DRAM1 was a target of miR-29b-3p. Downregulation of LINC00511 restrained proliferation and invasion of A549 cells and promoted cell apoptosis. The development of NSCLC could be prompted by increasing the presentation of LINC00511 through increasing presentation of DRAM1 and being targeted with miR-29b-3p. It could be restrained through reducing the presentation of LINC00511.