The landscape of immune checkpoint-related long non-coding RNAs core regulatory circuitry reveals implications for immunoregulation and immunotherapy responses

LncRNA AF117829.1 is correlated with prognosis and immune infiltration and facilitates tumor progression by targeting OR7C1 in colorectal cancer

Background

Colorectal cancer (CRC) is one of the most common malignant tumors in the digestive system with a high incidence, a poor prognosis and an unsatisfactory therapeutic effect. Long non-coding RNAs (lncRNAs) play crucial roles in various biological processes related to tumor progression. Immune-related lncRNA gene AF117829.1 has been reported to participate in the construction of clinical predictive signature in CRC patients, suggesting that it may be involved in regulating the immune landscape and progression of CRC. However, the clinical and immunological significance and biological function of AF117829.1 in CRC remain unclear. In this study, we aim to explore the roles of AF117829.1 in CRC progression by bioinformatics analysis and experimental studies, thereby providing new targets for CRC treatment.

Methods

This study collected data from The Cancer Genome Atlas (TCGA) database and explored the role of AF117829.1 in CRC by bioinformatics analysis. Cell-type Identification By Estimating Relative Subsets Of known RNA Transcripts (CIBERSORT) and Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE) methods estimated the immune infiltration. Gene Set Enrichment Analysis (GSEA) was performed to evaluate the enrichment of functional pathways and gene signatures. The biological functions and mechanism of AF117829.1 in CRC progression were validated using CRC tissues and in vitro experiments.

Results

In our study, high expression of AF117829.1 was found in pan-cancer including CRC and was positively associated with tumor (T) stage and tumor-node-metastasis (TNM) stage in CRC. The survival analysis results showed that CRC patients with high-AF117829.1 expression had significantly shorter overall survival (OS) time than those with low-AF117829.1 expression. Moreover, AF117829.1 expression was negatively associated with microsatellite instability (MSI) in colon adenocarcinoma (COAD). Subsequently, AF117829.1 expression was confirmed to be significantly associated with StromalScore, immune cell infiltration (ICI) levels and immune checkpoints (ICP) genes expression in CRC. The immunophenoscore (IPS) results indicated that immunotherapy could be more effective in CRC patients with low-AF117829.1 expression. Then we confirmed that AF117829.1 was highly expressed in CRC cell lines and tissues. Furthermore, our GSEA results showed that olfactory transduction-related signaling pathways were significantly enriched in the high-AF117829.1 expression group. Finally, in vitro experiments confirmed that AF117829.1 overexpression promoted the proliferation, migration and invasion of CRC cells by targeting olfactory receptor family 7 subfamily C member 1 (OR7C1).

Conclusions

LncRNA AF117829.1 is closely related to the prognosis, immunological characteristics and immunotherapy response of CRC patients and promotes malignant progression of CRC by targeting OR7C1. Moreover, AF117829.1 may be a potential therapeutic target for CRC patients.

Non-Coding RNA-Targeted Therapy: A State-of-the-Art Review

The use of non-coding RNAs (ncRNAs) as drug targets is being researched due to their discovery and their role in disease. Targeting ncRNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), is an attractive approach for treating various diseases, such as cardiovascular disease and cancer. This seminar discusses the current status of ncRNAs as therapeutic targets in different pathological conditions. Regarding miRNA-based drugs, this approach has made significant progress in preclinical and clinical testing for cardiovascular diseases, where the limitations of conventional pharmacotherapy are evident. The challenges of miRNA-based drugs, including specificity, delivery, and tolerability, will be discussed. New approaches to improve their success will be explored. Furthermore, it extensively discusses the potential development of targeted therapies for cardiovascular disease. Finally, this document reports on the recent advances in identifying and characterizing microRNAs, manipulating them, and translating them into clinical applications. It also addresses the challenges and perspectives towards clinical application.

The landscape of immune checkpoint-related long non-coding RNAs core regulatory circuitry reveals implications for immunoregulation and immunotherapy responses

Long non-coding RNAs (lncRNAs) could modulate expression of immune checkpoints (ICPs) by cooperating with immunity genes in tumor immunization. However, precise functions in immunity and potential for predicting ICP inhibitors (ICI) response have been described for only a few lncRNAs. Here we present an integrated framework that leverages network-based analyses and Bayesian network inference to identify the regulated relationships including lncRNA, ICP and immunity genes as ICP-related LncRNAs mediated Core Regulatory Circuitry Triplets (ICP-LncCRCTs) that can make robust predictions. Hub ICP-related lncRNAs such as MIR155HG and ADAMTS9-AS2 were highlighted to play central roles in immune regulation. Specific ICP-related lncRNAs could distinguish cancer subtypes. Moreover, the ICP-related lncRNAs are likely to significantly correlated with immune cell infiltration, MHC, CYT. Some ICP-LncCRCTs such as CXCL10-MIR155HG-ICOS could better predict one-, three- and five-year prognosis compared to single molecule in melanoma. We also validated that some ICP-LncCRCTs could effectively predict ICI-response using three kinds of machine learning algorithms follow five independent datasets. Specially, combining ICP-LncCRCTs with the tumor mutation burden (TMB) improves the prediction of ICI-treated melanoma patients. Altogether, this study will improve our grasp of lncRNA functions and accelerating discovery of lncRNA-based biomarkers in ICI treatment.