Comprehensive characterization genetic regulation and chromatin landscape of enhancer-associated long non-coding RNAs and their implication in human cancer

Ferroptosis-related lncRNAs: Distinguishing heterogeneity of the tumour microenvironment and predicting immunotherapy response in bladder cancer

Ferroptosis, a cell death pathway dependent on iron, has been shown in research to play a role in the development, advancement, and outlook of tumours through ferroptosis-related lncRNAs (FRLRs). However, the value of the FRLRs in bladder cancer (BLCA) has not been thoroughly investigated. This research project involved developing a predictive model using ten specific FRLRs (AC099850.4, AL731567.1, AL133415.1, AC021321.1, SPAG5-AS1, HMGA2-AS1, RBMS3-AS3, AC006160.1, AL583785.1, and AL662844.4) through univariate COX and LASSO regression techniques. The validation of this signature as a standalone predictor was confirmed in a group of 65 patients from the urology bladder tumour database at the First Affiliated Hospital of Wenzhou Medical University in Wenzhou, China. Patients were categorized based on their median risk score into either a low-risk group or a high-risk group. Enrichment analysis identified possible molecular mechanisms that could explain the variations in clinical outcomes observed in high-risk and low-risk groups. Moreover, we explored the correlation between FLPS and immunotherapy-related indicators. The ability of FLPS to forecast the effectiveness of immunotherapy was validated by the elevated levels of immune checkpoint genes (PD-L1, CTLA4, and PD-1) in the group at high risk. We also screened the crucial FRLR (HMGA2-AS1) through congruent expression and prognostic conditions and established a ceRNA network, indicating that HMGA2-AS1 may affect epithelial-mesenchymal transition by modulating the Wnt signalling pathway through the ceRNA mechanism. We identified the top five mRNAs (NFIB, NEGR1, JAZF1, JCAD, and ESM1) based on random forest algorithm and analysed the relationship between HMGA2-AS1, the top five mRNAs, and immunotherapy, and their interactions with drug sensitivities. Our results suggest that patients with BLCA have a greater sensitivity to four drugs (dasatinib, pazopanib, erismodegib and olaparib). Our study provides new insights into the TME, key signalling pathways, genome, and potential therapeutic targets of BLCA, with future guidance for immunotherapy and targeted precision drugs.

Machine learning-based integration develops an immunogenic cell death-derived lncRNA signature for predicting prognosis and immunotherapy response in lung adenocarcinoma

Accumulating evidence demonstrates that lncRNAs are involved in the regulation of the immune microenvironment and early tumor development. Immunogenic cell death occurs mainly through the release or increase of tumor-associated antigen and tumor-specific antigen, exposing "danger signals" to stimulate the body's immune response. Given the recent development of immunotherapy in lung adenocarcinoma, we explored the role of tumor immunogenic cell death-related lncRNAs in lung adenocarcinoma for prognosis and immunotherapy benefit, which has never been uncovered yet. Based on the lung adenocarcinoma cohorts from the TCGA database and GEO database, the study developed the immunogenic cell death index signature by several machine learning algorithms and then validated the signature for prognosis and immunotherapy benefit of lung adenocarcinoma patients, which had a more stable performance compared with published signatures in predicting the prognosis, and demonstrated predictive value for benefiting from immunotherapy in multiple cohorts of multiple cancers, and also guided the utilization of chemotherapy drugs.

Non-coding RNAs in disease: from mechanisms to therapeutics

Non-coding RNAs (ncRNAs) are a heterogeneous group of transcripts that, by definition, are not translated into proteins. Since their discovery, ncRNAs have emerged as important regulators of multiple biological functions across a range of cell types and tissues, and their dysregulation has been implicated in disease. Notably, much research has focused on the link between microRNAs (miRNAs) and human cancers, although other ncRNAs, such as long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), are also emerging as relevant contributors to human disease. In this Review, we summarize our current understanding of the roles of miRNAs, lncRNAs and circRNAs in cancer and other major human diseases, notably cardiovascular, neurological and infectious diseases. Further, we discuss the potential use of ncRNAs as biomarkers of disease and as therapeutic targets.

Identifying immune checkpoint-related lncRNA biomarkers for immunotherapy response and prognosis in cancers

Long non-coding RNAs (lncRNAs) could modulate expression of immune checkpoints (ICPs) in tumor-immune. However, precise functions in immunity and potential for predicting ICP inhibitors (ICI) response have been described for only a few lncRNAs. Here, a multiple-step pipeline was developed to identify cancer- and immune-context ICP and lncRNA cooperative regulation pairs (ICPaLncCRPs) across cancers. Immune-related ICPs and lncRNAs were extracted follow immune cell lines and immunologic constant of rejection groups. ICPaLncCRP networks were constructed, which likely to modulate tumor-immune by specific patterns. Common and specific hub ICPaLncs such as MIR155HG, TRG-AS1 and PCED1B-AS1 maybe play central roles in prognosis and circulating. Moreover, these hub ICPaLncs were significantly correlated with immune cell infiltration based on bulk and single-cell RNA sequencing data. Some ICPaLncCRPs such as IDO1-MIR155HG could predict three- and five-year prognosis of melanoma in two independent datasets. We also validated that some ICPaLncCRPs could effectively predict ICI-response follow six independent datasets. Collectively, this study will enhance our understanding of lncRNA functions and accelerate discovery of lncRNA-based biomarkers in ICI treatment.

HOTAIR in colorectal cancer: structure, function, and therapeutic potential

lncRNAs play a vital part in cancer development by regulating gene expression. Among these, the lncRNA HOTAIR has gained considerable attention due to its entanglement in multiple cellular processes, including chromatin remodeling and gene regulation. HOTAIR has a complex structure consisting of multiple domains that interact with various protein complexes and RNA molecules. In colorectal cancer (CRC), HOTAIR expression is upregulated, and its overexpression has been correlated with poor patient prognosis and resistance to chemotherapy. HOTAIR has been found to regulate gene expression and promote cancer growth by interacting with specific miRNAs. In addition, HOTAIR has been implicated in the development of treatment resistance in colorectal cancer. To develop effective treatments, it's important to understand how HOTAIR regulates gene expression. This article discusses HOTAIR's structure, functions, and mechanisms in CRC and its potential as a target for therapy. The author also suggests future research directions to better understand HOTAIR's role in CRC progression and drug resistance.

Proteogenomic characterization of ferroptosis regulators reveals therapeutic potential in glioblastoma

BACKGROUND

Ferroptosis is iron-dependent non-apoptotic cell death, that is characterized by the excessive accumulation of lipid peroxides. Ferroptosis-inducing therapy also shows promise in the treatment of cancers. However, ferroptosis-inducing therapy for glioblastoma multiforme (GBM) is still in the exploratory stage.

METHODS

We identified the differentially expressed ferroptosis regulators using Mann-Whitney U test in the proteome data from Clinical Proteomic Tumor Analysis Consortium (CPTAC). We next analyzed the effect of mutation on protein abundance. A multivariate Cox model was constructed to identify the prognostic signature.

RESULTS

In this study, we systemically portrayed the proteogenomic landscape of ferroptosis regulators in GBM. We observed that some mutation-specific ferroptosis regulators, such as down-regulated ACSL4 in EGFR-mutated patients and up-regulated FADS2 in IDH1-mutated patients, were linked to the inhibited ferroptosis activity in GBM. To interrogate the valuable treatment targets, we performed the survival analysis and identified five ferroptosis regulators (ACSL3, HSPB1, ELAVL1, IL33, and GPX4) as the prognostic biomarkers. We also validated their efficiency in external validation cohorts. Notably, we found overexpressed protein and phosphorylation abundances of HSPB1 were poor prognosis markers for overall survival of GBM to inhibit ferroptosis activity. Alternatively, HSPB1 showed a significant association with macrophage infiltration levels. Macrophage-secreted SPP1 could be a potential activator for HSPB1 in glioma cells. Finally, we recognized that ipatasertib, a novel pan-Akt inhibitor, could be a potential drug for suppressing HSPB1 phosphorylation, inducing ferroptosis of glioma cells.

CONCLUSION

In summary, our study characterized the proteogenomic landscape of ferroptosis regulators and identified that HSPB1 could be a candidate target for ferroptosis-inducing therapy strategy for GBM.

A cuproptosis-related long non-coding RNA signature to predict the prognosis and immune microenvironment characterization for lung adenocarcinoma

BACKGROUND

Cuproptosis or copper-dependent cell death is a newly identified non-apoptotic cell death pathway which plays a critical role in the development of multiple cancers. Long non-coding RNAs (lncRNAs) are increasingly recognized as crucial regulators of programmed cell death and lung adenocarcinoma (LUAD) development, and a comprehensive understanding of cuproptosis-related lncRNAs may improve prognosis prediction of LUAD. However, few studies have explored the association of cuproptosis-related lncRNAs with the prognosis of LUAD.

METHODS

The RNA sequencing data and corresponding clinical information of patients were extracted from The Cancer Genome Atlas (TCGA) database. Five hundred LUAD patients were randomly divided into a training (n=250) and a testing cohort (n=250). Pearson correlations were performed to identify cuproptosis-related lncRNAs, and univariate Cox regression was performed to screen prognostic lncRNAs. A cuproptosis-related lncRNAs prognostic signature (CLPS) was constructed by the least absolute shrinkage and selection operator Cox regression. Kaplan-Meier analysis, receiver operating characteristic curves, and multivariate Cox regression were performed to verify the prognostic performance of CLPS. Additionally, immune cell infiltration was estimated using the single-sample gene-set enrichment analysis. pRRophetic algorithm and Tumor Immune Dysfunction and Exclusion algorithm were used to assess the immunotherapy and chemotherapy response, respectively.

RESULTS

CLPS was established based on 61 cuproptosis-related prognostic lncRNAs and exhibited a satisfactory performance predicting LUAD patients' survival (area under the curve at 1, 3, 5 years was 0.784, 0.749, 0.775, respectively). multivariate Cox analysis confirmed the independent prognostic effect of CLPS (hazard ratio: 1.128; 95% confidence interval: 1.071-1.189; P<0.001), and a nomogram containing it exhibited robust validity in prognostic prediction. We further demonstrated a higher CLPS-risk score was associated with lower levels of signatures including immune cell infiltration, immune activation, and immune checkpoints.

CONCLUSIONS

The CLPS serves as an effective predictor for the prognosis and therapeutic responses of LUAD patients. Our findings provide promising novel biomarkers and therapeutic targets for LUAD.

Ferroptosis-Related Long Non-Coding RNA Signature Contributes to the Prediction of Prognosis Outcomes in Head and Neck Squamous Cell Carcinomas

Background: Head and neck squamous cell carcinoma (HNSCC) is a malignant tumor, which makes the prognosis prediction challenging. Ferroptosis is an iron-dependent form of non-apoptotic regulated cell death, which could affect cancer development. However, the prognostic value of ferroptosis-related long non-coding RNA (lncRNA) in HNSCC is still limited.

Methods: In the current study, we employed the DESeq2 method to characterize the differentially expressed ferroptosis-related genes (FEGs) between cancer and normal samples. Next, the FEG-related lncRNAs (FElncRNAs) were identified using Spearman’s correlation analysis and multiple permutation hypotheses. Subsequently, LASSO and stepwise multivariate Cox regression analyses were undertaken to recognize the prognosis-related FElncRNA signature (PFLS) and risk scores.

Results: Herein, we first identified 60 dysregulated FEGs and their co-expressed FElncRNAs in HNSCC. Then, we recognized a set of six FElncRNAs PFLS (SLCO4A1-AS1, C1RL-AS1, PCED1B-AS1, HOXB-AS3, MIR9-3HG, and SFTA1P) for predicting patients’ prognostic risks and survival outcomes. We also assessed the efficiency of PFLS in the test set and an external validation cohort. Further parsing of the tumor immune microenvironment showed the PFLS was closely associated with immune cell infiltration abundances. Notably, the low-risk group of the PFLS showed a higher MHC score and cytolytic activity (CYT) score than the high-risk group, implying the low-risk group may have greater tumor surveillance and killing ability. In addition, we observed that the expression levels of two immune checkpoints (ICPs), i.e., programmed cell death protein 1 (PD-1) and programmed cell death 1 ligand 1 (PD-L1), showed significant associations with patients’ risk score, prompting the role of the PFLS in ICP blockade therapy. Finally, we also constructed a drug–PFLS network to reinforce the clinical utilities of the PFLS.

Conclusion: In summary, our study indicated that FElncRNAs played an important role in HNSCC survival prediction. Identification of PFLS will contribute to the development of novel anticancer therapeutic strategies.