Long Noncoding RNA and Cancer: A New Paradigm

HOTAIR Participation in Glycolysis and Glutaminolysis Through Lactate and Glutamate Production in Colorectal Cancer

Metabolic reprogramming plays a crucial role in cancer biology and the mechanisms underlying its regulation represent a promising study area. In this regard, the discovery of non-coding RNAs opened a new regulatory landscape, which is in the early stages of investigation. Using a differential expression model of HOTAIR, we evaluated the expression level of metabolic enzymes, as well as the metabolites produced by glycolysis and glutaminolysis. Our results demonstrated the regulatory effect of HOTAIR on the expression of glycolysis and glutaminolysis enzymes in colorectal cancer cells. Specifically, through the overexpression and inhibition of HOTAIR, we determined its influence on the expression of the enzymes PFKFB4, PGK1, LDHA, SLC1A5, GLUD1, and GOT1, which had a direct impact on lactate and glutamate production. These findings indicate that HOTAIR plays a significant role in producing "oncometabolites" essential to maintaining the bioenergetics and biomass necessary for tumor cell survival by regulating glycolysis and glutaminolysis.

Development of a PANoptosis-related LncRNAs for prognosis predicting and immune infiltration characterization of gastric Cancer

PANoptosis is a newly discovered form of programmed cell death (PCD), involving the interaction of cellular pyroptosis, apoptosis, and necroptosis. Although PANoptosis plays a significant role in carcinogenesis process, the impact of PANoptosis-related lncRNAs (PANlncRNAs) on the prognostic value and mechanism of immune infiltration of gastric cancer have not been studied. All information of gastric cancer (GC) patients was downloaded from the TCGA database. PANoptosis-related genes were obtained from molecular characteristic databases, and PANlncRNAs were screened through Pearson correlation analysis. Based on this, PANlncRNAs were subjected to univariate Cox regression analysis using the least absolute shrinkage and selection operator (LASSO) algorithm to obtain lncRNA associated with survival outcomes, which were subsequently used to calculate survival scores and to construct signatures. Through further analysis of clinical subgroups, immune infiltration, drug sensitivity analysis, tumor mutation burden testing, and GSEA enrichment pathway analysis, their clinical significance was comprehensively analyzed. This study constructed a prognosis model for gastric cancer based on 8 PANlncRNAs and validated its prognostic value. The study showed that the survival time and outcome of the high-risk subgroup was significantly worse than that of the low-risk subgroup. The bar graph showed satisfactory predictive results, and the calibration curve showed good consistency between the prognostic model and actual prognostic outcomes. TIDE and drug sensitivity analysis showed significant differences between high and low-risk subgroups. The prognosis model based on PANlncRNAs has important implications for the judgment and precision treatment of gastric cancer.

HOXA10-AS Enhances Gastric Cancer Cell Proliferation, Migration, and Invasion via the p38 MAPK/STAT3 Signaling Pathway

Gastric cancer (GC) represents a major global health concern, with over 1 million new cases diagnosed annually worldwide. Emerging studies have highlighted the significant correlation between long noncoding RNAs (lncRNAs) and the progression of GC. The objective of the current study is to investigate the roles and mechanism of lncRNA homeobox A10 antisense RNA (HOXA10-AS) in modulating malignant properties of GC cells. RT-qPCR was employed to detect HOXA10-AS expression in GC cells or human normal gastric epithelium cells. The cellular localization of HOXA10-AS and mRNA HOXA10 were detected using RNA fractionation assays. Colony forming assays and Transwell assays were performed to assess the proliferative, invasive, and migratory capabilities of GC cells. Western blot analysis was used to determine protein levels of epithelial mesenchymal transition (EMT) markers in GC cells. RNA immunoprecipitation, RNA pulldown assays and luciferase assays were conducted to explore gene interaction. As shown by experimental results, HOXA10-AS showed high expression in GC cells. The silencing of HOXA10-AS led to weakened proliferative, invasive, and migratory abilities of GC cells, as well as inhibition of the EMT process. Moreover, HOXA10-AS positively regulated HOXA10 expression by interacting with miR-29a/b/c-3p. Additionally, overexpression of HOXA10 counteracted the repressive impacts on malignant cellular process caused by the knockdown of HOXA10-AS. Furthermore, HOXA10-AS activated the p38 MAPK/STAT3 signaling pathway via upregulation of HOXA10. In conclusion, HOXA10-AS upregulates HOXA10 expression through interaction with miR-29a/b/c-3p. The resultant increase in HOXA10 expression activates the p38 MAPK/STAT3 signaling, thereby promoting GC cell growth, migration, invasion, and EMT process.

Integrating Bioinformatics and Experimental Validation to Identify Mitochondrial Permeability Transition-Driven Necrosis-Related lncRNAs that can Serve as Prognostic Biomarkers and Therapeutic Targets in Endometrial Carcinoma

Endometrial carcinoma (EC) is a common malignant tumor in women with high mortality and relapse rates. Mitochondrial permeability transition (MPT)-driven necrosis is a novel form of programmed cell death. The MPT-driven necrosis related lncRNAs (MRLs) involved in EC development remain unclear. We aimed to predict the outcomes of patients with EC by constructing a novel prognostic model based on MRLs and explore potential molecular functions. A risk prognostic model was developed utilizing multi-Cox regression in conjunction with the Least Absolute Shrinkage and Selection Operator (LASSO) regression algorithm, which was based on MRLs. The predictive efficacy of the model was evaluated through receiver operating characteristic (ROC) curve analysis, as well as nomogram and concordance index (C-index) assessments. Patients were categorized into high- and low-risk groups based on their median risk scores. Notably, the high-risk group exhibited significantly poorer overall survival (OS) outcomes. Gene ontology (GO) and Gene set enrichment analysis (GSEA) demonstrated that Hedgehog and cell cycle pathways were enriched in the high-risk group. Tumor Immune Dysfunction and Exclusion (TIDE) displayed that patients in the high-risk group showed a high likelihood of immune evasion and less effective immunotherapy. A significant disparity in immune function was also observed between two groups. Based on the nine-MRLs, drug sensitivity analysis identified several anticancer drugs with potential efficacy in prognosis. Meanwhile, the results demonstrated that OGFRP1 plays a carcinogenic role by affecting mitochondrial membrane permeability in EC. Therefore, the risk model constructed by nine MRLs could be used to predict the clinical outcomes and therapeutic responses in patients with EC effectively.

Non-coding RNAs as mediators of epithelial to mesenchymal transition in metastatic colorectal cancers

Colorectal cancer (CRC) remains a leading cause of cancer-related mortality globally, necessitating the development of innovative treatment strategies. Recent research has underscored the significant role of non-coding RNAs (ncRNAs) in CRC pathogenesis, offering new avenues for diagnosis and therapy. In this review, we delve into the intricate roles of various ncRNAs, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), in CRC progression, epithelial-mesenchymal transition (EMT), metastasis, and drug resistance. We highlight the interaction of these ncRNAs with and regulation of key signaling pathways, such as Wnt/β-catenin, Notch, JAK-STAT, EGFR, and TGF-β, and the functional relevance of these interactions in CRC progression. Additionally, the review highlights the emerging applications of nanotechnology in enhancing the delivery and efficacy of ncRNA-based therapeutics, which could address existing challenges related to specificity and side effects. Future research directions, including advanced diagnostic tools, targeted therapeutics, strategies to overcome drug resistance, and the integration of personalized medicine approaches are discussed. Integrating nanotechnology with a deeper understanding of CRC biology offers the potential for more effective, targeted, and personalized strategies, though further research is essential to validate these approaches.

The emerging landscape of small nucleolar RNA host gene 10 in cancer mechanistic insights and clinical relevance

Small nucleolar RNA host gene 10 (SNHG10) is a newly recognized long non-coding RNA (lncRNA) with significant implications in cancer biology. Abnormal expression of SNHG10 has been observed in various solid tumors and hematological malignancies. Research conducted in vivo and in vitro has revealed that SNHG10 plays a pivotal role in numerous biological processes, including cell proliferation, apoptosis, invasion and migration, drug resistance, energy metabolism, immune evasion, as well as tumor growth and metastasis. SNHG10 regulates tumor development through several mechanisms, such as competing with microRNA (miRNA) for binding sites, modulating various signaling pathways, influencing transcriptional activity, and affecting epigenetic regulation. The diverse biological functions and intricate mechanisms of SNHG10 highlight its considerable clinical relevance, positioning it as a potential pan-cancer biomarker and therapeutic target. This review aims to summarize the role of SNHG10 in tumorigenesis and cancer progression, clarify the molecular mechanisms at play, and explore its clinical significance in cancer diagnosis and prognosis prediction, along with its therapeutic potential.

Survival expectations in melanoma patients: a molecular prognostic model associated with aging

BACKGROUND

Aging and long non-coding RNAs (lncRNAs) are research hotspots in melanoma. However, no study has so far explored the relationship between melanoma prognosis and aging-related lncRNAs (ARLs).

METHODS

The Cancer Genome Atlas database, the GTEx database, and the HAGR database were used in this study in a combined manner. Univariate and multivariate cox regression analyses were used to screen out lncRNA signatures associated with overall survival (OS) in the primary dataset. The risk scoring model was analyzed by risk stratification and tested internally. The protein expression levels of possible target genes of ARLs were verified by immunohistochemistry analysis in HPA database. Finally, gene enrichment analysis was performed.

RESULTS

In the primary dataset, five OS-related lncRNA signatures (AC011481.1, USP30-AS1, EBLN3P, LINC01527, HLA-DQB1-AS1) were screened out. The survival curve showed that the high-risk group had a worse prognosis than the low-risk group. The immunohistochemical analysis revealed that reduced expression of Epidermal Growth Factor Receptor (EGFR), along with increased expression of Activating Transcription Factor 2 (ATF2) and DNA Polymerase Delta 1 (POLD1), was linked to a worse prognosis. Finally, enrichment analysis revealed that OS-related DELs were significantly enriched in the regulation of reactive oxygen metabolism, etc. The ARGs were significantly activated in the SKCM tissues. The regulation of aging in melanoma cells may be realized through ferroptosis, immunity, and autophagy and so on.

CONCLUSION

The ARL signature obtained in this study had better prognostic ability than individual clinical features.

Identification and validation of an m5C-related lncRNA signature for predicting prognosis and immune response in clear cell renal cell carcinoma

This study investigated whether m5C-related Long non-coding RNAs (lncRNAs) can predict clear cell renal cell carcinoma (ccRCC) patient prognosis. Co-expression and Cox regression analyses identified 9 prognostic lncRNAs, which were closely associated with tumor immune characteristics and immune escape. The model also predicted the sensitivity of drugs, including Entinostat, SB216763, and Sapitinib. In vitro experiments showed that GNG12-AS1 inhibited ccRCC cell proliferation and migration by reducing the activity of the ERK/GSK-3β/β-catenin pathway. Overall, these findings suggest that the 9 m5C-related lncRNAs can accurately predict ccRCC patient prognosis, providing potential applications for clinical and immunotherapy approaches. GNG12-AS1 emerges as a promising prognostic biomarker for predicting survival outcomes in ccRCC, potentially influencing cell migration through the activation of the ERK/GSK-3β/β-catenin signaling pathway.

Prognostic implications of ERLncRNAs in ccRCC: a novel risk score model and its association with tumor mutation burden and immune microenvironment

INTRODUCTION/BACKGROUND

The specific role of efferocytosis-related long noncoding RNAs (ERLncRNAs) in Clear Cell Renal Cell Carcinoma (ccRCC) has not been thoroughly examined. This study aims to identify and validate a signature of ERLncRNAs for prognostic prediction and characterization of the immune landscape in individuals with ccRCC.

MATERIALS AND METHODS

Analysis of ccRCC samples was conducted by utilizing clinical and RNA sequencing information obtained from The Cancer Genome Atlas (TCGA). Pearson correlation analysis was utilized to identify lncRNAs associated with efferocytosis, which was then used to create a new prognostic model through univariate Cox regression, Least Absolute Shrinkage and Selection Operator (LASSO) regression, and stepwise multivariate Cox analysis. In order to investigate the biological significance, we performed a functional enrichment analysis to assess how well the model predicts outcomes. Differences in the immune landscape were observed through a comparison of immune cell infiltration, tumor mutational burden (TMB), and tumor microenvironment (TME) characteristics. Following this, drug sensitivity analysis was conducted.

RESULTS

This led to the identification of a unique signature consisting of seven ERLncRNAs (LINC01615, RUNX3-AS1, FOXD2-AS1, AC002070.1, LINC02747, LINC00944, and AC092296.1). Model performance was measured by Kaplan-Meier curves and receiver operating characteristic (ROC) curves. The nomogram and C-index provided additional validation of the strong correlation between the risk signature and clinical decision-making.

CONCLUSION

On the whole, our innovative signature exhibits potential for prognostic prediction and assessment of immunotherapeutic response in patients with ccRCC.

AL365181.3 as a novel prognostic biomarker for lung adenocarcinoma

As a lncRNA, AL365181.3 is aberrantly expressed in multiple cancer types, including lung adenocarcinoma (LUAD). However, the biological process underlying the ability of AL365181.3 to promote the progression of LUAD is unclear. Here, the pancancer expression level of AL365181.3 was analyzed via the TCGA and GTEx databases, as well as its clinical characteristics and prognostic value. We investigated the biological functions of AL365181.3 in LUAD using various in vitro and in vivo assays. We found that AL365181.3 was significantly more highly expressed in many types of cancer tissues, including LUAD tissues, than in adjacent normal tissues. LUAD patients with high AL365181.3 expression had poor prognoses. Functional enrichment analyses indicated that AL365181.3 is involved in the regulation of metabolism, MAPK signaling and other tumor regulatory signaling pathways. Finally, we found that AL365181.3 knockdown reduced the proliferation, migration and invasion capacity of LUAD cells, and AL365181.3 knockdown resulted in a reduced in vivo tumorigenic capacity of LUAD cells. These findings provide a comprehensive understanding of the role of AL365181.3 in LUAD.

Single-Cell RNA Sequencing Reveals Extensive Heterogeneity and Unique Gene Trajectories in Non-Transformed and Transformed Human Lung Epithelial Cells: Insights into the Role of LncRNAs in Tumor Heterogeneity

Lung cancer exhibits substantial inter- and intra-tumor heterogeneity, with features that present significant challenges in advancing biomarker discovery and the development of targeted therapeutics. To fill this gap, we employed single-cell RNA sequencing (scRNA-seq) and advanced bioinformatics tools to evaluate the transcriptomic heterogeneity of immortalized, non-transformed (BEAS2B) and transformed (H460) lung epithelial cell lines and their responses to carcinogen challenge. Gene expression profiles resolved four primary clusters further discretized into unique subclusters based on genetic signatures and phenotypic profiles. Profiles of long non-coding RNAs (lncRNAs) identified microRNA host genes, antisense RNA genes, divergent transcript, and long intergenic non-coding RNAs as contributors to cellular heterogeneity. These findings indicate that distinct patterns of gene expression, remarkably in lncRNAs, define cellular heterogeneity in non-transformed versus transformed cells. These features can be exploited for the development of therapies directed at specific cell subpopulations in precancerous lesions and within lung tumors.

LINC00870 promotes imatinib resistance in gastrointestinal stromal tumor via inhibiting PIGR glycosylation modifications

Imatinib is the first-line targeted therapy for gastrointestinal stromal tumor (GIST), but resistance frequently occurs during treatment, limiting its efficacy and clinical application. We performed high-throughput sequencing of tissue specimens from imatinib-resistant GIST patients, and identified significantly high expression of polymeric immunoglobulin receptor (PIGR) in imatinib-resistant cell lines. Further investigation revealed that PIGR binds specifically to LINC00870. The findings from in vitro cell functional experiments provide evidence of a strong association between LINC00870 and PIGR and the processes of proliferation and metastasis in GIST. Overexpression of LINC00870 in GIST significantly inhibits the glycosylation modification and secretion of the extracellular region of PIGR, leading to immune dysregulation. The inhibition of PIGR or LINC00870 effectively surmounts imatinib resistance. Our study identified PIGR as a critical molecule in regulating GIST imatinib resistance and elucidated the mechanism by which PIGR promotes imatinib resistance through LINC00870 inhibition of PIGR glycosylation modifications. These findings provide a new theoretical basis for blocking drug resistance and improving prognosis in GIST.

METTL14-mediated m6A modification of LINC00340 exerts oncogenic role in retinoblastoma by regulating Notch signaling pathway

PURPOSE

Retinoblastoma (RB) is a common primary intraocular cancer developed in early childhood. The N6-methyladenosine (m6A) modification of long non-coding RNAs (lncRNAs) have been reported to participate in tumorigenesis. However, the study on the m6A modification of lncRNA in RB is still limited. This study proposed to reveal the role of lncRNA LINC00340 in RB depending on m6A modification.

METHODS

The levels of LINC00340 and methyltransferase-like 14 (METTL14) were detected using qRT-PCR. The effects of LINC00340 interacting with METTL14 on RB cells were assessed by CCK8, colony formation, and flow cytometry assays. The changes of proteins associated with Notch signaling pathway were detected using western blotting. The regulatory mechanism of LINC00340 interacting with METTL14 in RB cells was confirmed by MeRIP, qRT-PCR, and actinomycin D treatment assays.

RESULTS

The expression of LINC00340 and METTL14 in RB samples were elevated, as well as their levels in RB samples showed the positive correlation. Silencing LINC00340 in RB cells could impair RB cell growth and enhance apoptosis via activating Notch signaling pathway, but overexpressing LINC00340 in RB cells showed the opposite effects. In addition, upregulating METTL14 effectively relieved the repressive effects of silencing LINC00340 on RB cells due to METTL14-mediated m6A modification of LINC00340.

CONCLUSIONS

The findings of study reveal that METTL14-mediated m6A modification of LINC00340 exerts oncogenic function in RB via Notch signaling pathway, which may uncover a novel molecular mechanism driving RB progression and identify a potential therapeutic target for RB.

Long non-coding RNA involved in the carcinogenesis of human female cancer - a comprehensive review

Recent years have seen an increase in our understanding of lncRNA and their role in various disease states. lncRNA molecules have been shown to contribute to carcinogenesis and influence the various cancer hallmarks and signalling pathways. It is pertinent to understand the specific contributions and mechanisms of action of these molecules in various cancers. This review provides an overview of the various lncRNA entities that influence and regulate the gynaecological cancers, namely, cervical, breast, ovarian and uterine cancers. The review curates a list of the key players and their effect on cellular processes. lncRNA molecules show immense potential to be used as diagnostic and prognostic indicators and in therapeutic strategies. Several phytochemicals, small molecules, RNA-based regulators, oligos and gene editing tools show promise as a therapeutic strategy. While this review highlights the promising developments in this field, it also underscores the necessity for further research to delineate the complex role of lncRNAs in cancer.

RNF144A-AS1 stabilizes TAF15 and promotes malignant biological behaviors of skin cutaneous melanoma

LncRNAs have been demonstrated to regulate biological processes in malignant tumors. In our previous study, we identified the immune-related LncRNA RNF144A-AS1 as a potential regulator in SKCM. However, its precise function and regulatory mechanism remain unclear. In this study, we observed upregulation of RNF144A-AS1 in SKCM and found that knockdown of RNF144A-AS1 suppressed proliferation, migration, invasion, and epithelial-mesenchymal transition abilities of melanoma cells. Mechanistically, as a high-risk prognostic factor, RNF144A-AS1 regulated biological processes of SKCM by interacting with TAF15 through an RNA-binding protein-dependent (RBP-dependent) manner. Furthermore, we confirmed that TAF15 activated downstream transcriptional regulation of YAP1 to modulate malignant behaviors in melanoma cells. In vivo experiments revealed that knockdown of RNF144A-AS1 inhibited tumorigenic capacity of melanoma cells and exhibited promising therapeutic effects. Collectively, these findings highlight the significance of the RNF144A-AS1/TAF15/YAP1 axis in promoting malignant behaviors in SKCM and provide novel insights into potential prognostic biomarkers and therapeutic targets for this disease.

LncRNA RNF144A-AS1 gene polymorphisms and their influence on lung cancer patients in the Chinese Han population

Lung cancer is primarily classified as NSCLC, which is distinguished by a wide range of genetic variations. This study focused on RNF144A-AS1, a relatively unexplored lncRNA, to explore the impact of its genetic polymorphisms on the susceptibility to NSCLC. We detected RNF144A-AS1 expression and its correlation with prognosis and clinical pathological features using bioinformatics analysis. The association between RNF144A-AS1 polymorphism and NSCLC susceptibility was evaluated using case-control methods. This investigation featured a cohort of 700 NSCLC individuals and 700 healthy controls. The genotype of genetic variation was detected by PCR-RFLP and iMLDR, followed by subsequent calculation of OR and 95 % CI. Our data show that RNF144A-AS1 exhibits high expression levels in LUAD tissues and its expression is closely linked to LUAD progression and prognosis. Carrier of RNF144A-AS1 rs3806609 TT genotype increased NSCLC susceptibility compared to carrier of rs3806609 CC genotype (OR = 2.21, 95%CI = 1.57-3.13). Our study identifies RNF144A-AS1 genetic variants as potential susceptibility markers in NSCLC. RNF144A-AS1 promotes cell proliferation and migration in LUAD through the IFN-γ/JAK2/STAT1 signalling pathway. Collectively, these findings pave the way for developing targeted therapies and diagnostic tools based on RNF144A-AS1 and its variants.

Targeting LINC00665/miR-199b-5p/SERPINE1 axis to inhibit trastuzumab resistance and tumorigenesis of gastric cancer via PI3K/AKt pathway

Long noncoding RNAs (lncRNAs) serve as critical mediators of tumor progression and drug resistance in cancer. Herein, we identified a lncRNA, LINC00665, associated with trastuzumab resistance and development in gastric cancer (GC). LINC00665 was highly expressed in GC tissues and high expression of LINC00665 was correlated with poor prognosis. LINC00665 knockdown was verified to suppress migration, invasion, and resistance to trastuzumab in GC. Furthermore, we found that LINC00665 participates in the infiltration of naive B cells, mast cells, and T follicular helper (Tfh) cells. Mechanistically, LINC00665 was confirmed to regulate tumorigenesis and trastuzumab resistance by activating PI3K/AKt pathway. LINC00665 sponged miR-199b-5p to interact with SERPINE1 expression, resulting in the increase of phosphorylation of AKt, thus participating in the PI3K/AKt pathway. To summarize, LINC00665 facilitated the tumorigenesis and trastuzumab resistance of GC by sponging miR-199b-5p and promoting SERPINE1 expression, which further activated PI3K/AKt signaling; this finding reveals a new mechanism by which LINC00665 modulates tumor development and drug resistance in GC.

Unveiling the hidden gem: A review of long non-coding RNA NBAT-1 as an emerging tumor suppressor and prognostic biomarker in cancer

Previously considered junk or non-functional, long non-coding RNAs (lncRNAs) have emerged over the past few decades as pivotal components in both physiological and pathological processes, including cancer. Neuroblastoma-associated transcript-1 (NBAT-1) was initially discovered a decade ago as a risk-associated tumor suppressor lncRNA in neuroblastoma (NB). Subsequent studies have consistently demonstrated that NBAT-1 serves as a dedicated tumor suppressor in many cancers. NBAT-1 is significantly downregulated in cancer, which is closely linked to higher histological grades, increased metastasis, and poor survival in cancer patients suggesting NBAT-1's potential as a prognostic biomarker. In this review, we delve into the current body of literature, elucidating the tumor-suppressive roles of NBAT-1 and the underlying regulatory mechanisms in the context of human malignancies. Additionally, we shed light on the mechanisms contributing to the diminished expression of NBAT-1 and its potential as both a prognostic biomarker and a promising therapeutic target in cancer.

HoxBlinc lncRNA reprograms CTCF-independent TADs to drive leukemic transcription and HSC dysregulation in NUP98-rearranged leukemia

Although nucleoporin 98 (NUP98) fusion oncogenes often drive aggressive pediatric leukemia by altering chromatin structure and expression of homeobox (HOX) genes, underlying mechanisms remain elusive. Here, we report that the Hoxb-associated lncRNA HoxBlinc was aberrantly activated in NUP98-PHF23 fusion-driven leukemias. HoxBlinc chromatin occupancies led to elevated mixed-lineage leukemia 1 (MLL1) recruitment and aberrant homeotic topologically associated domains (TADs) that enhanced chromatin accessibilities and activated homeotic/hematopoietic oncogenes. HoxBlinc depletion in NUP98 fusion-driven leukemia impaired HoxBlinc binding, TAD integrity, MLL1 recruitment, and the MLL1-driven chromatin signature within HoxBlinc-defined TADs in a CCCTC-binding factor-independent (CTCF-independent) manner, leading to inhibited homeotic/leukemic oncogenes that mitigated NUP98 fusion-driven leukemogenesis in xenografted mouse models. Mechanistically, HoxBlinc overexpression in the mouse hematopoietic compartment induced leukemias resembling those in NUP98-PHF23-knockin (KI) mice via enhancement of HoxBlinc chromatin binding, TAD formation, and Hox gene aberration, leading to expansion of hematopoietic stem and progenitor cell and myeloid/lymphoid cell subpopulations. Thus, our studies reveal a CTCF-independent role of HoxBlinc in leukemic TAD organization and oncogene-regulatory networks.

Long Intergenic Non-Coding RNAs and BRCA1 in Breast Cancer Pathogenesis: Neighboring Companions or Nemeses?

Breast cancer is one of the leading causes of mortality among women, primarily due to its complex molecular landscape and heterogeneous nature. The tendency of breast cancer patients to develop metastases poses significant challenges in clinical management. Notably, mutations in the breast cancer gene 1 (BRCA1) significantly elevate breast cancer risk. The current research endeavors employ diverse molecular approaches, including RNA, DNA, and protein studies, to explore avenues for the early diagnosis and treatment of breast cancer. Recent attention has shifted towards long non-coding RNAs (lncRNAs) as promising diagnostic, prognostic, and therapeutic targets in the multifaceted progression of breast cancer. Among these, long intergenic non-coding RNAs (lincRNAs), a specific class of lncRNAs, play critical roles in regulating various aspects of tumorigenesis, including cell proliferation, apoptosis, epigenetic modulation, tumor invasion, and metastasis. Their distinctive expression patterns in cellular and tissue contexts underscore their importance in breast cancer development and progression. Harnessing lincRNAs' sensitivity and precision as diagnostic, therapeutic, and prognostic markers holds significant promise for the clinical management of breast cancer. However, the potential of lincRNAs remains relatively underexplored, particularly in the context of BRCA1-mutated breast cancer and other clinicopathological parameters such as receptor status and patient survival. Consequently, there is an urgent need for comprehensive investigations into novel diagnostic and prognostic breast cancer biomarkers. This review examines the roles of lincRNAs associated with BRCA1 in the landscape of breast cancer, highlighting the potential avenues for future research and clinical applications.

LncRNAs in serum-derived extracellular vesicles are potential biomarker and correlated with immune infiltration in gastric cancer

Background

Long non-coding RNAs (lncRNAs) in extracellular vesicles (EVs) have been confirmed as effective non-invasive biomarkers for multiple diseases. However, their expression and clinical value in gastric cancer (GC) remain poorly understood.

Materials and methods

Serum EV RNA was extracted from four patients with GC and four healthy controls, followed by high-throughput RNA sequencing. LncRNAs were further validated in training and validation sets using quantitative real-time reverse transcription polymerase chain reaction.

Results

A total of 37,684 lncRNAs were obtained, and 10 lncRNAs were selected based on the criteria (P < 0.05 and |log2FoldChange| ≥1). Serum EV lncRNA RMRP, RPPH1, and linc-ROR were significantly higher in patients with GC than in those with chronic gastritis, atypical hyperplasia, or healthy control (all P < 0.05). Three lncRNAs were also significantly correlated with tumor diameter, lymphatic metastasis, distal metastasis, and TNM stage (all P < 0.05). The area under the curve (AUC) values for lncRNA RMRP, RPPH1, and linc-ROR were 0.727, 0.774, and 0.811, respectively. Corresponding sensitivity and specificity were 63.4% and 85.4%, 50.7% and 89.6%, and 78.5% and 66.7%. The combination of these three lncRNAs with carcinoembryonic antigen (CEA) yielded an AUC of 0.909, with a sensitivity and specificity of 83.3% each. Furthermore, high EV linc-ROR and RMRP expression levels were associated with worse disease-free survival and overall survival (OS). Univariate and multivariate Cox regression analyses confirmed that linc-ROR was the only independent prognostic factor for GC. Finally, the lncRNA-miRNA-mRNA network showed that three lncRNAs were predicted to interact with 15 miRNAs and 69 mRNAs. In addition, lncRNA RMRP and linc-ROR were correlated with immune cell infiltration, including neutrophils, central memory CD4 T cells, macrophage, and natural kill T cells.

Conclusion

EV lncRNAs are prospective biomarker and correlated with immune cell infiltration in GC. It provides a foundation for the development of serum EV-targeted novel biomarkers and immunotherapy targets of GC.

Identification of PANoptosis associated lncRNAs associated with clinical prognosis and immune infiltration microenvironment in colon adenocarcinoma

Early diagnosis and disease management based on risk stratification have a very positive impact on colon adenocarcinoma (COAD) prognosis. It is of positive significance to further explore risk stratification of COAD patients and identify predictive molecular biomarkers. PANoptosis is defined as a form of inflammatory cell death regulated by PANoptosome, with common features of pyroptosis, apoptosis and necroptosis. The role of PANoptosis in COAD has not been fully studied. In this study, we analyzed significant differences in the expression of PANoptosis-related gene (PRG) features in COAD. Subsequently, the PANoptosis associated lncRNAs (PALs) associated with PRGs were analyzed by LASSO algorithm and multivariate Cox analysis, and PALs related to the prognosis of COAD were selected. Based on the expression patterns of prognostic PAL features, we performed unsupervised consensus cluster analysis to categorize COAD samples into distinct PAL molecular subtypes and investigate their associated immune infiltration characteristics. We subsequently constructed PAL score model based on prognostic characteristics and verified its independent prognostic value for COAD. The nomogram diagnostic model was established to confirm the prognostic value of PAL scoring system again. Pathway enrichment analysis, somatic mutation profiling, and drug sensitivity analysis were employed to comprehensively assess the clinical value of the PAL score. Additionally, qRT-PCR was used to further validate the abnormal expression of the selected targets in COAD. Our results provide a new idea for clinical risk stratification and new evidence for the role of PANoptosis in COAD.

Role of long non-coding RNAs and natural products in prostate cancer: insights into key signaling pathways

Prostate cancer (PC) ranks among the most prevalent cancers in males. Recent studies have highlighted intricate connections between long non-coding RNAs (lncRNAs), natural products, and cellular signaling in PC development. LncRNAs, which are RNA transcripts without protein-coding function, influence cell growth, programmed cell death, metastasis, and resistance to treatments through pathways like PI3K/AKT, WNT/β-catenin, and androgen receptor signaling. Certain lncRNAs, including HOTAIR and PCA3, are associated with PC progression, with potential as diagnostic markers. Natural compounds, such as curcumin and resveratrol, demonstrate anticancer effects by targeting these pathways, reducing tumor growth, and modulating lncRNA expression. For instance, curcumin suppresses HOTAIR levels, hindering PC cell proliferation and invasion. The interaction between lncRNAs and natural compounds may open new avenues for therapy, as these substances can simultaneously impact multiple signaling pathways. These complex interactions offer promising directions for developing innovative PC treatments, enhancing diagnostics, and identifying new biomarkers for improved prevention and targeted therapy. This review aims to map the multifaceted relationship among natural products, lncRNAs, and signaling pathways in PC pathogenesis, focusing on key pathways such as AR, PI3K/AKT/mTOR, WNT/β-catenin, and MAPK, which are crucial in PC progression and therapy resistance. Regulation of these pathways by natural products and lncRNAs could lead to new insights into biomarker identification, preventive measures, and targeted PC therapies.

Long non-coding RNAs and their role in breast cancer pathogenesis and drug resistance: Navigating the non-coding landscape review

Despite the progress made in the development of targeted therapies, breast cancer (BC) continues to pose a significant threat to the health of women. Transcriptomics has emerged due to the advancements in high-throughput sequencing technology. This provides crucial information about the role of non-coding RNAs (ncRNAs) in human cells, particularly long ncRNAs (lncRNAs), in disease development and function. When the control of these ncRNAs is disrupted, various illnesses emerge, including cancer. Numerous studies have produced empirical data on the function of lncRNAs in tumorigenesis and disease development. However, the roles and mechanisms of numerous lncRNAs remain unidentified at the molecular level because their regulatory role and the functional implications of abnormalities in cancer biology have yet to be thoroughly defined. The review gives an itemized summary of the most current developments in the role of lncRNA in BC, focusing on three main pathways, PI3K, MAPK, NF-kB, and hypoxia, and their resistance mechanisms.

OTUD6B-AS1: a multifaceted regulator of cancer with critical clinical implications

OTU Deubiquitinase 6B-Antisense Transcript 1 (OTUD6B-AS1), a novel long non-coding RNA (lncRNA), has recently emerged as a critical regulator in various tumors. Current research underscores its dual functionality, acting either as an oncogene or a tumor suppressor depending on the tumor context. In this work, we compile and discuss findings from a range of studies investigating the expression patterns of OTUD6B-AS1 in different cancers and its consequent effects on tumor behavior, both in vitro and in vivo. We delve into the mechanisms through which OTUD6B-AS1 influences cancer initiation and progression, focusing on its role in regulating essential cellular processes such as cell growth, migration, invasion, angiogenesis, ferroptosis, and treatment resistance. Operating through complex interactions with microRNAs (miRNAs), proteins, and pivotal signaling pathways - most notably Wnt/β-catenin - OTUD6B-AS1 exhibits variable roles across cancer types and cellular environments. Additionally, we assess the clinical relevance of OTUD6B-AS1 expression levels, evaluating its potential as a biomarker for cancer prognosis and diagnosis, as well as a target for therapeutic intervention. By consolidating existing knowledge, this work aims to highlight the clinical implications of OTUD6B-AS1 and encourage further research in oncology, ultimately contributing to the advancement of targeted cancer therapies.

Crosstalk between non-coding RNAs and programmed cell death in colorectal cancer: implications for targeted therapy

BACKGROUND

Colorectal cancer (CRC) remains one of the most common causes of cancer-related mortality worldwide. Its progression is influenced by complex interactions involving genetic, epigenetic, and environmental factors. Non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), have been identified as key regulators of gene expression, affecting diverse biological processes, notably programmed cell death (PCD).

OBJECTIVE

This review aims to explore the relationship between ncRNAs and PCD in CRC, focusing on how ncRNAs influence cancer cell survival, proliferation, and treatment resistance.

METHODS

A comprehensive literature analysis was conducted to examine recent findings on the role of ncRNAs in modulating various PCD mechanisms, including apoptosis, autophagy, necroptosis, and pyroptosis, and their impact on CRC development and therapeutic response.

RESULTS

ncRNAs were found to significantly regulate PCD pathways, impacting tumor growth, metastasis, and treatment sensitivity in CRC. Their influence on these pathways highlights the potential of ncRNAs as biomarkers for early CRC detection and as targets for innovative therapeutic interventions.

CONCLUSION

Understanding the involvement of ncRNAs in PCD regulation offers new insights into CRC biology. The targeted modulation of ncRNA-PCD interactions presents promising avenues for personalized cancer treatment, which may improve patient outcomes by enhancing therapeutic effectiveness and reducing resistance.

lncRNA CASC7 contributes to the progression of LPS-induced liver injury by targeting miRNA-217/TLR4 axis

It has been reported that long non-coding RNAs (lncRNAs) are involved in sepsis-induced liver injury, while the role of cancer susceptibility candidate 7 (CASC7) in liver injury induced by sepsis remains elusive. In our study, 62 patients and 55 healthy controls were enrolled from our hospital, from whom CASC7 and microRNA-217 (miR-217) in serum samples were detected by quantitative real-time PCR (qRT-PCR). Then the sepsis-induced liver injury mice model was established by lipopolysaccharide (LPS). The effect of CASC7 on liver injury induced by sepsis was confirmed by hematoxylin and eosin (HE) staining, ELISA assay, TUNEL assay, Annexin V-FITC apoptosis assay and cell counting kit-8 (CCK-8) assay, respectively. Besides, RNA pull-down, luciferase reporter gene assay, qRT-PCR, and western blot were used to evaluate the underlying mechanisms. In this study, lncRNA CASC7 was significantly increased while miR-217 was significantly decreased in patients with sepsis-induced liver injury compared with that in healthy controls. There was a negative association of CASC7 and miR-217 in serum samples from patients with sepsis-induced liver injury and healthy controls. CASC7 was upregulated in a time-dependent manner in liver tissues of LPS-treated mice. It was found that knockdown of CASC7 reduced the liver injury induced by LPS in mice. In vitro, LPS treatment enhanced cell apoptosis, while knockdown of CASC7 inhibited the role of LPS in cell apoptosis. Moreover, knockdown of CASC7 suppressed the LPS-enhanced tumor necrosis factor alpha (TNF-α) and interleukin 1 beta (IL-1β) expression. In addition, miR-217 was found to be a target of CASC7, and miR-217 mimic could reverse CASC7-promoted liver injury. Furthermore, toll-like receptor 4 (TLR4) was identified as the target of miR-217, and both CASC7 and miR-217 could downregulate the mRNA and protein level of TLR4. Additionally, TLR4 overexpression could reverse miR-217-inhibited or CASC7-promoted liver injury. Taken together, CASC7 contributes to the progression of LPS-induced liver injury via the miR-217/TLR4 axis.

AL161431.1 is identified as a biomarker for bladder cancer progression and immunotherapy response

LncRNA AL161431.1 is currently known as a factor that can promote epithelial-mesenchymal transition. However, its role in the prognosis, immune infiltration and progression of bladder cancer (BLCA)patients is still unclear. The expression of AL161431.1 is elevated in BLCA tissues compared to normal tissues according to the TCGA database. By combining this data with clinical information, patients with high AL161431.1 expression have more advanced clinicopathological stages and shorter survival periods. Furthermore, AL161431.1 was identified as an independent prognostic factor for bladder cancer. We further analyzed the differences in immune infiltration, tumor mutation burden (TMB), immune checkpoints, and sensitivity to immunotherapy between groups with different levels of AL161431.1 expression. Enrichment analysis demonstrated that AL161431.1 is associated with numerous immune signaling pathways. High expression of AL161431.1 in cancer tissues was confirmed by qRT-PCR. CCK8, transwell, and wound healing demonstrated the oncogenic effects of AL161431.1. In conclusion, AL161431.1 is associated with immune infiltration in bladder cancer and has the potential to become a biomarker for predicting the prognosis of BLCA.

Genome-wide identification of long non-coding RNA for Botrytis cinerea during infection to tomato (Solanum lycopersicum) leaves

Long non-coding RNA (lncRNA) plays important roles in animals and plants. In filamentous fungi, however, their biological function in infection stage has been poorly studied. Here, we investigated the landscape and regulation of lncRNA in the filamentous plant pathogenic fungus Botrytis cinerea by strand-specific RNA-seq of multiple infection stages. In total, 1837 lncRNAs have been identified in B. cinerea. A large number of lncRNAs were found to be antisense to mRNAs, forming 743 sense-antisense pairs, of which 55 antisense lncRNAs and their respective sense transcripts were induced in parallel as the infection stage. Although small RNAs were produced from these overlapping loci, antisense lncRNAs appeared not to be involved in gene silencing pathways. In addition, we found the alternative splicing events occurred in lncRNA. These results highlight the developmental stage-specific nature and functional potential of lncRNA expression in the infection stage and provide fundamental resources for studying infection stage-induced lncRNAs.

LncRNA HOXA10-AS as a novel biomarker and therapeutic target in human cancers

Long non-coding RNAs (lncRNAs) are crucial regulatory molecules that participate in numerous cellular development processes, and they have gathered much interest recently. HOXA10 antisense RNA (HOXA10-AS, also known as HOXA-AS4) is a novel lncRNA that was identified to be dysregulated in some prevalent malignancies. In this review, the clinical significance of HOXA10-AS for the prognosis of various cancers is analyzed. In addition, the major advances in our understanding of the cellular biological functions and mechanisms of HOXA10-AS in different human cancers are summarized. These cancers include esophageal carcinoma (ESCA), gastric cancer (GC), glioma, laryngeal squamous cell carcinoma (LSCC), acute myeloid leukemia (AML), lung adenocarcinoma (LUAD), nasopharyngeal carcinoma (NPC), oral squamous cell carcinoma (OSCC), and pancreatic cancer. We also note that the aberrant expression of HOXA10-AS promotes malignant progression through various underlying mechanisms. In conclusion, HOXA10-AS is expected to serve as an ideal clinical biomarker and an effective cancer therapy target.

Identification of MYC and STAT3 for early diagnosis based on the long noncoding RNA-mRNA network and bioinformatics in colorectal cancer

Background

Colorectal cancer (CRC) ranks among the top three cancers globally in both incidence and mortality, posing a significant public health challenge. Most CRC cases are diagnosed at intermediate to advanced stages, and reliable biomarkers for early detection are lacking. Long non-coding RNAs (lncRNAs) have been implicated in various cancers, including CRC, playing key roles in tumor development, progression, and prognosis.

Methods

A comprehensive search of the PubMed database was conducted to identify relevant studies on the early diagnosis of CRC. Bioinformatics analysis was performed to explore lncRNA-mRNA networks, leading to the identification of five potential blood biomarkers. Expression analysis was carried out using the GEPIA and GEO online databases, focusing on MYC and STAT3. Differential expression between normal and CRC tissues was assessed, followed by Receiver Operating Characteristic (ROC) analysis to evaluate the diagnostic potential of these markers. Quantitative Real-Time PCR (qRT-PCR) was performed to validate MYC and STAT3 expression levels, and findings were further confirmed using the Human Protein Atlas (HPA) database.

Results

Database analysis revealed significant differential expression of MYC and STAT3 between normal and CRC tissues. ROC analysis demonstrated the diagnostic potential of these markers. qRT-PCR validation confirmed the differential expression patterns observed in the databases. Validation through the HPA database further supported these findings, confirming the potential of MYC and STAT3 as diagnostic biomarkers for CRC.

Conclusion

Our results suggest that MYC and STAT3 are promising diagnostic biomarkers for CRC, offering new insights into its pathophysiology and potential for targeted therapies.

Cuproptosis related lncRNA signature as a prognostic and therapeutic biomarker in osteosarcoma immunity

Osteosarcoma is one of the most common malignant bone tumours in children. In this study, we aimed to construct a cuproptosis-related lncRNAs signature to predict the prognosis and immune landscape of osteosarcoma patients. Databases from TARGET were used to acquire osteosarcoma patient datasets, which included clinical information and RNA sequencing data. Cuproptosis-related lncRNAs was obtained by correlation analysis. Through univariate Cox regression analysis, prognosis-related lncRNAs were obtained. We used nonnegative matrix factorization clustering to identify potential molecular subgroups with different cuproptosis-related lncRNA expression patterns. The least absolute shrinkage and selection operator algorithm and multivariate Cox regression analysis were used to construct the prognostic signature. The ESTIMATE algorithm, Gene Ontology and Kyoto Encyclopaedia of Genes and Genomes were applied to explore the underlying mechanisms in the immune landscape of osteosarcoma. We used gene set enrichment analysis to compare the different enrichments in the high-risk group and the low-risk group. Furthermore, we predicted the response to targeted drugs in patients with different risk groups. Using multivariable analysis, we developed a risk scoring model based on 7 long noncoding RNAs and calculated two molecular subgroups from osteosarcoma patients from the database. There is a better immune microenvironment in the low-risk group compared to the high-risk group. At the same time, the gene functional enrichment analysis based on the differently expressed genes obtained by grouping showed they were mainly related to immunity, indicating that cuproptosis-related lncRNAs may affect the prognosis of osteosarcoma by regulating immunity. Moreover, these patients in high-risk group were more susceptible to targeted drugs than the low-risk group. We identified a cuproptosis-related lncRNA prognostic signature for osteosarcoma and showed a close connection in terms of immunity. Moreover, we provided some potential targeted drugs for the treatment of osteosarcoma.

LncRNA LINC00466 Promotes the Progression of Breast Cancer via miR-4731-5p/EPHA2 Pathway

BACKGROUND

Breast Cancer (BC) is a female malignancy with a high mortality rate. Novel diagnostic and prognostic biomarkers are valuable for reducing BC mortality. Our study is designed to undrape the precise role of the LINC00466/miR-4731-5p/EPHA2 axis in BC.

METHODS

The Cancer Genome Atlas (TCGA) sequencing dataset was utilized to compare the levels of LINC00466. The levels of LINC00466, miR-4731-5p, and EPHA2 were tested by qRTPCR. Cell proliferation and cycle were detected by CCK-8 assay and flow cytometer. In vivo role of LINC00466 was tested by Xenograft nude models. Binding sites were predicted by TargetScan and Starbase. The binding relationship was employed by Dual-luciferase reporter gene assay and RNA pull-down assay.

RESULTS

LINC00466 was increased in human breast cancer tissues. LINC00466 was negatively associated with miR-4731-5p and positively correlated with EPHA2 in human breast cancer tissues. Down-regulation of LINC00466 suppressed the proliferation and arrested the cell cycle of breast cancer cells, and inhibited tumor growth in vivo.

CONCLUSION

LINC00466 promoted BC development via mediating the miR-4731-5p/EPHA2 axis, which has the potential value as a promising therapeutic target in BC.

Role of non-coding RNA in lineage plasticity of prostate cancer

The treatment of prostate cancer (PCa) has made great progress in recent years, but treatment resistance always develops and can even lead to fatal disease. Exploring the mechanism of drug resistance is of great significance for improving treatment outcomes and developing biomarkers with predictive value. It is increasingly recognized that mechanism of drug resistance in advanced PCa is related to lineage plasticity and tissue differentiation. Specifically, one of the mechanisms by which castration-resistant prostate cancer (CRPC) cells acquire drug resistance and transform into neuroendocrine prostate cancer (NEPC) cells is lineage plasticity. NEPC is a subtype of PCa that is highly aggressive and lethal, with a median survival of only 7 months. With the development of high-throughput RNA sequencing technology, more and more non-coding RNAs have been identified, which play important roles in different diseases through different mechanisms. Several ncRNAs have shown great potential in PCa lineage plasticity and as biomarkers. In the review, the role of ncRNA in PCa lineage plasticity and its use as biomarkers were reviewed.

Prospective Study of lncRNA NORAD for Predicting Cerebrovascular Events in Asymptomatic Patients with Carotid Artery Stenosis

BACKGROUND

Carotid artery stenosis (CAS) may cause many cerebrovascular diseases, and a biomarker for screening and monitoring is needed. This study focused on the clinical significance of long-chain non-coding RNA (lncRNA) non-coding RNA activated by DNA damage (NORAD) in patients with CAS and aimed to search for potential biomarkers of CAS.

METHODS

Eighty-six asymptomatic patients with CAS and 60 healthy individuals were enrolled, with corresponding clinical data and serum samples collected. The expression of NORAD was detected by reverse transcription-quantitive PCR (RT-qPCR). All patients were followed up for 2 years to collected the occurrence data of cerebrovascular events, and Kaplan-Meier and Cox regression were used for data analysis. Receiver operator characteristic curve was used to analyze the diagnostic value of NORAD in distinguishing CAS patients from healthy people, and to evaluate the prediction accuracy of NORAD.

RESULTS

NORAD is overexpressed in the serum of CAS patients, and associated with patients' hypertension, TC, LDL-C levels and stenosis degree. NORAD has high sensitivity (88.37%) and specificity (80.00%) in the identification of CAS patients (AUC = 0.917). NORAD was independently related to the occurrence of cerebrovascular events (HR = 2.435, P = .003). a logistic regression risk model for predicting cerebrovascular events was constructed with the parameters including NORAD, TC and LDL.

CONCLUSION

NORAD can be used as a diagnostic and prognostic biomarker for CAS, and NORAD, total cholesterol (TC), and low density lipoprotein cholesterol (LDL-C) can be independently correlated to predict cerebrovascular events.

Elucidating the Role of LINC01980 in Laryngeal Cancer: From Expression Profiling to Regulatory Network Prediction

Laryngeal squamous cell carcinoma (LSCC) remains a significant global health challenge despite advances in treatment. This study investigated the involvement of LINC01980, a long non-coding RNA, in LSCC pathogenesis. We conducted an integrative analysis of transcriptomic data sourced from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases to identify genes that are differentially expressed in LSCC. LINC01980 expression was evaluated in 32 matched pairs of advanced-stage LSCC and adjacent normal tissues using quantitative real-time PCR (qRT-PCR). The potential competing endogenous RNA (ceRNA) network involving LINC01980 was explored through bioinformatics analyses. Findings revealed significant upregulation of LINC01980 in LSCC tissues compared to normal adjacent tissues (p < 0.0001), with elevated expression in 78.125% of tumor samples. Receiver Operating Characteristic (ROC) curve analysis demonstrated LINC01980's potential as a diagnostic biomarker (AUC = 0.7666, p = 0.0002). While no significant correlations were found between LINC01980 expression and clinicopathological features, bioinformatics analyses identified potential LINC01980/ miRNA/ mRNA regulatory network involving hsa-let-7e-5p and hub gene MMP9. This study provides insights into LINC01980's role in LSCC and suggests its potential as a diagnostic biomarker and therapeutic target. Further research is warranted to elucidate the precise molecular mechanisms of LINC01980 in LSCC progression.

Revealing the Complex Interaction of Noncoding RNAs, Sirtuin Family, and Mitochondrial Function

Mitochondria are key organelles that perform and coordinate various metabolic processes in the cell, and their homeostasis is essential for the maintenance of eukaryotic life. To maintain mitochondrial homeostasis and cellular health, close communication between noncoding RNAs (ncRNAs) and proteins is required. For example, there are numerous crosstalk between ncRNAs and the sirtuin (SIRT1-7) family, which is a group of nicotinamide adenine dinucleotides (NAD(+))-dependent Type III deacetylases. NcRNAs are involved in the regulation of gene expression of sirtuin family members, and deacetylation of sirtuin family members can also influence the generation of ncRNAs. This review focuses on the relationship between the two mentioned above and summarizes the impact of their interactions on mitochondrial metabolism, oxidative stress, mitochondrial apoptotic pathways, mitochondrial biogenesis, mitochondrial dynamics, and other mitochondria-related pathophysiological processes. Finally, the review also describes targeted and appropriate treatment strategies. In conclusion, we provide an overview of the ncRNA-sirtuins/mitochondria relationship that could provide a reference for related research in the mitochondrial field and help the future development of new biomedical applications in this area.

LINC01614 Accelerates CRC Progression via STAT1/LINC01614/miR-4443/PFKFB3-Mediated Aerobic Glycolysis

BACKGROUND

Colorectal cancer (CRC) is an aggressive malignancy among malignant tumours, with a high incidence globally. LINC01614, a long non-coding RNA, has been identified as an essential regulator in multiple cancer types. However, its biological functions and underlying molecular mechanisms in CRC remain largely unknown.

METHODS

In this study, we employed RT-qPCR to assess the expression levels of LINC01614 in CRC samples. In vitro, glucose metabolism experiments were conducted to evaluate glucose metabolism in cells. The binding relationship between miR-4443, PFKFB3, and LINC01614 was confirmed through fluorescence reporter gene detection. The subcellular localization of LINC01614 in CRC cells was determined using FISH and subcellular fractionation experiments. Additionally, a mouse subcutaneous tumor model was established for in vivo experiments.

RESULTS

Our findings reveal that LINC01614 is upregulated in CRC tissues. Silencing of LINC01614 suppresses the malignant behaviors of CRC cells, including cell proliferation, invasion, migration, and aerobic glycolysis. Furthermore, we discovered that LINC01614 promotes the expression of PFKFB3. Additional experiments demonstrated that LINC01614 binds to miR-4443, leading to the upregulation of PFKFB3 expression. Further experiments confirmed that the LINC01614/miR-4443/PFKFB3 axis promotes CRC cell malignancy by enhancing aerobic glycolysis. Additionally, we found that STAT1 promotes the transcription of LINC01614.

CONCLUSION

These findings uncover a novel regulatory pathway wherein STAT1-induced LINC01614 enhances PFKFB3 expression by sponging miR-4443, thereby accelerating CRC development. This understanding may lead to novel therapeutic strategies for CRC treatment.

Expression and Significance of the Long Non-Coding RNA APTR in the Occurrence and Development of Lung Adenocarcinoma

As one of the three major malignant tumors, lung adenocarcinoma (LUAD), with its rapid progression and high mortality rate, has become the most dangerous factor endangering human health. This study aims to explore new potential molecular targets, explore the regulatory role of lncRNA APTR in LUAD, and provide a more theoretical basis for the selection of LUAD therapeutic targets. The expression of APTR in LUAD was detected by PCR experiments, and the relationship between APTR and patients' clinical conditions and prognosis was analyzed by chi-square test, multifactor Cox regression, and Kaplan-Meier. The interaction between APTR and miR-298 and the regulation of LUAD cellular activities by APTR/miR-298 were explored by the luciferase reporter gene system. APTR expression was found to be upregulated in LUAD tissues and cells, and the expression of APTR was revealed to be substantially linked with lymph node metastases and TNM stage. High expression of LUAD also predicted a poor prognosis for patients. Downregulation of APTR expression significantly inhibited the activities of LUAD cells. In addition, APTR targeted miR-298 and negatively regulated miR-298 expression. The inhibitory effect of APTR knockdown on LUAD cell activity was also reversed after transfection with miR-298 inhibitor. Increasing expression of APTR is associated with patients' poor prognosis, APTR targets miR-298 and promotes LUAD cellular activity through negative regulation of miR-298.

The Multifaceted Role of lncRNA GAS5: A Pan-Cancer Analysis of Its Diagnostic, Prognostic, and Therapeutic Potential

INTRODUCTION

Cancer is a significant global health problem characterized by increased incidence and large disparities in outcomes. There is a compelling need to identify novel biomarkers to enhance early detection, prognosis, and tailored therapies. Growth arrest-specific transcript 5 (GAS5) is a long noncoding RNA (lncRNA) with potential as a tumor suppressor in a subset of cancers. Its roles in the diagnosis, prognosis, and therapy across cancer types remain underexplored.

METHODS

In this study, a pan-cancer comprehensive analysis of the expression status of GAS5 was conducted using various bioinformatics tools and genomic datasets, including Tumor Immune Estimation Resource (TIMER), Gene Expression Profiling Interactive Analysis (GEPIA), University of Alabama at Birmingham Cancer Data Analysis Portal (UALCAN), and Gene Expression Omnibus (GEO). The expression of GAS5 in different types of cancers was determined and then evaluated for its correlation with clinicopathological parameters, immune cell infiltration, survival outcome, and the methylation status of its promoter. Additionally, the Kaplan-Meier plotter (KMP) was used for overall survival assessment, and the cBioPortal tool was applied for genetic alteration and radiation therapy response assessment. Functional analyses were performed using data from the Long Noncoding RNA Cancer Arrays (lnCAR) database, which included coexpression networks, competing endogenous RNA (ceRNA) interactions, and pathway enrichment.

RESULTS

Our analysis, based on three large datasets, showed that GAS5 was significantly upregulated mainly in cholangiocarcinoma (CHOL), kidney renal clear cell carcinoma (KIRC), and liver hepatocellular carcinoma (LIHC) (p < 0.05). On the contrary, it was downregulated in breast invasive carcinoma (BRCA), kidney chromophobe (KICH), and uterine corpus endometrial carcinoma (UCEC). High GAS5 expression was associated with poor overall survival in LIHC and KIRC (p < 0.05). Promoter hypomethylation was identified as a key regulatory mechanism in CHOL, KIRC, and LIHC (p < 0.05). GAS5 expression exhibited positive correlations with immune cell infiltration (e.g., CD4+ T cells, CD8+ T cells, and macrophages) in LIHC and negative correlations (e.g., B cells, dendritic cells) in KIRC. Our network analysis has established GAS5 as a ceRNA that interacts with 36 miRNAs and 95 protein-coding genes, affecting pathways like metabolism, mitogen-activated protein kinase (MAPK) signaling, and cytokine-cytokine receptor interactions in LIHC (p < 0.05). The genetic alterations may have an impact on GAS5 expression levels and how it functions during radiation treatment. Furthermore, the epigenetic control of GAS5 by DNA methylation suggests possible targets for personalized treatment methods.

CONCLUSION

This comprehensive analysis across various cancers offers a significant foundation for GAS5 as a potential diagnostic and prognostic biomarker, especially prominent in LIHC, with additional relevance in KIRC. Identification of tissue-specific regulatory mechanisms and correlations with immune cells opens new perspectives into the context-dependent functionality of GAS5. These findings highlight the potential of GAS5 for developing targeted therapies and advancing personalized medicine, paving the way for future research into GAS5-based treatment strategies in cancer.

Dysregulated LINC01133 expression in laryngeal carcinoma: Prognostic implications and predicted ceRNA interactome

Long non-coding RNAs (lncRNAs) have recently emerged as critical regulators of oncogenic or tumor-suppressive pathways in human cancers. LINC01133 is a lncRNA that has exhibited dichotomous roles in various malignancies but to the best of our knowledge, the role of LINC01133 in laryngeal squamous cell carcinoma (LSCC) has not been previously investigated. This study aimed to investigate the expression, clinical significance, and potential functions of the LINC01133 in LSCC. Integrative bioinformatics analysis of sequencing data obtained from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets revealed LINC01133 as a differentially expressed lncRNA in head and neck/laryngeal cancers. Experimental validation via quantitative real-time PCR in 41 pairs of stage III and IV LSCC tissues and normal tissues adjacent to the tumor (NAT) demonstrated significant downregulation of LINC01133 in tumors (p<0.0001). Decreased LINC01133 expression associated with advanced tumor stage (p=0.0206) and lymph node metastasis (p=0.0203). The receiver operating characteristic analysis indicated potential diagnostic utility (AUC=0.7115, p=0.001). Bioinformatic predictions and literature mining suggested two potential competing endogenous RNA (ceRNA) mechanisms whereby LINC01133 may act as a tumor suppressor by sponging miR-205-5p to derepress the leucine-rich repeat kinase 2 (LRRK2) and androgen receptor, leading to dysregulation of cancer-related signaling cascades. This study provides initial evidence that loss of lncRNA LINC01133 expression may promote LSCC tumorigenesis, possibly by dysregulating microRNA interactions. Further verification of its regulatory mechanisms and diagnostic value is warranted.

Involvement of PDGFR-integrin interactions in the regulation of anoikis resistance in glioblastoma progression

The interactions between platelet-derived growth factor/PDGF receptor and integrin signaling are crucial for cells to respond to extracellular stimuli. Integrin interactions with PDGFR within the lipid rafts activate downstream cellular signaling pathways that regulate cell proliferation, cell migration, cell differentiation, and cell death processes. The mechanisms underlying PDGFR activation mediated receptor internalization, interactions with other cell-surface receptors, particularly extracellular matrix receptors, integrins, and how these cellular mechanisms switch on anchorage-independent cell survival, leading to anoikis resistance are discussed. The role of regulatory molecules such as noncoding RNAs, that can modulate several molecular and cellular processes, including autophagy, in the acquisition of anoikis resistance is also discussed. Overall, the review provides a new perspective on a complex interplay of regulatory cellular machineries involving autophagy, noncoding RNAs and cellular mechanisms of PDGFR activation, PDGFR-integrin interactions, and involvement of lipids rafts in the acquisition of anoikis resistance that regulates glioblastoma progression along with potential future strategies to develop novel therapeutics for glioblastoma multiforme.

Liquid Biomarkers in Prostate Cancer Diagnosis: Current Status and Emerging Prospects

Prostate cancer (PCa) is a major health concern that necessitates appropriate diagnostic approaches for timely intervention. This review critically evaluates the role of liquid biopsy techniques, focusing on blood- and urine-based biomarkers, in overcoming the limitations of conventional diagnostic methods. The 4Kscore test and Prostate Health Index have demonstrated efficacy in distinguishing PCa from benign conditions. Urinary biomarker tests such as PCa antigen 3, MyProstateScore, SelectMDx, and ExoDx Prostate IntelliScore test have revolutionized risk stratification and minimized unnecessary biopsies. Emerging biomarkers, including non-coding RNAs, circulating tumor DNA, and prostate-specific antigen (PSA) glycosylation, offer valuable insights into PCa biology, enabling personalized treatment strategies. Advancements in non-invasive liquid biomarkers for PCa diagnosis may facilitate the stratification of patients and avoid unnecessary biopsies, particularly when PSA is in the gray area of 4 to 10 ng/mL.

Role of long non‑coding RNA leucine‑rich repeat containing 75 A‑antisense RNA1 in the invasion and progression of renal cell carcinoma

Long noncoding RNAs (lncRNAs) serve pivotal roles in cancer biology. The present study investigated the oncogenic roles of lncRNAs in renal cell carcinoma (RCC) and their potential as prognostic biomarkers. The lncRNA leucine‑rich repeat containing 75 A‑antisense RNA1 (LRRC75A‑AS1) was identified through lncRNA microarray as a potential lncRNA that may predict the efficacy of immune checkpoint inhibitor therapy and cancer progression in RCC. The present study subsequently assessed the expression of LRRC75A‑AS1 in 212 patients with clear cell RCC (ccRCC) who underwent nephrectomy, and performed in vitro functional analysis of LRRC75A‑AS1 in RCC cell lines. Additionally, the interactions between LRRC75A‑AS1, microRNA (miR)‑370‑5p and ADAMTS5 were explored. LRRC75A‑AS1 was revealed to be significantly upregulated in ccRCC tissues compared with in adjacent normal tissues, and high LRRC75A‑AS1 expression was associated with poor prognosis, including lower progression‑free survival, in patients with RCC. The knockdown of LRRC75A‑AS1 in RCC cell lines resulted in reduced cell proliferation and invasion, highlighting its role in promoting tumorigenesis. Furthermore, the interaction among LRRC75A‑AS1, miR‑370‑5p and ADAMTS5 was suggested as a regulatory mechanism underlying RCC progression. These findings indicated that LRRC75A‑AS1 may function as an oncogene in RCC, promoting cell proliferation and invasion. Its significant upregulation in ccRCC tissues and association with poor prognosis underscore its potential as a prognostic biomarker for RCC. Understanding the regulatory interactions among LRRC75A‑AS1, miR‑370‑5p and ADAMTS5 may provide new insights into the molecular mechanisms underlying RCC and facilitate the identification of novel therapeutic targets.

Lnc NBAT1 Inhibits the Proliferation and Migration of Liver Cancer Cells Through the miR-21/PDCD4/AP-1 Signaling Axis

Long non-coding RNAs (Lnc RNAs) are proven to participate in liver cancer (LC) regulation. The regulation of miR-21 by lnc NBAT1 has been studied in other cancers. However, the effect of this regulation on LC and its specific mechanism remains unclear. Lnc NBAT1 and miR-21 expressions in clinical tissues were measured by RT-qPCR. PDCD4, AP-1, p-c-Fos, p-c-Jun, and cyclin D1 expressions were analyzed by Western blot. Overexpression of lnc NBAT1 was studied to explore its influence on malignant behaviors of Bel7402 cells and the development of LC in the xenograft mouse model (XMM). The regulation mechanism of lnc NBAT1 in LC was explored by lnc NBAT1 overexpression, miR-21 mimic treatment, or PDCD4 silencing in Bel7402 cells. Lnc NBAT1 expression was downregulated while miR-21 expression was upregulated in LC tissues and cell lines. In comparison with LX-2 cells, the expressions of PDCD4 and AP-1 were downregulated in Bel7402 cells, while those of p-c-Fos, p-c-Jun, and cyclin D1 were upregulated. Further, lnc NBAT1 was found to localize primarily in the cytoplasm of Bel7402 cells. Overexpression of lnc NBAT1 enhanced cell apoptosis, blocked the cell cycle, suppressed malignant behaviors of Bel7402 cells, and inhibited tumor progression in the XMM. Mechanistically, lnc NBAT1 functioned as a competing endogenous RNA (ceRNA) by binding to the downstream target miR-21 to stabilize the expressions of PDCD4 and AP-1, thereby inhibiting malignant behaviors of Bel7402 cells. Lnc NBAT1 suppressed malignant behaviors of LC cells through the miR-21/PDCD4/AP-1 axis. Lnc NBAT1 might be a promising biomarker for LC treatment.

Transcriptional landscape and predictive potential of long noncoding RNAs in peritoneal recurrence of gastric cancer

BACKGROUND

Long noncoding RNAs (lncRNAs) play a critical role in gastric cancer (GC) progression and metastasis. However, research comprehensively exploring tissue-derived lncRNAs for predicting peritoneal recurrence in patients with GC remains limited. This study aims to investigate the transcriptional landscape of lncRNAs in GC with peritoneal metastasis (PM) and to develop an integrated lncRNA-based score to predict peritoneal recurrence in patients with GC after radical gastrectomy.

METHODS

We analyzed the transcriptome profile of lncRNAs in paired peritoneal, primary gastric tumor, and normal tissue specimens from 12 patients with GC in the Sun Yat-sen University Cancer Center (SYSUCC) discovery cohort. Key lncRNAs were identified via interactive analysis with the TCGA database and SYSUCC validation cohort. A score model was constructed using the LASSO regression model and nomogram COX regression and evaluated using receiver operating characteristic curves. The role of lncRNAs in the PM of GC was then examined through wound healing, Transwell, 3D multicellular tumor spheroid invasion, and peritoneal cavity xenograft tumorigenicity assays in mice.

RESULT

Five essential lncRNAs were screened and incorporated into the PM risk score to predict peritoneal recurrence-free survival (pRFS). We developed a comprehensive, integrated nomogram score, including the PM risk score, pT, pN, and tumor size, which could effectively predict the 5-year pRFS with an Area under the curve of 0.79 (95% CI: 0.71-0.88). Subsequently, we demonstrated that one of these lncRNAs, CASC15, promoted the invasion and migration of GC cells in vitro and facilitated the PM of GC cells in vivo, initially verifying that lncRNAs contribute to the PM of GC. Mechanistic analysis demonstrated that CASC15 promoted EMT and metastasis by activating the JNK and p38 pathways.

CONCLUSION

A lncRNA-based integrated score was constructed in this study to predict peritoneal recurrence in patients clinically.

Diagnostic and Therapeutic Advances of RNAs in Precision Medicine of Gastrointestinal Tumors

Gastrointestinal tumors present a significant challenge for precision medicine due to their complexity, necessitating the development of more specific diagnostic tools and therapeutic agents. Recent advances have positioned coding and non-coding RNAs as emerging biomarkers for these malignancies, detectable by liquid biopsies, and as innovative therapeutic agents. Many RNA-based therapeutics, such as small interfering RNA (siRNA) and antisense oligonucleotides (ASO), have entered clinical trials or are available on the market. This review provides a narrative examination of the diagnostic and therapeutic potential of RNA in gastrointestinal cancers, with an emphasis on its application in precision medicine. This review discusses the current challenges, such as drug resistance and tumor metastasis, and highlights how RNA molecules can be leveraged for targeted detection and treatment. Additionally, this review categorizes specific diagnostic biomarkers and RNA therapeutic targets based on tissue type, offering a comprehensive analysis of their role in advancing precision medicine for gastrointestinal tumors.

Novel insights into the interaction between IGF2BPs and ncRNAs in cancers

Insulin-like growth factor II mRNA-binding proteins (IGF2BPs), a family of RNA-binding proteins, are pivotal in regulating RNA dynamics, encompassing processes such as localization, metabolism, stability, and translation through the formation of ribonucleoprotein complexes. First identified in 1999 for their affinity to insulin-like growth factor II mRNA, IGF2BPs have been implicated in promoting tumor malignancy behaviors, including proliferation, metastasis, and the maintenance of stemness, which are associated with unfavorable outcomes in various cancers. Additionally, non-coding RNAs (ncRNAs), particularly long non-coding RNAs, circular RNAs, and microRNAs, play critical roles in cancer progression through intricate protein-RNA interactions. Recent studies, predominantly from 2018 onward, indicate that IGF2BPs can recognize and modulate ncRNAs via N6-methyladenosine (m6A) modifications, enriching the regulatory landscape of RNA-protein interactions in the context of cancer. This review explores the latest insights into the interplay between IGF2BPs and ncRNAs, emphasizing their potential influence on cancer biology.

LncRNA DNM1P35 sponges hsa-mir-326 to promote ovarian cancer progression

Long non-coding RNAs (lncRNAs) have emerged as crucial regulators in cancer progression. We found lncRNA DNM1P35 is elevated in ovarian tumors compared to normal tissues, and demonstrated that lncRNA DNM1P35 promoted cancer cell proliferation, migration and invasion in SK-OV-3 and OVCAR-3 cell lines. Furthermore, lncRNA DNM1P35 also facilitated the epithelial-mesenchymal transition (EMT) of ovarian cancer cells. Mechanistic studies identified microRNA-326 (miR-326) as a target of lncRNA DNM1P35. Overexpression of miR-326 diminished the tumor-promoting activity of lncRNA DNM1P35, resulting in reduction of Zinc finger E-box-binding homeobox 1 (ZEB1) expression and EMT features. We further revealed that ZEB1, a master transcription factor for EMT that is negatively regulated by miR-326, was essential for lncRNA DNM1P35-mediated cancer cell progression and EMT. Loss of ZEB1 led to compromised pro-tumoral activity of lncRNA DNM1P35. In vivo studies using a xenograft mouse model of ovarian cancer revealed that tumors with higher levels of lncRNA DNM1P35 led to shorter survival, increased tumor burden, as well as elevated expression of proliferative marker Ki67 and EMT marker ZEB1. Our comprehensive study underscored the significance of lncRNA DNM1P35 in ovarian cancer progression, elucidating the underlying mechanism through miR-326/ZEB1 axis to promote ovarian cancer progression.

CDH3-AS1 antisense RNA enhances P-cadherin translation and acts as a tumor suppressor in melanoma

Thousands of regulatory noncoding RNAs (ncRNAs) have been annotated; however, their functions in gene regulation and contributions to cancer formation remain poorly understood. To gain a better understanding of the influence of ncRNAs on gene regulation during melanoma progression, we mapped the landscape of ncRNAs in melanocytes and melanoma cells. Nearly half of deregulated genes in melanoma are ncRNAs, with antisense RNAs (asRNAs) comprising a large portion of deregulated ncRNAs. CDH3-AS1, the most significantly downregulated asRNA, overlaps the CDH3 gene, which encodes P-cadherin, a transmembrane glycoprotein involved in cell adhesion that was also reduced in melanoma. Overexpression of CDH3-AS1 increased cell aggregation and reduced xenograft tumor growth, mimicking the tumor-suppressive effects of CDH3. CDH3-AS1 interacted with CDH3 mRNA and enhanced P-cadherin protein levels. Interestingly, secondary structures at the CDH3 5' end regulated P-cadherin translation, and ribosome profiling revealed that CDH3-AS1 promotes ribosome occupancy at the CDH3 mRNA. Notably, ribosome occupancy was generally increased in mRNAs having cognate asRNA that are complementary to the 5'UTR. Taken together, this study revealed the CDH3-AS1-mediated enhancement of P-cadherin translation, underscoring the broader potential of asRNAs as regulators of protein-coding genes and their role in diseases like melanoma.