Long Noncoding RNA and Cancer: A New Paradigm

Construction of a novel prognostic model based on lncRNAs-related to DNA damage repair for predicting the prognosis of clear cell renal cell carcinoma

BACKGROUND

CcRCC has the characteristics of high aggression, high metastasis, high mortality, wide tumour heterogeneity and variable clinical course. The purpose of this study was to explore the potential value of lncRNAs-related to DNA damage repair (DDR) in predicting the prognosis of ccRCC by construction and verification a novel prognostic model.

METHODS

RNA-seq data and clinical data of ccRCC were downloaded from public databases. Subsequently, Pearson correlation analysis and differential expression analysis were performed to identify DElncRNAs-related to DDR. Then, through univariate Cox analysis and LASSO analysis, the DElncRNAs-related to DDR associated with prognosis were screened for the construction of novel risk score prognostic model. In addition, functional annotation, tumour mutation burden, immune correlation and drug sensitivity analyses were performed based on risk score to assess the characteristics of patients in different risk score groups.

RESULTS

Based on univariate Cox analysis and LASSO analysis, four best DElncRNAs-related to DDR were selected. Subsequently, a novel risk score prognostic model based on these four DElncRNAs was constructed through LASSO. Multivariate Cox analysis showed that risk score and age were independent prognostic factors for ccRCC (p < 0.05). Functional enrichment analysis showed that DDR-related biological processes were mainly enriched in the high risk group. The highly mutated genes in the high and low risk groups were the same (VHL, PBRM1 and TTN), but they also had their own unique mutated genes. Pearson correlation analysis showed that the risk score was significantly (p < 0.05) positively correlated with the infiltration degree of CD8 T cells evaluated by six algorithms. In addition, it was found that the high and low risk groups had different sensitivities to the drugs Etoposide, Imatinib, Sorafenib, Bosutinib and Sunitinib.

CONCLUSION

A novel prognostic model was constructed based on four DElncRNAs-related to DDR. The model has satisfactory accuracy in predicting survival of ccRCC patients.

In vitro investigation of epigenetic regulators related to chemo-resistance and stemness of CD133+VE cells sorted from U87MG cell line

Glioblastoma (GBM) is the most common and malignant adult primary brain tumor with frequent relapse and resistance to therapies. Glioma stem cells, a rare population, is thought to be the reason behind the treatment's failure. It is imperative to investigate the disease mechanisms and identify the biomarkers by which glioma stem cells would contribute to treatment relapse and resistance to already available chemotherapeutic agents. The CD133+VE cells were isolated from U87MG cell line and characterized by morphological features, cell viability, self-renewal efficiency, migration potential and karyotyping. Doxorubicin Cisplatin, Irinotecan, Etoposide and Temozolomide were used to determine the anti-proliferative effect on CD133+VE cells. Confocal microcopy was used to localize the chemotherapeutic agents in the CD133+VE cells. In quest of epigenetic biomarkers, RNA sequencing was performed to find the role of lncRNAs in stemness and resistance to therapies. U87cell line and CD133-VE cells were kept as controls for all the experiments. It was found that CD133+VEcells were highly proliferative with increased migration potential, elevated IC50 values against chemotherapeutic agents and showed distinct karyotyping related to pluripotency. Chemotherapeutic agent such as Doxorubicin was localized outside the nucleus revealing the drug resistance as evident by confocal microscopy. RNA sequencing revealed 126 differentially expressed lncRNAs (DELs) in CD133+VEcells among which lncRNA LOXL1-AS1 was highly upregulated and lncRNA PAX8-AS1 was significantly downregulated. These lncRNAs has been reported to be related to drug resistance, migration and epithelial- to- mesenchymal transmission (EMT), self-renewal and stemness properties contributing to poor prognosis and disease relapse.

Application of non‑coding RNAs in tumors (Review)

Tumors are associated with the highest mortality rates worldwide. For more than a decade, research has focused on the genetic involvement of proteins in cancer; however, a complete class of molecular non‑coding (nc)RNAs have been discovered in recent years, and these are considered to be associated with cancer. Notably, ncRNAs are highly conserved and multifunctional. These interact with multiple signaling pathways, influencing cell cycle progression and various physiological processes. Therefore, the present review aimed to investigate ncRNA, microRNA, transfer RNA‑derived small RNA, PIWI‑interacting RNA and long non‑coding RNA to further understand the associated generation processes, functional mechanisms and therapeutic roles in tumors. The present review demonstrated the critical role of ncRNAs in tumors, and may provide a novel theoretical basis for the role of ncRNAs as biomarkers or therapeutic tools in the treatment of cancer.

Long noncoding RNAs and HPV-related cervical cancer: Uncovering molecular mechanisms and clinical applications

Cervical cancer (CC) is the primary cause of cancer-related mortality among women in developing countries and is the most prevalent disease linked to human papillomavirus (HPV). Over 70 % of CC cases result from persistent infections with high-risk HPV types. The virus typically targets the mucocutaneous epithelium, generating viral particles in mature epithelial cells, which leads to disruptions in normal cell-cycle regulation and promotes uncontrolled cellular proliferation. This unchecked cell division results in the accumulation of genetic damage, contributing to the pathogenesis of CC. While HPV infection is a key etiological factor, the disease's progression also necessitates the involvement of genetic and epigenetic influences. One of the epigenetic regulators, long noncoding RNAs (lncRNAs), are characterized by transcripts exceeding 200 nucleotides. These molecules play crucial roles in various cellular processes, including transcription regulation, RNA metaboli35 per 100,000sm, and apoptosis. Investigating the specific roles of lncRNAs in modulating gene expression related to the oncogenic mechanisms of CC, particularly in the context of high-risk HPV infections, may provide valuable insights for diagnostic and therapeutic advancements. Herein, we first review key molecular mechanisms by which lncRNAs interfere with CC-related HPV development. Then, diagnostic, prognostic, and therapeutic potentials of these lncRNA molecules will be highlighted in depth. The focus of this article is on the role of lncRNAs associated with HPV-related CC, emphasizing the investigation of signaling pathways and their underlying molecular mechanisms. Furthermore, we explore the therapeutic potential and diagnostic relevance of the most significant lncRNAs in the context of CC, thereby highlighting their importance in advancing treatment strategies and improving patient outcomes.

The Regulatory Role of NcRNAs in Pyroptosis and Disease Pathogenesis

Non-coding RNAs (ncRNAs), as critical regulators of gene expression, play a pivotal role in the modulation of pyroptosis and exhibit a close association with a wide range of diseases. Pyroptosis is a form of programmed cell death mediated by inflammasomes, characterized by cell membrane perforation, release of inflammatory cytokines, and a robust immune response. Recent studies have revealed that ncRNAs influence the initiation and execution of pyroptosis by regulating the expression of pyroptosis-related genes or modulating associated signaling pathways. This review systematically summarizes the molecular mechanisms and applications of ncRNAs in diseases such as cancer, infectious diseases, neurological disorders, cardiovascular diseases, and metabolic disorders. It further explores the potential of ncRNAs as diagnostic biomarkers and therapeutic targets, elucidates the intricate interactions among ncRNAs, pyroptosis, and diseases, and provides novel strategies and directions for the precision treatment of related diseases.

Association of long non-coding RNA in lipid metabolism: Implications in leukemia

Cancer has high mortality rate and occupies second position among major diseases. Despite extensive research and therapies, in every nook and corner of the world, death rate is increasing exponentially. Hallmarks of cancer are benchmarks of cancer cells describing the fundamental principle and capabilities of the cells transforming from normal to malignant tumour. One of the major ones among them is the deregulation of cellular metabolism or metabolic reprogramming, involving alterations in glucose and lipid metabolism. Progressive research in this area has visualized the vital role of lncRNAs in lipid metabolism with respect to AML. lncRNAs involve in various cellular processes and also contribute for significant functions of the cell like chromatin remodelling, transcriptional activation and repression, gene regulation, immune response, cell differentiation, and cell cycle regulation, in addition to oncogenic processes such as proliferation, angiogenesis, migration, and apoptosis. Structural similarities are observed among mRNAs and lncRNAs in terms of poly A-tail and 5' cap however protein-coding regions are lacking. A large body of evidence has shown that lncRNAs directly or indirectly mediate lipid metabolism by activating downstream genes. Considering their potential involvement in leukemia, these lncRNAs can be explored and considered as biomarkers for therapeutics, prognosis, and diagnosis. The present review is planned to summarize the functional classification of lncRNAs, the role of lipid metabolism in cancer, different lncRNAs involved in leukemia, and different cancer types related to lipid metabolism.

Liver cancer-specific prognostic model developed using endoplasmic reticulum stress-related LncRNAs and LINC01011 as a potential therapeutic target

Liver cancer is a serious malignancy worldwide, and long noncoding RNAs (lncRNAs) have been implicated in its prognosis.It remains unclear how lncRNAs related to endoplasmic reticulum stress (ERS) influence liver cancer prognosis. Here, we analyzed RNA and clinical data from the Cancer Genome Atlas and sourced ERS-related genes from the Molecular Signatures Database. Co-expression analysis identified ERS-related lncRNAs, and Cox regression analysis as well as least absolute shrinkage and selection operator regression highlighted three lncRNAs for a prognostic model. Based on median risk scores, we classified patients into two risk groups. The high-risk group displayed poor prognosis, and this finding was validated in the test set. According to consistency clustering, the patients were assigned to two clusters, and tumor microenvironment scores were computed. Patients with a high mutation burden had worse outcomes. Furthermore, immune infiltration analysis indicated more immune cells and mutations in checkpoint molecules among high-risk individuals. Drug sensitivity varied between the risk groups. LINC01011 was selected for functional assays. Colony formation assay and CCK-8 assay revealed that silencing LINC01011 suppressed liver cancer cell proliferation. Transwell and scratch assays indicated that silencing LINC01011 inhibited liver cancer cell migration. Western blotting assay revealed that inhibiting LINC01011 induced apoptosis and simultaneously inhibited epithelial-mesenchymal transition. These findings confirm the validity of the prognostic model and indicate that LINC01011 could serve as a potential research target.

Frequent dysregulation of multiple circular RNA isoforms with diverse regulatory mechanisms in cancer - Insights from circFNDC3B and beyond: Why unique circular RNA identifiers matter

Circular RNAs (circRNAs) are post-transcriptional regulators generated through backsplicing of pre-mRNAs, primarily comprising exons of host genes. A single host gene may produce multiple circRNA isoforms with distinct structures and sequences. Dysregulated circRNA expression has been implicated in tumorigenesis. This review aims to investigate the selection and regulatory roles of circRNA isoforms in cancer using the extensively studied hsa_circFNDC3B and thirteen other circRNAs as study models. Interrogation of literature and databases, particularly the circBase, confirms that host genes generate a plethora of circRNA isoforms; however, only a small subset of isoforms is validated as dysregulated in tumor tissues. Notably, two or more isoforms of the same circRNA are frequently dysregulated in cancer. Structurally, short isoforms retaining 5'-proximal exons are preferentially selected, but for long host genes, circRNAs may arise from mid- or 3'-regions. We identify dysregulation of seven circFNDC3B isoforms across twelve cancer types and multi-isoforms in nine of the other thirteen circRNAs also in multiple cancers. MicroRNA sponging appears to be the major regulatory mechanism, but possible biased study designs raise concerns. Using circFNDC3B and circZFR as examples, we show inconsistency and inadequacy in circRNA nomenclature in different databases and the literature, underscoring the urgent need for a universally accepted standardized central circRNA database. As an interim measure, we propose guidelines for circRNA nomenclature in journal publications. Our findings caution against indiscriminate clinical use of specific circRNA isoforms as biomarkers or therapeutic targets without further validation.

Development and validation of a novel endoplasmic reticulum stress-related lncRNA signature in laryngeal squamous cell carcinoma

Endoplasmic reticulum stress (ERS) is an intracellular process in which improperly folded proteins lead to a cellular stress response. How endoplasmic reticulum stress contributes to the onset and progression of laryngeal squamous cell carcinoma remains unclear. Our research aimed to find an ERS signature to forecast the prognosis of laryngeal squamous cell carcinoma and to investigate its potential biological functions. LSCC sample data obtained from The Cancer Genome Atlas (TCGA) database were co-expressed with ERS- related genes, and then a prognostic signature on the basis of endoplasmic reticulum stress- related lncRNAs (ERS-related lncRNAs) was constructed by differential analysis and Cox regression analysis. Survival analysis, TMB, consensus cluster analysis, drug sensitivity analysis, immune analysis and clinical drug prediction were carried out on the model. Finally, the function of LHX1-DT was verified by in vitro experiments. From the TCGA-LSCC cohort, 35 significantly different ERS-related lncRNAs were identified. A prognostic signature consisting of three lncRNAs (AC110611.2, LHX1-DT, and AL157373.2) was identified. Kaplan-Meier analysis demonstrated the predictive ability of the model for overall survival. Calibration curves and receiver operating characteristic curves were validated and showed high predictive accuracy. Ultimately, the experimental results verified the expression of LHX1-DT in LSCC.

Unveiling EIF5A2: A multifaceted player in cellular regulation, tumorigenesis and drug resistance

The eukaryotic initiation factor 5A2 gene (EIF5A2) is a highly conserved and multifunctional gene that significantly influences various cellular processes, including translation elongation, RNA binding, ribosome binding, protein binding and post-translational modifications. Overexpression of EIF5A2 is frequently observed in multiple cancers, where it functions as an oncoprotein. Additionally, EIF5A2 is implicated in drug resistance through the regulation of various molecular pathways. In the review, we describe the structure and functions of EIF5A2 in normal cells and its role in tumorigenesis. We also elucidate the molecular mechanisms associated with EIF5A2 in the context of tumorigenesis and drug resistance. We propose that the biological roles of EIF5A2 in regulating diverse cellular processes and tumorigenesis are clinically significant and warrant further investigation.

Bone metastases of prostate cancer: Molecular mechanisms, targeted diagnosis and targeted therapy (Review)

Prostate cancer (PCa) is second only to lung cancer in terms of death among men worldwide. Advanced PCa frequently results in bone metastases, which occur in ~90% of patients and frequently result in severe skeleton‑related events. Currently, the treatment for this disease is limited to alleviating its clinical symptoms and cannot provide a complete cure. Therefore, the development of novel treatment strategies is particularly important. In recent years, numerous novel strategies for the diagnosis and treatment of PCa have emerged, resulting in good clinical efficacy. For example, strategies targeting prostate specific membrane antigen, poly ADP‑ribose polymerase and programmed cell death protein 1 have been applied to PCa‑induced bone metastasis, and have shown initial efficacy and great potential. Therefore, understanding the molecular mechanisms underlying the formation of bone metastases in patients with PCa is of importance for the effective management of this disease. The purpose of the present review is to comprehensively outline the roles of protein‑coding genes and non‑coding RNAs in the development of bone metastases of PCa to elucidate their significance in the management of PCa. The aim is to offer clinicians and researchers a comprehensive understanding of this topic.

The Long Noncoding RNA Gall Bladder Cancer-Associated Suppressor of Pyruvate Carboxylase Inhibits the Proliferation, Migration, and Invasion of Colorectal Cancer Cells and Induces Their Apoptosis

This study aimed to determine the role of the long noncoding RNA (lncRNA) gall bladder cancer-associated suppressor of pyruvate carboxylase (SOD2-1) in the progression of colorectal cancer (CRC). A total of 23 pairs of specimens, including CRC tissues and adjacent normal tissues, were collected, and the expression of lncRNA SOD2-1 (lnc-SOD2-1) was measured. lnc-SOD2-1 function was examined using HCT15 and HCT116 cells. A lnc-SOD2-1 overexpression vector was designed and transfected into both cell lines. MTS and colony formation assays were used to determine cell viability. Flow cytometry and terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end-labeling assays were performed to measure apoptosis. Cell migration and invasion were evaluated using the Transwell assay. Migration and invasion markers were validated using quantitative reverse transcription-polymerase chain reaction and western blot analysis. The results indicated that the expression of lnc-SOD2-1 was downregulated in CRC tissues. lnc-SOD2-1 overexpression evidently decreased cell viability and led to the formation of fewer cell colonies. lnc-SOD2-1 overexpression induced ~ twofold higher apoptosis than the control group. lnc-SOD2-1 overexpression reduced the proportion of migratory and invasive cells to 50% and 75% of the control group, respectively. lnc-SOD2-1 overexpression significantly decreased the expression of matrix metalloproteinase-2 and -9. In conclusion, lnc-SOD2-1 may act as a tumor suppressor that inhibits the proliferation, migration, and invasion of CRC cells and induces their apoptosis.

Dysregulation of GAS5-miRNA-Mediated Signaling Pathways in Cancer Pathobiology: A Comprehensive Exploration of Pathways Influenced by this Axis

The long non-coding RNA Growth Arrest-Specific 5 (GAS5) is pivotal in modulating key signaling pathways by functioning as a molecular sponge for microRNAs (miRNAs). GAS5 is notably recognized for its antitumor properties, primarily through its ability to sequester oncogenic miRNAs, thereby influencing critical pathways such as p53, Wnt/β-catenin, and PI3K/Akt, all of which are integral to cell proliferation, apoptosis, and metastasis. The disruption of GAS5-miRNA interactions has been implicated in various malignancies, reinforcing its potential as both a biomarker and a therapeutic target. This paper delves into the intricate signaling cascades affected by GAS5-miRNA interactions and thoroughly investigates the diagnosis and treatment prospects associated with GAS5. Moreover, it addresses both the challenges and opportunities for translational applicability of these findings in clinical environments. The study emphasizes GAS5's significance within the cancer molecular landscape and posits that precise modulation of GAS5-miRNA interactions could catalyze transformative developments in cancer diagnostics and therapeutic approaches. This comprehensive review not only highlights the critical role of non-coding RNAs in cancer biology but also aims to lay the groundwork for future investigations aimed at harnessing these insights for therapeutic interventions.

CTCF enhances pancreatic cancer progression via FLG-AS1-dependent epigenetic regulation and macrophage polarization

CCCTC-binding factor (CTCF) regulates chromatin organization and is upregulated in pancreatic ductal adenocarcinoma (PDAC). We found that CTCF interacts with HNRNPU through a FLG-AS1-dependent mechanism, facilitating the recruitment of EP300 and activation of the m6A reader IGF2BP2. This activation promotes histone lactylation at the promoter region of IGF2BP2 stimulating the proliferation of PDAC cells. IGF2BP2 enhanced the mRNA stability of CSF1 and MYC. Moreover, FLG-AS1 directly interacts with HNRNPU to modulate alternative splicing of CSF1, thus promoting the M2 polarization of tumor associated macrophages (TAMs) in PDAC. The results indicated that CTCF-induced oncogenic modification of histone lactylation, m6A and alternative spilcing as multi-regulation modes of TAMs reprogramming in PDAC and identifies CTCF as a potential therapeutic target for PDAC immunotherapy whose inhibition M2 polarization through the IGF2BP2/CSF1/CSF1R axis. Curaxin combined with gemcitabine treatment has shown promising antitumor efficacy against PDAC.

N4-Acetylcytidine-Mediated CD2BP2-DT Drives YBX1 Phase Separation to Stabilize CDK1 and Promote Breast Cancer Progression

Long noncoding RNAs (lncRNAs) play critical roles in the initiation and progression of breast cancer. However, the specific mechanisms and biological functions of lncRNAs in breast cancer remain incompletely understood. Bioinformatics analysis identifies a novel lncRNA, CD2BP2-DT, that is overexpressed in breast cancer and correlates with adverse clinicopathological features and poor overall survival. Both in vivo and in vitro experiments demonstrate that CD2BP2-DT promotes proliferation of breast cancer cells. Mechanistically, NAT10 mediates the N4-acetylcytidine (ac4C) modification of CD2BP2-DT, enhancing its RNA stability and expression. More importantly, CD2BP2-DT enhances the stability of CDK1 mRNA by mediating YBX1 phase separation, thereby promoting the proliferation of breast cancer cells. In conclusion, the lncRNA CD2BP2-DT is identified as a crucial driver of breast cancer cell proliferation through the YBX1/CDK1 axis, highlighting its potential as a promising biomarker and therapeutic target for breast cancer.

Gene and transcript expression patterns, coupled with isoform switching and long non-coding RNA dynamics in adipose tissue, underlie the longevity of Ames dwarf mice

Our study investigates gene expression in adipose tissue of Ames dwarf (df/df) mice, whose deficiency in growth hormone is linked to health and extended lifespan. Recognizing adipose tissue influence on metabolism, aging, and related diseases, we aim to understand its contribution to the health and longevity of df/df mice. We have identified gene and transcript expression patterns associated with critical biological functions, including metabolism, stress response, and resistance to cancer. Intriguingly, we identified genes that, despite maintaining unchanged expression levels, switch between different isoforms, impacting essential cellular functions such as tumor suppression, oncogenic activity, ATP transport, and lipid biosynthesis and storage. The isoform switching is associated with changes in protein domains, retention of introns, initiation of nonsense-mediated decay, and emergence of intrinsically disordered regions. Moreover, we detected various alternative splicing events that may drive these structural alterations. We also found changes in the expression of long non-coding RNAs (lncRNAs) that may be involved in the aging process and disease resistance by regulating crucial genes in survival and metabolism. Through weighted gene co-expression network analysis, we have linked four lncRNAs with 29 genes, which contribute to protein complexes such as the Mili-Tdrd1-Tdrd12 complex. Beyond safeguarding DNA integrity, this complex also has a wider impact on gene regulation, chromatin structure, and metabolic control. Our detailed investigation provides insight into the molecular foundations of the remarkable health and longevity of df/df mice, emphasizing the significance of adipose tissue in aging and identifying new avenues for health-promoting therapeutic strategies.

D-bait: A siDNA for regulation of DNA-protein kinases against DNA damage and its implications in cancer

siDNA fragments, also called Dbait and Pbait, are small DNA oligonucleotides of 30-32 base pairs that cause impairment in DNA repair pathways. Like siRNA and miRNA molecules, which lead to the degradation of mRNA molecules through the Argonaute and Drosha machinery, respectively, Dbait molecules act as false DNA damage signals and trigger and exhaust the DNA repair machinery. In normal cells with no significant DNA damage, the influence of these molecules is negligible. However, in cancer, when there is heavy DNA damage due to replication and anticancer therapies, the cancer cell is heavily dependent on DNA repair proteins to keep the genome intact and limit breaks. This phenomenon primarily occurs during radiation therapy, as significant DNA damage surpasses several DNA repair mechanisms, causing an accumulation of unrepaired lesions and ultimately leading to cell death. This review explores the therapeutic capacity of siDNA molecules in cancer treatment by stimulating the repair mechanisms in cells that depend on DNA repair pathways. For aggressive malignancies such as glioblastoma, prostate cancer, and colorectal cancer, the use of siDNA as a radiosensitizer, especially when combined with other treatments, increases the vulnerability of tumor cells to radiation-induced DNA damage, hence potentially enhancing therapy results.

Comprehensive identification of a migrasomes-associated long non-coding RNA signature to predict the prognosis and treatment options in colon adenocarcinoma

BACKGROUND

Migrasomes, recently discovered cellular substructures, may play a crucial role in cancer progression, treatment response, and prognosis. However, the prognostic value of migrasome-associated long non-coding RNAs (lncRNAs) in colon adenocarcinoma (COAD) remains unexplored.

METHODS

RNA-seq data from 459 COAD patients, including clinical characteristics and outcome information, were obtained from The Cancer Genome Atlas. A risk model was constructed through co-expression analysis of migrasome genes and lncRNAs, followed by Cox regression and least absolute shrinkage and selection operator analysis to identify prognostic lncRNAs. Functional enrichment analyses were performed to elucidate underlying biological mechanisms. Immune landscape characterization utilized ESTIMATE, CIBERSORT, Tumor Immune Estimation Resource (TIME), and single-sample Gene Set Enrichment Analysis (ssGSEA). Drug sensitivity analysis was conducted for select therapeutic agents.

RESULTS

Nine prognostic lncRNAs (AC010463.3, AL590483.4, AP005264.1, ZEB1-AS1, AC104088.1, PRKAR1B-AS2, AC009315.1, SUCLG2-AS1, and AC006111.2) were identified and incorporated into a risk model. Low-risk patients demonstrated significantly improved survival outcomes. The model exhibited independent prognostic capability, with AUCs of 0.783, 0.749, and 0.713 for one-, three-, and five-year survival, respectively, in the training cohort. High-risk patients displayed reduced overall survival and elevated tumor mutation burden. Additionally, these patients showed decreased sensitivity to therapeutic agents, including Oxaliplatin, Irinotecan, and 5-Fluorouracil.

CONCLUSION

Our novel migrasome-associated lncRNA signature demonstrates robust predictive capacity for both prognosis and chemotherapeutic sensitivity in COAD, potentially facilitating personalized treatment strategies and improved patient management.

Identification of mitochondrial permeability transition-related lncRNAs as quantitative biomarkers for the prognosis and therapy of breast cancer

Breast cancer (BC) continues to pose a global health threat and presents challenges for treatment due to its high heterogeneity. Recent advancements in the understanding of mitochondrial permeability transition (MPT) and the regulatory roles of long non-coding RNAs (lncRNAs) offer potential insights for the stratification and personalized treatment of BC. Although the association between MPT and lncRNAs has not been widely studied, a few research studies have indicated a regulatory impact of lncRNAs on MPT, further deepening the understanding of the tumor. To identify reliable biomarkers associated with MPT for managing BC, bulk RNA-seq data of MPT-related lncRNAs acquired from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) project were utilized to assess BC patients. A scoring system, termed the MPT-related score (MPTRscore), was developed using LASSO-Cox regression on data from 1,029 BC patients from TCGA-BRCA. Meanwhile, the superior prognostic accuracy of the MPTRscore was demonstrated by comparing it with biomarkers, including PAM50 subtyping for standardization. Subsequently, a clinical prediction model was created by incorporating the MPTRscore and clinical variables. This analysis revealed two distinct MPTRscore groups characterized by different biomolecular processes, tumor microenvironment (TME) patterns, and clinical outcomes. The MPTRscore was further investigated through unsupervised consensus clustering of TCGA-BRCA based on MPTRscore-related prognostic genes. Additionally, the MPTRscore was identified as an independent prognostic factor for BC and showed guiding utility in immunotherapy and chemotherapy response. Specifically, patients with a low MPTRscore exhibited better prognosis and treatment responses compared to those with a high MPTRscore. Significantly, the relevance of clustering results and MPTRscore was found to be mediated by lncRNA transcript RP11-573D15.8-018. In conclusion, MPTRscore-related clusters were identified in BC, and an integrative score was developed as a biomarker for predicting BC prognosis and therapeutic response. Additionally, molecular interactions underlying the relationship between MPTRscore-related clusters and MPTRscore were uncovered, proving insights for BC stratification. These findings may aid in prognosis determination and therapeutic decision-making for BC patients.

Non-coding RNAs as key regulators of epithelial-mesenchymal transition in breast cancer

This study examines the critical role of non-coding RNAs (ncRNAs) in regulating epithelial-mesenchymal transition (EMT) in breast cancer, a prevalent malignancy with significant metastatic potential. EMT, wherein cancer cells acquire mesenchymal traits, is fundamental to metastasis. ncRNAs-such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs)-modulate EMT by influencing gene expression and signaling pathways, affecting cancer cell migration and invasion. This review consolidates recent findings on ncRNA-mediated EMT regulation and explores their diagnostic and therapeutic potential. Specifically, miRNAs inhibit EMT-related transcription factors, while lncRNAs and circRNAs regulate gene expression through interactions with miRNAs, impacting EMT progression. Given the influence of ncRNAs on metastasis and therapeutic resistance, advancing ncRNA-based biomarkers and treatments holds promise for improving breast cancer outcomes.

LINC02154 Promotes Esophageal Squamous Cell Carcinoma Progression via the PI3K-AKT-mTOR Signaling Pathway by Interacting With IGF2BP2

As important types of noncoding RNAs, long noncoding RNAs (lncRNAs) have been found to be involved in the progression of various cancers. Accumulating evidence indicates that LINC02154 plays a critical role in cancer progression, but the underlying mechanisms regulating esophageal squamous cell carcinoma (ESCC) remain unclear. Here, we found that LINC02154 is significantly upregulated in ESCC cell lines and ESCC tissues. LINC02154 knockdown significantly inhibited the proliferation and migration of ESCC cells in vitro and suppressed the progression of ESCC in vivo. Mechanistically, LINC02154 can bind to IGF2BP2 and activate the PI3K-AKT-mTOR signaling pathway. High expression of LINC02154 is positively correlated with poor prognosis in ESCC patients. In conclusion, LINC02154 functions as an oncogenic factor to facilitate ESCC progression through the IG2BP2-PI3K-AKT-mTOR pathway and has the potential to be a promising diagnostic marker and therapeutic target for ESCC patients.

Curcumin: Epigenetic Modulation and Tumor Immunity in Antitumor Therapy

Curcumin (turmeric) is the main ingredient of the Chinese herbal turmeric rhizome, used to treat tumors, diabetes, inflammation, neurodegenerative diseases, cardiovascular diseases, metabolic syndrome, and liver diseases. The antitumor effects of curcumin have received even more attention. One of the main mechanisms of the antitumor effects includes inhibition of tumor invasion and migration, induction of tumor cell apoptosis, and inhibition of various cell signaling pathways. It has been found that the antitumor biological activity of curcumin in the body is associated with epigenetic mechanisms. That also implies that curcumin may act as a potential epigenetic modulator to influence the development of tumor diseases. The immune system plays an essential role in the development of tumorigenesis. Tumor immunotherapy is currently one of the most promising research directions in the field of tumor therapy. Curcumin has been found to have significant regulatory effects on tumor immunity and is expected to be a novel adjuvant for tumor immunity. This paper summarizes the antitumor effects of curcumin from four aspects: molecular and epigenetic mechanisms of curcumin against a tumor, mechanisms of curcumin modulation of tumor immunotherapy, reversal of chemotherapy resistance, and a novel drug delivery system of curcumin, which provide new directions for the development of new antitumor drugs.

A novel prognostic signature based on m5C‑related LncRNAs and its immunological characteristics in colon adenocarcinoma

BACKGROUND

Colon adenocarcinoma (COAD) has high mortality rates due to frequent resistance to treatment. 5-methylcytosine (m5C) is a crucial epigenetic modification of RNA, closely associated with tumorigenesis in various cancers. This study focuses on developing an m5C-related long non-coding RNA (lncRNA) signature to predict prognosis and explore potential therapeutic targets.

METHODS

Using data from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO), we analyzed 18 m5C regulatory genes and their associated lncRNAs in COAD samples. Prognostic lncRNAs were identified through univariate Cox regression, and a risk model was constructed through LASSO regression analyses. Kaplan-Meier survival and receiver operating characteristic analyses were employed to validate the prognostic ability of the signature. Additionally, functional enrichment and immune infiltration analyses were conducted to investigate underlying biological pathways and immune characteristics of the risk groups. Tumor mutation burden and drug sensitivity analyses were also performed. Functional validation of NR2F2-AS1 was conducted through in vitro experiments.

RESULTS

We established a risk score signature comprising six lncRNAs associated with m5C regulators. Patients were classified into high- and low-risk groups based on the median risk score. This prognostic signature demonstrated significant accuracy and was independent of other clinical features. Immune cell infiltration analysis revealed correlations between the risk signature and various immune cell subtypes. Drug sensitivity analysis indicated the potential therapeutic value of our prognostic signature. Functional experiments confirmed that NR2F2-AS1 acts as a risk factor in the proliferation of colon cancer cells.

CONCLUSIONS

The m5C-related lncRNA signature serves as a reliable prognostic indicator for colon adenocarcinoma and provides new insights into the tumor immune microenvironment.

Analysis of Long Noncoding RNA in Fatty Acid Metabolism to Identify Prognostic Markers and Predict Immunotherapy Response in Low-Grade Glioma

BACKGROUND

Low-grade gliomas (LGGs) are notorious for their difficult early-stage diagnosis, limited treatment options, and poor prognosis, making them a focal point in cancer research. Long noncoding RNAs (lncRNAs) have been identified as regulators of metabolic reprogramming in tumor cells, offering new directions for LGG treatment.

METHODS

This study employed data from The Cancer Genome Atlas, focusing on key fatty acid metabolism-related lncRNA. A risk scoring model was developed using univariate/multifactorial and least absolute shrinkage and selection operator Cox regression. Additionally, the study evaluated the role of these prognostic lncRNAs in LGG progression by assessing associations between LGG immune markers and tumor drug resistance. Finally, functional enrichment analysis highlighted the molecular roles of these lncRNAs.

RESULTS

In this study, a total of 14 prognostic lncRNAs were obtained. The risk model demonstrated excellent validity and reliability, making it a superior predictor of prognosis among patients with varying LGG risks. Among the identified lncRNAs, GHET-1 was notably associated with LGG sensitivity to current chemotherapy options and might be a crucial lncRNA affecting LGG progression. High-risk patients exhibited T-helper cell-mediated immunosuppression, potentially paving new paths for future LGG immunotherapy.

CONCLUSIONS

Focusing on lncRNA regulation and fatty acid metabolism reprogramming, this study established an innovative prognostic prediction model for LGGs, showing outstanding validity and reliability. The findings offer new molecular and cellular targets for the future development of LGG treatments.

Analysis of expression characteristics of ferroptosis-related lncRNAs in gastrointestinal cancer patients in Asia

BACKGROUND

Asian cancer patients have become the highest morbidity and mortality group, and gastrointestinal tumors account for the majority of them, so it is urgent to find effective targets. Therefore, ferroptosis-related lncRNAs models were established to predict the prognosis and clinical immune characteristics of GI cancer.

METHODS

RNA sequencing and clinical data were collected from the TCGA database (LIHC, STAD, ESCA, PAAD, COAD, CHOL, and READ) of patients with gastrointestinal cancer in Asia. Download ferrodroptosis genes from FerrDb. Through R language, differential genes were identified, prognostic related LncRNAs were screened, and risk scores were obtained by risk formula to build models. Survival analysis, risk heat map, COX regression and ROC were used to evaluate the risk model. Establish Nomogram and clinically relevant heat maps. GSEA software was used to analyze gene enrichment and immune-related characteristics in high and low risk groups. LncRNA expression was validated through paired sample differential analysis and qRT-PCR, and the drug sensitivity of genes was also analyzed.

RESULTS

The transcriptome data of 297 cases and clinical data of 322 cases were downloaded from TCGA, and the intersection of ferroptosis-related genes were obtaine. Cox analysis revealed 48 ferroptosis-related LncRNAs associated with prognosis. Through survival analysis, risk heatmap, COX regression and ROC, it was found that the risk model was highly accurate and efficient in predicting prognosis. KEGG-related GSEA enrichment analysis showed that 12 related pathways were significantly expressed in the low-risk group. Four immune-related functions were significantly higher in the high-risk group than in the low-risk group, and the expression of all immune checkpoints were significantly higher in the high-risk group than in the low-risk group. The three LncRNAs in the model exhibited varying expression levels across different tumors and obtained drug sensitivity data.

CONCLUSIONS

Our results reveal innovative and strong evidence that ferroptosis-related lncRNAs can be used as biomarkers for the treatment and prognosis of Asian GI cancer.

Development of LncRNA Biomarkers in Extracellular Vesicle of Amniotic Fluid Associated with Antenatal Hydronephrosis

Background: Antenatal hydronephrosis (ANH) is the most common congenital renal and urinary tract anomaly, and parenchymal damage and renal fibrosis due to pathological hydronephrosis are the main causes of end-stage renal disease in children and chronic kidney disease in adults. At present, there is no validated biomarker for ANH, and diagnostic criteria other than prenatal ultrasonography (US) assessment are lacking. Therefore, we assessed to determine if biomarkers extracted from amniotic fluid small extracellular vesicles (sEVs) might be used as ANH diagnosis. Methods: With congenital ureteropelvic junction obstruction (UPJO) as the ultimate diagnosis, 10 pregnant women with Grade III-IV ANH and 10 normal pregnant women were recruited. The sEVs were extracted from amniotic fluid supernatant of all samples. Transcriptomic sequencing of sEVs in the discovery cohort identified the differential expression profiles for ANH. The known differentially expressed lncRNAs (DE-lncRNAs) were assessed by qRT-PCR in the validation cohort. Results: We explored the global RNA expression in sEVs from amniotic fluid. The differential expression profiles of both mRNAs and lncRNAs were related to fetal kidney development. Six known DE-lncRNAs were identified for ANH, and three of those with high expression were verified in more ANH samples. In particular, the upregulated LINC02863 and its target genes were associated with renal development and morphogenesis. The four predicted novel lncRNAs in high expression were also related to mesenchymal morphogenesis and the STAT3 signaling pathway and may play roles in ANH. Conclusions: We identified differentially expressed RNAs of all species in the sEVs from amniotic fluid, and the validated known DE-lncRNAs might serve as promising diagnostic biomarkers for ANH.

Prognostic modeling of disulfidptosis gene-associated lncRNAs aids in identifying the tumor microenvironment and guiding the selection of therapy

INTRODUCTION

Gliomas, a type of malignant tumor, are marked by a short survival period and an unfavorable prognosis. Disulfide stress, which arises from an overabundance of intracellular cystine, can initiate disulfidoptosis, an emerging form of cell death. The link between gliomas and disulfidoptosis has not been extensively explored. This study breaks new ground by investigating the correlation between glioma prognosis and lncRNAs associated with disulfidoptosis, with the aim of improving glioma treatment strategies.

METHODS

We analyzed 10 long non-coding RNAs (lncRNAs) co-expressed with disulfidoptosis genes, retrieved clinical information and gene expression profiles from glioma and normal groups in the TCGA database, and developed a prognostic model for lncRNAs based on this data. The receiver operating characteristic curve (ROC) was used to evaluate and validate the model's reliability. Furthermore, the Kaplan-Meier survival curve was employed to assess the disparity in overall survival (OS) among patients with varying risk scores. We also examined the tumor microenvironment (TME), immune cell infiltration, immune-related functions, tumor mutational burden (TMB), and OncoPredict in samples with differing risk scores. To confirm the expression variations of genes associated with prognostic models in cell lines, quantitative polymerase chain reaction (qPCR) was employed.

RESULTS

Eleven long non-coding RNAs (lncRNAs) were identified for constructing prognostic models by analyzing lncRNAs associated with disulfidoptosis genes using Cox regression and LASSO regression analyses. The study's findings indicate that these 11 key lncRNAs serve as independent predictors of overall survival (OS) in glioma patients. Moreover, the frequency with which patients of varying risk scores opt for immune checkpoint blockade (ICB) therapy and chemotherapy not only differs but also their responses to these treatments are significantly distinct, suggesting that the risk score could be a predictive factor for treatment response.

CONCLUSIONS

This research sheds light on the characteristics of disulfidoptosis in glioma, revealing that patterns of disulfidoptosis in patients can be effectively assessed using a risk score. Consequently, the judicious application of this prognostic model can significantly inform clinical treatment strategies and precision medicine for glioma, potentially improving patient outcomes.

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.

Unlocking the Mysteries of Breast Cancer: The Role of Epigenetics in Diagnosis, Treatment, and Beyond

OBJECTIVES

Breast cancer is an intricate and varied disease exhibiting a range of molecular subgroups and clinical consequences. Epigenetic alterations have become essential players in the pathophysiology of breast cancer because they control gene expression without changing the DNA sequence. This review provides a comprehensive overview of epigenetics' diagnostic, prognostic, and therapeutic implications in breast cancer. This review aims to present a comprehensive study of the function of epigenetics in breast cancer, emphasizing current developments and potential avenues for future research.

METHODS

A narrative review methodology involved an extensive literature search and selection to gather relevant studies and trial data. PubMed, Embase, and Web of Science databases were searched using relevant keywords such as "epigenetics," "breast cancer," "DNA methylation," "histone modification," "noncoding RNA," and "linical trials." Relevant studies and clinical trial data were selected and synthesized to summarize the topic comprehensively.

RESULTS

The review synthesizes critical findings from current research, underscoring the pivotal role of epigenetic mechanisms in breast cancer initiation, progression, and therapeutic response. It highlights the potential of epigenetic biomarkers for diagnosis and prognosis and the promise of epigenetic-targeted therapies in breast cancer management. Furthermore, the review outlines future directions for research, emphasizing the importance of elucidating the dynamic interplay between epigenetic alterations and tumor microenvironments in shaping breast cancer phenotypes.

CONCLUSIONS

Epigenetic modifications influence breast cancer progression, diagnosis, and therapy. Emerging biomarkers and targeted treatments hold promise, but further research is essential to refine their clinical application and improve personalized cancer management strategies.

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.