NEAT1 is essential for metabolic changes that promote breast cancer growth and metastasis

LURAP1L-AS1 long noncoding RNA promotes breast cancer progression and associates with poor prognosis

Long noncoding RNAs (lncRNAs) are emerging as critical regulators of cancer biology, yet their roles in breast cancer, particularly in triple-negative breast cancer (TNBC), remain incompletely understood. Through a custom siRNA library screen targeting TNBC-associated lncRNAs in MDA-MB-231 and BT-549 TNBC cell models, we identified LURAP1L-AS1 as a key modulator of TNBC progression. Survival analysis of TNBC patients demonstrated a significant association between elevated LURAP1L-AS1 expression and poor clinical outcomes. LURAP1L-AS1 knockdown significantly impaired colony formation and organoid growth of TNBC models, associated with increased apoptosis thus highlighting its role in promoting tumorigenicity. RNA sequencing of LURAP1L-AS1-depleted cells revealed dysregulation of pathways related to cell proliferation, apoptosis, migration, and RNA processing. Bioinformatics analysis predicted LURAP1L-AS1 to function as a competitive endogenous RNA (ceRNA), sponging key microRNAs, such as miR-7a-5p, miR-101-3p, miR-181a-5p, and miR-27a-3p, thereby modulating oncogenes including EZH2, MCL1, and KRAS, which are linked to increased cancer cell survival, proliferation, and metastasis. In addition to its role in TNBC, correlation analysis using breast cancer patient datasets revealed a significant association between LURAP1L-AS1 and ESR1 expression, suggesting its broader impact across breast cancer subtypes. Concordantly, LURAP1L-AS1 depletion inhibited estrogen receptor-positive (ER+) MCF7 breast cancer cells colony formation and organotypic growth. Our findings establish LURAP1L-AS1 as a functional lncRNA that promotes breast cancer progression, highlighting its potential for use in RNA-based therapies for breast cancer.

LncRNA NEAT1 regulation of the miR-101-3p/RAC1 axis affects cervical cancer aerobic glycolysis and progression

Cervical cancer is a prevalent malignancy among women worldwide. Long-chain non-coding rna (lncRNAs) play a key role in the development of several cancers. Here, we found that the expression of lncRNA NEAT1 was significantly increased in cervical cancer cells and tissues and was closely associated with poor patient prognosis. Subsequently, we found that down-regulation of NEAT1 inhibited the proliferation, migration and invasion of cervical cancer cells. Subsequent studies showed that NEAT1, a competitive endogenous RNA, effectively enhanced RAC1 expression by adsorbing miR-101-3p. Glycolysis-related genes were predicted to be enriched in cervical cancers with high NEAT1 expression by bioinformatics analysis and confirmed by in vivo experiments. Our results suggest that NEAT1 enhances the Warburg effect through the miR-101-3p/RAC1 axis and promotes the proliferation, migration and invasion of cervical cancer cells. Therefore, elucidating this potential mechanism and targeting the NEAT1/miR-101-3p/RAC1 pathway may provide valuable insights.

Defining the transcriptional routes controlling lncRNA NEAT1 expression: implications in cellular stress response, inflammation, and differentiation

NEAT1 (Nuclear Enriched Abundant Transcript 1) is a long non-coding RNA playing a critical role in both physiological and pathological settings by directly modulating a variety of biological events, including transcriptional regulation, RNA processing, and chromatin remodeling. Multiple evidence demonstrated that different transcription factors and signaling pathways modulate biological processes by tightly regulating NEAT1 expression. These regulatory mechanisms act at different levels, allowing cells to rapidly modulate NEAT1 expression and dynamically respond to sudden changes in cellular conditions. In this review, we summarize and discuss the transcriptional routes controlling NEAT1 expression, emphasizing recent evidence showing the pivotal role of NEAT1 in regulating important biological processes, such as cellular stress response, inflammation, and cell differentiation.

Scorpion Venom Heat-Resistant Synthetic Peptide Alleviates Neuronal Necroptosis in Alzheimer's Disease Model by Regulating Lnc Gm6410 Under PM2.5 Exposure

Recent epidemiological studies have indicated that exposure to particulate matter with an aerodynamic diameter of 2.5 μm or less in the ambient air (PM2.5) is significantly associated with an elevated risk of developing Alzheimer's disease (AD) and its progression. Scorpion venom heat-resistant synthetic peptide (SVHRSP) exhibits anti-inflammatory and neuroprotective properties. However, the exact ways in which SVHRSP mitigates the progression of AD induced by PM2.5 are still unknown. Long non-coding RNA (lncRNA) plays a crucial role in various biological processes. Necroptosis, a form of programmed cell death, has garnered considerable attention in recent years. This study aims to investigate whether Lnc Gm16410 and neuronal necroptosis are involved in PM2.5-exacerbated AD progression and the mechanisms of SVHRSP in alleviating this process. Through the establishment of a PM2.5 exposure model in AD mice and an in vitro model, it was found that PM2.5 exposure could promote necroptosis and the down-regulation of Lnc Gm16410, thereby promoting the progression of AD. Behavioral tests showed that SVHRSP alleviated cognitive impairment in PM2.5-induced AD mice. WB, qRT-PCR, and other molecular biological assays indicate that Lnc Gm16410 regulates neuronal necroptosis under PM2.5 exposure via the p38 MAPK pathway. SVHRSP is a potential regulator of AD progression by regulating Lnc Gm16410 to alleviate PM2.5 exposure-induced necroptosis. These findings offer new insights into the mechanism through which PM2.5 exposure accelerates the progression of AD, examined from the perspective of LncRNA. Furthermore, we offer new targets for the treatment and prevention of AD following PM2.5 exposure by investigating the mechanism of action of SVHRSP in alleviating AD.

LncRNA OIP5-AS1 Modulates the Biological Behaviour of Lung Cancer Cells by Regulating the hsa-miR-29b-3p/ZIC5 Axis

Existing knowledge regarding the involvement of lncRNA OIP5-AS1 in lung adenocarcinoma (LUAD) development is still incomplete and requires further investigation. Our research aimed to reveal the function of OIP5-AS1 in LUAD. We evaluated the level of OIP5-AS1 and its association with clinicopathological factors in LUAD. The research examined the potential implications of targeting OIP5-AS1 in mitigating the invasive properties of lung cancer cells. A nude mouse xenograft model was utilised to examine tumour growth. We used bioinformatics data and a dual-luciferase reporter assay to study the interactions between OIP5-AS1 and hsa-miR-29b-3p. OIP5-AS1 was significantly overexpressed in LUAD, with a higher level correlating with adverse clinicopathological features. Knockdown of OIP5-AS1 resulted in notable decreases in LUAD cell growth, movement, and aggressive behaviour, accompanied by a decrease in tumour size in vivo. Furthermore, OIP5-AS1 was confirmed to act as a molecular sponge for hsa-miR-29b-3p. The elevated expression of hsa-miR-29b-3p intensified the inhibitory outcomes of OIP5-AS1 knockdown on LUAD cell properties. ZIC5 was experimentally determined to be a direct molecular target of hs-miR-29b-3p, emphasising its integral position in the regulatory interaction. This study reveals a new regulatory route involving OIP5-AS1, hsa-miR-29b-3p and ZIC5 in LUAD pathogenesis. Given its oncogenic traits, OIP5-AS1 presents a promising predictive biomarker and therapeutic target for optimising lung cancer treatment.

Long non-coding RNA LRTOR drives osimertinib resistance in non-small cell lung cancer by boosting YAP positive feedback loop

The therapeutic efficacy of osimertinib (OSI) in EGFR-mutant lung cancer is ultimately limited by the onset of acquired resistance, of which the mechanisms remain poorly understood. Here, we identify a novel long non-coding RNA, LRTOR, as a key driver of OSI resistance in non-small cell lung cancer (NSCLC). Clinical data indicate that elevated LRTOR expression correlates with poor prognosis in OSI-resistant patients. Functionally, LRTOR promotes tumor growth and confers OSI resistance both in vitro and in vivo. Mechanistically, LRTOR shields YAP from LATS-mediated phosphorylation at Ser127 and Ser381, preventing its proteasomal degradation. Furthermore, LRTOR facilitates the interaction between YAP and KCMF1, promoting K63-linked ubiquitination, nuclear translocation of YAP, and formation of the YAP/TEAD1 transcriptional complex, which in turn triggers the transcription of LRTOR, establishing a positive feedback loop that amplifies oncogenic signaling of YAP and consequently induces OSI resistance. LRTOR depletion by siRNA restores OSI sensitivity in resistant tumors, as demonstrated in patient-derived organoid xenograft models. Our findings unveil LRTOR as a central regulator of OSI resistance in NSCLC and propose it as a promising therapeutic and prognostic target for overcoming acquired OSI resistance in EGFR-mutant lung cancer.

CAF-derived exosomal LINC01711 promotes breast cancer progression by activating the miR-4510/NELFE axis and enhancing glycolysis

Breast cancer (BRCA) is among the most prevalent malignancies in women, characterized by a complex tumor microenvironment significantly influenced by cancer-associated fibroblasts (CAFs). CAFs contribute to tumor progression by secreting exosomes that can modulate cancer cell behavior. This study highlights how CAF-derived exosomes transmit the long non-coding RNA (lncRNA) LINC01711, which activates TXN through the miR-4510/NELFE axis, thereby enhancing glycolysis in BRCA cells. Utilizing BRCA single-cell sequencing data from the GEO database, the study employed dimensionality reduction, clustering, and cell annotation techniques to uncover the central role of NELFE in BRCA. Experimental findings revealed that LINC01711 is highly expressed in CAF-derived exosomes, which upregulate TXN via the miR-4510/NELFE axis, promoting the glycolytic pathway and subsequently increasing the proliferation, migration, and invasion potential of BRCA cells. These results shed light on a novel molecular mechanism underlying BRCA progression and suggest potential targets for therapeutic intervention.

YTHDC1 phase separation drives the nuclear export of m6A-modified lncNONMMUT062668.2 through the transport complex SRSF3-ALYREF-XPO5 to aggravate pulmonary fibrosis

Fibroblast-to-myofibroblast differentiation is the main cytopathologic characteristic of pulmonary fibrosis. However, its underlying molecular mechanism remains poorly understood. This study elucidated that the nuclear export of lncNONMMUT062668.2 (lnc668) exacerbated pulmonary fibrosis by activating fibroblast-to-myofibroblast differentiation. Mechanistic research revealed that histone H3K9 lactylation in the promoter region of the N6-methyladenosine (m6A) writer METTL3 was enriched to enhance METTL3 transcription, leading to the lnc668 m6A modification. Meanwhile, the m6A reader YTHDC1 recognized m6A-modified lnc668 and elevated the METTL3-mediated lnc668 modification. Subsequently, phase-separating YTHDC1 promoted the nuclear export of m6A-modified lnc668. In this process, the phase-separating YTHDC1 formed a nuclear pore complex with serine/arginine-rich splicing factor 3, Aly/REF export factor, and exportin-5 to assist the translocation of m6A-modified lnc668 from nucleus to cytoplasm. After nuclear export, lnc668 facilitated the translation and stability of its host gene phosphatidylinositol-binding clathrin assembly protein to activate fibroblast-to-myofibroblast differentiation, leading to the aggravation of pulmonary fibrosis, which also depended on YTHDC1 phase separation. This study first clarified that YTHDC1 phase separation is crucial for the m6A modification, nuclear export, and profibrotic role of lnc668 in exacerbating pulmonary fibrosis. These findings provide new insights into the nuclear export of cytoplasmic lncRNAs and identified potential targets for pulmonary fibrosis therapy.

LncRNA HCG11 regulates selinexor sensitivity in multiple myeloma

Multiple myeloma (MM) is an incurable plasma cell caner featured by monoclonal plasma cell proliferation in bone marrow. The patients inevitably encounter drug resistance and the cancer relapse. Selinexor, a selective inhibitor of nuclear export by targeting exportin-1 (XPO1), is a novel medication in MM treatment. However, there were still many MM patients who did not respond to selinexor without mechanisms being fully demonstrated. In this study, we found that a long noncoding RNA (lncRNA), HLA complex Group 11 (HCG11), regulated MM cell growth and sensitivity to selinexor. MM cell lines and primary MM cell expressed HCG11. High HCG11 expression in MM correlated with inferior patients' overall survival. HCG11 knockdown (HCG11-KD) MM cells were more sensitive to selinexor-induced apoptosis. Mechanistically, HCG11 bound to XPO1 mRNA and promoted the mRNA stability and translation in cells. Thus, HCG11-KD MM cells had reduced XPO1 expression. Animal study showed that HCG11-KD MM was more sensitivity to selinexor than control knockdown in vivo. Overall, our study suggested a regulation of selinexor sensitivity in MM by lncRNA HCG11.

Discovery of lncRNA-Based ProsRISK Score in Serum as Potential Biomarkers for Improved Accuracy of Prostate Cancer Detection

Circulating lncRNAs have emerged as promising biomarkers for the diagnosis of various cancers. This study aimed to establish an accurate risk prediction model based on serum lncRNAs to facilitate the detection of prostate cancer (PCA). RT-qPCR was used to analyse the levels of candidate lncRNAs, and four lncRNAs (NEAT1, ARLNC1, FOXP4-AS1 and DSCAM-AS1) were identified to be differently expressed in serum from 190 PCA patients, 140 benign controls, and 170 healthy controls. A ProsRISK score based on four lncRNAs and prostate-specific antigen (PSA) was established in the training set. ROC analysis in the validation set revealed that the ProsRISK demonstrated more powerful capacity in discriminating PCA from healthy and benign controls, with an AUC of 0.926 (95% CI: 0.882-0.970) and 0.837 (95% CI: 0.770-0.904), which were significantly higher than those of the lncRNA panel or PSA alone (all at p < 0.05). Moreover, the ProsRISK showed good diagnostic performance for PCA I-II patients compared with healthy and benign controls, and the corresponding AUCs were 0.905 (95% CI: 0.843-0.968) and 0.819 (95% CI: 0.732-0.907). Our findings indicated that the constructed ProsRISK could be a reliable risk stratification model and have great potential for clinical use to improve the precision surveillance for PCA.

Non-coding RNAs, a double-edged sword in breast cancer prognosis

Cancer is a rising issue worldwide, and numerous studies have focused on understanding the underlying reasons for its occurrence and finding proper ways to defeat it. By applying technological advances, researchers are continuously uncovering and updating treatments in cancer therapy. Their vast functions in the regulation of cell growth and proliferation and their significant role in the progression of diseases, including cancer. This review provides a comprehensive analysis of ncRNAs in breast cancer, focusing on long non-coding RNAs such as HOTAIR, MALAT1, and NEAT1, as well as microRNAs such as miR-21, miR-221/222, and miR-155. These ncRNAs are pivotal in regulating cell proliferation, metastasis, drug resistance, and apoptosis. Additionally, we discuss experimental approaches that are useful for studying them and highlight the advantages and challenges of each method. We then explain the results of these clinical trials and offer insights for future studies by discussing major existing gaps. On the basis of an extensive number of studies, this review provides valuable insights into the potential of ncRNAs in cancer therapy. Key findings show that even though the functions of ncRNAs are vast and undeniable in cancer, there are still complications associated with their therapeutic use. Moreover, there is an absence of sufficient experiments regarding their application in mouse models, which is an area to work on. By emphasizing the crucial role of ncRNAs, this review underscores the need for innovative approaches and further studies to explore their potential in cancer therapy.

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.

Prognosis model of patients with breast cancer based on metabolism-related LncRNAs

OBJECTIVE

Metabolism-related lncRNAs may play a significant role in the occurrence and development of breast cancer. This study aims to identify metabolism-related lncRNAs with high predictive value for prognosis and to construct a model that can predict the prognosis of breast cancer individually.

METHODS

Transcriptome data and clinical data of patients with breast cancer were retrieved from the TCGA database, and metabolism-related genes were sourced from the GSEA database. Metabolism-related lncRNAs in breast cancer were obtained through differential expression analysis and Pearson correlation analysis. Prognostic-related lncRNAs were further screened using Univariate Cox regression and LASSO regression. Kaplan-Meier survival analysis was performed and the survival curve of the two groups was drawn. Univariate and Multivariate Cox regression analyses were conducted to identify the independent prognostic factors, which were subsequently integrated into a nomogram for individualized prognostic prediction.

RESULTS

Through differential analysis, 2135 differential lncRNAs were obtained, of which 231 were metabolism-related lncRNAs. Using Univariate Cox regression and LASSO regression, a risk prediction model incorporating 19 metabolism-related lncRNAs was constructed. The survival curve suggested that patients with high-risk scores had a poor prognosis compared to those with low-risk scores (P < 0.05). Cox regression analysis further identified that age, stage classification, distant metastasis and risk score as independent prognostic factors to construct a nomogram. KEGG pathway enrichment analysis revealed that differential lncRNAs may be related to JAK-STAT signaling pathway, MAPK signaling pathway and mTOR signaling pathway. Finally, based on the analysis of the CIBERSORT algorithm, lncRNAs used in the construction of the model had a strong correlation with CD8+T cells, activated CD4+T cells and the polarization of M2 macrophages.

CONCLUSION

Bioinformatics methods were utilized to identify metabolism-related lncRNAs associated with breast cancer prognosis, and a prognostic risk model was constructed, laying a solid foundation for the study of metabolism-related lncRNAs in breast cancer.

M2-polarized tumor-associated macrophage-secreted exosomal lncRNA NEAT1 upregulates galectin-3 by recruiting KLF5 and promotes HCC immune escape

HCC cell immune escape is a critical element in the evolution of HCC malignancy. Herein, the regulatory mechanism of lncRNA NEAT1 in regulating HCC immune escape was investigated. Exosomes were isolated from M2 TAMs using ExoQuick-TC. Then, HCC cells were incubated with M2 TAMs-derived exosomes (M2-exos). The activation of perforin+CD8+ T cells was measured using flow cytometry. The secretion of IFN-γ was assessed using ELISA. Cell viability and migration were detected using CCK8 and Transwell assays, respectively. RIP and RNA pull-down assays were used to investigate the link between NEAT1 and KLF5. ChIP and dual-luciferase reporter assays were used to investigate the interaction between KLF5 and the LGALS3 promoter. Our results showed that NEAT1, KLF5 and galectin-3 were overexpressed in HCC tissues. M2-exos treatment promoted HCC proliferation, migration, and immune escape. It was found that NEAT1 was enriched in M2-TAMs and M2-exos. M2-exos facilitated HCC immune escape, whereas NEAT1 silencing reversed this effect. NEAT1 upregulated galectin-3 in HCC cells by recruiting KLF5. Mechanically, M2-TAM-derived exosomal NEAT1 induced HCC immune escape by upregulating KLF5/galectin-3 axis. M2-TAM-derived exosomal NEAT1 upregulated galectin-3 in HCC cells by recruiting KLF5 to promote perforin+CD8+ T cell depletion and further accelerate HCC immune escape.

Exosomal lncRNA Mir100hg from lung cancer stem cells activates H3K14 lactylation to enhance metastatic activity in non-stem lung cancer cells

The mean survival of metastatic lung adenocarcinoma is less than 1 year, highlighting the urgent need to understand the mechanisms underlying its high mortality rate. The role of Extracellular vesicles (EVs) in facilitating the interactions between cancer cells and the metastatic microenvironment has garnered increasing attention. Previous studies on the role of EVs in metastasis have been primarily focused on cancer cell-derived EVs in modulating the functions of stromal cells. However, whether cancer stem cells (CSCs) can alter the metastatic properties of non-CSC cells, and whether EV crosstalk can mediate such interaction, have not been demonstrated prior to this report. In the present study, we integrated multi-omics sequencing and public database analysis with experimental validation to demonstrate, for the first time, the exosomal Mir100hg, derived from CSCs, could enhance the metastatic potential of non-CSCs both in vitro and in vivo. Mechanistically, HNRNPF and HNRNPA2B1 directly binds to Mir100hg, facilitating its trafficking via exosomes to non-CSCs. In non-CSCs, Mir100hg upregulates ALDOA expression, subsequently leading to elevated lactate production. Consequently, the increased lactate levels enhance H3K14 lactylation by 2.5-fold and promote the transcription of 169 metastasis-related genes. This cascade of events ultimately results in enhanced ALDOA-driven glycolysis and histone lactylation-mediated metastatic potential of non-CSC lung cancer cells. We have delineated a complex regulatory network utilized by CSCs to transfer their high metastatic activity to non-CSCs through exosomal Mir100hg, providing new mechanistic insights into the communication between these two heterogeneous tumor cell populations. These mechanistic insights provide novel therapeutic targets for metastatic lung cancer, including HNRNPF/HNRNPA2B1-mediated Mir100hg trafficking and the histone lactylation pathway, advancing our understanding of CSC-mediated metastasis while suggesting promising strategies for clinical intervention.

Long non-coding RNA NEAT1 promotes colorectal cancer progression via interacting with SIRT1

Nuclear-enriched abundant transcript 1 (NEAT1), a long noncoding RNA, is found to be significantly dysregulated in different types of cancer, including colorectal cancer (CRC). Nevertheless, there is still much to learn about the precise functions and processes of NEAT1 in the progression of CRC. Using The Cancer Genome Atlas (TCGA) database and 50 CRC specimens from the First Affiliated Hospital of Dali University, we assessed the expression of NEAT1 to determine its clinical impact. Through gene set enrichment analysis (GSEA), Cancer Single-cell State Atlas (CancerSEA), and immune infiltration studies, we elucidated key functions of NEAT1. We utilized Cell Counting Kit-8 (CCK8), wound healing, and Transwell assays to investigate the role of NEAT1 in the progression of CRC. Through the use of GSEA and immunohistochemistry, additional investigations were conducted to unveil the downstream targets of NEAT1 and gain insights into their regulatory dynamics. Our in vitro studies confirmed the regulatory role of NEAT1 in CRC. Findings indicate that increased NEAT1 expression correlates with adverse outcomes in colorectal tissues. In the CRC model, reduced levels of NEAT1 lead to reduced cell proliferation, invasion, and migration. Additionally, NEAT1 influenced immune cell infiltration in CRC and functioned as an oncogene by upregulating Sirtuin 1 (SIRT1) expression. This study demonstrates that NEAT1 promotes CRC progression and metastasis through a SIRT1-mediated mechanism, suggesting its potential as a prognostic biomarker and therapeutic target for CRC.

HSP90 co-regulates the formation and nuclear distribution of the glycolytic output complex to promote resistance and poor prognosis in gastric cancer patients

BACKGROUND

Resistance to treatment is a critical factor contributing to poor prognosis in gastric cancer patients. HSP90 has emerged as a promising therapeutic target; however, its role in regulating tumor metabolic pathways, particularly glycolysis, remains poorly understood, which limits its clinical application.

METHODS

We identified proteins that directly interact with HSP90 using immunoprecipitation (IP) followed by mass spectrometry. The relationship between HSP90 and glycolysis was further investigated through transcriptomic analyses and in vitro experiments. Mechanistic insights were obtained through mass spectrometry, co-immunoprecipitation (Co-IP) assays, drug sensitivity tests, and bioinformatics analyses. Additionally, we developed a scoring system based on transcriptomic data to evaluate its prognostic significance and association with treatment resistance in gastric cancer patients.

RESULTS

Our multi-omics and in vitro studies revealed that HSP90 regulates glycolysis and influences the stemness properties of gastric cancer cells. Mechanistically, HSP90 facilitates the assembly of a glycolytic multi-enzyme complex, termed the HGEO complex, which enhances glycolytic metabolism. Mechanistically, HSP90 facilitates the formation of a multienzyme complex comprising key enzymes including PGK1, PKM2, ENO1, and LDHA, thereby facilitating the production of the final glycolytic products. We refer to this as the "HSP90-Glycolytic Output Complex" (HGEO Complex). We quantified this phenomenon with a scoring system (HGScore), finding that patients with a high HGScore exhibited more malignant signatures, increased resistance to treatment, and poorer prognoses. Furthermore, we demonstrated that the HGEO complex is localized in the nucleus, regulated by the nuclear lamina protein LMNA, which further contributes to treatment resistance and adverse outcomes. In vitro experiments indicated that inhibiting the formation of this complex sensitizes gastric cancer cells to chemotherapy.

CONCLUSION

Our findings suggest that HSP90 and LMNA mediated the formation and nuclear localization of the HGEO complex, thereby enhancing the malignant traits and resistance mechanisms in gastric cancer. Targeting this pathway may offer a novel therapeutic strategy to improve treatment outcomes.

LINC01224 promotes the Warburg effect in gastric cancer by activating the miR-486-5p/PI3K axis

The Warburg effect, a common feature of solid tumors, rewires the metabolism and promotes growth, survival, proliferation, and long-term maintenance in gastric cancer (GC). We performed in vitro and in vivo studies of the pathogenesis of GC to investigate the effects and mechanism of LINC01224 in this cancer. qRT-PCR was used to measure the expression of LINC01224 or miR-486-5p in GC cells, and the expression of LINC01224 in GC tissues by FISH (Fluorescence in situ hybridization) analysis was evaluated. Bioinformatics predicted the target gene of LINC01224, Western blotting was used to measure the protein expression of genes in the PI3K/AKT/mTOR/HIF-1α axis and Warburg effect in GC cells. The function of LINC01224 in GC cells was determined using measurements of EDU assay, colony formation, apoptosis, cell migration, and cell invasion. Glucose metabolism was evaluated using a glucose uptake assay and measurements of lactate. A tumor xenograft model was used to examine the effect of LINC01224 on GC growth in vivo. We found that upregulation of LINC01224 in GC cells activated the miR-486-5p/PI3K axis and promoted aerobic glycolysis, thereby increasing cell viability, proliferation, migration, invasion and anti-apoptosis. LINC01224 downregulation had the opposite effect. LINC01224 expression promoted the in vitro and in vivo pathogenesis of GC by promoting aerobic glycolysis. LINC01224 is a promising target in the treatment of GC.

DDX50 cooperates with STAU1 to effect stabilization of pro-differentiation RNAs

Glucose binding can alter protein oligomerization to enable differentiation. Here, we demonstrate that glucose binding is a general capacity of DExD/H-box RNA helicases, including DDX50, which was found to be essential for the differentiation of diverse cell types. Glucose binding to conserved DDX50 ATP binding sequences altered protein conformation and dissociated DDX50 dimers. DDX50 monomers bound STAU1 to redirect STAU1 from an RNA-decay-promoting complex with UPF1 to a DDX50-STAU1 ribonuclear complex. DDX50 and STAU1 bound and stabilized a common set of essential pro-differentiation RNAs, including JUN, OVOL1, CEBPB, PRDM1, and TINCR, whose structures they also modified. These findings uncover a DDX50-mediated mechanism of reprograming STAU1 from its canonical role in Staufen-mediated mRNA decay to an opposite role stabilizing pro-differentiation RNAs and establish an activity for glucose in controlling RNA structure and stability.

Development and validation of a glycolysis-associated gene signature for predicting the prognosis, immune landscape, and drug sensitivity in bladder cancer

Background

Bladder cancer (BCa) is one of the most common malignancies worldwide, and its prognostication and treatment remains challenging. The fast growth of various cancer cells requires reprogramming of its energy metabolism using aerobic glycolysis as a major energy source. However, the prognostic and therapeutic value of glycolysis-related genes in BCa remains to be determined.

Methods

The fused merge dateset from TCGA, GSE13507 and GSE31684 were used for the analysis of glycolysis-related genes expression or subtyping; and corresponding clinical data of these BCa patients were also collected. In the merge cohort, we constructed a 18 multigene signature using the least absolute shrinkage and selection operator (LASSO) Cox regression model. The four external cohorts (i.e., IMvigor210, GSE32894, GSE48276 and GSE48075) of BCa patients were used to validate the accuracy. We evaluated immune infiltration using seven published algorithms: CIBERSORT, QUANTISEQ, XCELL, TIMER, CIBERSORT-ABS, EPIC, and MCPCOUNTER. Subsequently, in order to analyze the correlation between risk groups(scores) and overall survival, recognised immunoregolatory cells or common chemotherapeutic agents, clinicopathological data and immune checkpoint-related genes of BCa patients, Wilcox rank test, chi-square test, cox regression and spearman's correlation were performed.

Results

Conspicuously, we could see that CD8+ T, cancer associated fibroblast, macrophage M2, NK, endothelial cells and so on were significantly dysregulated between the two risk groups. In addition, compared with the low-risk group, high-risk group predicted poor prognosis and relatively weak sensitivity of chemotherapy. Additionally, we also found that the expression level of partial genes in the model was significantly correlated with objective responses to anti-PD-1 or anti-PD-L1 treatment in the IMvigor210, GSE111636, GSE176307, GSE78220 or GSE67501 cohort; and its expression level was also varied in different objective response cases receiving tislelizumab combined with low-dose nab-paclitaxel therapy based on our mRNA sequencing (TRUCE-01). According to "GSEA" algorithm of R package "clusterProfiler", the most significantly enriched HALLMARK, KEGG pathway and GO term was separately the 'Epithelial Mesenchymal Transition', 'Ecm Receptor Interaction' and 'MF_Extracellular_matrix_structural_constitunet' in the high- vs. low-risk group. Subsequently, we verified the protein and mRNA expression of interested model-related genes from the Human Protein Atlas (HPA) and 10 paired BCa tissues collected by us. Furthermore, in vitro functional experiments demonstrated that FASN was a functional oncogene in BCa cells through promoting cell proliferation, migration, and invasion abilities.

Conclusion

In summary, the glycolysis-associated gene signature established by us exhibited a high predictive performance for the prognosis, immunotherapeutic responsiveness, and chemotherapeutic sensitivity of BCa. And, The model also might function as a chemotherapy and immune checkpoint inhibitor (ICI) treatment guidance.

Mechanical Remodeling of Nuclear Biomolecular Condensates

Organism health relies on cell proliferation, migration, and differentiation. These universal processes depend on cytoplasmic reorganization driven notably by the cytoskeleton and its force-generating motors. Their activity generates forces that mechanically agitate the cell nucleus and its interior. New evidence from reproductive cell biology revealed that these cytoskeletal forces can be tuned to remodel nuclear membraneless compartments, known as biomolecular condensates, and regulate their RNA processing function for the success of subsequent cell division that is critical for fertility. Both cytoskeletal and nuclear condensate reorganization are common to numerous physiological and pathological contexts, raising the possibility that mechanical remodeling of nuclear condensates may be a much broader mechanism regulating their function. Here, we review this newfound mechanism of condensate remodeling and venture into the contexts of health and disease where it may be relevant, with a focus on reproduction, cancer, and premature aging.

RNA Decay Assay: 5-Ethynyl-Uridine Labeling and Chasing

Eukaryotic RNA synthesis and degradation are intricately regulated, impacting on gene expression dynamics. RNA stability varies in individual transcripts and is modulated by trans-acting factors such as microRNAs, long noncoding RNAs, and RNA-binding proteins, which determine protein output and subsequent cellular processes. To measure RNA decay rate, accurate and reliable methodologies are essential in the field of RNA biology. Transcription inhibition and metabolic labeling enable comprehensive investigations on RNA decay, offering critical insights into dynamic regulation of RNA decay. Transcription shut-off has been employed widely by using various approaches, such as treatment with chemical inhibitors or generation of temperature-sensitive mutants of RNA polymerases. However, it has limitations, providing a static view and lacking real-time dynamics as well as precise measurement of decay rate. Metabolic labeling, a method of incorporating modified nucleotides into RNA transcripts, complements shut-off approaches, allowing selective monitoring of newly synthesized RNA and tracing decay intermediates. The purpose of the protocol described in this chapter is to assess the kinetics and statics of newly synthesized RNA and its decay by 5-ethynyl uridine labeling.

LncRNA Expression Profiles in C6 Ceramide Treatment Reveal lnc_025370 as a Promoter in Canine Mammary Carcinoma CHMp Cells Progression

Canine mammary carcinomas (CMCs) represent the most prevalent form of cancer in female dogs, characterized by a high incidence and mortality rate. C6 ceramide is recognized for its multifaceted anti-cancer properties, yet its specific influence on CMCs remains to be elucidated. Long noncoding RNAs (lncRNAs), now recognized as functional "dark matter" in precision oncology, are particularly intriguing, with 44% of canine lncRNAs exhibiting tissue-specific expression. In this study, we performed a thorough analysis of lncRNA expression profiles to uncover the mechanisms behind C6 ceramide's anti-cancer activity in CHMp cells. Our findings reveal that C6 ceramide notably inhibits the proliferation of CHMp cells. RNA sequencing identified 4522 lncRNAs with expression changes following C6 ceramide treatment, of which 2936 were upregulated and 1586 were downregulated. Further investigation into Lnc_025370 showed that it is predominantly nuclear-localized and is significantly downregulated by C6 ceramide treatment. Functional studies discovered that overexpression of Lnc_025370 enhances the growth and metastatic capabilities of CHMp cells, which is associated with an increase in NRG1, and concurrently diminishes the anti-cancer effectiveness of C6 ceramide in vitro. Mouse xenograft models also showed that Lnc_025370 overexpression promotes tumor growth and Ki67 expression. Together, our results suggest that Lnc_025370 acts as a pivotal target mediator of C6 ceramide's anti-cancer effects, facilitating the malignant progression of CHMp cells.

CircRREB1 Mediates Metabolic Reprogramming and Stemness Maintenance to Facilitate Pancreatic Ductal Adenocarcinoma Progression

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal tumor with limited treatment options and poor patient survival. Circular RNAs (circRNA) play crucial regulatory roles in the occurrence and development of various cancers, including PDAC. In this study, using circRNA sequencing of diverse PDAC samples, we identified circRREB1 as an oncogenic circRNA that is significantly upregulated in PDAC and is correlated with an unfavorable patient prognosis. Functionally, loss of circRREB1 markedly inhibited glycolysis and stemness, whereas elevated circRREB1 elicited the opposite effects. Mechanistically, circRREB1 interacted with PGK1, disrupting the association between PTEN and PGK1 and increasing PGK1 phosphorylation to activate glycolytic flux. Moreover, circRREB1 promoted WNT7B transcription by directly interacting with YBX1 and facilitating its nuclear translocation, consequently activating the Wnt/β-catenin signaling pathway to maintain PDAC stemness. Overall, these results highlight circRREB1 as a key regulator of metabolic and stemness properties of PDAC. Significance: CircRREB1 stimulates PGK1 to induce glycolysis and activates the Wnt/β-catenin signaling pathway to maintain stemness in pancreatic cancer, indicating the potential of circRREB1 as a biomarker and therapeutic target.

Functional roles of conserved lncRNAs and circRNAs in eukaryotes

Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) have emerged as critical regulators in essentially all biological processes across eukaryotes. They exert their functions through chromatin remodeling, transcriptional regulation, interacting with RNA-binding proteins (RBPs), serving as microRNA sponges, etc. Although non-coding RNAs are typically more species-specific than coding RNAs, a number of well-characterized lncRNA (such as XIST and NEAT1) and circRNA (such as CDR1as and ciRS-7) are evolutionarily conserved. The studies on conserved lncRNA and circRNAs across multiple species could facilitate a comprehensive understanding of their roles and mechanisms, thereby overcoming the limitations of single-species studies. In this review, we provide an overview of conserved lncRNAs and circRNAs, and summarize their conserved roles and mechanisms.

Analysis on the involvement of phosphoglycerate mutase 1 in the aerobic glycolysis of melanoma cells

BACKGROUND

The aim of this study was to investigate the mechanism through which phosphoglycerate mutase 1 (PGAM1) drives aerobic glycolysis and promotes tumor aggressiveness in melanoma and to evaluate its potential as a therapeutic target.

METHODS

The survival of patients with skin cutaneous melanoma was predicted. The expression of PGAM1 in melanoma cells was measured, and then the levels of markers related to apoptosis, glycolysis and immune responses in melanoma cells cultured with or without CD8+ T cells were detected. The effects of PGAM1 knockdown on the malignant phenotypes and extracellular acidification rate (ECAR) of melanoma cells were analyzed.

RESULTS

High-expressed PGAM1 was predictive of a poor prognosis of melanoma. The viability, proliferation and invasion as well as glycolysis of PGAM1-silenced melanoma cells were suppressed. PGAM1 silencing lowered the expressions of glycolysis-related markers and anti-apoptosis marker BCL2 but promoted that of BAX, a pro-apoptosis marker. Downregulated levels of immune responses-related markers were observed after PGAM1 knockdown. POMHEX, a glycolysis inhibitor, reduced glycolysis and suppressed the levels of immune responses-related markers and anti-apoptosis marker BCL2.

CONCLUSION

This study revealed the involvement of PGAM1 in the aerobic glycolysis of melanoma, providing novel insights into the molecular mechanisms of melanoma progression.

Single-Cell Transcriptome Sequencing and Analysis Provide a New Approach for the Treatment of Small Cell Neuroendocrine Carcinoma of the Cervix

INTRODUCTION

Small cell neuroendocrine carcinoma of the cervix (SCNECC) is a rare gynecologic malignant tumor, which has lack of systematic research. In order to investigate its molecular characteristics, origin, and pathogenesis, single-cell transcriptome sequencing (scRNA-Seq) of SCNECC was performed for the first time, the cellular and molecular landscape was revealed, and the key genes for clinical prognosis were screened.

METHODS

This article initially performed the scRNA-Seq on a tumor tissue sample from an SCNECC patient, combined with scRNA-Seq data from a healthy cervical tissue sample downloaded from a public database; the single-cell transcriptome landscape was constructed. Then, we investigated the cell types, intratumoral heterogeneity, characteristics of tumor microenvironment, and potential predictive markers of SCNECC.

RESULTS

We identified two malignant cell populations, tumor stem cells and malignant carcinoma cells, and revealed two tumor progression pathways of SCNECC. By analyzing gene expression levels in the pathophysiology of SCNECC, we found that the expression levels of ERBB4 and NRG1, as well as the expression profile of mTOR signaling pathway mediated by them, were significantly upregulated in malignant carcinoma cells. In addition, we also found that carcinoma cells were able to stimulate malignant cell proliferation through the FN1 signaling pathway. The immune cells were in a stress state, with T-cell depletion, macrophage polarization, and mast cell glycolysis. These results suggested that carcinoma cells could interfere with immune response and promote tumor escape through MIF, TGFb, and other immunosuppressive-related signaling pathways.

CONCLUSION

This study revealed the mechanism of genesis and progression in SCNECC and the related important signaling pathways, such as mTOR, and provided new insights into the treatment of SCNECC.

LncRNAs SOX2-OT and NEAT1 act as a potential biomarker for esophageal squamous cell carcinoma

Despite strides in diagnostic and therapeutic approaches for ESCC, patient survival rates remain relatively low. Recent studies highlight the pivotal role of long non-coding RNAs (lncRNAs) in regulating diverse cellular activities in humans. Dysregulated lncRNAs have emerged as potential diagnostic indicators across various cancers, including ESCC. However, further research is necessary to effectively leverage ESCC-associated lncRNAs in clinical settings. Understanding their clinical significance for ESCC diagnosis and their mechanisms can pave the way for more effective therapeutic strategies. Our qRT-PCR analysis revealed significant downregulation of SOX2-OT (~ 2.02-fold) and NEAT1 (~ 1.53-fold) in ESCC blood samples. These lncRNAs show potential as biomarkers for distinguishing ESCC patients from healthy individuals, with ROC curves and AUC values of 0.736 for SOX2-OT and 0.621 for NEAT1. Further analysis examined the correlation between SOX2-OT and NEAT1 expression and various clinicopathological factors, including age, gender, smoking, alcohol use, hot beverage intake, tumor grade, and TNM stages. In-silico studies highlighted their roles in miRNA sponging via mTOR and MAPK pathways, while co-expression network analysis identified associated genes. This research paves the way for future studies on ESCC prognosis using SOX2-OT and NEAT1 as predictive markers. By thoroughly investigating the functions of these lncRNAs, we aim to deepen our understanding of their potential as diagnostic markers and their role in facilitating effective therapeutic interventions for esophageal squamous cell carcinoma (ESCC) within clinical contexts.

Spatially Resolved in vivo CRISPR Screen Sequencing via Perturb-DBiT

Perturb-seq enabled the profiling of transcriptional effects of genetic perturbations in single cells but lacks the ability to examine the impact on tissue environments. We present Perturb-DBiT for simultaneous co-sequencing of spatial transcriptome and guide RNAs (gRNAs) on the same tissue section for in vivo CRISPR screen with genome-scale gRNA libraries, offering a comprehensive understanding of how genetic modifications affect cellular behavior and tissue architecture. This platform supports a variety of delivery vectors, gRNA library sizes, and tissue preparations, along with two distinct gRNA capture methods, making it adaptable to a wide range of experimental setups. In applying Perturb-DBiT, we conducted un-biased knockouts of tens of genes or at genome-wide scale across three cancer models. We mapped all gRNAs in individual colonies and corresponding transcriptomes in a human cancer metastatic colonization model, revealing clonal dynamics and cooperation. We also examined the effect of genetic perturbation on the tumor immune microenvironment in an immune-competent syngeneic model, uncovering differential and synergistic perturbations in promoting immune infiltration or suppression in tumors. Perturb-DBiT allows for simultaneously evaluating the impact of each knockout on tumor initiation, development, metastasis, histopathology, and immune landscape. Ultimately, it not only broadens the scope of genetic inquiry, but also lays the groundwork for developing targeted therapeutic strategies.

Role of ENO1 and its targeted therapy in tumors

ENO1, also called 2-phospho-D-glycerate hydrolase in cellular glycolysis, is an enzyme that converts 2-phosphoglycerate to phosphoenolpyruvate and plays an important role in the Warburg effect. In various tumors, ENO1 overexpression correlates with poor prognosis. ENO1 is a multifunctional oncoprotein that, when located on the cell surface, acts as a "moonlighting protein" to promote tumor invasion and metastasis. When located intracellularly, ENO1 facilitates glycolysis to dysregulate cellular energy and sustain tumor proliferation. Additionally, it promotes tumor progression by activating oncogenic signaling pathways. ENO1 is a tumor biomarker and represents a promising target for tumor therapy. This review summarizes recent advances from 2020 to 2024 in understanding the relationship between ENO1 and tumors and explores the latest targeted therapeutic strategies involving ENO1.

Lnc NEAT1 facilitates the progression of melanoma by targeting the miR-152-3p/CDK6 axis: An observational study

Long noncoding (Lnc) RNAs are novel regulators in melanoma. Lnc nuclear enriched autosomal transcript 1 (NEAT1) was reportedly upregulated in melanoma; however, the functional roles and mechanisms of Lnc NEAT1 need further investigation. Therefore, we used quantitative real-time PCR to determine the mRNA levels of Lnc NEAT1, miR-152-3p, and cyclin-dependent protein kinase 6 (CDK6). The protein level of CDK6 was determined by Western blot. Cell counting kit 8 and colony formation assays were used to assess cell proliferation. Cell migration was measured by wound healing and Transwell assays. Direct binding of the indicated molecules was verified by an RNA-binding protein immunoprecipitation assay and a dual luciferase reporter assay. The results revealed that Lnc NEAT1 and CDK6 were elevated, while miR-152-3p was downregulated in melanoma. Furthermore, Lnc NEAT1 was positively correlated with CDK6 expression and negatively correlated with miR-152-3p level. Furthermore, Lnc NEAT1 facilitated proliferation, migration, and invasion of melanoma cells. The underlying mechanism is that Lnc NEAT1 serves as a sponge for miR-152-3p to suppress the inhibitory effect of miR-152-3p on CDK6. Furthermore, the miR-152-3p/ CDK6 axis was implicated in the progression of melanoma accelerated by Lnc NEAT1. Taken together, Lnc NEAT1 may promote melanoma development by serving as an endogenous sponge of miR-152-3p, increasing CDK6 expression, and identifying a new target for the treatment of melanoma.

Targeting glucose metabolism for HPV-associated cervical cancer: A sweet poison

More than 99 % of precancerous cervical lesions are associated with human papillomavirus (HPV) infection, with HPV types 16 and 18 (especially type 16) found in over 70 % of cervical cancer cases globally. The growth of HPV-positive cervical cancer depends on the sustained expression of the viral oncogenes E6 and E7, which are key factors in maintaining the malignant phenotype of HPV-positive tumor cells. E6 and E7 oncoproteins can cause the degradation of the tumor suppressor gene p53 and the inactivation of pRb, respectively, thereby inducing carcinogenesis. However, the inhibition of p53 and pRb cannot fully explain the oncogenic mechanism of cervical cancer. Although the development of the HPV vaccine has controlled the incidence of HPV infection, its application and widespread adoption remain limited. In addition, many developing countries cannot afford the cost of vaccines. More importantly, the vaccine only prevents HPV infection and does not provide an effective treatment for patients who are already infected or have cervical cancer. Therefore, HPV-related diseases, especially cervical cancer, remain a serious challenge. This article reviews the role of glucose metabolism changes and key molecular events in HPV-induced cervical cancer, summarizes potential targets for the treatment of cervical cancer, and provides strategies for future clinical treatment. It also offers a theoretical basis for research into cervical cancer and other HPV-related tumors. Furthermore, we discuss potential treatments for HPV-associated cervical cancer through targeted metabolic pathways and analyze the risks and challenges of current targeted glucose metabolism therapies for cervical cancer.

Regulatory function of glycolysis-related lncRNAs in tumor progression: Mechanism, facts, and perspectives

Altered metabolism is a hallmark of cancer, and reprogramming of energy metabolism, known as the "Warburg effect", has long been associated with cancer. Cancer cells use the process of glycolysis to quickly manufacture energy from glucose, pyruvic acid, and lactate, which in turn accelerates the growth of cancer and glycolysis becomes a key target for anti-cancer therapies. Recent groundbreaking discoveries regarding long noncoding RNAs (lncRNAs) have opened a new chapter in the mechanism of cancer occurrence. It is widely recognized that lncRNAs regulate energy metabolism through glycolysis in cancer cells. LncRNAs have been demonstrated to engage in several cancer processes such as proliferation, apoptosis, migration, invasion, and chemoresistance, whereas glycolysis is enhanced or inhibited by the dysregulation of lncRNAs. As a result, cancer survival and development are influenced by different signaling pathways. In this review, we summarize the roles of lncRNAs in a variety of cancers and describe the mechanisms underlying their role in glycolysis. Additionally, the predictive potential of glycolysis and lncRNAs in cancer therapy is discussed.

LncRNA-Mediated TPI1 and PKM2 Promote Self-Renewal and Chemoresistance in GBM

Temozolomide (TMZ) resistance is one of the major reasons for poor prognosis in patients with glioblastoma (GBM). Long noncoding RNAs (lncRNAs) are involved in multiple biological processes, including TMZ resistance. Linc00942 is a potential regulator of TMZ sensitivity in GBM cells is shown previously. However, the underlying mechanism of TMZ resistance induced by Linc00942 is unknown. In this study, the sequence of Linc00942 by rapid amplification of cDNA ends assay in TMZ-resistant GBM cells is identified and confirmed that Linc00942 contributes to self-renewal and TMZ resistance in GBM cells. Chromatin isolation by RNA purification followed by mass spectrometry (ChIRP-MS) and followed by Western blotting (ChIRP-WB) assays shows that Linc00492 interacted with TPI1 and PKM2, subsequently promoting their phosphorylation, dimerization, and nuclear translocation. The interaction of Linc00942 with TPI1 and PKM2 leads to increased acetylation of H3K4 and activation of the STAT3/P300 axis, resulting in the marked transcriptional activation of SOX9. Moreover, the knockdown of SOX9 reversed TMZ resistance induced by Linc00492 both in vitro and in vivo. In summary, Linc00942 strongly promotes SOX9 expression by interacting with TPI1 and PKM2 is found, thereby driving self-renewal and TMZ resistance in GBM cells. These findings suggest potential combined therapeutic strategies to overcome TMZ resistance in patients with GBM.

Peptidylprolyl isomerase A guides SENP5/GAU1 DNA-lncRNA triplex generation for driving tumorigenesis

The three-stranded DNA-RNA triplex hybridization is involved in various biological processes, including gene expression regulation, DNA repair, and chromosomal stability. However, the DNA-RNA triplex mediating mechanisms underlying tumorigenesis remain to be fully elucidated. Here, we show that peptidylprolyl isomerase A (PPIA) serves as anchor to recruit GAU1 lncRNA by interacting with exon 4 of GAU1 and enhances the formation of SENP5/GAU1 DNA-lncRNA triplex. Intriguingly, TFR4 region of GAU1 exon 3 and TTS4 region of SENP5 promoter DNA constitute fragments forming the SENP5/GAU1 triplex. The SENP5/GAU1 triplex subsequently triggers the recruitment of the methyltransferase SET1A to exon 1 of GAU1, leading to the enrichment of H3K4 trimethylation and the activation of SENP5 transcription for driving the tumorigenesis of gastric cancer in vitro and in vivo. Our study reveals a mechanism of PPIA-guided SENP5/GAU1 DNA-lncRNA triplex formation in tumorigenesis and providing a concept in the dynamics of isomerase assisted DNA-RNA hybridization.

Replenishment of TCA cycle intermediates and long-noncoding RNAs regulation in breast cancer

The tricarboxylic acid (TCA) cycle is an essential interface that coordinates cellular metabolism and is as a primary route determining the fate of a variety of fuel sources, including glucose, fatty acid and glutamate. The crosstalk of nutrients replenished TCA cycle regulates breast cancer (BC) progression by changing substrate levels-induced epigenetic alterations, especially the methylation, acetylation, succinylation and lactylation. Long non-coding RNAs (lncRNA) have dual roles in inhibiting or promoting energy reprogramming, and so altering the metabolic flux of fuel sources to the TCA cycle, which may regulate epigenetic modifications at the cellular level of BC. This narrative review discussed the central role of the TCA cycle in interconnecting numerous fuels and the induced epigenetic modifications, and the underlying regulatory mechanisms of lncRNAs in BC.

The role of exosomes derived from stem cells in nerve regeneration: A contribution to neurological repair

Stem cell-derived exosomes have gained attention in regenerative medicine for their role in encouraging nerve regeneration and potential use in treating neurological diseases. These nanosized extracellular vesicles act as carriers of bioactive molecules, facilitating intercellular communication and enhancing the regenerative process in neural tissues. This comprehensive study explores the methods by which exosomes produced from various stem cells contribute to nerve healing, with a particular emphasis on their role in angiogenesis, inflammation, and cellular signaling pathways. By examining cutting-edge developments and exploring the potential of exosomes in delivering disease-specific miRNAs and proteins, we highlight their versatility in tailoring personalized therapeutic strategies. The findings presented here highlight the potential of stem cell-produced exosomes for use in neurological diseases therapy, establishing the door for future research into exosome-based neurotherapies.

LncOCMRL1 promotes oral squamous cell carcinoma growth and metastasis via the RRM2/EMT pathway

BACKGROUND

Long noncoding RNAs (lncRNAs) are widely involved in cancer development and progression, but the functions of most lncRNAs have not yet been elucidated. Metastasis is the main factor restricting the therapeutic outcomes of various cancer types, including oral squamous cell carcinoma (OSCC). Therefore, exploring the key lncRNAs that regulate OSCC metastasis and elucidating their molecular mechanisms will facilitate the development of new strategies for effective OSCC therapy.

METHODS

We analyzed the lncRNA expression profiles of tumor tissues from OSCC patients with and without cervical lymph node metastasis, and OSCC cell lines. We revealed high expression of oral squamous cell carcinoma metastasis-related lncRNA 1 (lncOCMRL1) in OSCC patient tumor tissues with lymph node metastasis and highly metastatic OSCC cell lines. The effects of lncOCMRL1 knockdown on the invasion, migration and proliferation abilities of OSCC cells were explored through qRT-PCR, Transwell, colony formation, and cell proliferation experiments. The mechanism by which lncOCMRL1 promotes OSCC metastasis and proliferation was explored through RNA pull-down, silver staining, mass spectrometry, RIP, and WB experiments. To increase its translational potential, we developed a reduction-responsive nanodelivery system to deliver siRNA for antitumor therapy.

RESULTS

We determined that lncOCMRL1 is highly expressed in OSCC metastatic tumor tissues and cells. Functional studies have shown that high lncOCMRL1 expression can promote the growth and metastasis of OSCC cells both in vivo and in vitro. Mechanistically, lncOCMRL1 could induce epithelial-mesenchymal transition (EMT) via the suppression of RRM2 ubiquitination and thereby promote the proliferation, invasion, and migration of OSCC cells. We further constructed reduction-responsive nanoparticles (NPs) for the systemic delivery of siRNAs targeting lncOCMRL1 and demonstrated their high efficacy in silencing lncOCMRL1 expression in vivo and significantly inhibited OSCC tumor growth and metastasis.

CONCLUSIONS

Our results suggest that lncOCMRL1 is a reliable target for blocking lymph node metastasis in OSCC.

ZFP64 drives glycolysis-mediated stem cell-like properties and tumorigenesis in breast cancer

BACKGROUND

Breast cancer (BC) is a great clinical challenge because of its aggressiveness and poor prognosis. Zinc Finger Protein 64 (ZFP64), as a transcriptional factor, is responsible for the development and progression of cancers. This study aims to investigate whether ZFP64 regulates stem cell-like properties and tumorigenesis in BC by the glycolytic pathway.

RESULTS

It was demonstrated that ZFP64 was overexpressed in BC specimens compared to adjacent normal tissues, and patients with high ZFP64 expression had shorter overall survival and disease-free survival. The analysis of the association of ZFP64 expression with clinicopathological characteristics showed that high ZFP64 expression is closely associated with N stage, TNM stage, and progesterone receptor status. Knockdown of ZFP64 suppressed the viability and colony formation capacity of BC cells by CCK8 and colony formation assays. The subcutaneous xenograft models revealed that ZFP64 knockdown reduced the volume of formatted tumors, and decreased Ki67 expression in tumors. The opposite effects on cell proliferation and tumorigenesis were demonstrated by ZFP64 overexpression. Furthermore, we suggested that the stem cell-like properties of BC cells were inhibited by ZFP64 depletion, as evidenced by the decreased size and number of formatted mammospheres, the downregulated expressions of OCT4, Nanog, and SOX2 proteins, as well as the reduced proportion of CD44+/CD24- subpopulations. Mechanistically, glycolysis was revealed to mediate the effect of ZFP64 using mRNA-seq analysis. Results showed that ZFP64 knockdown blocked the glycolytic process, as indicated by decreasing glycolytic metabolites, inhibiting glucose consumption, and reducing lactate and ATP production. As a transcription factor, we identified that ZFP64 was directly bound to the promoters of glycolysis-related genes (ALDOC, ENO2, HK2, and SPAG4), and induced the transcription of these genes by ChIP and dual-luciferase reporter assays. Blocking the glycolytic pathway by the inhibition of glycolytic enzymes ENO2/HK2 suppressed the high proliferation and stem cell-like properties of BC cells induced by ZFP64 overexpression.

CONCLUSIONS

These data support that ZFP64 promotes stem cell-like properties and tumorigenesis of BC by activating glycolysis in a transcriptional mechanism.

PGAM1 suppression remodels the tumor microenvironment in triple-negative breast cancer and synergizes with anti-PD-1 immunotherapy

Triple-negative breast cancer is a high-risk form of breast cancer with a high metastatic potential and lack of effective therapies. Immunotherapy has shown encouraging clinical benefits, and its efficacy in triple-negative breast cancer is affected by immunocyte infiltration in the tumor microenvironment. PGAM1 is a key enzyme involved in cancer metabolism; however, its role in the tumor microenvironment remains unclear. In this study, we aimed to investigate the role of PGAM1 in triple-negative breast cancer and determine the potential of PGAM1 inhibition in combination with anti-PD-1 immunotherapy. Our results showed that PGAM1 is highly expressed in triple-negative breast cancer and is associated with poor prognosis. In vivo experiments demonstrated that PGAM1 inhibition synergizes with anti-PD-1 immunotherapy, significantly remodeling the tumor microenvironment and leading to an increase in antitumor immunocytes, such as CD8+ T cells and M1 macrophages, and a reduction in immunosuppressive cell infiltration, including myeloid-derived suppressor cells, M2 macrophages, and regulatory T cells. Functional and animal experiments showed that this synergistic mechanism inhibited tumor growth in vitro and in vivo. We identified PGAM1 as a novel target that exhibits an antitumor effect via the regulation of immunocyte infiltration. Our results show that PGAM1 can synergize with anti-PD-1 immunotherapy, providing a novel treatment strategy for triple-negative breast cancer.

Advanced Insights into Competitive Endogenous RNAs (ceRNAs) Regulated Pathogenic Mechanisms in Metastatic Triple-Negative Breast Cancer (mTNBC)

Triple-negative breast cancer is aggressive and challenging to treat because of a lack of targets and heterogeneity among tumors. A paramount factor in the mortality from breast cancer is metastasis, which is driven by genetic and phenotypic alterations that drive epithelial-mesenchymal transition, stemness, survival, migration and invasion. Many genetic and epigenetic mechanisms have been identified in triple-negative breast cancer that drive these metastatic phenotypes; however, this knowledge has not yet led to the development of effective drugs for metastatic triple-negative breast cancer (mTNBC). One that may not have received enough attention in the literature is post-translational regulation of broad sets of cancer-related genes through inhibitory microRNAs and the complex competitive endogenous RNA (ceRNA) regulatory networks they are influenced by. This field of study and the resulting knowledge regarding alterations in these networks is coming of age, enabling translation into clinical benefit for patients. Herein, we review metastatic triple-negative breast cancer (mTNBC), the role of ceRNA network regulation in metastasis (and therefore clinical outcomes), potential approaches for therapeutic exploitation of these alterations, knowledge gaps and future directions in the field.

Long Non-Coding RNAs, Nuclear Receptors and Their Cross-Talks in Cancer-Implications and Perspectives

Long non-coding RNAs (lncRNAs) play key roles in various epigenetic and post-transcriptional events in the cell, thereby significantly influencing cellular processes including gene expression, development and diseases such as cancer. Nuclear receptors (NRs) are a family of ligand-regulated transcription factors that typically regulate transcription of genes involved in a broad spectrum of cellular processes, immune responses and in many diseases including cancer. Owing to their many overlapping roles as modulators of gene expression, the paths traversed by lncRNA and NR-mediated signaling often cross each other; these lncRNA-NR cross-talks are being increasingly recognized as important players in many cellular processes and diseases such as cancer. Here, we review the individual roles of lncRNAs and NRs, especially growth factor modulated receptors such as androgen receptors (ARs), in various types of cancers and how the cross-talks between lncRNAs and NRs are involved in cancer progression and metastasis. We discuss the challenges involved in characterizing lncRNA-NR associations and how to overcome them. Furthering our understanding of the mechanisms of lncRNA-NR associations is crucial to realizing their potential as prognostic features, diagnostic biomarkers and therapeutic targets in cancer biology.

Transcription factor ZEB1 coordinating with NuRD complex to promote oncogenesis through glycolysis in colorectal cancer

Background

Colorectal cancer (CRC) is an aggressive primary intestinal malignancy with the third-highest incidence and second-highest mortality among all cancer types worldwide. Transcription factors (TFs) regulate cell development and differentiation owing to their ability to recognize specific DNA sequences upstream of genes. Numerous studies have demonstrated a strong correlation between TFs, the etiology of tumors, and therapeutic approaches. Here, we aimed to explore prognosis-related TFs and comprehend their carcinogenic mechanisms, thereby offering novel insights into the diagnosis and management of CRC.

Materials and Methods

Differentially expressed TFs between CRC and normal tissues were identified leveraging The Cancer Genome Atlas database, Weighted correlation network analysis and Cox regression analysis were performed to identify prognosis-related TFs. The cellular functions of hub TF zinc finger E-box binding homeobox 1 (ZEB1) were determined using by 5-ethynyl-2'-deoxyuridine and cell invasion assays in CRC cells. RNA-sequencing, Kyoto Encyclopedia of Genes and Genomes enrichment, and gene set enrichment analyses were used to identify the cellular processes in which ZEB1 participates. Immunoaffinity purification, silver staining mass spectrometry, and a chromatin immunoprecipitation assay were conducted to search for proteins that might interact with ZEB1 and the target genes they jointly regulate.

Results

Thirteen central TFs related to prognosis were identified through bioinformatics analysis techniques. Among these TFs, ZEB1 emerged as the TF most closely associated with CRC, as determined through a combination of regulatory network diagrams, survival curves, and phenotype analyses. ZEB1 promotes CRC cell growth by recruiting the NuRD(MTA1) complex, and the ZEB1/NuRD(MTA1) complex transcriptionally represses glycolysis-associated tumor suppressor genes.

Conclusion

Our study not only identified a hub biomarker related to CRC prognosis but also revealed the specific molecular mechanisms through which ZEB1 affects cancer progression. These insights provide crucial evidence for the diagnosis of CRC and potential treatment opportunities.

Mechanism insights and therapeutic intervention of tumor metastasis: latest developments and perspectives

Metastasis remains a pivotal characteristic of cancer and is the primary contributor to cancer-associated mortality. Despite its significance, the mechanisms governing metastasis are not fully elucidated. Contemporary findings in the domain of cancer biology have shed light on the molecular aspects of this intricate process. Tumor cells undergoing invasion engage with other cellular entities and proteins en route to their destination. Insights into these engagements have enhanced our comprehension of the principles directing the movement and adaptability of metastatic cells. The tumor microenvironment plays a pivotal role in facilitating the invasion and proliferation of cancer cells by enabling tumor cells to navigate through stromal barriers. Such attributes are influenced by genetic and epigenetic changes occurring in the tumor cells and their surrounding milieu. A profound understanding of the metastatic process's biological mechanisms is indispensable for devising efficacious therapeutic strategies. This review delves into recent developments concerning metastasis-associated genes, important signaling pathways, tumor microenvironment, metabolic processes, peripheral immunity, and mechanical forces and cancer metastasis. In addition, we combine recent advances with a particular emphasis on the prospect of developing effective interventions including the most popular cancer immunotherapies and nanotechnology to combat metastasis. We have also identified the limitations of current research on tumor metastasis, encompassing drug resistance, restricted animal models, inadequate biomarkers and early detection methods, as well as heterogeneity among others. It is anticipated that this comprehensive review will significantly contribute to the advancement of cancer metastasis research.

Reciprocal interactions between lncRNAs and MYC in colorectal cancer: partners in crime

Proto-oncogenic MYC is frequently dysregulated in colorectal cancer (CRC). In the past decades, long noncoding RNAs (lncRNAs) have emerged as important regulators in cancers, acting as scaffolds, molecular decoys, post-transcriptional regulators, and others. Interestingly, lncRNAs are able to control MYC expression both at transcriptional and post-transcriptional levels. It is suggested that the reciprocal interaction of MYC and lncRNAs often occurs in CRC. MYC can affect the cell fate by promoting or inhibiting the transcription of some lncRNAs. At the same time, some lncRNAs can also affect MYC expression or transcriptional activity, and in turn decide the cell fate. In this review we summarized the current knowledge about the MYC and lncRNA axis, focusing on its mutual regulation, roles in CRC, and proposed potential therapeutic prospects for CRC treatment.

LncRNA NEAT1 promotes proliferation, migration, and invasion of laryngeal squamous cell carcinoma cells through miR-411-3p/FZD3-mediated Wnt signaling pathway

The lncRNA NEAT1 has been shown to promote the progression of several cancers, containing laryngeal squamous cell carcinoma (LSCC). However, the precise mechanism by which it promotes LSCC progression remains unclear. In this study, we verified the high expression of lncRNA NEAT1 in LSCC tissues and cells using RT-qPCR. Analysis of clinical data exhibited that high expression of lncRNA NEAT1 was associated with a history of smoking, worse T stage, lymph node metastasis, and later TNM stage in patients with LSCC. The promotion effect of lncRNA NEAT1 on LSCC cell proliferation, migration, invasion, and tumor growth in vivo was verified by CCK-8, plate clone formation, Transwell, and nude mouse tumorigenicity assays. Bioinformatics prediction and double luciferase reporter gene assay verified the binding of miR-411-3p to lncRNA NEAT1 and FZD3 mRNA, and inhibition of miR-411-3p reversed the inhibitory effect of lncRNA NEAT1 on FZD3 expression in LSCC cells. We also verified that lncRNA NEAT1-mediated FZD3 activation in the Wnt pathway affects LSCC development. In conclusion, we demonstrate that lncRNA NEAT1 promotes the progression of LSCC, and propose that the lncRNA NEAT1/miR-411-3p/FZD3 axis may be an effective target for LSCC therapy.

The Potential Links between lncRNAs and Drug Tolerance in Lung Adenocarcinoma

Lung cancer patients treated with targeted therapies frequently respond well but invariably relapse due to the development of drug resistance. Drug resistance is in part mediated by a subset of cancer cells termed "drug-tolerant persisters" (DTPs), which enter a dormant, slow-cycling state that enables them to survive drug exposure. DTPs also exhibit stem cell-like characteristics, broad epigenetic reprogramming, altered metabolism, and a mutagenic phenotype mediated by adaptive mutability. While several studies have characterised the transcriptional changes that lead to the altered phenotypes exhibited in DTPs, these studies have focused predominantly on protein coding changes. As long non-coding RNAs (lncRNAs) are also implicated in the phenotypes altered in DTPs, it is likely that they play a role in the biology of drug tolerance. In this review, we outline how lncRNAs may contribute to the key characteristics of DTPs, their potential roles in tolerance to targeted therapies, and the emergence of genetic resistance in lung adenocarcinoma.

Emerging roles of long noncoding RNAs in enzymes related intracellular metabolic pathways in cancer biology

Metabolic reprogramming plays critical roles in the development and progression of tumor by providing cancer cells with a sufficient supply of nutrients and other factors needed for fast-proliferating. Emerging evidence indicates that long noncoding RNAs (lncRNAs) are involved in the initiation of metastasis via regulating the metabolic reprogramming in various cancers. In this paper, we aim to summarize that lncRNAs could participate in intracellular nutrient metabolism including glucose, amino acid, lipid, and nucleotide, regardless of whether lncRNAs have tumor-promoting or tumor-suppressor function. Meanwhile, modulation of lncRNAs in glucose metabolic enzymes in glycolysis, pentose phosphate pathway and tricarboxylic acid cycle (TCA) in cancer is reviewed. We also discuss therapeutic strategies targeted at interfering with enzyme activity to decrease the utilization of glucoses, amino acid, nucleotide acid and lipid in tumor cells. This review focuses on our current understanding of lncRNAs participating in cancer cell metabolic reprogramming, paving the way for further investigation into the combination of such approaches with existing anti-cancer therapies.

Fokker-Planck diffusion maps of multiple single cell microglial transcriptomes reveals radial differentiation into substates associated with Alzheimer's pathology

The identification of microglia subtypes is important for understanding the role of innate immunity in neurodegenerative diseases. Current methods of unsupervised cell type identification assume a small noise-to-signal ratio of transcriptome measurements that would produce well-separated cell clusters. However, identification of subtypes is obscured by gene expression noise, diminishing the distances in transcriptome space between distinct cell types and blurring boundaries. Here we use Fokker-Planck (FP) diffusion maps to model cellular differentiation as a stochastic process whereby cells settle into local minima, corresponding to cell subtypes, in a potential landscape constructed from transcriptome data using a nearest neighbor graph approach. By applying critical transition fields, we identify individual cells on the verge of transitioning between subtypes, revealing microglial cells in inactivated, homeostatic state before radially transitioning into various specialized subtypes. Specifically, we show that cells from Alzheimer's disease patients are enriched in a microglia subtype associated to antigen presentation and T-cell recruitment.

SPACA6P-AS: a trailblazer in breast cancer pathobiology and therapeutics

OBJECTIVE

The primary objective of this investigation is to delve into the involvement of the long noncoding RNA (lncRNA) SPACA6P-AS in breast cancer (BC) development, focusing on its expression pattern, association with clinical-pathological features, impact on prognosis, as well as its molecular and immunological implications.

METHODS

Bioinformatics analysis was conducted utilizing RNA sequencing data of 1083 BC patients from the TCGA database. Functional exploration of SPACA6P-AS was carried out through the construction of survival curves, GO and KEGG enrichment analysis, and single-sample gene set enrichment analysis (ssGSEA). Furthermore, its functionality was validated through in vitro cell experiments and in vivo nude mouse model experiments.

RESULTS

SPACA6P-AS showed a remarkable increase in expression levels in BC tissues (p < 0.001) and demonstrated a close relationship to poor prognosis (overall survival HR = 1.616, progression-free interval HR = 1.40, disease-specific survival HR = 1.54). Enrichment analysis revealed that SPACA6P-AS could impact biological functions such as protease regulation, endopeptidase inhibitor activity, taste receptor activity, taste transduction, and maturity-onset diabetes of the young pathway. ssGSEA analysis indicated a negative correlation between SPACA6P-AS expression and immune cell infiltration like dendritic cells and neutrophils, while a positive correlation was observed with central memory T cells and T helper 2 cells. Results from in vitro and in vivo experiments illustrated that silencing SPACA6P-AS significantly inhibited the proliferation, migration, and invasion capabilities of BC cells. In vitro experiments also highlighted that dendritic cells with silenced SPACA6P-AS exhibited enhanced capabilities in promoting the proliferation of autologous CD3 + T cells and cytokine secretion. These discoveries elucidate the potential multifaceted roles of SPACA6P-AS in BC, including its potential involvement in modulating immune cell infiltration in the tumor microenvironment.

CONCLUSION

The high expression of lncRNA SPACA6P-AS in BC is closely linked to poor prognosis and may facilitate tumor progression by influencing specific biological processes, signaling pathways, and the immune microenvironment. The regulatory role of SPACA6P-AS positions it as a prospective biomarker and target for therapeutic approaches for BC diagnosis and intervention.