Analyzing MiRNA-LncRNA Interactions

miR-660: A novel regulator in human cancer pathogenesis and therapeutic implications

MicroRNAs (miRNAs) are non-coding RNAs that regulate gene expression. Among these, miR-660, located on chromosome Xp11.23, is increasingly studied for its role in cancer due to its abnormal expression in various biological contexts. It is regulated by 8 competing endogenous RNAs (ceRNAs), which adds complexity to its function. miR- 660 targets 19 genes involved in 6 pathways such as PI3K/AKT/mTOR, STAT3, Wnt/β-catenin, p53, NF‑κB, and RAS, influencing cell cycle, proliferation, apoptosis, and invasion/migration. It also plays a role in resistance to chemotherapies like cisplatin, gemcitabine, and sorafenib in lung adenocarcinoma (LUAD), pancreatic ductal adenocarcinoma (PDAC), and hepatocellular carcinoma (HCC), thus highlighting its clinical importance. Additionally, leveraging liposomes as nanocarriers presents a promising avenue for enhancing cancer drug delivery. Our comprehensive study not only elucidates the aberrant expression patterns, biological functions, and regulatory networks of miR-660 and its ceRNAs but also delves into the intricate signaling pathways implicated. We envisage that our findings will furnish a robust framework and serve as a seminal reference for future investigations of miR-660, fostering advancements in cancer research and potentially catalyzing breakthroughs in cancer diagnosis and treatment paradigms.

The role and research progress of epigenetic modifications in obstructive sleep apnoea-hypopnea syndrome and related complications

Epigenetic modifications are heritable changes in gene expression that do not alter the DNA sequence. Histone modifications, non-coding RNA expression, and DNA methylation are examples of common epigenetic changes. Obstructive sleep apnoea-hypopnea syndrome (OSAHS) is the most common sleep-related breathing disorder, and its incidence is increasing annually, making it a hotspot of clinical research and significantly impacting health and well-being. The main cause of OSAHS is related to complications caused by repeated chronic intermittent hypoxia (CIH). Currently, polysomnography (PSG) and continuous positive airway pressure (CPAP) remain the gold standards for the diagnosis and treatment of OSAHS. However, their limitations-such as time consumption, high cost, and poor patient comfort-contribute to the paradox of high disease prevalence yet low rates of diagnosis and treatment, resulting in a substantial disease burden. In recent years, rapid advances in epigenetics have revealed that biomarkers such as microRNAs (miRNAs), circular RNAs (circRNAs), and other epigenetic modifications hold promise as non-invasive tools for the diagnosis and treatment of OSAHS and its related complications. Although numerous studies have explored epigenetic modifications in other diseases, this study focuses on how epigenetic modifications participate in the process of OSAHS and its related complications, with an aim of elucidating the pathogenesis of OSAHS from an epigenetic perspective and provide new directions for identifying molecular targets for the diagnosis and treatment of OSAHS and related complications.

Predictive Value of LncRNA LINC01184 in Papillary Thyroid Cancer Development and Prognosis and Its Regulatory Effect on Cellular Processes

INTRODUCTION

This study assessed the potential of lncRNA LINC01184 in predicting PTC progression and prognosis and its regulatory mechanism in PTC cellular processes, aiming to explore a novel biomarker for PTC.

METHODS

The study enrolled 111 PTC patients and collected paired tissue samples. Using PCR, the expression of LINC01184 was analyzed, and its association with patients' clinicopathological features and prognosis was evaluated. The regulatory effects of LINC01184 on cell growth and metastasis were assessed by CCK8 and Transwell assays.

RESULTS

LINC01184 was significantly downregulated in PTC, which was closely correlated with poor differentiation, advanced TNM stage, the occurrence of lymph node metastasis, and poor overall survival. In PTC cells, LINC01184 negatively regulated miR-296-3p, and its overexpression suppressed cell growth and metastasis of PTC, which was reversed by overexpressing miR-296-3p.

CONCLUSION

Downregulated LINC01184 served as a biomarker for PTC. Overexpressing LINC01184 suppressed PTC cell progression via suppressing miR-296-3p.

The Preconditioning with Sevoflurane Alleviates Hypoxia-Reoxygenation-Induced Myocardial Cell Injury by Regulating the lncRNA LINC00265/miR-370-3p Axis

In recent years, the cardioprotective effects of the volatile anesthetic sevoflurane (SEV) have been confirmed, yet its underlying molecular mechanisms remain incompletely elucidated. Notably, lncRNA LINC00265 has been identified as dysregulated in damaged cardiomyocytes, potentially contributing to disease progression. However, limited research has focused on the interplay between SEV and lncRNA LINC00265. The main objective of this study was to explore the mechanism and role of lncRNA LINC00265 in mediating the cardioprotective effects of SEV against myocardial injury. An in vitro hypoxia/reoxygenation (H/R) model was created in AC16 cells following pretreatment with varying concentrations of SEV. RT-qPCR was used to evaluate the levels of lncRNA LINC00265, miR-370-3p, IL-6, and TNF-α. The concentrations of CK-MB and cTnI were determined using ELISA. Cell viability was evaluated using CCK-8, and apoptosis was quantified by flow cytometry. Additionally, the relationship between lncRNA LINC00265 and miR-370-3p was confirmed using a dual-luciferase reporter assay. Prolonged hypoxia gradually rose in lncRNA LINC00265 levels, which was reversed by SEV pretreatment. SEV pretreatment mitigated H/R-induced decreases in cell viability, increases in apoptosis, and excessive production of IL-6, TNF-α, CK-MB, and cTnI. However, the protective effects of SEV were counteracted by lncRNA LINC00265 overexpression. A negative regulatory relationship between lncRNA LINC00265 and miR-370-3p was discovered. miR-370-3p overexpression mitigated diminished protective effects of SEV by elevated lncRNA LINC00265 in myocardial injury. lncRNA LINC00265 could diminish the protective effects of SEV against myocardial injury by functioning as a sponge for miR-370-3p.

LncRNA TUSC7 Inhibits Cell Proliferation in Chronic Lymphocytic Leukemia by Modulating the miR-211-5p/SLC37A3 Axis

Chronic lymphocytic leukemia (CLL) is a malignant lymphoproliferative disorder. Long non-coding RNAs (lncRNAs) have been implicated in various regulatory processes and cancer development. Among these, lncRNA tumor suppressor candidate 7 (TUSC7) has been identified as a tumor suppressor gene. We herein measured TUSC7 expression using RT-qPCR and investigated its biological role in CLL through gain-of-function experiments. Our results revealed that TUSC7 expression was significantly lower in CLL patients compared to healthy controls, and its downregulation was associated with poor prognosis. Meanwhile, TUSC7 overexpression inhibited cell proliferation while promoting cell apoptosis. Mechanistically, TUSC7 interacted with miR-211-5p, thereby regulating the downstream target gene, solute carrier family 37 member 3 (SLC37A3). Further rescue experiments demonstrated that silencing SLC37A3 or upregulating miR-211-5p reversed the effects of TUSC7 elevation on cell proliferation and apoptosis. In conclusion, our findings suggest that TUSC7 regulates cell proliferation in CLL through the miR-211-5p/SLC37A3 axis.

Exploring the microRNA-mitochondrial nexus in hepatocellular carcinoma

MicroRNAs (miRNAs) are double-edged swords in hepatocellular carcinoma (HCC) that play a dual role in disease progression and suppression. The pivotal role of miRNAs in gene regulation emphasizes their potential to disrupt critical cellular processes, including mitochondrial function. Given the indispensable role of mitochondria in energy production, apoptosis, and metabolic control, all of which are central to HCC progression, understanding the miRNA-mitochondria axis is crucial. MiRNAs emerge as pivotal regulators of mitochondrial function, exerting profound influence over HCC progression. This comprehensive review delves into the multifaceted roles of miRNAs in modulating mitochondrial biogenesis, dynamics, and apoptosis. MiRNA impacts key metabolic pathways, including energy metabolism, fatty acid metabolism, and oxidative stress. The intricate interplay between miRNAs and mitochondrial function extends to the regulation of mitophagy and ferroptosis. By exploring the microRNA-mitochondrial axis, this review offers insights for identifying novel diagnostic and therapeutic targets.

Sevoflurane reduces cardiomyocyte injury in a hypoxia/reoxygenation model of cardiomyocytes through the linc01278/miR-134-5pt regulatory axis

BACKGROUND

Ischemia-reperfusion leads to varying degrees of myocardial cell injury. Notably, long noncoding RNA was associated with the protective effect of sevoflurane (Sev) preconditioning against myocardial ischemic injury. Therefore, we further investigated the protective mechanism of Sev-mediated linc01278 against damaged cardiomyocytes by constructing a hypoxia/reoxygenation (HR) model of cardiomyocytes.

METHODS

The expression of linc01278, miR-134-5p, and apoptotic biomarkers in cardiomyocytes was detected by RT-qPCR. The proliferation was detected by CCK8; apoptosis was observed by flow cytometry; and the degree of cardiomyocyte injury and the level of oxidative stress was observed by ELISA. Dual luciferase reporter assay and RIP verified linc01278 and miR-134-5p interactions.

RESULTS

linc01278 was down-regulated in the HR group and up-regulated after Sev pretreatment. Sev markedly mitigated the HR-impaired cell proliferation, reduced apoptosis, and oxidative stress, and downregulated the expression of myocardial injury markers including cTnI, CK-MB, and LDH. However, this protection was noticeably reversed by the downregulation of the linc01278 expression. Mechanistically, linc01278 binds to miR-134-5p. miR-134-5p was highly expressed in cardiomyocytes of the HR, and lowly expressed in the Sev groups. The cardioprotective effect of Sev weakened by si-linc01278 was typically restored by miR-134-5p inhibitor.

CONCLUSIONS

Sev attenuates HR-stimulated myocardial injury through linc01278/miR-134-5p axis-mediated proliferation, apoptosis, and oxidative stress.

DLEU2 facilitates bladder cancer progression through miR-103a-2-5p/SOS1 axis

Background

Bladder cancer (BC) represents a life-threatening malignancy within the urinary system. Dysregulated long non-coding RNAs (lncRNAs) play pivotal roles in the advancement of BC. LncRNA deleted in lymphocytic leukemia 2 (DLEU2) is implicated in the development of various cancers. However, its role and regulatory mechanisms in BC remain unclear. This research aimed to explore the expression, biological function, and molecular mechanisms of DLEU2 In BC progression.

Methods

Expression profiles of lncRNAs, microRNAs (miRNAs), and mRNAs in normal and BC tissues were examined by leveraging the raw data sourced from the NCBI GEO database. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) validated expression levels in BC cells. To evaluate the proliferation and migration capabilities of BC cells, assays such as CCK-8, EdU, Transwell, and scratch were carried out. Luciferase reporter assays examined interactions between DLEU2 and miR-103a-2-5p and between miR-103a-2-5p with SOS1. Protein expression of SOS1 in BC cells was analyzed via western blotting.

Results

DLEU2 was markedly increased in BC tissues. Functionally, DLEU2 overexpression elevated BC cell proliferation and migration, while its knockdown produced the opposite effects. Mechanistically, DLEU2 acted as a molecular sponge for miR-103a-2-5p, which targeted SOS1. miR-103a-2-5p knockdown enhanced proliferation and migration, while co-knockdown of miR-103a-2-5p and DLEU2 reversed these effects. Overexpression of SOS1 also promoted proliferation and migration, which were counteracted by miR-103a-2-5p overexpression. Conversely, SOS1 knockdown inhibited these processes, with miR-103a-2-5p knockdown reversing this inhibition.

Conclusions

These findings demonstrate that DLEU2 facilitates BC progression via the miR-103a-2-5p/SOS1 axis. This study reveals a novel regulatory mechanism underlying BC development and highlights DLEU2 as a potential therapeutic target for BC treatment.

lncRNA HCP5 regulates inflammation and oxidative stress of neonatal sepsis via modulating miR-93-5p

BACKGROUND

Due to the high sensitivity to pathogenic microorganisms, newborns showed a high incidence and mortality of sepsis. The dysregulation of non-coding RNAs may play a key role in the immune regulation of neonatal sepsis. This study aimed to evaluate the potential function of lncRNA human histocompatibility leukocyte antigen complex P5 (HCP5) in the inflammation and oxidative stress of neonatal and to disclose its potential molecular mechanism.

METHODS

The neonatal sepsis animal models were established with newborn rat pups by cecal ligation and perforation (CLP). The macrophage cells were induced by lipopolysaccharide (LPS) to mimic the sepsis injury. The expression of HCP5 was detected by polymerase chain reaction (PCR) and regulated by corresponding transfections. The inflammatory response was estimated by the levels of interleukin-6 (IL-6), interleukin-8 (IL-8), and tumor necrosis factor-α (TNF-α) using enzyme-linked immunosorbent assay (ELISA); and the oxidative stress was assessed by the levels of malondialdehyde (MDA) and superoxide dismutase (SOD). The proliferation of macrophage cells was evaluated by the CCK8 assay.

RESULTS

HCP5 was significantly upregulated in neonatal sepsis rat models, of which the knockdown suppressed the inflammation and oxidative stress induced by CLP. In vitro, HCP5 was found to negatively regulate miR-93-5p in LPS-induced macrophage cells, which co-regulated the proliferation, inflammatory response, and oxidative stress in macrophage cells.

CONCLUSION

Upregulated HCP5 in neonatal sepsis rats regulated inflammation and oxidative stress, and it also modulated macrophage cell via regulating miR-93-5p.

The Role of Exosomes in Central Immune Tolerance and Myasthenia Gravis

BACKGROUND

Immune homeostasis plays a crucial role in immunology andis dependent on both central and peripheral tolerance. Centraltolerance and peripheral tolerance occur in the thymus and thesecondary lymphoid tissues, respectively. Tolerance breakdown andimmune regulation defects can lead to autoimmune disorders. In thisreview article, we aimed to describe the role of exosomes inregulating central tolerance and provide a summary of their effectson the pathogenesis, diagnosis, and therapeutic potential inmyasthenia gravis (MG).

METHODS

Articles for this review wereidentified using the PubMed database.

RESULTS

As the primarylymphoid organ, the thymus is responsible for building an immunecompetent, yet self-tolerant of T-cell population. Thymic statesinclude thymoma, thymic hyperplasia, and thymic atrophy, which canexert a significant influence on the central immune tolerance andrepresent specific characteristics of MG. Previous studies have foundthat exosomes derived from human thymic epithelial cells carryantigen-presenting molecules and a wide range of tissue restrictedantigens, which may indicate a vital role of thymic exosomes in MG.Besides, exosomal miRNAs and lncRNAs may also play a critical role inthe pathophysiology of MG.

CONCLUSION

This review provides thetherapeutic and diagnostic potential of exosomes in MG patients.

Expression level and clinical significance of NEAT1 in patients with chronic periodontitis

Background/purpose

Previous studies have shown that lncRNA nuclear autosomal transcript 1 (NEAT1) is abnormally expressed in periodontitis patients. However, the pathological mechanism of NEAT1 regulating periodontitis is still not clear. This study attempted to explore the expression of NEAT1 in periodontitis patients and its effect on periodontitis cell model and inflammatory response.

Materials and methods

The expressions of NEAT1 and miR-205-5p in gingival crevicular fluid (GCF) and cell samples were analyzed by qRT-PCR. The diagnostic value of NEAT1 in periodontitis was evaluated by constructing an ROC curve. The efficacy of NEAT1 on cell function and inflammatory response were assessed in LPS-induced PDLSCs. Luciferase reporter gene assay verified the targeting relationship between miR-205-5p and NEAT1.

Results

In the clinical section of this study, it was observed that NEAT1 expression was increased in GCF of periodontitis patients, and NEAT1 was found to be useful for periodontitis diagnosis. Besides, in vitro experiments suggested that inhibition of NEAT1 could improve cell viability and attenuated cell apoptosis and generation of inflammatory factors. Subsequently, luciferase reporter gene assay revealed that miR-205-5p was the target gene of NEAT1, and was negatively regulated by NEAT1.

Conclusion

High expression of NEAT1 has diagnostic value for periodontitis, and NEAT1 knockdown may reduce LPS-induced cell damage by increasing the level of miR-205-5p, which may provide a new breakthrough for the diagnosis and treatment of periodontitis.

POGZ targeted by LINC01355/miR-27b-3p retards thyroid cancer progression via interplaying with MAD2L2

Despite the high morbidity of thyroid cancer (THCA), the underlying molecular pathology remains elusive. That autism-associated protein POGZ has recently been involved in tumorigenesis intrigues us exploring its relevant molecular regulatory network in THCA. Clinical characteristics and intermolecular relationships were dissected by bioinformatics. Interaction between POGZ and MAD2L2 was examined by Co-IP assay. Targeting relationships between miR-27b-3p and POGZ/LINC01355 was verified by sequence prediction and dual-luciferase reporter detection. Cellular effects of genes were assessed by CCK-8 assay, clone formation assay, and Transwell assay, and further confirmed by a tumor-bearing nude mice model. Our results demonstrated a decrease in POGZ expression in THCA tissues and cell lines, and an interaction between POGZ and MAD2L2 protein. POGZ inhibited both the proliferation and motility of THCA cells, with these effects being reversed upon MAD2L2 silencing. LINC01355 exhibited low expression level and a positive correlation with POGZ in THCA. Both miR-27b-3p and LINC01355 were identified as regulators of POGZ through targeting. Elevated miR-27b-3p suppressed POGZ expression. LINC01355 promoted POGZ and counteracted the inhibitory effects of miR-27b-3p. Furthermore, miR-27b-3p increased the proliferation and motility of THCA cells, an effect that was blocked by LINC01355. At the animal level, POGZ, LINC01355, and MAD2L2 all attenuated tumor growth in THCA. Collectively, POGZ restrains THCA growth by interacting with MAD2L2 protein, and POGZ modulation involves a complex interplay orchestrated by LINC01355-targeted miR-27b-3p. By reporting the first POGZ-focused ceRNA network involving noncoding RNA in THCA, our study paves the way for exploring POGZ-related pathways and developing new therapeutic strategies in cancer.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-025-04231-7.

The BCL2 family: from apoptosis mechanisms to new advances in targeted therapy

The B cell lymphoma 2 (BCL2) protein family critically controls apoptosis by regulating the release of cytochrome c from mitochondria. In this cutting-edge review, we summarize the basic biology regulating the BCL2 family including canonical and non-canonical functions, and highlight milestones from basic research to clinical applications in cancer and other pathophysiological conditions. We review laboratory and clinical development of BH3-mimetics as well as more recent approaches including proteolysis targeting chimeras (PROTACs), antibody-drug conjugates (ADCs) and tools targeting the BH4 domain of BCL2. The first BCL2-selective BH3-mimetic, venetoclax, showed remarkable efficacy with manageable toxicities and has transformed the treatment of several hematologic malignancies. Following its success, several chemically similar BCL2 inhibitors such as sonrotoclax and lisaftoclax are currently under clinical evaluation, alone and in combination. Genetic analysis highlights the importance of BCL-XL and MCL1 across different cancer types and the possible utility of BH3-mimetics targeting these proteins. However, the development of BH3-mimetics targeting BCL-XL or MCL1 has been more challenging, with on-target toxicities including thrombocytopenia for BCL-XL and cardiac toxicities for MCL1 inhibitors precluding clinical development. Tumor-specific BCL-XL or MCL1 inhibition may be achieved by novel targeting approaches using PROTACs or selective drug delivery strategies and would be transformational in many subtypes of malignancy. Taken together, we envision that the targeting of BCL2 proteins, while already a success story of translational research, may in the foreseeable future have broader clinical applicability and improve the treatment of multiple diseases.

Comparative structural insights and functional analysis for the distinct unbound states of Human AGO proteins

The four human Argonaute (AGO) proteins, critical in RNA interference and gene regulation, exhibit high sequence and structural similarity but differ functionally. We investigated the underexplored structural relationships of these paralogs through microsecond-scale molecular dynamics simulations. Our findings reveal that AGO proteins adopt similar, yet unsynchronized, open-close states. We observed similar and unique local conformations, interdomain distances and intramolecular interactions. Conformational differences at GW182/ZSWIM8 interaction sites and in catalytic/pseudo-catalytic tetrads were minimal. Tetrads display conserved movements, interacting with distant miRNA binding residues. We pinpointed long common protein subsequences with consistent molecular movement but varying solvent accessibility per AGO. We observed diverse conformational patterns at the post-transcriptional sites of the AGOs, except for AGO4. By combining simulation data with large datasets of experimental structures and AlphaFold's predictions, we identified proteins with genomic and proteomic similarities. Some of the identified proteins operate in the mitosis pathway, sharing mitosis-related interactors and miRNA targets. Additionally, we suggest that AGOs interact with a mitosis initiator, zinc ion, by predicting potential binding sites and detecting structurally similar proteins with the same function. These findings further advance our understanding for the human AGO protein family and their role in central cellular processes.

Integrated analysis of the expression profiles of the lncRNA-miRNA-mRNA ceRNA network in CASMCs under hypoxia and normoxia conditions in yak heart

Hypoxia causes the occurrence of right heart hypertrophy and right heart failure. However, the yak living in the hypoxic environment, does not exhibit hypoxia-related pathological features. Therefore, It is of great significance to explore the hypoxia adaptation mechanism of yak heart. In this study, the yak heart coronary vascular smooth muscle cells (CASMCs) were treated with 21% O2 (normoxic group) and 5% O2 (hypoxic group). The results showed that hypoxia could promote the proliferation of CASMCs. Subsequently, we sequenced CASMCs in normoxic and hypoxic groups. The analysis revealed differential expression of 835 mRNAs, 285 lncRNAs and 126 miRNAs were between the two groups. GO and KEGG analysis showed that the differentially expressed genes were predominantly associated with extracellular matrix components, transcription factor activity, protein binding, immune system processes, metabolic processes and cell development processes and TGF-β, MAPK, cAMP, mTOR, PI3K-Akt and other signaling pathways. By constructing a network of mRNAs, miRNAs and lncRNAs based on the major differentially expressed RNAs, core regulatory elements associated with hypoxic adaptive function were identified. Our study may help to prove the potential role of differential genes related to hypoxic adaptation, and enhanced understanding of the molecular mechanisms of hypoxic adaptation in yak heart.

ESM1 suppresses LncRNA GAS5/miR-23a-3p/PTEN axis to promote the cisplatin-chemotherapy resistance of ovarian cancer cells via activating the PI3K/AKT pathway

BACKGROUND

Cisplatin chemotherapy is an important treatment for advanced ovarian cancer (OC). However, the development of cisplatin resistance greatly limits the survival time of OC patients. Endothelial cell-specific molecule 1 (ESM1) has been found to be an important proto-oncogene promoting OC, but its mediating OC cisplatin resistance remains unknown.

METHODS

We used quantitative polymerase chain reaction (qPCR) to measure transcription levels of ESM1, Growth arrest specific transcript 5 (GAS5), miR-23a-3p, and Phosphatase And Tensin Homolog (PTEN). A double luciferase reporter gene assay confirmed the direct binding of GAS5 to miR-23a-3p and miR-23a-3p to PTEN mRNA. The effects of ESM1, GAS5, miR-23a-3p, and PTEN on OC cisplatin resistance were tested with an Half Maximal Inhibitory Concentration (IC50) assay. Flow cytometry was used to assess the effects of ESM1, GAS5, and miR-23a-3p on cisplatin-induced OC apoptosis. Changes in apoptosis-related proteins and PI3K/AKT-related proteins were analyzed with western blot (WB).

RESULTS

ESM1 inhibits the levels of GAS5 and PTEN but increases miR-23a-3p. ESM1 and miR-23a-3p promote OC cisplatin resistance. GAS5 and miR-23a-3p promote cisplatin sensitivity for OC cells. Moreover, the main molecular mechanism is the ESM1/GAS5/miR-23a-3p/PTEN/PI3K/Akt signaling axis.

CONCLUSION

ESM1 promotes OC cisplatin resistance by activating the Phosphoinositide-3-Kinase (PI3K)/AKT Serine/Threonine Kinase (Akt) signaling pathway through the GAS5/miR-23a-3p/PTEN signaling axis. This suggests that prescriptive ESM1 regulates key downstream molecular mechanisms via non-coding RNA and can be used before neoadjuvant chemotherapy in OC is initiated.

Nanotechnology-leveraged CRISPR/Cas systems: icebreaking in trace cancer-related nucleic acids biosensing

As promising noninvasive biomarkers, nucleic acids provide great potential to innovate cancer early detection methods and promote subsequent diagnosis to improve the survival rates of patient. Accurate, straightforward and sensitive detection of such nucleic acid-based cancer biomarkers in complex biological samples holds significant clinical importance. However, the low abundance creates huge challenges for their routine detection. As the next-generation diagnostic tool, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein (Cas) with their high programmability, sensitivity, fidelity, single-base resolution, and precise nucleic acid positioning capabilities are extremely attractive for trace nucleic acid-based cancer biomarkers (NABCBs), permitting rapid, ultra-sensitive and specific detection. More importantly, by combing with nanotechnology, it can solve the long-lasting problems of poor sensitivity, accuracy and simplicity, as well as to achieve integrated miniaturization and portable point-of-care testing (POCT) detection. However, existing literature lacks specific emphasis on this topic. Thus, we intend to propose a timely one for the readers. This review will bridge this gap by providing insights for CRISPR/Cas-based nano-biosensing development and highlighting the current state-of-art, challenges, and prospects. We expect that it can provide better understanding and valuable insights for trace NABCBs detection, thereby facilitating advancements in early cancer screening/detection/diagnostics and win practical applications in the foreseeable future.

Areca catechu L. Extract Inhibits Colorectal Cancer Tumor Growth by Modulating Cell Apoptosis and Autophagy

Colorectal cancer (CRC) is a common cancer globally, and chemotherapy often causes severe complications, necessitating effective drugs with minimal side effects. As Areca catechu L. extract (ACE) is a Traditional Chinese Medicine that contains numerous active compounds with anticancer effects, in this study, the Cell Counting Kit-8 (CCK-8) assay was used to determine ACE's effect on CRC cell lines, revealing that it significantly inhibits CoLo320DM and HCT116 cells. In vivo experiments with NU-Foxn1nu mice indicated that ACE inhibits tumor growth, while a flow cytometry assay revealed that higher ACE concentrations increased cell apoptosis and ROS levels. Next-generation sequencing (NGS) showed that ACE increases the fold changes in apoptosis, DNA damage, and autophagy-related genes while inhibiting the fold changes in cell proliferation and Wnt signaling pathway genes. We conducted Western blotting to confirm these findings. Overall, ACE demonstrates potential as a drug candidate by promoting apoptosis and autophagy, and significantly reducing cell viability and tumor growth, thus offering a new approach for effective colorectal cancer treatment with minimal side effects.

Unveiling the role of lncRNA ERDR1 in immune cell regulation

Long non-coding RNAs (lncRNAs) are a class of RNA molecules that exceed 200 nucleotides in length and lack the capacity to encode proteins. In recent years, there has been a surge of interest in lncRNA research, leading to the discovery of their diverse structures and functions. This review focused on elucidating the regulatory roles of lncRNA erythroid differentiation regulatory 1 (Erdr1) within immune cells and its involvement in related disorders. By synthesizing findings from recent studies sourced from PubMed, this paper examined the biological functions and underlying mechanisms by which lncRNA Erdr1 influences immune cells and contributes to various diseases. Emerging research highlights that lncRNA Erdr1 exerts significant effects on the functionality of immune cells, particularly T lymphocytes (T cells), natural killer (NK) cells, and macrophages. Furthermore, Erdr1 has been implicated in the mitigation of several diseases, including acne, wound healing, osteoarthritis, melanoma, gastric cancer, obesity, and autism. Given its complex biological functions and mechanisms, Erdr1 presents itself as a promising biomarker and a potential therapeutic target for a range of immune cell-related disorders.

Wnt/β-catenin signaling pathway: an attractive potential therapeutic target in osteosarcoma

Osteosarcoma (OS) is the most common bone malignancy in children and adolescents, and although current neoadjuvant chemotherapy has shown efficacy against OS, the long-term survival rate for patients with OS remains low, highlighting the need to find more effective treatments. In cancer cells, abnormal activation of signaling pathways can widely affect cell activity from growth and proliferation to apoptosis, invasion and metastasis. Wnt/β-catenin is a complex and unique signaling pathway that is considered to be one of the most important carcinogenic pathways in human cancer. Research have confirmed that the Wnt/β-catenin signaling pathway is an important driving factor for the occurrence and development of osteosarcoma, and abnormal activation of this pathway can promote the pathological processes of cell proliferation, invasion, migration, tumor angiogenesis and chemical resistance of osteosarcoma. However, inhibition of Wnt/β-catenin signaling pathway can effectively inhibit or reverse the above pathological processes. Therefore, manipulating the expression or function of the Wnt/β-catenin pathway may be a potential targeted pathway for the treatment of OS. In this review, we describe the characteristics of the Wnt/β-catenin signaling pathway and summarize the role and mechanism of this pathway in OS. This paper discusses the therapeutic significance of inhibiting or targeting Wnt/β-catenin pathway in OS and the shortcomings of current studies on this pathway in OS and the problems to be solved. This review helps us to understand the role of Wnt/β-catenin on OS, and provides a theoretical basis and new ideas for targeting Wnt/β-catenin pathway as a therapeutic target for OS.

Macrophage-Derived Exosomes Promoted the Development and Stemness of Inflammatory Bowel Disease-Related Colorectal Cancer via nuclear paraspeckle assembly transcript 1-Mediated miRNA-34a-5p/phosphoprotein enriched in astrocytes 15 Axis

BACKGROUND

Inflammatory bowel disease (IBD) is closely associated with the development of colorectal cancer (CRC) due to the chronic inflammatory response. Macrophages play critical roles in regulating the microenvironment to facilitate tumor progression. Exosomes are key modulators for the communication between macrophages and tumor cells. The mechanism of macrophage-derived exosomes in IBD-related CRC development remains unclear.

METHODS

The macrophages were isolated using fluorescence activating cell sorter (FACS). The RNA and protein expressions in exosomes and CRC cells were examined by quantitative real-time polymerase chain reaction and western blot assays, respectively. CRC cell development was assessed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay, BrdU staining, Transwell assay, and spheroid formation assay. The level of stemness was determined by detecting the proportion of leucine-rich repeat-containing G-protein-coupled receptor 5 (LGR5)-positive CRC cells and the expression of LGR5, CD133, and CD44. Molecular interaction experiments were done using luciferase reporter assay and RNA immunoprecipitation assay. Xenograft tumor model in vivo and immunohistochemistry were used to observe the pathological changes.

RESULTS

Macrophage-derived exosomes from IBD-related CRC tissues were enriched with nuclear paraspeckle assembly transcript 1 (NEAT1) and able to promote the progression and stemness of CRC both in vitro and in vivo. The exosomal NEAT1 could sponge miR-34a-5p, leading to the restoration of PEA15 expression in CRC cells and promoting the development of CRC. Inhibition of NEAT1 in exosomes could effectivity inhibit the tumor growth in the CRC xenograft model.

CONCLUSIONS

These findings provide novel insights into how macrophages affect CRC development and highlight exosomal NEAT1 as a therapeutic target for CRC treatment.

Deciphering the Interplay of the PD-L1/MALT1/miR-200a Axis During Lung Cancer Development

Lung cancer remains a leading cause of cancer-related mortality worldwide. Our study investigates the involvement of the PD-L1/MALAT1/miR-200a-3p axis in lung tumor progression using a murine model of lung carcinogenesis. Lung tumors were induced in rats, which were divided into groups and sacrificed at different stages of tumor development. A histopathological examination was performed to assess tumor progression. Immunohistochemistry was applied to evaluate the expression of Ki-67 and programmed death-ligand 1 (PD-L1). The level of carcinoembryonic antigen (CEA) and expression analysis of metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), miR-200a-3p, and zinc finger E-box binding homeobox 1 (ZEB1) were evaluated for each stage of induction. Immunohistochemical analysis demonstrated a progressive upregulation of the proliferative marker Ki-67 and the immune checkpoint protein PD-L1 during the induction process, indicative of enhanced tumor proliferation and immune evasion. Additionally, CEA levels revealed a progressive increase across induction stages, with a significant increase in advanced tumor stages, highlighting its clinical relevance as a biomarker for lung cancer progression. Expression analysis revealed dynamic upregulation of MALAT1 and downregulation of miR-200a during lung tumor induction, which correlated with advanced tumor stages and elevated PD-L1 expression, suggesting that the negative correlation between MALAT1 and miR-200a is involved in the development of lung tumors. ZEB1 expression exhibited a notable increase in the advanced stages of induction, consistent with its association with aggressive lung cancer. Our findings underscore the interplay between molecular pathways involved in lung tumor development and the potential diagnostic and therapeutic implications of the PD-L1/MALAT1/miR-200a-3p axis.

LncRNA EGFR‑AS1 promotes lung cancer cell proliferation, invasion and metastasis via regulation of miR‑449a/HDAC1

There is increasing evidence that long non-coding (lnc)RNA EGFR-AS1 is involved in the development of numerous types of cancer, including non-small-cell lung cancer (NSCLC). The Cancer Genome Atlas (TCGA) demonstrates that EGFR-AS1 is highly expressed in NSCLC. Downregulation of EGFR-AS1 in A549 and PC9 NSCLC cells demonstrates inhibition of NSCLC proliferation, invasion and metastasis. The present study demonstrated that lncRNA EGFR-AS1 was essential for the development of NSCLC through its function as a competitive endogenous RNA binding to miR-449a and upregulating histone deacetylase 1. In brief, it identified a novel signaling pathway that mediated the invasion and metastasis of NSCLC and may therefore provide a new treatment target for NSCLC.

LINC00941 affects the proliferation, apoptosis and differentiation of osteoblasts by regulating the miR-335-5p/KAT7 axis

BACKGROUND

Fractures are the prevalent traumatic conditions encountered in orthopedic practices. The rising incidence of fractures has emerged as a pressing global health concern. Although the majority of individuals with fractures experience complete recovery of bone structure and function, approximately 10% of those with fractures exhibit delayed fracture healing (DFH). The objective of this investigation was to explore the function and underlying mechanisms of LINC00941 in the advancement of DFH, as well as its involvement in the regulation of osteoblastic differentiation by regulating the miR-335-5p/KAT7 axis.

METHODS

The expression levels of LINC00941, miR-335-5p, KAT7 and osteoblast differentiation-related markers were assessed using RT-qPCR. The proliferation of MC3T3-E1 cells was evaluated through the CCK-8 assay, and cell apoptosis was analyzed via flow cytometry. The targeted regulatory relationships between LINC00941 and miR-335-5p, as well as between miR-335-5p and KAT7 were verified by a dual-luciferase reporter gene assay.

RESULT

The expression of LINC00941 was significantly up regulated, while miR-335-5p exhibited a notable downregulation in DFH patients, both of LINC00941 and miR-335-5p have been identified as potential predicted markers for DFH. Furthermore, LINC00941 has been demonstrated to inhibit osteoblast proliferation, promote apoptosis, and suppress osteoblast differentiation through the regulation of the miR-335-5p/KAT7 axis.

CONCLUSION

LINC00941/ miR-335-5p/KAT7 axis may be a therapeutic target for DFH.

Integrated bioinformatics and experimental analysis of CHAF1B as a novel biomarker and immunotherapy target in LUAD

The prognosis and treatment efficacy of lung adenocarcinoma (LUAD), a disease with a high incidence, remains unsatisfactory. Identifying new biomarkers and therapeutic targets for LUAD is essential. Chromosomal assembly factor 1B (CHAF1B), a p60 component of the CAF-1 complex, is closely linked to tumor incidence and cell proliferation. However, CHAF1B's biological role and molecular mechanism in LUAD remain unclear. Here, CHAF1B expression in LUAD was examined using the GEPIA2 and UALCAN databases. Using The Cancer Genome Atlas (TCGA) LUAD database, we analyzed the diagnostic and prognostic significance of CHAF1B and its association with immune infiltration and immunological checkpoints. Gene ontology (GO) enrichment and single-cell function analyses were employed to investigate CHAF1B's possible biological roles. Drug sensitivity analysis predicted CHAF1B's effect on chemotherapeutic drug sensitivity. We also predicted lncRNAs-miRNA-CHAF1B axis to explore the molecular mechanism of CHAF1B in LUAD. Preliminary in vitro studies using qRT-PCR, CCK8, Transwell, glucose, and lactate metabolism confirmed CHAF1B's expression and role in LUAD. Its expression is associated with drug sensitivity, immunological checkpoints, and immune cell infiltration. We predicted that three miRNAs (miR-29c-3p, miR-145-5p, miR-1247-5p) and three lncRNAs (AL139287.1, NEAT1, SHG1) may be target miRNAs and target lncRNAs that regulate CHAF1B. In vitro tests showed that CHAF1B suppression decreased LUAD's migration, invasion, proliferation, and glycolysis. Overall, CHAF1B may be an innovative biomarker and therapeutic target for LUAD.

Long non-coding RNA OSTM1-AS1 promotes renal cell carcinoma progression by sponging miR-491-5p and upregulating MMP-9

Long noncoding RNAs (lncRNAs) have been recognized as essential regulators in various human malignancies. Hundreds of lncRNAs were known to be abnormally expressed in renal cell carcinoma (RCC) through a lncRNA expression microarray, among which lncRNA OSTM1 antisense RNA 1(OSTM1-AS1) was revealed as one of the most abundant lncRNAs. However, the function of OSTM1-AS1 in RCC remains unknown. Here, we examined OSTM1-AS1 functional roles and mechanism in RCC development. OSTM1-AS1 expression was significantly highly expressed among RCC tissue specimens and cell lines. Functionally, OSTM1-AS1 knockdown significantly suppressed cell proliferation, migration along with metastasis of RCC cells. Mechanistically, miR-491-5p was targeted via OSTM1-AS1, and down-regulation of miR-491-5p reversed OSTM1-AS1 knockdown impact on RCC migration and invasion. MMP-9 was targeted via miR-491-5p, and MMP-9 overexpression reversed miR-491-5p or OSTM1-AS1 knockdown impact on cell migration and invasion. MMP-9 abundance was decreased by OSTM1-AS1 silence, that was reduced by miR-491-5p deficiency. Importantly, our investigation revealed that OSTM1-AS1 has the ability to interact with miR-491-5p, thereby increasing the MMP-9 expression. The in vivo trial demonstrated that OSTM1-AS1 suppression resulted in tumor growth inhibition among nude mice. In summary, our findings indicate, for the first time, at least to the best of our knowledge, that OSTM1-AS1 serves as an oncogene among RCC by promoting proliferation, invasion, and metastasis through its targeting of the miR-491-5p/MMP9 axis. Therefore, this axis could represent a promising alternative therapeutic target for RCC treatment.

lncRNA-056298 Regulates GAP43 and Promotes Cardiac Intrinsic Autonomic Nerve Remodelling in a Canine Model of Atrial Fibrillation Induction after Ganglionated Plexus Ablation

BACKGROUND

Cardiac intrinsic autonomic nerve remodelling has been reported to play an important role in the recurrence of atrial fibrillation after radiofrequency ablation, which significantly affects the long-term efficacy of this procedure. lncRNAs have been shown to interact in the pathological processes underlying heart diseases. However, the roles and mechanisms of lncRNAs in cardiac intrinsic autonomic nerve remodelling during atrial fibrillation reduction after ganglionated plexus ablation remain unknown.

OBJECTIVE

The aim of this study was to investigate the mechanism by which lncRNA- 056298 modulates GAP43 to affect cardiac intrinsic autonomic nerve remodelling and facilitate the induction of atrial fibrillation after ganglionated plexus ablation.

METHODS

A canine model of right atrial ganglionated plexus ablation was established. The atrial electrophysiological characteristics and neural markers were detected before and after 6 months of ganglionated plexus ablation. High-throughput sequencing was used to screen differentially expressed lncRNAs in target atrial tissues, and lncRNA- 056298 was selected to further explore its effects and mechanisms on cardiac intrinsic autonomic nerve remodelling.

RESULTS

The induction rate of atrial fibrillation increased in dogs after ganglionated plexus ablation. Overexpression of lncRNA-056298 by lentivirus can shorten the atrial effective refractory period and increase the induction of atrial fibrillation. lncRNA- 056298 promoted cardiac intrinsic autonomic nerve remodelling via endogenous competition with cfa-miR-185 to induce transcription of its target gene GAP43, thereby affecting the induction of atrial fibrillation.

CONCLUSION

lncRNA-056298 regulates GAP43 by sponging miR-185, which affects cardiac intrinsic autonomic nerve remodelling and mediates atrial fibrillation induction after ganglionated plexus ablation.

Inhibition of Taurine-upregulated Gene 1 Upregulates MiR-34a-5p to Protect against Myocardial Ischemia/Reperfusion via Autophagy Regulation

BACKGROUND

Taurine upregulated gene 1 (TUG1) has been identified on long noncoding RNA (lncRNA); however, its function in myocardial cells following ischemia/ reperfusion (I/R) injury has not been explored. This study aimed to investigate the role of LncTUG1 in I/R injury by focusing on its relationship with autophagy induction by regulating miR-34a-5p expression.

METHODS

We established a myocardial I/R model and H9C2 hypoxia-ischemic and reoxygenation (HI/R) conditions to induce I/R injury. TTC, Western blot, CCK-8 assay, quantitative reverse transcription PCR, flow cytometry, and confocal microscopy were used to assess the size of myocardial infarct, level of some apoptotic-related and autophagy-associated proteins, cell viability, the level of LncRNA TUG1, apoptosis, and autophagy, respectively.

RESULTS

The results revealed that a TUG1 knockdown protected against I/R-induced myocardial injury by decreasing the impairment in cardiac function. LncRNA TUG1 expression was increased in a myocardial I/R model and HI/R in H9C2 cells. Moreover, inhibition of LncTUG1 enhanced H9C2 cell viability and protected the cells from HI/R-induced apoptosis. Silencing LncRNA TUG1 promoted HI/R-induced autophagy. Furthermore, TUG1 siRNA upregulated the level of miR-34a-5p compared to the HI/R group. The protective effect of LncRNA TUG1 inhibition on H9C2 cells following HI/R was eliminated by blocking autophagy with an miR-34a-5p inhibitor.

CONCLUSION

These findings indicated that inhibiting TUG1 may reduce the extent of myocardial I/R injury by regulating miR-34a-5p. Taken together, these results suggest that LncRNA TUG1 may represent a novel therapeutic target for myocardial I/R injury.

Advancements in Antioxidant-Based Therapeutics for Spinal Cord Injury: A Critical Review of Strategies and Combination Approaches

Spinal cord injury (SCI) initiates a cascade of secondary damage driven by oxidative stress, characterized by the excessive production of reactive oxygen species and other reactive molecules, which exacerbate cellular and tissue damage through the activation of deleterious signaling pathways. This review provides a comprehensive and critical evaluation of recent advancements in antioxidant-based therapeutic strategies for SCI, including natural compounds, RNA-based therapies, stem cell interventions, and biomaterial applications. It emphasizes the limitations of single-regimen approaches, particularly their limited efficacy and suboptimal delivery to injured spinal cord tissue, while highlighting the synergistic potential of combination therapies that integrate multiple modalities to address the multifaceted pathophysiology of SCI. By analyzing emerging trends and current limitations, this review identifies key challenges and proposes future directions, including the refinement of antioxidant delivery systems, the development of multi-targeted approaches, and strategies to overcome the structural complexities of the spinal cord. This work underscores the pressing need for innovative and integrative therapeutic approaches to advance the clinical translation of antioxidant-based interventions and improve outcomes for SCI patients.

Long non-coding RNA NEAT1 promotes multiple myeloma malignant transformation via targeting miR-485-5p/ABCB8

Multiple myeloma (MM) is the second most common hematological cancer all over the world. Long non-coding RNA (lncRNA) nuclear-enriched autosomal transcript-1 (NEAT1) have been reported to play important roles in the development and progression of multiple human malignancies like MM. However, the functional role and molecular mechanism of NEAT1 in MM progression still needs more support to identify potential targets of MM. In the present study, we focused on the clinical and biological significance of NEAT1 in MM. We demonstrated that NEAT1 was up-regulated in MM tissues and cell line. NEAT1 silencing significantly inhibited cell proliferation and promoted cell apoptosis in vitro. And we illustrated that miR-485-5p was a direct target of NEAT1 and the effect of down-regulated NEAT1 on MM cells was partially reversed by the miR-485-5p antisense oligonucleotide (ASO-miR-485-5p). Further investigation revealed that ABCB8 directly interacted with miR-485-5p. Similarly, in vivo experiments confirmed that down-regulated NEAT1 inhibited tumor growth and ABCB8 expression. Taken together, our results demonstrate for the first time that NEAT1/miR-485-5p/ABCB8 axis may be a key pathway for the development and progression of MM, and they may provide a novel avenue for targeted therapy.

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.

LncRNA AP001007 protects human renal tubular epithelial HK-2 cells and kidney organoids from LPS-induced injury

The regulation of long non-coding RNAs (lncRNAs) has been implicated in the pathogenesis of sepsis-induced acute kidney injury (SI-AKI). Nevertheless, the specific roles of individual lncRNAs in this process remain unclear. This study investigated the expression of lncRNA AP001007 in lipopolysaccharide (LPS)-induced HK-2 cells and in the peripheral blood of sepsis patients. The result shows that LPS treatment downregulated the expression of AP001007 in HK-2 cells and that circulating levels of AP001007 were lower in sepsis patients. Furthermore, overexpressing AP001007 in HK-2 cells improved cell viability, mitochondrial activity, and survival when exposed to LPS. Additionally, LPS-treated HK-2 cells secreted fewer pro-inflammatory cytokines when AP001007 was overexpressed. Similar protective effects were observed in human kidney organoids (HKOs) subjected to LPS. These findings suggest that AP001007 confers protection against LPS-induced damage in HK-2 cells and HKOs, highlighting its potential as a regulator of SI-AKI.

LncRNA DDX11-AS1 promotes breast cancer progression by targeting the miR-30c-5p/MTDH axis

Long noncoding RNAs (lncRNAs) play a significant role in the occurrence and development of malignant tumours. However, ceRNAs, which are significantly associated with the prognosis of breast cancer (BC), need to be further investigated. Therefore, the current study aimed to investigate the effect of the lncRNA DDX11-AS1 on BC progression. Bioinformatics analysis via a public microarray revealed that DDX11-AS1 was upregulated in BC. The above findings were verified via RT‒qPCR analysis of BC tissues. Additionally, our study revealed that the expression levels of DDX11-AS1 increased with increasing pathological grade and lymph node metastasis. Furthermore, DDX11-AS1 knockdown markedly inhibited the proliferation, migration and invasion abilities of BC cells. Mechanistically, DDX11-AS1 could prevent the degradation of MTDH in BC via competitively binding with miR-30c-5p, which could act as a tumour promoter factor. Additionally, miR-30c-5p was downregulated and MTDH was upregulated in BC cells and tissues. The promoting effect of DDX11-AS1 on BC cells was enhanced by miR-30c-5p silencing and reduced by treatment with MTDH inhibitors. Collectively, the above results suggest that the DDX11-AS1/miR-30c-5p/MTDH axis could be associated with the progression of BC and that DDX11-AS1 could be a potential biomarker and therapeutic target for BC.

The role of lncRNA TSIX in osteoarthritis pathogenesis: mechanistic insights and clinical biomarker potential

BACKGROUND

This study seeks to elucidate the expressions of lncRNA TSIX in Osteoarthritis (OA) and to explore its mechanisms in regulating OA progression.

METHODS

RT-qPCR was employed to analyze the expression of TSIX in OA patients classified by Kellgren-Lawrence (K-L) grades. Receiver operator characteristic (ROC) was conducted to evaluate the diagnostic value of TSIX. Correlation between TSIX levels and clinical scores such as Lysholm and visual analogue scale (VAS) score was evaluated using Pearson method. IL-1β-induced SW1353 cells served as an in vitro model. The cell function were assessed by flow cytometry and cell counting kit-8 (CCK-8) assay. The relationship between TSIX and miR-320a was verified by luciferase reporting system, while bioinformatics approaches were utilized to predict the downstream target genes of miR-320a.

RESULTS

The findings revealed that TSIX level in OA patients was elevated compared to that of the control group, with a notable progressive increase in TSIX expression correlated with higher K-L grades. In OA patients, the Lysholm score showed a negative correlation with TSIX expression, while the VAS score displayed a positive correlation with TSIX levels. Cell studies demonstrated that inhibition of TSIX enhanced cell viability and mitigated IL-1β-induced apoptosis by targeting miR-320a, in addition to promoting Aggrecan and Collagen II secretion. Luciferase reporter assay further validated the targeting interaction among TSIX, miR-320a, and PTEN.

CONCLUSIONS

This study demonstrated an increased expression of TSIX in OA patients. It suggests that TSIX may play a role in chondrocyte dysfunction during OA by modulating the miR-320a/PTEN axis.

EZH2 Promotes Glioma Cell Proliferation, Invasion, and Migration via Mir-142-3p/KCNQ1OT1/HMGB3 Axis : Running Title: EZH2 Promotes Glioma cell Malignant Behaviors

This study investigates the role and molecular mechanism of EZH2 in glioma cell proliferation, invasion, and migration. EZH2, miR-142-3p, lncRNA KCNQ1OT1, LIN28B, and HMGB3 expressions in glioma tissues and cells were determined using qRT-PCR or Western blot, followed by CCK-8 assay detection of cell viability, Transwell detection of invasion and migration, ChIP analysis of the enrichment of EZH2 and H3K27me3 on miR-142-3p promoter, dual-luciferase reporter assay and RIP validation of the binding of miR-142-3p-KCNQ1OT1 and KCNQ1OT1-LIN28B, and actinomycin D detection of KCNQ1OT1 and HMGB3 mRNA stability. A nude mouse xenograft model and a lung metastasis model were established. EZH2, KCNQ1OT1, LIN28B, and HMGB3 were highly expressed while miR-142-3p was poorly expressed in gliomas. EZH2 silencing restrained glioma cell proliferation, invasion, and migration. EZH2 repressed miR-142-3p expression by elevating the H3K27me3 level. miR-142-3p targeted KCNQ1OT1 expression, and KCNQ1OT1 bound to LIN28B to stabilize HMGB3 mRNA, thereby promoting its protein expression. EZH2 silencing depressed tumor growth and metastasis in nude mice via the miR-142-3p/KCNQ1OT1/HMGB3 axis. In conclusion, EZH2 curbed miR-142-3p expression, thereby relieving the inhibition of KCNQ1OT1 expression by miR-142-3p, enhancing the binding of KCNQ1OT1 to LIN28B, elevating HMGB3 expression, and ultimately accelerating glioma cell proliferation, invasion, and migration.

Genomic analyses of intricate interaction of TE-lncRNA overlapping genes with miRNAs in human diseases

BACKGROUND

Transposable elements (TEs) are known to be inserted into genome to create transcript isoforms or to generate long non-coding RNA (lncRNA) sequences. The insertion of TEs generates a gene protein sequence within the genome, but also provides a microRNA (miRNA) regulatory region.

OBJECTIVE

To determine the effect of gene sequence changes caused by TE insertion on miRNA binding and to investigate the formation of an overlapping lncRNA that represses it.

METHODS

The distribution of overlapping regions between exons and TE regions with lncRNA was examined using the Bedtools. miRNAs that can bind to those overlapping regions were identified through the miRDB web program. For TE-lncRNA overlapping genes, bioinformatic analysis was conducted using DAVID web database. Differential expression analysis was conducted using data from the GEO dataset and TCGA.

RESULTS

Most TEs were distributed more frequently in untranslated regions than open reading frames. There were 30 annotated TE-lncRNA overlapping genes with same strand that could bind to the same miRNA. As a result of identifying the association between these 30 genes and diseases, TGFB2, FCGR2A, DCTN5, and IFI6 were associated with breast cancer, and HMGCS1, FRMD4A, EDNRB, and SNCA were associated with Alzheimer's disease. Analysis of the GEO and TCGA data showed that the relevant expression of miR-891a and miR-28, which bind to the TE overlapping region of DCTN5 and HMGCS1, decreased.

CONCLUSION

This study indicates that the interaction between TE-lncRNA overlapping genes and miRNAs can affect disease progression.

LINC00342 regulates the PI3K-AKT signaling pathway via the miR-149-5p/FGF11 axis and affects the progression of oral cancer

BACKGROUND

A large number of long non-coding RNAs (lncRNAs) have been implicated in the progression of oral cancer (OC). This study aimed to investigate the role of a novel lncRNA, LINC00342, in OC and elucidate its molecular mechanism.

METHODS

Differential expression of lncRNA/miRNA/mRNA was analyzed using the Gene Expression Omnibus database and validated with RT-qPCR. Additionally, the expression levels of these molecules in OC cells and their effects on cell viability and cell cycle were assessed using the Cell Counting Kit-8 and flow cytometry. RNA bindings was analyzed by dual luciferase, and Western blot was used to detect the activation of relevant pathways.

RESULTS

This study showed that, in contrast to miR-149-5p, the expression of LINC00342 and fibroblast growth factor 11 (FGF11) were upregulated in OC cells (LINC00342: 10.00 ± 1.06 (FaDu) and 3.55 ± 0.25 (CAL-27) vs 1.00 ± 0.07 (HOECs), P < 0.05; FGF11: 7.31 ± 0.33 (FaDu) and 3.43 ± 0.08 (CAL-27) vs 1.00 ± 0.10 (HOECs), P < 0.05). Dual-luciferase assays confirmed that LINC00342 bind to miR-149-5p in a direct targeting manner. Furthermore, inhibition of LINC00342 expression resulted in decreased proliferation rate (FaDu: 136.22 ± 22.10% vs 59.36 ± 8.98% (control), P < 0.05; CAL-27: 131.40 ± 11.58% vs 49.83 ± 11.19 (control), P < 0.05) and migration ability of OC cells, cell cycle arrest in G1 phase, and inhibition of PI3K-AKT signaling. Inhibition of miR-149-5p or overexpression of FGF11 reversed the effects of si-LINC00342.

CONCLUSIONS

LINC00342 promotes PI3K-AKT signaling by activating FGF11 through adsorption of miR-149-5p, thereby regulating the progression of OC.

Cardiomyopathies: The Role of Non-Coding RNAs

Cardiomyopathies are the structural and functional disorders of the myocardium. Etiopathogenesis is complex and involves an interplay of genetic, environmental, and lifestyle factors eventually leading to myocardial abnormalities. It is known that non-coding (Nc) RNAs, including micro (mi)-RNAs and long non-coding (lnc) RNAs, play a crucial role in regulating gene expression. Several studies have explored the role of miRNAs in the development of various pathologies, including heart diseases. In this review, we analyzed various patterns of ncRNAs expressed in the most common cardiomyopathies: dilated cardiomyopathy, hypertrophic cardiomyopathy and arrhythmogenic cardiomyopathy. Understanding the role of different ncRNAs implicated in cardiomyopathic processes may contribute to the identification of potential therapeutic targets and novel risk stratification models based on gene expression. The analysis of ncRNAs may also be helpful to unveil the molecular mechanisms subtended to these diseases.

Regulation of autophagy by non-coding RNAs in human glioblastoma

Glioblastoma, a lethal form of brain cancer, poses substantial challenges in treatment due to its aggressive nature and resistance to standard therapies like radiation and chemotherapy. Autophagy has a crucial role in glioblastoma progression by supporting cellular homeostasis and promoting survival under stressful conditions. Non-coding RNAs (ncRNAs) play diverse biological roles including, gene regulation, chromatin remodeling, and the maintenance of cellular homeostasis. Emerging evidence reveals the intricate regulatory mechanisms of autophagy orchestrated by non-coding RNAs (ncRNAs) in glioblastoma. The diverse roles of these ncRNAs in regulating crucial autophagy-related pathways, including AMPK/mTOR signaling, the PI3K/AKT pathway, Beclin1, and other autophagy-triggering system regulation, sheds light on ncRNAs biological mechanisms in the proliferation, invasion, and therapy response of glioblastoma cells. Furthermore, the clinical implications of targeting ncRNA-regulated autophagy as a promising therapeutic strategy for glioblastoma treatment are in the spotlight of ongoing studies. In this review, we delve into our current understanding of how ncRNAs regulate autophagy in glioblastoma, with a specific focus on microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), and their intricate interplay with therapy response.

Non-coding RNAs as modulators of radioresponse in triple-negative breast cancer: a systematic review

Triple-negative breast cancer (TNBC), characterized by high invasiveness, is associated with poor prognosis and elevated mortality rates. Despite the development of effective therapeutic targets for TNBC, systemic chemotherapy and radiotherapy (RdT) remain prevalent treatment modalities. One notable challenge of RdT is the acquisition of radioresistance, which poses a significant obstacle in achieving optimal treatment response. Compelling evidence implicates non-coding RNAs (ncRNAs), gene expression regulators, in the development of radioresistance. This systematic review focuses on describing the role, association, and/or involvement of ncRNAs in modulating radioresponse in TNBC. In adhrence to the PRISMA guidelines, an extensive and comprehensive search was conducted across four databases using carefully selected entry terms. Following the evaluation of the studies based on predefined inclusion and exclusion criteria, a refined selection of 37 original research articles published up to October 2023 was obtained. In total, 33 different ncRNAs, including lncRNAs, miRNAs, and circRNAs, were identified to be associated with radiation response impacting diverse molecular mechanisms, primarily the regulation of cell death and DNA damage repair. The findings highlighted in this review demonstrate the critical roles and the intricate network of ncRNAs that significantly modulates TNBC's responsiveness to radiation. The understanding of these underlying mechanisms offers potential for the early identification of non-responders and patients prone to radioresistance during RdT, ultimately improving TNBC survival outcomes.

LncRNA-miRNA interactions prediction based on meta-path similarity and Gaussian kernel similarity

Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are two typical types of non-coding RNAs that interact and play important regulatory roles in many animal organisms. Exploring the unknown interactions between lncRNAs and miRNAs contributes to a better understanding of their functional involvement. Currently, studying the interactions between lncRNAs and miRNAs heavily relies on laborious biological experiments. Therefore, it is necessary to design a computational method for predicting lncRNA-miRNA interactions. In this work, we propose a method called MPGK-LMI, which utilizes a graph attention network (GAT) to predict lncRNA-miRNA interactions in animals. First, we construct a meta-path similarity matrix based on known lncRNA-miRNA interaction information. Then, we use GAT to aggregate the constructed meta-path similarity matrix and the computed Gaussian kernel similarity matrix to update the feature matrix with neighbourhood information. Finally, a scoring module is used for prediction. By comparing with three state-of-the-art algorithms, MPGK-LMI achieves the best results in terms of performance, with AUC value of 0.9077, AUPR of 0.9327, ACC of 0.9080, F1-score of 0.9143 and precision of 0.8739. These results validate the effectiveness and reliability of MPGK-LMI. Additionally, we conduct detailed case studies to demonstrate the effectiveness and feasibility of our approach in practical applications. Through these empirical results, we gain deeper insights into the functional roles and mechanisms of lncRNA-miRNA interactions, providing significant breakthroughs and advancements in this field of research. In summary, our method not only outperforms others in terms of performance but also establishes its practicality and reliability in biological research through real-case analysis, offering strong support and guidance for future studies and applications.

Epigenetic regulation of megakaryopoiesis and platelet formation

Platelets, produced by megakaryocytes, play unique roles in physiological processes, such as hemostasis, coagulation, and immune regulation, while also contributing to various clinical diseases. During megakaryocyte differentiation, the morphology and function of cells undergo significant changes due to the programmed expression of a series of genes. Epigenetic changes modify gene expression without altering the DNA base sequence, effectively affecting the inner workings of the cell at different stages of growth, proliferation, differentiation, and apoptosis. These modifications also play important roles in megakaryocyte development and platelet biogenesis. However, the specific mechanisms underlying epigenetic processes and the vast epigenetic regulatory network formed by their interactions remain unclear. In this review, we systematically summarize the key roles played by epigenetics in megakaryocyte development and platelet formation, including DNA methylation, histone modification, and non-coding RNA regulation. We expect our review to provide a deeper understanding of the biological processes underlying megakaryocyte development and platelet formation and to inform the development of new clinical interventions aimed at addressing platelet-related diseases and improving patients' prognoses.

LncRNA CYTOR knockdown inhibits tumor development via regulating miR-503-5p/PCSK9 in lung adenocarcinoma

BACKGROUND

The intricate biological mechanism underlying lung adenocarcinoma (LUAD), characterized by a deficiency of distinctive biomarkers, remain elusive. The presence of Long non-coding RNAs (lncRNAs) have been established to play a role in carcinogenesis. Nevertheless, the regulatory effects and mechanisms of lncRNA CYTOR in LUAD have yet to be elucidated.

METHODS

In this study, RT-qPCR and Western blot were adopted to examine gene mRNA and protein expression, respectively. Cell proliferation was evaluated by CCK-8 assays. Transwell was performed to assay cell migration and invasion. The function of CYTOR in vivo was investigated through a xenograft animal model.

RESULTS

We observed an apparent upregulation of CYTOR in LUAD. Silencing CYTOR significantly reduced proliferation, migration, and invasion capabilities of LUAD cells. Mechanism analysis indicated that CYTOR targeted the miR-503-5p/PCSK9 axis. Additionally, inhibiting of miR-503-5p partially reversed the inhibitory effects of CYTOR silencing on the malignant progression of LUAD cells. Animal experiments revealed that CYTOR/miR-503-5p/PCSK9 curbed tumor formation of nude mice in vivo.

CONCLUSION

These findings demonstrated that lncRNA CYTOR acted as an oncogene in LUAD, regulating tumor malignant progression through the miR-503-5p/PCSK9 axis. This study unveiled a new regulation mechanism of LUAD progression, offering potential therapeutic targets for LUAD.

Long Non-Coding RNA Nuclear-Enriched Abundant Transcript 1 (NEAT1) Facilitates Foam Cell Formation and Atherosclerosis Progression Through the miR-17-5p/Itchy E3 Ubiquitin Protein Ligase (ITCH)/Liver Kinase B1 (LKB1) Axis

BACKGROUND

Foam cell formation is an important step for atherosclerosis (AS) progression. We investigated the mechanism by which the long non-coding RNA (lncRNA) nuclear-enriched abundant transcript 1 (NEAT1) regulates foam cell formation during AS progression.

METHODS AND RESULTS

An in vivo AS model was created by feeding ApoE-/-mice a high-fat diet. Oxidized low-density lipoprotein (ox-LDL)-stimulated macrophages were used as a cellular AS model. Interactions between NEAT1, miR-17-5p, itchy E3 ubiquitin protein ligase (ITCH) and liver kinase B1 (LKB1) were analyzed. NEAT1 and ITCH were highly expressed in clinical samples collected from 10 AS patients and in ox-LDL-treated macrophages, whereas expression of both miR-17-5p and LKB1 was low. ITCH knockdown inhibited ox-LDL-induced lipid accumulation and LDL uptake in macrophages. Mechanistically speakingly, ITCH promoted LDL uptake and lipid accumulation in macrophages by mediating LKB1 ubiquitination degradation. NEAT1 knockdown reduced LDL uptake and lipid accumulation in macrophages and AS progression in vivo. NEAT1 promoted ITCH expression in macrophages by acting as a sponge for miR-17-5p. Inhibition of miR-17-5p facilitated ox-LDL-induced increase in LDL uptake and lipid accumulation in macrophages, which was reversed by NEAT1/ITCH knockdown.

CONCLUSIONS

NEAT1 accelerated foam cell formation during AS progression through the miR-17-5p/ITCH/LKB1 axis.

Antisense Oligonucleotide Embedded Context Responsive Nanoparticles Derived from Synthetic Ionizable Lipids for lncRNA Targeted Therapy of Breast Cancer

The long noncoding RNAs (lncRNA) are primarily associated with several essential gene regulations but are also connected to cancer metabolism and progression. HOTAIR and MALAT1 are two such lncRNAs that are detected in malignancies of various origins and are responsible for the poor prognosis of cancer patients. Due to these factors, the lncRNAs have emerged as prime targets for the development of anticancer therapeutics. However, nonviral delivery of lncRNA-targeted antisense oligonucleotides (ASOs) still remains a critical challenge while maintaining their structural and functional integrity. Herein, we have designed and synthesized a new series of ionizable lipids with variations in their head groups to prepare lipid nanoparticle (LNP) formulation along with cholesterol-based twin cationic lipid and amphiphilic zwitterionic lipid. The context responsiveness of these formulations in delivering the ASOs has been thoroughly investigated by various bioanalytical techniques, and an optimum formulation has been identified. The LNPs are utilized to deliver the ASOs targeting HOTAIR lncRNA in human cancer cell lines and MALAT1 lncRNA in mouse models. This study thus standardizes an advanced nanomaterial system for nonviral gene delivery that has been validated by a considerable reduction in the target lncRNA level under in vitro and a significant reduction in tumor volume under in vivo settings.

The roles of long non-coding RNAs in Alzheimer's disease diagnosis, treatment, and their involvement in Alzheimer's disease immune responses

Alzheimer's disease (AD) is the most frequent type of dementia, presenting a substantial danger to the health and well-being of the aged population. It has arisen as a significant public health problem with considerable socioeconomic repercussions. Unfortunately, no effective treatments or diagnostic tools are available for Alzheimer's disease. Despite substantial studies on the pathophysiology of Alzheimer's, the molecular pathways underpinning its development remain poorly understood. Long non-coding RNAs (lncRNAs) vary in size from 200 nucleotides to over 100 kilobytes and have been found to play critical roles in various vital biological processes that play critical in developing Alzheimer's disease. This review intends to examine the functions of long non-coding RNAs in diagnosing and treating Alzheimer's disease and their participation in immunological responses associated with AD.

Diagnostic value of lncRNAs LINC00152 and LARS2-AS1 and their regulatory roles in macrophage immune response in tuberculosis

OBJECTIVES

To determine the usefulness of LINC00152 and LARS2-AS1 as potential biomarkers for latent tuberculosis (LTB) and active tuberculosis (ATB), as well as their effect on Mycobacterium (Mtb) infection.

METHODS

The expression levels of LINC00152 and LARS2-AS1 in the health, patients with LTB and ATB were detected by qRT-PCR. The ROC curves were constructed to show their potential as biomarkers. The intracellular survival assays for Mtb and the levels of immune-related cytokines were determined to discover the effect of LINC00152 and LARS2-AS1 on Mtb infection. The relationships of miR-485-5p with LINC00152 and LARS2-AS1 were explored.

RESULTS

LINC00152 and LARS2-AS1 levels were significantly elevated in patients with ATB and LTB, and Mtb-infected macrophages. LINC00152 and LARS2-AS1 can distinguish the LTB from the health and ATB from LTB. LARS2-AS1 and LINC00152 knock-down reduced the intracellular Mtb survival and induced cellular immune response after Mtb challenge. miR-485-5p was a targeting miRNA for LINC00152 and LARS2-AS1.

CONCLUSIONS

LINC00152 and LARS2-AS1 can be considered as potential biomarkers for tuberculosis disease. LINC00152 and LARS2-AS1 have anti-Mtb effects.

Long non-coding RNA TMEM147 antisense RNA 1/microRNA-124/signal transducer and activator of transcription 3 axis in estrogen receptor-positive breast cancer

OBJECTIVE

This research aimed to probe the expression of long noncoding RNA TMEM147 antisense RNA 1 (TMEM147-AS1)/micro-RNA (miR)-124/signal transducer and activator of transcription 3 (STAT3) axis in estrogen receptor (ER)-positive breast cancer (BC).

METHODS

Sixty ER-positive BC patients undergoing surgical treatment were gathered. TMEM147-AS1, miR-124, and STAT3 expression levels in BC cells and tissues were measured. The binding sites of TMEM147-AS1 and miR-124, miR-124, and STAT3 were analyzed and validated. The miR-124, STAT3 overexpression (oe) sequences, TMEM147-AS1 oe, and interference sequences and their control sequences were planned and cells were transfected to assess their functions in BC cells biological functions.

RESULTS

TMEM147-AS1, as well as STAT3 was extremely expressed and miR-124 was lowly expressed in BC cells and tissues. Interference with TMEM147-AS1 restrained ER-positive BC cell malignant activities. Mechanistically, TMEM147-AS1 could competitively bind miR-124 in refraining miR-124 expression, and STAT3 was a target gene of miR-124. Oe of miR-124 effectively reversed the enhancement of BC cell proliferation and invasion induced by TMEM147-AS1 upregulation. Oe of STAT3 could reverse the inhibitory effect of miR-124 on BC cell malignant behaviors.

CONCLUSION

TMEM147-AS1 has oncogenic activity in ER-positive BC, which may be a result of the altered miR-124/STAT3 axis. Therefore, targeting the TMEM147-AS1/miR-124/STAT3 axis may be a target for ER-positive BC therapy.

Long non-coding RNAs in ferroptosis, pyroptosis and necroptosis: from functions to clinical implications in cancer therapy

As global population ageing accelerates, cancer emerges as a predominant cause of mortality. Long non-coding RNAs (lncRNAs) play crucial roles in cancer cell growth and death, given their involvement in regulating downstream gene expression levels and numerous cellular processes. Cell death, especially non-apoptotic regulated cell death (RCD), such as ferroptosis, pyroptosis and necroptosis, significantly impacts cancer proliferation, invasion and metastasis. Understanding the interplay between lncRNAs and the diverse forms of cell death in cancer is imperative. Modulating lncRNA expression can regulate cancer onset and progression, offering promising therapeutic avenues. This review discusses the mechanisms by which lncRNAs modulate non-apoptotic RCDs in cancer, highlighting their potential as biomarkers for various cancer types. Elucidating the role of lncRNAs in cell death pathways provides valuable insights for personalised cancer interventions.

A Holistic Analysis of Alzheimer's Disease-Associated lncRNA Communities Reveals Enhanced lncRNA-miRNA-RBP Regulatory Triad Formation Within Functionally Segregated Clusters

Recent studies on the regulatory networks implicated in Alzheimer's disease (AD) evince long non-coding RNAs (lncRNAs) as crucial regulatory players, albeit a poor understanding of the mechanism. Analyzing differential gene expression in the RNA-seq data from the post-mortem AD brain hippocampus, we categorized a list of AD-dysregulated lncRNA transcripts into functionally similar communities based on their k-mer profiles. Using machine-learning-based algorithms, their subcellular localizations were mapped. We further explored the functional relevance of each community through AD-dysregulated miRNA, RNA-binding protein (RBP) interactors, and pathway enrichment analyses. Further investigation of the miRNA-lncRNA and RBP-lncRNA networks from each community revealed the top RBPs, miRNAs, and lncRNAs for each cluster. The experimental validation community yielded ELAVL4 and miR-16-5p as the predominant RBP and miRNA, respectively. Five lncRNAs emerged as the top-ranking candidates from the RBP/miRNA-lncRNA networks. Further analyses of these networks revealed the presence of multiple regulatory triads where the RBP-lncRNA interactions could be augmented by the enhanced miRNA-lncRNA interactions. Our results advance the understanding of the mechanism of lncRNA-mediated AD regulation through their interacting partners and demonstrate how these functionally segregated but overlapping regulatory networks can modulate the disease holistically.