On the classification of long non-coding RNAs

Exosome-mediated Transfer of lncRNA in Liver Associated Diseases; Uncovered Truths

Exosomes are extracellular vesicles with a diameter ranging from 40 to 160 nm. They are produced by hepatocytes, cholangiocytes, hepatic stellate cells (HSCs), liver sinusoidal endothelial cells (LSECs) and Kupffer cells in liver tissue. The secretion of exosomes might vary in quantity and composition in reaction to multiple triggers and various stages of disease. They transport various payloads, such as proteins, DNAs, and RNAs, and enable cell interaction to regulate myriad physiological and pathological processes in liver tissue. Long non-coding RNAs (lncRNAs) are a crucial component of exosomes with an excellent capability to regulate multiple cellular activities such as differentiation, development, metabolism, proliferation, apoptosis, and activation. With the advancements in transcriptomic and genomic study methods and database management technology, the functions and mechanisms of exosomal lncRNAs in liver diseases have been well-studied. This article delves into the detailed role of exosomal lncRNAs in liver disease onset and progression, ranging from hepatocellular carcinoma (HCC) to liver fibrosis drug-induced liver damage (DILI) and steatotic liver diseases.

Non-coding RNA RMRP governs RAB31-dependent MMP secretion, enhancing ovarian cancer invasion

Non-coding RNAs (ncRNAs) are frequently dysregulated in various cancers and have been implicated in the etiology and progression of cancer. Ovarian cancer, the most fatal gynecological cancer, has a poor prognosis and a high patient fatality rate due to metastases. In this study, we classified patients with ovarian cancer into three groups based on their ncRNA expression levels. Notably, an ncRNA transcribed by RNA polymerase III, RNA component of mitochondrial RNA processing endoribonuclease (RMRP), is highly expressed in a group with a poor prognosis. Functional assays using SKOV3 and HeyA8 human ovarian cancer cell lines revealed that while RMRP modulation had no significant effect on cell viability, it markedly enhanced cell invasion. Knockdown and ectopic expression experiments demonstrated that RMRP promotes the secretion of matrix metalloproteinase (MMP)-2 and -9, thereby facilitating ovarian cancer cell invasiveness. Transcriptomic analysis further revealed a positive correlation between RMRP expression and genes involved in cellular localization, including RAB31, a member of the Ras-related protein family. Notably, RAB31 knockdown abrogated the pro-invasive effects of RMRP, identifying it as a key downstream effector in SKOV3 and HeyA8 cells. In addition, MechRNA analysis identified RAB31 as a putative RMRP-interacting transcript. These findings establish RMRP as a critical regulator of RAB31-dependent MMP secretion and ovarian cancer cell invasion. Moreover, our results suggest that RMRP could serve as a promising prognostic biomarker for ovarian cancer.

Exploring the roles and clinical potential of exosome-derived non-coding RNAs in glioma

Non-coding accounts for 98 %-99 % of the human genome and performs many essential regulatory functions in eukaryotes, involved in cancer development and development. Non-coding RNAs are abundantly enriched in exosomes, which play a biological role as vectors. Some biofunctional non-coding RNAs are specifically designed as exosomes for the treatment of cancers such as glioma. Glioma is one of the most common primary tumors within the skull and has varying degrees of malignancy and histologic subtypes of grades I-IV. Gliomas are characterized by high malignancy and an abundant blood supply due to rapid cell proliferation and vascularization, often with a poor prognosis. Exosomal non-coding RNAs can be involved in the tumorigenesis process of glioma from multiple directions, such as angiogenesis, tumor proliferation, metastatic invasion, immune evasion, apoptosis, and autophagy. Therefore, non-coding RNAs in exosomes are suitable as markers or therapeutic targets for early diagnosis of diseases and for predicting the prognosis of a variety of diseases. Regulating exosome production and the level of exosomal non-coding RNA expression may be a new approach to prevent or eliminate glioma. In this review, we review the origin and characteristics of exosomal non-coding RNAs, and introduce the functional studies of exosomal non-coding RNAs in glioma and their potential clinical applications, in order to broaden new ideas for the treatment of glioma.

Genome-wide identification of long non-coding RNAs reveals potential association with Phytophthora infestans asexual and sexual development

Long non-coding RNAs (lncRNAs) play pivotal roles in regulating diverse biological processes across plants, mammals, and fungi. However, the information on lncRNAs in oomycete asexual and sexual reproduction, which are two pivotal processes in the pathogenic cycle, has not been elucidated. In this present study, strand-specific RNA sequencing data of Phytophthora infestans with asexual development and sexual reproduction were reanalyzed, and a total of 4,399 lncRNAs were systematically identified. Compared to messenger RNAs (mRNAs), lncRNAs had a higher proportion of transcripts containing more than one exon, shorter nucleotide lengths, and lower expression levels. Target analysis showed that although only 280 lncRNA-mRNA pairs were shared, the functional pathways in which cis and trans targets participated were similar. Weighted gene co-expression network analysis of differentially expressed lncRNAs (DElncRs) and differentially expressed mRNAs (DEmRs) of asexual development stages indicated that lncRNAs might participate in different asexual stages and transformation of the growth stages via regulating functional genes. Expression trend analysis of DElncRs and DEmRs showed that lncRNAs may promote asexual development via upregulating mRNAs encoding development- and invasion-related proteins, such as INF6, triosephosphate isomerase, and glycoprotein elicitor. Co-expression analysis of DElncRs and DEmRs of sexual reproduction showed that lncRNAs could increase the level of mRNAs related to mating, such as M96 mating-specific protein and Crinkler family protein, which meant that lncRNAs might participate in sexual reproduction by regulating mating-related genes. Our study conducted a comprehensive analysis of lncRNAs in P. infestans and suggested a potential function of lncRNAs in asexual and sexual development.

IMPORTANCE

This study systematically analyzed lncRNAs in Phytophthora infestans, revealing the associations between lncRNAs and functional genes. The potential regulatory roles of lncRNAs in the asexual and sexual reproduction stages were clarified, providing a new perspective for in-depth understanding of the reproductive regulatory network of oomycetes. This not only expands the understanding of the functions of non-coding RNAs in different biological groups but also provides potential targets for the development of new disease prevention and control strategies, promoting related research in the fields of agriculture and biology.

A novel lncRNA ABCE1-5 regulates pulmonary fibrosis by targeting KRT14

Idiopathic pulmonary fibrosis (IPF) is a progressive and degenerative interstitial lung disease characterized by complex etiology, unclear pathogenesis, and high mortality. Long noncoding RNAs (lncRNAs) have been identified as key regulators in modulating the initiation, maintenance, and progression of pulmonary fibrosis. However, the precise pathological mechanisms through which lncRNAs are involved in IPF remain limited and require further elucidation. A novel lncABCE1-5 was identified as significantly decreased by an ncRNA microarray analysis in our eight IPF lung samples compared with three donor tissues and validated by quantitative real-time polymerase chain reaction (qRT-PCR) analysis in clinical lung samples. To investigate the biological function of ABCE1-5, we performed loss- and gain-of-function experiments in vitro and in vivo. LncABCE1-5 silencing promoted A549 cell migration and A549 and bronchial epithelial cell line (BEAS-2B) cell apoptosis while enhancing the expression of proteins associated with extracellular matrix deposition, whereas overexpression of ABCE1-5 partially attenuated transforming growth factor-beta (TGF-β)-induced fibrogenesis. Forced ABCE1-5 expression by intratracheal injection of adeno-associated virus 6 revealing the antifibrotic effect of ABCE1-5 in bleomycin (BLM)-treated mice. Mechanistically, RNA pull-down (RPD)-mass spectrometry and RNA immunoprecipitation assay demonstrated that ABCE1-5 directly binds to keratin14 (krt14) sequences, potentially impeding its expression by perturbing mRNA stability. Furthermore, decreased ABCE1-5 levels can promote krt14 expression and enhance the phosphorylation of both mTOR and Akt; overexpression of ABCE1-5 in BLM mouse lung tissue significantly attenuated the elevated levels of p-mTOR and p-AKT. Knockdown of krt14 reversed the activation of mTOR signaling mediated by ABCE1-5 silencing. Collectively, the downregulation of ABCE1-5 mediated krt14 activation, thereby activating mTOR/AKT signaling, to facilitate pulmonary fibrosis progression in IPF.NEW & NOTEWORTHY In the present study, our data first reveal that a novel lncRNA ABCE1-5 could inhibit pulmonary fibrosis through interacting with krt14 and negative regulation of its expression, and indicated ABCE1-5 also regulates the phosphorylation of mTOR and Akt, thus acting on extracellular matrix remodeling in lung fibrosis procession. These results suggest that novel molecules within the ABCE1-5-krt14-mTOR axis may serve as potential candidates for clinical application in IPF.

Non-coding RNA regulatory networks underlying intestinal degradation in Apostichopus japonicus under starvation stress: Insights from transcriptome analysis

Starvation stress is one of the most common environmental challenges faced by aquatic animals, often leading to compensatory growth, a widespread phenomenon in the animal kingdom, especially among aquatic species. The sea cucumber (Apostichopus japonicus), a key marine economic species in China, has been shown to utilize long non-coding RNAs (lncRNAs) in responding to environmental changes, pathogen infections, and tissue regeneration. In this study, strand-specific high-throughput sequencing was employed to analyze transcriptomic data from degenerated intestines of A. japonicus under starvation conditions. High-quality lncRNAs were identified and classified, and key differentially expressed mRNAs and lncRNAs associated with intestinal degradation were screened. A gene interaction network model based on the competing endogenous RNA (ceRNA) theory was then constructed. The analysis revealed that the "AjSOX9/Aja-miR-2012-5p/MSTRG.2956.1 and MSTRG.5699.1" axes, as well as the "AjWNT9B/Aja-miR-200-3p/MSTRG.19757.1 and MSTRG.21788.1" axes, play significant roles in degraded intestines and may promote intestinal regeneration during compensatory growth. Additionally, the "AjFABP2/Aja-miR-9-5p/MSTRG.9667.1" axis appears to regulate energy metabolism under starvation stress. These findings provide valuable insights into the non-coding gene regulatory networks in invertebrates under starvation stress and offer a scientific foundation for developing stress-resistant sea cucumber strains, contributing to the sustainable development of the sea cucumber aquaculture industry.

Genome-Wide Mining of lncRNAs Reveals Their Potential Regulatory Role in the Evolution of Viviparity

Reproduction in vertebrates usually involves egg-laying (oviparity) or live-bearing (viviparity). Oviparity is the ancestral trait from which viviparity has independently evolved more than 100 times in squamate reptiles. This transition involves a series of physiological and structural changes, including the degeneration of eggshell and the evolution of a placenta and differences in the temporal and spatial expression patterns of some functional genes that drive the structural transformation. Long non-coding RNAs (lncRNAs) play important roles in the regulation of gene expression, yet it remains unclear whether they participate in gene expression shifts during the transition from oviparity to viviparity, and if so how. Therefore, we employ deep mining to identify novel lncRNAs of a closely related oviparous-viviparous pair of lizards (Phrynocephalus przewalskii and P. vlangalii). We construct cis- and trans-regulatory networks between lncRNAs and target genes using the transcriptomic data of oviduct or uteri tissues across reproductive periods. Results show that lncRNAs that regulate eggshell gland developmental genes in the oviparous lizard are lost or less expressed in the viviparous lizard. A number of lncRNAs involved in the regulation of placental development and embryo attachment in viviparous species have no orthologs in oviparous species, and others show little or no expression. Accordingly, lncRNAs may play important regulatory roles in the physiological and structural changes in the transition from oviparity to viviparity. These results open doors to the further elucidation of genetic regulatory networks.

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.

Long non-coding RNA transcripts in Mycobacterium tuberculosis-host interactions

Tuberculosis (TB) persists as a significant health threat, affecting millions of people all over the world. Despite years of control measures, the elimination of TB has become a difficult task as morbidity and mortality rates remain unaffected for several years. Developing new diagnostics and therapeutics is paramount to keeping TB under control. However, it largely depends upon understanding the pathogenic mechanisms of Mycobacterium tuberculosis (Mtb), the causative agent of TB. Mtb is an intracellular pathogen capable of subverting the defensive functions of the immune cells, and it can survive and multiply within humans' mononuclear phagocytes. Emerging evidence indicates that long non-coding RNAs (lncRNAs), a class of RNA molecules with limited coding potential, are critical players in this intricate game as they regulate gene expression at transcriptional and post-transcriptional levels and also by chromatin modification. Moreover, they have been shown to regulate cellular processes by controlling the function of other molecules, such as DNA, RNA, and protein, through binding with them. Recent studies have shown that lncRNAs are differentially regulated in the tissues of TB patients and cells infected in vitro with Mtb. Some dysregulated lncRNAs are associated with essential roles in modulating immune response, apoptosis, and autophagy in the host cells, adding a new dimension to TB pathogenesis. In this article, we provide a comprehensive review of the recent literature in this field and the impact of lncRNAs in unraveling pathogenic mechanisms in TB. We also discuss how the studies involving lncRNAs provide insight into TB pathogenesis, especially Mtb-host interactions.

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

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

The role of long non-coding RNAs in cardiovascular diseases: A comprehensive review

Cardiovascular diseases (CVDs) are the leading cause of morbidity and mortality worldwide, posing significant challenges to healthcare systems. Despite advances in medical interventions, the molecular mechanisms underlying CVDs are not yet fully understood. For decades, protein-coding genes have been the focus of CVD research. However, recent advances in genomics have highlighted the importance of long non-coding RNAs (lncRNAs) in cardiovascular health and disease. Changes in lncRNA expression specific to tissues may result from various internal or external factors, leading to tissue damage, organ dysfunction, and disease. In this review, we provide a comprehensive discussion of the regulatory mechanisms underlying lncRNAs and their roles in the pathogenesis and progression of CVDs, such as coronary heart disease, atherosclerosis, heart failure, arrhythmias, cardiomyopathies, and diabetic cardiomyopathy, to explore their potential as therapeutic targets and diagnostic biomarkers.

The Role of M6A LncRNA Modification in Papillary Thyroid Cancer

Thyroid Cancer (TC) is the most common endocrine cancer, of which papillary thyroid cancer (PTC), a well-differentiated type of TC, accounts for 80-90%. Long non-coding RNAs (lncRNAs), which comprise non-protein-coding segments of the genome, have been found to play a crucial role in various biological processes, including cancer development. The activity of lncRNAs is modified through epigenetic modifications, with N6-Methyladenosine (m6A) modifications implicated in the progression of several malignancies. The activity of m6A is further regulated by modifying enzymes classified as "readers", writers", and "erasers", of which specific enzymes have been found to play a role in various aspects of PTC. Recent research has highlighted the significance of m6A modification in regulating the expression and function of lncRNAs associated with PTC pathogenesis. Dysregulation of this process implicates tumor proliferation, invasion, and metastasis, with subsequent impact on prognosis. Therefore, understanding the interplay between m6A modification and lncRNAs provides valuable insights into the molecular mechanisms underlying PTC progression. This narrative review aims to explore the established role of several prominent m6A modifying enzymes and lncRNAs on cancer pathogenesis and seeks to clarify the function of these enzymes in PTC pathogenesis.

Epigenetic Regulation of Chromatin Functions by MicroRNAs and Long Noncoding RNAs and Implications in Human Diseases

The bulk of RNA produced from the genome of complex organisms consists of a very large number of transcripts lacking protein translational potential and collectively known as noncoding RNAs (ncRNAs). Initially thought to be mere products of spurious transcriptional noise, ncRNAs are now universally recognized as pivotal players in cell regulatory networks across a broad spectrum of biological processes. Owing to their critical regulatory roles, ncRNA dysfunction is closely associated with the etiopathogenesis of various human malignancies, including cancer. As such, ncRNAs represent valuable diagnostic biomarkers as well as potential targets for innovative therapeutic intervention. In this review, we focus on microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), the two most extensively studied classes in the field of ncRNA biology. After outlining key concepts of miRNA and lncRNA biogenesis pathways, we examine their multiple roles in mediating epigenetic regulation of gene expression and chromatin organization. Finally, by providing numerous examples of specific miRNAs and lncRNAs, we discuss how dysregulation of these mechanisms contributes to the onset and/or progression of various human diseases.

Epigenetic code underlying EGFR-TKI resistance in non-small cell lung cancer: Elucidation of mechanisms and perspectives on therapeutic strategies

Non-small-cell lung cancer (NSCLC) is the most common lung cancer subtype, and epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) are the core drugs used for its treatment. However, the emergence of drug resistance poses a significant challenge to their clinical efficacy. As a significant role-player in cancer development and maintenance, histone modifications, DNA methylation and noncoding RNA (ncRNA) changes have been proven to play a crucial part in driving EGFR-TKI resistance, which provides promising potential therapeutic targets and biomarkers for overcoming drug resistance. This review delves into the complex epigenetic mechanisms that cause EGFR-TKI resistance and emphasizes the potential of combined epigenetic therapies, aiming to provide better-targeted treatment options for NSCLC patients with NSCLC and drive innovative strategies to overcome the challenges of drug resistance.

RNA damage and its implications in genome stability

Endogenous and environmental stressors can damage DNA and RNA to compromise genome and transcriptome stability and integrity in cells, leading to genetic instability and diseases. Recent studies have demonstrated that RNA damage can also modulate genome stability via RNA-templated DNA synthesis, suggesting that it is essential to maintain RNA integrity for the sustainment of genome stability. However, little is known about RNA damage and repair and their roles in modulating genome stability. Current efforts have mainly focused on revealing RNA surveillance pathways that detect and degrade damaged RNA, while the critical role of RNA repair is often overlooked. Due to their abundance and susceptibility to nucleobase damaging agents, it is essential for cells to evolve robust RNA repair mechanisms that can remove RNA damage, maintaining RNA integrity during gene transcription. This is supported by the discovery of the alkylated RNA nucleobase repair enzyme human AlkB homolog 3 that can directly remove the methyl group on damaged RNA nucleobases, predominantly in the nucleus of human cells, thereby restoring the integrity of the damaged RNA nucleobases. This is further supported by the fact that several DNA repair enzymes can also process RNA damage. In this review, we discuss RNA damage and its effects on cellular function, DNA repair, genome instability, and potential RNA damage repair mechanisms. Our review underscores the necessity for future research on RNA damage and repair and their essential roles in modulating genome stability.

A novel lncRNA PDG1 targets NADP-ME to modulate TCA cycle and JH in Aspongopus chinensis diapause

Diapause is essential for insect survival under adverse environmental conditions and plays a crucial role in regulating reproduction. However, the role of long non-coding RNAs (lncRNAs) in this process remains unclear. In this study, we investigated the function of lncRNAs in the diapause of Aspongopus chinensis. A total of 28,360 lncRNAs were identified across the transcriptomes, with 814 upregulated and 512 downregulated during diapause. Analysis revealed 48 key mRNAs regulated by these lncRNAs, primarily associated with energy metabolism. Among them, the NADP+-dependent malic enzyme (NADP-ME) gene was notably enriched in these pathways. Knockdown of NADP-ME resulted in decreased pyruvate levels and TCA activity. We identified a novel lncRNA, PDG1, which regulates NADP-ME expression, and RNA interference targeting PDG1 increased NADP-ME levels, leading to enhanced pyruvate levels and elevated TCA cycle activity, with dual luciferase assays confirming that PDG1 directly targeted NADP-ME and downregulated its expression. Furthermore, secondary structure analysis revealed that PDG1 exhibited significantly lower free energy compared to NADP-ME, with fewer hairpins and stem-loops. These findings highlight PDG1's critical role in regulating TCA cycle activity by targeting NADP-ME during A. chinensis diapause, revealing a novel mechanism through which lncRNAs modulate metabolic pathways to control insect diapause.

Emerging Roles of Long Non-Coding RNAs in Cardiovascular Diseases

Cardiovascular diseases (CVDs) are the leading cause of morbidity and mortality worldwide. Over the past decade, studies have demonstrated that circulating long non-coding RNAs (lncRNAs)-recognised for their stability and ease of detection-serve as crucial regulators and potential biomarkers in multiple diseases. LncRNAs regulate key processes, including endothelial function, vascular remodelling, and myocardial hypertrophy, all of which influence CVD progression. Additionally, lncRNAs display cell-, tissue-, and disease-specific expression patterns, making them ideal therapeutic targets or tools. This review presents a comprehensive overview of the current understanding of lncRNAs in CVDs, examining their mechanisms of action and recent research advances. It also addresses the use of lncRNAs as diagnostic and prognostic markers, as well as potential applications of RNA therapeutics in novel treatment strategies.

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

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

Cancer brain metastasis: molecular mechanisms and therapeutic strategies

Brain metastases (BMs) are the most common intracranial tumors in adults and the major cause of cancer-related morbidity and mortality. The occurrence of BMs varies according to the type of primary tumors with most frequence in lung cancer, melanoma and breast cancer. Among of them, lung cancer has been reported to have a higher risk of BMs than other types of cancers with 40 ~ 50% of such patients will develop BMs during the course of disease. BMs lead to many neurological complications and result in a poor quality of life and short life span. Although the treatment strategies were improved for brain tumors in the past decades, the prognosis of BMs patients is grim. Poorly understanding of the molecular and cellular characteristics of BMs and the complicated interaction with brain microenvironment are the major reasons for the dismal prognosis of BM patients. Recent studies have enhanced understanding of the mechanisms of BMs. The newly identified potential therapeutic targets and the advanced therapeutic strategies have brought light for a better cure of BMs. In this review, we summarized the mechanisms of BMs during the metastatic course, the molecular and cellular landscapes of BMs, and the advances of novel drug delivery systems for overcoming the obstruction of blood-brain barrier (BBB). We further discussed the challenges of the emerging therapeutic strategies, such as synergistic approach of combining targeted therapy with immunotherapy, which will provide vital clues for realizing the precise and personalized medicine for BM patients in the future.

Innovative perspectives on glioblastoma: the emerging role of long non-coding RNAs

Glioblastoma (GBM) is a highly aggressive and treatment-resistant brain tumor. Recent advancements have highlighted the crucial role of long noncoding RNAs (lncRNAs) in GBM's molecular biology. Unlike protein-coding RNAs, lncRNAs regulate gene expression through transcription, post-transcriptional modifications, and chromatin remodeling. Some lncRNAs, like HOTAIR, CCAT2, CRNDE, and MALAT1, promote GBM development by affecting tumor suppressors and various signaling pathways like PI3K/Akt, mTOR, EGFR, NF-κB, and Wnt/β-catenin. Conversely, certain lncRNAs such as TUG1, MEG3, and GAS8-AS1 act as tumor suppressors and are associated with better prognosis. The study presented in the manuscript aims to explore the involvement of lncRNAs in GBM, focusing on their roles in tumor progression, proliferation, invasion, and potential implications for early detection and immunotherapy. The research seeks to elucidate the mechanisms by which specific lncRNAs influence GBM characteristics and highlight their potential as therapeutic targets or biomarkers in managing this aggressive form of brain cancer.

Unveiling Racial Disparities in Localized Prostate Cancer: A Systems-Level Exploration of the lncRNA Landscape

BACKGROUND/OBJECTIVES

Prostate cancer (PC) is the most common non-cutaneous cancer in men globally, and one which displays significant racial disparities. Men of African descent (AF) are more likely to develop PC and face higher mortality compared to men of European descent (EU). The biological mechanisms underlying these differences remain unclear. Long non-coding RNAs (lncRNAs), recognized as key regulators of gene expression and immune processes, have emerged as potential contributors to these disparities. This study aimed to investigate the regulatory role of lncRNAs in localized PC in AF men relative to those of EU and assess their involvement in immune response and inflammation.

METHODS

A systems biology approach was employed to analyze differentially expressed (DE) lncRNAs and their roles in prostate cancer (PC). Immune-related pathways were investigated through over-representation analysis of lncRNA-mRNA networks. The study also examined the effects of vitamin D supplementation on lncRNA expression in African descent (AF) PC patients, highlighting their potential regulatory roles in immune response and inflammation.

RESULTS

Key lncRNAs specific to AF men were identified, with several being implicated for immune response and inflammatory processes. Notably, 10 out of the top 11 ranked lncRNAs demonstrated strong interactions with immune-related genes. Pathway analysis revealed their regulatory influence on antigen processing and presentation, chemokine signaling, and ribosome pathways, suggesting their critical roles in immune regulation.

CONCLUSIONS

These findings highlight the pivotal role of lncRNAs in PC racial disparities, particularly through immune modulation. The identified lncRNAs may serve as potential biomarkers or therapeutic targets to address racial disparities in PC outcomes.

Non-coding RNAs in Cancer: Mechanistic insights and therapeutic implications

Non-coding RNAs have gathered significant attention for their unique roles in biological regulation. Across a broad spectrum of developmental processes and diseases, particularly in human malignancies, ncRNAs play pivotal roles in regulatory mechanisms. MicroRNAs, long noncoding RNAs, and small nucleolar RNAs stand out among the diverse forms of ncRNAs that have been implicated in cancer. MiRNAs, classified as short non-coding RNAs, modulate gene expression by binding to messenger RNA molecules, thereby inhibiting their translation. Altered miRNA expression has been associated with the onset and progression of various malignancies, including lung, breast, and prostate cancer. In contrast, lncRNAs, characterized as longer ncRNAs, exert control over gene expression through various mechanisms, such as chromatin remodelling and gene silencing. This review offers a comprehensive examination of the numerous ncRNAs that have emerged as crucial regulators of gene expression, playing implicated roles in the initiation and progression of diverse cancers.

Exploring the interplay of natural products and long non-coding RNAs in colorectal cancer: pathogenesis, diagnosis, and overcoming drug resistance

Colorectal cancer (CRC) is recognized as one of the most prevalent malignancies, both in terms of incidence and mortality rates. Current research into CRC has shed light on the molecular mechanisms driving its development. Several factors, including lifestyle, environmental influences, genetics, and diet, play significant roles in its pathogenesis. Natural compounds such as curcumin, tanshinone, lycorine, sinomenine, kaempferol, verbascoside, quercetin, berberine, and fisetin have shown great promise in the prevention and treatment of CRC. Research has also highlighted the significance of non-coding RNAs (ncRNAs) as biomarkers and therapeutic targets in CRC. Among these, long non-coding RNAs (lncRNAs) have been found to regulate the transcription of genes involved in cancer. LncRNAs contribute to cancer stem cell (CSC) proliferation, angiogenesis, epithelial-mesenchymal transition (EMT), and chemoresistance. Specific lncRNAs, including GAS5, LNC00337, HOTAIR, TPT1-AS1, cCSC1, BCAR4, TUG1, and Solh2, play crucial roles in these processes. They hold potential as novel biomarkers, detectable in bodily fluids and tissues, and could serve as therapeutic targets due to their involvement in drug resistance and sensitivity. These insights could improve CRC treatment strategies, addressing resistance to chemotherapy and radiotherapy. This review article aims to provide a comprehensive analysis of the current knowledge regarding the effectiveness of natural anti-cancer agents in CRC treatment. Additionally, it offers an in-depth evaluation of lncRNAs in CRC, their role in the disease's progression, and their potential applications in its management.

The role of long non-coding RNA NORAD in digestive system tumors

In recent years, it has been discovered that the expression of long non-coding RNAs is highly deregulated in several types of cancer and contributes to its progression and development. Recently, it has been described that in tumors of the digestive system, such as colorectal cancer, pancreatic cancer, and gastric cancer, DNA damage-activated lncRNA (NORAD) was frequently up-regulated. The purpose of this review is to elucidate the functions of NORAD in tumors of the digestive system, emphasizing its involvement in important cellular processes such as invasion, metastasis, proliferation, and apoptosis. NORAD acts as a ceRNA (competitive endogenous RNA) that sponges microRNAs and regulates the expression of target genes involved in tumorigenesis. Thus, the mechanisms underlying the effects of NORAD are complex and involve multiple signaling pathways. This review consolidates current knowledge on the role of NORAD in digestive cancers and highlights the need for further research to explore its potential as a therapeutic target. Understanding the intricate functions of NORAD could elucidate the way for innovative approaches to cancer treatment.

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

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

Long Non-Coding RNAs in Ovarian Cancer: Mechanistic Insights and Clinical Applications

Background/Objectives: Ovarian cancer is a leading cause of gynecological cancer mortality worldwide, often diagnosed at advanced stages due to vague symptoms and the lack of effective early detection methods. Long non-coding RNAs (lncRNAs) have emerged as key regulators in cancer biology, influencing cellular processes such as proliferation, apoptosis, and chemoresistance. This review explores the multifaceted roles of lncRNAs in ovarian cancer pathogenesis and their potential as biomarkers and therapeutic targets. Methods: A comprehensive literature review was conducted to analyze the structural and functional characteristics of lncRNAs and their contributions to ovarian cancer biology. This includes their regulatory mechanisms, interactions with signaling pathways, and implications for therapeutic resistance. Advanced bioinformatics and omics approaches were also evaluated for their potential in lncRNA research. Results: The review highlights the dual role of lncRNAs as oncogenes and tumor suppressors, modulating processes such as cell proliferation, invasion, and angiogenesis. Specific lncRNAs, such as HOTAIR and GAS5, demonstrate significant potential as diagnostic biomarkers and therapeutic targets. Emerging technologies, such as single-cell sequencing, provide valuable insights into the tumor microenvironment and the heterogeneity of lncRNA expression. Conclusions: LncRNAs hold transformative potential in advancing ovarian cancer diagnosis, prognosis, and treatment. Targeting lncRNAs or their associated pathways offers promising strategies to overcome therapy resistance and enhance personalized medicine. Continued research integrating omics and bioinformatics will be essential to unlock the full clinical potential of lncRNAs in ovarian cancer management.

Investigating the role of exosomal long non-coding RNAs in drug resistance within female reproductive system cancers

Exosomes, as key mediators of intercellular communication, have been increasingly recognized for their role in the oncogenic processes, particularly in facilitating drug resistance. This article delves into the emerging evidence linking exosomal lncRNAs to the modulation of drug resistance mechanisms in cancers such as ovarian, cervical, and endometrial cancer. It synthesizes current research findings on how these lncRNAs influence cancer cell survival, tumor microenvironment, and chemotherapy efficacy. Additionally, the review highlights potential therapeutic strategies targeting exosomal lncRNAs, proposing a new frontier in overcoming drug resistance. By mapping the interface of exosomal lncRNAs and drug resistance, this article aims to provide a comprehensive understanding that could pave the way for innovative treatments and improved patient outcomes in female reproductive system cancers.

Recent advances in investigation of circRNA/lncRNA-miRNA-mRNA networks through RNA sequencing data analysis

Non-coding RNAs (ncRNAs) are RNA molecules that are transcribed from DNA but are not translated into proteins. Studies over the past decades have revealed that ncRNAs can be classified into small RNAs, long non-coding RNAs and circular RNAs by genomic size and structure. Accumulated evidences have eludicated the critical roles of these non-coding transcripts in regulating gene expression through transcription and translation, thereby shaping cellular function and disease pathogenesis. Notably, recent studies have investigated the function of ncRNAs as competitive endogenous RNAs (ceRNAs) that sequester miRNAs and modulate mRNAs expression. The ceRNAs network emerges as a pivotal regulatory function, with significant implications in various diseases such as cancer and neurodegenerative disease. Therefore, we highlighted multiple bioinformatics tools and databases that aim to predict ceRNAs interaction. Furthermore, we discussed limitations of using current technologies and potential improvement for ceRNAs network detection. Understanding of the dynamic interplay within ceRNAs may advance the biological comprehension, as well as providing potential targets for therapeutic intervention.

Non-coding RNAs in BRAF-mutant melanoma: targets, indicators, and therapeutic potential

Melanoma, a highly aggressive skin cancer, is often driven by BRAF mutations, such as the V600E mutation, which promotes cancer growth through the MAPK pathway and contributes to treatment resistance. Understanding the role of non-coding RNAs (ncRNAs) in these processes is crucial for developing new therapeutic strategies. This review aims to elucidate the relationship between ncRNAs and BRAF mutations in melanoma, focusing on their regulatory roles and impact on treatment resistance. We comprehensively reviewed current literature to synthesize evidence on ncRNA-mediated regulation of BRAF-mutant melanoma and their influence on therapeutic responses. Key ncRNAs, including microRNAs and long ncRNAs, were identified as significant regulators of melanoma development and therapy resistance. MicroRNAs such as miR-15/16 and miR-200 families modulate critical pathways like Wnt signaling and melanogenesis. Long ncRNAs like ANRIL and SAMMSON play roles in cell growth, invasion, and drug susceptibility. Specific ncRNAs, such as BANCR and RMEL3, intersect with the MAPK pathway, highlighting their potential as therapeutic targets or biomarkers in BRAF-mutant melanoma. Additionally, ncRNAs involved in drug resistance, such as miR-579-3p and miR-1246, target processes like autophagy and immune checkpoint regulation. This review highlights the pivotal roles of ncRNAs in regulating BRAF-mutant melanoma and their contribution to drug resistance. These findings underscore the potential of ncRNAs as biomarkers and therapeutic targets, paving the way for innovative treatments to improve outcomes for melanoma patients.

Non-coding RNA Networks in Infection

In the face of global health challenges posed by infectious diseases and the emergence of drug-resistant pathogens, the exploration of cellular non-coding RNA (ncRNA) networks has unveiled new dimensions in infection research. Particularly microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) have emerged as instrumental players in ensuring a balance between protection against hyper-inflammatory conditions and the effective elimination of pathogens. Specifically, ncRNAs, such as the miRNA miR-155 or the lncRNAs MaIL1 (macrophage interferon-regulatory lncRNA 1), and LUCAT1 (lung cancer-associated transcript 1) have been recurrently linked to infectious and inflammatory diseases. Together with other ncRNAs, discussed in this chapter, they form a complex regulatory network shaping the host response to pathogens. Additionally, some pathogens exploit these ncRNAs to establish and sustain infections, underscoring their dual roles in host protection and colonization. Despite the substantial progress made, the vast majority of ncRNA loci remains unexplored, with ongoing research likely to reveal novel ncRNA categories and expand our understanding of their roles in infections. This chapter consolidates current insights into ncRNA-mediated regulatory networks, highlighting their contributions to severe diseases and their potential as targets and biomarkers for innovative therapeutic strategies.

Vegetal memory through the lens of transcriptomic changes - recent progress and future practical prospects for exploiting plant transcriptional memory

Plant memory plays an important role in the efficient and rapid acclimation to a swiftly changing environment. In addition, since plant memory can be inherited, it is also of adaptive and evolutionary importance. The ability of a plant to store, retain, retrieve and delete information on acquired experience is based on cellular, biochemical and molecular networks in the plants. This review offers an up-to-date overview on the formation, types, checkpoints of plant memory based on our current knowledge and focusing on its transcriptional aspects, the transcriptional memory. Roles of long and small non-coding RNAs are summarized in the regulation, formation and the cooperation between the different layers of the plant memory, i.e. in the establishment of epigenetic changes associated with memory formation in plants. The RNA interference mechanisms at the RNA and DNA level and the interplays between them are also presented. Furthermore, this review gives an insight of how exploitation of plant transcriptional memory may provide new opportunities for elaborating promising cost-efficient, and effective strategies to cope with the ever-changing environmental perturbations, caused by climate change. The potentials of plant memory-based methods, such as crop priming, cross acclimatization, memory modification by miRNAs and associative use of plant memory, in the future's agriculture are also discussed.

Localization is the key to action: regulatory peculiarities of lncRNAs

To understand the transcriptomic profile of an individual cell in a multicellular organism, we must comprehend its surrounding environment and the cellular space where distinct molecular stimuli responses are located. Contradicting the initial perception that RNAs were nonfunctional and that only a few could act in chromatin remodeling, over the last few decades, research has revealed that they are multifaceted, versatile regulators of most cellular processes. Among the various RNAs, long non-coding RNAs (LncRNAs) regulate multiple biological processes and can even impact cell fate. In this sense, the subcellular localization of lncRNAs is the primary determinant of their functions. It affects their behavior by limiting their potential molecular partner and which process it can affect. The fine-tuned activity of lncRNAs is also tissue-specific and modulated by their cis and trans regulation. Hence, the spatial context of lncRNAs is crucial for understanding the regulatory networks by which they influence and are influenced. Therefore, predicting a lncRNA's correct location is not just a technical challenge but a critical step in understanding the biological meaning of its activity. Hence, examining these peculiarities is crucial to researching and discussing lncRNAs. In this review, we debate the spatial regulation of lncRNAs and their tissue-specific roles and regulatory mechanisms. We also briefly highlight how bioinformatic tools can aid research in the area.

Non-coding RNA: A key regulator in the Glutathione-GPX4 pathway of ferroptosis

Ferroptosis, a form of regulated cell death, has emerged as a crucial process in diverse pathophysiological states, encompassing cancer, neurodegenerative ailments, and ischemia-reperfusion injury. The glutathione (GSH)-dependent lipid peroxidation pathway, chiefly governed by glutathione peroxidase 4 (GPX4), assumes an essential part in driving ferroptosis. GPX4, as the principal orchestrator of ferroptosis, has garnered significant attention across cancer, cardiovascular, and neuroscience domains over the past decade. Noteworthy investigations have elucidated the indispensable functions of ferroptosis in numerous diseases, including tumorigenesis, wherein robust ferroptosis within cells can impede tumor advancement. Recent research has underscored the complex regulatory role of non-coding RNAs (ncRNAs) in regulating the GSH-GPX4 network, thus influencing cellular susceptibility to ferroptosis. This exhaustive review endeavors to probe into the multifaceted processes by which ncRNAs control the GSH-GPX4 network in ferroptosis. Specifically, we delve into the functions of miRNAs, lncRNAs, and circRNAs in regulating GPX4 expression and impacting cellular susceptibility to ferroptosis. Moreover, we discuss the clinical implications of dysregulated interactions between ncRNAs and GPX4 in several conditions, underscoring their capacity as viable targets for therapeutic intervention. Additionally, the review explores emerging strategies aimed at targeting ncRNAs to modulate the GSH-GPX4 pathway and manipulate ferroptosis for therapeutic advantage. A comprehensive understanding of these intricate regulatory networks furnishes insights into innovative therapeutic avenues for diseases associated with perturbed ferroptosis, thereby laying the groundwork for therapeutic interventions targeting ncRNAs in ferroptosis-related pathological conditions.

Epigenetic modulation of immune cells: Mechanisms and implications

Epigenetic modulation of the immune response entails modifiable and inheritable modifications that do not modify the DNA sequence. While there have been many studies on epigenetic changes in tumor cells, there is now a growing focus on epigenetically mediated changes in immune cells of both the innate and adaptive systems. These changes have significant implications for both the body's response to tumors and the development of potential therapeutic vaccines. This study primarily discusses the key epigenetic alterations, with a specific emphasis on pseudouridination, as well as non-coding RNAs and their transportation, which can lead to the development of cancer and the acquisition of new phenotypic traits by immune cells. Furthermore, the advancement of therapeutic vaccinations targeting the tumor will be outlined.

Comprehensive Quality Analysis of Conventional and Novel Biomarkers in Diagnosing and Predicting Prognosis of Coronary Artery Disease, Acute Coronary Syndrome, and Heart Failure, a Comprehensive Literature Review

Coronary artery disease (CAD), acute coronary syndrome (ACS), and heart failure (HF) are major global health issues with high morbidity and mortality rates. Biomarkers like cardiac troponins (cTn) and natriuretic peptides (NPs) are crucial tools in cardiology, but numerous new biomarkers have emerged, proving increasingly valuable in CAD/ACS. These biomarkers are classified based on their mechanisms, such as fibrosis, metabolism, inflammation, and congestion. The integration of established and emerging biomarkers into clinical practice is an ongoing process, and recognizing their strengths and limitations is crucial for their accurate interpretation, incorporation into clinical settings, and improved management of CVD patients. We explored established biomarkers like cTn, NPs, and CRP, alongside newer biomarkers such as Apo-A1, IL-17E, IgA, Gal-3, sST2, GDF-15, MPO, H-FABP, Lp-PLA2, and ncRNAs; provided evidence of their utility in CAD/ACS diagnosis and prognosis; and empowered clinicians to confidently integrate these biomarkers into clinical practice based on solid evidence.

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.

The role of long noncoding RNAs in the diagnosis, prognosis and therapeutic biomarkers of acute myeloid leukemia

Acute myeloid leukemia (AML) is the abnormal proliferation of immature myeloid blast cells in the bone marrow. Currently, there are no universally recognized biomarkers for the early diagnosis, prognosis and effective treatment of AML to improve the overall survival of patients. Recent studies, however, have demonstrated that long noncoding RNAs (lncRNAs) are promising targets for the early diagnosis, prognosis and treatment of AML. A critical review of available data would be important to identify study gaps and provide perspectives. In this review, we explored comprehensive information on the potential use of lncRNAs as targets for the diagnosis, prognosis, and treatment of AML. LncRNAs are nonprotein-coding RNAs that are approximately 200 nucleotides long and play important roles in the regulation, metabolism and differentiation of tissues. In addition, they play important roles in the diagnosis, prognosis and treatment of different cancers, including AML. LncRNAs play multifaceted roles as oncogenes or tumor suppressor genes. Recently, deregulated lncRNAs were identified as novel players in the development of AML, making them promising prognostic indicators. Given that lncRNAs could have potential diagnostic marker roles, the lack of sufficient evidence identifying specific lncRNAs expressed in specific cancers hampers the use of lncRNAs as diagnostic markers of AML. The complex roles of lncRNAs in the pathophysiology of AML require further scrutiny to identify specific lncRNAs. This review, despite the lack of sufficient literature, discusses the therapeutic, diagnostic and prognostic roles of lncRNAs in AML and provides future insights that will contribute to studies targeting lncRNAs in the diagnosis, treatment, and management of AML.

An anti-sense lncRNA of the A-FABP gene regulates the proliferation of hair follicle stem cells via the chi-miR-335-5p/DKK1/β-catenin axis

Hair follicle development relies on both the epithelial-mesenchymal interaction (EMI) and the proliferation of hair follicle stem cells (HFSCs). This intricate process involves numerous regulatory molecules. Increasing evidence suggests that long non-coding RNAs (lncRNAs) play a crucial role in hair follicle development. However, the functions and molecular mechanisms of many lncRNAs in hair follicle development of cashmere goats remain unclear. Based on our previous lncRNA sequencing results in cashmere goats, an unannotated lncRNA differentially expressed at various stages of hair follicle development, named FABP_AS, was detected. Consequently, we aimed at exploring the function and molecular mechanisms of FABP_AS. We constructed a CRISPR/Cas9 knockout system to specifically knock down FABP_AS, providing a reference model for target lncRNA knockout in animal primary cells. Functional experiment results demonstrated that FABP_AS significantly inhibited HFSCs proliferation. Mechanism experiment results revealed that FABP_AS competitively bond to chi-miR-335-5p, promoted DKK1 gene expression, and reduced Wnt/β-catenin signaling pathway activity. In summary, our findings indicated that FABP_AS acted as a miRNA sponge, sequestering chi-miR-335-5p away from the DKK1 gene, thereby suppressing HFSCs proliferation, which would lay the groundwork for a better understanding of the molecular mechanisms of hair follicle development and provide therapeutic targets for hair loss.

Transcriptome Analysis Reveals the lncRNA-mRNA Co-expression Network Regulating the Aestivation of Sea Cucumber

LncRNAs are long non-coding RNAs that are widely recognized as crucial regulators of gene expression and metabolic control, involved in numerous dormancy-related processes. Aestivation is a common hypometabolism strategy of sea cucumber (Apostichopus japonicus) in response to high-temperature conditions and is typically characterized by the degradation of the intestine and respiratory tree. Although the aestivation process has been extensively studied in sea cucumbers, the role of lncRNAs in the context of aestivation states remains a conspicuous knowledge gap. Here, we identified and characterized 14,711 lncRNAs in A. japonicus and analyzed their differential expression patterns during the aestivation process in the intestine and respiratory tree. The results revealed the physiological differences, especially the metabolic processes, between the intestine and respiratory tree during the aestivation. The co-expression network of lncRNA-mRNA suggested the dominant role of lncRNA in regulating the differential response of the intestine and respiratory trees. Differentially co-expressed factors were significantly enriched in the deep-aestivation stage-specific modules. Conserved co-expressed factors included several transcription factors known to be involved in rhythm regulation, such as Klf2 and Egr1. Furthermore, a specific trans-acting lncRNA (lncrna.1393.1) was identified as a potential regulator of Klf2 and Egr1. Overall, the systematic identification, characterization, and expression analysis of lncRNAs in A. japonicus enhanced our knowledge of long non-coding regulation of aestivation in sea cucumber and provided new clues for understanding the common "toolkit" of dormancy regulatory mechanisms.

SVALKA: A Long Noncoding Cis-Natural Antisense RNA That Plays a Role in the Regulation of the Cold Response of Arabidopsis thaliana

RNA plays important roles in the regulation of gene expression in response to environmental stimuli. SVALKA, a long noncoding cis-natural antisense RNA, is a key component of regulating the response to cold temperature in Arabidopsis thaliana. There are three mechanisms through which SVALKA fine tunes the transcriptional response to cold temperatures. SVALKA regulates the expression of the CBF1 (C-Repeat Dehydration Binding Factor 1) transcription factor through a collisional transcription mechanism and a dsRNA and DICER mediated mechanism. SVALKA also interacts with Polycomb Repressor Complex 2 to regulate the histone methylation of CBF3. Both CBF1 and CBF3 are key components of the COLD REGULATED (COR) regulon that direct the plant's response to cold temperature over time, as well as plant drought adaptation, pathogen responses, and growth regulation. The different isoforms of SVALKA and its potential to form dynamic RNA conformations are important features in regulating a complex gene network in concert with several other noncoding RNA. This review will summarize the three mechanisms through which SVALKA participates in gene regulation, describe the ways that dynamic RNA structures support the function of regulatory noncoding RNA, and explore the potential for improving agricultural genetic engineering with a better understanding of the roles of noncoding RNA.

Biological Insights and Recent Advances in Plant Long Non-Coding RNA

Long non-coding RNA (lncRNA) refers to an RNA molecule longer than 200 nucleotides (nt) that plays a significant role in regulating essential molecular and biological processes. It is commonly found in animals, plants, and viruses, and is characterized by features such as epigenetic markers, developmental stage-specific expression, and tissue-specific expression. Research has shown that lncRNA participates in anatomical processes like plant progression, while also playing a crucial role in plant disease resistance and adaptation mechanisms. In this review, we provide a concise overview of the formation mechanism, structural characteristics, and databases related to lncRNA in recent years. We primarily discuss the biological roles of lncRNA in plant progression as well as its involvement in response to biotic and abiotic stresses. Additionally, we examine the current challenges associated with lncRNA and explore its potential application in crop production and breeding. Studying plant lncRNAs is highly significant for multiple reasons: It reveals the regulatory mechanisms of plant growth and development, promotes agricultural production and food security, and drives research in plant genomics and epigenetics. Additionally, it facilitates ecological protection and biodiversity conservation.

Endothelial cell-cardiomyocyte cross-talk: understanding bidirectional paracrine signaling in cardiovascular homeostasis and disease

To maintain homeostasis in the heart, endothelial cells and cardiomyocytes engage in dynamic cross-talk through paracrine signals that regulate both cardiac development and function. Here, we review the paracrine signals that endothelial cells release to regulate cardiomyocyte growth, hypertrophy and contractility, and the factors that cardiomyocytes release to influence angiogenesis and vascular tone. Dysregulated communication between these cell types can drive pathophysiology of disease, as seen in ischemia-reperfusion injury, diabetes, maladaptive hypertrophy, and chemotherapy-induced cardiotoxicity. Investingating the role of cross-talk is critical in developing an understanding of tissue homeostasis, regeneration, and disease pathogenesis, with the potential to identify novel targets for diagnostic and therapeutic purposes.

Non-coding RNAs as therapeutic targets in Parkinson's Disease: A focus on dopamine

Parkinson's Disease is a highly complicated neurological disorder, with a key manifestation of loss of dopaminergic neurons. Despite the plethora of medicines that alleviate the symptoms, there is an urgent need for new treatments acting on the fundamental pathology of PD. Non-coding RNAs are becoming increasingly important in gene regulation and various cellular processes and are found to play a role in PD pathophysiology. This review analyzes the cross-talk of distinct ncRNAs with dopamine signaling. We attempt to constrain the various ncRNA networks that can activate dopamine production. First, we describe the deregulation of miRNAs that target dopamine receptors and have been implicated in PD. Next, we turn to the functions of lncRNAs in dopaminergic neurons and the connections to susceptibility genes for PD. Finally, we will analyze the novel circRNAs, such as ciRS-7, which may modulate dopamine-linked processes and serve as possible PD biomarkers. In this review, we describe recent progress in dopamine neuron revival to treat PD and the therapeutic potential of ncRNA. This review critically evaluates the available data, and we predict the role of some ncRNAs, such as PTBP1, to become candidate treatment targets in the future. Thus, this review aims to summarize the molecular causes for the deficit in dopamine signaling in PD and point to novel ncRNAs-linked therapeutic directions in neuroscience.

Mechanistic role of long non-coding RNAs in the pathogenesis of metabolic dysfunction-associated steatotic liver disease and fibrosis

Metabolic dysfunction-associated steatotic liver disease (MASLD), previously referred to as non-alcoholic fatty liver disease, encompasses a broad range of hepatic metabolic disorders primarily characterised by the disruption of hepatic lipid metabolism, hepatic lipid accumulation and steatosis. Severe cases of MASLD might progress to metabolic dysfunction-associated steatohepatitis, characterised by hepatic inflammation, hepatocyte ballooning degeneration, activation of hepatic stellate cells (HSCs) and fibrogenesis. It may further progress to hepatocellular carcinoma. In the liver, long non-coding RNAs (lncRNAs) target multiple metabolic pathways in hepatocytes, HSCs, and Kupffer cells at different stages of MASLD and liver fibrosis. In this study, we overview recent findings on the potential role of lncRNAs in the pathogenesis of MASLD and liver fibrosis via modulation of de novo lipid synthesis, fatty acid β-oxidation, lipotoxicity, oxidative stress, metabolic inflammation, mammalian target of rapamycin signalling, apoptosis, ubiquitination and fibrogenesis. We critically assess the literature reports that investigate the complex interplay between lncRNA, microRNA and key mediators in liver injury, in both human participants and animal models of MASLD and liver fibrosis. We also highlight the therapeutic potential of lncRNAs in chronic liver diseases.

Long noncoding RNA network for lncRNA-mRNA interactions throughout swine estrous cycle reveals developmental and hormonal regulations in reproductive tissues

The mechanism of estrous cycles of pigs should be explored because their reproductive traits are useful for manipulating productivity and solving problems such as infertility. These estrous cycles should be elucidated to understand the complex interactions between various reproductive tissues (including the ovary, oviduct, and endometrium) and the complex range of hormone secretions during estrous cycles. Long non-coding RNAs (lncRNAs) regulate target genes at transcriptional, post-transcriptional, and post-translational regulation levels in various species. However, unlike mRNAs, lncRNAs in pigs have not been sufficiently annotated, and understanding the protein level of coding genes has limitations in determining the mechanism of the reproductive traits of porcine. In this study, the lncRNAs of the porcine ovary, oviduct, and endometrium were investigated on days 0, 3, 6, 9, 12, 15, and 18 of the estrous cycle. In addition, the characteristics and functions of the identified lncRNAs were explored. 19,021 novel lncRNA transcripts were selected, and the comparison of the characteristics of the newly identified lncRNA and mRNA showed that similar to those of previous studies. Four lncRNA networks were chosen through network analysis. The cis-acting genes of lncRNAs included in each network were identified, and expression patterns were compared. The main lncRNAs (XLOC_021792, XLOC_017111, ENSSSCG00000050977, XLOC_000342, ENSSSCG00000050380, ENSSSCG00000045111, XLOC_008338, XLOC_004128, and ENSSSCG00000040267) were determined from the network by considering the cis-acting genes. Specific novel lncRNAs were discovered in the reproductive tissues during the swine estrous cycle, and their time-serial expression dynamics were confirmed. As the main lncRNAs are involved in the development of each reproductive tissue and hormone action, they can be utilized as potential biomarkers to help improve and develop the reproductive traits of pigs.

Analysis of lncRNAs and Their Regulatory Network in Skeletal Muscle Development of the Yangtze River Delta White Goat

lncRNA (long non-coding RNA) has been confirmed to be associated with growth, development, cell proliferation, and other biological processes. This study explored the potential role and dynamic change process of lncRNAs and related ceRNA (competitive endogenous RNA) networks in skeletal muscle development of the Yangtze River Delta White (YDW) goat, and to analyze the differences in muscle fiber characteristics and meat quality levels of goats at different growth stages. In this study, we compared the expression profiles of lncRNAs in the M. Longissimus dorsi of the YDW goats at different stages of growth and development by RNA sequencing. The results revealed that, in terms of muscle fiber characteristics, muscle fiber diameter and muscle fiber area were significantly larger in 6-month-old and 10-month-old goats than those in 2-month-old goats (p < 0.01). In terms of muscle quality, a* and b* values of 6-month-old goats were significantly higher than those of 2-month-old goats (p < 0.01). Additionally, the a*, b*, and L* values of 6-month-old goats were significantly higher than those of 10-month-old goats (p < 0.01). The pH at 45 min post-mortem (pH45min) in 10-month-old goats was significantly higher than that in 2-month-old goats (p = 0.006). However, the pH at 24 h post-mortem (pH24h) in 10-month-old goats was significantly lower than that in both 2-month-old and 6-month-old goats (p < 0.01). Shear force increased gradually with age (p < 0.05), while there was no significant difference in drip loss among the different age groups (p > 0.05). Among the identified lncRNA expression profiles, a total of 3073 lncRNAs were found, including 2676 known lncRNAs and 397 novel lncRNAs. Of these, 110, 93, and 99 lncRNAs were specifically expressed in 2-month-old, 6-month-old, and 10-month-old goats, respectively. The lncRNA target gene enrichment analysis showed that they were mainly involved in actin binding, the actin cytoskeleton, the myocardin complex, as well as the AMPK, FoxO, and GnRH signaling pathways. When constructing the lncRNA-miRNA-mRNA ceRNA network, it was found that the ceRNA networks centered on chi-miR-758 and chi-miR-127-5p were involved in muscle development across all three periods, suggesting that they may play an important role in goat muscle growth and development.

The Role of Long Intergenic Noncoding RNA in Fetal Development

The role of long intergenic noncoding RNAs (lincRNAs) in fetal development has emerged as a significant area of study, challenging the traditional protein-centric view of gene expression. While messenger RNAs (mRNAs) have long been recognized for their role in encoding proteins, recent advances have illuminated the critical functions of lincRNAs in various biological processes. Initially identified through high-throughput sequencing technologies, lincRNAs are transcribed from intergenic regions between protein-coding genes and exhibit unique regulatory functions. Unlike mRNAs, lincRNAs are involved in complex interactions with chromatin and chromatin-modifying complexes, influencing gene expression and chromatin structure. LincRNAs are pivotal in regulating tissue-specific development and embryogenesis. For example, they are crucial for proper cardiac, neural, and reproductive system development, with specific lincRNAs being associated with organogenesis and differentiation processes. Their roles in embryonic development include regulating transcription factors and modulating chromatin states, which are essential for maintaining developmental programs and cellular identity. Studies using RNA sequencing and genetic knockout models have highlighted the importance of lincRNAs in processes such as cell differentiation, tissue patterning, and organ development. Despite their functional significance, the comprehensive annotation and understanding of lincRNAs remain limited. Ongoing research aims to elucidate their mechanisms of action and potential applications in disease diagnostics and therapeutics. This review summarizes current knowledge on the functional roles of lincRNAs in fetal development, emphasizing their contributions to tissue-specific gene regulation and developmental processes.

Mechanisms of tamoxifen resistance: insight from long non-coding RNAs

Breast cancer(BC) is the second most prevalent tumor in the world and one of the most lethal tumors in women. Patients with estrogen receptor-positive breast cancer can obtain significant advantages from endocrine therapies including tamoxifen, aromatase inhibitors, and others. However, the development of primary or acquired drug resistance ultimately leads to discontinuation of treatment with adverse consequences for breast cancer patients, and the underlying mechanisms have not been fully elucidated. Long non-coding RNAs (lncRNAs) play pivotal roles in orchestrating fundamental biochemical and cellular processes. They exert regulatory control over various processes including epigenetics, gene transcription, post-transcriptional modifications, and translation. Additionally, they influence key biological events like cell cycle progression, cell differentiation, and development. For the past few years, the relationship between lncRNAs and endocrine resistance has gained increasing attention, leading to a surge in related studies. LncRNAs mediate tamoxifen resistance in cancer by utilizing a variety of molecular mechanisms, including enhanced estrogen receptor (ER) signaling, inhibition of apoptosis, autophagy, exosome-mediated transfer, epigenetic alterations, epithelial-to-mesenchymal transition, and acting as competitive endogenous RNAs(ceRNAs). In this comprehensive review, we systematically summarize the critical role and intricate molecular mechanisms by which lncRNAs influence the development of tamoxifen resistance in breast cancer. Furthermore, we propose the potential clinical significance of lncRNAs as innovative therapeutic targets and prognostic biomarkers for breast cancer.

Schistosoma japonicum infection-mediated downregulation of lncRNA Malat1 contributes to schistosomiasis hepatic fibrosis by the Malat1/miR-96/Smad7 pathway

BACKGROUND

Schistosoma japonicum infection causes hepatic fibrosis, a primary cause of morbidity and mortality associated with the disease, and effective treatments are still lacking. Long non-coding RNAs (lncRNAs) have been implicated in the pathogenic process of various tissue fibroses. However, the role of lncRNAs in schistosomiasis hepatic fibrosis (HF) is poorly understood. Understanding the role of lncRNAs in schistosomiasis HF will enhance knowledge of disease processes and aid in the discovery of therapeutic targets and diagnostic biomarkers.

METHODS

Differentially expressed lncRNA profiles in primary hepatic stellate cells (HSCs) of mice infected with S. japonicum were identified using high-throughput lncRNA sequencing. Primary HSCs were isolated from infected mice using collagenase digestion and density-gradient centrifugation, cultured in DMEM with 10% fetal bovine serum. Dual-luciferase reporter assays, nuclear cytoplasm fractionation and RIP assays were employed to assess the relationship between Malat1 and miRNA-96. Malat1 lentivirus and ASO-Malat1 were constructed for forced expression and downregulated expression of Malat1. The Malat1-KO mouse was constructed by CRISPR/Cas9 technology. Pathological features of the liver were evaluated by hematoxylin-eosin (HE), Masson's trichrome staining and immunohistochemistry (IHC). The expression levels of fibrosis-related genes were determined by quantitative real-time PCR (qRT-PCR) and Western blot.

RESULTS

A total of 1561 differentially expressed lncRNAs were identified between infected and uninfected primary HSCs. Among the top altered lncRNAs, the downregulated Malat1 was observed in infected HSCs and verified by qPCR. Treatment of infected mice with praziquantel (PZQ) significantly increased the Malat1 expression. Elevated Malat1 expression in infected primary HSC reduced the expressions of profibrogenic genes, whereas Malat1 knockdown had the opposite effect. Moreover, Malat1 was found to interact with miR-96, a profibrotic miRNA, by targeting Smad7. Forced Malat1 expression reduced miR-96 levels in infected primary HSCs, attenuating fibrogenesis and showing negative correlation between Malat1 expression and the expression levels of miR-96 and profibrogenic genes α-SMA and Col1α1. Notably, in Malat1-KO mice, knockout of Malat1 aggravates schistosomiasis HF, while restored Malat1 expression in the infected HSCs reduced the expression of profibrogenic genes.

CONCLUSIONS

We demonstrate that lncRNA is involved in regulation of schistosomiasis HF. Elevated lncRNA Malat1 expression in infected HSCs reduces fibrosis via the Malat1/miR-96/Smad7 pathway, thus providing a novel therapeutic target for schistosomiasis HF. Furthermore, Malat1 expression is sensitive to PZQ treatment, thus offering a potential biomarker for assessing the response to chemotherapy.