Long noncoding RNAs: functional surprises from the RNA world

Prognostic gene expression profile of colorectal cancer

Colorectal cancer is a major global health burden, with significant heterogeneity in clinical outcomes among patients. Identifying robust prognostic gene expression signatures can help stratify patients, guide treatment decisions, and improve clinical management. This review provides an overview of current prognostic gene expression profiles in colorectal cancer research. We have synthesized evidence from numerous published studies investigating the association between tumor gene expression patterns and patient survival outcomes. The reviewed literature reveals several promising gene signatures that have demonstrated the ability to predict disease-free survival and overall survival in CRC patients, independent of standard clinicopathological risk factors. These genes are crucial in fundamental biological processes, including cell cycle control, epithelial-mesenchymal transition, and immune regulation. The implementation of prognostic gene expression tests in clinical practice holds great potential for enabling more personalized management strategies for colorectal cancer.

Non-coding RNA-mediated granulosa cell dysfunction during ovarian aging: From mechanisms to potential interventions

As the earliest aging organ in the reproductive system, the ovary has both reproductive and endocrine functions, which are closely related to overall female health. The exact pathogenesis of ovarian aging (OA) remains incompletely understood, with granulosa cells (GCs) dysfunction playing a significant role in this process. Recent advancements in research and biotechnology have highlighted the importance of non-coding RNAs (ncRNAs), including micro RNAs, long non-coding RNAs, and circular RNAs, in regulating the biological functions of GCs through gene expression modulation. This paper provides a comprehensive overview of the role of ncRNAs in various cellular functions such as apoptosis, autophagy, proliferation, and steroid synthesis in GCs, and explores the underlying regulatory mechanisms. Additionally, the therapeutic potential of ncRNAs, particularly those carried by exosomes derived from mesenchymal stem cells, in delaying OA is discussed. Understanding the regulatory mechanisms of ncRNAs in GC function and the current progress in this field is crucial for identifying effective biomarkers and therapeutic targets, ultimately aiding in the early diagnosis, prognostic assessment, and individualized treatment of OA.

Analysis of gonadal transcriptome reveals core long non-coding RNA-mRNA regulatory network in sea cucumber Apostichopus japonicus

Apostichopus japonicus is a representative temperate sea cucumber species, that mainly inhabits in coastal zone of the continental shelf. With high nutritional value and important medical value, A. japonicus become an important commercial aquaculture species and produce significant economic value in recent years. A. japonicus has no sexual dimorphism that can be used to distinguish female and male individuals by external appearance and morphology. The phenotype sex can be only detected by dissecting and observing gonad tissue, thus the breeding efficiency could be greatly reduced. This limitation has hindered the advancement of selective breeding programs and sea cucumber industry. To investigate the genetic basis of reproductive biology in A. japonicus, advanced sequencing techniques, such as next- and third-generation sequencing, have been employed to explore the roles of non-coding RNAs and other genetic factors, offering new insights into sex determination mechanisms. To further gain a deeper understanding of the knowledge underlying lncRNAs in gonadal differentiation, we conducted a comparative transcriptome sequencing analysis of gonadal tissues from both sexes. In our research, a total of 3990 novel lncRNAs and 1441 differentially expressed lncRNAs were identified between female and male gonads. Additionally, a molecular regulatory network indicating lncRNA-mRNA interactions was constructed based on transcriptional profiles, which provide insights into the potential cis- and trans- target genes of lncRNAs. The gonadal transcriptome analysis identified a number of novel long non-coding RNAs involved in female and male reproduction process. Both cis- and trans-acting regulatory networks indicating lncRNA-mRNA interaction were constructed based on transcriptional profiles. These findings provide new insights into the lncRNA-mediated regulation of reproductive biology in marine invertebrates, indicating the crucial roles of long non-coding sequences in regulating expression profiles. Further, the GO and KEGG enrichment analyses of cis- and trans- targeted mRNA for differentially expressed lncRNA indicated that sexual reproduction (GO:0019953), germ cell development (GO:0007281), and negative regulation of hormone secretion (GO:0046888) are potentially involved in gonadal differentiation through the regulation of long non-coding sequences. Notably, besides the classical reproduction related signaling pathway like Gonadotropin-releasing hormone (GnRH) secretion (ko04929), several regulatory pathways, such as Epidermal growth factor receptor (ErbB) signaling pathway (ko04012), TGF-beta signaling pathway (ko04350), and neurotrophin signaling pathway (ko04722) were also enriched and potentially involved in sex differentiation and gonadal development.

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.

LncRNA TCONS_00067339 as a key regulatory factor inducing decreased cell viability and ferroptosis in neonatal hypoxic-ischemic brain damage

Newborn hypoxic-ischemic brain damage (HIBD) is a major cause of mortality and neurological disabilities. Ferroptosis, characterized by lipid peroxidation, is implicated in HIBD pathogenesis. The role of lncRNA TCONS_00067339 in ferroptosis regulation in HIBD is understudied. This study investigates its mechanisms using a HIBD rat model and PC12 high differentiation cells oxygen-glucose deprivation (OGD) model. We identified upregulated lncRNA TCONS_00067339 in HIBD, associated with cells viability and ferroptosis-related mitochondrial changes. RNA sequencing revealed differential lncRNA expression in hippocampal, and enrichment analyses suggested involvement in ferroptosis pathways. Knockdown of lncRNA TCONS_00067339 increased OGD-treated PC12 cells viability and reduced cell death. These findings indicate that lncRNA TCONS_00067339 is a key regulator in ferroptosis and cell survival in HIBD, offering a potential target for therapeutic intervention.

Comprehensive transcriptome of muscle development in Sichuan white rabbit

BACKGROUND

The Sichuan white rabbit is a unique domestic breed and is famous for its high meat production. Muscle development is a complicated biological process, but the underlying regulatory mechanisms have not been elucidated. Here, we generated comprehensive transcriptome datasets (i.e., mRNAs, miRNAs and lncRNAs) in three developmental stages of Sichuan white rabbits, and aim to systematically explore the regulatory network in myogenesis.

RESULTS

We generated extensive transcriptome datasets (mRNAs, miRNAs and lncRNAs) revealing the myogenic regulatory network at different time points. Our differential expression analysis identified 2,995 DE genes, 1,211 DE-lncRNAs, and 305 DE-miRNAs with distinct expression patterns across developmental stages. In addition, functional enrichment analysis of DE mRNAs and miRNAs indicates their involvement in muscle growth, development, and regeneration, highlighting biological processes and muscle-specific functions. Interaction analysis between DE-lncRNAs and mRNAs uncovered a complex regulatory network, especially between 21 and 27 days of development. These findings contribute to better understanding of the transcriptomic changes during muscle development and have implications for breeding improvement in Sichuan white rabbits.

CONCLUSIONS

Our study provides a comprehensive overview of the transcriptomic changes during muscle development in Sichuan white rabbits. The identification and functional annotation of DE genes, miRNAs, and lncRNAs provide valuable insights into the molecular mechanisms underlying this process. These findings pave the way for targeted investigations into the role of non-coding RNAs in muscle biology.

Long non coding RNA function in epigenetic memory with a particular emphasis on genomic imprinting and X chromosome inactivation

Cells preserve and convey certain gene expression patterns to their progeny through the mechanism called epigenetic memory. Epigenetic memory, encoded by epigenetic markers and components, determines germline inheritance, genomic imprinting, and X chromosome inactivation. First discovered long non coding RNAs were implicated in genomic imprinting and X-inactivation and these two phenomena clearly demonstrate the role of lncRNAs in epigenetic memory regulation. Undoubtedly, lncRNAs are well-suited for regulating genes in close proximity at imprinted loci. Due to prolonged association with the transcription site, lncRNAs are able to guide chromatin modifiers to certain locations, thereby enabling accurate temporal and spatial regulation. Nevertheless, the current state of knowledge regarding lncRNA biology and imprinting processes is still in its nascent phase. Herein, we provide a synopsis of recent scientific advancements to enhance our comprehension of lncRNAs and their functions in epigenetic memory, with a particular emphasis on genomic imprinting and X chromosome inactivation, thus gaining a deeper understanding of the role of lncRNAs in epigenetic regulatory networks.

MSC exosomes and MSC exosomes loaded with LncRNA H19 as nanotherapeutics regulate the neurogenetic potential of Müller Glial Cells in dry age-related macular degeneration

In retinal degeneration diseases such as dry age-related macular degeneration (AMD), Müller Glial Cells (MGCs) in mammals undergo a process of reactive gliosis leading to the progression of dry AMD. Here, It is demonstrated that exosomes derived from mesenchymal stem cells (MSC exosomes) and MSC exosomes loaded with LncRNA H19, acting as nanotherapeutics, can be regulated by MGCs in dry AMD. In the in vivo study, MSC exosomes were administered via intravitreal injection. MSC exosomes effectively redirected MGCs from gliosis to dedifferentiation and alleviated MGCs-to-epithelial transition by inhibiting oxidative stress in mice with dry AMD induced by NaIO3. In the in vitro study, MSC exosomes promoted MGCs dedifferentiation by activating Wnt/β-catenin signaling pathway and prevented oxidative stress-induced MGCs gliosis and MGCs-to-epithelial transition by inhibiting TGFβ1 signaling pathway. MSC exosomes loaded with LncRNA H19 enhanced the activation of Wnt/β-catenin signaling pathway and the inhibition of the TGFβ1 signaling pathway compared with MSC exosomes. These results suggest that MSC exosomes regulate the neurogenetic potential of MGCs by redirecting MGCs from gliosis to dedifferentiation and alleviating the transformation of MGCs to epithelial cells through regulating oxidative stress. Regulating LncRNA H19 in MGCs to promote mammalian retinal regeneration in dry AMD was suggested for the first time.

Identification and validation of lncRNA mutation hotspot SNPs associated with myasthenia gravis susceptibility

Background

Myasthenia gravis (MG) is an autoimmune disorder caused by antibodies that target the postsynaptic muscle membrane. Recent evidence suggests that genetic variants and long noncoding RNAs (lncRNAs) play crucial roles in the pathogenesis of MG. The purpose of this study was to investigate the associations between lncRNA-related single-nucleotide polymorphisms (SNPs) and MG susceptibility in Chinese populations.

Methods

First, we identified lncRNA mutation hotspot regions based on the improved Kolmogorov‒Smirnov test and the cumulative hypergeometric distribution principle. Next, we further identified lncRNA mutation hotspot SNPs by calculating conservative scores. Finally, experiments were conducted to verify the associations between lncRNA mutation hotspot SNPs and MG susceptibility. A total of 82 patients with MG and 82 healthy controls were recruited for genotyping of lncRNA mutation hotspot SNPs using the SNaPshot technique. Quantitative real-time PCR was used to investigate lncRNA expression in 34 patients with MG and 37 healthy controls.

Results

In the multistep calculation, 14 candidate SNPs of 3 lncRNAs (AL031686.1, NONHSAT028539.2 and AC245014.3) in MG were identified as mutation hotspot SNPs. The genotyping results of the 14 SNPs in our study revealed no statistically significant differences in the frequencies of genotypes and alleles between patients with MG and controls. However, in the lncRNA AL031686.1, rs1000383 and rs6094353 were in perfect linkage disequilibrium (LD) and were associated with an increased risk of ocular MG. Additionally, rs6094347 was associated with an increased risk of ocular MG. Nevertheless, no SNP was found to be associated with factors such as sex, age, the presence or absence of thymoma, or the genetic model of MG. Further experiments revealed that NONHSAT028539.2 expression was upregulated in peripheral blood mononuclear cells (PBMCs) from patients with MG compared with those from healthy controls.

Conclusion

In our study, we did not find an association between the 14 mutation hotspot SNPs of lncRNAs and susceptibility to MG. However, we observed that the rs6094347 and rs1000383/rs6094353 polymorphisms in the lncRNA AL031686.1 were associated with the risk of ocular MG.

Identification of lncRNA expression profiles associated with ovarian development and ageing process in mice

Long non-coding RNA (lncRNA) participates in various biological processes, however, neither the expression profile nor the biological role of lncRNAs in mammalian ovaries has been fully studied. In this work, the lncRNA transcriptomic analysis of postnatal mice ovaries was performed by using bulk RNA sequencing in C57BL/6 mice. A total of 5302 lncRNAs were found in mouse ovaries, and 1836 lncRNAs were differentially expressed during the development and ageing process, of which targets were enriched in the developmental process, reproduction, etc. Developmental stage specific lncRNAs showed functions in system development, inflammatory response, myeloid leukocyte activation, etc. Moreover, a co-expression network analysis based on reproduction-related genes reveals lncRNAs that may regulate multiple mRNA targets in ovaries, including Neat1, Gm11613 and Gm43915. Two cis-acting lncRNAs, Ptgs2os and Gm14705, showed correlated expression pattern with their potential targets Ptgs2 and Aff2 respectively, and these lncRNA-mRNA pairs were conserved in mice and humans. WGCNA further identified 10 co-expressed modules with distinct expression patterns associated with ovarian development and ageing. Taken together, our results reveal a transcriptomic profile of mouse ovaries over the reproductive lifespan, providing insights into the molecular mechanisms of ovarian development and ageing.

Harnessing the potential of long non-coding RNAs in the pathophysiology of Alzheimer's disease

Alzheimer's disease (AD), a diverse neurodegenerative disease, is the leading cause of dementia, accounting for 60-80 % of all cases. The pathophysiology of Alzheimer's disease is unknown, and there is no cure at this time. Recent developments in transcriptome-wide profiling have led to the identification of a number of non-coding RNAs (ncRNAs). Among these, long non-coding RNAs (lncRNAs)-long transcripts that don't seem to be able to code for proteins-have drawn attention because they function as regulatory agents in a variety of biological processes. Recent research suggests that lncRNAs play a role in the pathogenesis of Alzheimer's disease by modulating tau hyperphosphorylation, amyloid production, synaptic impairment, neuroinflammation, mitochondrial dysfunction, and oxidative stress, though their precise effects on the disorder are unknown. The biology and modes of action of the best-characterized lncRNAs in AD will be outlined here, with an emphasis on their possible involvement in the pathophysiology of the disease. As lncRNAs may offer prospective prognostic/diagnostic biomarkers and therapeutic targets for the treatment of AD, a greater comprehension of the molecular processes and the intricate network of interactions in which they are implicated could pave the way for future research.

Roles of lncRNA in the crosstalk between osteogenesis and angiogenesis in the bone microenvironment

Bone is a highly calcified and vascularized tissue. The vascular system plays a vital role in supporting bone growth and repair, such as the provision of nutrients, growth factors, and metabolic waste transfer. Moreover, the additional functions of the bone vasculature, such as the secretion of various factors and the regulation of bone-related signaling pathways, are essential for maintaining bone health. In the bone microenvironment, bone tissue cells play a critical role in regulating angiogenesis, including osteoblasts, bone marrow mesenchymal stem cells (BMSCs), and osteoclasts. Osteogenesis and bone angiogenesis are closely linked. The decrease in osteogenesis and bone angiogenesis caused by aging leads to osteoporosis. Long noncoding RNAs (lncRNAs) are involved in various physiological processes, including osteogenesis and angiogenesis. Recent studies have shown that lncRNAs could mediate the crosstalk between angiogenesis and osteogenesis. However, the mechanism by which lncRNAs regulate angiogenesis‒osteogenesis crosstalk remains unclear. In this review, we describe in detail the ways in which lncRNAs regulate the crosstalk between osteogenesis and angiogenesis to promote bone health, aiming to provide new directions for the study of the mechanism by which lncRNAs regulate bone metabolism.

Long noncoding RNA SNHG4 promotes glioma progression via regulating miR-367-3p/MYO1B axis in zebrafish xenografts

Glioma is one of the most malignancy and prevalent tumor in the human central nervous system, which is associated with severe morbidity and high mortality. Numerous studies have explained the clear correlation between abnormal expression of lncRNA and progression of Glioma. LncRNA small nucleolar RNA host gene 4 (SNHG4) have been proved to play oncogenesis roles in various tumors, however, the underlying mechanism remains to be explored deeply. In this study, by analysis of the public database, we found that SNHG4 was upregulated in multiple cancer tissues, including glioma. Subsequently, the functional roles of SNHG4 were investigated, and we found that knockdown of SNHG4 remarkedly inhibited cell proliferation, migration. While, overexpression of SNHG4 enhanced these functions of glioma cells in vitro. Meanwhile, as the in vivo tool, zebrafish xenograft model was used to verify the functions of SNHG4 in glioma cells. Mechanically, we identified that SNHG4 or MYO1B could bind with miR-367-3p by the luciferase reporter assays. Furthermore, the rescue experiments showed that the inhibition of miR-367-3p or the expression of MYO1B partially rescue the inhibition effects of SNHG4 in glioma cells. Our study reveals that SNHG4 promotes the proliferation, migration of glioma via regulating miR-367-3p/MYO1B axis.

Comprehensive insights and In silico analysis into the emerging role of LincRNAs in lung diseases pathogenesis; a step toward ncRNA precision

Long non-coding RNAs (lncRNAs) have emerged as essential regulators of gene expression, significantly influencing various biological processes. Approximately half of all lncRNAs are classified as long intergenic non-coding RNAs (lincRNAs), which are situated among coding genes. Recent studies have documented the role of lincRNAs in the pathogenesis of lung diseases, including lung cancer, pulmonary fibrosis, and pulmonary arterial hypertension. These lincRNAs can modulate gene expression through various mechanisms, including epigenetic modifications, transcriptional regulation, and post-transcriptional regulation. By functioning as competing endogenous RNAs (ceRNAs), lincRNAs can affect the activity of microRNAs (miRNAs) and their corresponding target genes. This review delves into the intricate mechanisms by which lincRNAs contribute to the development and progression of various lung diseases. Furthermore, it discusses the potential of lincRNAs as therapeutic targets.

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

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

Systematic review and meta-analysis of the impact of abnormal expression of long non coding RNA on the prognosis of acute myeloid leukemia

Objective

Long non-coding RNA (lncRNA) is aberrantly expressed in a variety of tumor diseases. To date, its specific role in acute myeloid leukemia (AML) has not been fully elucidated. This study aims to evaluate the association between aberrant lncRNA expression and poor prognosis in AML patients, and to systematically assess the relationship between aberrant lncRNA expression and AML prognosis.

Methods

We conducted a comprehensive literature search in PubMed, Embase, Cochrane Library, CNKI (China National Knowledge Infrastructure), WanFang (China Wanfang Database), VIP (China VIP Database), and Sinomed (China Biomedical Literature Database) to identify relevant Chinese and English articles. The search period covered from the inception of these databases to 4 August 2024. Articles were screened according to predefined inclusion and exclusion criteria, and meta-analysis was performed using Stata.

Results

A total of 25 articles were included in the analysis. Aberrant lncRNA expression was significantly associated with reduced overall survival (univariate HR = 2.46, 95%CI 2.11-2.88, P < 0.001; multivariate HR = 2.46, 95%CI 2.11-2.88, P < 0.001), event-free survival (HR = 1.51, 95%CI 1.19-1.90, P = 0.001), recurrence-free survival (HR = 2.82, 95%CI 2.03-3.91, P < 0.001), and disease-free survival (HR = 2.390, 95%CI 1.037-5.507, P = 0.041). These findings were statistically significant. The 25 articles collectively identified 22 lncRNAs whose aberrant expression was associated with AML prognosis. Notably, multiple studies highlighted the aberrant expression of lncRNA CRNDE, ZEB2-AS1, and TUG1 as being particularly relevant to AML prognosis. Our meta-analysis revealed that high expression of lncRNA CRNDE and TUG1 was associated with reduced overall survival, while high expression of lncRNA ZEB2-AS1 was linked to decreased disease-free survival, both with statistically significant differences.

Conclusion

The expression levels of lncRNAs are closely associated with the prognosis of AML patients and may serve as important indicators for monitoring prognosis in the future. However, further high-quality studies are needed to validate these findings.

memerna: Sparse RNA folding including coaxial stacking

Determining RNA secondary structure is a core problem in computational biology. Fast algorithms for predicting secondary structure are fundamental to this task. We describe a modified formulation of the Zuker-Stiegler algorithm with coaxial stacking, a stabilising interaction in which the ends of helices in multi-loops are stacked. In particular, optimal coaxial stacking is computed as part of the dynamic programming state, rather than in an inner loop. We introduce a new notion of sparsity, which we call replaceability. Replaceability is a more general condition and applicable in more places than the triangle inequality that is used by previous sparse folding methods. We also introduce non-monotonic candidate lists as an additional sparsification tool. Existing usages of the triangle inequality for sparsification can be thought of as an application of both replaceability and monotonicity together. The modified recurrences along with replaceability allows sparsification to be applied to coaxial stacking as well, which increases the speed of the algorithm. We implemented this algorithm in software we call memerna, which we show to have the fastest exact (non-heuristic) implementation of RNA folding under the complete Turner 2004 model with coaxial stacking, out of several popular RNA folding tools supporting coaxial stacking. We also introduce a new notation for secondary structure which includes coaxial stacking, terminal mismatches, and dangles (CTDs) information. The memerna package 0.1 release is available at https://github.com/Edgeworth/memerna/tree/release/0.1.

Long non-coding RNAs as promising targets for controlling disease vector mosquitoes

Hematophagous female mosquitoes are important vectors of numerous devastating human diseases, posing a major public health threat. Effective prevention and control of mosquito-borne diseases rely considerably on progress in understanding the molecular mechanisms of various life activities, and accordingly, the molecules that regulate the various life activities of mosquitoes are potential targets for implementing future vector control strategies. Many long non-coding RNAs (lncRNAs) have been identified in mosquitoes and significant progress has been made in determining their functions. Here, we present a comprehensive overview of the research advances on mosquito lncRNAs, including their molecular identification, function, and interaction with other non-coding RNAs, as well as their synergistic regulatory roles in mosquito life activities. We also highlight the potential roles of competitive endogenous RNAs in mosquito growth and development, as well as in insecticide resistance and virus-host interactions. Insights into the biological functions and mechanisms of lncRNAs in mosquito life activities, viral replication, pathogenesis, and transmission will contribute to the development of novel drugs and safe vaccines.

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.

The urinary eccDNA landscape in prostate cancer reveals associations with genome instability and vital roles in cancer progression

INTRODUCTION

Extrachromosomal circular DNA (eccDNA) plays significant roles in cancer progression and prognosis. However, it remains unclear whether cell-free eccDNA, considered more stable than linear DNA, possesses cancer-specific genomic features. Furthermore, the biogenesis and function of eccDNAs are not yet fully understood.

OBJECTIVES

This study aims to characterize the genomic landscape of urinary cell-free eccDNAs in prostate cancer (PCa) and non-cancer (NC) individuals, elucidate their biogenesis and PCa-specific genomic features, and investigate their roles in PCa progression.

METHODS

We conducted urine Circle-seq for 21 PCa patients and 16 NC individuals, performed integrated analysis with other omics datasets, and finally validated the function of eccDNA by in vitro transfection and RNA-seq.

RESULTS

We pioneered the profiling of urinary cell-free eccDNAs landscape in PCa and uncovered a high association between eccDNA generation and active chromatin status as well as gene transcription. Double strand breaks and R-loops, which preferentially occur in active genomic sites and cause genome instability, can promote eccDNA generation. Genome instability frequently results in genomic mutations, and our study further established a link between eccDNA generation and oncogenic mutations. Additionally, genes specifically exhibiting high eccDNA generation frequency (HFGs) in PCa contributed to PCa progression and were associated with poorer survival outcomes in PCa patients. Finally, we demonstrated that eccDNAs derived from PCa-specific HFGs, in contrast to intergenic eccDNAs, could suppress PCa cell proliferation and migration, which was independent of their host gene expression.

CONCLUSION

Our study illustrated the biogenesis of eccDNAs from DSBs in active genes, revealed PCa-specific eccDNA features and suggested new mechanisms underlying eccDNA function.

Silencing of lncRNA Gm26917 Attenuates Alveolar Macrophage-mediated Inflammatory Response in LPS-induced Acute Lung Injury Via Inhibiting NKRF Ubiquitination

The inflammatory response mediated by alveolar macrophages plays a crucial role in the development of acute lung injury. Numerous studies have reported that lncRNAs are highly expressed in acute lung injury in mouse models and cell lines, and acute lung injury (ALI) can be effectively alleviated by targeting these lncRNAs. The aim of this study was to explore the mechanism by LncRNA Gm26917 regulates the inflammatory response in alveolar macrophages during acute lung injury mouse model. We initially observed a significant upregulation of Gm26917 expression in both ALI conditions and in MH-S cells treated with LPS. Furthermore, the silencing of Gm26917 via lentivirus-mediated methods conferred protection against LPS-induced ALI. Additionally, siRNA-mediated knockdown of Gm26917 attenuated LPS-induced inflammatory responses and modulated the function of alveolar macrophages. Subsequent mechanistic studies revealed that Gm26917 interacts with NKRF, and its knockdown suppressed NKRF ubiquitination, thereby enhancing NKRF binding to p50 and subsequently inhibiting the NF-κB signaling pathway. In conclusion, our findings demonstrate that silencing Gm26917 can mitigate LPS-induced ALI by modulating the NF-κB signaling pathway in alveolar macrophages through interactions with NKRF.

Exploring the Mechanisms of Iron Overload-Induced Liver Injury in Rats Based on Transcriptomics and Proteomics

Iron is a trace element that is indispensable for the growth and development of animals. Excessive iron supplementation may lead to iron overload and elevated reactive oxygen species (ROS) production in animals, causing cellular damage. Nevertheless, the precise mechanism by which iron overload causes cell injury remains to be fully elucidated. In this study, 16 male SD rats aged 6 to 7 weeks were randomly assigned to either a control group (CON) or an iron overload group (IO). Rats in the iron overload group received 150 mg/kg iron dextran injections every three days for a duration of four weeks. The results indicated that iron treatment with iron dextran significantly increased the scores of steatosis (p < 0.05) and inflammation (p < 0.05) in the NAS score. The integrated transcriptomic and proteomic analysis suggests that HO-1 and Lnc286.2 are potentially significant in iron overload-induced liver injury in rats. In vitro experiments utilizing ferric ammonium citrate (FAC) were conducted to establish an iron overload model in rat liver-derived BRL-3A cells. The result found that FAC treatment can significantly increase the BRL-3A cell's Fe2+ content (p < 0.05), ROS (p < 0.01), lipid ROS (p < 0.01) levels, and the expression of the HO-1 gene and protein (p < 0.01), aligning with proteomic and transcriptomic findings. HO-1 inhibition can significantly decrease BRL-3A cell vitality (p < 0.01) and promote ROS (p < 0.05) and lipid ROS (p < 0.01), thus aggravating FAC-induced BRL-3A cell iron overload damage. Using the agonist of HO-1 agonist cobalt protoporphyrin (CoPP) to induce HO-1 overexpression can significantly alleviate the decrease in FAC-induced BRL-3A cell viability (p < 0.01), ROS (p < 0.01), and lipid ROS (p < 0.01). In addition, siLnc286.2 treatment can increase HO-1 expression, alleviate the decline of FAC-induced BRL-3A cell activity, and increase lipid ROS (p < 0.05) content. In conclusion, the findings of this study suggest that by suppressing the expression of Lnc286.2, we can enhance the expression of HO-1, which in turn alleviates lipid peroxidation in cells and increases their antioxidant capacity, thereby exerting a protective effect against liver cell injury induced by iron overload.

Identification and expression analysis of lncRNAs in rice roots (Oryza sativa L.) under elevated CO2 concentration and/or cadmium stress

The gradual rise of CO2 is one of the global climate changes, Cd stress is also a major abiotic stress factor that affects rice (Oryza sativa L.). The rice seedlings were treated under two CO2 concentrations and two CdCl2 concentrations for 7 days (treatments names: 400 ± 20 μmol mol-1 CO2 and 0 μmol L-1 CdCl2 concentrations, AC; 400 ± 20 μmol mol-1 CO2 and 150 μmol L-1 CdCl2 concentrations, Cd; 800 ± 20 μmol mol-1 CO2 and 0 μmol L-1 CdCl2 concentrations, EC; 800 ± 20 μmol mol-1 CO2 and 150 μmol L-1 CdCl2 concentrations, EC + Cd). The lncRNAs informations were analyzed and excavated using high-throughput sequencing, target genes annotation, and qRT-PCR analysis techniques so as to reveal the regulatory mechanism of lncRNAs in rice roots under high CO2 concentrations and/or Cd stress. The results show that: (1) 326 (AC vs Cd), 331 (AC vs EC), 343 (AC vs EC + Cd), 112 (Cd vs EC + Cd) DE-lncRNAs were identified. (2) MAPK signaling pathway-plant (relevant genes Os04g0534166, Os05g0399800 regulated by MSTRG.18576.11, MSTRG.20864.1) and diterpenoid biosynthesis (relevant genes Os12g0491800, Os02g0570400 regulated by MSTRG.8965.1, MSTRG.11509.1) were annotated in AC vs Cd; Under EC relative to AC, DE-lncRNAs were annotated significantly to the flavonoid biosynthesis (relevant genes Os10g0196100, Os10g0320100, Os11g0116300, Os03g0819600 regulated by MSTRG.4612.1, MSTRG.4668.1, MSTRG.6051.1, MSTRG.16669.1); Under composite treatments, relative to AC, DE-lncRNAs were mainly annotated in the plant hormone signal transduction pathway (relevant genes Os03g0180800, Os03g0180900, Os03g0181100 regulated by MSTRG.13776.1). Under combined treatment, elevated CO2 alleviates Cd stress damage by regulating phenylpropanoid biosynthesis through DE-lncRNAs (relevant genes Os09g0419200 regulated by MSTRG. 29,573.1).

Long non-coding RNA OIP5-AS1 protects neurons from ischemia-reperfusion injury and inhibits neuronal apoptosis through TAB-2

Ischemic stroke represents a highly perilous cerebrovascular disorder, involving a variety of complex pathophysiological mechanisms. OIP5 antisense RNA 1 (OIP5-AS1) is a long non-coding RNA (LncRNA) that has been shown to play a pivotal role in a variety of disease systems. However, there are relatively few studies on ischemic stroke. This research aimed to elucidate the direct impact of OIP5-AS1 on neuronal cells following cerebral ischemia-reperfusion. Our study revealed a significant reduction in OIP5-AS1 expression in mouse neurons following middle cerebral artery occlusion/reperfusion (MCAO/R). Overexpression of OIP5-AS1 in neurons inhibits neuronal apoptosis induced by cerebral ischemia-reperfusion injury (CIRI) and exerts a neuroprotective role. Mechanistically, OIP5-AS1 may play a neuroprotective role after CIRI by up-regulating the expression of TAK1 binding protein 2 (TAB-2), reducing neuronal mitochondrial damage, and inhibiting apoptosis. OIP5-AS1 may become a novel therapeutic target for ischemic stroke.

Scientific investigation of non-coding RNAs in mitochondrial epigenetic and aging disorders: Current nanoengineered approaches for their therapeutic improvement

Genetic control is vital for the growth of cells and tissues, and it also helps living things, from single-celled organisms to complex creatures, maintain a stable internal environment. Within cells, structures called mitochondria act like tiny power plants, producing energy and keeping the cell balanced. The two primary categories of RNA are messenger RNA (mRNA) and non-coding RNA (ncRNA). mRNA carries the instructions for building proteins, while ncRNA does various jobs at the RNA level. There are different kinds of ncRNA, each with a specific role. Some help put RNA molecules together correctly, while others modify other RNAs or cut them into smaller pieces. Still others control how much protein is made from a gene. Scientists have recently discovered many more ncRNAs than previously known, and their functions are still being explored. This article analyzes the RNA molecules present within mitochondria, which have a crucial purpose in the operation of mitochondria. We'll also discuss how genes can be turned on and off without changing their DNA code, and how this process might be linked to mitochondrial RNA. Finally, we'll explore how scientists are using engineered particles to silence genes and develop new treatments based on manipulating ncRNA.

Interplay of cell death pathways and immune responses in ischemic stroke: insights into novel biomarkers

Stroke is a severe neurological disease and a major worldwide issue, mostly manifesting as ischemic stroke (IS). In order to create effective treatments for IS, it is imperative to fully understand the underlying pathologies, as the existing therapeutic choices are inadequate. Recent investigations have shown the complex relationships between several programmed cell death (PCD) pathways, including necroptosis, ferroptosis, and pyroptosis, and their correlation with immune responses during IS. However, this relationship is still unclear. To address this gap, this review study explored the cellular interactions in the immune microenvironment of IS. Then, to validate prior findings and uncover biomarkers, the study investigated bioinformatics studies. Several pathways, including nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), Toll-like receptor 4 (TLR4), and receptor-interacting protein kinase (RIPK), were involved in PCD-immune interactions. The bioinformatics studies reported key biomarkers such as glutathione peroxidase 4 (GPX4), NOD-like receptor family pyrin domain containing 3 (NLRP3), gasdermin D (GSDMD), and TLR4, which have important implications in ferroptosis, cuproptosis, pyroptosis, and necroptosis respectively. These biomarkers were associated with PCD mechanisms such as oxidative stress and inflammatory reactions. The immune infiltration analysis consistently revealed a significant correlation between PCD pathways and detrimental immune cells, such as neutrophils and γδ T cells. Conversely, M2 macrophages and T helper cells showed protective effects. In conclusion, considering the intricate network of interactions between immune responses and PCD pathways, this study emphasized the necessity of a paradigm shift in therapeutic approaches to address the injuries that are related to this complex network.

The implications for urological malignancies of non-coding RNAs in the the tumor microenvironment

Urological malignancies are a major global health issue because of their complexity and the wide range of ways they affect patients. There's a growing need for in-depth research into these cancers, especially at the molecular level. Recent studies have highlighted the importance of non-coding RNAs (ncRNAs) – these don't code for proteins but are crucial in controlling genes – and the tumor microenvironment (TME), which is no longer seen as just a background factor but as an active player in cancer progression. Understanding how ncRNAs and the TME interact is key for finding new ways to diagnose and predict outcomes in urological cancers, and for developing new treatments. This article reviews the basic features of ncRNAs and goes into detail about their various roles in the TME, focusing specifically on how different ncRNAs function and act in urological malignancies.

Transposable Elements Contribute to the Regulation of Long Noncoding RNAs in Drosophila melanogaster

Background: Transposable elements (TEs) and noncoding sequences are major components of the genome, yet their functional contributions to long noncoding RNAs (lncRNAs) are not well understood. Although many lncRNAs originating from TEs (TE-lncRNAs) have been identified across various organisms, their characteristics and regulatory roles, particularly in insects, remain largely unexplored. This study integrated multi-omics data to investigate TE-lncRNAs in D. melanogaster, focusing on the influence of transposons across different omics levels. Results: We identified 16,118 transposons overlapping with lncRNA sequences that constitute 2119 TE-lncRNAs (40.4% of all lncRNAs) using 256 public RNA-seq samples and 15 lncRNA-seq samples of Drosophila S2 cells treated with heavy metals. Of these, 67.2% of TE-lncRNAs contain more than one TE. The LTR/Gypsy family was the most common transposon insertion. Transposons preferred to insert into promoters, transcription starting sites, and intronic regions, especially in chromosome ends. Compared with lncRNAs, TE-lncRNAs showed longer lengths, a lower conservation, and lower levels but a higher specificity of expression. Multi-omics data analysis revealed positive correlations between transposon insertions and chromatin openness at the pre-transcriptional level. Notably, a total of 516 TE-lncRNAs provided transcriptional factor binding sites through transposon insertions. The regulatory network of a key transcription factor was rewired by transposons, potentially recruiting other transcription factors to exert regulatory functions under heavy metal stress. Additionally, 99 TE-lncRNAs were associated with m6A methylation modification sites, and 115 TE-lncRNAs potentially provided candidate small open reading frames through transposon insertions. Conclusions: Our data analysis demonstrated that TEs contribute to the regulation of lncRNAs. TEs not only promote the transcriptional regulation of lncRNAs, but also facilitate their post-transcriptional and epigenetic regulation.

Roles of the lncRNAs MEG3, PVT1 and H19 tagSNPs in gastric cancer susceptibility

BACKGROUND

Improper expression of long noncoding RNAs (lncRNAs) can cause various cancers. Single nucleotide polymorphisms (SNPs) affect the expression and function of several key lncRNAs. We assessed the associations of MEG3, PVT1, and H19 lncRNA polymorphisms with susceptibility to gastric cancer (GC).

METHODS

In Ardabil (a high-risk area in North‒West Iran), 795 blood samples were collected from 396 cases and 399 controls. The control subjects were randomly selected from individuals receiving regular physical examinations in this hospital with no self-reported cancer history and were frequency-matched to the case group by sex and 5-year age intervals. All the samples were genotyped via the Infinium HTS platform, which was subsequently followed by rigorous data quality control, as well as statistical and bioinformatic analyses.

RESULTS

The H19 rs2107425 SNP was associated with GC risk in a recessive model of inheritance (TT vs. CC + CT: OR = 1.87). The PVT1 rs13255292 variant in the overdominant model significantly reduced GC risk (CT vs. CC + TT: OR = 0.74). There was no significant association between H19 rs2839698, MEG3 rs116907618, or rs11160608, or PVT1 rs7017386, rs13254990 tagSNPs and susceptibility to GC. The interaction between H19 rs2107425 TT and PVT1 rs7017386 TC increased GC risk (OR = 3.73; pbon < 0.05). The MEG3, PVT1, and H19 variants were not associated with clinicopathologic characteristics.

CONCLUSIONS

We revealed significant associations of the H19 rs2107425 and PVT1 rs13255292 genetic variants with GC. Interestingly, the novel SNP‒SNP interaction of H19 and PVT1 tagSNPs had a greater effect than single SNP impacts did on GC risk, providing us with invaluable data to identify potential biological mechanisms involved in the development of GC.

Roles of noncoding RNAs in diabetic retinopathy: Mechanisms and therapeutic implications

Diabetic retinopathy (DR) is a microvascular complication of diabetes that leads to vision loss. The striking features of DR are hard exudate, cotton-wool spots, hemorrhage, and neovascularization. The dysregulated retinal cells, encompassing microvascular endothelial cells, pericytes, Müller cells, and adjacent retinal pigment epithelial cells, are involved in the pathological processes of DR. According to recent research, oxidative stress, inflammation, ferroptosis, pyroptosis, apoptosis, and angiogenesis contribute to DR. Recent advancements have highlighted that noncoding RNAs could regulate diverse targets in pathological processes that contribute to DR. Noncoding RNAs, including long noncoding RNAs, microRNAs (miRNA), and circular RNAs, are dysregulated in DR, and interact with miRNA, mRNA, or proteins to control the pathological processes of DR. Hence, modulation of noncoding RNAs may have therapeutic effects on DR. Small extracellular vesicles may be valuable tools for transferring noncoding RNAs and regulating the genes involved in progression of DR. However, the roles of noncoding RNA in developing DR are not fully understood; it is critical to summarize the mechanisms for noncoding RNA regulation of pathological processes and pathways related to DR. This review provides a fundamental understanding of the relationship between noncoding RNAs and DR, exploring the mechanism of how noncoding RNA modulates different signaling pathways, and pave the way for finding potential therapeutic strategies for DR.

The role of circular RNA targeting IGF2BPs in cancer-a potential target for cancer therapy

Circular RNAs (circRNAs) are an interesting class of conserved single-stranded RNA molecules derived from exon or intron sequences produced by the reverse splicing of precursor mRNA. CircRNAs play important roles as microRNA sponges, gene splicing and transcriptional regulators, RNA-binding protein sponges, and protein/peptide translation factors. Abnormal functions of circRNAs and RBPs in tumor progression have been widely reported. Insulin-like growth factor-2 mRNA-binding proteins (IGF2BPs) are a highly conserved family of RBPs identified in humans that function as post-transcriptional fine-tuners of target transcripts. Emerging evidence suggests that IGF2BPs regulate the processing and metabolism of RNA, including its stability, translation, and localization, and participate in a variety of cellular functions and pathophysiology. In this review, we have summarized the roles and molecular mechanisms of circRNAs and IGF2BPs in cancer development and progression. In addition, we briefly introduce the role of other RNAs and IGF2BPs in cancer, discuss the current clinical applications and challenges faced by circRNAs and IGF2BPs, and propose future directions for this promising research field.

Bibliometric and visualization analysis in the field of epigenetics and glioma (2009-2024)

Introduction

Glioma represents the most prevalent primary malignant tumor in the central nervous system, a deeper understanding of the underlying molecular mechanisms driving glioma is imperative for guiding future treatment strategies. Emerging evidence has implicated a close relationship between glioma development and epigenetic regulation. However, there remains a significant lack of comprehensive summaries in this domain. This study aims to analyze epigenetic publications pertaining to gliomas from 2009 to 2024 using bibliometric methods, consolidate the extant research, and delineate future prospects for investigation in this critical area.

Methods

For the purpose of this study, publications spanning the years 2009 to 2024 were extracted from the esteemed Web of Science Core Collection (WoSCC) database. Utilizing advanced visualization tools such as CiteSpace and VOSviewer, comprehensive data pertaining to various aspects including countries, authors, author co-citations, countries/regions, institutions, journals, cited literature, and keywords were systematically visualized and analyzed.

Results

A thorough analysis was conducted on a comprehensive dataset consisting of 858 publications, which unveiled a discernible trend of steady annual growth in research output within this specific field. The nations of the United States, China, and Germany emerged as the foremost contributors to this research domain. It is noteworthy that von Deimling A and the Helmholtz Association were distinguished as prominent authors and institutions, respectively, in this corpus of literature. A rigorous keyword search and subsequent co-occurrence analysis were executed, ultimately leading to the identification of seven distinct clusters: "epigenetic regulation", "DNA repair", "DNA methylation", "brain tumors", "diffuse midline glioma (DMG)", "U-87 MG" and "epigenomics". Furthermore, an intricate cluster analysis revealed that the primary foci of research within this field were centered around the exploration of glioma pathogenesis and the development of corresponding treatment strategies.

Conclusion

This article underscores the prevailing trends and hotspots in glioma epigenetics, offering invaluable insights that can guide future research endeavors. The investigation of epigenetic mechanisms primarily centers on DNA modification, non-coding RNAs (ncRNAs), and histone modification. Furthermore, the pursuit of overcoming temozolomide (TMZ) resistance and the exploration of diverse emerging therapeutic strategies have emerged as pivotal avenues for future research within the field of glioma epigenetics.

Experimental and in silico analysis of LINC01279 expression in tumor of patients with breast cancer

Breast cancer (BC) is characterized by the increase of malignant cells in the breast. The malignant cells begin in the lining of the breast milk glands or ducts (ductal epithelium). BC is the most frequent cancer in women, but it may also occur in males. Long non-coding RNAs (lncRNA) have been demonstrated to control the development and incidence of cancer. However, some lncRNAs experience potential changes in BC, but their role has not been well studied. LINC01279 is known as a valuable biomarker in gastric cancer but has not yet been studied in BC. Changes in LINC01279 expression levels in BC samples were investigated by microarray. Q-PCR was also used to evaluate the expression of LINC01279 in the tumor and normal adjacent samples of 30 BC patients. The LINC01279 co-expressed gene module was discovered using weighted gene correlation network analysis (WGCNA) on the relevant dataset. The top ten hub genes were determined using gene ontology (GO) functional enrichments on the co-expressed gene module. The results of the bioinformatics study showed an increase in LINC01279 expression levels (log2FC = 3.228749561, adj.P.Val = 1.69E - 12) in tumor samples compared to normal marginal tissue. Q-PCR results also showed a significant increase in LINC01279 expression (P-value = 0.0005) in tumor samples. WGCNA analysis identified that the black module is the LINC01279 co-expressed module, and functional annotation analysis of black module genes enriched in significant cancer-related pathways and processes, including cell growth and/or maintenance, regulation of immune response, regulation of cell proliferation, and epithelial-to-mesenchymal transition (EMT). Regarding the real-time PCR results, the analysis of expression patterns has illuminated a distinct association between the heightened expression levels of LINC01279, and the stages of cancer progression as well as the metastatic potential of tumors. However, intriguingly, our observations have failed to reveal any statistically significant correlations between the relative expression of LINC01279 and tumor grade classification, or the presence of ER, PR, and HER2 biomarkers. The present study could provide a new perspective on the molecular regulatory. Processes associated with BC pathogenic mechanisms are linked to the LINC01279, although further research is needed on the possible role of this lncRNA in BC.

Colon Cancer-Derived Exosomal LncRNA-XIST Promotes M2-like Macrophage Polarization by Regulating PDGFRA

Colon cancer ranks second in overall cancer-related deaths and poses a serious risk to human life and health. In recent years, exosomes are believed to play an important and significant role in cancer, especially tumor-derived exosomes (TDEs). Previous studies have highlighted the pivotal role of exosomes in tumor development, owing to their ability to mediate communication between tumor cells and macrophages, induce macrophage M2 polarization, and facilitate the progression of tumorigenesis. In this study, we revealed that colon cancer-derived exosomes promoted M2-like macrophage polarization. Moreover, exosome-induced M2-like macrophages, in turn, promoted the proliferation, migration, and invasion abilities of colon cancer cells. Specifically, CT26- and HCT116-derived exosomes led to the activation of AKT, ERK, and STAT3/6 signaling pathways in THP-1(Mφ) cells. Furthermore, our findings showed that colon cancer-derived exosomes secreted lncXIST to sponge miR-17-5p, which, in turn, promoted the expression of PDGFRA, a common gene found in all three signaling pathways, to facilitate M2-like macrophage polarization. Dual-luciferase reporter assays confirmed the binding relationship between lncXIST and miR-17-5p, as well as miR-17-5p and PDGFRA. Collectively, our results highlight the novel role of lncXIST in facilitating macrophage polarization by sponging miR-17-5p and regulating PDGFRA expression.

Epigenetic regulation of targeted ferroptosis: A new strategy for drug development

Ferroptosis is a newly discovered form of cell death that is influenced by iron levels and is triggered by cellular metabolism and excessive lipid peroxidation. Epigenetic regulation plays a crucial role in the development and progression of diseases, making it essential to understand these mechanisms in order to identify potential targets for drug development and clinical treatment. The intersection of ferroptosis and epigenetics has opened up new avenues for research in drug development, offering innovative strategies for combating diseases. Recent studies have shown that epigenetic modifications can impact pathways related to ferroptosis, potentially leading to organ dysfunction. Despite the increasing focus on this relationship, the role of epigenetic regulation in drug development remains largely unexplored. This article explores current research on the interplay between epigenetic regulation and ferroptosis, delving into their regulatory mechanisms and discussing the effects of existing epigenetic modification regulators on diseases. Additionally, we highlight ongoing research on epigenetic factors involved in targeting ferroptosis in cancer, providing new insights for the development of cancer treatments.

Endothelial derived, secreted long non-coding RNAs Gadlor1 and Gadlor2 aggravate cardiac remodeling

Pathological cardiac remodeling predisposes individuals to developing heart failure. Here, we investigated two co-regulated long non-coding RNAs (lncRNAs), termed Gadlor1 and Gadlor2, which are upregulated in failing hearts of patients and mice. Cardiac overexpression of Gadlor1 and Gadlor2 aggravated myocardial dysfunction and enhanced hypertrophic and fibrotic remodeling in mice exposed to pressure overload. Compound Gadlor1/2 knockout (KO) mice showed markedly reduced myocardial hypertrophy, fibrosis, and dysfunction, while exhibiting increased angiogenesis during short and prolonged periods of pressure overload. Paradoxically, Gadlor1/2 KO mice suffered from sudden death during prolonged overload, possibly due to cardiac arrhythmia. Gadlor1 and Gadlor2, which are mainly expressed in endothelial cells (ECs) in the heart, where they inhibit pro-angiogenic gene expression, are strongly secreted within extracellular vesicles (EVs). These EVs transfer Gadlor lncRNAs to cardiomyocytes, where they bind and activate calmodulin-dependent kinase II, and impact pro-hypertrophic gene expression and calcium homeostasis. Therefore, we reveal a crucial lncRNA-based mechanism of EC-cardiomyocyte crosstalk during heart failure, which could be specifically modified in the future for therapeutic purposes.

The functions and mechanisms of piRNAs in mediating mammalian spermatogenesis and their applications in reproductive medicine

As the most abundant small RNAs, piwi-interacting RNAs (piRNAs) have been identified as a new class of non-coding RNAs with 24-32 nucleotides in length, and they are expressed at high levels in male germ cells. PiRNAs have been implicated in the regulation of several biological processes, including cell differentiation, development, and male reproduction. In this review, we focused on the functions and molecular mechanisms of piRNAs in controlling spermatogenesis, including genome stability, regulation of gene expression, and male germ cell development. The piRNA pathways include two major pathways, namely the pre-pachytene piRNA pathway and the pachytene piRNA pathway. In the pre-pachytene stage, piRNAs are involved in chromosome remodeling and gene expression regulation to maintain genome stability by inhibiting transposon activity. In the pachytene stage, piRNAs mediate the development of male germ cells via regulating gene expression by binding to mRNA and RNA cleavage. We further discussed the correlations between the abnormalities of piRNAs and male infertility and the prospective of piRNAs' applications in reproductive medicine and future studies. This review provides novel insights into mechanisms underlying mammalian spermatogenesis and offers new targets for diagnosing and treating male infertility.

FOXCUT regulates the malignant phenotype of triple-negative breast Cancer via the miR-337-3p/ANP32E Axis

BACKGROUND

The lack of specific molecular targets and the rapid spread lead to a worse prognosis of triple-negative breast cancer (TNBC). Therefore, identifying new therapeutic and prognostic biomarkers helps to develop effective treatment strategies for TNBC.

METHODS

Through preliminary bioinformatics analysis, FOXCUT was found to be significantly overexpressed in breast cancer, especially in TNBC. Tissue samples were collected from 15 TNBC patients, and qRT-PCR was employed to validate the expression of FOXCUT in both TNBC patient tissues and TNBC cell lines. We also carried out the GSEA analysis and KEGG enrichment analysis of FOXCUT. Additionally, the effects of FOXCUT knockdown on TNBC cell malignant behaviors, and aerobic glycolysis were assessed by methods including CCK-8, Transwell, western blot, and Seahorse XF 96 analyses. Moreover, utilizing databases predicting interactions between ceRNAs, corresponding lncRNA-miRNA binding relationships, and miRNA-mRNA interactions were predicted. These predictions were subsequently validated through RNA immunoprecipitation and dual-luciferase reporter assays.

RESULTS

FOXCUT exhibited high expression in both TNBC tissues and cell lines, fostering cell malignant behaviors and glycolysis. FOXCUT was found to sponge miR-337-3p, while miR-337-3p negatively regulated the expression of ANP32E. Consequently, FOXCUT ultimately facilitated the malignant phenotype of TNBC by upregulating ANP32E expression.

CONCLUSION

This study elucidated the role of FOXCUT in elevating aerobic glycolysis levels in TNBC and driving malignant cancer cell development via the miR-337-3p/ANP32E regulatory axis.

LncRNA MALAT-1 modulates EGFR-TKI resistance in lung adenocarcinoma cells by downregulating miR-125

Molecular targeted therapy resistance remains a major challenge in treating lung adenocarcinoma (LUAD). The resistance of Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs, epidermal growth factor receptor-tyrosine kinase inhibitor) plays a dominant role in molecular targeted therapy. Our previous research demonstrated the role of MALAT-1 (Metastasis-associated lung adenocarcinoma transcript 1) in the formation of Erlotinib-resistant LUAD cells. This study aims to uncover the mechanism of MALAT-1 overexpression in Erlotinib-resistant LUAD cells. The RT2 LncRNA PCR array system was used to explore MALAT-1 regulation in Erlotinib-resistant LUAD cells through patient serum analysis. Dual luciferase reporter experiments confirmed the binding between MALAT-1 and miR-125, leading to regulation of miR-125 expression. Functional assays were performed to elucidate the impact of MALAT1 on modulating drug resistance, growth, and Epithelial-mesenchymal transition (EMT, Epithelial-mesenchymal transition) in both parental and Erlotinib-resistant LUAD cells. The investigation unveiled the mechanism underlying the competing endogenous RNA (ceRNA, competing endogenouse RNA) pathway. MALAT1 exerted its regulatory effect on miR-125 as a competing endogenous RNA (ceRNA). Moreover, MALAT1 played a role in modulating the sensitivity of LUAD cells to Erlotinib. Rab25 was identified as the direct target of miR-125 and mediated the functional effects of MALAT1 in Erlotinib-resistant LUAD cells. In conclusion, our study reveals overexpress MALAT-1 cause the drug resistance of EGFR-TKIs in non-small cell lung cancer (NSCLC) through the MALAT-1/miR-125/Rab25 axis. These findings present a potential novel therapeutic target and perspective for the treatment of LUAD.

Glycolysis and chemoresistance in acute myeloid leukemia

While traditional high-dose chemotherapy can effectively prolong the overall survival of acute myeloid leukemia (AML) patients and contribute to better prognostic outcomes, the advent of chemoresistance is a persistent challenge to effective AML management in the clinic. The therapeutic resistance is thought to emerge owing to the heterogeneous and adaptable nature of tumor cells when exposed to exogenous stimuli. Recent studies have focused on exploring metabolic changes that may afford novel opportunities to treat AML, with a particular focus on glycolytic metabolism. The Warburg effect, a hallmark of cancer, refers to metabolism of glucose through glycolysis under normoxic conditions, which contributes to the development of chemoresistance. Despite the key significance of this metabolic process in the context of malignant transformation, the underlying molecular mechanisms linking glycolysis to chemoresistance in AML remain incompletely understood. This review offers an overview of the current status of research focused on the relationship between glycolytic metabolism and AML resistance to chemotherapy, with a particular focus on the contributions of glucose transporters, key glycolytic enzymes, signaling pathways, non-coding RNAs, and the tumor microenvironment to this relationship. Together, this article will provide a foundation for the selection of novel therapeutic targets and the formulation of new approaches to treating AML.

Mitochondrial sequencing identifies long noncoding RNA features that promote binding to PNPase

Extranuclear localization of long noncoding RNAs (lncRNAs) is poorly understood. Based on machine learning evaluations, we propose a lncRNA-mitochondrial interaction pathway where polynucleotide phosphorylase (PNPase), through domains that provide specificity for primary sequence and secondary structure, binds nuclear-encoded lncRNAs to facilitate mitochondrial import. Using FVB/NJ mouse and human cardiac tissues, RNA from isolated subcellular compartments (cytoplasmic and mitochondrial) and cross-linked immunoprecipitate (CLIP) with PNPase within the mitochondrion were sequenced on the Illumina HiSeq and MiSeq, respectively. lncRNA sequence and structure were evaluated through supervised [classification and regression trees (CART) and support vector machines (SVM)] machine learning algorithms. In HL-1 cells, quantitative PCR of PNPase CLIP knockout mutants (KH and S1) was performed. In vitro fluorescence assays assessed PNPase RNA binding capacity and verified with PNPase CLIP. One hundred twelve (mouse) and 1,548 (human) lncRNAs were identified in the mitochondrion with Malat1 being the most abundant. Most noncoding RNAs binding PNPase were lncRNAs, including Malat1. lncRNA fragments bound to PNPase compared against randomly generated sequences of similar length showed stratification with SVM and CART algorithms. The lncRNAs bound to PNPase were used to create a criterion for binding, with experimental validation revealing increased binding affinity of RNA designed to bind PNPase compared to control RNA. The binding of lncRNAs to PNPase was decreased through the knockout of RNA binding domains KH and S1. In conclusion, sequence and secondary structural features identified by machine learning enhance the likelihood of nuclear-encoded lncRNAs binding to PNPase and undergoing import into the mitochondrion.NEW & NOTEWORTHY Long noncoding RNAs (lncRNAs) are relatively novel RNAs with increasingly prominent roles in regulating genetic expression, mainly in the nucleus but more recently in regions such as the mitochondrion. This study explores how lncRNAs interact with polynucleotide phosphorylase (PNPase), a protein that regulates RNA import into the mitochondrion. Machine learning identified several RNA structural features that improved lncRNA binding to PNPase, which may be useful in targeting RNA therapeutics to the mitochondrion.

The response of LncRNAs associated with photosynthesis-and pigment synthesis-related genes to green light in Chlamydomonas reinhardtii

The quality of light is an important abiotic factor that affects the growth and development of green plants. Ultraviolet, red, blue, and far-red light all have demonstrated roles in regulating green plant growth and development, as well as light morphogenesis. However, the mechanism underlying photosynthetic organism responses to green light throughout the life of them are not clear. In this study, we exposed the unicellular green alga Chlamydomonas reinhardtii to green light and analyzed the dynamics of transcriptome changes. Based on the whole transcriptome data from C. reinhardtii, a total of 9974 differentially expressed genes (DEGs) were identified under green light. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that these DEGs were mainly related to "carboxylic acid metabolic process," "enzyme activity," "carbon metabolism," and "photosynthesis and other processes." At the same time, 253 differentially expressed long non-coding RNAs (DELs) were characterized as green light responsive. We also made a detailed analysis of the responses of photosynthesis- and pigment synthesis-related genes in C. reinhardtii to green light and found that these genes exhibited obvious dynamic expression. Lastly, we constructed a co-expression regulatory network, comprising 49 long non-coding RNAs (lncRNAs) and 20 photosynthesis and pigment related genes, of which 9 mRNAs were also the predicted trans/cis-targets of 8 lncRNAs, these results suggested that lncRNAs may affect the expression of mRNAs related to photosynthesis and pigment synthesis. Our findings give a preliminary explanation of the response mechanism of C. reinhardtii to green light at the transcriptional level.

Lnc-PIK3R1, transcriptionally suppressed by YY1, inhibits hepatocellular carcinoma progression via the Lnc-PIK3R1/miR-1286/GSK3β axis

Hepatocellular carcinoma (HCC) poses a significant threat due to its highly aggressive and high recurrence characteristics, necessitating urgent advances in diagnostic and therapeutic approaches. Long non-coding RNAs exert vital roles in HCC tumorigenesis, however the mechanisms of their expression regulation and functions are not fully elucidated yet. Herein, we identify that a novel tumor suppressor 'lnc-PIK3R1' was significantly downregulated in HCC tissues, which was correlated with poor prognosis. Functionally, lnc-PIK3R1 played tumor suppressor roles to inhibit the proliferation and mobility of HCC cells, and to impede the distant implantation of xenograft in mice. Mechanistic studies revealed that lnc-PIK3R1 interacted with miR-1286 and alleviated the repression on GSK3B by miR-1286. Notably, pharmacological inhibition of GSK3β compromised the tumor suppression effect by lnc-PIK3R1, confirming their functional relevance. Moreover, we identified that oncogenic YY1 acts as a specific transcriptional repressor to downregulate the expression of lnc-PIK3R1 in HCC. In summary, this study highlights the tumor-suppressive effect of lnc-PIK3R1, and provides new insights into the regulation of GSK3β expression in HCC, which would benefit the development of innovative intervention strategies for HCC.

Implications of lncRNAs in Helicobacter pylori-associated gastrointestinal cancers: underlying mechanisms and future perspectives

Helicobacter pylori (H. pylori) is a harmful bacterium that is difficult to conveniently diagnose and effectively eradicate. Chronic H. pylori infection increases the risk of gastrointestinal diseases, even cancers. Despite the known findings, more underlying mechanisms are to be deeply explored to facilitate the development of novel prevention and treatment strategies of H. pylori infection. Long noncoding RNAs (lncRNAs) are RNAs with more than 200 nucleotides. They may be implicated in cell proliferation, inflammation and many other signaling pathways of gastrointestinal cancer progression. The dynamic expression of lncRNAs indicates their potential to be diagnostic or prognostic biomarkers. In this paper, we comprehensively summarize the processes of H. pylori infection and the treatment methods, review the known findings of lncRNA classification and functional mechanisms, elucidate the roles of lncRNAs in H. pylori-related gastrointestinal cancer, and discuss the clinical perspectives of lncRNAs.

Deciphering epigenetic regulations in the inflammatory pathways of atopic dermatitis

Atopic dermatitis, commonly referred to as atopic eczema, is a persistent inflammatory skin disorder that predominantly manifests in children but may endure into adulthood. Its clinical management poses challenges due to the absence of a definitive cure, and its prevalence varies across ethnicities, genders, and geographic locations. The epigenetic landscape of AD includes changes in DNA methylation, changes in histone acetylation and methylation, and regulation by non-coding RNAs. These changes affect inflammatory and immune mechanisms, and research has identified AD-specific variations in DNA methylation, particularly in the affected epidermis. Histone modifications, including acetylation, have been associated with the disruption of skin barrier function in AD, suggesting the potential therapeutic benefit of histone deacetylase inhibitors such as belinostat. Furthermore, non-coding RNAs, particularly microRNAs and long non-coding RNAs (lncRNAs), have been implicated in modulating various cellular processes central to AD pathogenesis. Therapeutic implications in AD include the potential use of DNA methylation inhibitors and histone deacetylase inhibitors to correct aberrant methylation patterns and modulate gene expression related to immune responses and skin barrier functions. Additionally, the emerging role of lncRNAs suggests the possibility of using small interfering RNAs or antisense oligonucleotides to inhibit lncRNAs and adjust their regulatory impact on gene expression. In conclusion, the importance of epigenetic elements in AD is becoming increasingly clear as studies highlight the contribution of DNA methylation, histone modifications and, control by non-coding RNAs to the onset and progression of the disease. Understanding these epigenetic changes provides valuable insights for developing targeted therapeutic strategies.

The Long Non-Coding RNA Obesity-Related (Obr) Contributes To Lipid Metabolism Through Epigenetic Regulation

Obesity is a multifactorial disease that is part of today's epidemic and also increases the risk of other metabolic diseases. Long noncoding RNAs (lncRNAs) provide one tier of regulatory mechanisms to maintain metabolic homeostasis. Although lncRNAs are a significant constituent of the mammalian genome, studies aimed at their metabolic significance, including obesity, are only beginning to be addressed. Here, a developmentally regulated lncRNA, termed as obesity related (Obr), whose expression in metabolically relevant tissues such as skeletal muscle, liver, and pancreas is altered in diet-induced obesity, is identified. The Clone 9 cell line and high-fat diet-induced obese Wistar rats are used as a model system to verify the function of Obr. By using stable expression and antisense oligonucleotide-mediated downregulation of the expression of Obr followed by different molecular biology experiments, its role in lipid metabolism is verified. It is shown that Obr associates with the cAMP response element-binding protein (Creb) and activates different transcription factors involved in lipid metabolism. Its association with the Creb histone acetyltransferase complex, which includes the cAMP response element-binding protein (CBP) and p300, positively regulates the transcription of genes involved in lipid metabolism. In addition, Obr is regulated by Pparγ in response to lipid accumulation.

Novel insights on the positive correlation between sense and antisense pairs on gene expression

A considerable proportion of the eukaryotic genome undergoes transcription, leading to the generation of noncoding RNA molecules that lack protein-coding information and are not subjected to translation. These noncoding RNAs (ncRNAs) are well recognized to have essential roles in several biological processes. Long noncoding RNAs (lncRNAs) represent the most extensive category of ncRNAs found in the human genome. Much research has focused on investigating the roles of cis-acting lncRNAs in the regulation of specific target gene expression. In the majority of instances, the regulation of sense gene expression by its corresponding antisense pair occurs in a negative (discordant) manner, resulting in the suppression of the target genes. The notion that a negative correlation exists between sense and antisense pairings is, however, not universally valid. In fact, several recent studies have reported a positive relationship between corresponding cis antisense pairs within plants, budding yeast, and mammalian cancer cells. The positive (concordant) correlation between anti-sense and sense transcripts leads to an increase in the level of the sense transcript within the same genomic loci. In addition, mechanisms such as altering chromatin structure, the formation of R loops, and the recruitment of transcription factors can either enhance transcription or stabilize sense transcripts through their antisense pairs. The primary objective of this work is to provide a comprehensive understanding of both aspects of antisense regulation, specifically focusing on the positive correlation between sense and antisense transcripts in the context of eukaryotic gene expression, including its implications towards cancer progression. This article is categorized under: RNA Processing > 3' End Processing Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.

CYTOR-NFAT1 feedback loop regulates epithelial-mesenchymal transition of retinal pigment epithelial cells

Epithelial mesenchymal transition (EMT) occurring in retinal pigment epithelial cells (RPE) is a crucial mechanism that contributes to the development of age-related macular degeneration (AMD), a pivotal factor leading to permanent vision impairment. Long non-coding RNAs (lncRNAs) have emerged as critical regulators orchestrating EMT in RPE cells. In this study, we explored the function of the lncRNA CYTOR (cytoskeleton regulator RNA) in EMT of RPE cells and its underlying mechanisms. Through weighted correlation network analysis, we identified CYTOR as an EMT-related lncRNA associated with AMD. Experimental validation revealed that CYTOR orchestrates TGF-β1-induced EMT, as well as proliferation and migration of ARPE-19 cells. Further investigation demonstrated the involvement of CYTOR in regulating the WNT5A/NFAT1 pathway and NFAT1 intranuclear translocation in the ARPE-19 cell EMT model. Mechanistically, CHIP, EMSA and dual luciferase reporter assays confirmed NFAT1's direct binding to CYTOR's promoter, promoting transcription. Reciprocally, CYTOR overexpression promoted NFAT1 expression, while NFAT1 overexpression increased CYTOR transcription. These findings highlight a mutual promotion between CYTOR and NFAT1, forming a positive feedback loop that triggers the EMT phenotype in ARPE-19 cells. These discoveries provide valuable insights into the molecular mechanisms of EMT and its association with AMD, offering potential avenues for targeted therapies in EMT-related conditions, including AMD.

The effects of exercise on epigenetic modifications: focus on DNA methylation, histone modifications and non-coding RNAs

Physical activity on a regular basis has been shown to bolster the overall wellness of an individual; research is now revealing that these changes are accompanied by epigenetic modifications. Regular exercise has been proven to make intervention plans more successful and prolong adherence to them. When it comes to epigenetic changes, there are four primary components. This includes changes to the DNA, histones, expression of particular non-coding RNAs and DNA methylation. External triggers, such as physical activity, can lead to modifications in the epigenetic components, resulting in changes in the transcription process. This report pays attention to the current knowledge that pertains to the epigenetic alterations that occur after exercise, the genes affected and the resulting characteristics.

The RNA world: from experimental laboratory to "in silico" approach. Part 1: User friendly RNA expression databases portals

Cellular information about "life instruction" is stored, transferred, and modified using different types of RNA molecules. During the last decades, a growing number of RNA data has been generated thanks to the development of microarray chips and next-generation sequencing (NGS) methods. Improvement of bioinformatics contributed to the discovery of many types of new non-coding RNAs (ncRNAs), mostly with regulatory functions that supplemented the knowledge about the world of RNA. All of it, as well as the Human Genome Project (HGP) and the Cancer Genome Atlas (TCGA) project, has resulted in the formation of data storage and analysis portals which are widely used in cancer research and moved science from in vitro to in silico research. In this review we presented and discussed the data storage and analysis portals used by us, such as cBioPortal, UALCAN, ENCORI, and others. During the revision of these sites, we paid attention to data integration, simplicity of analysis, and results visualization, which are important for users without bioinformatic or statistical skills. In our opinion, the RNA analysis online tools will rapidly develop during the next decade and it seems to be a way for personalization of cancer treatment.