The multidimensional mechanisms of long noncoding RNA function

LncRNA XIST inhibits mitophagy and increases mitochondrial dysfunction by promoting BNIP3 promoter methylation to facilitate the progression of KBD

The primary mechanisms underlying cartilage destruction in Kashin-Beck disease (KBD) involve excessive chondrocyte death and extracellular matrix (ECM) degradation. While long non-coding RNA XIST (lncRNA XIST) has been implicated in promoting chondrocyte injury in osteoarthritis (OA), its role in KBD-related chondrocyte injury remains poorly understood. In this study, joint tissues were collected from four healthy and four KBD-affected children, as well as five healthy and five KBD-affected adults, to assess the expression of lncRNA XIST. The results revealed a significant upregulation of lncRNA XIST in the cartilage tissues of KBD patients. To model KBD-induced chondrocyte damage in vitro, hypertrophic ATDC5 cells were exposed to 10 ng/ml T-2 toxin for 24 hours, which resulted in increased lncRNA XIST expression. Silencing lncRNA XIST was found to mitigate T-2 toxin-induced ECM degradation and chondrocyte apoptosis by alleviating defects in mitochondrial autophagy and dysfunction. Mechanistically, lncRNA XIST promoted the methylation of the BNIP3 promoter by recruiting DNA methyltransferases (DNMTs) to the BNIP3 promoter region, thereby suppressing BNIP3-mediated mitophagy and exacerbating mitochondrial dysfunction. To establish a KBD rat model, rats were fed a low-selenium diet supplemented with T-2 toxin for four weeks. Knockdown of lncRNA XIST in these rats attenuated articular cartilage damage and apoptosis, while enhancing collagen II expression. In conclusion, lncRNA XIST accelerates KBD progression by inhibiting mitophagy and promoting mitochondrial dysfunction through increased BNIP3 promoter methylation.

A review on the lncRNA-miRNA-mRNA regulatory networks involved in inflammatory processes in Alzheimer's disease

Alzheimer's disease is a progressive neurodegenerative condition that is the most frequent reason for dementia. Due to the increasing trend of aging in societies, it will place a large social and financial burden on society. Although beta amyloid plaques and the formation of neurofibrillary tangles are mentioned as the main events in this disorder, the exact molecular pathology and inflammatory regulatory networks involved in neuroinflammatory events, as a fundamental pathogenic mechanism remain unknown. Understanding these molecular network pathways in addition to helping to understand the pathogenesis of Alzheimer's disease, can also help in the early diagnosis as well as the control of inflammatory processes that are involved in its progression. So, in this study, we intend to have an overview on the regulatory lncRNAs of Alzheimer's disease and their related miRNA and mRNAs, as well as the relationship of these regulatory pathways with inflammatory processes, so that we can provide a perspective for future studies in the field of diagnosis and possibly treatment of this disorder.

Machine learning identifies SRD5A3 as a propionate-related prognostic biomarker in triple-negative breast cancer

The increased risk of recurrence and metastasis are obstacles to treating TNBC. Propionate-related genes play an important role in tumor development and immune cell infiltration. The study was to identify the association between propionate-related genes and the prognosis of TNBC patients. Propionate-related genes were collected and analyzed to establish propionate-related gene characteristics. Then, the survival analysis was performed, and the responses to immunotherapies were evaluated. Furthermore, the drug sensitivity of some traditional chemotherapeutic drugs was evaluated. Finally, the hub genes were discovered and validated by in vitro experiments. Based on the five-propionate-related gene signature, TNBC patients were divided into high and low-risk groups. In addition, DEGs between the different risk groups were enriched in the biological activities associated with immunity. TNBC patients in the high-risk groups were suggested to have worse responses to immunotherapies and a poorer prognosis. SRD5A3 was finally found to be a hub gene, and in vitro experiments revealed that silencing SRD5A3 inhibited tumor cell proliferation, invasion, and migration. The five-propionate-related risk model presented novel insights into the efficacy of immunotherapy. It was found that down-regulation of SRD5A3 inhibited the growth and invasion of tumor cells, thereby affecting the prognosis of TNBC.

Macrophage polarization in hepatocellular carcinoma: a lncRNA-centric perspective on tumor progression and metastasis

Hepatocellular carcinoma (HCC) represents a multifaceted and aggressive cancer frequently associated with chronic inflammation and immune cell activation. The pathogenesis of HCC is influenced by a variety of factors such as long non-coding RNAs (lncRNAs). LncRNAs, a significant class of non-coding RNAs, contribute to the intricate nature of the transcriptome and are extensively distributed across various tissues and cell types in mammals. In HCC, these transcripts are crucial not only for deepening our molecular understanding but also for advancing clinical outcomes, as they serve as both oncogenes and tumor suppressors by dysregulating essential genes and signaling pathways. Additionally, macrophage polarization is crucial in HCC tumor progression. The study explores the role of lncRNAs in hepatocellular carcinoma (HCC) and elucidates the specific molecular mechanisms by which key lncRNAs such as HULC and MALAT1 regulate macrophage polarization in the tumor microenvironment. These lncRNAs modulate cytokine profiles and influence immune regulators including IL-10 and TGF-β, steering macrophages toward an M2-like, pro-tumor phenotype that fosters aggressive tumor characteristics and progression. Mechanistically, these transcripts interact with epigenetic modifiers like EZH2 to alter histone modifications and chromatin accessibility, while also stabilizing mRNAs that encode inflammatory mediators, thereby reinforcing an immunosuppressive response. The clinical implications of these findings are substantial. The detection of such lncRNAs in patient samples offers a minimally invasive diagnostic avenue, while their pivotal role in complex immune cell behavior positions them as promising prognostic biomarkers. Moreover, targeting these lncRNAs may lead to innovative therapeutic strategies aimed at disrupting tumor-supportive inflammatory cascades and restoring an effective antitumor immune response. Understanding the intricate interplay between lncRNA-mediated epigenetic regulation and macrophage polarization not only refines our grasp of HCC progression but also opens new pathways for interventions designed to improve patient outcomes.

Phenylacetylglutamine produced from injury lung alveolar epithelial cells promotes the function of BMSCs by regulating NONRATT006276.2/Mapt pathway

Mesenchymal stem cell (MSC)-based therapy regenerates damaged structures of the respiratory system and restores lung function, thus providing a promising therapeutic approach for chronic obstructive pulmonary disease. Understanding the communication between injured alveolar cells and MSCs can improve the efficiency of MSC-based therapies. The present study analyzed the untargeted metabolomics of the supernatant of AEC-II injury induced by cigarette smoke extract and identified 205 differential metabolites. Phenotypic assays indicated that phenylacetylglutamine (PAG) significantly promoted the migration and mitochondrial function of bone marrow MSCs (BMSCs). Whole-transcriptome sequencing (WT-seq) was used to analyze the long noncoding RNA (lncRNA) and mRNA expression profiles of BMSCs treated with PAG. The upregulated lncNRA NONRATT006276.2 (NRT6276.2) and its trans-regulated gene, microtubule-associated protein tau (Mapt), were identified based on the lncRNA-mRNA co-expression network and bioinformatics analysis. The knockdown of NRT6276.2 or Mapt inhibited the positive effects of PAG on BMSCs. Furthermore, Mapt overexpression reversed the phenotype of BMSCs inhibited by silencing NRT6276.2. In conclusion, PAG enhanced the migration and mitochondrial function of BMSCs by regulating the NRT6276.2/Mapt pathway. This study clarified the positive effects of PAG produced by injured lung cells on transplanted MSCs, providing a potential new strategy to enhance the efficiency of MSC-based therapies.

Long non-coding RNAs in bipolar disorder

Bipolar disorder is characterized by alternating episodes of mania or hypomania and depression, encompassing various forms such as cyclothymia, bipolar I disorder, and bipolar II disorder. Manic periods present with increased energy and decreased sleep, whereas depressive episodes involve poor energy and extended sleep duration. Despite the availability of treatments, approximately 30% of patients with bipolar disorder are drug resistant and require alternative strategies. Recent research highlights the role of long noncoding RNAs (lncRNAs) as potential biomarkers for bipolar disorder, aiding in distinguishing it from other mood disorders and improving diagnostic accuracy. LncRNAs such as GAS5 and FOXD3-AS1 are downregulated in bipolar disorder patients, suggesting their utility as diagnostic tools. LncRNAs regulate gene expression through interactions with DNA, RNA, and proteins, influencing various biological processes. Studies have identified several lncRNAs linked to bipolar disorder, including lincRNA-p21, lincRNA-ROR, and lincRNA-PINT. These findings underscore the potential of lncRNAs as biomarkers and therapeutic targets, facilitating more personalized treatment strategies. This review explores the diagnostic and therapeutic potential of lncRNAs in bipolar disorder, aiming to enhance the current understanding and management of this condition.

Profiling Long Noncoding RNA in Psoriatic Skin Using Single-Cell RNA Sequencing

The expressions of long noncoding RNAs (lncRNAs) and their roles in epidermal differentiation have been previously defined using bulk RNA sequencing. Despite their tissue-specific expression profiles, most lncRNAs are not well-annotated at the single-cell level. In this study, we evaluated the use of single-cell RNA sequencing to profile and characterize lncRNAs using data from 6 patients with psoriasis with paired uninvolved and lesional psoriatic skin. Despite their overall lower expression, we were able to detect >7000 skin-expressing lncRNAs and their cellular sources. Differential gene expression analysis revealed 137 differentially expressed lncRNAs in lesional psoriasis skin and identified 169 cell-type-specific lncRNAs. Keratinocytes had the highest number of differentially expressed lncRNA in psoriatic skin, which we validated using spatial transcriptomic data. We further showed that expression of the keratinocyte-specific lncRNA, AC020916.1, upregulated in lesional skin, is significantly correlated with expressions of genes participating in cell proliferation/epidermal differentiation, including SPRR2E and transcription factor ZFP36, particularly in the psoriatic skin. Our study highlights the potential for using single-cell RNA sequencing to profile skin-expressing lncRNA transcripts and to infer their cellular origins, providing a crucial approach that can be applied to the study of other inflammatory skin conditions.

Construction and significance of a breast cancer prognostic model based on cuproptosis-related genotyping and lncRNAs

BACKGROUND/PURPOSE

Cuproptosis may play a significant role in breast cancer (BC). We aimed to investigate the prognostic impact of cuproptosis-related lncRNAs in BC.

METHODS

Consensus clustering analysis categorized TCGA-BRCA samples into 3 clusters, followed by survival and immune analyses of the 3 clusters. LASSO-COX analysis was performed on cuproptosis-related lncRNAs differentially expressed in BC to construct a BC prognostic model. Gene Ontology/Kyoto Encyclopedia of Genes and Genomes (GO/KEGG) enrichment, immune, and drug prediction analyses were performed on the high-risk and low-risk groups. Cell experiments were conducted to analyze the results of drug prediction and two cuproptosis-related lncRNAs (AC104211.1 and LINC01863).

RESULTS

Significant differences were observed in survival outcomes and immune infiltration levels among the three clusters (p < 0.05). The validation of the model showed significant differences in survival outcomes between the high-risk and low-risk groups in both the training and validation sets (p < 0.05). Differential mRNAs between the two groups were significantly enriched in the Neuroactive ligand-receptor interaction and cAMP signaling pathway. Additionally, significant differences were found in immune infiltration levels, human leukocyte antigen (HLA) expression, Immunophenoscore (IPS) scores, and Tumor Immune Dysfunction and Exclusion (TIDE) scores between the two groups (p < 0.05). Drug prediction and corresponding cell experimental results showed that Trametinib, 5-fluorouracil, and AICAR significantly inhibited the viability of MCF-7 cells (p < 0.05). AC104211.1 and LINC01863 were found to impact the proliferation of BC cells.

CONCLUSION

The risk-scoring model obtained in this study may serve as a robust prognostic biomarker, potentially aiding in clinical decision-making for BC patients.

Long noncoding RNA PARAL1 regulates myeloid dendritic cell differentiation and TLR signaling

Dendritic cells (DCs) are professional antigen presentation cells (APCs) that bridge innate and adaptive immune functions to contain pathogenic threats. Long noncoding RNAs (lncRNAs) are implicated in regulating biological processes, including inflammation and immunity. However, the knowledge of myeloid DC-expressed lncRNA repertoire and their regulatory functions is limited. Here we profiled lncRNA expression kinetics during monocyte-to-DC (moDC) differentiation and characterized their functional roles. Our RNA-seq data identified a repertoire of differentially expressed lncRNAs associated with moDC differentiation and a large subset of these lncRNAs are distinct from M1 or M2 macrophages. We selected two DC-enriched lncRNAs and observed that PARAL1 silencing, or overexpression modulates DC surface markers expression. Importantly, PARAL1 RNAi significantly reduced, while its overexpression upregulated the levels of multiple TLRs. Upon treatment with TLR agonists PARAL1 knockdown cells exhibit reduced NF-κB, IRF3 and IRF7 phosphorylation substantiating its role in potentiating TLR signaling. Mechanistically, PARAL1 silencing showed significant downregulation of multiple NF-κB-induced genes and time-dependent inhibition of proinflammatory cytokine secretion upon challenge with TLR agonists. Finally, PARAL1 RNAi in DCs significantly impaired antigen processing and presentation to T cells. Overall, this study characterized novel functions of PARAL1 in regulating DC differentiation, TLR-dependent innate immunity and activation of adaptive immune response.

Epigenetic and epitranscriptomic role of lncRNA in carcinogenesis (Review)

Long non‑coding RNAs (lncRNAs) are key players in the regulation of gene expression by mediating epigenetic and epitranscriptomic modification. Dysregulation of lncRNAs is implicated in tumor initiation, progression and metastasis. lncRNAs modulate chromatin structure and gene transcription by recruiting epigenetic regulators, including DNA‑ or histone‑modifying enzymes. Additionally, lncRNAs mediate chromatin remodeling and enhancer‑promoter long‑range chromatin interactions to control oncogene expression by recruiting chromatin organization‑associated proteins, thereby promoting carcinogenesis. Furthermore, lncRNAs aberrantly induce oncogene expression by mediating epitranscriptomic modifications, including RNA methylation and RNA editing. The present study aimed to summarize the regulatory mechanisms of lncRNAs in cancer to unravel the complex interplay between lncRNAs and epigenetic/epitranscriptomic regulators in carcinogenesis. The present review aimed to provide a novel perspective on the epigenetic and epitranscriptomic roles of lncRNAs in carcinogenesis to facilitate identification of potential biomarkers and therapeutic targets for cancer diagnosis and treatment.

Harnessing the Role of ESR1 in Breast Cancer: Correlation with microRNA, lncRNA, and Methylation

Breast cancer (BC) is a multifactorial condition and it primarily expresses the estrogen receptor α (ERα) that is encoded by the gene estrogen receptor 1 (ESR1), which modulates estrogen signaling. ESR1, by facilitating estrogen overproduction, plays an indispensable role in the progression and survival of the majority of BCs. To obtain molecular insights into these phenomena, we analyzed The Cancer Genome Atlas (TCGA) breast invasive carcinoma (BRCA) RNA-Seq datasets for the expression of ESR1 and its correlation to microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), along with its methylation patterns. Regulation of ESR1 was also assessed with a total of 43 cancerous and non-cancerous breast cell lines. Analyses of both TCGA BRCA and breast cell line RNA-Seq data revealed that specific lncRNAs, i.e., MEG3, BIK, MLL, and FAS are negatively correlated with the ESR1, in which PARP1 demonstrates a positive association. Additionally, both miR-30a and miR-145 showed negative correlations with the ESR1 expression. Of the 54 ESR1 methylation loci analyzed, the majority of them exhibited a negative correlation with the ESR1 expression, highlighting a potentially modifiable regulatory mechanism. These findings underscore the complex regulatory events influencing ESR1 expression and its interaction with diverse signaling pathways, demonstrating novel insights into breast pathogenesis and its potential therapeutics.

The NcRNA/Wnt axis in lung cancer: oncogenic mechanisms, remarkable indicators and therapeutic targets

Early diagnosis of lung cancer (LC) is challenging, treatment options are limited, and treatment resistance leads to poor prognosis and management in most patients. The Wnt/β-catenin signaling pathway plays a vital role in the occurrence, progression, and therapeutic response of LC. Recent studies indicate that non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) function as epigenetic regulators that can promote or inhibit Wnt/β-catenin signaling by interacting with Wnt proteins, receptors, signaling transducers, and transcriptional effectors, thereby affecting LC cell proliferation, metastasis, invasion, and treatment resistance. Deepening our understanding of the regulatory network between ncRNAs and the Wnt/β-catenin signaling pathway will help overcome the limitations of current LC diagnosis and treatment methods. This article comprehensively reviews the regulatory mechanisms related to the functions of ncRNAs and the Wnt/β-catenin pathway in LC, examining their potential as diagnostic and prognostic biomarkers and therapeutic targets, aiming to offer new promising perspectives for LC diagnosis and treatment.

EGFR-induced lncRNA TRIDENT promotes drug resistance in non-small cell lung cancer via phospho-TRIM28-mediated DNA damage repair

Long noncoding RNAs (lncRNAs) play numerous roles in cellular biology and alterations in lncRNA expression profiles have been implicated in a variety of cancers. Here, we identify and characterize a lncRNA, TRIM28 Interacting DNA damage repair Enhancing Noncoding Transcript (TRIDENT), whose expression is induced upon epithelial growth factor receptor (EGFR) activation, and which exerts pro-oncogenic functions in EGFR-driven non-small cell lung cancer. Knocking down TRIDENT leads to decreased tumor-cell proliferation in both in vitro and in vivo model systems and induces sensitization to chemotherapeutic drugs. Using ChIRP-MS analysis we identified TRIM28 as a protein interactor of TRIDENT. TRIDENT promotes phosphorylation of TRIM28 and knocking down TRIDENT leads to accumulation of DNA damage in cancer cells via decreased TRIM28 phosphorylation. Altogether, our results reveal a molecular pathway in which TRIDENT regulates TRIM28 phosphorylation to promote tumor cell growth and drug resistance. Our findings suggest that TRIDENT can be developed as a biomarker or therapeutic target for EGFR mutant non-small cell lung cancer.

Comprehensive identification of hub mRNAs and lncRNAs in colorectal cancer using galaxy: an in silico transcriptome analysis

Colorectal cancer (CRC) is the second leading cause of cancer-related mortality. Using the Galaxy platform, the present study aimed to assess the differentially expressed genes (DEGs) in CRC patients. The expression data was obtained from the Gene Expression Omnibus database (GSE137327). DEGs were analyzed using Gene Ontology (GO) and GeneMANIA databases to detect the most critical biological pathways and processes. Protein-Protein Interaction Studies (PPIS) identified four hub genes (CCN1, CCL2, FLNC, MYH11). This article presents findings on three mRNAs (CEMIP, MMP7, and DPEP1) and also two notable lncRNAs, EVADR and DLX6-AS1, that have an impact on CRC pathogenesis and play a role in the epithelial-mesenchymal transition in tumor cells. The identified genes and lncRNAs are putative therapeutic targets and diagnostic markers. For instance, CRISPR/Cas9 editing systems can be designed in order to modulate expression of these genes, or edit them for the purpose of inducing sensitivity to conventional therapies. Besides, these genes can be incorporated into clinical prognostic models, offering panels of genes to choose appropriate personalized methods of treatment. Together, these genes represent novel markers and possible therapeutic targets for CRC.

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.

A novel lncRNA enhances autophagy to suppress extracellular matrix via modulating TP53INP1 in human trabecular meshwork cells under oxidative stress

Primary open-angle glaucoma (POAG) can result in irreversible blindness. As an important etiological factor, oxidative stress can elicit extraordinary increase of extracellular matrix (ECM) in trabecular meshwork-schlemm canal, to increase aqueous humor outflow resistance and elevate intraocular pressure. Although autophagy plays an important role in clearing ECM, the functions of long non-coding RNAs (lncRNAs) in autophagy induced by oxidative stress in human trabecular meshwork cells (HTMCs) remain unclear. In our study, oxidative stress induced the expression of ECM and autophagy in TMCs after H2O2 treatment. Meanwhile, a novel lncRNA ENST00000523905 and tumor protein 53-induced nuclear protein 1 (TP53INP1) were elevated in TMCs treated with H2O2. Similar to treatment with 3-MA (an inhibitor of autophagy), knocking-down the expression of TP53INP1 or ENST00000523905 could suppress the autophagy of TMCs induced by H2O2, which increased the level of ECM. Furthermore, the inhibition of ENST00000523905 decreased the expression of TP53INP1. ENST00000523905 could recruit and directly bind with CCAAT/enhancer (C/EBPβ), which can promote the expression of TP53INP1. Taken together, our findings demonstrated that ENST00000523905 may increase autophagy via enhancing TP53INP1 expression through binding with C/EBPβ, resulting in oxidative stress-induced decrease in ECM in HTMCs.

MALAT1 is important for facilitating HIV-1 latency reversal in latently infected monocytes

Long non-coding RNAs (lncRNAs) are long RNA transcripts with length >200 nucleotides that do not encode proteins. They play a crucial role in regulating HIV-1 infection, yet their involvement in myeloid cells remains underexplored. Myeloid cells are susceptible to HIV infection and contribute substantially to the latent HIV reservoir. Therefore, disruption of latency within these reservoirs is crucial for achieving a definite cure. In this study, we aimed to ascertain the role of MALAT1 lncRNA in reversal of HIV-1 latency. Latently HIV-infected cell line, U1 was treated with SAHA, followed by qRT-PCR assays to confirm HIV-1 reactivation, and MALAT1 expression was assessed. The in vitro experiments revealed a significant increase in MALAT1 expression following latency reactivation and HIV-1 infection, while its knockdown using siRNA resulted in suppression of HIV transcription, which implies that MALAT1 play a significant role in facilitating the reversal of HIV-1 latency by promoting HIV transcription. Clinical samples were analysed to measure MALAT1 and pro-inflammatory cytokines expression. The elevated MALAT1 expression in treatment-naïve subjects compared to those on ART and HIV-negative controls suggests its association with HIV replication. Moreover, correlation analysis revealed a positive association between MALAT1 expression and pro-inflammatory cytokines, TNF-α and IP-10. To conclude, MALAT1 lncRNA emerged as a crucial facilitator of HIV-1 latency reversal in latently infected monocytes by inducing the expression of pro-inflammatory factors. These findings highlight that MALAT1 could potentially be explored as the therapeutic intervention to reactivate latent cells in monocytes.

LncRNA MEG9 Promotes Inflammation and Liver Fibrosis Through S100A9 in Biliary Atresia

BACKGROUND

The pathogenesis of biliary atresia (BA) remains elusive. We aimed to investigate the role of long noncoding RNA (lncRNA) MEG9 in BA.

METHODS

LncRNA microarray was conducted to identify differentially expressed lncRNAs in three BA and three para-hepatoblastoma liver tissues. RT-qPCR validated the results. Human intrahepatic bile duct epithelial cells (HIBECs) were stably transfected with lncRNA MEG9 knockdown/overexpression to investigate its cellular localization and function. RNA sequencing (RNA-seq), differentially expressed genes (DEGs) analysis and gene set enrichment analysis were applied to MEG9-overexpresed HIBECs. RNA pull-down and mass spectrometry explored the interacting protein of MEG9, while clinical information was reviewed.

RESULTS

436 differentially expressed lncRNAs were identified, with MEG9 highly upregulated in BA. RT-qPCR further confirmed MEG9's overexpression in BA and diagnostic potential (AUC = 0.9691). MEG9 was predominantly located in the nucleus and significantly promoted cell proliferation and migration. RNA-seq revealed inflammation- and extracellular matrix-related pathways enriched in MEG9-overexpressing HIBECs, with upregulated cytokine genes like CXCL6 and IL6. MMP-7 and collagen I were also overexpressed. Furthermore, 38 proteins were identified to specifically interact with MEG9, and S100A9 was highly expressed in cell models. S100A9 was also significantly upregulated in BA liver tissue and correlated with MEG9 expression (r = 0.313, p < 0.05), albumin level (r = -0.349, p < 0.05), and platelet level (r = -0.324, p < 0.05).

CONCLUSION

MEG9 influences cholangiocyte proliferation, migration, and cytokine production, potentially regulating BA inflammation and fibrosis via S100A9 interaction.

The triple code model for advancing research in rare and undiagnosed diseases beyond the base pairs

Rare and undiagnosed diseases pose significant challenges for understanding their mechanisms, diagnosis, and treatment. The Triple Code Model, an integrative paradigm described here, considers the combined influence of the genetic code, epigenetic code, and nuclear structure (an emerging code), as fundamental biochemical mechanisms underlying many rare diseases. Studies demonstrate dysfunctional membrane and cytoplasmic signals instruct the epigenome to ultimately impact the 3D structure and dynamics of the nucleus, highlighting their close interrelationships. Consequently, this model offers a holistic perspective on rare and undiagnosed diseases by moving beyond a solely genetic view. We propose that this integrated framework will efficiently guide rare disease research by taking it 'Beyond the Base Pairs,' leading to improved diagnostics and personalized treatments.

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.

MicroRNA functions in osteogenic differentiation of periodontal ligament stem cells: a scoping review

This scoping review aimed to describe the differential microRNA (miRNA) functions in osteogenic differentiation of periodontal ligament stem cells (PDLSCs), and then analyze the potential of applying PDLSCs and miRNAs in bone regeneration. The databases of PubMed, Google Scholar and EBSCO search were performed by the 4 themes, including periodontal ligament stem cells, miRNA, osteogenic differentiation, and tissue regeneration. The original articles described miRNA functions in osteogenic differentiation of PDLSCs were identified and selected for content analyze. The articles suggested that PDLSCs have high potential in bone regeneration because of their multipotency and immunomodulation. PDLSCs are conveniently accessible and obtained from extracted teeth. However, recent evidence reported that PDLSCs of various origins demonstrate differential characteristics of osteogenic differentiation. Exosomal miRNAs of PDLSCs demonstrate a regulatory role in tissue regeneration. The properties of PDLSCs associated to miRNA functions are altered in differential microenvironmental conditions such as infection, inflammation, high-glucose environment, or mechanical force. Therefore, these factors must be considered when inflamed PDLSCs are used for tissue regeneration. The results suggested inflammation-free PDLSCs harvested from the middle third of root surface provide the best osteogenic potential. Alternatively, the addition of miRNA as a bioactive molecule also increases the success of PDLSCs therapy to enhance their osteogenic differentiation. In conclusion, Exosome-derived miRNAs play a key role in PDLSCs osteogenic differentiation during tissue regeneration. While the success of PDLSCs in tissue regeneration could be uncertain by many factors, the use of miRNAs as an adjunct is beneficial for new bone regeneration.

OTUD6B-AS1: a multifaceted regulator of cancer with critical clinical implications

OTU Deubiquitinase 6B-Antisense Transcript 1 (OTUD6B-AS1), a novel long non-coding RNA (lncRNA), has recently emerged as a critical regulator in various tumors. Current research underscores its dual functionality, acting either as an oncogene or a tumor suppressor depending on the tumor context. In this work, we compile and discuss findings from a range of studies investigating the expression patterns of OTUD6B-AS1 in different cancers and its consequent effects on tumor behavior, both in vitro and in vivo. We delve into the mechanisms through which OTUD6B-AS1 influences cancer initiation and progression, focusing on its role in regulating essential cellular processes such as cell growth, migration, invasion, angiogenesis, ferroptosis, and treatment resistance. Operating through complex interactions with microRNAs (miRNAs), proteins, and pivotal signaling pathways - most notably Wnt/β-catenin - OTUD6B-AS1 exhibits variable roles across cancer types and cellular environments. Additionally, we assess the clinical relevance of OTUD6B-AS1 expression levels, evaluating its potential as a biomarker for cancer prognosis and diagnosis, as well as a target for therapeutic intervention. By consolidating existing knowledge, this work aims to highlight the clinical implications of OTUD6B-AS1 and encourage further research in oncology, ultimately contributing to the advancement of targeted cancer therapies.

Integrative Analysis of Whole-Genome and Transcriptomic Data Reveals Novel Variants in Differentially Expressed Long Noncoding RNAs Associated with Asthenozoospermia

Background/Objectives: Asthenozoospermia, characterized by reduced sperm motility, is a common cause of male infertility. Emerging evidence suggests that noncoding RNAs, particularly long noncoding RNAs (lncRNAs), play a critical role in the regulation of spermatogenesis and sperm function. Coding regions have a well-characterized role and established predictive value in asthenozoospermia. However, this study was designed to complement previous findings and provide a more holistic understanding of asthenozoospermia, this time focusing on noncoding regions. This study aimed to identify and prioritize variants in differentially expressed (DE) lncRNAs found exclusively in asthenozoospermic men, focusing on their impact on lncRNA structure and lncRNA-miRNA-mRNA interactions. Methods: Whole-genome sequencing (WGS) was performed on samples from asthenozoospermic and normozoospermic men. Additionally, an RNA-seq dataset from normozoospermic and asthenozoospermic individuals was analyzed to identify DE lncRNAs. Bioinformatics analyses were conducted to map unique variants on DE lncRNAs, followed by prioritization based on predicted functional impact. The structural impact of the variants and their effects on lncRNA-miRNA interactions were assessed using computational tools. Gene ontology (GO) and KEGG pathway analyses were employed to investigate the affected biological processes and pathways. Results: We identified 4173 unique variants mapped to 258 DE lncRNAs. After prioritization, 5 unique variants in 5 lncRNAs were found to affect lncRNA structure, while 20 variants in 17 lncRNAs were predicted to disrupt miRNA-lncRNA interactions. Enriched pathways included Wnt signaling, phosphatase binding, and cell proliferation, all previously implicated in reproductive health. Conclusions: This study identifies specific variants in DE lncRNAs that may play a role in asthenozoospermia. Given the limited research utilizing WGS to explore the role of noncoding RNAs in male infertility, our findings provide valuable insights and a foundation for future studies.

Lnc-Pim1 Promotes Neurite Outgrowth and Regeneration of Neuron-Like Cells Following ACR-Induced Neuronal Injury

Decreased regenerative capacity of central nervous system neurons is the main cause for failure of damaged neuron regeneration and functional recovery. Long noncoding RNAs (lncRNAs) are abundant in mammalian transcriptomes, and many time- and tissue-specific lncRNAs are thought to be closely related to specific biological functions. The promoting effect of Pim-1 gene on neural differentiation and regeneration has been documented, but the effect and mechanism of its neighbor gene Lnc-Pim1 in regulating the response of central neurons to injury remain unclear. RT-PCR in this study demonstrated that the expression of Lnc-Pim1 was upregulated in acrylamide (ACR)-induced neuronal injury. FISH and nucleus-cytoplasmic assay demonstrated that Lnc-Pim1 was mainly expressed in the neuron cytoplasm, with a small amount in the nucleus. Western blot analysis proved that Lnc-Pim1 overexpression induced by the lentivirus vector could promote neurite outgrowth in Neuro-2a cells by activating the Erk1/2 signal pathway, and improve neurite regeneration of injured neurons by upregulating GAP-43 and β-Ⅲ tubulin protein expression. However, silencing Lnc-Pim1 expression by interfering RNA could effectively downregulate the GAP-43 and β-Ⅲ tubulin protein expression, and inhibit neurite growth of neurons. In addition, CHIRP-MS was performed to identify several potential targets of Lnc-Pim1 involved in the regulation of neurite regeneration of injured neurons. In conclusion, our study demonstrated that Lnc-Pim1 is a potential lnc-RNA, playing an important role in regulating central nerve regeneration.

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).

LINC00667: A Novel Vital Oncogenic LincRNA

Long intergenic noncoding RNAs (lincRNAs) have a variety of properties that differ from those of messenger RNAs (mRNAs) encoding proteins. Long intergenic nonprotein coding RNA 667 (LINC00667) is a non-coding transcript located on chromosome 18p11.31. Recently, many studies have found that LINC00667 can enhance the progression of various cancers and play a key part in a lot of diseases, such as tumorigenesis. Therefore, LINC00667 can be recognized as a potential biomarker and therapeutic target. So, we reviewed the biological functions, relevant mechanisms, as well as clinical significance of LINC00667 in several human cancers in detail.

Computational Prediction of Gene Regulation by lncRNAs

High-throughput sequencing technologies and innovative bioinformatics tools discovered that most of the genome is transcribed into RNA. However, only a fraction of the RNAs in cell translates into proteins, while the majority of them are categorized as noncoding RNAs (ncRNAs). The ncRNAs with more than 200 nt without protein-coding ability are termed long noncoding RNAs (lncRNAs). Hundreds of studies established that lncRNAs are a crucial RNA family regulating gene expression. Regulatory RNAs, including lncRNAs, modulate gene expression by interacting with RNA, DNA, and proteins. Several databases and computational tools have been developed to explore the functions of lncRNAs in cellular physiology. This chapter discusses the tools available for lncRNA functional analysis and provides a detailed workflow for the computational analysis of lncRNAs.

The novel role of LOC344887 in the enhancement of hepatocellular carcinoma progression via modulation of SHP1-regulated STAT3/HMGA2 signaling axis

Pseudogene-derived long non-coding RNAs (lncRNAs) have become crucial regulators in cancer progression. Extensive research highlights the pivotal role of signal transducer and activator of transcription 3 (STAT3) in promoting hepatocellular carcinoma (HCC) progression. As a result, targeting aberrant STAT3 activation presents a promising therapeutic strategy for HCC. Our study aims to identify the key pseudogene-derived lncRNA involved in modulating STAT3 activation and driving HCC progression. Our study is the first to identify a significant upregulation of LOC344887, a pseudogene-derived lncRNA, in HCC tissues. Elevated LOC344887 levels correlated with poor overall survival (OS) and recurrence-free survival (RFS), highlighting its potential as a biomarker for HCC. The rapid amplification of cDNA ends (RACE) and RT-PCR experiments revealed the expression of a novel LOC344887 transcript, named LOC344887-v2, alongside the annotated RefSeq transcript NR_151491 (LOC344887-v1) in both HCC tissues and hepatoma cell lines. Functional assays demonstrated that LOC344887 enhances cellular migration and invasion, with its variant LOC344887-v2 exhibiting a more pronounced effect. Further, LOC344887 mechanistically regulates STAT3 phosphorylation at tyrosine 705, which is crucial for maintaining STAT3 activation in HCC. Our findings unravel that LOC344887 not only physically interacts with p-STAT3 but also prevents its dephosphorylation by src homology region 2 domain-containing phosphatase 1 (SHP-1), thereby sustaining oncogenic signaling. In addition, we identified HMGA2 as a target of the LOC344887/SHP-1/STAT3 axis, with higher HMGA2 expression correlating with poorer prognosis in HCC patients. The ability of LOC344887 to regulate HMGA2 through direct binding of STAT3 to its promoter underlines its role in HCC progression. Collectively, these findings elucidate a novel oncogenic role of LOC344887 in HCC and suggest that targeting this lncRNA and its associated pathways may provide novel therapeutic strategies for improving patient outcomes in HCC.

Analysis of differential expression of hair follicle tissue transcriptome in Hetian sheep undergoing different periodic changes

Background

This study provides new information on long non-coding RNA (lncRNA) and messenger RNA (mRNA) expression profiles in the hair follicles of Hetian sheep via the sequencing and analysis of the transcriptome of skin hair follicles during three periods of periodicity change. This is important for improving the quality of carpet wool, providing a preliminary basis for further research on the targeting relationship of these mRNAs and their target genes, and providing a scientific basis for marker-assisted selection of Hetian sheep.

Methods

The periodic variation of anagen (P I, May, n = 3), catagen (p II, October, n = 3), and telogen (p III, January, n = 3) of the skin hair follicle tissue of three Hetian sheep ewes were selected. Skin samples were collected from the right mid-side of each sampled sheep at three hair follicle developmental stages. The three sheep were used for each developmental stage as biological and technical replicates for transcriptome sequencing and analysis.

Results

The statistical power of this experimental design, calculated in RNASeqPower, was 0.92. Differential expression analysis revealed 81 lncRNAs that were differentially expressed (46 up-regulated and 35 down-regulated) and 129 mRNAs that were differentially expressed (46 up-regulated and 83 down-regulated) during the PI and PII periods. Between the PI and PIII periods, a total of 144 differentially expressed lncRNAs and 693 differentially expressed mRNAs were identified. Of these, 73 lncRNAs were significantly up-regulated and 71 were significantly down-regulated, while 474 mRNAs were significantly up-regulated and 219 were down-regulated. Additionally, a total of 87 lncRNAs were found to be differentially expressed, with 40 up-regulated and 47 down-regulated, along with 39 differentially expressed mRNAs (23 up-regulated and 16 down-regulated), between the PII and PIII stages. The functional assessment revealed that the mRNA expressed in the cells is related to the membrane, cell processes, metabolism, extracellular region, and other GO items. It is enriched in thyroid hormone synthesis, choline metabolism, cancer, AMPK, Hedgehog, and other signaling pathways.

Conclusion

A total of 2,286 lncRNAs (including 965 known and 1,321 novel lncRNAs) and 20,879 mRNAs were identified. These co-expressed differentially expressed genes could be used as candidate genes for studying the periodic changes of the hair follicles in Hetian sheep.

Non-coding RNAs in bladder cancer, a bridge between gut microbiota and host?

In recent years, the role of gut microbiota (GM) in bladder cancer has attracted significant attention. Research indicates that GM not only contributes to bladder carcinogenesis but also influences the efficacy of adjuvant therapies for bladder cancer. Despite this, interventions targeting GM have not been widely employed in the prevention and treatment of bladder cancer, mainly due to the incomplete understanding of the complex interactions between the host and gut flora. Simultaneously, aberrantly expressed non-coding RNAs (ncRNAs) have been frequently associated with bladder cancer, playing crucial roles in processes such as cell proliferation, invasion, and drug resistance. It is widely known that the regulation of GM-mediated host pathophysiological processes is partly regulated through epigenetic pathways. At the same time, ncRNAs are increasingly regarded as GM signaling molecules involved in GM-mediated epigenetic regulation. Accordingly, this review analyzes the ncRNAs that are closely related to the GM in the context of bladder cancer occurrence and treatment, and summarizes the role of their interaction with the GM in bladder cancer-related phenotypes. The aim is to delineate a regulatory network between GM and ncRNAs and provide a new perspective for the study and prevention of bladder cancer.

LncRNA FAISL Inhibits Calpain 2-Mediated Proteolysis of FAK to Promote Progression and Metastasis of Triple Negative Breast Cancer

Triple negative breast cancer (TNBC) is the most aggressive subtype in breast tumors. When re-analyzing TCGA breast cancer dataset, we found cell adhesion molecules are highly enriched in differentially expressed genes in TNBC samples, among which Focal Adhesion Kinase (FAK) is most significantly associated with poor survival of TNBC patients. FAK is precisely modulated in the focal adhesion dynamics. To investigate whether lncRNAs regulate FAK signaling, we performed RNA immunoprecipitation sequencing and found FAISL (FAK Interacting and Stabilizing LncRNA) abundantly enriched in FAK-interacting lncRNAs and frequently overexpressed in TCGA TNBC tissues. FAISL promotes TNBC cell adhesion, cytoskeleton spreading, proliferation, and anchor-independent survival. FAISL doesn't affect FAK mRNA but positively regulates FAK protein level by blocking Calpain 2-mediated proteolysis. FAISL interacts with the C-terminus domain of FAK, whereby masks the binding site of Calpain 2 and prevents FAK cleavage. High level of FAISL correlates with FAK expression in tumor tissues and poor prognosis of TNBC patients. A siRNA delivery system targeting FAISL using reduction-responsive nanoparticles effectively inhibits tumor growth and metastasis in TNBC mouse models. Together, these findings uncover a lncRNA-mediated mechanism of regulating FAK proteolysis in the TNBC progression, and highlight the potential of targeting lncRNA FAISL for TNBC treatment.

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.

Long non-coding RNA (LncRNA) and epigenetic factors: their role in regulating the adipocytes in bovine

Investigating the involvement of long non-coding RNAs (lncRNAs) and epigenetic processes in bovine adipocytes can provide valuable new insights into controlling adipogenesis in livestock. Long non-coding RNAs have been associated with forming chromatin loops that facilitate enhancer-promoter interactions during adipogenesis, as well as regulating important adipogenic transcription factors like C/EBPα and PPARγ. They significantly influence gene expression regulation at the post-transcriptional level and are extensively researched for their diverse roles in cellular functions. Epigenetic modifications such as chromatin reorganization, histone alterations, and DNA methylation subsequently affect the activation of genes related to adipogenesis and the progression of adipocyte differentiation. By investigating how fat deposition is epigenetically regulated in beef cattle, scientists aim to unravel molecular mechanisms, identify key regulatory genes and pathways, and develop targeted strategies for modifying fat deposition to enhance desirable traits such as marbling and meat tenderness. This review paper delves into lncRNAs and epigenetic factors and their role in regulating bovine adipocytes while focusing on their potential as targets for genetic improvement to increase production efficiency. Recent genomics advancements, including molecular markers and genetic variations, can boost animal productivity, meeting global demands for high-quality meat products. This review establishes a foundation for future research on understanding regulatory networks linked to lncRNAs and epigenetic changes, contributing to both scholarly knowledge advancement and practical applications within animal agriculture.

A novel long non-coding RNA connects obesity to impaired adipocyte function

BACKGROUND

Long non-coding RNAs (lncRNAs) can perform tasks of key relevance in fat cells, contributing, when defective, to the burden of obesity and its sequelae. Here, scrutiny of adipose tissue transcriptomes before and after bariatric surgery (GSE53378) granted identification of 496 lncRNAs linked to the obese phenotype. Only expression of linc-GALNTL6-4 displayed an average recovery over 2-fold and FDR-adjusted p-value <0.0001 after weight loss. The aim of the present study was to investigate the impact on adipocyte function and potential clinical value of impaired adipose linc-GALNTL6-4 in obese subjects.

METHODS

We employed transcriptomic analysis of public dataset GSE199063, and cross validations in two large transversal cohorts to report evidence of a previously unknown association of adipose linc-GALNTL6-4 with obesity. We then performed functional analyses in human adipocyte cultures, genome-wide transcriptomics, and untargeted lipidomics in cell models of loss and gain of function to explore the molecular implications of its associations with obesity and weight loss.

RESULTS

The expression of linc-GALNTL6-4 in human adipose tissue is adipocyte-specific and co-segregates with obesity, being normalized upon weight loss. This co-segregation is demonstrated in two longitudinal weight loss studies and two cross-sectional samples. While compromised expression of linc-GALNTL6-4 in obese subjects is primarily due to the inflammatory component in the context of obesity, adipogenesis requires the transcriptional upregulation of linc-GALNTL6-4, the expression of which reaches an apex in terminally differentiated adipocytes. Functionally, we demonstrated that the knockdown of linc-GALNTL6-4 impairs adipogenesis, induces alterations in the lipidome, and leads to the downregulation of genes related to cell cycle, while propelling in adipocytes inflammation, impaired fatty acid metabolism, and altered gene expression patterns, including that of apolipoprotein C1 (APOC1). Conversely, the genetic gain of linc-GALNTL6-4 ameliorated differentiation and adipocyte phenotype, putatively by constraining APOC1, also contributing to the metabolism of triglycerides in adipose.

CONCLUSIONS

Current data unveil the unforeseen connection of adipocyte-specific linc-GALNTL6-4 as a modulator of lipid homeostasis challenged by excessive body weight and meta-inflammation.

Long non-coding RNA LINC-PINT is associated with favorable prognosis in cancer patients: a systematic review and meta-analysis

Background

There is growing evidence that long non-coding RNA long iatrogenic non-protein-coding RNA p53-induced transcript (LINC-PINT) is highly expressed in cancer tissue and is associated with the prognosis of cancer patients. The present study systematically analyzed the prognostic significance of LINC-PINT expression in cancer patients. We aimed to reveal the association between LINC-PINT expression and survival in cancer patients.

Methods

We collected eligible studies through the PubMed, Embase, and Cochrane library searches until February 1, 2024. We collected the following data from the enrolled studies: first author, publication year, country, cancer type, case number, cancer stage, detection method and cut-off value of LINC-PINT expression, follow-up period, and survival outcome. The prognostic significance of LINC-PINT expression was evaluated by conducting a meta-analysis. StataSE17 (Stata, College Station, TX, USA) was used for all analyses.

Results

Eleven eligible studies with 2,876 cancer patients were collected. The pooled results revealed that LINC-PINT expression was associated with favorable overall survival (OS) and disease-free survival (DFS) in cancer patients [for OS, hazard ratio (HR) =0.72, 95% confidence interval (CI): 0.64-0.80, P<0.001; for DFS, HR =0.70, 95% CI: 0.60-0.82, P<0.001].

Conclusions

LINC-PINT expression was associated with favorable OS and DFS, and it may serve as a valuable prognostic marker in cancer patients.

LINC00665 aggravates the malignant phenotypes in chondrosarcoma cells through miR-665/FGF9 pathway

Long non-coding RNAs (lncRNAs) have been demonstrated to participate in a variety of physiological and pathological processes, including tumor initiation and development. Nevertheless, few of them have been investigated in chondrosarcoma. Here, we were intended to unveil the role of long intergenic non-protein coding RNA 665 (LINC00665) in chondrosarcoma. RT-qPCR was adopted for gene expression detection. The biological processes in chondrosarcoma cells were detected by CCK-8, EdU, TUNEL, Transwell and wound healing assays. The relationships between genes in chondrosarcoma cells were evaluated by a series of mechanism experiments including RIP, luciferase reporter assays and so on.LINC00665 expressed at a high level in chondrosarcoma cell lines. LINC00665 interference suppressed cell proliferation, migration and invasion in chondrosarcoma. Besides, LINC00665 interacted with microRNA-665 (miR-665), which was then verified to be down-regulated in chondrosarcoma cells. Additionally, LINC00665 and miR-665 were mutually inhibited by each other in chondrosarcoma cells. Importantly, LINC00665 stimulated fibroblast growth factor 9 (FGF9) expression in chondrosarcoma cells via sponging miR-665. Furthermore, FGF9 participated in the regulation of LINC00665-promoted chondrosarcoma development. CONCLUSION: LINC00665 facilitates chondrosarcoma progression via miR-665/FGF9 axis, which might indicate a new path for the treatment of chondrosarcoma.

Resveratrol shields against cisplatin-induced ototoxicity through epigenetic lncRNA GAS5 modulation of miR-455-5p/PTEN pathway

BACKGROUND

Our previous research demonstrated that resveratrol counters DDP-induced ototoxicity by upregulating miR-455-5p, which targets PTEN. This study aimed to elucidate the underlying mechanisms involving GAS5 and DNA methyltransferase 1 (DNMT1) in resveratrol's protective action.

METHODS

A luciferase reporter assay and RNA immunoprecipitation (RIP) assay were employed to study the binding between GAS5 and miR-455-5p, as well as between miR-455-5p and PTEN. HEI-OC1 cells treated with DDP were transfected with vectors for GAS5, si-GAS5, DNMT1, si-DNMT1, and miR-455-5p mimics, as well as PTEN. Subsequently, they were treated with resveratrol and exposed to DDP, both separately and in combination. The distribution of CpG islands in the GAS5 promoter was identified using MethyPrimer, and methylation-specific PCR (MSP) was conducted to determine the methylation levels of GAS5. Chromatin immunoprecipitation (ChIP) was utilized to examine the interaction between DNMT1 and GAS5. The viability of HEI-OC1 cells, catalase (CAT) activity, apoptosis, and ROS levels were assessed using the CCK-8 assay, CAT assay, TUNEL staining, and flow cytometry, respectively. An in vivo mouse model was developed to measure auditory brainstem response (ABR) thresholds, while RT-qPCR and Western blot analysis were employed to evaluate molecular levels.

RESULTS

Our study discovered that GAS5 acts as a sponge for miR-455-5p, thereby increasing PTEN expression in DDP-treated HEI-OC1 cells. This process was reversed upon treatment with resveratrol. Importantly, DNMT1 promoted the methylation of the GAS5 promoter, leading to the suppression of GAS5 expression. This suppression enhanced the effectiveness of resveratrol in combating DDP-induced apoptosis and ROS in HEI-OC1 cells and amplified its protective effect against DDP's ototoxicity in vivo.

CONCLUSIONS

Our research emphasizes the significance of the DNMT1/GAS5/miR-455-5p/PTEN axis as a promising new route to boost resveratrol's effectiveness against DDP-induced ototoxicity.

Guidelines for mitochondrial RNA analysis

Mitochondria are the energy-producing organelles of mammalian cells with critical involvement in metabolism and signaling. Studying their regulation in pathological conditions may lead to the discovery of novel drugs to treat, for instance, cardiovascular or neurological diseases, which affect high-energy-consuming cells such as cardiomyocytes, hepatocytes, or neurons. Mitochondria possess both protein-coding and noncoding RNAs, such as microRNAs, long noncoding RNAs, circular RNAs, and piwi-interacting RNAs, encoded by the mitochondria or the nuclear genome. Mitochondrial RNAs are involved in anterograde-retrograde communication between the nucleus and mitochondria and play an important role in physiological and pathological conditions. Despite accumulating evidence on the presence and biogenesis of mitochondrial RNAs, their study continues to pose significant challenges. Currently, there are no standardized protocols and guidelines to conduct deep functional characterization and expression profiling of mitochondrial RNAs. To overcome major obstacles in this emerging field, the EU-CardioRNA and AtheroNET COST Action networks summarize currently available techniques and emphasize critical points that may constitute sources of variability and explain discrepancies between published results. Standardized methods and adherence to guidelines to quantify and study mitochondrial RNAs in normal and disease states will improve research outputs, their reproducibility, and translation potential to clinical application.

Importance of Transcript Variants in Transcriptome Analyses

RNA sequencing (RNA-Seq) has become a widely adopted technique for studying gene expression. However, conventional RNA-Seq analyses rely on gene expression (GE) values that aggregate all the transcripts produced under a single gene identifier, overlooking the complexity of transcript variants arising from different transcription start sites or alternative splicing. Transcript variants may encode proteins with diverse functional domains, or noncoding RNAs. This study explored the implications of neglecting transcript variants in RNA-Seq analyses. Among the 1334 transcription factor (TF) genes expressed in mouse embryonic stem (ES) or trophoblast stem (TS) cells, 652 were differentially expressed in TS cells based on GE values (365 upregulated and 287 downregulated, ≥absolute 2-fold changes, false discovery rate (FDR) p-value ≤ 0.05). The 365 upregulated genes expressed 883 transcript variants. Further transcript expression (TE) based analyses identified only 174 (<20%) of the 883 transcripts to be upregulated. The remaining 709 transcripts were either downregulated or showed no significant changes. Meanwhile, the 287 downregulated genes expressed 856 transcript variants and only 153 (<20%) of the 856 transcripts were downregulated. The other 703 transcripts were either upregulated or showed no significant change. Additionally, the 682 insignificant TF genes (GE values < absolute 2-fold changes and/or FDR p-values > 0.05) between ES and TS cells expressed 2215 transcript variants. These included 477 (>21%) differentially expressed transcripts (276 upregulated and 201 downregulated, ≥absolute 2-fold changes, FDR p-value ≤ 0.05). Hence, GE based RNA-Seq analyses do not represent accurate expression levels due to divergent transcripts expression from the same gene. Our findings show that by including transcript variants in RNA-Seq analyses, we can generate a precise understanding of a gene's functional and regulatory landscape; ignoring the variants may result in an erroneous interpretation.

Identification of lysine lactylation (kla)-related lncRNA signatures using XGBoost to predict prognosis and immune microenvironment in breast cancer patients

Breast cancer (BC) stands as a predominant global malignancy, significantly contributing to female mortality. Recently uncovered, histone lysine lactylation (kla) has assumed a crucial role in cancer progression. However, the correlation with lncRNAs remains ambiguous. Scrutinizing lncRNAs associated with Kla not only improves clinical breast cancer management but also establishes a groundwork for antitumor drug development. We procured breast tissue samples, encompassing both normal and cancerous specimens, from The Cancer Genome Atlas (TCGA) database. Utilizing Cox regression and XGBoost methods, we developed a prognostic model using identified kla-related lncRNAs. The model's predictive efficacy underwent validation across training, testing, and the overall cohort. Functional analysis concerning kla-related lncRNAs ensued. We identified and screened 8 kla-related lncRNAs to formulate the risk model. Pathway analysis disclosed the connection between immune-related pathways and the risk model of kla-related lncRNAs. Significantly, the risk scores exhibited a correlation with both immune cell infiltration and immune function, indicating a clear association. Noteworthy is the observation that patients with elevated risk scores demonstrated an increased tumor mutation burden (TMB) and decreased tumor immune dysfunction and exclusion (TIDE) scores, suggesting heightened responses to immune checkpoint blockade. Our study uncovers a potential link between Kla-related lncRNAs and BC, providing innovative therapeutic guidelines for BC management.

microRNA 21 and long non-coding RNAs interplays underlie cancer pathophysiology: A narrative review

Non-coding RNAs (ncRNAs) are a diverse group of functional RNA molecules that lack the ability to code for proteins. Despite missing this traditional role, ncRNAs have emerged as crucial regulators of various biological processes and have been implicated in the development and progression of many diseases, including cancer. MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are two prominent classes of ncRNAs that have emerged as key players in cancer pathophysiology. In particular, miR-21 has been reported to exhibit oncogenic roles in various forms of human cancer, including prostate, breast, lung, and colorectal cancer. In this context, miR-21 overexpression is closely associated with tumor proliferation, growth, invasion, angiogenesis, and chemoresistance, whereas miR-21 inactivation is linked to the regression of most tumor-related processes. Accordingly, miR-21 is a crucial modulator of various canonical oncogenic pathways such as PTEN/PI3K/Akt, Wnt/β-catenin, STAT, p53, MMP2, and MMP9. Moreover, interplays between lncRNA and miRNA further complicate the regulatory mechanisms underlying tumor development and progression. In this regard, several lncRNAs have been found to interact with miR-21 and, by functioning as competitive endogenous RNAs (ceRNAs) or miRNA sponges, can modulate cancer tumorigenesis. This work presents and discusses recent findings highlighting the roles and pathophysiological implications of the miR-21-lncRNA regulatory axis in cancer occurrence, development, and progression. The data collected indicate that specific lncRNAs, such as MEG3, CASC2, and GAS5, are strongly associated with miR-21 in various types of cancer, including gastric, cervical, lung, and glioma. Indeed, these lncRNAs are well-known tumor suppressors and are commonly downregulated in different types of tumors. Conversely, by modulating various mechanisms and oncogenic signaling pathways, their overexpression has been linked with preventing tumor formation and development. This review highlights the significance of these regulatory pathways in cancer and their potential for use in cancer therapy as diagnostic and prognostic markers.

LncRNA-536 and RNA Binding Protein RBM25 Interactions in Pulmonary Arterial Hypertension

OBJECTIVE

Hyperproliferation of pulmonary artery smooth muscle cells (PASMCs) is one of the essential features of the maladaptive inward remodeling of the pulmonary arteries in pulmonary arterial hypertension (PAH). In this study, we define the mechanistic association between long-noncoding RNA: ENST00000495536 (Lnc-536) and anti-proliferative HOXB13 in mediating smooth muscle hyperplasia.

METHODS

Antisense oligonucleotide-based GapmeRs or plasmid overexpressing lnc-536 were used to evaluate the role of lnc-536 in mediating hyperproliferation of PDGF-treated or idiopathic PAH (IPAH) PASMCs. Further, we pulled down lnc536 to identify the proteins directly interacting with lnc536. The in-vivo role of lnc-536 was determined in Sugen-hypoxia and HIV-transgenic pulmonary hypertensive rats.

RESULTS

Increased levels of lnc-536 in PDGF-treated or IPAH PASMCs promote hyperproliferative phenotype by downregulating the HOXB13 expression. Knockdown of lnc-536 in-vivo prevented increased RVSP, Fulton Index, and pulmonary vascular remodeling in Sugen-Hypoxia rats. The lncRNA-536 pull-down assay demonstrated the interactions of RNA binding protein: RBM25 with SFPQ, a transcriptional regulator that has a binding motif on HOXB13 exon Further, The RNA-IP experiment using the SFPQ antibody showed direct interaction of RBM25 with SFPQ and knockdown of RBM25 resulted in increased interactions of SFPQ and HOXB13 mRNA while attenuating PASMC proliferation. Finally, we examined the role of lnc-536 and HOXB13 axis in the PASMCs exposed to the dual hit of HIV and a stimulant: cocaine as well.

CONCLUSION

lnc-536 acts as a decoy for RBM25, which in turn sequesters SFPQ, leading to the decrease in HOXB13 expression and hyperproliferation of smooth muscle cells associated with PAH development.

On the Power and Challenges of Atomistic Molecular Dynamics to Investigate RNA Molecules

RNA molecules play a vital role in biological processes within the cell, with significant implications for science and medicine. Notably, the biological functions exerted by specific RNA molecules are often linked to the RNA conformational ensemble. However, the experimental characterization of such three-dimensional RNA structures is challenged by the structural heterogeneity of RNA and by its multiple dynamic interactions with binding partners such as small molecules, proteins, and metal ions. Consequently, our current understanding of the structure-function relationship of RNA molecules is still limited. In this context, we highlight molecular dynamics (MD) simulations as a powerful tool to complement experimental efforts on RNAs. Despite the recognized limitations of current force fields for RNA MD simulations, examining the dynamics of selected RNAs has provided valuable functional insights into their structures.

The Association between Long Non-Coding RNAs and Alzheimer's Disease

Neurodegeneration occurs naturally as humans age, but the presence of additional pathogenic mechanisms yields harmful and consequential effects on the brain. Alzheimer's disease (AD), the most common form of dementia, is a composite of such factors. Despite extensive research to identify the exact causes of AD, therapeutic approaches for treating the disease continue to be ineffective, indicating important gaps in our understanding of disease mechanisms. Long non-coding RNAs (lncRNAs) are an endogenous class of regulatory RNA transcripts longer than 200 nucleotides, involved in various regulatory networks, whose dysregulation is evident in several neural and extraneural diseases. LncRNAs are ubiquitously expressed across all tissues with a wide range of functions, including controlling cell differentiation and development, responding to environmental stimuli, and other physiological processes. Several lncRNAs have been identified as potential contributors in worsening neurodegeneration due to altered regulation during abnormal pathological conditions. Within neurological disease, lncRNAs are prime candidates for use as biomarkers and pharmacological targets. Gender-associated lncRNA expression is altered in a gender-dependent manner for AD, suggesting more research needs to be focused on this relationship. Overall, research on lncRNAs and their connection to neurodegenerative disease is growing exponentially, as commercial enterprises are already designing and employing RNA therapeutics. In this review we offer a comprehensive overview of the current state of knowledge on the role of lncRNAs in AD and discuss the potential implications of lncRNA as potential therapeutic targets and diagnostic biomarkers in patients with Alzheimer's disease.

Exploring the Utility of Long Non-Coding RNAs for Assessing the Health Consequences of Vaping

Electronic cigarette (e-cig) use, otherwise known as "vaping", is widespread among adolescent never-smokers and adult smokers seeking a less-harmful alternative to combustible tobacco products. To date, however, the long-term health consequences of vaping are largely unknown. Many toxicants and carcinogens present in e-cig vapor and tobacco smoke exert their biological effects through epigenetic changes that can cause dysregulation of disease-related genes. Long non-coding RNAs (lncRNAs) have emerged as prime regulators of gene expression in health and disease states. A large body of research has shown that lncRNAs regulate genes involved in the pathogenesis of smoking-associated diseases; however, the utility of lncRNAs for assessing the disease-causing potential of vaping remains to be fully determined. A limited but growing number of studies has shown that lncRNAs mediate dysregulation of disease-related genes in cells and tissues of vapers as well as cells treated in vitro with e-cig aerosol extract. This review article provides an overview of the evolution of e-cig technology, trends in use, and controversies on the safety, efficacy, and health risks or potential benefits of vaping relative to smoking. While highlighting the importance of lncRNAs in cell biology and disease, it summarizes the current and ongoing research on the modulatory effects of lncRNAs on gene regulation and disease pathogenesis in e-cig users and in vitro experimental settings. The gaps in knowledge are identified, priorities for future research are highlighted, and the importance of empirical data for tobacco products regulation and public health is underscored.

Comprehensive Analysis for Predicting Prognoses and Immune Responses of m6A-Related lncRNAs in Women with Lung Adenocarcinoma

During the past decade, the average 5-year survival rate of patients with Lung adenocarcinoma (LUAD) has remained < 20%, although the targeted therapies and novel immunotherapy approaches have held promise. Epigenetic modifications could provide prognostic value as molecular biomarkers, and we aimed to identify the independent risk of m6A-related lncRNAs to establish a risk model for the clinical prediction of prognoses in women with LUAD. In this study, we first assessed 31 N6-methyladenosine (m6A)-related lncRNAs associated with overall survival. Moreover, we evaluated the expression of the oncogenic driver and the tumor immune microenvironment (TIME) in two female LUAD subtypes (clusters 1 and 2) using consensus clustering. We also found 16 m6A-related lncRNAs as the independent prognostic indicator of women with LUAD and established a risk model developed from these lncRNAs. We comprehensively investigated the correlation between the TIME and m6A-related lncRNA and found that m6A-related lncRNA may significantly affect the immune cell infiltration level in LUAD. In conclusion, our study provides evidence on the prognostic prediction in women with LUAD and may help elucidate the processes and mechanisms of m6A-regulated lncRNAs.

Non-coding RNA in exosomes: Regulating bone metastasis of lung cancer and its clinical application prospect

Lung cancer is a highly prevalent malignancy with poor prognosis and rapid progression. It most frequently metastasizes to the bone, where it can pose a severe threat to the patient's survival. Once metastasized, the disease is often incurable and can result in severe complications such as hypercalcemia, bone pain, fractures, spinal cord compression, and subsequent paralysis. Exosomes are bilayer vesicle nanoparticles secreted by most of the extracellular vesicles, which can be found in almost all organisms and play an essential role in intercellular communication. Through their ability to regulate related bone cells, exosomes carry bioactive molecules, including proteins, lipids, and non-coding RNAs (ncRNAs), that can be extremely important in bone remodeling. Studies have been conducted on the role play by proteins, lncRNA, and microRNA-all ncRNAs-carried by exosomes in the bone metastases of lung cancer. In this review, the latest progress of the regulatory mechanism of ncRNAs carried by exosomes in lung cancer bone metastasis has been reviewed. The clinical use of exosomes as a promising biomarker, drug transporter, and therapeutic target was highlighted to offer a novel diagnostic and treatment approach for patients with lung cancer bone metastases.

Clustering of RNA co-expression network identifies novel long non-coding RNA biomarkers in squamous cell carcinoma

Long non-coding RNAs (lncRNAs) have emerged as important players in cancer progression. Cutaneous squamous cell carcinoma (cSCC) is the most common metastatic skin cancer with increasing incidence worldwide. The prognosis of the metastatic cSCC is poor, and currently there are no established biomarkers to predict metastasis risk or specific therapeutic targets for advanced or metastatic cSCC. To elucidate the role of lncRNAs in cSCC, RNA sequencing of patient derived cSCC cell lines and normal human epidermal keratinocytes was performed. The correlation analysis of differentially expressed lncRNAs and protein-coding genes revealed six distinct gene clusters with one of the upregulated clusters featuring genes associated with cell motility. Upregulation of the expression of lncRNAs linked to cSCC cell motility in cSCC and head and neck SCC (HNSCC) cells was confirmed using qRT-PCR. Elevated expression of HOTTIP and LINC00543 was also noted in SCC tumors in vivo and was associated with poorer prognosis in HNSCC and lung SCC cohorts within TCGA data, respectively. Altogether, these findings uncover a novel set of lncRNAs implicated in cSCC cell locomotion. These lncRNAs may serve as potential novel biomarkers and as putative therapeutic targets for locally advanced and metastatic cSCC.

Discovery and functional characterization of LncRNAs associated with inflammation and macrophage activation

Long noncoding RNAs (lncRNA) are emerging players in regulation of gene expression and cell signaling and their dysregulation has been implicated in a multitude of human diseases. Recent studies from our laboratory revealed that lncRNAs play critical roles in cytokine regulation, inflammation, and metabolism. We demonstrated that lncRNA HOTAIR, which is a well-known regulator of gene silencing, plays critical roles in modulation of cytokines and proinflammatory genes, and glucose metabolism in macrophages during inflammation. In addition, we recently discovered a series of novel lncRNAs that are closely associated with inflammation and macrophage activation. We termed these as long-noncoding inflammation associated RNAs (LinfRNAs). We are currently engaged in the functional characterization of these hLinfRNAs (human LinfRNAs) with a focus on their roles in inflammation, and we are investigating their potential implications in chronic inflammatory human diseases. Here, we have summarized experimental methods that have been utilized for the discovery and functional characterization of lncRNAs in inflammation and macrophage activation.