The landscape of long noncoding RNAs in the human transcriptome. Nat Genet. 2015;47:199-208. [PMID: 25599403 DOI: 10.1038/ng.3192]

A novel cinnamic acid derivative for hepatocellular carcinoma therapy by degrading METTL16 protein

The RNA methyltransferase methyltransferaselike protein 16 (METTL16) is upregulated in a large proportion of hepatocellular carcinoma (HCC), and its high expression is associated with poor clinical outcomes. METTL16 deletion inhibits HCC growth in vitro and in vivo. Referencing the structure of cinnamic acid, here we designed and synthesized a novel series of small molecular compounds, and found through bioactivity screening that compound 15a effectively reduced METTL16 level and modulated oncogenic PI3K/AKT pathway signaling. Compound 15a inhibited the proliferation and migration of HepG2 cells, and induced apoptosis in vitro. Furthermore, compound 15a significantly inhibited the growth of patient-derived HCC xenografts in nude mice with greater efficacy than the multi-kinase inhibitor lenvatinib. The promising efficacy and good biosafety profile of compound 15a enables us to further develop this compound for treating patients with HCC and possibly other cancers in clinic.

Unveiling EIF5A2: A multifaceted player in cellular regulation, tumorigenesis and drug resistance

The eukaryotic initiation factor 5A2 gene (EIF5A2) is a highly conserved and multifunctional gene that significantly influences various cellular processes, including translation elongation, RNA binding, ribosome binding, protein binding and post-translational modifications. Overexpression of EIF5A2 is frequently observed in multiple cancers, where it functions as an oncoprotein. Additionally, EIF5A2 is implicated in drug resistance through the regulation of various molecular pathways. In the review, we describe the structure and functions of EIF5A2 in normal cells and its role in tumorigenesis. We also elucidate the molecular mechanisms associated with EIF5A2 in the context of tumorigenesis and drug resistance. We propose that the biological roles of EIF5A2 in regulating diverse cellular processes and tumorigenesis are clinically significant and warrant further investigation.

Landscape of lncRNAs expressed in Mexican patients with triple‑negative breast cancer

Long non‑coding RNAs (lncRNAs) are key regulators of gene expression, that can regulate a range of carcinogenic processes. Moreover, they exhibit stability in biological fluids, with some displaying tissue specificity. As their expression depends on specific conditions or is linked to the regulation of particular signaling pathways, lncRNAs are promising candidates for providing insights into the likely progression of the disease. This allows for the stratification of patients based on their risk of progression, making them potential prognostic biomarkers in various types of cancer. In addition, the tissue‑specific expression profile of lncRNAs renders them ideal candidates for detection, prognosis and monitoring of cancer progression. The present study aims to provide an overview of differentially expressed lncRNAs in Mexican patients with triple‑negative breast cancer (TNBC), a subtype of breast cancer. The aim was to identify potential prognostic biomarkers that can be applied to improve the clinical management of Mexican patients with TNBC. Human Transcriptome Array 2.0 microarrays were used to analyze the transcriptome of TNBC and luminal tumors, which are reported to have a good prognosis amongst aggressive tumor types. Subsequently, results from these microarrays were validated in a cohort from The Cancer Genome Atlas, an independent cohort of Mexican patients and in breast cancer cell lines (MCF7, ZR75, T47D, MDA‑MB‑231, MDA‑MB‑468 and BT20). A total of 746 differentially expressed transcripts were identified, including 102 lncRNAs in TNBC compared with luminal tumors. Among the lncRNAs with the most significant changes in expression levels, SOX9‑AS was highly expressed in TNBC, whereas the expression of Lnc‑peroxidasin‑3:1 (Lnc‑PXDN‑3:1), Lnc‑RNA Synapse Defective Rho GTPase Homolog (Lnc‑SYDE) and long intergenic non‑coding RNA (LINC)01087 were decreased. In addition, the low expression of lncRNA LINC01087, LINC02568, ACO22196, and lncRNA eosinophil granule ontogeny transcript (Lnc‑EGOT) was associated with poor overall survival (OS). Further analysis revealed that the high expression levels of Lnc‑PXDN‑3:1, Lnc RNA fibrous sheath interacting protein 1‑6:3 and (LINC)00182 were associated with reduced survival in patients with the luminal subtype of breast cancer. Similarly, low expression levels of lncRNAs such as GATA binding protein 3‑1 (Lnc‑GATA‑3‑1), LINC01087, and BX679671.1 in luminal subtypes of breast cancer, as well as LINC00504 and LncRNA rho guanine nucleotide exchange factor 38 intronic transcript 1 (Lnc‑ARHGEF38‑IT1) in basal subtypes have been linked to poorer survival. The interactions and functions of LINC01087 were then investigated, revealing the interaction of LINC01087 with RNAs and transcription factors, highlighting their potential involvement in the estrogen receptor pathway. The present study provided a detailed analysis of the expression of lncRNAs in TNBC, which highlights the role of lncRNAs as a biomarker in the survival outcomes of patients with breast cancer to improve the understanding of transcriptional regulation in TNBC.

A potential therapeutic molecule target: lncRNA AK023507 inhibits the metastasis of breast cancer by regulating the WNT/DOCK4/β-catenin axis

PURPOSE

Breast cancer (BC) has become the most common malignant tumor in women worldwide. This study was carried out to find and validate a novel molecular therapeutic target for BC.

METHODS

Long non-coding RNA (lncRNA) AK023507 was selected as the study objects through microarray analysis. The function of lncRNA AK023507 was verified by various cell function experiments in vitro, subcutaneous tumorigenesis experiments, and lung metastasis model experiments in vivo. The RNA pull-down experiment and Western blot experiment were used to confirm the mechanism regulation pathway and the recovery experiment was used to verify it. TCGA datasets were used for clinical and immune function prediction analysis.

RESULTS

In vitro cell function tests and in vivo experiments suggested that overexpression of lncRNA AK023507 inhibited the proliferation and metastasis of BC cells. The RNA pull-down experiment and Western blot analysis validated that lncRNA AK023507 interacted with the dedicator of cytokinesis 4 (DOCK4) protein. Analysis of public databases predicted that DOCK4 is a potential prognostic risk factor associated with epithelial-mesenchymal transition (EMT) and central memory T cell (TCM) cellular immune infiltration.

CONCLUSIONS

LncRNA AK023507 inhibits the proliferation and metastasis of BC by regulating the DOCK4/β-catenin axis. This discovery will provide new potential therapeutic targets for BC.

A novel nuclear RNA HSD52 scaffolding NONO/SFPQ complex modulates DNA damage repair to facilitate temozolomide resistance

BACKGROUND

Temozolomide (TMZ) is used in the treatment of glioblastoma (GBM). However, the primary obstacle remains the emergence of TMZ chemotherapy resistance. Non-POU domain-containing octamer-binding protein (NONO) and splicing factor proline/glutamine rich (SFPQ) are multifunctional nuclear proteins involved in genome stability and gene regulation. However, the specific role of NONO and SFPQ in TMZ resistance of GBM remains to be explored.

METHODS

RNA-binding protein immunoprecipitation-microarray and RNA microarray of TMZ-resistant and parental cells were performed for the gain of HSD52. The effects of HSD52 on TMZ resistance were investigated through in vitro assays, intracranial xenograft, and GBM organoid models. The underlying mechanisms were explored by DNA methylation chip, RNA immunoprecipitation, RNA pull-down assays, among others. GBM clinical samples were rolled in to investigate the clinical significance of HSD52.

RESULTS

We identified a novel noncoding RNA, HSD52, that was highly expressed in TMZ-resistant GBM and facilitated the interaction between NONO and SFPQ. H3 ubiquitination attenuation and reduced DNA methyltransferase 1 (DNMT1) recruitment increased HSD52 transcription via DNA hypo-methylation. HSD52 formed an RNA duplex with UFM1 specific ligase 1 (UFL1) mRNA, thereby promoting NONO/SFPQ complex binding to UFL1 mRNA and enhancing its stability, and then contributed to TMZ resistance through activating the ataxia telangiectasia mutated signaling pathway. In vivo xenograft and GBM organoid models showed significant repression in tumor growth after HSD52 knockout with TMZ treatment. In GBM clinical samples, HSD52 was responsible for the malignant progression and TMZ resistance.

CONCLUSIONS

Our results revealed that HSD52 could serve as a promising therapeutic target to overcome TMZ resistance, improving the clinical efficacy of TMZ chemotherapy in GBM.

Peak analysis of cell-free RNA finds recurrently protected narrow regions with clinical potential

BACKGROUND

Cell-free RNAs (cfRNAs) can be detected in biofluids and have emerged as valuable disease biomarkers. Accurate identification of the fragmented cfRNA signals, especially those originating from pathological cells, is crucial for understanding their biological functions and clinical value. However, many challenges still need to be addressed for their application, including developing specific analysis methods and translating cfRNA fragments with biological support into clinical applications.

RESULTS

We present cfPeak, a novel method combining statistics and machine learning models to detect the fragmented cfRNA signals effectively. When test in real and artificial cfRNA sequencing (cfRNA-seq) data, cfPeak shows an improved performance compared with other applicable methods. We reveal that narrow cfRNA peaks preferentially overlap with protein binding sites, vesicle-sorting sites, structural sites, and novel small non-coding RNAs (sncRNAs). When applied in clinical cohorts, cfPeak identified cfRNA peaks in patients' plasma that enable cancer detection and are informative of cancer types and metastasis.

CONCLUSIONS

Our study fills the gap in the current small cfRNA-seq analysis at fragment-scale and builds a bridge to the scientific discovery in cfRNA fragmentomics. We demonstrate the significance of finding low abundant tissue-derived signals in small cfRNA and prove the feasibility for application in liquid biopsy.

Role of noncoding RNA and protein interaction in pancreatic cancer

ABSTRACT

Noncoding RNAs (ncRNAs) are a class of RNA molecules with little or no protein-coding potential. Emerging evidence indicates that ncRNAs are frequently dysregulated and play pivotal roles in the pathogenesis of pancreatic cancer. Their aberrant expression can arise from chromosomal abnormalities, dysregulated transcriptional control, and epigenetic modifications. ncRNAs function as protein scaffolds or molecular decoys to modulate interactions between proteins and other biomolecules, thereby regulating gene expression and contributing to pancreatic cancer progression. In this review, we summarize the mechanisms underlying ncRNA dysregulation in pancreatic cancer, emphasize the biological significance of ncRNA-protein interactions, and highlight their clinical relevance. A deeper understanding of ncRNA-protein interactions is essential to elucidate molecular mechanisms and advance translational research in pancreatic cancer.

Archetypal Analysis of Kidney Allograft Biopsies Using Next-generation Sequencing Technology

BACKGROUND

In kidney transplantation, molecular diagnostics may be a valuable approach to improve the precision of the diagnosis. Using next-generation sequencing (NGS), we aimed to identify clinically relevant archetypes.

METHODS

We conducted an Illumina bulk RNA sequencing on 770 kidney biopsies (540 kidney recipients) collected between 2006 and 2021 from 11 European centers. Differentially expressed genes were determined for 11 Banff lesions. An ElasticNet model was used for feature selection, and 4 machine learning classifiers were trained to predict the probability of presence of the lesions. NGS-based classifiers were used in an unsupervised archetypal analysis to different archetypes. The association of the archetypes with allograft survival was assessed using the iBox risk prediction score.

RESULTS

The ElasticNet feature selection reduced the number of the genes from a range of 859-10 830 to a range of 52-867 genes. NGS-based classifiers demonstrated robust performances (precision-recall area under the curves 0.708-0.980) in predicting the Banff lesions. Archetypal analysis revealed 8 distinct phenotypes, each characterized by distinct clinical, immunological, and histological features. Although the archetypes confirmed the well-defined Banff rejection phenotypes for T cell-mediated rejection and antibody-mediated rejection, equivocal histologic antibody-mediated rejection, and borderline diagnoses were reclassified into different archetypes based on their molecular signatures. The 8 NGS-based archetypes displayed distinct allograft survival profiles with incremental graft loss rates between archetypes, ranging from 90% to 56% rates 7 y after evaluation ( P < 0.0001).

CONCLUSIONS

Using molecular phenotyping, 8 archetypes were identified. These NGS-based archetypes might improve disease characterization, reclassify ambiguous Banff diagnoses, and enable patient-specific risk stratification.

Mechanisms and progress of LncRNAs in prostate cancer development and diagnostic therapy

Prostate cancer (PCa) is a leading cause of cancer-related morbidity and mortality in men worldwide. Despite advancements in diagnosis and treatment, challenges such as late-stage detection, therapeutic resistance, and the complexity of castration-resistant prostate cancer (CRPC) persist. Long non-coding RNAs (LncRNAs) play critical roles in PCa progression through epigenetic regulation, transcriptional and post-transcriptional modulation, and immune response regulation. This review highlights the molecular mechanisms by which LncRNAs influence PCa development, treatment resistance, and immune regulation, emphasizing their potential as biomarkers and therapeutic targets. We also discuss future research directions to advance precision medicine in PCa.

An ultraconserved snoRNA-like element in long noncoding RNA CRNDE promotes ribosome biogenesis and cell proliferation

Cancer cells frequently upregulate ribosome production to support tumorigenesis. While small nucleolar RNAs (snoRNAs) are critical for ribosome biogenesis, the roles of other classes of noncoding RNAs in this process remain largely unknown. Here, we performed CRISPR interference (CRISPRi) screens to identify essential long noncoding RNAs (lncRNAs) in renal cell carcinoma (RCC) cells. This revealed that an alternatively spliced isoform of lncRNA colorectal neoplasia differentially expressed (CRNDE) containing an ultraconserved element (UCE), referred to as CRNDEUCE, is required for RCC cell proliferation. CRNDEUCE localizes to the nucleolus and promotes 60S ribosomal subunit biogenesis. The UCE of CRNDE functions as an unprocessed C/D box snoRNA that directly interacts with ribosomal RNA precursors. This facilitates delivery of eukaryotic initiation factor 6 (eIF6), a key 60S biogenesis factor, which binds to CRNDEUCE through a sequence element adjacent to the UCE. These findings highlight the functional versatility of snoRNA sequences and expand the known mechanisms through which noncoding RNAs orchestrate ribosome biogenesis.

High tissue specificity of lncRNAs maximises the prediction of tissue of origin of circulating DNA

Several studies have made it possible to envision a translational application of plasma DNA sequencing in cancer diagnosis and monitoring. However, the extremely low concentration of circulating tumour DNA (ctDNA) fragments among the total cell-free DNA (cfDNA) remains a formidable challenge to overcome and statistical models have yet to be improved enough to become of practical use. In this study, we set about appraising the predictive value of a variety of binary classification models based on cfDNA sequencing using fragmentation features extracted around transcription start sites (TSSs). We investigated (1) features summarising mapped fragment density around each TSS, (2) long non-coding RNA (lncRNA) genes versus coding genes and (3) selection criteria to generate gene classes to be assigned by the model. Given that, in healthy samples, most of the cfDNA comes from lymphomyeloid lineages, we could identify the model parametrisation with the best accuracy in those lineages using publicly available datasets of healthy patients' cfDNA. Our results show that (1) the way tissue-specific gene classes are defined matters more than what fragmentation features are included, and (2) in particular, lncRNAs are more tissue specific than coding genes and stand out in terms of both sensitivity and specificity in our results.

The role of exosomal lncRNAs in mediating apoptosis and inflammation in UV-induced skin photoaging

The skin, as the body's largest organ, functions as a vital barrier against environmental insults. Chronic exposure to ultraviolet (UV) radiation significantly contributes to premature aging, or photoaging, which leads to DNA damage and disrupts repair mechanisms. Exosomes, which are small extracellular vesicles, play a key role in cell-to-cell communication and might help mitigate the effects of photoaging by transporting bioactive molecules to skin cells. Long non-coding RNAs (lncRNAs) are increasingly recognized for their regulatory roles in the photoaging process, influencing stress responses and DNA repair; however, their involvement in exosomes in the context of skin aging is not yet well understood. In this study, we developed a photoaging model using SD rats subjected to UVA and UVB irradiation, which led to significant changes in the dermis such as increased dryness, wrinkles, pigmentation, and vascular alterations. Histological evaluations showed uneven thickening of the epidermis, degradation of collagen and elastic fibers, and cellular infiltration. Exosomes isolated from the dermal tissues exposed to UV radiation displayed altered size distributions. Transcriptomic analyses of the UV-treated rats identified 2,332 lncRNAs and 5,906 mRNAs that were differentially expressed, revealing significant involvement in pathways related to oxidative stress, apoptosis, and cellular stress responses. A cis-regulatory analysis identified 1,327 essential interactions between lncRNAs and mRNAs, highlighting their role in controlling inflammation and apoptosis. Importantly, both IL-1B and GADD45B levels were significantly increased in the exosomes and UV-challenged HaCaT cells, indicating their crucial roles in responding to UV-induced stress. This study highlights the significant role of exosomal lncRNAs in managing cellular reactions to UV-induced stress, impacting regulatory pathways associated with apoptosis, inflammation, and oxidative stress. These insights pave the way for the development of lncRNA-focused therapeutic approaches to address UV-induced skin damage.

Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation

Long-read sequencing (LRS) technologies have revolutionized transcriptomic research by enabling the comprehensive sequencing of full-length transcripts. Using these technologies, researchers have reported tens of thousands of novel transcripts, even in well-annotated genomes, while developing new algorithms and experimental approaches to handle the noisy data. The Long-read RNA-seq Genome Annotation Assessment Project community effort benchmarked LRS methods in transcriptomics and validated many novel, lowly expressed, often times sample-specific transcripts identified by long reads. These molecules represent deviations of the major transcriptional program that were overlooked by short-read sequencing methods but are now captured by the full-length, single-molecule approach. This Perspective discusses the challenges and opportunities associated with LRS' capacity to unravel this fraction of the transcriptome, in terms of both transcriptome biology and genome annotation. For transcriptome biology, we need to develop novel experimental and computational methods to effectively differentiate technology errors from rare but real molecules. For genome annotation, we must agree on the strategy to capture molecular variability while still defining reference annotations that are useful for the genomics community.

Androgen receptor-regulated lncRNA PRCAT71 promotes AR signaling through the interaction with KHSRP in prostate cancer

Mounting evidence indicates that long noncoding RNAs (lncRNAs) play vital roles in tumorigenesis and progression of cancers. However, the functions and regulatory mechanisms of lncRNAs in prostate cancer (PCa) are still largely unknown. In this study, we found an lncRNA, PCa-associated transcript 71 (PRCAT71), highly expressed in metastatic and primary PCa compared to benign prostate tissues. Silencing PRCAT71 inhibited cancerous properties of PCa cells and androgen receptor (AR) signaling. Mechanistically, PRCAT71 acts as a scaffold to recruit K homology (KH)-type splicing regulatory protein (KHSRP) to AR messenger RNA (mRNA) and stabilize AR mRNA, leading to activated AR signaling. KHSRP plays a critical role in PCa progression. PRCAT71 is transcriptionally regulated by AR-driven enhancers, forming a positive regulatory loop between AR and PRCAT71 in PCa. Our study demonstrates a coordinated regulation of AR mRNA by lncRNA PRCAT71 and RNA binding protein KHSRP and provides insight that the PRCAT71-KHSRP-AR axis is a promising therapeutic target for treating PCa.

Identification of a PANoptosis-related long noncoding rna risk signature for prognosis and immunology in colon adenocarcinoma

BACKGROUND

PANoptosis, a complex programmed cell death (PCD) pathway that includes apoptosis, pyroptosis and necroptosis, is significantly involved in the progression of cancers. Long noncoding RNAs (lncRNAs) play crucial roles in PCD. However, the predictive value of PANoptosis-related lncRNAs (PRlncRNAs) for colon adenocarcinoma (COAD) has not been established.

METHODS

Gene expression data and clinical characteristics of patients with COAD were obtained from The Cancer Genome Atlas database. Differential expression analysis and Pearson correlation analysis were used to identify PRlncRNAs. In addition to least absolute shrinkage and selection operator, univariate and multivariate Cox regression analyses were employed to obtain PRlncRNAs for constructing a risk signature. Patients with COAD in the training set, testing set and entire set were stratified into high- and low-risk groups for further comparison of survival prognosis, using the median risk score as the cut-off point. Time-dependent receiver operating characteristic curves, a nomogram and multivariate Cox regression analysis were conducted to validate the risk signature in the testing set and the entire set. In addition, critical pathways, immune infiltration cells, immune checkpoint-related genes, Tumor Immune Dysfunction and Exclusion (TIDE) scores and antitumour drugs were compared between the two risk groups in the entire set. Correlations between ferroptosis, cuproptosis, disulfidptosis and the PRlncRNA risk score were evaluated. Finally, a competitive endogenous RNA (ceRNA) network was established, and enrichment analysis of the predicted mRNAs was performed using Gene Ontology (GO) analysis. The Kaplan-Meier plotter database was used as an external database to confirm the accuracy of the risk signature in predicting patient prognosis. Additionally, small interfering RNA (siRNA), a cell counting kit- 8 assay, a cell colony formation assay, quantitative polymerase chain reaction (qPCR) and an apoptosis assay were further employed to investigate the roles of AP003555.1 in colon cancer.

RESULTS

A risk signature comprising four PRlncRNAs (LINC01133, FOXD3-AS1, AP001066.1, and AP003555.1) was developed to predict the prognosis of patients with COAD. Kaplan‒Meier curves demonstrated significant differences in prognosis between the high- and low-risk groups across the three sets. Multivariate Cox regression analysis confirmed that the risk signature was an independent prognostic factor across the three sets. A nomogram, receiver operating characteristic curves and calibration curves indicated strong confidence in the risk signature. Using the CIBERSORT algorithm and gene set enrichment analysis, variations in infiltrating immune cells and immune processes were observed between the two risk groups. Furthermore, TIDE algorithm suggested that the high-risk group exhibited a lower risk of immunotherapy escape and better immunotherapy outcomes than the low-risk group. Distinct responses to various antitumour drugs were observed between the two risk groups. Additionally, we constructed a ceRNA network based on PRlncRNAs, and GO enrichment analysis of the predicted mRNAs revealed different functions. In addition, the results of the Kaplan‒Meier plotter database revealed that patients who exhibited high levels of LINC01133 and FOXD3-AS1 experienced significantly shorter overall survival than those with low levels of these lncRNAs. Specifically, in terms of functionality, AP003555.1 was found to be highly expressed in colon cancer tissue and promoted viability and proliferation while suppressing the apoptosis of colon cancer cells.

CONCLUSION

We identified a novel risk signature consisting of four PRlncRNAs, which is an independent prognostic indicator for patients with COAD. This PRlncRNA risk signature is potentially relevant for immunotherapy and could serve as a therapeutic target for COAD.

Interactions Between Non-Coding RNAs and HIF-1alpha in the Context of Colorectal Cancer

Hypoxia-inducible factor-1α (HIF-1α), a master regulator of cellular adaptation to hypoxia, drives colorectal cancer (CRC) progression by fueling angiogenesis, metastasis, and therapy resistance. Emerging evidence delineates intricate crosstalk between non-coding RNAs (ncRNAs)-including microRNAs, long non-coding RNAs, and circular RNAs-and HIF-1α, forming bidirectional regulatory networks that orchestrate CRC pathogenesis. By interacting with HIF-1α, these non-coding RNAs contribute to the orchestration of the aggressive hypoxic tumor microenvironment. Recent studies have evaluated the clinical potential of lncRNAs and miRNAs in the realms of non-invasive liquid biopsies and RNA-targeted therapies. This review offers a comprehensive synthesis of recent investigations into the mechanisms by which lncRNAs and miRNAs interact with HIF-1α to modulate CRC progression. Additionally, we further explore the clinical implications of ncRNA/HIF-1α crosstalk, emphasizing their potential as diagnostic biomarkers and therapeutic targets, while also spotlighting intriguing and promising areas of ncRNA research. Methods: In this study, our search strategy employed in databases such as PubMed, Web of Science, and EMBASE is as follows: we will specify search terms, including combinations of "non-coding RNA", "HIF-1α", and "colorectal cancer", along with a date range for the literature search (for example, from 2000 to 2025) to capture the most relevant and up-to-date research.

N4-Acetylcytidine-Mediated CD2BP2-DT Drives YBX1 Phase Separation to Stabilize CDK1 and Promote Breast Cancer Progression

Long noncoding RNAs (lncRNAs) play critical roles in the initiation and progression of breast cancer. However, the specific mechanisms and biological functions of lncRNAs in breast cancer remain incompletely understood. Bioinformatics analysis identifies a novel lncRNA, CD2BP2-DT, that is overexpressed in breast cancer and correlates with adverse clinicopathological features and poor overall survival. Both in vivo and in vitro experiments demonstrate that CD2BP2-DT promotes proliferation of breast cancer cells. Mechanistically, NAT10 mediates the N4-acetylcytidine (ac4C) modification of CD2BP2-DT, enhancing its RNA stability and expression. More importantly, CD2BP2-DT enhances the stability of CDK1 mRNA by mediating YBX1 phase separation, thereby promoting the proliferation of breast cancer cells. In conclusion, the lncRNA CD2BP2-DT is identified as a crucial driver of breast cancer cell proliferation through the YBX1/CDK1 axis, highlighting its potential as a promising biomarker and therapeutic target for breast cancer.

Circular RNAs in neurological conditions - computational identification, functional validation, and potential clinical applications

Non-coding RNAs (ncRNAs) have gained significant attention in recent years due to advancements in biotechnology, particularly high-throughput total RNA sequencing. These developments have led to new understandings of non-coding biology, revealing that approximately 80% of non-coding regions in the genome possesses biochemical functionality. Among ncRNAs, circular RNAs (circRNAs), first identified in 1976, have emerged as a prominent research field. CircRNAs are abundant in most human cell types, evolutionary conserved, highly stable, and formed by back-splicing events which generate covalently closed ends. Notably, circRNAs exhibit high expression levels in neural tissue and perform diverse biochemical functions, including acting as molecular sponges for microRNAs, interacting with RNA-binding proteins to regulate their availability and activity, modulating transcription and splicing, and even translating into functional peptides in some cases. Recent advancements in computational and experimental methods have enhanced our ability to identify and validate circRNAs, providing valuable insights into their biological roles. This review focuses on recent developments in circRNA research as they related to neuropsychiatric and neurodegenerative conditions. We also explore their potential applications in clinical diagnostics, therapeutics, and future research directions. CircRNAs remain a relatively underexplored area of non-coding biology, particularly in the context of neurological disorders. However, emerging evidence supports their role as critical players in the etiology and molecular mechanisms of conditions such as schizophrenia, bipolar disorder, major depressive disorder, Alzheimer's disease, and Parkinson's disease. These findings suggest that circRNAs may provide a novel framework contributing to the molecular dysfunctions underpinning these complex neurological conditions.

Increased expression of an isoform of the long non-coding RNA, lnc37707, is associated with malathion resistance in Bactrocera dorsalis

The oriental fruit fly, Bactrocera dorsalis (Hendel) is an invasive pest threatening global fruit industries. Field populations of B. dorsalis exhibit complex insecticide resistance, hindering pest control efforts and exacerbating damage. Long non-coding RNAs (lncRNAs) are critical regulators of multiple bioprocess in insects, including insecticide resistance, and have potentials as novel target for pest management. Here, the candidate lncRNAs associated with malathion resistance in B. dorsalis were identified through RNA-seq. One of the isoforms of lnc37707, designated as lnc37707.10, was significantly enriched in the detoxification tissues of malathion-resistant (MR) strain. A specific fragment of lnc37707.10 (sflnc37707) was strongly associated with malathion resistance, and silencing sflnc37707 increased the susceptibility, whereas overexpressing it decreased susceptibility to malathion. Silencing sflnc37707 resulted in the down-regulation of 248 genes, but none of them included the four adjacent genes as its potential target. Instead, pathway analysis revealed significant enrichment of down-regulated genes involved in drug and xenobiotics metabolism, including P450s and GSTs. Bioinformatic analysis suggested a potential regulatory role of miRNA in the function of lnc37707. Further combining silence or overexpression sflnc37707 with miRNA mimic treatment identified that BdGSTd10 (an important gene involved in malathion resistance) and miR-1000 was strongly linked to lnc37707.10. Finally, a ceRNA (competing endogenous RNA) regulatory axis was proposed, where lnc37707.10 might indirectly modulate BdGSTd10 by sponging miR-1000 to regulate the malathion resistance in B. dorsalis. These findings provide a new insight into insecticide resistance and a potential lncRNA target for the sustainable pest management.

Fat mass and obesity-associated protein in mesenchymal stem cells inhibits osteoclastogenesis via lnc NORAD/miR-4284 axis in ankylosing spondylitis

BACKGROUND

Ankylosing spondylitis (AS) is recognized as a long-term inflammatory disorder that leads to inflammation in the spine and joints, alongside abnormal bone growth. In previous studies, we reported that mesenchymal stem cells (MSCs) derived from individuals with AS demonstrated a remarkable inhibition in the formation of osteoclasts compared to those obtained from healthy donors. The mechanism through which MSCs from AS patients achieve this inhibition remains unclear.

AIM

To investigate the potential underlying mechanism by which MSCs from individuals with ankylosing spondylitis (AS-MSCs) inhibit osteoclastogenesis.

METHODS

We analysed fat mass and obesity-associated (FTO) protein levels in AS-MSCs and MSCs from healthy donors and investigated the effects and mechanism by which FTO in MSCs inhibits osteoclastogenesis by coculturing and measuring the levels of tartrate-resistant acid phosphatase, nuclear factor of activated T cells 1 and cathepsin K.

RESULTS

We found that FTO, an enzyme responsible for removing methyl groups from RNA, was more abundantly expressed in MSCs from AS patients than in those from healthy donors. Reducing FTO levels was shown to diminish the capacity of MSCs to inhibit osteoclast development. Further experimental results revealed that FTO affects the stability of the long non-coding RNA activated by DNA damage (NORAD) by altering its N6-methyladenosine methylation status. Deactivating NORAD in MSCs significantly increased osteoclast formation by affecting miR-4284, which could regulate the MSC-mediated inhibition of osteoclastogenesis reported in our previous research.

CONCLUSION

This study revealed elevated FTO levels in AS-MSCs and found that FTO regulated the ability of AS-MSCs to inhibit osteoclast formation through the long noncoding RNA NORAD/miR-4284 axis.

Non-coding RNAs as key regulators of epithelial-mesenchymal transition in breast cancer

This study examines the critical role of non-coding RNAs (ncRNAs) in regulating epithelial-mesenchymal transition (EMT) in breast cancer, a prevalent malignancy with significant metastatic potential. EMT, wherein cancer cells acquire mesenchymal traits, is fundamental to metastasis. ncRNAs-such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs)-modulate EMT by influencing gene expression and signaling pathways, affecting cancer cell migration and invasion. This review consolidates recent findings on ncRNA-mediated EMT regulation and explores their diagnostic and therapeutic potential. Specifically, miRNAs inhibit EMT-related transcription factors, while lncRNAs and circRNAs regulate gene expression through interactions with miRNAs, impacting EMT progression. Given the influence of ncRNAs on metastasis and therapeutic resistance, advancing ncRNA-based biomarkers and treatments holds promise for improving breast cancer outcomes.

Systemic Identification of Functionally Conserved Long Noncoding RNA Metabolic Regulators in Human and Mouse Livers

BACKGROUND & AIMS

Unlike protein-coding genes, most human long noncoding RNAs (lncRNAs) lack conservation based on their sequences, posing a challenge for investigating their role in a pathophysiological context for clinical translation. This study explores the hypothesis that nonconserved lncRNAs in human and mouse livers may share similar metabolic functions, giving rise to functionally conserved lncRNA metabolic regulators (fcLMRs).

METHODS

We developed a sequence-independent strategy to select putative fcLMRs and performed extensive analysis to determine the functional similarities of putative human and mouse (h/m)LMR pairs.

RESULTS

We found that several pairs of putative fcLMRs share similar functions in regulating gene expression. We further demonstrated that a pair of fcLMRs, h/mLMR1, robustly regulated triglyceride levels by modulating the expression of a similar set of lipogenic genes. Mechanistically, h/mLMR1 binds to poly(A)-binding protein cytoplasmic 1 (PABPC1), a regulator of protein translation, via short motifs on either lncRNA with divergent sequences but similar structures. This interaction inhibits protein translation, activating an amino acid- mechanistic target of rapamycin-sterol regulatory element-binding transcription factor 1 axis to regulate lipogenic gene expression. Intriguingly, PABPC1-binding motifs on each lncRNA fully rescued the functions of their corresponding LMRs in the opposite species. Given the elevated expression of h/mLMR1 in humans and mice with hepatic steatosis, the PABPC1-binding motif on hLMR1 emerges as a potential nonconserved human drug target whose functions can be fully validated in a physiologically relevant setting before clinical studies.

CONCLUSIONS

Our study supports that fcLMRs represent a novel and prevalent biological phenomenon and that deep phenotyping of genetic mLMR mouse models constitutes a powerful approach to understand the pathophysiological role of lncRNAs in the human liver.

Prognostic modeling of disulfidptosis gene-associated lncRNAs aids in identifying the tumor microenvironment and guiding the selection of therapy

INTRODUCTION

Gliomas, a type of malignant tumor, are marked by a short survival period and an unfavorable prognosis. Disulfide stress, which arises from an overabundance of intracellular cystine, can initiate disulfidoptosis, an emerging form of cell death. The link between gliomas and disulfidoptosis has not been extensively explored. This study breaks new ground by investigating the correlation between glioma prognosis and lncRNAs associated with disulfidoptosis, with the aim of improving glioma treatment strategies.

METHODS

We analyzed 10 long non-coding RNAs (lncRNAs) co-expressed with disulfidoptosis genes, retrieved clinical information and gene expression profiles from glioma and normal groups in the TCGA database, and developed a prognostic model for lncRNAs based on this data. The receiver operating characteristic curve (ROC) was used to evaluate and validate the model's reliability. Furthermore, the Kaplan-Meier survival curve was employed to assess the disparity in overall survival (OS) among patients with varying risk scores. We also examined the tumor microenvironment (TME), immune cell infiltration, immune-related functions, tumor mutational burden (TMB), and OncoPredict in samples with differing risk scores. To confirm the expression variations of genes associated with prognostic models in cell lines, quantitative polymerase chain reaction (qPCR) was employed.

RESULTS

Eleven long non-coding RNAs (lncRNAs) were identified for constructing prognostic models by analyzing lncRNAs associated with disulfidoptosis genes using Cox regression and LASSO regression analyses. The study's findings indicate that these 11 key lncRNAs serve as independent predictors of overall survival (OS) in glioma patients. Moreover, the frequency with which patients of varying risk scores opt for immune checkpoint blockade (ICB) therapy and chemotherapy not only differs but also their responses to these treatments are significantly distinct, suggesting that the risk score could be a predictive factor for treatment response.

CONCLUSIONS

This research sheds light on the characteristics of disulfidoptosis in glioma, revealing that patterns of disulfidoptosis in patients can be effectively assessed using a risk score. Consequently, the judicious application of this prognostic model can significantly inform clinical treatment strategies and precision medicine for glioma, potentially improving patient outcomes.

Comparative Analysis of Transcription Factors TWIST2, GATA3, and HES5 in Glioblastoma Multiforme : Evaluating Biomarker Potential and Therapeutic Targets Using in Silico Methods

OBJECTIVE

Glioblastoma multiforme (GBM) is characterized by substantial heterogeneity and limited therapeutic options. As molecular approaches to central nervous system tumors have gained prominence, this study examined the roles of three genes, TWIST2, GATA3, and HES5, known to be involved in oncogenesis, developmental processes, and maintenance of cancer stem cell properties, which have not yet been extensively studied in GBM. This study is the first to present gene expression data for TWIST2, GATA3, and HES5 specifically within the context of GBM patient survival.

METHODS

Gene expression data for TWIST2, GATA3, and HES5 were collected from GBM and normal brain tissues using datasets from The Cancer Genome Atlas via the Genomic Data Commons portal and the Genotype-Tissue Expression database. These data were rigorously analyzed using in silico methods.

RESULTS

All three genes were significantly more expressed in GBM tissues than in normal tissues. TWIST2 and GATA3 were linked to lower survival rates in GBM patients. Interestingly, higher HES5 levels were associated with better survival rates, suggesting a complex role that needs more investigation.

CONCLUSION

This study shows that TWIST2, GATA3, and HES5 could help predict outcomes in GBM patients. Our multigene model offers a better understanding of GBM and points to new treatment options, bringing hope for improved therapies and patient outcomes. This research advances our knowledge of GBM and highlights the potential of molecular diagnostics in oncology.

HIF-1α-induced long noncoding RNA LINC02776 promotes drug resistance of ovarian cancer by increasing polyADP-ribosylation

BACKGROUND

Chemoresistance remains a major hurdle in ovarian cancer (OC) treatment, as many patients eventually develop resistance to platinum-based chemotherapy and/or PARP inhibitors (PARPi).

METHODS

We performed transcriptome-wide analysis by RNA sequencing (RNA-seq) data of platinum-resistant and -sensitive OC tissues. We demonstrated the role of LINC02776 in platinum resistance in OC cells, mice models and patient-derived organoid (PDO) models.

RESULTS

We identify the long noncoding RNA LINC02776 as a critical factor of platinum resistance. Elevated expression of LINC02776 is observed in platinum-resistant OC and serves as an independent prognostic factor for OC patients. Functionally, silencing LINC02776 reduces proliferation and DNA damage repair in OC cells, thereby enhancing sensitivity to platinum and PARPi in both xenograft mouse models and patient-derived organoid (PDO) models with acquired chemoresistance. Mechanistically, LINC02776 binds to the catalytic domain of poly (ADP-ribose) polymerase 1 (PARP1), promoting PARP1-dependent polyADP-ribosylation (PARylation) and facilitating homologous recombination (HR) restoration. Additionally, high HIF-1α expression in platinum-resistant tissues further stimulates LINC02776 transcription.

CONCLUSIONS

Our findings suggest that targeting LINC02776 represents a promising therapeutic strategy for OC patients who have developed resistance to platinum or PARPi.

KEY POINTS

LINC02776 promotes OC cell proliferation by regulating DNA damage and apoptosis signaling pathways. LINC02776 binds PARP1 to promote DNA damage-triggered PARylation in OC cells. LINC02776 mediates cisplatin and olaparib resistance in OC cells by enhancing PARP1-mediated PARylation activity and regulating the PARP1-mediated HR pathway. The high expression of LINC02776 is induced by HIF-1α in platinum-resistant OC cells and tissues.

Comprehensive discovery and functional characterization of the noncanonical proteome

The systematic identification and functional characterization of noncanonical translation products, such as novel peptides, will facilitate the understanding of the human genome and provide new insights into cell biology. Here, we constructed a high-coverage peptide sequencing reference library with 11,668,944 open reading frames and employed an ultrafiltration tandem mass spectrometry assay to identify novel peptides. Through these methods, we discovered 8945 previously unannotated peptides from normal gastric tissues, gastric cancer tissues and cell lines, nearly half of which were derived from noncoding RNAs. Moreover, our CRISPR screening revealed that 1161 peptides are involved in tumor cell proliferation. The presence and physiological function of a subset of these peptides, selected based on screening scores, amino acid length, and various indicators, were verified through Flag-knockin and multiple other methods. To further characterize the potential regulatory mechanisms involved, we constructed a framework based on artificial intelligence structure prediction and peptide‒protein interaction network analysis for the top 100 candidates and revealed that these cancer-related peptides have diverse subcellular locations and participate in organelle-specific processes. Further investigation verified the interacting partners of pep1-nc-OLMALINC, pep5-nc-TRHDE-AS1, pep-nc-ZNF436-AS1 and pep2-nc-AC027045.3, and the functions of these peptides in mitochondrial complex assembly, energy metabolism, and cholesterol metabolism, respectively. We showed that pep5-nc-TRHDE-AS1 and pep2-nc-AC027045.3 had substantial impacts on tumor growth in xenograft models. Furthermore, the dysregulation of these four peptides is closely correlated with clinical prognosis. Taken together, our study provides a comprehensive characterization of the noncanonical proteome, and highlights critical roles of these previously unannotated peptides in cancer biology.

Long non‑coding RNA signatures in breast cancer: Properties as biomarkers?

Breast cancer represents the most common type of cancer in females worldwide. The survival rates for breast cancer patients have been increasing since 1990. However, in 2023 breast cancer is still the second most common cause of malignancy-associated death in women. One decisive reason is the increase of treatment resistance and low therapy response. Therefore, new therapy targets and predictive markers for the response to treatment are needed. The present study analyzed the potential effects triggered by different breast cancer treatments on the transcriptional expression of 12 pre-selected long non-coding (lnc) RNAs and the proliferation markers Cyclin D1 and Ki-67 in six different breast cancer cell lines (BT-474, MDA-MB-231, BT-20, T-47D, SKBR-3 and MCF-7). The results revealed that lncRNA cytoskeleton regulator RNA may be an appropriate biomarker for the response to treatment with both epirubicin and gemcitabine (P<0.001). NF-ĸB interacting lnc RNA may be a marker for therapy response (P<0.001), while HOX transcript antisense RNA overexpression suggested resistance to treatment (P<0.001) with epirubicin. The transcriptional expression of lncRNA BC4 increased during treatment with epirubicin and gemcitabine, which indicated therapy response. Overall, the present data suggested that the aforementioned lncRNAs have a promising potential as biomarkers to detect early therapy response or resistance in and therefore should be analyzed in more detail.

Goose multi-omics database: A comprehensive multi-omics database for goose genomics

Multi-omics has helped elucidate the gene expression patterns and genomic variations closely associated with economically significant traits in geese. Despite the substantial genomic data generated through extensive goose studies, a unified platform for integrating these datasets is lacking. To address this gap, we introduced the Goose Multi-omics Database (GMD), which is accessible at http://goosedb.com/. The GMD is a comprehensive resource enabling streamlined search, analysis, and visualization of genetic information through a unified interface, providing insights into phenotypic traits, gene sequences, structures, expression profiles, genomic variations, gene families, homology, and collinearity. Equipped with robust analytical tools such as GBrowse and BLAST, the GMD facilitates rapid access to target gene information, significantly enhancing the efficiency and productivity of genomic research. By serving as a versatile and intuitive online repository, the GMD offers transformative potential for advancing goose biology, fostering multi-omics investigations, and integrating cutting-edge methodologies such as deep learning to accelerate discoveries in goose genomics.

LncRNAs, RNA Therapeutics, and Emerging Technologies in Liver Pathobiology

The field of ribonucleic acid (RNA) biology has revealed an array of noncoding RNA species, particularly long noncoding RNAs (lncRNAs), which play crucial roles in liver disease pathogenesis. This review explores the diverse functions of lncRNAs in liver pathology, including metabolic-associated steatotic liver disease, hepatocellular carcinoma, alcohol-related liver disease, and cholangiopathies such as primary sclerosing cholangitis and cholangiocarcinoma. We highlight key lncRNAs that regulate lipid metabolism, inflammation, fibrosis, and oncogenesis in the liver, demonstrating their diagnostic and therapeutic potential. Emerging RNA-based therapies, such as mRNA therapy, RNA interference, and antisense oligonucleotides, offer approaches to modulate lncRNA activity and address liver disease at a molecular level. Advances in sequencing technologies and bioinformatics pipelines are simultaneously enabling the identification and functional characterization of novel lncRNAs, driving innovation in personalized medicine. In conclusion, this review highlights the potential of lncRNAs as biomarkers and therapeutic targets in liver disease and emphasizes the need for further research into their regulatory mechanisms and clinical applications.

Detection of human unannotated microproteins by mass spectrometry-based proteomics: a community assessment

Thousands of short open reading frames (sORFs) are translated outside of annotated coding sequences. Recent studies have pioneered searching for sORF-encoded microproteins in mass spectrometry (MS)-based proteomics and peptidomics datasets. Here, we assessed literature-reported MS-based identifications of unannotated human proteins. We find that studies vary by three orders of magnitude in the number of unannotated proteins they report. Of nearly 10,000 reported sORF-encoded peptides, 96% were unique to a single study, and 12% mapped to annotated proteins or proteoforms. Manual curation of a benchmark dataset of 406 manually evaluated spectra from 204 sORF-encoded proteins revealed large variation in peptide-spectrum match (PSM) quality between studies, with immunopeptidomics studies generally reporting higher quality PSMs than conventional enzymatic digests of whole cell lysates. We estimate that 65% of predicted sORF-encoded protein detections in immunopeptidomics studies were supported by high-quality PSMs versus 7.8% in non-immunopeptidomics datasets. Our work stresses the need for standardized protocols and analysis workflows to guide future advancements in microprotein detection by MS towards uncovering how many human microproteins exist.

Clinical implications and molecular mechanism of long noncoding RNA LINC00518 and protein-coding genes in skin cutaneous melanoma by genome‑wide investigation

Skin cutaneous melanoma (SKCM) is a cancer with serious global impact. Long non-coding RNA was previously found to be associated with tumor prognosis. This research focuses on long intergenic non-protein coding (LINC) RNAs, and correlated protein-coding genes (PCGs), to explore their diagnostic and prognostic value, function and mechanism. Gene expression data was obtained from TCGA and Oncomine for analysis; in total there were 458 cases included in this study. LIN00518 and the 10 most highly correlated PCGs were selected to determine the diagnostic and prognostic value. We undertook bioinformatic analysis with LINC00518 and the prognostic-related PCGs in order to explore their molecular mechanism. The Connectivity Map was carried out for pharmacological target prediction and drug selection. Among the top 10 correlated PCGs, trafficking kinesin protein 2 (TRAK2), epilepsy of progressive myoclonus type 2 gene A (EPM2A) and melanocyte inducing transcription factor (MITF) had significant diagnostic value (all AUC > 0.7, P < 0.05). LINC00518, ras association domain family member 3 (RASSF3), cdk5 and Abl enzyme substrate 1 (CABLES1), kazrin, periplakin interacting protein (KAZN), EF-hand calcium binding domain 5 (EFCAB5) and MITF were significantly associated with prognosis (all adjusted P < 0.05). LINC00518 was associated with cell cycle process, melanogenesis, MAPK signaling pathway, cell division and DNA repair(all P < 0.05). Pharmacological targets analysis suggested results acquired eight potential target drugs. Up-regulation of LINC00518 is significantly associated with poor prognosis. TRAK2, EPM2A and MITF had diagnostic significance. RASSF3, CABLES1, KAZN, EFCAB5 and MITF had prognostic significance. This study provided novel biomarkers for SKCM.

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.

Long Non-Coding RNAs: Key Regulators of Tumor Epithelial/Mesenchymal Plasticity and Cancer Stemness

Long non-coding RNAs (lncRNAs) are a class of non-coding RNA molecules with transcripts longer than 200 bp, which were initially thought to be noise from genomic transcription without biological function. However, since the discovery of H19 in 1980 and Xist in 1990, increasing evidence has shown that lncRNAs regulate gene expression at epigenetic, transcriptional, and post-transcriptional levels through specific regulatory actions and are involved in the development of cancer and other diseases. Despite many lncRNAs being expressed at lower levels than those of protein-coding genes with less sequence conservation across species, lncRNAs have become an intense area of RNA research. They exert diverse biological functions such as inducing chromatin remodeling, recruiting transcriptional machinery, acting as competitive endogenous RNAs for microRNAs, and modulating protein-protein interactions. Epithelial-mesenchymal transition (EMT) is a developmental process, associated with embryonic development, wound healing, and cancer progression. In the context of oncogenesis, the EMT program is transiently activated and confers migratory/invasive and cancer stem cell (CSC) properties to tumor cells, which are crucial for malignant progression, metastasis, and therapeutic resistance. Accumulating evidence has revealed that lncRNAs play crucial roles in the regulation of tumor epithelial/mesenchymal plasticity (EMP) and cancer stemness. Here, we summarize the emerging roles and molecular mechanisms of lncRNAs in regulating tumor cell EMP and their effects on tumor initiation and progression through regulation of CSCs. We also discuss the potential of lncRNAs as diagnostic and prognostic biomarkers and therapeutic targets.

Long non-coding RNAs as key regulators of neurodegenerative protein aggregation

The characteristic events in neurodegenerative diseases (NDDs) encompass protein misfolding, aggregation, accumulation, and their related cellular dysfunction, synaptic function loss. While distinct proteins are implicated in the pathological processes of different NDDs, the process of protein misfolding and aggregation remains notably similar across various conditions. Specifically, proteins undergo misfolding into beta-folded (β-folded) conformation, resulting in the formation of insoluble amyloid proteins. Despite advancements in comprehending protein aggregation, certain facets of this intricate process remain incompletely elucidated. In recent years, the concept that long non-coding RNAs (lncRNAs) contribute to protein aggregation has gained recognition. LncRNAs influence the formation of protein aggregates by facilitating protein overexpression through the regulation of gene transcription and translation, inhibiting protein degradation via lysosomal and autophagic pathways, and targeting aberrant modifications and phase transitions of proteins. A better understanding of the relationship between lncRNAs and aberrant protein aggregation is an important step in dissecting the underlying molecular mechanisms and will contribute to the discovery of new therapeutic targets and strategies. HIGHLIGHTS: NDDs are marked by protein misfolding, aggregation, and accumulation, leading to cellular dysfunction and loss of synaptic function. Despite different proteins being involved in various NDDs, the process of misfolding into β-folded conformations and forming insoluble amyloid proteins is consistent across conditions. The role of lncRNAs in protein aggregation has gained attention, as they regulate gene transcription and translation, inhibit protein degradation, and target aberrant protein modifications. Understanding the link between lncRNAs and protein aggregation is crucial for uncovering molecular mechanisms and developing new therapeutic targets.

Role of epigenetic regulation in diminished ovarian reserve

Diminished ovarian reserve (DOR) is characterized by a decrease in the number and quality of oocytes, with its incidence increasing annually. Its pathogenesis remains unclear, making it one of the most challenging problems in the field of assisted reproduction. Epigenetic modification, a molecular mechanism affecting genomic activity and expression without altering the DNA sequence, has been widely studied in reproductive medicine and has attracted considerable attention regarding DOR. This review comprehensively examines the various epigenetic regulatory changes in ovarian granulosa cells (OGCs) and oocytes during DOR. DNA methylation plays a crucial role in regulating granulosa cell function, hormone production, and oocyte development, maturation, and senescence. Histone modifications are involved in regulating follicular activation, while non-coding RNAs, such as long noncoding RNAs (lncRNAs) and microRNAs (miRNAs), regulate granulosa cell function and oocyte development. N6-methyladenosine (m6A) modifications are associated with age-related oocyte senescence. Epigenetic clocks based on DNA methylation show potential in predicting ovarian reserve in DOR. Furthermore, it discusses the potential for utilizing epigenetic mechanisms to better diagnose and manage DOR.

Biological functions and affected signaling pathways by Long Non-Coding RNAs in the immune system

Recently, the various regulative functions of long non-coding RNAs (LncRNAs) have been well determined. Recently, the vital role of LncRNAs as gene regulators has been identified in the immune system, especially in the inflammatory response. All cells of the immune system are governed by a complex and ever-changing gene expression program that is regulated through both transcriptional and post-transcriptional processes. LncRNAs regulate gene expression within the cell nucleus by influencing transcription or through post-transcriptional processes that affect the splicing, stability, or translation of messenger RNAs (mRNAs). Recent studies in immunology have revealed substantial alterations in the expression of lncRNAs during the activation of the innate immune system as well as the development, differentiation, and activation of T cells. These lncRNAs regulate key aspects of immune function, including the manufacturing of inflammatory molecules, cellular distinction, and cell movement. They do this by modulating protein-protein interactions or through base pairing with RNA and DNA. Here we review the current understanding of the mechanism of action of lncRNAs as novel immune-related regulators and their impact on physiological and pathological processes related to the immune system, including autoimmune diseases. We also highlight the emerging pattern of gene expression control in important research areas at the intersection between immunology and lncRNA biology.

Nrf2 Signaling Pathway: Focus on Oxidative Stress in Spinal Cord Injury

Spinal cord injury (SCI) is a serious, disabling injury to the central nervous system that can lead to motor, sensory, and autonomic dysfunction below the injury plane. SCI can be divided into primary injury and secondary injury according to its pathophysiological process. Primary injury is irreversible in most cases, while secondary injury is a dynamic regulatory process. Secondary injury involves a series of pathological events, such as ischemia, oxidative stress, inflammatory events, apoptotic pathways, and motor dysfunction. Among them, oxidative stress is an important pathological event of secondary injury. Oxidative stress causes a series of destructive events such as lipid peroxidation, DNA damage, inflammation, and cell death, which further worsens the microenvironment of the injured site and leads to neurological dysfunction. The nuclear factor erythrocyte 2-associated factor 2 (Nrf2) is considered to be a key pathway of antioxidative stress and is closely related to the pathological process of SCI. Activation of this pathway can effectively inhibit the oxidative stress process and promote the recovery of nerve function after SCI. Therefore, the Nrf2 pathway may be a potential therapeutic target for SCI. This review deeply analyzed the generation of oxidative stress in SCI, the role and mechanism of Nrf2 as the main regulator of antioxidant stress in SCI, and the influence of cross-talk between Nrf2 and related pathways that may be involved in the pathological regulation of SCI on oxidative stress, and summarized the drugs and other treatment methods based on Nrf2 pathway regulation. The objective of this paper is to provide evidence for the role of Nrf2 activation in SCI and to highlight the important role of Nrf2 in alleviating SCI by elucidating the mechanism, so as to provide a theoretical basis for targeting Nrf2 pathway as a therapy for SCI.

Landscape of Noncoding RNA in the Hypoxic Tumor Microenvironment

Amidst the prevalent and notable characteristic of a hypoxic microenvironment present in the majority of solid tumors, a burgeoning number of studies have revealed the significance of noncoding RNAs (ncRNAs) in hypoxic tumor regions. The transcriptome of cancers is highly heterogeneous, with noncoding transcripts playing crucial roles. Long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) are two distinctive classes of ncRNA that are garnering increasing attention. Biologically, they possess intriguing properties and possess significant regulatory functions. Clinically, they present as promising biomarkers and therapeutic targets. Additionally, recent research has evaluated the clinical applications of these ncRNAs in RNA-based treatments and noninvasive liquid biopsies. This review provides a comprehensive summary of recent studies on lncRNAs and circRNAs within the hypoxic tumor microenvironment. Furthermore, the clinical significance of lncRNAs and circRNAs in cancer diagnosis and treatment is emphasized, which could pave the way for the development of effective targeted therapies.

Expression study of Wnt/β-catenin signaling pathway associated lncRNAs in schizophrenia

Schizophrenia is one of the most debilitating mental illnesses affecting any age group. The mechanism and etiology of schizophrenia are extremely complex and multiple signaling pathways recruit genes implicated in the etiology of this disease. While the role of Wnt/β-catenin signaling in this disorder has been verified, the impact of long noncoding RNAs (lncRNAs) associated with this pathway has not been studied in schizophrenia. The objective of this study was to examine the expression levels of Wnt/β-catenin-related lncRNAs, namely CCAT2, SNHG5, PTCSC3, and DANCR, as well as the CTNNB1 gene encoding beta-catenin protein in two groups of schizophrenia patients (drug-naïve and medicated) compared with healthy individuals. This study included 50 medicated patients in the remission phase of the disease, 25 drug-naive patients in the acute phase, and 50 control subjects. There was no significant difference in CTNNB1 gene expression in the medicated patients compared to controls (P value = 0.9754). However, the expression of this gene was significantly decreased in drug-naïve first-episode patients compared with controls (P value < 0.001). In contrast, expression of DANCR, PTCSC3, SNHG5, and CCAT2 genes was significantly higher in medicated (P values < 0.001, < 0.001, = 0.01, < 0.001, respectively) and drug-naive first-episode patients (P value < 0.001) compared to control subjects. ROC curve analysis revealed that DANCR, PTCSC3, SNHG5, and CCAT2 genes had diagnostic power with specificity and sensitivity of 80% and above in separation between study subgroups. In brief, our data demonstrated dysregulation of Wnt/β pathway related genes and lncRNAs in the peripheral blood of patients with schizophrenia and their potential as biomarkers for this disorder.

Genome-wide identification of long non-coding RNA for Botrytis cinerea during infection to tomato (Solanum lycopersicum) leaves

Long non-coding RNA (lncRNA) plays important roles in animals and plants. In filamentous fungi, however, their biological function in infection stage has been poorly studied. Here, we investigated the landscape and regulation of lncRNA in the filamentous plant pathogenic fungus Botrytis cinerea by strand-specific RNA-seq of multiple infection stages. In total, 1837 lncRNAs have been identified in B. cinerea. A large number of lncRNAs were found to be antisense to mRNAs, forming 743 sense-antisense pairs, of which 55 antisense lncRNAs and their respective sense transcripts were induced in parallel as the infection stage. Although small RNAs were produced from these overlapping loci, antisense lncRNAs appeared not to be involved in gene silencing pathways. In addition, we found the alternative splicing events occurred in lncRNA. These results highlight the developmental stage-specific nature and functional potential of lncRNA expression in the infection stage and provide fundamental resources for studying infection stage-induced lncRNAs.

Update of the FANTOM web resource: enhancement for studying noncoding genomes

The FANTOM web resource (https://fantom.gsc.riken.jp/) has been a unique resource for studying mammalian genomes, which is built on the research activities conducted in the international collaborative project FANTOM (Functional ANnoTation Of the Mammalian genome). In recent updates, we expanded annotations for long non-coding RNAs (lncRNAs) and transcribed cis-regulatory elements (CREs). The former was derived from the large-scale lncRNA perturbations in induced pluripotent stem cells (iPSCs) and integrative analysis of Hi-C data conducted in the sixth iteration of the project (FANTOM6). The resulting annotations of lncRNAs, according to the impact on cellular and molecular phenotypes and the potential RNA-chromatin interactions, are accessible via the interactive ZENBU-Reports framework. The latter involves a new platform, fanta.bio (https://fanta.bio/), which collects transcribed CREs identified via use of an extended dataset of CAGE profiles. The CREs, with their annotations including genetic and epigenetic information, are accessible via a dedicated interface as well as the UCSC Genome Browser Database. These updates offer enhanced opportunities to investigate the functions of non-coding regions within mammalian genomes.

Light-regulated microRNAs shape dynamic gene expression in the zebrafish circadian clock

A key property of the circadian clock is that it is reset by light to remain synchronized with the day-night cycle. An attractive model to explore light input to the circadian clock in vertebrates is the zebrafish. Circadian clocks in zebrafish peripheral tissues and even zebrafish-derived cell lines are entrainable by direct light exposure thus providing unique insight into the function and evolution of light regulatory pathways. Our previous work has revealed that light-induced gene transcription is a key step in the entrainment of the circadian clock as well as enabling the more general adaptation of zebrafish cells to sunlight exposure. However, considerable evidence points to post-transcriptional regulatory mechanisms, notably microRNAs (miRNAs), playing an essential role in shaping dynamic changes in mRNA levels. Therefore, does light directly impact the function of miRNAs? Are there light-regulated miRNAs and if so, which classes of mRNA do they target? To address these questions, we performed a complete sequencing analysis of light-induced changes in the zebrafish transcriptome, encompassing small non-coding RNAs as well as mRNAs. Importantly, we identified sets of light-regulated miRNAs, with many regulatory targets representing light-inducible mRNAs including circadian clock genes and genes involved in redox homeostasis. We subsequently focused on the light-responsive miR-204-3-3p and miR-430a-3p which are predicted to regulate the expression of cryptochrome genes (cry1a and cry1b). Luciferase reporter assays validated the target binding of miR-204-3-3p and miR-430a-3p to the 3'UTRs of cry1a and cry1b, respectively. Furthermore, treatment with mimics and inhibitors of these two miRNAs significantly affected the dynamic expression of their target genes but also other core clock components (clock1a, bmal1b, per1b, per2, per3), as well as the rhythmic locomotor activity of zebrafish larvae. Thus, our identification of light-responsive miRNAs reveals new intricacy in the multi-level regulation of the circadian clockwork by light.

The perinucleolar compartment and the oncogenic super-enhancers are part of the same phase-separated structure filled with phosphatidylinositol 4,5-bisphosphate and long non-coding RNA HANR

The liquid-liquid phase separation in the cell nucleus regulates various processes such as gene regulation and transcription control, chromatin organization, and DNA repair. A plethora of proteins and RNAs contribute to the formation of biomolecular condensates and recently, several nuclear phosphoinositides were shown to be a part of these membrane-less complexes within the nucleus as well. Here we lipid-interacting RNA sequencing (LIPRNAseq) and confocal microscopy to uncover the RNA-binding capacity and localization of phosphatidylinositol 4,5 bisphosphate (PIP2). We discovered the consensus PIP2-binding AU-rich RNA motif and identified long non-coding RNA HANR (lncHANR) to colocalize with PIP2 in the proximity to the nucleolus in the perinucleolar compartment (PNC). Colocalization studies with different nuclear markers reveal that PIP2-HANR presence in the PNC correlates with oncogenic super-enhancers, and both PNC and oncogenic enhancers are part of the same structure. As lncHANR, PNC, and oncogenic super-enhancers are associated with cancer cell lines and tumors, we suggest that they can serve as interchangeable prognostic markers. Understanding of the interplay between lipid metabolism, and lncRNAs in subnuclear compartment phase separation can lead to future improvement in treatment strategies and personalized cancer management approaches.

Architects and Partners: The Dual Roles of Non-coding RNAs in Gene Fusion Events

Extensive research into gene fusions in cancer and other diseases has led to the discovery of novel biomarkers and therapeutic targets. Concurrently, various bioinformatics tools have been developed for fusion detection in RNA sequencing data, which, in the age of increasing affordability of sequencing, have delivered a large-scale identification of transcriptomic abnormalities. Historically, the focus of fusion transcript research was predominantly on coding RNAs and their resultant proteins, often overlooking non-coding RNAs (ncRNAs). This chapter discusses how ncRNAs are integral players in the landscape of gene fusions, detailing their contributions to the formation of gene fusions and their presence in chimeric transcripts. We delve into both linear and the more recently identified circular fusion RNAs, providing a comprehensive overview of the computational methodologies used to detect ncRNA-involved gene fusions. Additionally, we examine the inherent biases and limitations of these bioinformatics approaches, offering insights into the challenges and future directions in this dynamic field.

Interplay between lncRNAs and the PI3K/AKT signaling pathway in the progression of digestive system neoplasms (Review)

Long non‑coding RNA (lncRNA) is a class of non‑coding RNA molecules located in the cytoplasm or nucleus, which can regulate chromosome structure and function by interacting with DNA, RNA, proteins and other molecules; binding to mRNA bases in a complementary manner, affecting the splicing, stabilization, translation and degradation of mRNA; acting as competing endogenous RNA competitively binds to microRNAs to regulate gene expression and participate in the regulation of various vital activities of the body. The PI3K/AKT signalling pathway plays a key role in numerous biological and cellular processes, such as cell proliferation, invasion, migration and angiogenesis. It has been found that the lncRNA/PI3K/AKT axis regulates the expression of cancer‑related genes and thus tumour progression. The abnormal regulation of lncRNA expression in the lncRNA/PI3K/AKT axis is clearly associated with clinicopathological features and plays an important role in regulating biological functions. In the present review, the expression and biological functions of PI3K/AKT‑related lncRNAs both in vitro and in vivo over recent years, were comprehensively summarized and analyzed. Their correlation with clinicopathological features was also evaluated, with the objective of furnishing a solid theoretical foundation for clinical diagnosis and the monitoring of efficacy in digestive system neoplasms. The present review aimed to provide a comprehensive overview of the expression and biological functions of PI3K/AKT‑related lncRNAs in digestive system neoplasms and to assess their correlation with clinicopathological features. This endeavor seeks to establish a solid theoretical foundation for the clinical diagnosis and efficacy monitoring of digestive system tumors.

The Emerging Role of LncRNA AWPPH in Multiple Cancers: A Review Study

Long non-coding RNAs (lncRNAs) are transcribed RNA molecules longer than 200 nucleotides in length that have no protein-coding potential. They are able to react with DNA, RNA, and protein. Hence they involve in regulating gene expression at the epigenetic, transcriptional, post-transcriptional, and translational levels. LncRNAs have been proven to play an important role in human malignancies and prognostic outcomes. In this review, we will comprehensively and functionally discuss the role of a novel identified lncRNA, namely lncRNA WAPPH located on human chromosome 2q13, in various cancers. Increasing research studies have shown that lncRNA AWPPH is deregulated in different malignancies, including breast cancer, gastric cancer, colorectal cancer, ovarian cancer, bladder cancer, leukemia, and others. LncRNA WAPPH serves as an oncogene in tumorigenesis and the development of cancer. Moreover, lncRNA AWPPH is involved in numerous biological processes of solid and blood cancers. Taken together, based on our scrutiny analysis, lncRNA AWPPH can be regarded as a putative biomarker for diagnosis or therapeutic target in human malignancies.

Computational Resources for lncRNA Functions and Targetome

Long non-coding RNAs (lncRNAs) are a type of non-coding RNA molecules exceeding 200 nucleotides in length and that do not encode proteins. The dysregulated expression of lncRNAs has been identified in various diseases, holding therapeutic significance. Over the past decade, numerous computational resources have been published in the field of lncRNA. In this chapter, we have provided a comprehensive review of the databases as well as predictive tools, that is, lncRNA databases, machine learning based algorithms, and tools predicting lncRNAs utilizing different techniques. The chapter will focus on the importance of lncRNA resources developed for different organisms specifically for humans, mouse, plants, and other model organisms. We have enlisted important databases, primarily focusing on comprehensive information related to lncRNA registries, associations with diseases, differential expression, lncRNA transcriptome, target regulations, and all-in-one resources. Further, we have also included the updated version of lncRNA resources. Additionally, computational identification of lncRNAs using algorithms like Deep learning, Support Vector Machine (SVM), and Random Forest (RF) was also discussed. In conclusion, this comprehensive overview concludes by summarizing vital in silico resources, empowering biologists to choose the most suitable tools for their lncRNA research endeavors. This chapter serves as a valuable guide, emphasizing the significance of computational approaches in understanding lncRNAs and their implications in various biological contexts.

LncSL: A Novel Stacked Ensemble Computing Tool for Subcellular Localization of lncRNA by Amino Acid-Enhanced Features and Two-Stage Automated Selection Strategy

Long non-coding RNA (lncRNA) is a non-coding RNA longer than 200 nucleotides, crucial for functions like cell cycle regulation and gene transcription. Accurate localization prediction from sequence information is vital for understanding lncRNA's biological roles. Computational methods offer an effective alternative to traditional experimental methods for annotating lncRNA subcellular positions. Existing machine learning-based methods are limited and often overlook regions with coding potential that affect the function of lncRNA. Therefore, we propose a new model called LncSL. For feature encoding, both lncRNA sequences and amino acid sequences from open reading frames (ORFs) are employed. And we selected the most suitable features by CatBoost and integrated them into a new feature set. Additionally, a voting process with seven feature selection algorithms identified the higher contributive features for training our final stacked model. Additionally, an automatic model selection strategy is constructed to find a better performance meta-model for assembling LncSL. This study specifically focuses on predicting the subcellular localization of lncRNA in the nucleus and cytoplasm. On two benchmark datasets called S1 and S2 datasets, LncSL outperformed existing methods by 6.3% to 12.3% in the Matthew's correlation coefficient on a balanced test dataset. On an unbalanced independent test dataset sourced from S1, LncSL improved by 4.7% to 18.6% in the Matthew's correlation coefficient, which further demonstrates that LncSL is superior to other compared methods. In all, this study presents an effective method for predicting lncRNA subcellular localization through enhancing sequence information, which is always overlooked by traditional methods, and addressing contributive meta-model selection problems, which can offer new insights for other bioinformatics problems.

lncRNA H19 plays a role in multiple myeloma via interacting with hnRNPA2B1 to stabilize BET proteins by targeting osteoclasts and osteoblasts

BACKGROUND

Multiple myeloma (MM), characterized with bone marrow microenvironment disorder, accounts for about 20% of hematological cancer deaths globally. Tissue extracellular communication, especially extracellular vesicles, has been defined as important mediator among cell-to-cell cross-talk. Our previous study revealed an elevated level of H19 in MM, whereas, its role in MM exosomes in the development of osteolysis remains largely unknown.

METHOD

MM exosomes referring to 5TGM1 cells were isolated and characterized using transmission electron microscopy (TEM), nanoparticle tracking and western blot analysis. The biological effects of blocking H19 were examined on osteolysis in vivo of C57Bl6/KalwRij mice, as well as on the osteoclast differentiation in vitro of RAW264.7 cells, by the application of TRAP, either with osteogenic differentiation in vitro of bone marrow mesenchymal stem cells (BMSCs), by the detection of alkaline phosphatase (ALP), alizarin red dye staining (ARS). The targeted relationships among H19/hnRNPA2B1/BET proteins were validated through RNA immunoprecipitation (RIP) and RNA pull-down assays.

RESULTS

5TGM1 cells derived-exosomes lacking H19 dramatically blocked osteolysis and boosted osteogeneis in C57Bl6/KalwRij mice, either with osteoclastic differentiation of RAW264.7 cells and osteogenic differentiation of BMSCs, thereby enhancing their resorptive activity. Physically, H19 interacted with hnRNPA2B1 by preferentially adhering to it and enhancing its nuclear-cytoplasmic translocation. Further mechanistic research validated that H19 promoted the stabilization of BET proteins through hnRNA2B1 to be involved in osteoclast differentiation for contributing to MM progression.

CONCLUSION

Altogether, our findings suggest that H19, serving as an essential role for exosomes in the bone marrow environment, might be a viable diagnostic and therapeutic target for MM therapy.

Posttranscriptional Regulation of Intestinal Mucosal Growth and Adaptation by Noncoding RNAs in Critical Surgical Disorders

The human intestinal epithelium has an impressive ability to respond to insults and its homeostasis is maintained by well-regulated mechanisms under various pathophysiological conditions. Nonetheless, acute injury and inhibited regeneration of the intestinal epithelium occur commonly in critically ill surgical patients, leading to the translocation of luminal toxic substances and bacteria to the bloodstream. Effective therapies for the preservation of intestinal epithelial integrity and for the prevention of mucosal hemorrhage and gut barrier dysfunction are limited, primarily because of a poor understanding of the mechanisms underlying mucosal disruption. Noncoding RNAs (ncRNAs), which include microRNAs (miRNAs), long ncRNAs (lncRNAs), circular RNAs (circRNAs), and small vault RNAs (vtRNAs), modulate a wide array of biological functions and have been identified as orchestrators of intestinal epithelial homeostasis. Here, we feature the roles of many important ncRNAs in controlling intestinal mucosal growth, barrier function, and repair after injury-particularly in the context of postoperative recovery from bowel surgery. We review recent literature surrounding the relationships between lncRNAs, microRNAs, and RNA-binding proteins and how their interactions impact cell survival, proliferation, migration, and cell-to-cell interactions in the intestinal epithelium. With advancing knowledge of ncRNA biology and growing recognition of the importance of ncRNAs in maintaining the intestinal epithelial integrity, ncRNAs provide novel therapeutic targets for treatments to preserve the gut epithelium in individuals suffering from critical surgical disorders.