A Peptide Encoded by a Putative lncRNA HOXB-AS3 Suppresses Colon Cancer Growth

LINC02593 impedes cell senescence via COP1-mediated p53 degradation in cervical cancer

Evasion of cellular senescence is one of the hallmarks of cervical carcinoma (CC) to maintain malignant development. Even though the regulators driving CC cell senescence are widely recognized, the underlying upstream mechanisms are still not fully understood. Long non-coding RNAs (lncRNAs) are emerging as important regulators in cell senescence. Here, we conducted a lncRNA profiling and identified LINC02593 as a significantly downregulated lncRNA in induced senescent cervical squamous cell carcinoma (CSCC) cells. LINC02593 is upregulated in CSCC tissues. Depletion of LINC02593 resulted in a marked cellular senescence phenotype and tumor growth inhibition in vitro and in vivo, whereas LINC02593 overexpression suppressed doxorubicin-induced cell senescence. LINC02593 was shown to impede cell senescence by inhibiting p21 expression, and this regulation was mainly dependent on p53 protein degradation. Mechanistically, LINC02593 served as a scaffold, bridging the coiled-coil domain of COP1 and the C-terminal domain of p53, enhancing the affinity between p53 and its E3 ubiquitin ligase COP1. The "scaffold" function facilitated p53 degradation by COP1 as well as the downstream p21 repression, eventually evading cell senescence. Overall, we characterized a previously unknown mechanism by which LINC02593 manipulated senescence to promote CC progression.

A Peptide Encoded by lncRNA HOXB-AS3 Promotes Cigarette Smoke-Induced Inflammation in Bronchial Epithelial Cells via EZH2-Mediated H3K27me3 Modification

Background

Chronic obstructive pulmonary disease (COPD) primarily results from cigarette smoke (CS)-induced chronic inflammation. Although numerous long non-coding ribonucleic acids (lncRNAs) have been extensively studied for their crucial roles in COPD, the peptides encoded by these lncRNAs have garnered limited attention. This study aimed to investigate the role of a peptide encoded by lncRNA HOXB-AS3 in cigarette smoke extract (CSE)-induced inflammation and in 16HBE cells.

Methods

Open reading frames (ORF) Find software was utilized to predict the encoding potential of HOXB-AS3. Quantitative real-time polymerase chain reaction (qRT-PCR) was employed to detect the levels of peptide HOXB-AS3-32aa in peripheral blood mononuclear cells (PBMCs) from both healthy controls and COPD patients and in 16HBE cells exposed to different CSE. To establish an in vitro inflammatory cell model of COPD, 16HBE cells were treated with 2% CSE. Enzyme-Linked Immunosorbent Assay (ELISA) measured inflammatory cytokines, while CCK-8 assay assessed cell viability. Flow cytometry was employed to assess cell apoptosis. Western blot analysis was performed to measure the expression of HOXB-AS3-32aa, EZH2, and H3K27me3 proteins. Co-Immunoprecipitation (Co-IP) was conducted to verify the interaction between EZH2 and HOXB-AS3-32aa.

Results

Our findings revealed elevated expression of HOXB-AS3-32aa in PBMCs of COPD patients compared to controls. CSE treatment dose-dependently increased HOXB-AS3-32aa expression. Overexpression of HOXB-AS3-32aa exacerbated CS-induced inflammation in bronchial epithelial cells, leading to inhibited cell proliferation and increased cell apoptosis. Furthermore, HOXB-AS3-32aa suppressed EZH2 and H3k27me3 protein levels in 16HBE cells. Co-IP results confirmed the interaction between HOXB-AS3-32aa and EZH2 protein.

Conclusion

Our results demonstrate that the novel peptide HOXB-AS3-32aa encoded by lncRNA HOXB-AS3 promotes CS-induced inflammation and apoptosis in 16HBE cells via EZH2-mediated H3K27me3 modification.

Beyond the Transcript: Translating Non-Coding RNAs and Their Impact on Cellular Regulation

Non-coding RNAs (ncRNAs) constitute the majority of the human transcriptome and play diverse structural, catalytic, and regulatory roles. The ability of ncRNAs to be translated into functional peptides and microproteins expands our understanding of their regulatory potential beyond their established non-coding functions. Our comprehensive search identified 86 translating "non-coding" RNAs. While translating ncRNAs have traditionally been categorized as "peptide-encoding", in this study, we introduce a novel classification based on amino acid length, distinguishing their products as ncRNA encoded peptides (ncRNA-PEPs), which are less than 60 amino acids, or ncRNA encoded microproteins (ncRNA-MPs) ranging from 61 to 200 amino acids. These peptides and microproteins act as co-regulators in cell signaling, transcriptional regulation, and protein complex assembly, playing a role in both health and disease. We outline the molecular pathways by which ncRNA-PEPs and ncRNA-MPs could govern cell cycle progression, highlighting their influence on cell cycle transitions, oncogenic and tumor suppressor pathways, metabolic homeostasis, autophagy, and on key cell cycle regulators like PCNA, Rad18, and CDK-cyclin complexes. Furthermore, we highlight recent advancements in their detection and characterization, exploring their evolutionary origins, species-specific conservation, and potential therapeutic applications. Our findings underscore the emerging significance of ncRNA-PEPs and ncRNA-MPs as integral regulators of cellular processes, highlighting their functional versatility and opening promising avenues for further research and potential therapeutic applications.

Harnessing Noncanonical Proteins for Next-Generation Drug Discovery and Diagnosis

Noncanonical proteins, encoded by previously overlooked genomic regions (part of the "dark genome"), are emerging as crucial players in human health and disease, expanding our understanding of the "dark proteome." This review explores their landscape, including proteins derived from long non-coding RNAs, circular RNAs, and alternative open reading frames. Recent advances in ribosome profiling, mass spectrometry, and proteogenomics have unveiled their involvement in critical cellular processes. We examine their roles in cancer, neurological disorders, cardiovascular diseases, and infectious diseases, highlighting their potential as novel biomarkers and therapeutic targets. The review addresses challenges in identifying and characterizing these proteins, particularly recently evolved ones, and discusses implications for drug discovery, including cancer immunotherapy and neoantigen sources. By synthesizing recent findings, we underscore the significance of noncanonical proteins in expanding our understanding of the human genome and proteome, and their promise in developing innovative diagnostic tools and targeted therapies. This overview aims to stimulate further research into this unexplored biological space, potentially revolutionizing approaches to disease treatment and personalized medicine.

From non-coding RNAs to cancer regulators: The fascinating world of micropeptides

Micropeptides are commonly identified as peptides encoded by non-coding RNAs (ncRNAs). In the short open reading frame (sORF) of ncRNAs, there is a base sequence encoding functional micropeptides, which is of great significance in the biological field. Recently, micropeptides regulate diverse processes, including mitochondrial metabolism, calcium transport, mRNA splicing, signal transduction, myocyte fusion, and cellular senescence, regulating the homeostasis of the internal environment and cancer's incidence and progression. Especially, the study of micropeptides in cancer about the potential regulatory mechanism will be conducive to further understanding of the process of cancer initiation and development. More and more research shows micropeptides have been confirmed to play an essential role in the emergence of multiple kinds of cancers, including Breast cancer, Colon cancer, Colorectal cancer, Glioma, Glioblastoma, and Liver cancer. This review presents a comprehensive synthesis of the latest advancements in our understanding of the biological roles of micropeptides in cancer cells, with a particular focus on the regulatory networks involving micropeptides in oncogenesis. The new mode of action of micropeptides provides innovative ideas for cancer diagnosis and treatment. Moreover, we explored the significant capacity of micropeptides as diagnostic biomarkers and targets for anti-cancer therapies in cancer clinical settings, highlighting their role in the development of innovative micropeptide-based diagnostic tools and anti-cancer therapeutics.

The intersection of ferroptosis and non-coding RNAs: a novel approach to ovarian cancer

Understanding the core principles of ovarian cancer has been significantly improved through the exploration of Ferroptosis, a type of cell death triggered by iron that leads to an increase in lipid peroxides. Current research has shed light on the critical functions of non-coding RNAs, such as circRNAs, lncRNAs, and miRNAs, in regulating ferroptosis in ovarian cancer. The aim of this paper is to comprehensively analyze how ncRNAs influence the development of ferroptosis in ovarian cancer cells. In-depth exploration is undertaken to understand the intricate ways in which ncRNAs regulate essential elements of ferroptosis, including iron management and lipid peroxidation levels. We also investigate their significant involvement in the progression of this type of cellular demise. It should be emphasized that ncRNAs can impact the synthesis of crucial proteins, such as GPX4, a key contributor to the cellular defense against oxidation, and ACSL4, involved in lipid formation. In addition, we examine the correlation between ncRNAs and well-known pathways associated with oxidative stress and cell death. The consequences of these discoveries are noteworthy, since focusing on particular ncRNAs could potentially render ovarian cancer cells more vulnerable to ferroptosis, effectively combating drug resistance problems. This discussion highlights the growing significance of ncRNAs in governing ferroptosis and their potential as useful biomarkers and treatment targets for ovarian cancer. We intend to promote additional research into the involvement of ncRNAs in controlling ferroptosis, based on current findings, with the ultimate goal of informing targeted therapeutic strategies and improving long-term treatment outcomes for individuals suffering from OC.

Inhibition of colorectal cancer cell growth by downregulation of M2-PK and reduction of aerobic glycolysis by clove active ingredients

Exploring the anti-tumor molecular mechanisms of traditional Chinese medicines has become an important strategy to develop novel anti-tumor drugs in the clinic. Several pharmacological studies have reported the antioxidant, antibacterial, anti-inflammatory, and anti-tumor effects of clove. Previously, we have shown that the active fraction from clove (AFC) can inhibit the growth of tumor cells, particularly colon cancer cells, in vitro. However, the mechanism of action regarding the anti-colon cancer activity of AFC, especially in aerobic glycolysis, has not been adequately investigated. In this study, we found that AFC significantly inhibited the growth of five types of colon cancer cells, downregulated the mRNA and protein levels of M2-type pyruvate kinase (PKM2), and reduced aerobic glycolysis capacity. Transfection of PKM2-siRNA mimicked the inhibitory effects of AFC on aerobic glycolysis in colon cancer cells. Furthermore, the highly expressed, tumor-specific targets c-myc and cyclin D1 in cells were also found to be downregulated following the action of AFC. In the HCT116 cell xenograft nude mice models, the results after AFC administration were consistent with those of the cellular experiments, while AFC caused less liver injury and weight loss than the conventional chemotherapeutic agent 5- fluorouracil (5-FU). In conclusion, AFC inhibits colon cancer growth by downregulating PKM2 to inhibit aerobic glycolysis and reduce the tumor-specific high expression of c-myc and cyclin D1. Future work should explore how it downregulates pyruvate kinase (PK) in the first place, along with the intrinsic mechanism between the downregulation of PKM2 and the downregulation of c-myc.

Main methods and tools for peptide development based on protein-protein interactions (PPIs)

Protein-protein interactions (PPIs) regulate essential physiological and pathological processes. Due to their large and shallow binding surfaces, PPIs are often considered challenging drug targets for small molecules. Peptides offer a viable alternative, as they can bind these targets, acting as regulators or mimicking interaction partners. This review focuses on competitive peptides, a class of orthosteric modulators that disrupt PPI formation. We provide a concise yet comprehensive overview of recent advancements in in-silico peptide design, highlighting computational strategies that have improved the efficiency and accuracy of PPI-targeting peptides. Additionally, we examine cutting-edge experimental methods for evaluating PPI-based peptides. By exploring the interplay between computational design and experimental validation, this review presents a structured framework for developing effective peptide therapeutics targeting PPIs in various diseases.

Current Perspectives on Functional Involvement of Micropeptides in Virus-Host Interactions

Micropeptides (miPEPs), encoded by short open reading frames (sORFs) within various genomic regions, have recently emerged as critical regulators of multiple biological processes. In particular, these small molecules are now increasingly being recognized for their role in modulating viral replication, pathogenesis, and host immune responses. Both host miPEPs and virus-derived miPEPs have been noted for their ability to regulate virus-host interactions through diversified mechanisms such as altering protein stability and modulating protein-protein interactions. Although thousands of sORFs have been annotated as having the potential to encode miPEPs, only a small number have been experimentally validated so far, with some directly linked to virus-host interactions and a small subset associated with immune modulation, indicating that the investigation of miPEPs is still in its infancy. The systematic identification, translational status assessment, in-depth characterization, and functional analysis of a substantial fraction of sORFs encoding miPEPs remain largely underexplored. Further studies are anticipated to uncover the intricate mechanisms underlying virus-host interactions, host immune modulation, and the broader biological functions of miPEPs. This article will review the emerging roles of miPEPs in virus-host interactions and host immunity, and discuss the challenges and future perspectives of miPEP studies.

Analysis of RNA translation with a deep learning architecture provides new insight into translation control

Accurate annotation of coding regions in RNAs is essential for understanding gene translation. We developed a deep neural network to directly predict and analyze translation initiation and termination sites from RNA sequences. Trained with human transcripts, our model learned hidden rules of translation control and achieved a near perfect prediction of canonical translation sites across entire human transcriptome. Surprisingly, this model revealed a new role of codon usage in regulating translation termination, which was experimentally validated. We also identified thousands of new open reading frames in mRNAs or lncRNAs, some of which were confirmed experimentally. The model trained with human mRNAs achieved high prediction accuracy of canonical translation sites in all eukaryotes and good prediction in polycistronic transcripts from prokaryotes or RNA viruses, suggesting a high degree of conservation in translation control. Collectively, we present TranslationAI (https://www.biosino.org/TranslationAI/), a general and efficient deep learning model for RNA translation that generates new insights into the complexity of translation regulation.

Endogenous micropeptides as potential diagnostic biomarkers and therapeutic drugs

Micropeptides, these small proteins derived from non-coding RNA, typically consist of no more than 100 amino acids in length. Despite the challenges in analysis and identification, their various critical functions within organisms cannot be overlooked. They play a significant role in maintaining energy metabolism balance, regulating the immune system, and influencing the development of tumors, which also gives them a decisive impact on the occurrence and development of various diseases. This review aims to outline the role and potential value of micropeptides, introducing their tissue classification and distribution, biological functions, and mechanisms, with a focus on their potential as diagnostic markers and therapeutic drugs.

Unveiling the multifaceted roles of long non-coding RNA CTBP1-DT in human diseases: Special attention to its microprotein-encoding potential

C-terminal binding protein 1 divergent transcript (CTBP1-DT) is a novel long non-coding RNA (lncRNA) located on human chromosome 4p16.3. Numerous studies have shown that CTBP1-DT plays a critical regulatory role in various human malignancies and non-malignant diseases. In several cancers, the expression of CTBP1-DT is upregulated, closely associated with the risk of 12 types of cancer, and strongly correlated with the clinical pathological features and poor prognosis of 10 of these cancers. Mechanistically, CTBP1-DT is stimulated by the transcription factors ETV5 and Sp1, or methylated by YTHDC1. By competitively inhibiting 12 microRNAs, it activates 3 signaling pathways that influence malignant behaviors of tumor cells, including proliferation, apoptosis, cell cycle arrest, migration, invasion, immune evasion, and chemoresistance. Importantly, it also encodes the microprotein DNA damage up-regulated protein (DDUP), which mediates cisplatin resistance through sustained response to DNA damage signals. Furthermore, CTBP1-DT has been implicated in the progression of non-malignant diseases such as diabetes and related conditions, cardiovascular diseases, and osteoarthritis. This review summarizes the latest research on the RNA and protein functions of CTBP1-DT in human diseases, outlines various molecular regulatory networks centered around CTBP1-DT, and discusses the opportunities and challenges of its clinical applications.

SERTM2: a neuroactive player in the world of micropeptides

In this study, we analyze the long noncoding RNA, lncMN3, that is predominantly expressed in motor neurons and shows potential coding capabilities. Utilizing custom antibodies, we demonstrate the production of a lncMN3-derived type I transmembrane micropeptide, SERTM2. Patch-clamp experiments performed on both wild-type and SERTM2 knockout motor neurons, differentiated in vitro from mouse embryonic stem cells, show a difference in the resting membrane potential and overall decreased excitability upon SERTM2 depletion. In vivo studies indicate that the absence of the peptide impairs treadmill test performance. At the mechanistic level, we identify a two-pore domain potassium channel, TASK1, known to be a major determinant of the resting membrane potential in motor neurons, as a SERTM2 interactor. Our study characterizes one of the first lncRNA-derived micropeptides involved in neuronal physiology.

Overexpression of lncRNA22524 from Dongxiang Wild Rice Reduces Drought and Salt Stress Tolerance in Cultivated Rice

Drought and salt stresses are major challenges to rice production, and a deep understanding of the mechanisms for tolerance could help deal with the challenges. Long non-coding RNAs (lncRNAs) play crucial roles in gene regulation. Previously, lncRNA22524 has been identified as a drought stress-responsive lncRNA from Dongxiang wild rice (DXWR). Nevertheless, its reactions to abiotic stresses in genetics and physiology remained unclear. In this study, we employed a rapid amplification of cDNA ends (RACE) to obtain the full-length cDNA of lncRNA22524 from DXWR, analyzed its cellular localization, built an overexpression vector to generate transgenic lines of cultivated rice and evaluated its impact in genetics and physiology. After treated with drought and salt stress, the overexpressed lines exhibited much more injuries and lower rates of survival, more reactive oxygen species (ROS) and malondialdehyde (MDA), lower antioxidant enzymes and lower proline (Pro) and soluble sugar (SS) than their wild-type (WT). Furthermore, transcriptome analysis of overexpressed lines with weaker tolerance than WT revealed 1,233 differentially expressed genes (DEGs), where most DEGs were involved in phenylpropanoid biosynthesis, photosynthesis and glutathione metabolism. These findings demonstrated that lncRNA22524 negatively regulated rice responses to drought and salt stress, which clear way of working from transcription to metabolic products should be worth of further study.

A large-scale sORF screen identifies putative microproteins involved in cancer cell fitness

The human genome contains thousands of potentially coding short open reading frames (sORFs). While a growing set of microproteins translated from these sORFs have been demonstrated to mediate important cellular functions, the majority remains uncharacterized. In our study, we performed a high-throughput CRISPR-Cas9 knock-out screen targeting 11,776 sORFs to identify microproteins essential for cancer cell line growth. We show that the CENPBD2P gene encodes a translated sORF and promotes cell fitness. We selected five additional candidate sORFs encoding microproteins between 11 and 63 amino acids in length for further functional assessment. Green fluorescent protein fusion constructs of these microproteins localized to distinct subcellular compartments, and the majority showed reproducible biochemical interaction partners. Studying the fitness and transcriptome of sORF knock-outs and complementation with the corresponding microprotein, we identify rescuable phenotypes while also illustrating the limitations and caveats of our pipeline for sORF functional screening and characterization.

The Long Noncoding RNA DUXAP8 Facilitates the Malignant Progression of Colon Cancer via the microRNA-378a-3p/FOXQ1 Axis

Background/Aims

The long noncoding RNA DUXAP8 is a pivotal regulator in cancer pathogenesis, but the molecular mechanism underlying the role of DUXAP8 in colon cancer progression is underexplored.

Methods

In addition to bioinformatic analyses, quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed to assess DUXAP8, microRNA-378a-3p, FOXQ1 expression in colon cancer tissues, and clinical data were analyzed to determine the correlation between DUXAP8 expression and colon cancer patient outcomes. Nuclear/cytoplasmic RNA fractionation was utilized to analyze the subcellular distribution of DUXAP8. Dual-luciferase and RNA immunoprecipitation assays were performed to confirm the binding of DUXAP8/FOXQ1 and microRNA-378a-3p. After cell transfection, qRT-PCR was performed to evaluate the modulatory relationship of DUXAP8/microRNA-378a-3p/FOXQ1. Cell Counting Kit-8, MTT, scratch healing, and Transwell assays were performed to evaluate the impact of DUXAP8/microRNA-378a-3p/FOXQ1 expression on colon cancer cell functions.

Results

The results revealed that the expression of DUXAP8 and FOXQ1 was upregulated in colon cancer tissues, while the expression of microRNA-378a-3p was down-regulated. The increased DUXAP8 expression was positively correlated with lymph node metastasis and TNM stage. Dual-luciferase and RNA immunoprecipitation assays demonstrated that DUXAP8 was a sponge for microRNA-378a-3p and targeted the ability of microRNA-378a-3p to regulate FOXQ1. In addition, functional experiment results revealed that overexpressed DUXAP8 facilitated the growth and migratory ability of colon cancer cells. DUXAP8 also reversed the tumor-suppressive effect of microRNA-378a-3p. However, silencing FOXQ1 could reverse the cancer-promoting effects of high DUXAP8 expression.

Conclusions

DUXAP8 expression was significantly increased in colon cancer, which was associated with lymph node metastasis and unfavorable outcomes in colon cancer patients. DUXAP8 may hasten malignant progression of colon cancer cells through its effects on microRNA-378a-3p/FOXQ1.

Splicing to orchestrate cell fate

Alternative splicing (AS) plays a critical role in gene expression by generating protein diversity from single genes. This review provides an overview of the role of AS in regulating cell fate, focusing on its involvement in processes such as cell proliferation, differentiation, apoptosis, and tumorigenesis. We explore how AS influences the cell cycle, particularly its impact on key stages like G1, S, and G2/M. The review also examines AS in cell differentiation, highlighting its effects on mesenchymal stem cells and neurogenesis, and how it regulates differentiation into adipocytes, osteoblasts, and chondrocytes. Additionally, we discuss the role of AS in programmed cell death, including apoptosis and pyroptosis, and its contribution to cancer progression. Importantly, targeting aberrant splicing mechanisms presents promising therapeutic opportunities for restoring normal cellular function. By synthesizing recent findings, this review provides insights into how AS governs cellular fate and offers directions for future research into splicing regulatory networks.

Analysis of long Non-Coding RNA and mRNA expression in Clostridium butyricum-Induced apoptosis in SW480 colon cancer cells

Colon cancer is a leading cause of cancer-related deaths worldwide and has been increasingly linked to the gut microbiome. Clostridium butyricum (CB), a probiotic, has demonstrated potential in influencing colon cancer cell behavior, particularly through the modulation of long non-coding RNAs (lncRNAs) and mRNAs. This study examines the effects of CB on the expression of lncRNAs and mRNAs in SW480 colon cancer cells and their association with apoptosis. SW480 cells were co-cultured with CB, and total RNA was extracted for microarray analysis to identify differentially expressed lncRNAs and mRNAs. Quantitative real-time PCR and fluorescence staining were utilized to validate the expression changes of selected lncRNAs and to assess markers of apoptosis. Pathway enrichment analysis was performed to explore the biological functions of genes with altered expression. Co-culture with CB resulted in significant changes in lncRNA and mRNA expression, with 50 lncRNAs upregulated and 152 downregulated by more than five-fold. Similarly, 738 mRNAs were upregulated, while 1,088 were downregulated. Apoptosis analysis revealed that CB treatment induced apoptosis in SW480 cells, as evidenced by the upregulation of pro-apoptotic genes such as CASP1, TNF, and BNIP3L, and the downregulation of anti-apoptotic BCL family members. Pathway analysis suggested the involvement of the MAPK signaling pathway, cytokine-cytokine receptor interactions, and other pathways associated with tumor progression. These findings suggest that CB regulates the expression of lncRNAs and mRNAs involved in apoptosis and tumor progression, highlighting their potential as biomarkers and therapeutic targets in colorectal cancer. This study provides a novel therapeutic strategy for colon cancer treatment.

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.

The translatome of glioblastoma

Glioblastoma (GB), the most common and aggressive brain tumor, demonstrates intrinsic resistance to current therapies, resulting in poor clinical outcomes. Cancer progression can be partially attributed to the deregulation of protein translation mechanisms that drive cancer cell growth. In this study, we present the translatome landscape of GB as a valuable data resource. Eight patient-derived GB sphere cultures (GSCs) were analyzed using ribosome profiling and messenger RNA (mRNA) sequencing. We investigated inter-cell-line differences through differential expression analysis at both the translatome and transcriptome levels. Translational changes post-radiotherapy were assessed at 30 and 60 min. The translation of non-coding RNAs (ncRNAs) was validated using in-house and public mass spectrometry (MS) data, whereas RNA expression was confirmed by quantitative PCR (qPCR). Our findings demonstrate that ribosome sequencing provides more detailed information than MS or transcriptional analyses. Transcriptional similarities among GSCs correlate with translational similarities, aligning with previously defined subtypes such as proneural and mesenchymal. Additionally, we identified a broad spectrum of open reading frame types in both coding and non-coding mRNA regions, including long non-coding RNAs (lncRNAs) and pseudogenes undergoing active translation. Translation of ncRNAs into peptides was independently confirmed by in-house data and external MS data. We also observed that translational regulation of histones (downregulated) and splicing factors (upregulated) occurs in response to radiotherapy. These data offer new insights into genome-wide protein synthesis, identifying translationally regulated genes and alternative translation initiation sites in GB under normal and radiotherapeutic conditions, providing a rich resource for GB research. Further functional validation of differentially expressed genes after radiotherapy is needed. Understanding translational control in GB can reveal mechanistic insights and identify currently unknown biomarkers, ultimately enhancing the diagnosis and treatment of this aggressive brain cancer.

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.

HPV E6/E7-Induced Acetylation of a Peptide Encoded by a Long Non-Coding RNA Inhibits Ferroptosis to Promote the Malignancy of Cervical Cancer

Although a fraction of functional peptides concealed within long non-coding RNAs (lncRNAs) is identified, it remains unclear whether lncRNA-encoded peptides are involved in the malignancy of cervical cancer (CC). Here, a 92-amino acid peptide is discovered, which is named TUBORF, encoded by lncRNA TUBA3FP and highly expressed in CC tissues. TUBORF inhibits ferroptosis to promote the malignant proliferation of CC cells. Mechanistically, human papillomavirus (HPV) oncogenes E6 and E7 upregulate TUBORF through CREB-binding protein (CBP)/E1A-binding protein p300 (p300)-mediated histone H3 lysine 27 acetylation (H3K27ac) of lncTUBA3FP enhancer. Furthermore, E6 and E7 elevate and recruit acetyltransferase establishment of sister chromatid cohesion N-acetyltransferase 1 (ESCO1) to bind to and acetylate TUBORF, which facilitates the degradation of immunity-related GTPase Q (IRGQ) via a ubiquitin-proteasome pathway, resulting in the inhibition of ferroptosis and promotion of the malignant proliferation of CC cells. Importantly, silencing ESCO1 or TURORF amplifies anticancer effects by paclitaxel both in CC cells and in vivo. These novel findings reveal oncopeptide TUBORF and its acetyltransferase ESCO1 as important regulators of ferroptosis and tumorigenesis during cervical cancer pathogenesis and establish the scientific basis for targeting these molecules for treating CC.

Micropeptide hSPAR regulates glutamine levels and suppresses mammary tumor growth via a TRIM21-P27KIP1-mTOR axis

mTOR plays a pivotal role in cancer growth control upon amino acid response. Recently, CDK inhibitor P27KIP1 has been reported as a noncanonical inhibitor of mTOR signaling in MEFs, via unclear mechanisms. Here, we find that P27KIP1 degradation via E3 ligase TRIM21 is inhibited by human micropeptide hSPAR through its C-terminus (hSPAR-C), causing P27KIP1's cytoplasmic accumulation in breast cancer cells. Furthermore, hSPAR/hSPAR-C also serves as an inhibitor of glutamine transporter SLC38A2 expression and thereby decreases the cellular glutamine levels specifically in cancer cells. The resultant glutamine deprivation sequentially triggers translocation of cytoplasmic P27KIP1 to lysosomes, where P27KIP1 disrupts the Ragulator complex and suppresses mTORC1 assembly. Administration of hSPAR or hSPAR-C significantly impedes breast cancer cell proliferation and tumor growth in xenograft models. These findings define hSPAR as an intrinsic control factor for cellular glutamine levels and as a novel tumor suppressor inhibiting mTORC1 assembly.

A novel micropeptide miPEP205 suppresses the growth and metastasis of TNBC

Triple negative breast cancer (TNBC) is the most aggressive subtype of breast cancer and poses a treatment challenge due to high recurrence risk. Consequently, there is an urgent need for novel and efficacious therapies targeting TNBC. In this context, our study delineates the identification and characterization of a long non-coding RNA (lncRNA)-derived micropeptide miPEP205. Notably, the micropeptide exerts a significant inhibitory effect on the growth and metastasis of TNBC. Moreover, we observed a substantial down-regulation of micropeptide expression in clinical samples, which was markedly associated with a poor prognosis. Mechanistically, our research demonstrated that EGR3 governs lncRNA MIR205HG and the micropeptide expression, while miPEP205 boosts GSK-3β phosphorylation at Tyr216. This cascade causes β-catenin degradation, deactivating the GSK-3β/β-catenin signaling pathway and ultimately inhibits TNBC progression. Remarkably, our experiments in the spontaneous breast cancer mice model MMTV-PyMT demonstrated that the introduction of the miPEP205 gene or exogenous administration of the micropeptide miPEP205 significantly curtailed tumor growth and lung metastasis, and enhanced the overall survival among tumor-bearing mice. In conclusion, our study uncovers a previously uncharacterized micropeptide derived from a lncRNA, showcasing potent antitumor properties. These findings position miPEP205 as a promising novel target for therapeutic intervention in TNBC.

Noncoding RNA-encoded peptides in cancer: biological functions, posttranslational modifications and therapeutic potential

In the present era, noncoding RNAs (ncRNAs) have become a subject of considerable scientific interest, with peptides encoded by ncRNAs representing a particularly promising avenue of investigation. The identification of ncRNA-encoded peptides in human cancers is increasing. These peptides regulate cancer progression through multiple molecular mechanisms. Here, we delineate the patterns of diverse ncRNA-encoded peptides and provide a synopsis of the methodologies employed for the identification of ncRNAs that possess the capacity to encode these peptides. Furthermore, we discuss the impacts of ncRNA-encoded peptides on the biological behavior of cancer cells and the underlying molecular mechanisms. In conclusion, we describe the prospects of ncRNA-encoded peptides in cancer and the challenges that need to be overcome.

GMRSP encoded by lncRNA H19 regulates metabolic reprogramming and alleviates aortic dissection

Metabolic disturbances are hallmarks of vascular smooth muscle cell (VSMC) phenotypic transitions, which play a critical role in the pathogenesis of aortic dissection (AD). In this study, we identify and characterize glucose metabolism regulatory protein (GMRSP), a protein encoded by lncRNA H19. Using VSMC-specific GMRSP induction in knock-in mice, adeno-associated virus-mediated GMRSP overexpression, and exosomal GMRSP delivery, we demonstrate significant improvements in AD and mitochondrial dysfunction. Mechanistically, GMRSP inhibits heterogeneous nuclear ribonucleoprotein (hnRNP) A2B1-mediated alternative splicing of pyruvate kinase M (PKM) pre-mRNA, leading to reduced PKM2 production and glycolysis. This reprogramming preserves the contractile phenotype of VSMCs and prevents their transition to a proliferative state. Importantly, pharmacological activation of PKM2 via TEPP-46 abrogates the protective effects of GMRSP in vivo and in vitro. Clinical relevance is shown by elevated plasma PKM2 levels in AD patients, which correlate with poor prognosis. Collectively, these findings indicate GMRSP as a key regulator of VSMC metabolism and phenotypic stability, highlighting its potential as a therapeutic target for AD.

Emerging role of endogenous peptides encoded by non-coding RNAs in cancer biology

Non-coding RNAs have long been recognized for their regulatory roles in various cellular processes, including cancer development and progression. Recent advancements have shed light on a novel aspect of non-coding RNA biology, revealing their ability to encode endogenous peptides also named micropeptides or microprotein through short open reading frames (sORFs). These small proteins play crucial roles in oncogenic processes, acting as either tumour suppressors or tumour promoters, and hold enormous potential as biomarkers for early diagnosis of cancer and as therapeutic targets. This comprehensive review highlights the state of the art on peptides encoded by long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs), elucidating their regulatory functions and implications in different cancer types, including breast cancer, hepatocellular carcinoma and colorectal cancer. The review also discusses challenges and future directions in the exploration of these emerging players in cancer biology, emphasizing the importance of further investigation for their clinical translation in diagnosis and therapy.

Microproteins in cancer: identification, biological functions, and clinical implications

Cancer continues to be a major global health challenge, accounting for 10 million deaths annually worldwide. Since the inception of genome-wide cancer sequencing studies 20 years ago, a core set of ~700 oncogenes and tumor suppressor genes has become the basis for cancer research. However, this research has been based largely on an understanding that the human genome encodes ~19 500 protein-coding genes. Complementing this genomic landscape, recent advances have described numerous microproteins which are now poised to redefine our understanding of oncogenic processes and open new avenues for therapeutic intervention. This review explores the emerging evidence for microprotein involvement in cancer mechanisms and discusses potential therapeutic applications, with an emphasis on highlighting recent advances in the field.

lncRNAs: the unexpected link between protein synthesis and cancer adaptation

Cancer progression relies on the ability of cells to adapt to challenging environments overcoming stresses and growth constraints. Such adaptation is a multifactorial process that depends on the rapid reorganization of many basic cellular mechanisms. Protein synthesis is often dysregulated in cancer, and translational reprogramming is emerging as a driving force of cancer adaptive plasticity. Long non-coding RNAs (lncRNAs) represent the main product of genome transcription. They outnumber mRNAs by an order of magnitude and their expression is regulated in an extremely specific manner depending on context, space and time. This heterogeneity is functional and allows lncRNAs to act as context-specific, fine-tuning controllers of gene expression. Multiple recent evidence underlines how, besides their consolidated role in transcription, lncRNAs are major players in translation control. Their capacity to establish multiple and highly dynamic interactions with proteins and other transcripts makes these molecules able to play a central role across all phases of protein synthesis. Even if through a myriad of different mechanisms, the action of these transcripts is dual. On one hand, by modulating the overall translation speed, lncRNAs participate in the process of metabolic adaptation of cancer cells under stress conditions. On the other hand, by prioritizing the synthesis of specific transcripts they help cancer cells to maintain high levels of essential oncogenes. In this review, we aim to discuss the most relevant evidence regarding the involvement of lncRNAs in translation regulation and to discuss how this specific function may affect cancer plasticity and resistance to stress. We also expect to provide one of the first collective perspectives on the way these transcripts modulate gene expression beyond transcription.

Micropeptides derived from long non-coding RNAs: Computational analysis and functional roles in breast cancer and other diseases

Long non-coding RNAs (lncRNAs), once thought to be mere transcriptional noise, are now revealing a hidden code. Recent advancements like ribosome sequencing have unveiled that many lncRNAs harbor small open reading frames and can potentially encode functional micropeptides. Emerging research suggests these micropeptides, not the lncRNAs themselves, play crucial roles in regulating homeostasis, inflammation, metabolism, and especially in breast cancer progression. This review delves into the rapidly evolving computational tools used to predict and validate lncRNA-encoded micropeptides. We then explore the diverse functions and mechanisms of action of these micropeptides in breast cancer pathogenesis, with a focus on their roles in various species. Ultimately, this review aims to illuminate the functional landscape of lncRNA-encoded micropeptides and their potential as therapeutic targets in cancer.

Small protein ERSP encoded by LINC02870 promotes triple negative breast cancer progression via IRE1α/XBP1s activation

Clinical treatment options for triple-negative breast cancer (TNBC) are currently limited to chemotherapy because of a lack of effective therapeutic targets. Recent evidence suggests that long noncoding RNAs (lncRNAs) encode bioactive peptides or proteins, thereby playing noncanonical yet significant roles in regulating cellular processes. However, the potential of lncRNA-translated products in cancer progression remains largely unknown. In this study, we identified a previously undocumented small protein encoded by the lncRNA LINC02870. This protein is localized at the endoplasmic reticulum (ER) and participates in ER stress, thus, we named it the endoplasmic reticulum stress protein (ERSP). ERSP was highly expressed in TNBC tissues, and elevated LINC02870 content was correlated with poor prognosis in TNBC patients. Loss of ERSP inhibited TNBC growth and metastasis both in vitro and in vivo. The pro-oncogenic effects of ERSP could be attributed to its selective activation of the IRE1α/XBP1s branch. ERSP enhances the unfolded protein response (UPR) by interacting with XBP1s, facilitating the nuclear accumulation of XBP1s, thereby promoting the expression of ER stress-related genes. These findings highlight the regulatory role of the lncRNA-encoded protein ERSP in ER stress and suggest that it is a potential therapeutic target for TNBC.

A Zea genus-specific micropeptide controls kernel dehydration in maize

Kernel dehydration rate (KDR) is a crucial production trait that affects mechanized harvesting and kernel quality in maize; however, the underlying mechanisms remain unclear. Here, we identified a quantitative trait locus (QTL), qKDR1, as a non-coding sequence that regulates the expression of qKDR1 REGULATED PEPTIDE GENE (RPG). RPG encodes a 31 amino acid micropeptide, microRPG1, which controls KDR by precisely modulating the expression of two genes, ZmETHYLENE-INSENSITIVE3-like 1 and 3, in the ethylene signaling pathway in the kernels after filling. microRPG1 is a Zea genus-specific micropeptide and originated de novo from a non-coding sequence. Knockouts of microRPG1 result in faster KDR in maize. By contrast, overexpression or exogenous application of the micropeptide shows the opposite effect both in maize and Arabidopsis. Our findings reveal the molecular mechanism of microRPG1 in kernel dehydration and provide an important tool for future crop breeding.

LncRNA HAGLROS: A Vital Oncogenic Propellant in Various Human Cancers

HAGLR Opposite Strand lncRNA (HAGLROS) is a long non-coding RNA (lncRNA) located on the long arm of human chromosome 2 at locus 2q31.1. Emerging evidence highlights HAGLROS as a pivotal player in human cancers, characterized by its significant upregulation across multiple malignancies where it functions as an oncogenic driver. Its aberrant expression is closely linked to the initiation and progression of 13 distinct cancer types, notably correlating with adverse clinical outcomes and reduced overall survival rates in 9 of these cancer types. Mechanistically, HAGLROS is under the regulatory influence of the transcription factor STAT3, exerts competitive binding to 9 miRNAs, activates 5 signaling pathways pivotal for cancer cell proliferation and metastasis, as well as intricately modulates gene expression profiles. Given its multifaceted roles, HAGLROS emerges as a promising candidate for cancer diagnostics and prognostics. Moreover, its potential as a therapeutic target holds considerable promise for novel treatment strategies in oncology. This review synthesizes current research on HAGLROS, covering its expression patterns, biological roles, and clinical significance in cancer. By shedding light on these aspects, this review aims to contribute new perspectives that advance our understanding of cancer biology, enhance diagnostic accuracy, refine prognostic assessments, and pave the way for targeted therapeutic interventions.

A peptide encoded by LINC00944 suppresses the growth of melanoma cells by diminishing EP400-MYC interaction

The peptides encoded by long noncoding RNAs (lncRNAs) have been shown to participate in cancer pathogenesis. In this study, lncRNA LINC00944 was validated to encode an endogenous 102-amino acid (aa) small peptide (named LINC00944 peptide). Functionally, LINC00944 peptide exerted an anti-growth effect in melanoma cells in vitro. Mechanistically, LINC00944 peptide interacted with the E1A binding protein p400 (EP400)/c-MYC complex. LINC00944 peptide also inhibited c-MYC protein expression. Furthermore, LINC00944 peptide repressed the transcriptional activity of MYC by reducing the EP400-MYC interaction, thereby reducing the levels of fatty acid metabolism- and glucose metabolism-related proteins. Our findings uncovered that LINC00944 peptide might be a promising adjuvant therapeutic agent for melanoma. Implications: This study provided the first evidence that LINC00944-encoded peptide played a critical role in the growth of melanoma cells.

Chimeric SFT2D2-TBX19 Promotes Prostate Cancer Progression by Encoding TBX19-202 Protein and Stabilizing Mitochondrial ATP Synthase through ATP5F1A Phosphorylation

Specific chimeric RNAs and their products are consistently regarded as ideal tumor diagnostic markers and therapeutic targets. Chimeric RNAs can mediate tumor cell plasticity, neuroendocrine processes, polarization of tumor-associated macrophages, and resistance to chemotherapy and immunotherapy. However, the discovery of chimeric RNAs in prostate cancer is still in its early stages. This study identifies the chimeric SFT2D2-TBX19 as a novel transcript encoding the TBX19-202 protein. Both TBX19-202 and its parental TBX19, which share homologous amino acid sequences, enhance prostate cancer cell proliferation, migration, and invasion. Additionally, SFT2D2-TBX19 also functions as a lncRNA, interacting with the ATP synthase F1 subunit ATP5F1A, thereby increasing ATP5F1A phosphorylation mediated by TNK2/ACK1, which stabilizes the interaction between ATP5F1A and ATP5F1B. The region spanning 1801-2400 bp of SFT2D2-TBX19 and the intermediate structural domain of ATP5F1A are crucial functional areas. This stabilization of ATP5F1A and ATP5F1B enhances mitochondrial ATP synthase activity and ATP production. Even under conditions of mitochondrial vulnerability, SFT2D2-TBX19 protects mitochondrial structural stability to maintain prostate cancer cell proliferation. This research provides comprehensive evidence that chimeric SFT2D2-TBX19 promotes prostate cancer progression by encoding the TBX19-202 protein and stabilizing mitochondrial ATP synthase via ATP5F1A phosphorylation. These findings highlight SFT2D2-TBX19 as a potential therapeutic target for prostate cancer.

Functional roles of conserved lncRNAs and circRNAs in eukaryotes

Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) have emerged as critical regulators in essentially all biological processes across eukaryotes. They exert their functions through chromatin remodeling, transcriptional regulation, interacting with RNA-binding proteins (RBPs), serving as microRNA sponges, etc. Although non-coding RNAs are typically more species-specific than coding RNAs, a number of well-characterized lncRNA (such as XIST and NEAT1) and circRNA (such as CDR1as and ciRS-7) are evolutionarily conserved. The studies on conserved lncRNA and circRNAs across multiple species could facilitate a comprehensive understanding of their roles and mechanisms, thereby overcoming the limitations of single-species studies. In this review, we provide an overview of conserved lncRNAs and circRNAs, and summarize their conserved roles and mechanisms.

Ferroptosis contributes to the progression of female-specific neoplasms, from breast cancer to gynecological malignancies in a manner regulated by non-coding RNAs: Mechanistic implications

Ferroptosis, a recently identified type of non-apoptotic cell death, triggers the elimination of cells in the presence of lipid peroxidation and in an iron-dependent manner. Indeed, ferroptosis-stimulating factors have the ability of suppressing antioxidant capacity, leading to the accumulation of reactive oxygen species (ROS) and the subsequent oxidative death of the cells. Ferroptosis is involved in the pathophysiological basis of different maladies, such as multiple cancers, among which female-oriented malignancies have attracted much attention in recent years. In this context, it has also been unveiled that non-coding RNA transcripts, including microRNAs, long non-coding RNAs, and circular RNAs have regulatory interconnections with the ferroptotic flux, which controls the pathogenic development of diseases. Furthermore, the potential of employing these RNA transcripts as therapeutic targets during the onset of female-specific neoplasms to modulate ferroptosis has become a research hotspot; however, the molecular mechanisms and functional alterations of ferroptosis still require further investigation. The current review comprehensively highlights ferroptosis and its association with non-coding RNAs with a focus on how this crosstalk affects the pathogenesis of female-oriented malignancies, from breast cancer to ovarian, cervical, and endometrial neoplasms, suggesting novel therapeutic targets to decelerate and even block the expansion and development of these tumors.

HCP5 Derived Novel Microprotein Triggers Progression of Gastric Cancer through Regulating Ferroptosis

The context of long noncoding RNAs (lncRNAs) contains many unannotated open reading frames (ORFs). These ORFs potentially encode novel proteins or peptides with crucial roles in various human cancers, yet the translational potential of these lncRNAs and the functions of the protein products remain largely unexplored, especially in gastric cancer (GC). In this study, a comprehensive analysis is performed and identified a GC associated lncRNA known as HCP5, which contains a non-canonical ORF. Further analysis showed that HCP5-132aa, a microprotein encoded by HCP5 harboring this ORF, is highly expressed in GC cells and tissues, and can promote the proliferation of GC cells by inhibiting ferroptosis. Mechanistically, HCP5-132aa enhances the interaction between YBX1 and ELAVL1, facilitates recognition of YBX1 at the m5C site in the 3'UTR of SLC7A11 and G6PD mRNA, and preserves their stability via ELAVL1. By employing a Cas9/sgRNA delivery system with AAV in vivo, effectively knocked out the HCP5-132aa and inhibition of tumor growth in a patient-derived xenograft model are achieved. These findings demonstrate that the novel protein HCP5-132aa, derived from lncRNA HCP5, mediates the repression of ferroptosis, thereby driving the progression of GC and identifying a new potential therapeutic target for its treatment.

Peptidomics and Machine Learning-based Evaluation of Noncoding RNA-Derived Micropeptides in Breast Cancer: Expression Patterns and Functional/Therapeutic Insights

Breast cancer is a highly heterogeneous disease characterized by different subtypes arising from molecular alterations that give the disease different phenotypes, clinical behaviors, and prognostic. The noncoding RNA (ncRNA)-derived micropeptides (MPs) represent a novel layer of complexity in cancer study once they can be biologically active and can present potential as biomarkers and also in therapeutics. However, few large-scale studies address the expression of these peptides at the peptidomics level or evaluate their functions and potential in peptide-based therapeutics for breast cancer. In this study, we propose deepening the landscape of ncRNA-derived MPs in breast cancer subtypes and advance the comprehension of the relevance of these molecules to the disease. First, we constructed a 16,349 unique putative MP sequence data set by integrating 2 previously published lists of predicted ncRNA-derived MPs. We evaluated its expression on high-throughput mass spectrometry data of breast tumor samples from different subtypes. Next, we applied several machine and deep learning tools, such as AntiCP 2.0, MULocDeep, PEPstrMOD, Peptipedia, and PreAIP, to predict its functions, cellular localization, tertiary structure, physicochemical features, and other properties related to therapeutics. We identified 58 peptides expressed on breast tissue, including 27 differentially expressed MPs in tumor compared with nontumor samples and MPs exhibiting tumor or subtype specificity. These peptides presented physicochemical features compatible with the canonical proteome and were predicted to influence the tumor immune environment and participate in cell communication, metabolism, and signaling processes. In addition, some MPs presented potential as anticancer, antiinflammatory, and antiangiogenic molecules. Our data demonstrate that MPs derived from ncRNAs have expression patterns associated with specific breast cancer subtypes and tumor specificity, thus highlighting their potential as biomarkers for molecular classification. We also reinforce the relevance of MPs as biologically active molecules that play a role in breast tumorigenesis, besides their potential in peptide-based therapeutics.

New mechanism of LncRNA: In addition to act as a ceRNA

Long non-coding RNAs (LncRNAs) are a class of RNA molecules with nucleic acid lengths ranging from 200 bp to 100 kb that cannot code for proteins, which are diverse and widely expressed in both animals and plants. Scholars have found that lncRNAs can regulate human physiological processes at the gene and protein levels, mainly through the regulation of epigenetic, transcriptional and post-transcriptional levels of genes and proteins, as well as in the immune response by regulating the expression of immune cells and inflammatory factors, and thus participate in the occurrence and development of a variety of diseases. From the downstream targets of lncRNAs, we summarize the new research progress of lncRNA mechanisms other than miRNA sponges in recent years, aiming to provide new ideas and directions for the study of lncRNA mechanisms.

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

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

Molecular leveraging of HOX-embedded non-coding RNAs in the progression of acute myeloid leukemia

Acute myeloid leukemia (AML) is characterized by impaired differentiation of myeloid cells leading to hematopoietic failure. Despite advances, the molecular mechanisms driving AML remain incompletely understood, limiting the identification and targeting of critical vulnerabilities in leukemic cells. Homeobox (HOX) genes, encoding transcription factors essential for myeloid and lymphoid differentiation, are distributed across four clusters: HOXA (chromosome 7), HOXB (chromosome 17), HOXC (chromosome 12), and HOXD (chromosome 2). In addition to protein-coding sequences, HOX clusters encode non-coding RNAs (ncRNAs), which are functional as transcripts and do not translate into proteins. This is the first study wherein we comprehensively reviewed the literature for HOX-embedded ncRNAs, encompassing long non-coding RNAs (lncRNAs), microRNAs, circular RNAs (circRNAs), and piwiRNAs with a role in AML. To date, there is no evidence of circular RNAs and piwi RNAs encoded from the HOX gene clusters. Our review focuses on how leukemic cells harness the regulatory mechanisms of HOX-cluster-derived ncRNAs, (predominantly HOXA and HOXB) to modulate expression of HOX transcription factors facilitating leukemogenesis. HOX ncRNAs either regulate genes on the same chromosome (e.g., lncRNA HOTTIP) or influence expression of genes on different chromosomes (e.g., HOTAIR, HOX10-AS, miR-196b, and miR-10a). We discuss how specific HOX ncRNA networks are leveraged by leukemic cells, presenting an opportunity to explore targeted therapies and address the molecular heterogeneity of AML. Additionally, the aberrant expression of HOX ncRNAs such as HOXB derived ncRNAs in NPM1 mutated AML suggests their potential utility as improved biomarkers and for prognostication of patients with specific molecular aberrations.

The role of polypeptides encoded by ncRNAs in cancer

It was previously thought that ncRNA could not encode polypeptides, but recent reports have challenged this notion. As research into ncRNA progresses, it is increasingly clear that it serves roles beyond traditional mechanisms, playing significant regulatory roles in various diseases, notably cancer, which is responsible for 70% of human deaths. Numerous studies have highlighted the diverse regulatory mechanisms of ncRNA that are pivotal in cancer initiation and progression. The role of ncRNA-encoded polypeptides in cancer regulation has gained prominence. This article explores the newly identified regulatory functions of these polypeptides in three types of ncRNA-lncRNA, pri-miRNA, and circRNA. These polypeptides can interact with proteins, influence signaling pathways, enhance miRNA stability, and regulate cancer progression, malignancy, resistance, and other clinical challenges. Furthermore, we discuss the evolutionary significance of these polypeptides in the transition from RNA to protein, examining their emergence and conservation throughout evolution.

Recent Advances in Peptide Drug Discovery: Novel Strategies and Targeted Protein Degradation

Recent technological advancements, including computer-assisted drug discovery, gene-editing techniques, and high-throughput screening approaches, have greatly expanded the palette of methods for the discovery of peptides available to researchers. These emerging strategies, driven by recent advances in bioinformatics and multi-omics, have significantly improved the efficiency of peptide drug discovery when compared with traditional in vitro and in vivo methods, cutting costs and improving their reliability. An added benefit of peptide-based drugs is the ability to precisely target protein-protein interactions, which are normally a particularly challenging aspect of drug discovery. Another recent breakthrough in this field is targeted protein degradation through proteolysis-targeting chimeras. These revolutionary compounds represent a noteworthy advancement over traditional small-molecule inhibitors due to their unique mechanism of action, which allows for the degradation of specific proteins with unprecedented specificity. The inclusion of a peptide as a protein-of-interest-targeting moiety allows for improved versatility and the possibility of targeting otherwise undruggable proteins. In this review, we discuss various novel wet-lab and computational multi-omic methods for peptide drug discovery, provide an overview of therapeutic agents discovered through these cutting-edge techniques, and discuss the potential for the therapeutic delivery of peptide-based drugs.

Lnc-H19-derived protein shapes the immunosuppressive microenvironment of glioblastoma

The immunosuppressive tumor microenvironment (TME) is a prominent feature of glioblastoma (GBM), the most lethal primary brain cancer resistant to current immunotherapies. The mechanisms underlying GBM-TME remain to be explored. We report that long non-coding RNA (LncRNA) H19 encodes an immune-related protein called H19-IRP. Functionally separated from H19 RNA, H19-IRP promotes GBM immunosuppression by binding to the CCL2 and Galectin-9 promoters and activating their transcription, thereby recruiting myeloid-derived suppressor cells (MDSCs) and tumor-associated macrophages (TAMs), leading to T cell exhaustion and an immunosuppressive GBM-TME. H19-IRP, overexpressed in clinical GBM samples, acts as a tumor-associated antigen (TAA) presented by major histocompatibility complex class I (MHC-I). A circular RNA vaccine targeting H19-IRP (circH19-vac) triggers a potent cytotoxic T cell response against GBM and inhibits GBM growth. Our results highlight the unrevealed function of H19-IRP in creating immunosuppressive GBM-TME by recruiting MDSCs and TAMs, supporting the idea of targeting H19-IRP with cancer vaccine for GBM treatment.

Small and long non-coding RNAs: Past, present, and future

Since the introduction of the central dogma of molecular biology in 1958, various RNA species have been discovered. Messenger RNAs transmit genetic instructions from DNA to make proteins, a process facilitated by housekeeping non-coding RNAs (ncRNAs) such as small nuclear RNAs (snRNAs), ribosomal RNAs (rRNAs), and transfer RNAs (tRNAs). Over the past four decades, a wide array of regulatory ncRNAs have emerged as crucial players in gene regulation. In celebration of Cell's 50th anniversary, this Review explores our current understanding of the most extensively studied regulatory ncRNAs-small RNAs and long non-coding RNAs (lncRNAs)-which have profoundly shaped the field of RNA biology and beyond. While small RNA pathways have been well documented with clearly defined mechanisms, lncRNAs exhibit a greater diversity of mechanisms, many of which remain unknown. This Review covers pivotal events in their discovery, biogenesis pathways, evolutionary traits, action mechanisms, functions, and crosstalks among ncRNAs. We also highlight their roles in pathophysiological contexts and propose future research directions to decipher the unknowns of lncRNAs by leveraging lessons from small RNAs.

Therapeutic Potential of lncRNAs in Regulating Disulfidptosis for Cancer Treatment

Non-coding RNAs (lncRNAs) play critical roles in various cellular processes, including a novel form of regulated cell death known as disulfidptosis, characterized by accumulating protein disulfide bonds and severe endoplasmic reticulum stress. This review highlights the therapeutic potential of lncRNAs in regulating disulfidptosis for cancer treatment, emphasizing their influence on key pathway components such as GPX4, SLC7A11, and PDIA family members. Recent studies have demonstrated that targeting specific lncRNAs can sensitize cancer cells to disulfidptosis, offering a promising approach to cancer therapy. The regulation of disulfidptosis by lncRNAs involves various signaling pathways, including oxidative stress, ER stress, and calcium signaling. This review also discusses the molecular mechanisms underlying lncRNA regulation of disulfidptosis, the challenges of developing lncRNA-based therapies, and the future potential of this rapidly advancing field in cancer research.

Mechanism research of non-coding RNA in immune checkpoint inhibitors therapy

Immune checkpoint inhibitor (ICI) therapies for tumors of different systems have attained significant achievements and have changed the current situation of tumor treatment due to their therapeutic characteristics of high specificity and low side effects. The immune checkpoint Programmed death 1/Programmed cell death-Ligand 1 (PD-1/PD-L1) axis exerts a vital role in the immune escape of tumor cells. As a result, it has become a key target for tumor immunotherapy. Therefore, to perfect research into potential regulatory factors for the PD-1/PD-L1 axis, in order to understand and illustrate tumor ICI therapy mechanisms, is a significant goal. Moreover, ncRNA has been verified to regulate the PD-1/PD-L1 axis in the tumor immune microenvironment to regulate tumor genesis and development. ncRNAs can improve or decrease the efficacy of ICI therapy by modulating PD-L1 expression. This review aimed to investigate the mechanisms of action of ncRNA in regulating the PD-1/PD-L1 axis in ICI therapy, to provide more efficient immunotherapy for tumors of different systems.

Long non-coding RNA-encoded micropeptides: functions, mechanisms and implications

Long non-coding RNAs (lncRNAs) are typically described as RNA transcripts exceeding 200 nucleotides in length, which do not code for proteins. Recent advancements in technology, including ribosome RNA sequencing and ribosome nascent-chain complex sequencing, have demonstrated that many lncRNAs retain small open reading frames and can potentially encode micropeptides. Emerging studies have revealed that these micropeptides, rather than lncRNAs themselves, are responsible for vital functions, including but not limited to regulating homeostasis, managing inflammation and the immune system, moderating metabolism, and influencing tumor progression. In this review, we initially outline the rapidly advancing computational analytical methods and public tools to predict and validate the potential encoding of lncRNAs. We then focus on the diverse functions of micropeptides and their underlying mechanisms in the pathogenesis of disease. This review aims to elucidate the functions of lncRNA-encoded micropeptides and explore their potential applications as therapeutic targets in cancer.

Integrative analysis of RNA-seq and Ribo-seq reveals that lncRNA-GRN regulates chicken follicular atresia through miR-103-3p/FBXW7 axis and encoding peptide

Follicular atresia in chickens seriously reduced the egg production and economic benefits of chickens. LncRNA plays a key role in the process of follicular atresia. In this study, RNA-seq and Ribo-seq were performed on normal and atretic follicles of Dahen broilers to screen out lncRNAs that may regulate follicle atresia, and to study the molecular mechanisms of their regulation. GRN granulin precursor (lncGRN, ID: 101748909) was highly expressed in atretic follicles with translational ability. A molecular regulatory network of lncGRN/miR-103-3p/FBXW7 was constructed through bioinformatics analysis and dual luciferase reporting. LncGRN promoted the expression of FBXW7 by adsorption of miR-103-3p, thereby inhibiting the proliferation of chicken granulosa cells (GCs), promoting apoptosis of chicken GCs and inhibiting steroid hormone synthesis thus induced follicular atresia. Meanwhile, we also found a micropeptide named GRN-122aa derived by lncGRN which can promote follicular atresia. In conclusion, our study found that lncGRN promoted follicular atresia through the lncGRN/miR-103-3p/FBXW7 axis and the translation micropeptide GRN-122aa. This study provided new insight into the post-transcriptional regulation mechanism of lncGRN suggesting that lncGRN may act as a potential to regulate chicken follicle development, and provided a theoretical argument for further improving the egg production of chickens through molecular breeding.