Emerging roles and functional mechanisms of PIWI-interacting RNAs

Carbon black induced pulmonary fibrosis through piR-713551/PIWIL4 targeting THBS2 signal pathway

Carbon black (CB) is a vital constituent of airborne pollutants, comprising diesel exhaust and fine particulate matter (PM2.5), as well as a prevalent manufacturing material. CB was known to cause pulmonary dysfunction and fibrosis. However, the detailed molecular mechanisms underlying fibrosis development are poorly understood. In this study, 18 C57BL/6 mice were randomized into two groups and exposed to CB and filtered air (FA) for 28 days, with 6 hr/day and 7 days per week exposure regimen, respectively. The human normal bronchial epithelial cell line (BEAS-2B) was subjected to CB treatment for 24 h in vitro, with CB concentrations in 0, 50, 100, and 200 µg/mL. Our study indicated that exposure to CB resulted in a reduction in lung function and the development of pulmonary fibrosis in mice. Furthermore, our results showed cytoskeleton rearrangement and epithelial-mesenchymal transition (EMT) phenotype in BEAS-2B cells were happened, after CB exposure. Subsequent studies revealed that elevated expression of THBS2 after CB primarily contributed to the development of pulmonary fibrosis. The research findings from both in vivo and in vitro studies provided evidence that piR-713551 was involved in CB exposure-induced EMT by targeting the THBS2 gene and activating the β-catenin pathway. Mechanically, piR-713551/PIWIL4 complex activated the THBS2 transcription by recruitment of histone demethyltransferase KDM4A to reduce H3K9me3 modification at the THBS2 gene promoter. Conclusively, our research showed that CB exposure could activate EMT and lead pulmonary fibrosis which was modulated by piR-713551/PIWIL4 targeting THBS2.

The significance of small noncoding RNAs in the pathogenesis of cardiovascular diseases

With the advancement of high-throughput sequencing and bioinformatics, an increasing number of overlooked small noncoding RNAs (sncRNAs) have emerged. These sncRNAs predominantly comprise transfer RNA-derived fragments (tsRNAs), PIWI-interacting RNAs (piRNAs), Ro-associated non-coding RNAs (RNYs or Y-RNAs), small nucleolar RNAs (snoRNAs), and small nuclear RNAs (snRNAs). Each of these RNA types possesses distinct biological properties and plays specific roles in both physiological and pathological processes. The differential expression of sncRNAs substantially affects the occurrence and progression of various systemic diseases. However, their roles in the cardiovascular system remain unclear. Therefore, understanding the functionality and mechanisms of sncRNAs in the cardiovascular system holds promise for identifying novel targets and strategies for the diagnosis, prevention, and treatment of cardiovascular diseases. This review examines the biological characteristics of sncRNAs and their potential roles in cardiovascular diseases.

miRNA and piRNA differential expression profiles in Alzheimer's disease: A potential source of pathology and tool for diagnosis

Alzheimer's Disease (AD) is the most prevalent form of dementia and one of the leading causes of death in the United States, and despite our best efforts and recent advancements, a treatment that stops or substantially slows its progression has remained elusive. Small extracellular vesicles (sEVs), hold the potential to alleviate some of the common issues in the field by serving to better differentiate AD and non-AD individuals. These vesicles could provide insights into therapeutic targets, and potentially an avenue towards early detection. We compared the sEV cargo profiles of AD and non-AD brains (n = 6) and identified significant differences in both the micro RNA (miRNA) and Piwi-interacting RNA (piRNA) cargo through sEV isolation from temporal cortex tissue, followed by small RNA sequencing, and differential expression analysis. Differentially expressed miRNAs targeting systems relevant to AD included miR-206, miR-4516, miR-219a-5p, and miR-486-5p. Significant piRNAs included piR-6,565,525, piR-2,947,194, piR-7,181,973, and piR-7,326,987. These targets warrant further study for their potential role in the progression of AD pathology by dysregulating cellular activity; additionally, future large-scale studies of neuronal sEV miRNA profiles may facilitate the development of diagnostic tools which can aid in clinical trial design and recruitment. Longitudinal analysis of sEV data, perhaps accessible through plasma surveyance, will help determine at what point these miRNA and/or piRNA profiles begin to diverge between AD and non-AD individuals.

Factories without walls: The molecular architecture and functions of non-membrane organelles in small RNA-guided genome protection

Non-membrane organelles, Yb body and nuage, play an essential role in piRNA-guided genome defense in Drosophila gonad by mediating piRNA biogenesis and transposon silencing. Yb body, found in somatic follicle cells, is responsible for primary piRNA processing, while nuage, located in germline cells, facilitates the ping-pong cycle to amplify the piRNAs corresponding to both sense and antisense strands of the expressed transposons. These organelles are assembled by liquid-liquid phase separation (LLPS) and protein-protein interactions, integrating RNA helicases (Vasa, Armitage), Tudor domain-containing proteins (Krimper, Tejas, Qin/Kumo), and proteins containing both domains (Yb, SoYb, Spn-E). Within these condensates, we summarize the protein-protein interactions experimentally validated and predicted by AlphaFold3, providing new structural insights into the non-membrane organelle assembly. This review highlights how the dynamic organization of Yb body and nuage enables efficient RNA processing, ensuring transposon suppression and genome stability.

Cancer-associated fibroblasts-derived exosomal piR-35462 promotes the progression of oral squamous cell carcinoma via FTO/Twist1 pathway

BACKGROUND

Cancer-associated fibroblasts (CAFs) represent a crucial component of tumor stroma and play critical roles in cancer progression. However, the role of CAFs derived exosomes in oral squamous cell carcinoma (OSCC) environment is unexplored. PIWI-interacting RNAs (piRNAs) serve as epigenetic effectors in cancer progression and constitute significant compositions of exosomes. Here, we explored the functional mechanism of exosomal piRNAs in OSCC development.

METHODS

We screened exosomal piRNAs derived from CAFs and normal fibroblasts (NFs) and assess their effect on tumor proliferation and metastasis. A nude mouse model was established to assess the impact of exosomal piR-35462 on tumor progression.

RESULTS

CAFs-derived exosomes showed an enhanced piR-35462 expression and promoted OSCC cell proliferation, migration and invasion. Additionally, elevated piR-35462 expression in OSCC tissues correlates with poor prognosis. Mechanistically, CAFs-derived exosomal piR-35462 increased the expression of fat mass and obesity-associated protein (FTO) in OSCC cells. By inhibiting N6-methyladenosine (m6A) RNA methylation, the overexpression of FTO further enhances the stability and expression levels of Twist1 mRNA, thereby contributing to epithelial-mesenchymal transition (EMT) and tumor progression. In vivo xenograft tumor model also confirmed the same results.

CONCLUSION

The achieved outcomes elucidate that CAFs can deliver piR-35462 containing exosomes to OSCC cells and promote OSCC progression via FTO/Twist mediated EMT pathways, and could represent a promising therapeutic target for OSCC.

piR-RCC Suppresses Renal Cell Carcinoma Progression by Facilitating YBX-1 Cytoplasm Localization

PIWI-interacting RNAs (piRNAs), a novel category of small non-coding RNAs, are widely expressed in eukaryotes and deregulated in several pathologies, including cancer. Little is known about their function and mechanism in renal cell carcinoma (RCC) progression. Herein, a down-regulated piRNA in RCC, termed piR-hsa-28489 (designated as piR-RCC), is identified to impede RCC progression both in vivo and in vitro. Mechanistically, piR-RCC directly interacts with Y-box binding protein 1 (YBX-1), thus impeding p-AKT-mediated YBX-1 phosphorylation and its subsequent nuclear translocation. Moreover, YBX-1 coordinates the transcription of ETS homologous factor (EHF) as a repressor factor. Consequently, piR-RCC enhances EHF expression, leading to the inhibition of RCC proliferation and metastasis. Based on these, a biomimetic nanoparticle platform is constructed to achieve RCC-specific targeted delivery of piR-RCC. The nanoparticles are fabricated using a cell membrane coating derived from cancer cells and used to encapsulate and deliver piR-RCC plasmids to renal orthotopic implantation in mice, hindering RCC progression. This study illustrates piR-RCC/YBX-1/EHF signaling axis in RCC, offering a promising therapeutic avenue for RCC.

iPiDA-LGE: a local and global graph ensemble learning framework for identifying piRNA-disease associations

BACKGROUND

Exploring piRNA-disease associations can help discover candidate diagnostic or prognostic biomarkers and therapeutic targets. Several computational methods have been presented for identifying associations between piRNAs and diseases. However, the existing methods encounter challenges such as over-smoothing in feature learning and overlooking specific local proximity relationships, resulting in limited representation of piRNA-disease pairs and insufficient detection of association patterns.

RESULTS

In this study, we propose a novel computational method called iPiDA-LGE for piRNA-disease association identification. iPiDA-LGE comprises two graph convolutional neural network modules based on local and global piRNA-disease graphs, aimed at capturing specific and general features of piRNA-disease pairs. Additionally, it integrates their refined and macroscopic inferences to derive the final prediction result.

CONCLUSIONS

The experimental results show that iPiDA-LGE effectively leverages the advantages of both local and global graph learning, thereby achieving more discriminative pair representation and superior predictive performance.

Sex-biased fertility degeneration induced by depletion of an auxiliary piRNA-pathway factor Qin in Bombyx mori

The PIWI-interacting RNA (piRNA) pathway is the major defense system for transposable elements (TEs) silencing in animal gonads, maintaining genomic integrity of germ cells and ensuring proper gametogenesis. An the piRNA-pathway factor, Qin, has been reported to participate in piRNA biogenesis in the lepidopteran model insect, Bombyx mori. Nevertheless, the physiological functions of Qin remain to be characterized. Here we demonstrated that Qin plays important roles in silkworm gonad development of both sexes. BmQin was predominantly expressed in gonads. Immunofluorescent staining revealed that BmQin is localized in the cytoplasm of both germ cells and somatic cells in gonads. Depletion of BmQin via CRISPR/Cas9 system induceed complete sterile in males, and partial sterile in females. Notably, mutants displayed severe defects in gonad development and gametogenesis. RNA-seq analysis revealed that the piRNA pathway was dysregulated in mutant gonads. In addition, apoptosis was significantly enhanced in mutant gonads. Our study revealed the physiological functions of BmQin in silkworm fertility and its auxiliary roles in the piRNA pathway in both male and female gonads.

piRNA gene density and SUMOylation organize piRNA transcriptional condensate formation

Piwi-interacting RNAs (piRNAs) are essential for maintaining genome integrity and fertility in various organisms. In flies and nematodes, piRNA genes are encoded in heterochromatinized genomic clusters. The molecular mechanisms of piRNA transcription remain intriguing. Through small RNA sequencing and chromatin editing, we discovered that spatial aggregation of piRNA genes enhances their transcription in nematodes. The facultative heterochromatinized piRNA genome recruits the piRNA upstream sequence transcription complex (USTC; including PRDE-1, SNPC4, TOFU-4 and TOFU-5) and the H3K27me3 reader UAD-2, which phase-separate into droplets to initiate piRNA transcription. We searched for factors that regulate piRNA transcription and isolated the SUMO E3 ligase GEI-17 as inhibiting and the SUMO protease TOFU-3 as promoting piRNA transcription foci formation, thereby regulating piRNA production. Our study revealed that spatial aggregation of piRNA genes, phase separation and deSUMOylation may benefit the organization of functional biomolecular condensates to direct piRNA transcription in the facultative heterochromatinized genome.

Paramutation-Like Behavior of Genic piRNA-Producing Loci in Drosophila virilis

Piwi-interacting RNAs (piRNAs) play a crucial role in silencing transposable elements (TEs) in the germ cells of Metazoa by acting as sequence-specific guides. Originating from distinct genomic loci, called piRNA clusters, piRNA can trigger an epigenetic conversion of TE insertions into piRNA clusters by means of a paramutation-like process. However, the variability in piRNA clusters' capacity to induce such conversions remains poorly understood. Here, we investigated two Drosophila virilis strains with differing capacities to produce piRNAs from the subtelomeric RhoGEF3 and Adar gene loci. We found that active piRNA generation correlates with high levels of the heterochromatic mark histone 3 lysine 9 trimethylation (H3K9me3) over genomic regions that give rise to piRNAs. Importantly, the maternal transmission of piRNAs drives their production in the progeny, even from homologous loci previously inactive in piRNA biogenesis. The RhoGEF3 locus, once epigenetically converted, maintained enhanced piRNA production in subsequent generations lacking the original allele carrying the active piRNA cluster. In contrast, piRNA expression from the converted Adar locus was lost in offspring lacking the inducer allele. The present findings suggest that the paramutation-like behavior of piRNA clusters may be influenced not only by piRNAs but also by structural features and the chromatin environment in the proximity to telomeres, providing new insights into the epigenetic regulation of the Drosophila genome.

Functions and mechanisms of eukaryotic RNA-guided programmed DNA elimination

Many eukaryotic organisms, from ciliates to mammals, employ programmed DNA elimination during their postmeiotic reproduction. The process removes specific regions from the somatic DNA and has broad functions, including the irreversible silencing of genes, sex determination, and genome protection from transposable elements or integrating viruses. Multiple mechanisms have evolved that explain the sequence selectivity of the process. In some cases, the eliminated sequences lack centromeres and are flanked by conserved sequence motifs that are specifically recognized and cleaved by designated nucleases. Upon cleavage, all DNA fragments that lack centromeres are lost during the following mitosis. Alternatively, specific sequences can be destined for elimination by complementary small RNAs (sRNAs) as in some ciliates. These sRNAs enable a PIWI-mediated recruitment of chromatin remodelers, followed up by the precise positioning of a cleavage complex formed from a transposase like PiggyBac or Tc1. Here, we review the known molecular interplay of the cellular machinery that is involved in precise sRNA-guided DNA excision, and additionally, we highlight prominent knowledge gaps. We focus on the modes through which sRNAs enable the precise localization of the cleavage complex, and how the nuclease activity is controlled to prevent off-target cleavage. A mechanistic understanding of this process could enable the development of novel eukaryotic genome editing tools.

Characterization and comparative profiling of piRNAs in serum biopsies of pediatric Wilms tumor patients

Piwi-interacting RNAs (piRNAs) are small non-coding RNAs involved in transposon silencing and linked to cancer progression. However, their role in Wilms tumors (WT) remains unexplored. We conducted a thorough analysis and characterization of piRNAs in serum liquid biopsies of WT patients. Our study examined their expression patterns and functional annotations related to WT pathogenesis, as well as their clinical potential for diagnosis and monitoring. We identified 307 piRNAs expressed in WT serum samples, with 4% classified as repeat-related and 96% as non-repeat-related. The most abundant repeat-related piRNAs originated from LINEs retrotransposon, while tRNA-derived piRNAs were the most prevalent among non-repeat-related piRNAs. Furthermore, a distinct profile of 34 piRNAs showed significant differential expression in WT patients compared to healthy controls-22 downregulated and 12 upregulated. The target genes of differentially expressed piRNAs exhibited significant enrichment in biological pathways related to cytokine activity, inflammatory responses, TGF-beta signaling, p38 MAPK, and ErbB signaling. These genes are also involved in DNA damage response, DNA methylation, cell cycle regulation, as well as kidney development and function. Low expression levels of several piRNAs, especially piR-hsa-1,913,711, piR-hsa-28,190, piR-hsa-28,849, piR-hsa-28,848, and piR-hsa-28,318, showed significant diagnostic potential as non-invasive biomarkers for WT (AUC > 0.8, p < 0.05). Their expression levels also significantly correlated with adverse pathological features, including metastasis, anaplasia, and bilateral WT development. In conclusion, non-transposon-related piRNAs may serve as reliable biomarkers for WT and possess potential non-germline functions, particularly in regulating DNA methylation, cell growth, immune responses, and immune responses. Further studies are warranted to elucidate their functional significance.

Zygotic activation of transposable elements during zebrafish early embryogenesis

Although previous studies have shown that transposable elements (TEs) are conservatively activated to play key roles during early embryonic development, the details of zygotic TE activation (ZTA) remain poorly understood. Here, we employ long-read sequencing to precisely identify that only a small subset of TE loci are activated among numerous copies, allowing us to map their hierarchical transcriptional cascades at the single-locus and single-transcript level. Despite the heterogeneity of ZTA across family, subfamily, locus, and transcript levels, our findings reveal that ZTA follows a markedly different pattern from conventional zygotic gene activation (ZGA): ZTA occurs significantly later than ZGA and shows a pronounced bias for nuclear localization of TE transcripts. This study advances our understanding of TE activation by providing a high-resolution view of TE copies and creating a comprehensive catalog of thousands of previously unannotated transcripts and genes that are activated during early zebrafish embryogenesis. Among these genes, we highlight two that are essential for zebrafish development.

Nested likelihood-ratio testing of the nonsynonymous:synonymous ratio suggests greater adaptation in the piRNA machinery of Drosophila melanogaster compared with Drosophila ananassae and Drosophila willistoni, two species with higher repeat content

Numerous studies have revealed a signature of strong adaptive evolution in the piwi-interacting RNA (piRNA) machinery of Drosophila melanogaster, but the cause of this pattern is not understood. Several hypotheses have been proposed. One hypothesis is that transposable element (TE) families and the piRNA machinery are co-evolving under an evolutionary arms race, perhaps due to antagonism by TEs against the piRNA machinery. A related, though not co-evolutionary, hypothesis is that recurrent TE invasion drives the piRNA machinery to adapt to novel TE strategies. A third hypothesis is that ongoing fluctuation in TE abundance leads to adaptation in the piRNA machinery that must constantly adjust between sensitivity for detecting new elements and specificity to avoid the cost of off-target gene silencing. Rapid evolution of the piRNA machinery may also be driven independently of TEs, and instead from other functions such as the role of piRNAs in suppressing sex-chromosome meiotic drive. We sought to evaluate the impact of TE abundance on adaptive evolution of the piRNA machinery in D. melanogaster and 2 species with higher repeat content-Drosophila ananassae and Drosophila willistoni. This comparison was achieved by employing a likelihood-based hypothesis testing framework based on the McDonald-Kreitman test. We show that we can reject a faster rate of adaptive evolution in the piRNA machinery of these 2 species. We propose that the high rate of adaptation in D. melanogaster is either driven by a recent influx of TEs that have occurred during range expansion or selection on other functions of the piRNA machinery.

Mechanistic insights into RNA cleavage by human Argonaute2-siRNA complex

In animals, AGO-clade Argonaute proteins utilize small interfering RNAs (siRNAs) as guides to recognize target with complete complementarity, resulting in target RNA cleavage that is a critical step for target silencing. These proteins feature a constricted nucleic acid-binding channel that limits base pairing between the guide and target beyond the seed region. How the AGO-siRNA complexes overcome this structural limitation and achieve efficient target cleavage remains unclear. We performed cryo-electron microscopy of human AGO-siRNA complexes bound to target RNAs of increasing lengths to examine the conformational changes associated with target recognition and cleavage. Initially, conformational transition propagates from the opening of the PAZ domain and extends through a repositioning of the PIWI-L1-N domain toward the binding channel, facilitating the capture of siRNA-target duplex. Subsequent extension of base pairing drives the downward movement of the PIWI-L1-N domain to enable catalytic activation. Finally, further base pairing toward the 3' end of siRNA destabilizes the PAZ-N domain, resulting in a "uni-lobed" architecture, which might facilitate the multi-turnover action of the AGO-siRNA enzyme complex. In contrast to PIWI-clade Argonautes, the "uni-lobed" structure of the AGO complex makes multiple contacts with the target in the central region of the siRNA-target duplex, positioning it within the catalytic site. Our findings shed light on the stepwise mechanisms by which the AGO-siRNA complex executes target RNA cleavage and offer insights into the distinct operational modalities of AGO and PIWI proteins in achieving such cleavage.

Protocol for assembling, prioritizing, and characterizing piRNA clusters using the piRNA Cluster Builder

PIWI-interacting RNAs (piRNAs) play a critical role in safeguarding genome integrity in germ cells, ensuring fertility. Here, we provide a protocol for processing piRNA sequencing data, identifying piRNA-rich genomic regions as piRNA clusters, and preparing these clusters for downstream analyses. We describe steps for assembling piRNA cluster regions using an R-based tool, the piRNA Cluster Builder (PICB), which integrates unique and multimapping piRNA reads stepwise. The protocol allows for parameter optimizations and generates normalized outputs for prioritization of piRNA clusters. For complete details on the use and execution of this protocol, please refer to Konstantinidou et al.1.

The eusocial non-code: Unveiling the impact of noncoding RNAs on Hymenoptera eusocial evolution

Eusociality, characterized by reproductive division of labor, cooperative brood care, and multi-generational cohabitation, represents a pinnacle of complex social evolution, most notably manifested within the Hymenoptera order including bees, ants, and wasps. The molecular underpinnings underlying these sophisticated social structures remain an enigma, with noncoding RNAs (ncRNAs) emerging as crucial regulatory players. This article delves into the roles of ncRNAs in exerting epigenetic control during the development and maintenance of Hymenopteran eusociality. We consolidate current findings on various classes of ncRNAs, underscoring their influence on gene expression regulation pertinent to caste differentiation, developmental plasticity, and behavioral modulation. Evidence is explored supporting the hypothesis that ncRNAs contribute to epigenetic landscapes fostering eusocial traits through genomic regulation. They are likely to play an important role in eusociality "point of no return". Critical analysis is provided on the functional insights garnered from ncRNA profiles correlated with caste-specific phenotypes, specifical for phylogenetic branches and transitional sociality models, drawing from comparative genomics and transcriptomics studies. Overall, ncRNA provides a missed understanding of both "genetic toolkit" and "unique genes" hypotheses of eusociality development. Moreover, it points to gaps in current knowledge, advocating for integrative approaches combining genomics, proteomics, and epigenetics to decipher the complexity of eusociality. Understanding the ncRNA contributions offers not only a window into the molecular intricacies of Hymenoptera sociality but also extends our comprehension of how complex biological systems evolve and function.

Regulatory roles of PIWI-interacting RNAs in cardiovascular disease

Cardiovascular disease remains the number one cause of death worldwide. Across the spectrum of cardiovascular pathologies, all are accompanied by changes in gene expression profiles spanning a variety of cellular components of the myocardium. Alterations in gene expression are regulated by small noncoding RNAs (sncRNAs), with P-element-induced WImpy testis (PIWI)-interacting RNAs (piRNAs) being the most abundant of the sncRNAs in the human genome. Composed of 21-35 nucleotides in length with a protective methyl group at the 3' end, piRNAs complex with highly conserved RNA-binding proteins termed PIWI proteins to recruit enzymes used for histone, DNA, RNA, and protein modifications. Thus, specific piRNA expression patterns can be exploited for early clinical diagnosis of cardiovascular disease and the development of novel RNA therapeutics that may improve cardiac health outcomes. This review summarizes the latest progress made on understanding how piRNAs regulate cardiovascular health and disease progression, including a discussion of their potential in the development of biomarkers and therapeutics.

Non-coding RNAs and regulation of the PI3K signaling pathway in lung cancer: Recent insights and potential clinical applications

Lung cancer (LC) is one of the most common causes of cancer-related death worldwide. It has been demonstrated that the prognosis of current drug treatments is affected by a variety of factors, including late stage, tumor recurrence, inaccessibility to appropriate treatments, and, most importantly, chemotherapy resistance. Non-coding RNAs (ncRNAs) contribute to tumor development, with some acting as tumor suppressors and others as oncogenes. The phosphoinositide 3-kinase (PI3Ks)/AKT serine/threonine kinase pathway is one of the most important common targets of ncRNAs in cancer, which is widely applied to modulate the cell cycle and a variety of biological processes, including cell growth, mobility survival, metabolic activity, and protein production. Discovering the biology of ncRNA-PI3K/AKT signaling may lead to advances in cancer diagnosis and treatment. As a result, we investigated the expression and role of PI3K/AKT-related ncRNAs in clinical characteristics of lung cancer, as well as their functions as potential biomarkers in lung cancer diagnosis, prognosis, and treatment.

Spatiotemporal single-cell architecture of gene expression in the Caenorhabditis elegans germ cells

Spermatogenesis is an intricate and tightly controlled process encompassing various layers of gene expression regulation. Despite the advance of our current understanding, the developmental trajectory and regulatory mechanisms dictating spermatogenesis remain elusive. In this study, we have generated single-cell gene expression profiles for Caenorhabditis elegans sperm cells and constructed gene regulatory networks alongside the developmental trajectories of these cells. Our findings indicate that each pre- and post-developmental stage is closely linked by co-expressed genes, while simultaneously being uniquely identified by the combined expression of specific gene families. To illustrate the applicability of this exhaustive gene expression catalog, we used gene regulatory networks to uncover potential transcription factors for (1) the expression of genes in the phosphorylation pathway, identifying NHR-23-to-phosphatase regulation for the meiotic cell division process; and (2) the expression of constituent components of small RNA pathways, identifying ELT-1-to-Argonaute protein regulation for siRNA maintenance and sperm activation. We expect that this sperm cell-specific gene expression directory will prompt investigations into the underlying mechanisms determining anatomy, differentiation, and function across the reproductive system. Finally, our expression data can be explored using the web application CelegansGermAtlas ( https://scgerm-atlas.sjtu.edu.cn/website/#/home ).

piRNA/PIWI pathways and epigenetic crosstalk in human diseases: Molecular insights into HIV-1 infection and drugs of abuse

P-element-induced wimpy (PIWI)-interacting RNAs (piRNAs) and PIWI proteins have long been studied in insects and germline cells for their roles in regulating transposable elements (TEs). However, emerging evidence suggests that piRNAs and PIWI proteins also play crucial roles in human diseases beyond gametocyte protection, and these molecules are implicated in the onset and progression of various human diseases, particularly those arising in somatic cells. Notably, piRNAs and PIWI proteins are increasingly recognized for their involvement in cancers, cardiovascular diseases, neurodegenerative disorders, and viral infections, including HIV. This review first provides an overview of piRNAs/PIWIs and their interactions with TEs and primary targets. We then explore the molecular mechanisms and signaling pathways through which piRNAs and PIWIs modulate human disease processes, focusing on neurodegeneration, cancers, and HIV. Special attention is given to the role of piRNA/PIWI complexes in regulating gene transcription, translation, and post-translational modifications in the context of disease. Additionally, we address emerging research into the role of piRNAs/PIWIs in HIV- and drug abuse or substance abuse-associated neurodegenerative diseases, highlighting existing knowledge gaps. Finally, we discuss future research directions to understand better the functions of piRNAs/PIWI proteins in human health and disease.

Structural insights into RNA cleavage by PIWI Argonaute

Argonaute proteins are categorized into AGO and PIWI clades. Across most animal species, AGO-clade proteins are widely expressed in various cell types, and regulate normal gene expression1. By contrast, PIWI-clade proteins predominantly function during gametogenesis to suppress transposons and ensure fertility1,2. Both clades use nucleic acid guides for target recognition by means of base pairing, crucial for initiating target silencing, often through direct cleavage. AGO-clade proteins use a narrow channel to secure a tight guide-target interaction3. By contrast, PIWI proteins feature a wider channel that potentially allows mismatches during pairing, broadening target silencing capability4,5. However, the mechanism of PIWI-mediated target cleavage remains unclear. Here we demonstrate that after target binding, PIWI proteins undergo a conformational change from an 'open' state to a 'locked' state, facilitating base pairing and enhancing target cleavage efficiency. This transition involves narrowing of the binding channel and repositioning of the PIWI-interacting RNA-target duplex towards the MID-PIWI lobe, establishing extensive contacts for duplex stabilization. During this transition, we also identify an intermediate 'comma-shaped' conformation, which might recruit GTSF1, a known auxiliary protein that enhances PIWI cleavage activity6. GTSF1 facilitates the transition to the locked state by linking the PIWI domain to the RNA duplex, thereby expediting the conformational change critical for efficient target cleavage. These findings explain the molecular mechanisms underlying PIWI-PIWI-interacting RNA complex function in target RNA cleavage, providing insights into how dynamic conformational changes from PIWI proteins coordinate cofactors to safeguard gametogenesis.

Flipons enable genomes to learn by intermediating the exchange of energy for information

Recent findings have confirmed the long-held belief that alternative DNA conformations encoded by genetic elements called flipons have important biological roles. Many of these alternative structures are formed by sequences originally spread throughout the human genome by endogenous retroelements (ERE) that captured 50% of the territory before being disarmed. Only 2.6% of the remaining DNA codes for proteins. Other organisms have instead streamlined their genomes by eliminating invasive retroelements and other repeat elements. The question arises, why retain any ERE at all? A new synthesis suggests that flipons enable genomes to learn and programme the context-specific readout of information by altering the transcripts produced. The exchange of energy for information is mediated through changes in DNA topology. Here I provide a formulation for how genomes learn and describe the underlying p-bit algorithm through which flipons are tuned. The framework suggests new strategies for the therapeutic reprogramming of cells.

PIWI-interacting RNA biomarkers in gastrointestinal disease

Detection and diagnosis of neoplastic and inflammatory gastrointestinal (GI) diseases are typically based on endoscopic and pathologic examination. In GI neoplastic diseases, diagnosis can be delayed due to the expense and invasive nature of this approach. Recently, PIWI-interacting RNAs (piRNAs), a group of small non-coding RNA molecules containing 24-31 nucleotides, have been thought to serve as biomarkers in many disease processes. For example, piRNAs are differentially expressed in GI cancer but their biologic role remains unclear. Using next-generation sequencing and microarray analyses, researchers have suggested that monitoring piRNAs could facilitate diagnosis and prognosis in GI disease. Herein, we reviewed the use of piRNAs in neoplastic, inflammatory, functional, and other diseases of the digestive system, which could shed new light on cancer screening, early detection, and personalized treatment.

Progress in research of non-coding RNAs in colorectal cancer and their application in early diagnosis

Colorectal cancer is one of the common malignant tumors in the digestive system worldwide, with its incidence and mortality rates ranking high among various diseases. Although certain advancements have been achieved in the diagnosis and treatment techniques of colorectal cancer in recent years, the existing diagnostic means and treatment methods still present numerous limitations, significantly influencing the early detection, precise diagnosis, and individualized treatment of colorectal cancer. With the in-depth research of molecular biology, non-coding RNAs (ncRNAs) have gained increasing attention in the development and prognosis evaluation of colorectal cancer. This paper summarizes some studies related to the expression of different types of ncRNAs in colorectal cancer and selects a portion of ncRNAs that are expected to serve as new diagnostic indicators for this malignancy. The emergence of new biological indicators will contribute to the early diagnosis of colorectal cancer, facilitating its early detection and even prevention.

Small RNA data sets of mouse testes and ovaries before and after sexual maturity

For a considerable period, reproductive health, fertility, and reproductive-related diseases have posed challenges to human well-being, as well as to the conservation of endangered species and the advancement of animal husbandry. PANDORA-seq, a recently introduced sequencing technique, demonstrates heightened sensitivity towards highly modified small RNAs like tsRNA and rsRNA. In this research endeavor, we leveraged PANDORA-seq to capture the small RNA expression profiles of mouse testes and ovaries pre- and post-sexual maturation. Our investigation successfully pinpointed an array of abundantly expressed small RNAs across various tissues, encompassing tsRNA, rsRNA, piRNA, miRNA, snoRNA, and ysRNA. Next, we conducted an expression profile analysis of these small RNAs to assist researchers in screening and validating them for various areas of interest. This dataset is poised to become an invaluable resource for exploring the postnatal development of testes and ovaries, offering new insights into the epigenetic mechanisms underlying germ cell production and differentiation.

Insights into the role of hnRNPK in spermatogenesis via the piRNA pathway

Deletion of hnRNPK in mouse spermatogonia leads to male sterility due to arrest permatogenesis, yet the underlying molecular mechanisms remain elusive. This study investigated the testicular proteome on postnatal day 28 (P28) to elucidate the infertility associated with Hnrnpk deficiency, identifying 791 proteins with altered expression: 256 were upregulated, and 535 were downregulated. Pathway enrichment analysis demonstrated that the downregulated proteins are primarily involved in spermatogenesis, fertilization, and piRNA metabolic processes. In Hnrnpk cKO mice, key proteins essential for piRNA metabolism, such as PIWIL1, TDRD7, DDX4, and MAEL, exhibited reduced expression, resulting in impaired piRNA production. Mechanistic studies employing RNA immunoprecipitation (RIP), dual-luciferase reporter assays, and fluorescence in situ hybridization/immunofluorescence (FISH/IF) assays demonstrated that hnRNPK directly interacts with the 3'UTR of piRNA pathway transcripts, enhancing their translational efficiency. These results establish that Hnrnpk deficiency disrupts the piRNA pathway by diminishing the expression of essential regulatory proteins, thereby impairing piRNA production and spermatogenesis. Our findings elucidate a novel molecular basis for infertility linked to hnRNPK dysfunction and advance understanding of post-transcriptional regulation in male germ cell development.

Small non-coding RNA profiling in patients with non-muscle invasive bladder cancer

The intricate regulatory roles of small non-coding RNAs (sncRNAs), including PIWI-interacting RNAs (piRNAs) and microRNAs (miRNAs), have been increasingly recognized in the modulation of cellular functions and are associated with the pathogenesis of various diseases, notably cancer. However, the specific dysregulation patterns of sncRNAs in non-muscle-invasive bladder cancer (NMIBC) have yet to be fully delineated, highlighting a significant gap in our current understanding. To elucidate the expressional dynamics of sncRNAs for patients with NMIBC, we characterized the profile of piRNAs and miRNAs by next-generation sequencing. We identified the differentially expressed sncRNAs between tumor and paracancerous tissues and characterized their distribution along the genome. We further revealed a set of immune-related piRNAs and dysregulated miRNAs that might be associated with NMIBC pathogenesis. Differentially expressed piRNAs were predominantly localized at the long arms of chromosomes 13, 1, and 6. Notably, the targets of specific piRNAs, including piR-hsa-2215234, piR-hsa-105306, piR-hsa-102066, and piR-hsa-236465, show significant associated with antigen processing and presentation pathway. Additionally, differentially expressed miRNAs are mainly located on chromosome 14 and their target genes tend to be involved in cancer-related pathways, suggesting their potential regulatory roles in NMIBC. Collectively, this study revealed the global sncRNA dysregulation in NMIBC, and the identified sncRNAs are implicated in the modulation of both immune and cancer pathways, suggesting their contribution to the pathogenesis and potential targets for immunotherapy.

tRNA intron-derived small regulatory RNAs fine-tune gene expression under oxidative stress

The intron sequences of certain tRNAs are evolutionarily conserved among specific organisms, implying potential cellular functions of such tRNA introns. In this issue, Nostramo et al.1 identify free introns of tRNAs (fitRNAs) in S. cerevisiae as small regulatory RNAs that dynamically control mRNA levels in response to oxidative stress.

Functional Investigation of a Novel PIWIL4 Mutation in Nonobstructive Azoospermia During the First Wave of Spermatogenesis

PIWI-interacting RNAs (piRNAs) are small noncoding RNAs that are almost exclusively expressed in germ cells to silence harmful transposons to maintain genome stability. PIWIL4 is guided by its associated piRNAs to transposable elements, where it recruits the DNA methylation apparatus and instructs de novo DNA methylation. Herein, we identified a missense variant of PIWIL4 (c.805 C>T p.R269W) in two infertile males. Homozygous male mice carrying the orthologous knock-in variant displayed elevated transposable element expression and aberrant gene expression during the first wave of spermatogenesis, despite exhibiting normal sperm counts and morphology. Mechanistically, the mutated site altered the piRNA-binding ability of PIWIL4 and led to the derepression of endogenous LINE-1 elements. In summary, we identified a piRNA binding mutation in PIWIL4 that may be involved in human nonobstructive azoospermia.

Mammalian piRNA target prediction using a hierarchical attention model

BACKGROUND

Piwi-interacting RNAs (piRNAs) are well established for monitoring and protecting the genome from transposons in germline cells. Recently, numerous studies provided evidence that piRNAs also play important roles in regulating mRNA transcript levels. Despite their significant role in regulating cellular RNA levels, the piRNA targeting rules are not well defined, especially in mammals, which poses obstacles to the elucidation of piRNA function.

RESULTS

Given the complexity and current limitation in understanding the mammalian piRNA targeting rules, we designed a deep learning model by selecting appropriate deep learning sub-networks based on the targeting patterns of piRNA inferred from previous experiments. Additionally, to alleviate the problem of insufficient data, a transfer learning approach was employed. Our model achieves a good discriminatory power (Accuracy: 98.5%) in predicting an independent test dataset. Finally, this model was utilized to predict the targets of all mouse and human piRNAs available in the piRNA database.

CONCLUSIONS

In this research, we developed a deep learning framework that significantly advances the prediction of piRNA targets, overcoming the limitations posed by insufficient data and current incomplete targeting rules. The piRNA target prediction network and results can be downloaded from https://github.com/SofiaTianjiaoZhang/piRNATarget .

A model that integrates the different piRNA biogenesis pathways based on studies in silkworm BmN4 cells

PIWI-interacting (pi) RNAs play an essential role in protecting the genomic integrity of germ cells from the disruptive transpositions of selfish genetic elements. One of the most important model systems for studying piRNA biogenesis is the ovary derived BmN4 cell line of the silkworm Bombyx mori. In recent years, many steps and components of the pathways involved in this process have been unraveled. However, a holistic description of piRNA biogenesis in BmN4 cells is still unavailable. In this paper, we review the state of the art and propose a novel model for piRNA biogenesis in BmN4 cells. This model was built considering the latest published data and will empower researchers to plan future experiments and interpret experimental results.

PIWI proteins and piRNAs: key regulators of stem cell biology

In this mini review, we discussed the functional roles of PIWI proteins and their associated small RNAs, piRNAs, in regulating gene expression within stem cell biology. Guided by piRNAs, these proteins transcriptionally and post-transcriptionally repress transposons using mechanisms such as the ping-pong amplification cycle and phasing to protect germline genomes. Initially identified in Drosophila melanogaster, the piRNA pathway regulate germline stem cell self-renewal and differentiation via cell-autonomous and non-cell-autonomous mechanisms. Precisely, in GSCs, PIWI proteins and piRNAs regulate gene expression by modulating chromatin states and directly influencing mRNA translation. For instance, the PIWI protein Aubergine loaded with piRNAs promotes and represses translation of certain mRNAs to balance self-renewal and differentiation. Thus, the piRNA pathway exhibits dual regulatory roles in mRNA stability and translation, highlighting its context-dependent functions. Moreover, PIWI proteins are essential in somatic stem cells to support the regenerative capacity of highly regenerative species, such as planarians. Similarly, in Drosophila intestinal stem cells, the PIWI protein Piwi regulates metabolic pathways and genome integrity, impacting longevity and gut homeostasis. In this case, piRNAs appear absent in the gut, suggesting piRNA-independent regulatory mechanisms. Together, PIWI proteins and piRNAs demonstrate evolutionary conservation in stem cell regulation, integrating TE silencing and gene expression regulation at chromatin and mRNA levels in somatic and germline lineages. Beyond their canonical roles, emerging evidence reveal their broader significance in maintaining stem cell properties and organismal health under physiological and pathological conditions.

Noncoding RNA profiling in omentum adipose tissue from obese patients and the identification of novel metabolic biomarkers

Background

Obesity, a prevalent metabolic disorder, is linked to perturbations in the balance of gene expression regulation. Noncoding RNAs (ncRNAs), including long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs), play pivotal roles in regulating gene expression. The aim of this study was to identify additional ncRNA candidates that are implicated in obesity, elucidating their potential as key regulators of the pathogenesis of obesity.

Methods

We identified distinct ncRNA expression profiles in omental adipose tissue in obese and healthy subjects through comprehensive whole-transcriptome sequencing. Subsequent analyses included functional annotation with GO and KEGG pathway mapping, validation via real-time quantitative polymerase chain reaction (qRT‒PCR), the exploration of protein‒protein interactions (PPIs), and the identification of key regulatory genes through network analysis.

Results

The results indicated that, compared with those in healthy individuals, various lncRNAs, circRNAs, and miRNAs were significantly differentially expressed in obese subjects. Further verifications of top changed gene expressions proved the most genes' consistence with RNA-sequencing including 11 lncRNAs and 4 circRNAs. Gene network analysis highlighted the most significant features associated with metabolic pathways, specifically ENST00000605862, ENST00000558885, and ENST00000686149. Collectively, our findings suggest potential ncRNA therapeutic targets for obesity, including ENST00000605862, ENST00000558885, and ENST00000686149.

Universal First-Trimester Screening Biomarkers for Diagnosis of Preeclampsia and Placenta Accreta Spectrum

BACKGROUND

Disruptions in epigenetic mechanisms regulating placentation, particularly imbalances in the levels of small non-coding RNAs, contribute to various pregnancy complications, including preeclampsia (PE) and placenta accreta spectrum (PAS). Given that abnormal trophoblast differentiation, invasiveness, and angiogenesis-reduced in PE and excessive in PAS-are central to the pathogenesis of these conditions, this study aimed to identify universal circulating piRNAs and their targets.

METHODS

Small RNA deep sequencing, quantitative reverse transcription combined with real-time polymerase chain reaction, magnetic bead-based multiplex immunoassay, ELISA, and Western blotting were employed to quantify circulating piRNAs and proteins in the blood serum of pregnant women during the 11th-14th weeks of gestation.

RESULTS

Statistically significant negative correlations were identified between PE- and PAS-associated piRNAs (hsa_piR_019122, hsa_piR_020497, hsa_piR_019949, and piR_019675) and several molecules, including Endoglin, IL-18, VEGF-A, VEGF-C, Angiopoietin-2, sFASL, HB-EGF, TGFα, and Clusterin. These molecules are involved in processes such as angiogenesis, inflammation, the epithelial-mesenchymal transition, cell proliferation, adhesion, and apoptosis. A first-trimester pregnancy screening algorithm was developed using logistic regression models based on Clusterin concentration and the levels of hsa_piR_020497, hsa_piR_019949, piR_019675, and hsa_piR_019122.

CONCLUSIONS

The proposed screening tool for early pregnancy monitoring may enable the prediction of PE or PAS in the first trimester, allowing timely interventions to reduce maternal and perinatal morbidity and mortality.

Mutation Rate Variation and Other Challenges in 2-LTR Dating of Primate Endogenous Retrovirus Integrations

The time of integration of germline-targeting Long Terminal Repeat (LTR) retroposons, such as endogenous retroviruses (ERVs), can be estimated by assessing the nucleotide divergence between the LTR sequences flanking the viral genes. Due to the viral replication mechanism, both LTRs are identical at the moment of integration, when the provirus becomes part of the host genome. After that time, proviral sequences evolve within the host DNA. When the mutation rate is known, nucleotide divergence between the LTRs would then be a measure of time elapsed since integration. Though frequently used, the approach has been complicated by the choice of host mutation rate and, to a lesser extent, by the method selected to estimate nucleotide divergence. As a result, outcomes can be incompatible with, for instance, speciation events identified from the fossil record. The review will give an overview of research reporting LTR-retroposon dating, and a summary of important factors to consider, including the quality, assembly, and alignment of sequences, the mutation rate of foreign DNA in host genomes, and the choice of a distance estimation method. Primates will here be the focus of the analysis because their genomes, ERVs, and fossil record have been extensively studied. However, most of the factors discussed have a wide applicability in the vertebrate field.

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

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

Hypoxic Postconditioning Offers Neuroprotection Against Transient Cerebral Ischemia via Down-Regulation of rno_piR_011022

BACKGROUND

Piwi-interacting RNAs (piRNAs) are differentially expressed after cerebral ischemia. However, little is known about their roles in transient global cerebral ischemia (tGCI). Herein, we aim to elucidate the roles and the underlying molecular mechanisms of piRNAs in tGCI and cerebral ischemic tolerance induced by hypoxic postconditioning (HPC).

METHODS

The male rat models of tGCI and HPC were established in vivo. Oxygen-glucose deprivation/reoxygenation (OGD/R) was developed from primary hippocampal neurons in vitro. RNA-sequencing, fluorescence in situ hybridization, and quantitative real-time PCR were used for detecting piRNA expression. Immunohistochemistry, TUNEL staining, CCK8 assay, etc., were used to evaluate neuronal damage. Western blot was used to measure protein levels of NR2B, PSD95, and cleaved-caspase 3.

RESULTS

The expression profiles of piRNAs in CA1 were significantly changed after tGCI. HPC downregulated the expression of the top 5 piRNAs associated with synaptic function. Notably, the knockdown of rno_piR_011022 not only alleviated neuronal apoptosis and enhanced synaptic plasticity after tGCI and OGD/R but also reduced methyl-D-aspartate (NMDA) receptor 2B (NR2B) expression and inhibited NR2B-postsynaptic density 95 (PSD95) interaction following tGCI. HPC enhanced these inhibitory effects.

CONCLUSION

This innovative study indicated that the down-regulation of rno_piR_011022 plays an important role in HPC-mediated neuroprotection against tGCI through inhibiting the NR2B-PSD95 interaction.

X-Chromosome-Linked miRNAs Regulate Sex Differences in Cardiac Physiology

BACKGROUND

Males and females exhibit distinct anatomic and functional characteristics of the heart, predisposing them to specific disease states.

METHODS

We identified microRNAs (miRNAs/miR) with sex-differential expression in mouse hearts.

RESULTS

Four conserved miRNAs are present in a single locus on the X-chromosome and are expressed at higher levels in females than males. We show miRNA, miR-871, is responsible for decreased expression of the protein SRL (sarcalumenin) in females. SRL is involved in calcium signaling, and we show it contributes to differences in electrophysiology between males and females. miR-871 overexpression mimics the effects of the cardiac physiology of conditional cardiomyocyte-specific Srl-null mice. Inhibiting miR-871 with an antagomir in females shortened ventricular repolarization. The human orthologue of miR-871, miR-888, coevolved with the SRL 3' untranslated region and regulates human SRL.

CONCLUSIONS

These data highlight the importance of sex-differential miRNA mechanisms in mediating sex-specific functions and their potential relevance to human cardiac diseases.

Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes

BACKGROUND

East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. We set out to bridge this gap and to understand the interactions between TEs and their cichlid hosts.

RESULTS

Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. Orthology inference revealed strong conservation of TE silencing factors in cichlids, and an expansion of piwil1 genes in Lake Malawi cichlids, likely driven by PiggyBac TEs. The expanded piwil1 copies have signatures of positive selection and retain amino acid residues essential for catalytic activity. Furthermore, the gonads of African cichlids express a Piwi-interacting RNA (piRNA) pathway that targets TEs. We define the genomic sites of piRNA production in African cichlids and find divergence in closely related species, in line with fast evolution of piRNA-producing loci.

CONCLUSIONS

Our findings suggest dynamic co-evolution of TEs and host silencing pathways in the African cichlid radiations. We propose that this co-evolution has contributed to cichlid genomic diversity.

Circulating Extracellular Vesicles as Promising Biomarkers for Precession Diagnostics: A Perspective on Lung Cancer

Extracellular vesicles (EVs) have emerged as promising biomarkers in liquid biopsy, owing to their ubiquitous presence in bodily fluids and their ability to carry disease-related cargo. Recognizing their significance in disease diagnosis and treatment, substantial efforts have been dedicated to developing efficient methods for EV isolation, detection, and analysis. EVs, heterogeneous membrane-encapsulated vesicles secreted by all cells, contain bioactive substances capable of modulating recipient cell biology upon internalization, including proteins, lipids, DNA, and various RNAs. Their prevalence across bodily fluids has positioned them as pivotal mediators in physiological and pathological processes, notably in cancer, where they hold potential as straightforward tumor biomarkers. This review offers a comprehensive examination of advanced nanotechnology-based techniques for detecting lung cancer through EV analysis. It begins by providing a brief overview of exosomes and their role in lung cancer progression. Furthermore, this review explores the evolving landscape of EV isolation and cargo analysis, highlighting the importance of characterizing specific biomolecular signatures within EVs for improved diagnostic accuracy in lung cancer patients. Innovative strategies for enhancing the sensitivity and specificity of EV isolation and detection, including the integration of microfluidic platforms and multiplexed biosensing technologies are summarized. The discussion then extends to key challenges associated with EV-based liquid biopsies, such as the standardization of isolation and detection protocols and the establishment of robust analytical platforms for clinical translation. This review highlights the transformative impact of EV-based liquid biopsy in lung cancer diagnosis, heralding a new era of personalized medicine and improved patient care.

Recent advances in the regulatory and non-coding RNA biology of osteogenic differentiation: biological functions and significance for bone healing

Injuries associated with contemporary life, such as automobile crashes and sports injuries, can lead to large numbers of traumatic neuromuscular injuries that are intimately associated with bone fractures. Regulatory and non-coding RNAs play essential roles in multiple cellular processes, including osteogenic differentiation and bone healing. In this review, we discuss the most recent advances in our understanding of the regulatory and non-coding RNA biology of osteogenic differentiation in stem, stromal and progenitor cells. We focused on circular RNAs, small nucleolar RNAs and PIWI-interacting RNAs and comprehensively summarized their biological functions as well as discussed their significance for bone healing and tissue regeneration.

From the cauldron of conflict: Endogenous gene regulation by piRNA and other modes of adaptation enabled by selfish transposable elements

Transposable elements (TEs) provide a prime example of genetic conflict because they can proliferate in genomes and populations even if they harm the host. However, numerous studies have shown that TEs, though typically harmful, can also provide fuel for adaptation. This is because they code functional sequences that can be useful for the host in which they reside. In this review, I summarize the "how" and "why" of adaptation enabled by the genetic conflict between TEs and hosts. In addition, focusing on mechanisms of TE control by small piwi-interacting RNAs (piRNAs), I highlight an indirect form of adaptation enabled by conflict. In this case, mechanisms of host defense that regulate TEs have been redeployed for endogenous gene regulation. I propose that the genetic conflict released by meiosis in early eukaryotes may have been important because, among other reasons, it spurred evolutionary innovation on multiple interwoven trajectories - on the part of hosts and also embedded genetic parasites. This form of evolution may function as a complexity generating engine that was a critical player in eukaryotic evolution.

Overview of the Different Classes of Small RNAs During B-Cell Development

B lymphocytes (B cells) are a type of white blood cell that play an essential role in the adaptive immune response. They are derived from pluripotent hematopoietic stem cells and undergo several developmental stages in the bone marrow and secondary lymphoid organs to become effector cells. B cells can act as antigen-presenting cells, secrete cytokines, generate immunological memory as memory B cells, and produce and secrete high-affinity antibodies as plasma B cells.B-cell development occurs in discontinuous steps within specific organs and niche environments, progressing through checkpoints controlled by the relative levels of numerous transcription factors, cytokines, and surface receptors. These complex interactions of distinct developmental programs operate through balanced control mechanisms rather than simple "on/off" signals.Over the past two decades, much has been learned about short non-coding RNA (ncRNA) molecules that play a critical role in fine-tuning gene expression by targeting specific messenger RNAs (mRNAs) for degradation or translational repression. In the intricate orchestration of B-cell development, ncRNAs contribute to the delicate balance between proliferation, differentiation, and apoptosis by influencing key checkpoints in the maturation process.Therefore, in this chapter, I will review the role of different classes of small ncRNAs, including microRNAs, glycoRNAs, tRNA-derived fragments, and ribosomal RNA-derived fragments, in modulating gene expression at the post-transcriptional level and their contribution to the intricate regulatory network that controls B-cell maturation.

piRNA processing within non-membrane structures is governed by constituent proteins and their functional motifs

Discovered two decades ago, PIWI-interacting RNAs (piRNAs) are crucial for silencing transposable elements (TEs) in animal gonads, thereby protecting the germline genome from harmful transposition, and ensuring species continuity. Silencing of TEs is achieved through transcriptional and post-transcriptional suppression by piRNAs and the PIWI clade of Argonaute proteins within non-membrane structured organelle. These structures are composed of proteins involved in piRNA processing, including PIWIs and other proteins by distinct functional motifs such as the Tudor domain, LOTUS, and intrinsic disordered regions (IDRs). This review highlights recent advances in understanding the roles of these conserved proteins and structural motifs in piRNA biogenesis. We explore the molecular mechanisms of piRNA biogenesis, with a primary focus on Drosophila as a model organism, identifying common themes and species-specific variations. Additionally, we extend the discussion to the roles of these components in nongonadal tissues.

Drosophila Piwi distinguishes transposons from mRNAs by piRNA complementarity and abundance

Piwi-interacting RNAs (piRNAs) are the main repressors of transposable elements (TEs) in animal germlines. In Drosophila, Piwi-piRNA complexes associate with nascent TE transcripts to drive heterochromatin formation and TE repression. However, previous studies have shown that Piwi also associates with large numbers of mRNAs, raising the question of how Piwi discriminates between mRNAs and TEs. To answer this question, we performed a comprehensive analysis of Piwi-associated RNAs, compositionally and functionally, to decipher the targeting rules of Piwi-piRNA complexes. While Piwi initially identifies its targets through the seed sequence, it requires pairing well beyond the seed, nearly a perfect match, to elicit a repressive response. In addition to the complementarity of piRNAs to their targets, their abundance must reach a certain threshold to be functional. Together, these findings explain large differences in the target repression of Piwi-associated RNAs and reveal how Piwi efficiently distinguishes TEs from mRNAs despite associating with both.

Somatic piRNA and PIWI-mediated post-transcriptional gene regulation in stem cells and disease

PIWI-interacting RNAs (piRNAs) are small non-coding RNAs that bind to the PIWI subclass of the Argonaute protein family and are essential for maintaining germline integrity. Initially discovered in Drosophila, PIWI proteins safeguard piRNAs, forming ribonucleoprotein (RNP) complexes, crucial for regulating gene expression and genome stability, by suppressing transposable elements (TEs). Recent insights revealed that piRNAs and PIWI proteins, known for their roles in germline maintenance, significantly influence mRNA stability, translation and retrotransposon silencing in both stem cells and bodily tissues. In the current review, we explore the multifaceted roles of piRNAs and PIWI proteins in numerous biological contexts, emphasizing their involvement in stem cell maintenance, differentiation, and the development of human diseases. Additionally, we discussed the up-and-coming animal models, beyond the classical fruit fly and earthworm systems, for studying piRNA-PIWIs in self-renewal and cell differentiation. Further, our review offers new insights and discusses the emerging roles of piRNA-dependent and independent functions of PIWI proteins in the soma, especially the mRNA regulation at the post-transcriptional level, governing stem cell characteristics, tumor development, and cardiovascular and neurodegenerative diseases.

PiRNA CFAPIR inhibits cardiac fibrosis by regulating the muscleblind-like protein MBNL2

Myocardial fibroblasts transform into myofibroblasts during the progression of cardiac fibrosis, together with excessive cardiac fibroblast proliferation. Hence, the prevention and treatment of cardiac fibrosis are significant factors for inhibiting the development of heart failure. P-element Induced WImpy testis-interacting RNAs (PiRNA) are widely expressed in the heart, but their involvement in cardiac fibrosis has not yet been confirmed. We identified differentially expressed PiRNAs using Arraystar PiRNA expression profiling in Angiotensin II models of cardiac fibrosis in vivo and in vitro. We then explored cardiac-fibrosis-associated PiRNA-related proteins, RNA-protein interactomes, immunoprecipitation, and pulldown. We detected fibrosis markers and pathway-related proteins using immunofluorescence, qRT-PCR, and Western blot. We uncovered cardiac fibrosis associated PiRNA (CFAPIR) that was obviously dysregulated during cardiac fibrosis, whereas its overexpression reversed fibrosis in vivo and in vitro. Mechanistically, CFAPIR competitively bound muscleblind like protein 2 (MBNL2) and the cyclin-dependent kinase inhibitor P21 to regulate the TGF-β1/SMAD3 signaling pathway.

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.

Databases and computational methods for the identification of piRNA-related molecules: A survey

Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs (ncRNAs) that plays important roles in many biological processes and major cancer diagnosis and treatment, thus becoming a hot research topic. This study aims to provide an in-depth review of computational piRNA-related research, including databases and computational models. Herein, we perform literature analysis and use comparative evaluation methods to summarize and analyze three aspects of computational piRNA-related research: (i) computational models for piRNA-related molecular identification tasks, (ii) computational models for piRNA-disease association prediction tasks, and (iii) computational resources and evaluation metrics for these tasks. This study shows that computational piRNA-related research has significantly progressed, exhibiting promising performance in recent years, whereas they also suffer from the emerging challenges of inconsistent naming systems and the lack of data. Different from other reviews on piRNA-related identification tasks that focus on the organization of datasets and computational methods, we pay more attention to the analysis of computational models, algorithms, and performances that aim to provide valuable references for computational piRNA-related identification tasks. This study will benefit the theoretical development and practical application of piRNAs by better understanding computational models and resources to investigate the biological functions and clinical implications of piRNA.