PIWI-interacting RNA Expression Research Articles

Influence of aging and maternal protein restriction on PIWI-interacting RNA expression in the offspring rat ventral prostate

The Developmental Origins of Health and Disease (DOHaD) concept explores the link between exposure to adverse conditions during fetal and early childhood development and the onset of chronic non-communicable diseases, such as prostate cancer (PCa). Changes in epigenetics that control gene expression have been identified as potential contributors to the developmental origin of PCa. Piwi-interacting RNAs (piRNAs), for example, control transposable elements (TEs) and maintain genome integrity in germ cells. However, stress-induced deregulation of TEs warrants investigating the role of piRNAs in the prostate gland from the DOHaD perspective, which remains underexplored. This study aimed to detect and characterize piRNA expression in the ventral prostate (VP) of Sprague Dawley rat offspring at 21 postnatal days (PND21) and PND540. The rats were subjected to maternal protein restriction during pregnancy and lactation to understand its impact on prostate development and aging. Histological analyses showed that the gestational and lactation low-protein diet (GLLP) group experienced a delay in prostate gland development, with increased stromal and epithelial compartments and decreased luminal compartments during early life. Aging in this group resulted in decreased luminal compartments and increased stromal areas. Epithelial atrophy was observed in both groups, with an increased incidence of carcinoma in situ in the GLLP group. Small RNA sequencing from control and restricted groups (at PND21 and PND540) identified piRNA clusters in both young and aged animals. We also detected the expression of PIWI genes (Riwi, Rili, Rili2) in the prostate. Our data highlight the key role of maternal malnutrition in modulating piRNA expression in the offspring’s VP, with the potential to influence prostate developmental biology and the risk of prostatic disorders with aging.

Polystyrene nanoplastics induce vascular stenosis via regulation of the PIWI-interacting RNA expression profile

Nanoplastics (NPs) have become common worldwide and attracted increasing attention due to their serious toxic effects. Owing to their higher surface area and volume ratios and ability to easily enter tissues, NPs impose more serious toxic effects than microplastics. However, the effect of NP exposure on vascular stenosis remains unclear. To measure the effects of polystyrene NP (PS-NP) exposure on vascular toxicity, we conducted analyses of blood biochemical parameters, pathological histology, high-throughput sequencing, and bioinformatics. Red fluorescent PS-NPs (100 nm) were effectively uptake by mouse vascular arterial tissue. The uptake of PS-NPs resulted in vascular toxicity, including alterations in lipid metabolism and thickening of the arterial wall. Based on PIWI-interacting RNA (piRNA) sequencing, 1547 and 132 differentially expressed piRNAs (DEpiRNAs) were detected in the PS-NP treatment group after 180 and 30 days, including 787 and 86 upregulated and 760 and 46 downregulated compared with the control group, respectively. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated that the target genes of DEpiRNAs were mostly involved in cell growth and cell motility-related signaling, such as the MAPK signaling pathway. This is the first study to highlight the alteration in piRNA levels in mouse vascular arterial tissue after PS-NP exposure. This study adds to the knowledge regarding the regulatory mechanism of pathological changes induced by PS-NP exposure.

PIWI-interacting RNA expression regulates pathogenesis in a Caenorhabditis elegans model of Lewy body disease

PIWI-interacting RNAs (piRNAs) are small noncoding RNAs that regulate gene expression, yet their molecular functions in neurobiology are unclear. While investigating neurodegeneration mechanisms using human α-syn(A53T)Tg and AβTg;α-syn(A53T)Tg pan-neuronal overexpressing strains, we unexpectedly observed dysregulation of piRNAs. RNAi screening revealed that knock down of piRNA biogenesis genes improved thrashing behavior; further, a tofu-1 gene deletion ameliorated phenotypic deficits in α-syn(A53T)Tg and AβTg;α-syn(A53T)Tg transgenic strains. piRNA expression was extensively downregulated and H3K9me3 marks were decreased after tofu-1 deletion in α-syn(A53T)Tg and AβTg;α-syn(A53T)Tg strains. Dysregulated piRNAs targeted protein degradation genes suggesting that a decrease of piRNA expression leads to an increase of degradation ability in C. elegans. Finally, we interrogated piRNA expression in brain samples from PD patients. piRNAs were observed to be widely overexpressed at late motor stage. In this work, our results provide evidence that piRNAs are mediators in pathogenesis of Lewy body diseases and suggest a molecular mechanism for neurodegeneration in these and related disorders.

Systematic evaluation of the effects of genetic variants on PIWI-interacting RNA expression across 33 cancer types.

PIWI-interacting RNAs (piRNAs) are an emerging class of non-coding RNAs involved in tumorigenesis. Expression quantitative trait locus (eQTL) analysis has been demonstrated to help reveal the genetic mechanism of single nucleotide polymorphisms (SNPs) in cancer etiology. However, there are no databases that have been constructed to provide an eQTL analysis between SNPs and piRNA expression. In this study, we collected genotyping and piRNA expression data for 10 997 samples across 33 cancer types from The Cancer Genome Atlas (TCGA). Using linear regression cis-eQTL analysis with adjustment of appropriate covariates, we identified millions of SNP-piRNA pairs in tumor (76 924 831) and normal (24 431 061) tissues. Further, we performed differential expression and survival analyses, and linked the eQTLs to genome-wide association study (GWAS) data to comprehensively decipher the functional roles of identified cis-piRNA eQTLs. Finally, we developed a user-friendly database, piRNA-eQTL (http://njmu-edu.cn:3838/piRNA-eQTL/), to help users query, browse and download corresponding eQTL results. In summary, piRNA-eQTL could serve as an important resource to assist the research community in understanding the roles of genetic variants and piRNAs in the development of cancers.

Trypanosoma cruzi Modulates PIWI-Interacting RNA Expression in Primary Human Cardiac Myocytes during the Early Phase of Infection.

Trypanosoma cruzi dysregulates the gene expression profile of primary human cardiomyocytes (PHCM) during the early phase of infection through a mechanism which remains to be elucidated. The role that small non-coding RNAs (sncRNA) including PIWI-interacting RNA (piRNA) play in regulating gene expression during the early phase of infection is unknown. To understand how T. cruzi dysregulate gene expression in the heart, we challenged PHCM with T. cruzi trypomastigotes and analyzed sncRNA, especially piRNA, by RNA-sequencing. The parasite induced significant differential expression of host piRNAs, which can target and regulate the genes which are important during the early infection phase. An average of 21,595,866 (88.40%) of clean reads mapped to the human reference genome. The parasite induced 217 unique piRNAs that were significantly differentially expressed (q ≥ 0.8). Of these differentially expressed piRNAs, 6 were known and 211 were novel piRNAs. In silico analysis showed that some of the dysregulated known and novel piRNAs could target and potentially regulate the expression of genes including NFATC2, FOS and TGF-β1, reported to play important roles during T. cruzi infection. Further evaluation of the specific functions of the piRNAs in the regulation of gene expression during the early phase of infection will enhance our understanding of the molecular mechanism of T. cruzi pathogenesis. Our novel findings constitute the first report that T. cruzi can induce differential expression of piRNAs in PHCM, advancing our knowledge about the involvement of piRNAs in an infectious disease model, which can be exploited for biomarker and therapeutic development.

Effects of fluoride on PIWI-interacting RNA expression profiling in testis of mice

Excessive fluoride intake can damage testis by breaking the integrity of sperm DNA and changing the expression profiles of testicular mRNAs and microRNAs. However, the effects of fluoride on the expression of PIWI-interacting RNAs (piRNAs) in mouse testes have not been reported. In this study, we determined the effect of fluoride on PIWI-interacting RNA expression profiling in testis of mice, using deep-sequencing technology. Compared to the control, 50 mg/L sodium fluoride (NaF) exposure led to a reduced testicular organ coefficient, semen quality, and testosterone level, and altered the testicular microstructure. Furthermore, NaF exposure also changed the expression of 28 piRNAs that regulate 182 target genes in mouse testes. In mice given water containing 50 mg/L NaF, the following four pathways were enriched and overexpressed: lysosomal, Jak-STAT, chemokine, and ubiquitin-mediated proteolysis. Among the piRNAs affecting the lysosomal pathway, piR-mmu-1277316, piR-mmu-8060747, and piR-mmu-1566415 levels were increased. We also observed increased levels of the following target gene mRNAs in lysosomal pathwa in the 50 mg/L NaF-treated group: Gga2, Ap4e1, Gla, and Ap1s3. These findings are in line with the results of piRNA-sequencing and suggest that piRNAs in the testis could be potential biomarkers for fluoride reproductive toxicity.

HPV status is associated with altered PIWI-interacting RNA expression pattern in head and neck cancer

As HPV-induced cases of oral malignancy increase, it is important to understand the molecular differences between HPV positive and negative head and neck squamous cell carcinoma (HNSCC). PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs aberrantly expressed in cancer. We analyzed global piRNA expression patterns to define the HNSCC piRNA transcriptome and assess whether HPV infection status associates with changes in piRNA levels. A total of 498 HNSCC small RNA sequencing libraries were acquired from the Cancer Genomics Hub (cgHUB) Data Repository and a custom sequence analysis pipeline was developed to deduce piRNA expression from raw sequencing data. Expression matrices were aligned to clinicopathological features in order to analyze piRNA expression patterns across different HNSCC groups. The association of a piRNA signature with HPV-positive patient survival was evaluated using a Cox proportional hazard model. Analysis of piRNA levels between HNSCC and non-malignant tissues revealed distinct expression patterns, with 87 piRNAs exclusively expressed in tumor samples. HPV infection status affected the expression of 41 of these piRNAs. Eleven (26.8%) piRNAs were significantly downregulated in HPV16/18 tumors compared to other HPV types. Remarkably, expression of a combination of five-piRNAs in HPV-positive HNSCC tumors was associated with worse overall survival. The expression of specific piRNAs is deregulated in HNSCC, and changes with both HPV status and type. Importantly, a five-piRNA signature is able to delineate a subset of HPV-positive HNSCC patients with poor outcome, highlighting the potential utility of piRNAs in patient management.