The burgeoning importance of PIWI-interacting RNAs in cancer progression

Triple‑negative breast cancer cell‑derived piR‑31115 promotes the proliferation and migration of endothelial cells via METTL3‑mediated m6A modification of YAP1

Triple‑negative breast cancer (TNBC), a highly malignant breast cancer subtype with a pronounced metastatic propensity, forms the focus of the present investigation. MDA‑MB‑231, a prevalently utilized TNBC cell line in cancer research, was employed. In accordance with the tumour angiogenesis theory, cancer cells are capable of instigating angiogenesis and the formation of a novel vascular system within the tumour microenvironment, which subsequently sustains malignant proliferation and metastasis. Consequently, impeding the growth of tumour blood vessels holds substantial significance in suppressing TNBC metastasis. Piwi‑interacting RNAs (piRNAs), a category of endogenous non‑coding RNAs, have been demonstrated to modulate cancer progression. However, studies regarding the role of piRNAs in regulating angiogenesis within cancer cells are relatively scant. In the present study, via cell co‑culture experiments, it was revealed that piR‑31115 (a kind of piRNA) in MDA‑MB‑231 cells notably enhanced the recruitment of a human microvascular endothelial cell line (HMEC‑1). Moreover, the conditioned medium (CM, which was obtained from MDA‑MB‑231 cells via a specific culturing methodology and was employed for the subsequent treatment of HMEC‑1 cells to explore its impacts on the biological behaviors such as the proliferation and migration of HMEC‑1 cells) derived from MDA‑MB‑231 cells with upregulated piR‑31115 expression stimulated the proliferation and migration of HMEC‑1 cells. These findings suggest that piR‑31115 in MDA‑MB‑231 cells may play a pivotal role in modulating tumour angiogenesis. Further studies disclosed that the CM from MDA‑MB‑231 cells augmented the N6‑methyladenosine (m6A) RNA modification level via METTL3 in HMEC‑1 cells. Transcriptome sequencing revealed that METTL3 functions as an m6A writer protein for Yes‑associated protein 1 (YAP1), which exerts a positive influence on promoting the proliferation and migration of HMEC‑1 cells. Concurrently, the IGF2BP plays a crucial role in stabilizing YAP1 protein expression. Collectively, the present findings identified a signalling pathway through which MDA‑MB‑231 cells induce HMEC‑1 cell proliferation and migration by regulating m6A RNA methylation.

Machine-learning diagnostics of breast cancer using piRNA biomarkers

BACKGROUND AND OBJECTIVES

Prior studies have shown that small non-coding RNAs (sncRNAs) are associated with cancer occurrence or development. Recently, a newly discovered class of small ncRNAs known as PIWI-interacting RNAs (piRNAs) have been found to play a vital role in physiological processes and cancer initiation. This study aims to utilize piRNAs as innovative, noninvasive diagnostic biomarkers for breast cancer. Our objective is to develop computational methods that leverage piRNA attributes for breast cancer prediction and its application in diagnostics.

METHODS

We created a set of piRNA sequence descriptors using information extracted from the piRNA sequences. To ensure accuracy, we found a path to convert non-standard piRNA names to standard ones to enable precise identification of these sequences. Using these descriptors, we applied machine-learning (ML) techniques in WEKA (Waikato Environment for Knowledge Analysis) to a dataset of piRNA to assess the predictive accuracy of the following classifiers: Logistic Regression model, Sequential Minimal Optimization (SMO), Random Forest classifier, and Logistic Model Tree (LMT). Furthermore, we performed Shapley additive explanations (SHAP) Analysis to understand which descriptors were the most relevant to the prediction accuracy. The ML models were then validated on an independent dataset to evaluate their effectiveness in predicting breast cancer.

RESULTS

The top three performing classifiers in WEKA were Logistic Regression, SMO, and LMT. The Logistic Regression model achieved an accuracy of 90.7% in predicting breast cancer, while SMO and LMT attained 89.7% and 85.65%, respectively.

CONCLUSIONS

Our study demonstrates the effectiveness of using ML-based piRNA classifiers in diagnosing breast cancer and contributes to the growing body of evidence supporting piRNAs as biomarkers in cancer diagnosis. However, additional research is needed to validate these findings and further assess the clinical applicability of this approach.

Palindrome-mediated DNA nanotubes with cell-specific aptamers to improve targeted antitumor effects and reduce toxicity on non-small cell lung cancer

Chemotherapy is regarded as a widely used and effective treatment strategy for lung cancer, although most conventional chemotherapeutics cause severe toxic side-effects due to their indiscriminate attacks on both cancerous and normal cells. Although nucleic acid nanomaterials are emerging as a promising drug delivery strategy, their clinical applications are limited by rapid degradation by nucleases and difficulties in targeting cancer cells. In this study, we have developed a Rhein-loaded aptamer-based DNA nanotube (DNT-S6@Rhein) for the targeted and efficient therapy of non-small cell lung cancer. Through the palindrome segments, two specified oligonucleotides were hybridized and folded into the well-defined nanotubes (DNT-S6), with the S6 aptamer distributed outside. The obtained nanotubes exhibited excellent serum stability and targeting ability towards A549 cells due to the firm structure and decoration of the S6 aptamer. Rhein, as an antitumor drug and DNA intercalator, can be effectively inserted into the DNT-S6. The drug-loaded nanotubes rapidly disassembled in intracellular environment and then the released Rhein was found to activate cellular apoptotic process and significantly suppress proliferation, migration and invasion of A549 cells. Moreover, DNT-S6@Rhein could efficiently accumulate in tumor regions, offering compelling therapeutic efficacy and biocompatibility under both in vitro and in vivo settings. These findings of this study provide a promising strategy for mitigating the inevitable systemic side-effects of chemotherapy and expand the potential application of DNA nanostructure on targeted drug delivery.

Dysregulation of transposable elements and PIWI-interacting RNAs in myelodysplastic neoplasms

BACKGROUND

Myelodysplastic neoplasms (MDS) are heterogeneous hematopoietic disorders characterized by ineffective hematopoiesis and genome instability. Mobilization of transposable elements (TEs) is an important source of genome instability leading to oncogenesis, whereas small PIWI-interacting RNAs (piRNAs) act as cellular suppressors of TEs. However, the roles of TEs and piRNAs in MDS remain unclear.

METHODS

In this study, we examined TE and piRNA expression through parallel RNA and small RNA sequencing of CD34+ hematopoietic stem cells from MDS patients.

RESULTS

Comparative analysis of TE and piRNA expression between MDS and control samples revealed several significantly dysregulated molecules. However, significant differences were observed between lower-risk MDS (LR-MDS) and higher-risk MDS (HR-MDS) samples. In HR-MDS, we found an inverse correlation between decreased TE levels and increased piRNA expression and these TE and piRNA levels were significantly associated with patient outcomes. Importantly, the upregulation of PIWIL2, which encodes a key factor in the piRNA pathway, independently predicted poor prognosis in MDS patients, underscoring its potential as a valuable disease marker. Furthermore, pathway analysis of RNA sequencing data revealed that dysregulation of the TE‒piRNA axis is linked to the suppression of processes related to energy metabolism, the cell cycle, and the immune response, suggesting that these disruptions significantly affect cellular activity.

CONCLUSIONS

Our findings demonstrate the parallel dysregulation of TEs and piRNAs in HR-MDS patients, highlighting their potential role in MDS progression and indicating that the PIWIL2 level is a promising molecular marker for prognosis.

Development and validation of a novel artificial intelligence algorithm for precise prediction the postoperative prognosis of esophageal squamous cell carcinoma

BACKGROUND

Esophageal squamous cell carcinoma (ESCC) is a highly aggressive malignancy, and current postoperative prognostic assessment methods remain unsatisfactory, underlining the urgent to develop a reliable approach for precision medicine. Given the similarities with gametogenesis, cancer/testis genes (CTGs) are acknowledged for regulation unrestrained multiplication and immune microenvironment during oncogenic processes. These processes are associated with advanced disease and poorer prognosis, indicating that CTGs could serve as ideal prognostic biomarkers in ESCC. The purpose of this study is to develop a novel clinically prognostic prediction system to facilitate the individualized postoperative care.

METHODS

We conducted LASSO regression analysis of protein-coding CTGs and clinical characteristics from 119 pathologically confirmed ESCC patients to recognize powerful predictive variables. We employed nine supervised machine learning classifiers and integrated best predictive machine learning classifiers by weighted voting method to construct an ensemble model called PPMESCC. Additionally, functional assay was conducted to examine the potential effect of top-ranking CTG HENMT1 in ESCC.

RESULTS

LASSO regression identified five CTGs and TNM stage as optimized prognostic features. Six machine learning classifiers were integrated to construct an ensemble model, PPMESCC, which exhibited outstanding performance in ESCC prediction. The AUC for PPMESCC was 0.9828 (95% confidence interval: 0.9608 to 0.9926), with an accuracy of 98.32% (95% CI: 96.64-99.16%) in the discovery cohort and 0.9057 (95% CI: 0.8897 to 0.9583) of AUC with an accuracy of 90% (95% CI: 89.08-93.28%) in validation cohort. In addition, the top-ranking CTG HENMT1 encodes 2'-O-methyltransferase of piRNAs that was confirmed positively correlated with the proliferation capacity of ESCC cells. Then we systematically screen piRNAs associated with esophageal carcinoma based on GWAS, eQTL-piRNA, and i2OM databases, and successfully discovered 8 piRNAs potentially regulated by HENMT1.

CONCLUSION

The study highlights the clinical utility of PPMESCC algorithm in prognostic prediction that may facilitate to establish the personalized screening and management strategies for postoperative ESCC patients.

Genes and proteins expressed at different life cycle stages in the model protist Euplotes vannus revealed by both transcriptomic and proteomic approaches

Sexual reproduction first appeared in unicellular protists and has continued to be an essential biological process in almost all eukaryotes. Ciliated protists, which contain both germline and somatic genomes within a single cell, have evolved a special form of sexual reproduction called conjugation that involves mitosis, meiosis, fertilization, nuclear differentiation, genome rearrangement, and the development of unique cellular structures. The molecular basis and mechanisms of conjugation vary dramatically among ciliates, and many details of the process and its regulation are still largely unknown. In order to better comprehend these processes and mechanisms from an evolutionary perspective, this study provides the first comprehensive overview of the transcriptome and proteome profiles during the entire life cycle of the newly-established marine model ciliate Euplotes vannus. Transcriptome analyses from 14 life cycle stages (three vegetative stages and 11 sexual stages) revealed over 26,000 genes that are specifically expressed at different stages, many of which are related to DNA replication, transcription, translation, mitosis, meiosis, nuclear differentiation, and/or genome rearrangement. Quantitative proteomic analyses identified 338 proteins with homologs associated with conjugation and/or somatic nuclear development in other ciliates, including dicer-like proteins, Hsp90 proteins, RNA polymerase II and transcription elongation factors, ribosomal-associated proteins, and ubiquitin-related proteins. Four of these homologs belong to the PIWI family, each with different expression patterns identified and confirmed by RT-qPCR, which may function in small RNA-mediated genome rearrangement. Proteins involved in the nonhomologous end-joining pathway are induced early during meiosis and accumulate in the developing new somatic nucleus, where more than 80% of the germline sequences are eliminated from the somatic genome. A number of new candidate genes and proteins likely to play roles in conjugation and its related genome rearrangements have also been revealed. The gene expression profiles reported here will be valuable resources for further studies of the origin and evolution of sexual reproduction in this new model species.

A comprehensive analysis of gene expression and the immune landscape in gastric cancer through single-cell and multi-omics approaches

Gastric cancer (GC) is a common malignant tumor worldwide, characterized by complex biological processes. The distribution of various cell types and gene expression profiles in the GC microenvironment remains unclear. This study uses single-cell RNA sequencing to explore gene expression patterns and identify differentially expressed genes in GC samples, offering new insights into cellular diversity and potential molecular mechanisms. We conducted temporal and clustering analyses with single-cell sequencing, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses to clarify their functions. Using machine learning, we identified relevant genes to create highly accurate prediction models. Additionally, ssGSEA analysis provided detailed insights into the immunosuppressive tumor microenvironment, revealing complex gene expression interactions and diverse immune infiltrates in cancer. Correlation analysis highlighted TIMP1 as having significant prognostic value across different immune cell subtypes. Single-cell RNA sequencing revealed the cellular landscape and gene expression profiles of the GC microenvironment, offering crucial data on how cell heterogeneity is regulated in relation to the tumor microenvironment. Moreover, new insights into the expression levels of AGT, INHBA, and TIMP1 showed distinct sex-biased gene functions within the tumor microenvironment. These findings enhance our understanding of the molecular mechanisms associated with gastric cancer development and may lay the groundwork for identifying novel therapeutic targets and diagnostic strategies.

Long non-coding RNAs: regulators of autophagy and potential biomarkers in therapy resistance and urological cancers

The non-coding RNAs (ncRNAs) comprise a large part of human genome that mainly do not code for proteins. Although ncRNAs were first believed to be non-functional, the more investigations highlighted tthe possibility of ncRNAs in controlling vital biological processes. The length of long non-coding RNAs (lncRNAs) exceeds 200 nucleotidesand can be present in nucleus and cytoplasm. LncRNAs do not translate to proteins and they have been implicated in the regulation of tumorigenesis. On the other hand, One way cells die is by a process called autophagy, which breaks down proteins and other components in the cytoplasm., while the aberrant activation of autophagy allegedly involved in the pathogenesis of diseases. The autophagy exerts anti-cancer activity in pre-cancerous lesions, while it has oncogenic function in advanced stages of cancers. The current overview focuses on the connection between lncRNAs and autophagy in urological cancers is discussed. Notably, one possible role for lncRNAs is as diagnostic and prognostic variablesin urological cancers. The proliferation, metastasis, apoptosis and therapy response in prostate, bladder and renal cancers are regulated by lncRNAs. The changes in autophagy levels can also influence the apoptosis, proliferation and therapy response in urological tumors. Since lncRNAs have modulatory functions, they can affect autophagy mechanism to determine progression of urological cancers.

tsRNA-GlyGCC promotes colorectal cancer progression and 5-FU resistance by regulating SPIB

BACKGROUND

tRNA-derived small RNAs (tsRNAs) are newly discovered non-coding RNA, which are generated from tRNAs and are reported to participate in several biological processes in diseases, especially cancer; however, the mechanism of tsRNA involvement in colorectal cancer (CRC) and 5-fluorouracil (5-FU) is still unclear.

METHODS

RNA sequencing was performed to identify differential expression of tsRNAs in CRC tissues. CCK8, colony formation, transwell assays, and tumor sphere assays were used to investigate the role of tsRNA-GlyGCC in 5-FU resistance in CRC. TargetScan and miRanda were used to identify the target genes of tsRNA-GlyGCC. Biotin pull-down, RNA pull-down, luciferase assay, ChIP, and western blotting were used to explore the underlying molecular mechanisms of action of tsRNA-GlyGCC. The MeRIP assay was used to investigate the N(7)-methylguanosine RNA modification of tsRNA-GlyGCC.

RESULTS

In this study, we uncovered the feature of tsRNAs in human CRC tissues and confirmed a specific 5' half tRNA, 5'tiRNA-Gly-GCC (tsRNA-GlyGCC), which is upregulated in CRC tissues and modulated by METTL1-mediated N(7)-methylguanosine tRNA modification. In vitro and in vivo experiments revealed the oncogenic role of tsRNA-GlyGCC in 5-FU drug resistance in CRC. Remarkably, our results showed that tsRNA-GlyGCC modulated the JAK1/STAT6 signaling pathway by targeting SPIB. Poly (β-amino esters) were synthesized to assist the delivery of 5-FU and tsRNA-GlyGCC inhibitor, which effectively inhibited tumor growth and enhanced CRC sensitive to 5-FU without obvious adverse effects in subcutaneous tumor.

CONCLUSIONS

Our study revealed a specific tsRNA-GlyGCC-engaged pathway in CRC progression. Targeting tsRNA-GlyGCC in combination with 5-FU may provide a promising nanotherapeutic strategy for the treatment of 5-FU-resistance CRC.

CircRNA-associated ceRNA regulatory networks as emerging mechanisms governing the development and biophysiopathology of epilepsy

The etiology of epilepsy is ascribed to the synchronized aberrant neuronal activity within the brain. Circular RNAs (circRNAs), a class of non-coding RNAs characterized by their circular structures and covalent linkage, exert a substantial influence on this phenomenon. CircRNAs possess stereotyped replication, transience, repetitiveness, and paroxysm. Additionally, MicroRNA (miRNA) plays a crucial role in the regulation of diverse pathological processes, including epilepsy. CircRNA is of particular significance due to its ability to function as a competing endogenous RNA, thereby sequestering or inhibiting miRNA activity through binding to target mRNA. Our review primarily concentrates on elucidating the pathological and functional roles, as well as the underlying mechanisms, of circRNA-miRNA-mRNA networks in epilepsy. Additionally, it explores the potential utility of these networks for early detection and therapeutic intervention.

Exosomal non-coding RNAs in colorectal cancer metastasis

Colorectal cancer (CRC) is a type of gastrointestinal cancer with high morbidity and mortality rates, and is often accompanied by distant metastases. Metastasis is a major cause of shortened survival time and poor treatment outcomes for patients with CRC. However, the molecular mechanisms underlying the metastasis of CRC remain unclear. Exosomes are a class of small extracellular vesicles that originate from almost all human cells and can transmit biological information (e.g., nucleic acids, lipids, proteins, and metabolites) from secretory cells to target recipient cells. Recent studies have revealed that non-coding RNAs (ncRNAs) can be released by exosomes into the tumour microenvironment or specific tissues, and play a pivotal role in tumorigenesis by regulating a series of key molecules or signalling pathways, particularly those involved in tumour metastasis. Exosomal ncRNAs have potential as novel therapeutic targets for CRC metastasis, and can also be used as liquid biopsy biomarkers because of their specificity and sensitivity. Therefore, further investigations into the biological function and clinical value of exosomal ncRNAs will be of great value for the prevention, early diagnosis, and treatment of CRC metastasis.