YRNAs: New Insights and Potential Novel Approach in Head and Neck Squamous Cell Carcinoma

Expression Levels of Plasma YRNAs in Colorectal Cancer as a Potential Noninvasive Biomarker

PURPOSE

Colorectal cancer (CRC) is identified as the second leading cause of cancer-associated deaths worldwide. Therefore, there is ongoing research to discover new potential biomarkers enabling early and noninvasive diagnosis of the disease. YRNAs, a novel class of non-coding RNAs, have been identified as a new player in carcinogenesis and an independent class of clinical biomarkers in various malignancies. Nevertheless, the role of plasma YRNAs in CRC diagnosis and prognosis remains unknown. Therefore, the current study aimed to investigate the clinical significance of plasma YRNAs as a noninvasive biomarker for CRC.

METHODS

Plasma YRNAs expression was assessed in 50 newly diagnosed CRC patients as well as 50 age- and sex-matched healthy controls using quantitative reverse transcription polymerase chain reaction.

RESULTS

All plasma YRNAs expression levels were significantly higher in CRC patients than in controls. A significant correlation was observed between YRNA1 and YRNA3, and between YRNA1 and YRNA4. However, no significant correlation between YRNA1 and YRNA5 was identified. Plasma YRNA1 expression showed the highest diagnostic performance for the detection of CRC using the receiver operating characteristic curve analysis, with a sensitivity of 92% and a specificity of 90%. Nevertheless, when the four YRNAs were combined in a single ROC analysis, sensitivity decreased to 80%, while the specificity remained virtually unchanged. Moreover, significant association was observed between plasma YRNA1 and YRNA3 and tumor stage, grade, lymph node presence, metastasis, and lymphovascular invasion.

CONCLUSIONS

Plasma YRNA may serve as a potential noninvasive biomarker for the diagnosis and prognosis of CRC with high sensitivity and specificity vs. healthy controls.

YRNAs: biosynthesis, structure, functions and involvment in cancer development

Y RNAs are a class of highly conserved small non-coding RNAs. Emerging evidences reported that Y RNAs and their Y RNA-derived small RNAs (YsRNAs) represent bioactive molecules and not simply structural RNAs involved in scaffolding and assembling. They can interact and regulate both localization and functions of several RNA-binding proteins implicated in a wide range of cellular processes such as DNA replication, RNA quality control and cellular stress responses. More evidences suggest functional involvement of Y RNAs in several type of disease such as cancer, immune related pathologies, neurological disorders and cardiovascular diseases. Nevertheless, there are many questions that still need to be answered for their functional and mechanistic understanding in a physiological and in a pathological context. In this review we will describe the current state of knowledge about YRNAs, their structure, biogenesis, functions and interaction with known proteins, as well their role in disease. The picture arising indicates their potential function as biomarkers for disease diagnosis, as well as therapeutical targets for building up tailored approaches in personalized medicine.

Non-Coding RNAs in Cancer: Structure, Function, and Clinical Application

We are on the brink of a paradigm shift in both theoretical and clinical oncology. Genomic and transcriptomic profiling, alongside personalized approaches that account for individual patient variability, are increasingly shaping discourse. Discussions on the future of personalized cancer medicine are mainly dominated by the potential of non-coding RNAs (ncRNAs), which play a prominent role in cancer progression and metastasis formation by regulating the expression of oncogenic or tumor suppressor proteins at transcriptional and post-transcriptional levels; furthermore, their cell-free counterparts might be involved in intercellular communication. Non-coding RNAs are considered to be promising biomarker candidates for early diagnosis of cancer as well as potential therapeutic agents. This review aims to provide clarity amidst the vast body of literature by focusing on diverse species of ncRNAs, exploring the structure, origin, function, and potential clinical applications of miRNAs, siRNAs, lncRNAs, circRNAs, snRNAs, snoRNAs, eRNAs, paRNAs, YRNAs, vtRNAs, and piRNAs. We discuss molecular methods used for their detection or functional studies both in vitro and in vivo. We also address the challenges that must be overcome to enter a new era of cancer diagnosis and therapy that will reshape the future of oncology.

The biomarkers for maintenance Cancer stem cell features can be applicable in precision medicine of head and neck squamous cell carcinoma

Cancer stem cells (CSCs) play a crucial role in tumor relapse, proliferation, invasion, and drug resistance in head and neck squamous cell carcinoma (HNSCC). This narrative review aims to synthesize data from articles published between 2019 and 2023 on biomarkers for detecting CSCs in HNSCC and changes in molecular pathways, genetics, epigenetics, and non-coding RNAs (ncRNAs) in CSCs relevant to precision medicine approaches in HNSCC management. The search encompassed 41 in vitro studies and 22 clinical studies. CSCs exhibit diverse molecular profiles and unique biomarker expression patterns, offering significant potential for HNSCC diagnosis, treatment, and prognosis, thereby enhancing patient survival. Their remarkable self-renewal ability and adaptability are closely linked to tumorigenicity development and maintenance. Assessing biomarkers before and after therapy can aid in identifying various cell types associated with cancer progression and relapse. Screening for CSCs, senescent tumor cells, and cells correlated with the senescence process post-treatment has proven highly beneficial. However, the clinical application of precision medicine in HNSCC management is hindered by the lack of specific and definitive CSC biomarkers. Furthermore, our limited understanding of CSC plasticity, governed by genomic, transcriptomic, and epigenomic alterations during tumorigenesis, as well as the bidirectional interaction of CSCs with the tumor microenvironment, underscores the need for further research. Well-designed studies involving large patient cohorts are, therefore, essential to establish a standardized protocol and address these unresolved queries.

Novel Y RNA-Derived Fragments Can Differentiate Canine Hepatocellular Carcinoma from Hepatocellular Adenoma

Hepatocellular carcinomas (HCC) are common tumors, whereas hepatocellular adenomas (HCA) are rare, benign tumors in dogs. The aberrant expression of noncoding RNAs (ncRNAs) plays a pivotal role in HCC tumorigenesis and progression. Among ncRNAs, micro RNAs have been widely researched in human HCC, but much less widely in canine HCC. However, Y RNA-derived fragments have yet to be investigated in canine HCC and HCA. This study targeted canine HCC and HCA patients. We used qRT-PCR to determine Y RNA expression in clinical tissues, plasma, and plasma extracellular vesicles, and two HCC cell lines (95-1044 and AZACH). Y RNA was significantly decreased in tissue, plasma, and plasma extracellular vesicles for canine HCC versus canine HCA and healthy controls. Y RNA was decreased in 95-1044 and AZACH cells versus normal liver tissue and in AZACH versus 95-1044 cells. In plasma samples, Y RNA levels were decreased in HCC versus HCA and Healthy controls and increased in HCA versus Healthy controls. Receiver operating characteristic analysis showed that Y RNA could be a promising biomarker for distinguishing HCC from HCA and healthy controls. Overall, the dysregulated expression of Y RNA can distinguish canine HCC from HCA. However, further research is necessary to elucidate the underlying Y RNA-related molecular mechanisms in hepatocellular neoplastic diseases. To the best of our knowledge, this is the first report on the relative expression of Y RNA in canine HCC and HCA.

The Impact of YRNAs on HNSCC and HPV Infection

HPV infection is one of the most important risk factors for head and neck squamous cell carcinoma among younger patients. YRNAs are short non-coding RNAs involved in DNA replication. YRNAs have been found to be dysregulated in many cancers, including head and neck squamous cell carcinoma (HNSCC). In this study, we investigated the role of YRNAs in HPV-positive HNSCC using publicly available gene expression datasets from HNSCC tissue, where expression patterns of YRNAs in HPV(+) and HPV(−) HNSCC samples significantly differed. Additionally, HNSCC cell lines were treated with YRNA1-overexpressing plasmid and RNA derived from these cell lines was used to perform a NGS analysis. Additionally, a deconvolution analysis was performed to determine YRNA1’s impact on immune cells. YRNA expression levels varied according to cancer pathological and clinical stages, and correlated with more aggressive subtypes. YRNAs were mostly associated with more advanced cancer stages in the HPV(+) group, and YRNA3 and YRNA1 expression levels were found to be correlated with more advanced clinical stages despite HPV infection status, showing that they may function as potential biomarkers of more advanced stages of the disease. YRNA5 was associated with less-advanced cancer stages in the HPV(−) group. Overall survival and progression-free survival analyses showed opposite results between the HPV groups. The expression of YRNAs, especially YRNA1, correlated with a vast number of proteins and cellular processes associated with viral infections and immunologic responses to viruses. HNSCC-derived cell lines overexpressing YRNA1 were then used to determine the correlation of YRNA1 and the expression of genes associated with HPV infections. Taken together, our results highlight the potential of YRNAs as possible HNSCC biomarkers and new molecular targets.

RNY3 modulates cell proliferation and IL13 mRNA levels in a T lymphocyte model: a possible new epigenetic mechanism of IL-13 regulation

Allergic asthma is the most common type of asthma. It is characterized by T_H2 cell-driven inflammation in which interleukin-13 (IL-13) plays a pivotal role. Cytoplasmic RNAs (Y-RNAs), a variety of non-coding RNAs that are dysregulated in many cancer types, are also differentially expressed in patients with allergic asthma. Their function in the development of the disease is still unknown. We investigated the potential role of RNY3 RNA (hY3) in the T_H2 cell inflammatory response using the Jurkat cell line as a model. hY3 expression levels were modulated to mimic the upregulation effect in allergic disease. We evaluated the effect of hY3 over cell stimulation and the expression of the T_H2 cytokine IL13. Total RNA was isolated and retrotranscribed, and RNA levels were assessed by qPCR. In Jurkat cells, hY3 levels increased upon stimulation with phorbol 12-myristate 13-acetate (PMA) and ionomycin. When transfecting with high levels of hY3 mimic molecules, cell proliferation rate decreased while IL13 mRNA levels increased upon stimulation compared to stimulated control cells. Our results show the effect of increased hY3 levels on cell proliferation and the levels of IL13 mRNA in Jurkat cells. Also, we showed that hY3 could act over other cells via exosomes. This study opens up new ways to study the potential regulatory function of hY3 over IL-13 production and its implications for asthma development.

Midsize noncoding RNAs in cancers: a new division that clarifies the world of noncoding RNA or an unnecessary chaos?

Most of the human genome is made out of noncoding RNAs (ncRNAs). These ncRNAs do not code for proteins but carry a vast number of important functions in human cells such as: modification and processing other RNAs (tRNAs, rRNAs, snRNAs, snoRNAs, miRNAs), help in the synthesis of ribosome proteins, initiation of DNA replication, regulation of transcription, processing of pre-messenger mRNA during its maturation and much more. The ncRNAs also have a significant impact on many events that occur during carcinogenesis in cancer cells, such as: regulation of cell survival, cellular signaling, apoptosis, proliferation or even influencing the metastasis process. The ncRNAs may be divided based on their length, into short and long, where 200 nucleotides is the "magic" border. However, a new division was proposed, suggesting the creation of the additional group called midsize noncoding RNAs, with the length ranging from 50-400 nucleotides. This new group may include: transfer RNA (tRNA), small nuclear RNAs (snRNAs) with 7SK and 7SL, small nucleolar RNAs (snoRNAs), small Cajal body-specific RNAs (scaRNAs) and YRNAs. In this review their structure, biogenesis, function and influence on carcinogenesis process will be evaluated. What is more, a question will be answered of whether this new division is a necessity that clears current knowledge or just creates an additional misunderstanding in the ncRNA world?

C10orf55, CASC2, and SFTA1P lncRNAs Are Potential Biomarkers to Assess Radiation Therapy Response in Head and Neck Cancers

Long non-coding RNAs have proven to be important molecules in carcinogenesis. Due to little knowledge about them, the molecular mechanisms of tumorigenesis are still being explored. The aim of this work was to study the effect of ionizing radiation on the expression of lncRNAs in head and neck squamous cell carcinoma (HNSCC) in patients responding and non-responding to radiotherapy. The experimental model was created using a group of patients with response (RG, n = 75) and no response (NRG, n = 75) to radiotherapy based on the cancer genome atlas (TCGA) data. Using the in silico model, statistically significant lncRNAs were defined and further validated on six HNSCC cell lines irradiated at three different doses. Based on the TCGA model, C10orf55, C3orf35, C5orf38, CASC2, MEG3, MYCNOS, SFTA1P, SNHG3, and TMEM105, with the altered expression between the RG and NRG were observed. Analysis of pathways and immune profile indicated that these lncRNAs were associated with changes in processes, such as epithelial-to-mesenchymal transition, regulation of spindle division, and the p53 pathway, and differences in immune cells score and lymphocyte infiltration signature score. However, only C10orf55, CASC2, and SFTA1P presented statistically altered expression after irradiation in the in vitro model. In conclusion, the expression of lncRNAs is affected by ionization radiation in HNSCC, and these lncRNAs are associated with pathways, which are important for radiation response and immune response. Potentially presented lncRNAs could be used as biomarkers for personalized radiotherapy in the future. However, these results need to be verified based on an in vitro experimental model to show a direct net of interactions.

The Landscape of Transmembrane Protein Family Members in Head and Neck Cancers: Their Biological Role and Diagnostic Utility

Simple Summary

Transmembrane proteins (TMEM) are a large group of integral membrane proteins whose molecular and biological functions are not fully understood. It is known that some of them are involved in tumor formation and metastasis. Here, we performed a panel of TCGA data analyses to investigate the role of different TMEM genes in head and neck squamous cell carcinoma (HNSCC) and define their potential as biomarkers. Based on changes in the expression levels in HNSCC tumors, we selected four TMEM genes: ANO1, TMEM156, TMEM173, and TMEM213 and associated them with patient survival. We also demonstrated that the expression of those TMEMs highly correlates with the enrichment of genes involved in numerous biological processes, especially metastasis formation and immune response. Thus, we propose ANO1, TMEM156, TMEM173, and TMEM213 as new biomarkers and potential targets for personalized therapy of HNSCC.

Abstract

Background: Transmembrane proteins (TMEM) constitute a large family of proteins spanning the entirety of the lipid bilayer. However, there is still a lack of knowledge about their function or mechanism of action. In this study, we analyzed the expression of selected TMEM genes in patients with head and neck squamous cell carcinoma (HNSCC) to learn their role in tumor formation and metastasis. Materials and Methods: Using TCGA data, we analyzed the expression levels of different TMEMs in both normal and tumor samples and compared those two groups depending on clinical-pathological parameters. We selected four TMEMs whose expression was highly correlated with patient survival status and subjected them to further analysis. The pathway analysis using REACTOME and the gene set enrichment analysis (GSEA) were performed to evaluate the association of those TMEMs with genes involved in hallmarks of cancer as well as in oncogenic and immune-related pathways. In addition, the fractions of different immune cell subpopulations depending on TMEM expression were estimated in analyzed patients. The results for selected TMEMs were validated using GEO data. All analyses were performed using the R package, Statistica, and Graphpad Prism. Results: We demonstrated that 73% of the analyzed TMEMs were dysregulated in HNSCC and depended on tumor localization, smoking, alcohol consumption, or HPV infection. The expression levels of ANO1, TMEM156, TMEM173, and TMEM213 correlated with patient survival. The four TMEMs were also upregulated in HPV-positive patients. The elevated expression of those TMEMs correlated with the enrichment of genes involved in cancer-related processes, including immune response. Specifically, overexpression of TMEM156 and TMEM173 was associated with immune cell mobilization and better survival rates, while the elevated ANO1 expression was linked with metastasis formation and worse survival. Conclusions: In this work, we performed a panel of in silico analyses to discover the role of TMEMs in head and neck squamous cell carcinoma. We found that ANO1, TMEM156, TMEM173, and TMEM213 correlated with clinical status and immune responses in HNSCC patients, pointing them as biomarkers for a better prognosis and treatment. This is the first study describing such the role of TMEMs in HNSCC. Future clinical trials should confirm the potential of those genes as targets for personalized therapy of HNSCC.

Circulating Non-Coding RNAs in Head and Neck Cancer: Roles in Diagnosis, Prognosis, and Therapy Monitoring

Head and neck cancer (HNC), the seventh most common form of cancer worldwide, is a group of epithelial malignancies affecting sites in the upper aerodigestive tract. The 5-year overall survival for patients with HNC has stayed around 40–50% for decades, with mortality being attributable mainly to late diagnosis and recurrence. Recently, non-coding RNAs, including tRNA halves, YRNA fragments, microRNAs (miRNAs), and long non-coding RNAs (lncRNAs), have been identified in the blood and saliva of patients diagnosed with HNC. These observations have recently fueled the study of their potential use in early detection, diagnosis, and risk assessment. The present review focuses on recent insights and the potential impact that circulating non-coding RNA evaluation may have on clinical decision-making in the management of HNC.

Liquid lncRNA Biopsy for the Evaluation of Locally Advanced and Metastatic Squamous Cell Carcinomas of the Head and Neck

Background: Long non-coding RNA (lncRNA) are RNA molecules that are more than 200 nucleotides long and have the ability to modify the activity of genes. They can be found in both healthy and cancer tissues, as well as in plasma, saliva and other bodily fluids. They can also be used as biomarkers of early detection, prognosis and chemotherapy resistance in several cancer types. Treatment of head and neck squamous cell carcinoma (HNSCC) patients with locally advanced disease is still difficult, and choice of treatment should be based on more precise and available biomarkers, such as those obtained from a liquid biopsy. For improvement of treatment efficacy, identification and clinical implementation of new biomarkers are of the utmost importance. Methods: Plasma samples drawn before (p1) and three cycles post (p2) (TPF: docetaxel, cisplatin, 5-fluorouracil/PF: cisplatin, 5-fluorouracil) chemotherapy from 53 HNSCC patients (17 with locally advanced and 36 with metastatic disease) and 14 healthy volunteers were studied. Expression levels of 90 lncRNA expression were analyzed using the qRT-PCR method, and the obtained results were compared between proper groups. Statistical analyses were carried out using Jupyter Notebooks (5.7.2), Python (ver. 3.6) and GraphPad Prism 8. Results: The study demonstrated the differences between the expressions of several lncRNA in cancer patients' and healthy volunteers' plasma, as well as between locally advanced and metastatic patients' groups. A correlation between the response to systemic therapy and lncRNA expression levels was observed. Patients with a (high/low) expression of Alpha 250 and Emx2os showed statistically significant differences in progression free survival (PFS), as well as for overall survival (OS) depending on the level of Alpha 250, snaR, SNHG1. The univariate and multivariate Cox regression model showed Alpha 250 as the best prognostic factor for HNSCC patients. Conclusions: Liquid biopsies based on lncRNAs are promising diagnostic tools that can be used to differentiate between those with cancer and healthy individuals. Additionally, they can also serve as biomarkers for chemotherapy resistance. An identified, circulating lncRNA Alpha 250 seems to prove the best prognostic biomarker, associated with extended PFS and OS, and should be validated in a larger cohort in the future.

YRNAs and YRNA-Derived Fragments as New Players in Cancer Research and Their Potential Role in Diagnostics

YRNAs are a type of short, noncoding RNAs. A total of four different transcripts can be distinguished, which are YRNA1, YRNA3, YRNA4 and YRNA5. All YRNAs are relatively small, made up of about 100 nucleotides each. YRNAs are characterized by a stem-loop structure and each part of that structure carries a different function. YRNAs are transcribed in the nucleus by RNA polymerase III. Then, the YRNA molecule is bound to the polyuridine tail of the La protein responsible for both its nuclear retention and protection from degradation. They also bind to the Ro60 protein, making the molecule more stable. In turn, YRNA-derived small RNAs (YsRNAs) are a class of YRNAs produced in apoptotic cells as a result of YRNA degradation. This process is performed by caspase-3-dependent pathways that form two groups of YsRNAs, with lengths of either approximately 24 or 31 nucleotides. From all four YRNA transcripts, 75 well-described pseudogenes are generated as a result of the mutation. However, available data indicates the formation of up to 1000 pseudogenes. YRNAs and YRNA-derived small RNAs may play a role in carcinogenesis due to their altered expression in cancers and influence on cell proliferation and inflammation. Nevertheless, our knowledge is still limited, and more research is required. The main aim of this review is to describe the current state of knowledge about YRNAs, their function and contribution to carcinogenesis, as well as their potential role in cancer diagnostics. To confirm the promising potential of YRNAs and YRNA-derived fragments as biomarkers, their significant role in several tumor types was taken into consideration.

The role of NEAT1 lncRNA in squamous cell carcinoma of the head and neck is still difficult to define

INTRODUCTION

Nuclear paraspeckle assembly transcript 1 (NEAT1) is considered an oncogene in various cancers, but the role in head and neck squamous cell carcinomas (HNSCC) is not clear.

MATERIAL AND METHODS

Expression of NEAT1 in HNSCC patients' samples and cell lines was analysed using qRT-PCR. The TCGA expression data of NEAT1 were analysed depending on the clinicopathological parameters and tumour localisation. Correlation and gene set enrichment analysis (GSEA) were conducted, and the results were analysed using the REACTOME and GeneMANIA tools. All statistical analyses were carried out using GraphPad Prism 5 and Statistica 13.

RESULTS

The NEAT1 was up-regulated in some patients' samples and HNSCC cell lines. Moreover, TCGA data analysis indicated that the expression of NEAT1 was up-regulated in tumour tissue in most of the analysed TCGA cancers, including HNSCC. There were no significant differences in levels of NEAT1 between various tumour localisations. Overall survival of individuals with high expression of NEAT1 was slightly longer than in the low-expression group (p = 0.0553). Analysis of genes that positively and negatively correlated with NEAT1 indicated that they are involved in mRNA metabolism and cellular transport. Moreover, the GSEA revealed that in patients with low NEAT1, the most up-regulated genes were in clusters associated with the cAMP-dependent pathway, the MYC pathway, unfolded protein response, the MTORC1 signalling pathway, oxidative phosphorylation, and DNA repair.

CONCLUSIONS

Patients with low expression of NEAT1 display worse overall survival, presumably due to up-regulation of certain oncogenic signalling pathways that are important for cancerogenesis.