Class Of Small RNAs Research Articles

Development of a Single-Molecule Biosensor Based on Polymerization-Transcription-Mediated Target Regeneration for Simultaneously One-Pot Detection of Multiple piRNAs.

PIWI-interacting RNAs (piRNAs) are a class of small noncoding RNAs associated with PIWI proteins within the male germline, and they play significant roles in maintaining genome stability via the modulation of gene expression. The piRNAs are implicated in the progression of various cancers, but the simultaneous monitoring of multiple piRNAs remains a challenge. Herein, we construct a single-molecule biosensor based on polymerization-transcription-mediated target regeneration for the simultaneous one-pot detection of multiple piRNAs. This assay involves two cycles. In step 1, target piRNAs hybridize with the template probe complexes to yield three-way junction (3WJ) structures. Then, KF DNA polymerase initiates the extension to generate a complete T7 promoter, and the extension product can act as an invading strand to displace signal probes, resulting in the release of fluorophores. Then, in step 2, the T7 promoter can be recognized by T7 RNA polymerase to initiate transcription, producing abundant transcripts with 3'-OH that are identical to piRNAs. The resultant transcripts can hybridize with free template probe complexes to obtain new 3WJ structures that can be elongated by KF polymerase for the recovery of fluorescence signals. This assay can be performed homogeneously in a one-pot format within 30 min, and it exhibits high sensitivity, with a limit of detection (LOD) of 19.26 aM for piRNA-36026 and 41.88 aM for piRNA-36743. Moreover, it can simultaneously detect endogenous piRNAs at the single-cell level and differentiate piRNA expression in the tissues of healthy individuals and breast cancer patients, offering a prospective platform for clinic diagnosis.

Mitochondrial microRNAs: Key Drivers in Unraveling Neurodegenerative Diseases.

MicroRNAs (miRNAs) are a class of small non-coding RNAs (ncRNAs) crucial for regulating gene expression at the post-transcriptional level. Recent evidence has shown that miRNAs are also found in mitochondria, organelles that produce energy in the cell. These mitochondrial miRNAs, also known as mitomiRs, are essential for regulating mitochondrial function and metabolism. MitomiRs can originate from the nucleus, following traditional miRNA biogenesis pathways, or potentially from mitochondrial DNA, allowing them to directly affect gene expression and cellular energy dynamics within the mitochondrion. While miRNAs have been extensively investigated, the function and involvement of mitomiRs in the development of neurodegenerative disorders like Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis remain to be elucidated. This review aims to discuss findings on the role of mitomiRs in such diseases and their potential as therapeutic targets, as well as to highlight future research directions.

Identification and characterisation of temporal abundance of microRNAs in synovial fluid from an experimental equine model of osteoarthritis.

MicroRNAs, a class of small noncoding RNAs, serve as post-transcriptional regulators of gene expression and are present in a stable and quantifiable form in biological fluids. MicroRNAs may influence intra-articular responses and the course of disease, but very little is known about their temporal changes in osteoarthritis. To identify miRNAs and characterise the temporal changes in their abundance in SF from horses with experimentally induced osteoarthritis. We hypothesised that the abundance of miRNA would change during disease progression. In vivo experiments. RNA extracted from synovial fluid obtained sequentially (Day 0, 28 and 70) from nine horses with experimentally induced osteoarthritis was subjected to small RNA sequencing using the Illumina Hiseq 4000 sequencing platform. Differentially abundant miRNAs underwent further validation and mapping of temporal abundance (Day 0, 14, 17, 21, 28, 35, 42, 49, 56, 63 and 70 days after osteoarthritis induction) by microfluidic reverse transcription quantitative real-time PCR. Bioinformatic analyses were performed to predict potential biological associations and target genes of the differentially abundant microRNAs. Small RNA sequencing revealed 61 differentially abundant microRNAs at an early osteoarthritis stage (Day 28), and subsequent reverse transcription quantitative real-time PCR analysis validated 20 of these. Significant biological functions of the differentially abundant microRNAs were apoptosis, necrosis, cell proliferation and cell invasion. Following validation, four microRNAs (miRNA-199b-3p, miRNA-139-5p, miRNA-1839 and miRNA-151-5p) were detected in more than 50% of the synovial fluid samples and had higher abundance in osteoarthritic than in control joints. Limited sample size. This is the first study to determine longitudinal changes in synovial fluid microRNA abundance in an equine model of osteoarthritis. Larger studies are needed in naturally occurring osteoarthritis to interrogate putative changes identified by this study.

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.

TRF-AspGTC Promotes Intracranial Aneurysm Formation by Controlling TRIM29-Mediated Galectin-3 Ubiquitination.

Transfer RNA-derived small RNAs, a recently identified class of small noncoding RNAs, play a crucial role in regulating gene expression and are implicated in cerebrovascular diseases. However, the specific biological roles and mechanisms of transfer RNA-derived small RNAs in intracranial aneurysms (IAs) remain unclear. In this study, we identified that the transfer RNA-Asp-GTC derived fragment (tRF-AspGTC) is highly expressed in the IA tissues of both humans and mice. tRF-AspGTC promotes IA formation by facilitating the phenotypic switching of vascular smooth muscle cells, increasing of matrix metalloproteinase 9 expression, and inducing of oxidative stress and inflammatory responses. Mechanistically, tRF-AspGTC binds to galectin-3, inhibiting tripartite motif 29-mediated ubiquitination and stabilizing galectin-3. This stabilization activates the toll-like receptor 4/MyD88/nuclear factor kappa B pathway, further driving phenotypic switching and inflammation. Clinically, circulating exosomal tRF-AspGTC demonstrates strong diagnostic efficacy for IAs and is identified as an independent risk factor for IA occurrence. These findings highlight the potential of tRF-AspGTC as a promising diagnostic biomarker and therapeutic target for IAs.

Temporal Expression Analysis to Unravel Gene Regulatory Dynamics by microRNAs.

MicroRNAs (miRNAs) are a class of small non-coding RNAs (sncRNAs) of length 21-25 nucleotides. These sncRNAs hybridize to repress their target genes and inhibit protein translation, thereby controlling regulatory functions in the cell. Integration of time-series matched small and RNA-seq data enables investigation of dynamic gene regulation through miRNAs during development or in response to a stimulus, such as stress. Here we summarize analysis strategies, such as probabilistic and regression-based models, that take advantage of the temporal dimension to investigate the complexity of miRNA regulation.

Recent Insights Into Wnt-Related tRNA-Derived Fragments (tRFs) in Human Diseases.

tRNA-derived fragments (tRFs) are a newly recognized class of small noncoding RNAs (sncRNAs) that play significant roles in various diseases. The Wnt pathway plays a key role in various physiological processes such as embryonic development, tissue renewal and regeneration. In the regulation of Wnt/β-catenin, Forkhead box k1(FOXK1), Frizzled class receptor 3 (FZD3), and Wnt5b can be targeted and inhibited by three tRFs: tRF3008A targets FOXK1 to inhibit colorectal cancer (CRC), 5'-tiRNAVal targets FZD3 to inhibit breast cancer (BrC), and tRF-22-8BWS7K092 targets Wnt5b to induce ferroptosis in lung cells. Additionally, tRF-24-V29K9UV3IU can inhibit the levels of FZD3, Van Gogh-like protein 1 (VANGL1), and cyclin D2 (CCND2) through an unexplained mechanism and play a role in inhibiting gastric cancer (GC). Clinical data has shown that the expression levels of certain tRFs are associated with the prognosis and pathological features of CRC and BrC patients. Low expression of tRF3008A is associated with poor prognosis and adverse pathological features in CRC patients, while high expression of tiRNA-Phe-GAA-003 and low expression of 5'-tiRNAVal are associated with poor prognosis and adverse pathological features in BrC patients. KEGG analysis has also shown that a variety of tRFs are involved in regulating the Wnt pathway and have been shown to play a role in a variety of diseases. For example, high expression of tRF-Gly-CCC-039 is associated with poor healing of diabetic foot, low expression of tsRNA-10277 is associated with high incidence of steroid-induced osteonecrosis of the femoral head (SONFH), high expression of tRF-22-8BWS7K092 is correlated with the severity of acute lung injury (ALI), and low expression of tsRNA-21109 is associated with the severity of systemic lupus erythematosus (SLE), and high expression of tRF-36-F900BY4D-84KRIME and tRF-23-87R8WP9IY, as well as low expression of tRF-40-86J8WPMN1E8Y7Z2R, were associated with high incidence of varicose vein (VV), and high expression of ts-34, was associated with high mortality of BrC. This article summarizes the biological function and mechanism of tRFs related to the Wnt pathway in cancer and other diseases, providing a new direction for subsequent translational medical research.

Metabolome and transcriptome profiling reveal tRNA-derived small RNAs regulated glutathione metabolism in intrauterine growth-restricted pigs liver.

Intrauterine growth retardation (IUGR) has become a difficult problem in animal husbandry and is often accompanied by the occurrence of metabolic syndrome. tRNA-derived small RNAs (tsRNAs) are a novel class of regulatory small noncoding RNAs. However, the involvement of tsRNA in regulating the mechanism of IUGR remains unclear. Here, we first characterized the tsRNA expression profiles in the liver of normal pigs and IUGR pigs through high-throughput sequencing. IUGR pigs exhibit significantly increased 17 tsRNA levels including tRF-Ile-GAT, tRF-Pro-TGG, tRF-Leu-CAA and tRF-Ala-TGC etc. Transcriptome sequencing further revealed 1244 upregulated and 762 downregulated differentially expressed genes in IUGR pig liver. Functional enrichment analysis found that DEGs were mainly involved in insulin resistance, metabolic pathways, etc. Metabolomics was performed to determine the metabolic changes between the normal and IUGR pigs. Then, We constructed a potential tsRNA regulatory network involved in metabolic pathways in IUGR pig liver. Moreover, combined metabolome and transcriptome analysis showed a disorder of glutathione metabolism in the IUGR pigs liver. We identified tRF-Ile-GAT as the potential target of interest. NCTC1469 liver cells were used to validate the preliminary function of tRF-Ile-GAT in vitro. Bioinformatics analyses and luciferase reporter assays further revealed that microsomal glutathione S-transferase 1 (MGST1) was the target gene of tRF-Ile-GAT. In addition, tRF-Ile-GAT overexpression inhibited antioxidant gene expression, glutathione and glutathione glutathione S-transferase levels in NCTC1469 cells, while an MGST1 overexpression reversed the above phenomenon. These findings provide new insights into the understanding of the molecular mechanisms of IUGR pathogenesis.

Advancing miRNA cancer research through artificial intelligence: from biomarker discovery to therapeutic targeting.

MicroRNAs (miRNAs), a class of small non-coding RNAs, play a vital role in regulating gene expression at the post-transcriptional level. Their discovery has profoundly impacted therapeutic strategies, particularly in cancer treatment, where RNA therapeutics, including miRNA-based targeted therapies, have gained prominence. Advances in RNA sequencing technologies have facilitated a comprehensive exploration of miRNAs-from fundamental research to their diagnostic and prognostic potential in various diseases, notably cancers. However, the manual handling and interpretation of vast RNA datasets pose significant challenges. The advent of artificial intelligence (AI) has revolutionized biological research by efficiently extracting insights from complex data. Machine learning algorithms, particularly deep learning techniques are effective for identifying critical miRNAs across different cancers and developing prognostic models. Moreover, the integration of AI has led to the creation of comprehensive miRNA databases for identifying mRNA and gene targets, thus facilitating deeper understanding and application in cancer research. This review comprehensively examines current developments in the application of machine learning techniques in miRNA research across diverse cancers. We discuss their roles in identifying biomarkers, elucidating miRNA targets, establishing disease associations, predicting prognostic outcomes, and exploring broader AI applications in cancer research. This review aims to guide researchers in leveraging AI techniques effectively within the miRNA field, thereby accelerating advancements in cancer diagnostics and therapeutics.

Recent Advances in the miRNA-Mediated Regulation of Neuronal Differentiation and Death.

The review aims to focus on the role of miRNA in gene regulation, related to differentiation and apoptosis of neurons, focusing on the array of miRNAs involved in the processes. miRNAs are a known class of small regulatory RNAs, which in association with RNA processing bodies, play major roles in different cellular events, such as neurogenesis and neuronal differentiation. miRNAs function in controlling neuronal events by targeting different important molecules of cellular signalling. The post-translational modification of Ago2 is crucial in modulating the neurons' miRNA-mediated regulation. Thus, understanding the crosstalk between cellular signalling and miRNA activity affecting neuronal events is very important to decipher novel targets and related signalling pathways, involved in neuronal survival and neurodegeneration.

TRF-16 Inhibits Lung Cancer Progression by Hindering the N6-Methyladenosine Modification of CPT1A mRNA.

Transfer RNA-derived fragments (tRFs) are a new class of small non-coding RNAs. Recent studies suggest that tRFs participate in some pathological processes. However, the biological activities and processes of tRFs in lung cancer cells remain mainly unclear. In the present investigation, we employed tRNA-derived small RNA (tsRNA) sequencing to predict differentially expressed tsRNAs in lung cancer cells, and nine tsRNAs with significant expression alterations were validated using qPCR. Wound healing, colony formation, transwell invasion and CCK-8 assays were performed to detect the effects of tRF-16 on cell function. Western blotting evaluated the relationship between tRF-16 and the IGF2BP1 axis. Our findings demonstrated that tRF-16 expression was substantially downregulated in lung cancer cells. TRF-16 could inhibit lung cancer cells' ability to increase, migrate, invade and obtain radiation resistance. Furthermore, tRF-16 decreases the stability of CPT1A by impairing the binding of IGF2BP1 to CPT1A. As a result, the fatty acid metabolism in lung cancer cells was inhibited. Finally, tRF-16 also inhibits lung cancer cell proliferation invivo. This study shows that tRF-16 plays a crucial regulatory role in the proliferation of lung cancer cells and may represent a novel avenue for their regulation.

Ultrasensitive electrochemical detection of miDNA-21 in human serum based on synergistic signal amplification by conducting polymers and bimetallic nanoparticles

MicroRNA-21 (miRNA-21) is a class of small non-coding RNAs that play a crucial role in the regulation of post-transcriptional gene expression. By leveraging the principle of base complementary pairing, the detection of miRNA-21 can be achieved through its analogue, MicroDNA-21 (miDNA-21), which possesses an identical sequence. Utilizing screen-printed carbon electrodes (SPCE), a conducting polymer (polypyrrole, Ppy), and metal nanocomposites (gold-platinum nanoparticles, Au@Pt NPs) were sequentially electrodeposited to create an electrochemical biosensor for the detection of miDNA-21. This biosensor employed ferrocyanide/ferricyanide (Fe(CN)63−/4−) as the electrochemical signaling probe, and its structure was elucidated via field emission scanning electron microscopy (FESEM) and Energy Dispersive Spectrometer (EDS). Quantitative detection was facilitated through differential pulse voltammetry (DPV), yielding a concentration range and linear fitting equation of 10.00–7.00 × 10.00−14 mol/L: ΔI = 0.5143 lgc + 9.191, R2 = 0.9986. The limit of detection (LOD) was determined to be 2.90 × 10−15 mol/L, with a sensitivity of 9.42 μA/μmol/L·cm2. Subsequent performance assessments confirmed the sensor’s excellent selectivity, reproducibility, and stability. Evaluation using the standard addition method, with normal human serum as the matrix, yielded recoveries ranging from 98.97 % to 102.70 %, and relative standard deviation (RSD) values below 1.00 %. These results demonstrate the method’s viability for practical application in detecting miRNA in human serum.

MiRNAs in HCC, pathogenesis, and targets.

Liver cancer is the third leading cause of cancer-related mortality worldwide. Hepatocellular carcinoma (HCC), the most common type of primary liver cancer is driven by complex genetic, epigenetic, and environmental factors. MicroRNAs, a class of naturally-occurring small non-coding RNAs play crucial roles in HCC by simultaneously modulating expression of multiple genes in a fine-tuning manner. Significant progress has been made in understanding how miRNAs influence key oncogenic pathways, including cell proliferation, apoptosis, angiogenesis, and epithelial-mesenchymal transition (EMT), as well as their role in modulating the immune microenvironment in HCC. Due to the unexpected stability of miRNAs in the blood and fixed HCC tumors, recent advancements also highlight their potential as non-invasive diagnostic tools. Restoring or inhibiting specific miRNAs have offered promising strategies for targeted HCC treatment by suppressing malignant hepatocyte growth and enhancing antitumor immunity. In this comprehensive review, we consolidate previous research and provide the latest insights into how miRNAs regulate HCC and their therapeutic and diagnostic potential. We delve into dysregulation of miRNA biogenesis in HCC, the roles of miRNAs in proliferation and apoptosis of malignant hepatocytes, angiogenesis and metastasis of HCC, immune microenvironment in HCC and drug resistance. We also discuss the therapeutic and diagnostic potential of miRNAs and delivery approaches of miRNA drugs to overcome the limitations of current HCC treatment options. By thoroughly summarizing the roles of miRNAs in HCC, our goal is to advance the development of effective therapeutic drugs with minimal adverse effects and to establish precise tools for early diagnosis of HCC.

Abstract I004: Systematic Discovery and Annotation of Cancer Emergent Orphan non-coding RNAs in human Cancers

Abstract We recently described orphan non-coding RNAs (oncRNAs) as a class of cancer-specific small RNAs with the potential to play functional roles in breast cancer progression1. Here, we report a systematic search to annotate and characterize cancer-emergent oncRNAs across 32 tumor types. We also leverage large-scale in vivo genetic screens in xenografted mice to functionally identify driver oncRNAs in multiple tumor types. We have not only discovered a large repertoire of oncRNAs, but also found that their presence and absence represent a digital molecular barcode that faithfully captures the types and subtypes of cancer. Importantly, we discovered that this molecular barcode is partially accessible from the cell-free space as some oncRNAs are secreted by cancer cells. In a large retrospective study across 192 breast cancer patients, we showed that oncRNAs can be reliably detected in the blood and that changes in the cell-free oncRNA burden captures both short-term and long-term clinical outcomes upon completion of a neoadjuvant chemotherapy regimen. Citation Format: Hani Goodarzi. Systematic Discovery and Annotation of Cancer Emergent Orphan non-coding RNAs in human Cancers [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr I004.

Profiling of 24-nt phasiRNAs in Rice Anther by Massively Parallel Sequencing and Stem-Loop Reverse Transcription PCR.

Small RNAs are highly abundant and play important roles in plant reproduction. Profiling of small RNAs in reproductive tissues is a critical step in understanding their biology. Here, we describe a protocol for small RNA profiling in rice anthers, with a focus on an abundantly expressed but little-understood reproductive small RNA class named 24-nucleotide phased secondary small interfering RNAs (24-nt phasiRNAs). The protocol details small RNA library preparation steps for high-throughput sequencing, with a subsequent bioinformatic analysis framework. A low-throughput stem-loop reverse transcription PCR protocol for quick semi-quantification of small RNAs is also included as a complementary approach. The collective protocol, although focused on 24-nt phasiRNAs, should be amenable to other small RNA classes in various plant reproductive tissues.

Stu-miR159a negatively regulates anthocyanin-specific MYB transcription factor to mediate drought stress tolerance in potato

MicroRNAs (miRNAs) are a class of small endogenous non-coding RNAs that direct post-transcriptional gene silencing. In plants, numerous miRNAs have been demonstrated to be regulated under drought-induced stress. However, the role of miRNAs in drought regulation remains unclear in potato. In this work, the function of stu-miR159a was investigated in responding to drought stress in potato. Upon examination, StGAMyb-like1 was identified as the target gene for stu-miR159a. Overexpression of stu-miR159a (stu-miR159a OE plants) increased sensitivity to drought, interference with stu-miR159a activity by target mimics (stu-miR159a ST plants) resulted in drought resistance. During drought treatment, the target gene StGAMyb-like1 showed increased activation in stu-miR159a ST plants compared to non-transgenic plants. In contrast, drought stress induced weaker activation of the target gene in stu-miR159a OE plants. In stu-miR159a ST plants, the expression of critical genes in the anthocyanin biosynthesis pathway (StF3'5'H, StF3'H and StCHS2) was increased by decreasing stu-miR159a activity and simultaneously increasing that of StGAMyb-like1. Meanwhile, with drought treatment, stu-miR159a ST plants exhibited higher anthocyanin accumulation than non-transgenic ones, indicating enhanced antioxidant capacity and improved drought tolerance. The above data support that stu-miR159a is a negative regulator of drought stress and provide new insights into the stu-miR159a-mediated regulation of the anthocyanin biosynthesis pathway in controlling drought tolerance in potato.

Assessment of heat tolerance and identification of miRNAs during high-temperature response in grapevine.

With global warming, heat stress has been recognized as a significant factor limiting grapevine development and fruit quality. MicroRNAs (miRNAs) are a class of small non-coding RNAs known to play crucial regulatory roles in stress resistance. Hence, there is an immediate requirement to cultivate and identify grapevine varieties that are resistant to heat and explore miRNA-mediated heat stress defense mechanisms. In this study, we assessed the thermal resistance of 38 grape germplasm resources and identified a series of miRNAs involved in heat stress resistance. The CK (25°C) and HS (45°C) groups of "Shenyue" cuttings of grapes were used as experimental materials for next-generation sequencing and construct libraries of small RNAs. A total of 177 known and 20 novel miRNAs were detected in the libraries. Differential expression analysis identified 65 differentially expressed miRNAs (DEMs) using the DE-Seq procedure. Furthermore, RT-qPCR validation confirmed complementary expression profiles of eight DEMs and their target genes between the HS and CK groups. Heterologous transformation further identified the function of Vvi-miR3633a downregulated under heat stress in Arabidopsis. In the heterologous expression lines, the survival rate was reduced by high temperature treatment indicating the ability of Vvi-miR3633a to regulate heat resistance. Assessing the heat resistance of grape species and the expression patterns of miRNA in response to high temperatures may reveal the molecular processes of heat resistance regulation mediated by miRNA in grapes under heat stress.

Computational Analysis Suggests That AsnGTT 3′-tRNA-Derived Fragments Are Potential Biomarkers in Papillary Thyroid Carcinoma

Transfer-RNA-derived fragments (tRFs) are a novel class of small non-coding RNAs that have been implicated in oncogenesis. tRFs may act as post-transcriptional regulators by recruiting AGO proteins and binding to highly complementary regions of mRNA at seed regions, resulting in the knockdown of the transcript. Therefore, tRFs may be critical to tumorigenesis and warrant investigation as potential biomarkers. Meanwhile, the incidence of papillary thyroid carcinoma (PTC) has increased in recent decades and current diagnostic technology stands to benefit from new detection methods. Although small non-coding RNAs have been studied for their role in oncogenesis, there is currently no standard for their use as PTC biomarkers, and tRFs are especially underexplored. Accordingly, we aim to identify dysregulated tRFs in PTC that may serve as biomarker candidates. We identified dysregulated tRFs and driver genes between PTC primary tumor samples (n = 511) and adjacent normal tissue samples (n = 59). Expression data were obtained from MINTbase v2.0 and The Cancer Genome Atlas. Dysregulated tRFs and genes were analyzed in tandem to find pairs with anticorrelated expression. Significantly anticorrelated tRF-gene pairs were then tested for potential binding affinity using RNA22—if a heteroduplex can form via complementary binding, this would support the hypothesized RNA silencing mechanism. Four tRFs were significantly dysregulated in PTC tissue (p < 0.05), with only AsnGTT 3′-tRF being upregulated. Binding affinity analysis revealed that tRF-30-RY73W0K5KKOV (AsnGTT 3′-tRF) exhibits sufficient complementarity to potentially bind to and regulate transcripts of SLC26A4, SLC5A8, DIO2, and TPO, which were all found to be downregulated in PTC tissue. In the present study, we identified dysregulated tRFs in PTC and found that AsnGTT 3′-tRF is a potential post-transcriptional regulator and biomarker.

Significance of miRNA-192 as a Prognostic Marker in Chronic Lymphocytic Leukemia

Abstract Background Chronic lymphocytic leukemia (CLL) is the most common human leukemia in western world. This disease can arise in two forms, aggressive and indolent, both characterized by the accumulation of incompetent CD5+ B lymphocytes. MicroRNAs (miRNAs): represent a class of small non-coding RNAs (ncRNAs) of 19–25 nucleotide (nt) length, which post-transcriptionally regulate protein expression, impacting on key cellular functions. miRNAs control numerous cellular/molecular processes such as apoptosis, cell proliferation and differentiation. Deregulated expression of miRNAs contributes to the initiation or development of numerous diseases such as cancer. One of these microRNA is miR-192 which has been suggested to be a positive regulator of p53 (a tumor suppressor gene) and its expression is deregulated in biological samples of cancer patients. Objective To evaluate miRNA-192 as a prognostic biomarker in CLL patients, correlate miRNA-192 expression levels to p53 gene in CLL and find out the association between miRNA- 192 and p53 genes expressions and prognostic criteria of CLL. Methods The present study was conducted on 40 newly diagnosed CLL patients who attended the Hematology outpatient clinic-Ain Shams University hospital during the years from 2018 to 2019 and were included in the study in addition to ten healthy subjects. Quantitation of plasma miR-192 and P53 expression levels were done by real-time quantitative polymerase chain reaction. Results A significant statistical association between poor patients’ outcome and advanced clinical Rai staging together with unfavorable cytogenetic profile was found. Moreover, significant statistical association was also observed in patients with poor outcome expressing low levels of miRNA-192 with p value (P = 0.00) and increased levels of P53. miRNA-192 expression levels in our work were significantly lower in patients with lymphadenopathy and in patients with unfavorable cytogenetic profile. However, it was significantly higher among patients with good prognosis in comparison to patients with worse one. Conclusion miRNA-192 expression levels was significantly correlated with some standard prognostic factors as TLC, Hb &insignificantly with platelets, P53 expression level and favorable cytogenetic profile indicated that circulating miR-192 can serve as non-invasive biomarker that can be used for predicting prognosis and monitoring of therapy in CLL patients.

MicroRNA and Rare Human Diseases

Background: The role of microRNAs (miRNAs) in the pathogenesis of rare genetic disorders has been gradually discovered. MiRNAs, a class of small non-coding RNAs, regulate gene expression by silencing target messenger RNAs (mRNAs). Their biogenesis involves transcription into primary miRNA (pri-miRNA), processing by the DROSHA–DGCR8 (DiGeorge syndrome critical region 8) complex, exportation to the cytoplasm, and further processing by DICER to generate mature miRNAs. These mature miRNAs are incorporated into the RNA-induced silencing complex (RISC), where they modulate gene expression. Methods/Results: The dysregulation of miRNAs is implicated in various Mendelian disorders and familial diseases, including DICER1 syndrome, neurodevelopmental disorders (NDDs), and conditions linked to mutations in miRNA-binding sites. We summarized a few mechanisms how miRNA processing and regulation abnormalities lead to rare genetic disorders. Examples of such genetic diseases include hearing loss associated with MIR96 mutations, eye disorders linked to MIR184 mutations, and skeletal dysplasia involving MIR140 mutations. Conclusions: Understanding these molecular mechanisms is crucial, as miRNA dysregulation is a key factor in the pathogenesis of these conditions, offering significant potential for the diagnosis and potential therapeutic intervention.