miR-15 and miR-16 induce apoptosis by targeting BCL2

Current updates regarding biogenesis, functions and dysregulation of microRNAs in cancer: Innovative approaches for detection using CRISPR/Cas13‑based platforms (Review)

MicroRNAs (miRNAs) are short non‑coding RNAs, which perform a key role in cellular differentiation and development. Most human diseases, particularly cancer, are linked to miRNA functional dysregulation implicated in the expression of tumor‑suppressive or oncogenic targets. Cancer hallmarks such as continued proliferative signaling, dodging growth suppressors, invasion and metastasis, triggering angiogenesis, and avoiding cell death have all been demonstrated to be affected by dysregulated miRNAs. Thus, for the treatment of different cancer types, the detection and quantification of this type of RNA is significant. The classical and current methods of RNA detection, including northern blotting, reverse transcription‑quantitative PCR, rolling circle amplification and next‑generation sequencing, may be effective but differ in efficiency and accuracy. Furthermore, these approaches are expensive, and require special instrumentation and expertise. Thus, researchers are constantly looking for more innovative approaches for miRNA detection, which can be advantageous in all aspects. In this regard, an RNA manipulation tool known as the CRISPR and CRISPR‑associated sequence 13 (CRISPR/Cas13) system has been found to be more advantageous in miRNA detection. The Cas13‑based miRNA detection approach is cost effective and requires no special instrumentation or expertise. However, more research and validation are required to confirm the growing body of CRISPR/Cas13‑based research that has identified miRNAs as possible cancer biomarkers for diagnosis and prognosis, and as targets for treatment. In the present review, current updates regarding miRNA biogenesis, structural and functional aspects, and miRNA dysregulation during cancer are described. In addition, novel approaches using the CRISPR/Cas13 system as a next‑generation tool for miRNA detection are discussed. Furthermore, challenges and prospects of CRISPR/Cas13‑based miRNA detection approaches are described.

Circulating MicroRNAs in association with urinary arsenic: A community-based multi-center study in China

The profile of plasma miRNAs in association with arsenic exposure remains largely unclear. We aim to identify plasma miRNAs assoicated with urinary arsenic using a two-stage design in Chinese population. The discovery group, Shimen panel, consists of 19 high vs. low arsenic-exposed pairs selected from 1095 residents in an arsenic-contaminated area. The validation group, Wuhan-Zhuhai panel, consists of 53 community-dwelling participants with moderate arsenic exposure. Plasma miRNAs were measured by microarray in the Shimen panel and by sequencing in the Wuhan-Zhuhai panel. Arsenic levels in urine and plasma were quantified using inductively coupled plasma mass spectrometry. During the discovery stage, 16 miRNAs were found to be differentially expressed between high and low urinary arsenic groups in the Shimen panel (fold change >2, P < 0.05). Seven miRNAs (miR-101-3p, miR-142-3p, miR-148a-3p, miR-15a-5p, miR-199a-3p, miR-27b-3p, and miR-340-5p) were validated to have a positive association with log-transformed urinary arsenic levels in the Wuhan-Zhuhai panel (P < 0.05). Furthermore, five of the seven miRNAs were also associated with arsenic in plasma. The identified miRNAs were primarily associated with cancer-related pathways. These identified miRNAs would serve as crucial biomarkers for arsenic exposure, elucidating the epigenetic mechanisms underlying arsenic-induced toxicity and carcinogenesis.

RBM24-mediated biogenesis of circ23679 protects cardiomyocytes against apoptosis via sponging miR-15b-5p

Circular RNAs (circRNAs) have emerged as significant members of gene regulatory networks and play important roles in normal heart biology and cardiac diseases. RNA binding proteins (RBPs) are key regulatory factors in circRNA formation; however, the mechanisms by which RBP regulate circRNA production remain unclear. RNA binding motif protein 24 (RBM24) is essential for alternative splicing of genes related to cardiac function, and its loss leads to dilated cardiomyopathy and heart failure. In this study, we performed circRNA profiling on hearts from wild-type and Rbm24 knockout mice, identifying the differential expression of circRNAs. We demonstrated that RBM24 could directly bind to pre-mRNA, facilitating the inclusion of specific exons to provide a substrate for circ23679 production. Moreover, RBM24-regulated circRNA production depended on its phosphorylation status. Further, we showed that RBM24-mediated circ23679 acted as a sponge of miR-15b-5p, and a deficient in circ23679-mediated 'sponging events' could drive cardiac apoptosis. Conversely, circ23679 overexpression inhibited cardiac apoptosis and alleviated the disease phenotype in mouse models of heart failure. Thus, our study not only proposes a novel model in which RBPs provide the substrate for circRNA formation but also reveals that RBM24-dependent circRNA production is a crucial post-transcriptional regulatory circuit in cardiac pathogenesis.

miR-126: a bridge between cancer and exercise

The microRNA miR-126 supports endothelial cells and blood vessel integrity. Recent research has shown that it also serves as a key link between exercise and cancer. This article delves into how exercise affects the expression of miR-126, impacting cardiovascular well-being and metabolic control. The article also examines the various contributions of miR-126 in cancer, acting as both a suppressor and an enhancer depending on the particular context. Regular aerobic exercises, including HIIT, consistently increase levels of miR-126, leading to enhanced angiogenesis, endothelial repair, and improved vascular function through mechanisms involving VEGF, HIF-1α, and EPC mobilization. Resistance training affects similar pathways, but does not cause a significant change in miR-126 levels.MiR-126 involves in cancer by suppressing tumor growth and controlling key pathways such as PI3K/Akt, ERK/MAPK, and EMT. Lower levels are associated with negative outcomes, later stages of the disease, and increased spread of different types of cancer like glioblastoma, CRC, ovarian, esophageal, gastric, and prostate cancer.The relationship between exercise and cancer suggests a possible therapeutic approach, where the regulation of miR-126 through exercise could help improve vascular function and slow tumor growth. Further studies should focus on understanding the specific molecular pathways through which miR-126 connects these areas, leading to potential interventions that utilize its regulatory network to promote cardiovascular well-being and enhance cancer treatment.

Impact of Tyrosine Kinase Inhibitors on the Expression Pattern of Epigenetic Regulators

Background: Advances in molecular genetic diagnostics and emerging opportunities for targeted treatment have opened new horizons in precision oncology. Tyrosine kinase inhibitors (TKI) are the subgroup of these agents with which the most clinical experience has been gathered so far. However, little data is available on the effect of TKI agents on the expression levels of molecules responsible for epigenetic regulation. Methods: In this study, we investigated the effect of in vitro and in vivo treatment with tyrosine kinase inhibitor agents on the expression of epigenetic regulators in hematological malignancies and solid tumors, based on data included in the functional genomics repository Gene Expression Omnibus. Results: Statistical analysis of datasets and series of gene expression patterns revealed numerous significant changes in the levels of epigenetic writers, erasers, microRNAs and members of chromatin-remodeling complexes following TKI treatment. Previously published data about the role of these epigenetic modifiers in malignant diseases has also been summarized. Conclusions: Our results may contribute to the establishment of novel treatment strategies aiming at the combinatorial administration of TKI and epidrugs in cancer, leading to less toxic therapy with further improved results.

Re-appraising assays on permeabilized blood cancer cells testing venetoclax or other BH3 mimetic agents selectively targeting pro-survival BCL2 proteins

BH3 mimetic drugs that selectively target the pro-survival BCL2 proteins are highly promising for cancer treatment, most notably for treating blood cancers. Venetoclax, which inhibits BCL2, is now approved for treating chronic lymphocytic leukemia (CLL) and acute myeloid leukemia (AML). Preferably, robust and validated assays would identify patients most likely to benefit from therapy with venetoclax itself or with inhibitors of other pro-survival proteins. A sophisticated method that has been developed is the BH3 profiling assay. In this assay, permeabilized, instead of intact, cells are treated for a few hours with inhibitors of the pro-survival BCL2 proteins, and the resultant mitochondrial depolarization measured. Sensitivity to a specific inhibitor (e.g., venetoclax or other BH3 mimetics) is then used to infer the reliance of a tumor (e.g., CLL) on one or more pro-survival BCL2 proteins. However, we found that this methodology cannot reliably identify such dependencies. In part, this is because almost all cells express multiple pro-survival BCL2 proteins that restrain BAX and BAK which must be inhibited before mitochondrial depolarization and apoptosis can proceed. Using genetic and pharmacological tools across multiple cell line models of blood cancer, we demonstrated that selective BCL2 inhibitors have important flow-on effects that includes the redistribution of BH3-only proteins to ancillary pro-survival proteins not directly engaged by the inhibitor. These secondary effects, critical to the biological action of selective inhibitors, were not accurately recapitulated in permeabilized cells, probably due to the limited time frame possible in such assays or the altered biophysical conditions when cells are permeabilized. While we could consistently define the sensitivity of a tumor cell to a particular BH3 mimetic drugs using intact cells, this was not reliable with permeabilized cells. These studies emphasize the need to carefully evaluate assays on permeabilized cells undertaken with inhibitors of the pro-survival BCL2 proteins.

Therapeutic potential of synthetic microRNA mimics based on the miR-15/107 consensus sequence

MicroRNA expression is frequently suppressed in cancer, and previously we demonstrated coordinate downregulation of multiple related microRNAs of the miR-15/107 group in malignant pleural mesothelioma (PM). From an alignment of the miR-15 family and the related miR-103/107, we derived a consensus sequence and used this to generate synthetic mimics. The synthetic mimics displayed tumour suppressor activity in PM cells in vitro, which was greater than that of a mimic based on the native miR-16 sequence. These mimics were also growth inhibitory in cells from non-small cell lung (NSCLC), prostate, breast and colorectal cancer, and sensitised all cell lines to the chemotherapeutic drug gemcitabine. The increased activity corresponded to enhanced inhibition of the expression of target genes and was associated with an increase in predicted binding to target sites, and proteomic analysis revealed a strong effect on proteins involved in RNA and DNA processes. Applying the novel consensus mimics to xenograft models of PM and NSCLC in vivo using EGFR-targeted nanocells loaded with mimic led to tumour growth inhibition. These results suggest that mimics based on the consensus sequence of the miR-15/107 group have therapeutic potential in a range of cancer types.

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.

Mapping Current Studies of tRNA Fragments onto Disease Landscape

Transfer-RNA-derived fragments (tRFs) are a relatively recently discovered class of non-coding RNAs derived from both precursor and mature transfer RNAs (tRNAs). Research on these molecules has been expanding rapidly, revealing their diverse roles in cellular processes, both in normal physiology and in disease states, often via post-transcriptional regulation of target genes. Altered tRFs abundances have been implicated in various conditions, where they may act as either drivers of disease progression or as protective agents. For instance, specific tRFs are associated with increased risk for cancer metastasis, while others may suppress tumor cell proliferation. Despite the growing recognition of tRFs as functional RNAs rather than sequencing noise, this field of study faces numerous challenges. Inconsistent naming conventions and variability in experimental approaches hinder the comparison of findings across studies, limiting our understanding of the common roles and mechanisms of tRFs. This review provides a comprehensive analysis of current literature on the various roles of tRFs in different diseases, particularly focusing on four broad areas: cancer, neurological, cardiovascular, and musculoskeletal disorders. We analyze studies that link specific tRFs to various aspects of human diseases and provide a convenient classification of these studies regarding the depth of the provided evidence. Further, we note gaps in current investigations and consider strategies to address methodological inconsistencies, including validation experiments and unified nomenclature. By consolidating research in this manner, we aim to facilitate comparisons across diverse studies, enhancing our ability to identify functional commonalities and furthering our understanding of the mechanisms by which tRFs act.

Non-coding RNAs, a double-edged sword in breast cancer prognosis

Cancer is a rising issue worldwide, and numerous studies have focused on understanding the underlying reasons for its occurrence and finding proper ways to defeat it. By applying technological advances, researchers are continuously uncovering and updating treatments in cancer therapy. Their vast functions in the regulation of cell growth and proliferation and their significant role in the progression of diseases, including cancer. This review provides a comprehensive analysis of ncRNAs in breast cancer, focusing on long non-coding RNAs such as HOTAIR, MALAT1, and NEAT1, as well as microRNAs such as miR-21, miR-221/222, and miR-155. These ncRNAs are pivotal in regulating cell proliferation, metastasis, drug resistance, and apoptosis. Additionally, we discuss experimental approaches that are useful for studying them and highlight the advantages and challenges of each method. We then explain the results of these clinical trials and offer insights for future studies by discussing major existing gaps. On the basis of an extensive number of studies, this review provides valuable insights into the potential of ncRNAs in cancer therapy. Key findings show that even though the functions of ncRNAs are vast and undeniable in cancer, there are still complications associated with their therapeutic use. Moreover, there is an absence of sufficient experiments regarding their application in mouse models, which is an area to work on. By emphasizing the crucial role of ncRNAs, this review underscores the need for innovative approaches and further studies to explore their potential in cancer therapy.

Single-cell analysis of a bi-clonal chronic lymphocytic leukemia reveals two clones with distinct gene expression pattern

Dual productive B-cell receptor (BCR) rearrangements have been repeatedly reported for chronic lymphocytic leukemia (CLL), but the standard population-based PCR analyses cannot distinguish whether these are bi-clonal CLL, or a monoclonal CLL with bi-allelic productive rearrangements. We investigated CLL cells by combined single-cell RNA and BCR sequencing. We identified two CLL clones using different immunoglobulin (Ig) heavy-chain V region genes (IGHV) genes and distinct Ig λ light chains. One clone is classified as Ig unmutated the other as mutated. The two CLL clones have distinct transcriptomes: Numerous genes were differentially expressed, with genes typical for unmutated or mutated CLL showing the expected representation in the two clones. Using PCR, cloning and Sanger sequencing of the IGHV rearrangements we detected both CLL clones over a period of three years without clinical progression of the CLL and thus giving insights into the disease biology of multi-clonal CLL.

Double Strike in Chronic Lymphocytic Leukemia-The Combination of BTK and BCL2 Inhibitors in Actual and Future Clinical Practice

In the recent 2024 ESMO guidelines, the combination of venetoclax and ibrutinib was listed as one of the first-line treatment options for CLL patients. These drugs were first-in-class medicines that revolutionized CLL management, extending patients' overall survival even in cases refractory to immunochemotherapy. However, since the approval of both compounds, more and more Bruton Tyrosine Kinase inhibitors (BTKis) and B-cell lymphoma 2 inhibitors (BCL2is) have been discovered. Their efficacy and safety are the reasons for their use in monotherapy among both treatment-naïve and relapsed patients with CLL. Currently, several ongoing clinical trials are investigating the rationale for the combination of BCL2is and BTKis. In this review, we discuss the recent advancements in the field of co-therapy with BTKis and BCL2is.

CD73 Molecule Inhibitor Upregulates miR16 Expression in Experimental Glioblastoma and Inhibits Angiogenesis by Targeting VEGF

The function of CD73 (Cluster of Differentiation 73), an enzyme involved in the formation of adenosine (ADO), in the development of glioblastomas has been demonstrated. Indeed, ADO helps tumor angiogenesis by stimulating endothelial cell migration, proliferation, and tube formation. However, the details of the molecular mechanisms are not yet fully understood. Given the importance of angiogenesis in cancer progression, invasion, and metastasis, this study aimed to investigate how the inhibition of CD73 by adenosine-5'-(α, β-methylene) diphosphate (APCP) affects the angiogenesis process of experimental orthotopic glioblastoma at mRNAs, microRNAs, and protein levels. According to the real-time-polymerase chain reaction (RT-PCR) results, inhibition of CD73 decreased the angiogenesis of glioblastoma by reducing the expression of vascular endothelial growth factor (VEGF) and hypoxia-inducible factor 1-alpha (HIF-1α) by ****P < 0.0001 and **P < 0.01, respectively. Furthermore, immunohistochemical staining showed that this treatment protocol attenuated the expression of VEGF and CD31. Moreover, APCP treatment significantly increased miR-16 expression in glioblastoma model rats by P < 0.001, but no significant change in miR-29A expression was observed. The results showed that the treatment did not lead to systemic damage or significant weight loss. Our results suggest that inhibition of CD73 may reduce the formation of new tumor vessels by inhibiting the VEGF, HIF-1α, and CD31 in this process. Therefore, CD73 may be a practical target and provide new opportunities to improve the treatment of malignant brain tumors.

Role of noncoding RNA as a pacemaker in cancer stem cell regulation: a review article

Accumulated evidence supported the crucial role of a tiny population of cells within the tumor called cancer stem cells (CSCs) in cancer origination, and proliferation. Additionally, these cells are distinguished by their self-renewal, differentiation, and therapeutic resistance capabilities. Interestingly, many studies recorded dysregulation of different types of noncoding RNAs, such as microRNA (miRNA) and long non-coding RNA (LncRNA), in cancer cells as well as CSCs. Moreover, several studies also supported the regulation of the transcription factors and signaling pathways required for CSC progression by these noncoding RNAs. However, the exact biological functions of all these noncoding RNAs are not well understood yet. These findings are of great interest, implying usage of noncoding RNA as therapeutic tool to target these cells. In this review, we provide an insight into how noncoding RNAs regulate CSCs and how this correlation is manipulated to develop new therapies to eradicate cancer cells successfully.

The BCL2 family: from apoptosis mechanisms to new advances in targeted therapy

The B cell lymphoma 2 (BCL2) protein family critically controls apoptosis by regulating the release of cytochrome c from mitochondria. In this cutting-edge review, we summarize the basic biology regulating the BCL2 family including canonical and non-canonical functions, and highlight milestones from basic research to clinical applications in cancer and other pathophysiological conditions. We review laboratory and clinical development of BH3-mimetics as well as more recent approaches including proteolysis targeting chimeras (PROTACs), antibody-drug conjugates (ADCs) and tools targeting the BH4 domain of BCL2. The first BCL2-selective BH3-mimetic, venetoclax, showed remarkable efficacy with manageable toxicities and has transformed the treatment of several hematologic malignancies. Following its success, several chemically similar BCL2 inhibitors such as sonrotoclax and lisaftoclax are currently under clinical evaluation, alone and in combination. Genetic analysis highlights the importance of BCL-XL and MCL1 across different cancer types and the possible utility of BH3-mimetics targeting these proteins. However, the development of BH3-mimetics targeting BCL-XL or MCL1 has been more challenging, with on-target toxicities including thrombocytopenia for BCL-XL and cardiac toxicities for MCL1 inhibitors precluding clinical development. Tumor-specific BCL-XL or MCL1 inhibition may be achieved by novel targeting approaches using PROTACs or selective drug delivery strategies and would be transformational in many subtypes of malignancy. Taken together, we envision that the targeting of BCL2 proteins, while already a success story of translational research, may in the foreseeable future have broader clinical applicability and improve the treatment of multiple diseases.

Circular RNAs and host genes act synergistically in regulating cellular processes and functions in skeletal myogenesis

Circular RNAs (circRNAs) are post-transcriptional regulators generated from backsplicing of pre-mRNAs of host genes. A major circRNA regulatory mechanism involves microRNA (miRNA) sequestering, relieving miRNA-blocked mRNAs for translation and functions. To investigate possible circRNA-host gene relationship, skeletal myogenesis is chosen as a study model for its developmental importance and for readily available muscle tissues from farm animals for studies at different myogenic stages. This review aims to provide an integrated interpretations on methodologies, regulatory mechanisms and possible host gene-circRNA synergistic functional relationships in skeletal myogenesis, focusing on myoblast differentiation and proliferation, core drivers of muscle formation in myogenesis, while other myogenic processes that play supportive roles in the structure, maintenance and function of muscle tissues are also briefly discussed. On literature review,thirty-two circRNAs derived from thirty-one host genes involved in various myogenic stages are identified; twenty-two (68.6 %) of these circRNAs regulate myogenesis by sequestering miRNAs to engage PI3K/AKT and other signaling pathways while four (12.5 %) are translated into proteins for functions. In circRNA-host gene relationship,ten (32.3 %) host genes are shown to regulate myogenesis,nine (29.0 %) are specific to skeletal muscle functions,and twelve (38.8 %) are linked to skeletal muscle disorders.Our analysis of skeletal myogenesis suggests that circRNAs and host genes act synergistically to regulate cellular functions. Such circRNA-host gene functional synergism may also be found in other major cellular processes. CircRNAs may have evolved later than miRNAs to counteract the suppressive effects of miRNAs and to augment host gene functions to further fine-tune gene regulation.

Mechanism of Action of circRNA/miRNA Network in DLBCL

Circular RNAs (circRNAs) make up approximately 10% of the human transcriptome. CircRNAs belong to the broad group of non-coding RNAs and characteristically are formed by backsplicing into a stable circular loop. Their main role is to regulate transcription through the inhibition of miRNAs' expression, termed miRNA sponging. CircRNAs promote tumorigenesis/lymphomagenesis by competitively binding to miRNAs at miRNA binding sites. In diffuse large B-cell lymphoma (DLBCL), several circRNAs have been identified and their expression is related to both progression and response to therapy. DLBCL is the most prevalent and aggressive subtype of B-cell lymphomas and accounts for about 25% to 30% of all non-Hodgkin lymphomas. DLBCL displays great heterogeneity concerning histopathology, biology, and genetics. Patients who have relapsed or have refractory disease after first-line therapy have a very poor prognosis, demonstrating an important unmet need for new treatment options. As more circRNAs are identified in the future, we will better understand their biological roles and potential use in treating cancer, including DLBCL. For example, circAmotl1 promotes nuclear translocation of MYC and upregulation of translational targets of MYC, thus enhancing lymphomagenesis. Another example is circAPC, which is significantly downregulated in DLBCL and correlates with disease aggressiveness and poor prognosis. CircAPC increases expression of the host gene adenomatous polyposis coli (APC), and in doing so inactivates the canonical Wnt/β-catenin signaling and restrains DLBCL growth. MiRNAs belong to the non-coding regulatory molecules that significantly contribute to lymphomagenesis through their target mRNAs. In DLBCL, among the highly expressed miRNAs, are miR-155-5p and miR-21-5p, which regulate NF-ĸB and PI3K/AKT signaling pathways. The aim of this review is to describe the function and mechanism of regulation of circRNAs on miRNAs' expression in DLBCL. This will help us to better understand the regulatory network of circRNA/miRNA/mRNA, and to propose novel therapeutic targets to treat DLBCL.

Chemokine Ligands and Receptors Regulate Macrophage Polarization in Atherosclerosis: A Comprehensive Database Mining Study

Background

Atherosclerosis is a systemic disease involving multiple blood vessels and a major cause of cardiovascular disease. Current treatment methods (eg, statins) for atherosclerosis can reduce the risk of cardiovascular diseases effectively, but they are insufficient to completely reverse existing atherosclerosis. Macrophages play a central role in development of atherosclerosis. Chemokines, the main mediators of macrophage chemotaxis, are important in immune and inflammatory responses. The effects of chemokines on mechanisms involved in atherosclerosis are unknown. This study preliminarily investigated these effects and mechanisms via bioinformatics methods.

Methods

In this study, data on chemokine ligands and receptors were obtained by mining public databases (the National Center of Biotechnology Information-Gene Expression Omnibus [NCBI-GEO] database, ArrayExpress database, and single-cell RNA sequencing [scRNA-seq] database), and an extensive literature search was performed. The expression levels of chemokines in mouse tissues were analyzed via Metascape software for signalling pathway enrichment, scRNA-seq data for chemokine expression in atherosclerotic plaque progression and regression, and GEO2R data for chemokine expression during macrophage polarization. Ingenuity Pathway Analysis (IPA) software was used to analyze regulatory factors such as transcription factors and microRNAs that are significantly differentially expressed upstream of chemokines in macrophage polarization. Finally, a model of the chemokine regulation of atherosclerosis was established on the basis of these results.

Results

There are 5 main findings: (1) In atherosclerosis, chemokines are regulated by transcription factors and microRNAs. (2) The transcription factor STAT1 promotes the polarization of dormant (M0) macrophages into classically activated (M1) macrophages and alternative activated (M2) macrophages by regulating chemokines. The transcription factors STAT1, IRF7 and IRF1 regulate the polarization of M0 macrophages into M2a and M2b macrophages via different chemokines. For example, some transcription factors promote M1 polarization of M0 macrophages through CCL4, but M2 macrophage polarization is regulated via CCL19, CCL5 and CCR7. (3) Transcription factors can promote and inhibit, whereas miRNAs can only inhibit atherosclerosis. (4) CCL4 existed in all 5 different chemokine-regulated macrophage models, whereas CXCL3 only existed in the M2b macrophage transcriptional regulation model, indicating that CXCL3 may promote the M2b type macrophages polarization of M0 macrophages. (5) CCL5 and CCR7 can promote the M2a macrophages and M2b macrophages polarization of M0 macrophages.

Conclusions

Atherosclerosis can be treated by regulating chemokines and regulating the polarization of macrophages. The chemokines CCL4, CCL5, CCL8, CCL19, CXCL3, CXCL10, CXCL13, and CCR7 may play key roles in the progression and regression of atherosclerosis.

The Heterogeneity of 13q Deletions in Chronic Lymphocytic Leukemia: Diagnostic Challenges and Clinical Implications

Chronic lymphocytic leukemia (CLL) is the most common type of adult leukemia, particularly in Western countries. CLL can present indolently or aggressively, influenced by various factors, including chromosomal alterations. Fluorescent in situ hybridization (FISH), targeting specific genes/loci frequently affected in CLL patients, has established a standard for stratifying five CLL prognostic groups: del(11q)/ATM, trisomy 12, del(13q) as a sole aberration, del(17p)/TP53, and normal CLL FISH panel results. Among these, del(13q) as a sole aberration is associated with a favorable prognosis, while the others are considered intermediate (normal CLL FISH panel result and trisomy 12) or unfavorable (del(11q)/ATM and del(17p)/TP53) prognostic markers. However, significant heterogeneity in del(13q) aberrations has been observed among CLL patients with isolated del(13q), which should be considered when predicting prognosis and planning clinical management for individual CLL patients with this aberration. This review discusses the variations in del(13q) aberrations in CLL, including a minimally deleted region (MDR), the anatomic sizes of deleted 13q regions, affected alleles, the clone sizes of del(13q), and their dynamic changes during disease progression. The impact of del(13q) heterogeneity on various diagnostic tests such as karyotyping, the FISH panel, chromosomal microarray (CMA), and optical genome mapping (OGM), prognostic prediction, and clinical management is illustrated through authentic clinical scenarios.

The functional correlation between mir-16-5p and BIRC5 gene in colorectal cancer: integrated analysis of transcriptomics and in vitro validation

BACKGROUND

This study explores the mechanisms of colorectal cancer (CRC) through bioinformatics and in vitro experiments. The goal is to find differentially expressed genes (DEGs) and miRNA-gene interactions, especially between miR-16-5p and BIRC5, in order to find biomarkers that can be used to diagnose, predict, and treat CRC.

METHODS AND RESULTS

Microarray data (GSE52060) from the GEO database was analysed using R software, applying LIMMA for log2 transformation and quantile normalization. Significant DEGs were identified, and miRNA targets were predicted with miRWalk v.3 and validated in CRC cell lines. Statistical analyses were conducted using R and GraphPad Prism. BIRC5's impact on survival was analysed via GEPIA2, and correlated genes were identified using Correlation AnalyzeR. The treatment of miR-16-5p mimic significantly reduced BIRC5 expression in HT-29, SW480, and HCT116 cells in a dose-dependent manner. Correlational analyses revealed a strong negative association between miR-16-5p levels and BIRC5 expression, emphasizing miR-16-5p's role as a tumor suppressor. While BIRC5 inhibits apoptosis and regulates cell division, miR-16-5p impacts apoptosis, the cell cycle, and angiogenesis. GEPIA2 analysis indicated that BIRC5 expression had no significant impact on CRC survival outcomes.

CONCLUSIONS

This study demonstrates miR-16-5p's regulatory role on BIRC5 in CRC cells and its therapeutic potential. Restoring miR-16-5p or targeting BIRC5 could improve CRC treatment strategies. To learn more about how miR-16-5p and BIRC5 can be used to diagnose and predict CRC, more clinical testing is needed. This will help us learn more about how CRC works at the molecular level.

Aberrantly Expressed Mitochondrial Lipid Kinase, AGK, Activates JAK2-Histone H3 Axis and BCR Signal: A Mechanistic Study with Implication in CLL Therapy

PURPOSE

Although the B-cell receptor (BCR) signal plays a critical role in chronic lymphocytic leukemia (CLL) cell survival and a target of current therapies (ibrutinib targets Bruton's tyrosine kinase; idelalisib targets PI3Kδ), contribution of the cytokine-driven JAK2 pathway to the "CLL cell-survival signaling network" is largely undefined.

EXPERIMENTAL DESIGN

Patients with CLL were enrolled to investigate expression/activation of JAK2 and acylglycerol kinase (AGK), and their functional implication in primary CLL cell survival. A series of biochemical and molecular biology assays were employed to uncover the underlying mechanism.

RESULTS

We detected that compared with normal B cells, CLL cells aberrantly express constitutively active JAK2. Mechanistically, HSP90 forms a chaperoning complex with JAK2, resulting in its aberrant accumulation in CLL cells. We also discovered aberrant upregulation of a novel mitochondrial lipid kinase, AGK, which remains complexed with HSP90 in CLL cells activating JAK2. Although AGK is typically mitochondrial, we detected its nuclear localization in association with JAK2 in some CLL cells. Functionally, JAK2 phosphorylates its noncanonical substrate, histone H3(Y41), but not STAT3, activating transcription of diverse sets of genes in a patient-specific manner. Additionally, JAK2 activates the BCR signal in CLL cells via LYN/Bruton's tyrosine kinase axis. Targeted inhibition of JAK2 as monotherapy, or in combination with the BCR inhibitors or venetoclax (a BCL2 inhibitor), induced apoptosis synergistically in CLL cells.

CONCLUSIONS

These findings suggest that aberrantly expressed AGK activates JAK2, independent of cytokine, leading to activation of diverse sets of gene transcription in CLL cells. Combined targeting of JAK2 and BCR signals or BCL2 may be effective in some patients with CLL.

MicroRNA Gets a Mighty Award

Recent advancements in microRNAs (miRNAs) research have revealed their key roles in both normal physiological processes and pathological conditions, leading to potential applications in diagnostics and therapeutics. However, the path forward is fraught with several scientific and technical challenges. This review article briefly explores the milestones of the discovery, biogenesis, functions, and application for clinical diagnostic and therapeutic strategies of miRNAs. The potential challenges and future directions are also discussed to fully harness their capabilities.

Role of miRNAs in Apoptosis Pathways of Immune Cells in Systemic Lupus Erythematosus

BACKGROUND

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by dysregulated immune responses and multi-organ involvement. Dysregulation of apoptosis, a key process for maintaining immune homeostasis, plays a critical role in the pathogenesis of SLE. MicroRNAs (miRNAs), small non-coding RNAs that regulate gene expression, have emerged as important modulators of apoptosis in immune cells, influencing the balance between immune tolerance and autoimmunity.

OBJECTIVES

This review aims to comprehensively summarize recent advancements in understanding the roles of miRNAs in apoptosis regulation within immune cells in SLE, highlighting their therapeutic potential for restoring immune balance and mitigating disease progression.

RESULTS

Aberrant expression of specific miRNAs contributes to the dysregulation of apoptosis in SLE immune cells. Pro-apoptotic miRNAs, such as miR-125b and miR-150, are often downregulated, leading to enhanced survival of autoreactive immune cells. Conversely, anti-apoptotic miRNAs, including miR-21, are upregulated, further disrupting the delicate balance of immune cell apoptosis. Dual-function miRNAs, such as miR-155, exhibit context-dependent roles based on cellular environments and target gene interactions. This dysregulation promotes the persistence of autoreactive immune cells and the development of autoimmunity.

CONCLUSIONS

miRNAs play critical roles in modulating apoptosis pathways, making them promising therapeutic targets for SLE. Restoring the balance of pro-apoptotic and anti-apoptotic miRNAs could help reinstate immune tolerance and reduce tissue damage. Future research should focus on elucidating miRNA targetomes, improving delivery systems, and addressing off-target effects to fully harness their therapeutic potential.

A review on gut microbiota and miRNA crosstalk: implications for Alzheimer's disease

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by cognitive decline and progressive neuronal damage. Recent research has highlighted the significant roles of the gut microbiota and microRNAs (miRNAs) in the pathogenesis of AD. This review explores the intricate interaction between gut microbiota and miRNAs, emphasizing their combined impact on Alzheimer's progression. First, we discuss the bidirectional communication within the gut-brain axis and how gut dysbiosis contributes to neuroinflammation and neurodegeneration in AD. Changes in gut microbiota composition in Alzheimer's patients have been linked to inflammation, which exacerbates disease progression. Next, we delve into the biology of miRNAs, focusing on their roles in gene regulation, neurodevelopment, and neurodegeneration. Dysregulated miRNAs are implicated in AD pathogenesis, influencing key processes like inflammation, tau pathology, and amyloid deposition. We then examine how the gut microbiota modulates miRNA expression, particularly in the brain, potentially altering neuroinflammatory responses and synaptic plasticity. The interplay between gut microbiota and miRNAs also affects blood-brain barrier integrity, further contributing to Alzheimer's pathology. Lastly, we explore therapeutic strategies targeting this gut microbiota-miRNA axis, including probiotics, prebiotics, and dietary interventions, aiming to modulate miRNA expression and improve AD outcomes. While promising, challenges remain in fully elucidating these interactions and translating them into effective therapies. This review highlights the importance of understanding the gut microbiota-miRNA relationship in AD, offering potential pathways for novel therapeutic approaches aimed at mitigating the disease's progression.

High Expression Levels of the Long Non-Coding RNAs Lnc-IRF2-3 and Lnc-KIAA1755-4 Are Markers of Poor Prognosis in Chronic Lymphocytic Leukemia

Long non-coding RNAs (lncRNAs) play complex roles at multiple levels of gene regulation, thus modulating key cellular processes involved in the pathogenesis and progression of cancer. Aberrant expression of lncRNAs has been reported in various malignancies, including chronic lymphocytic leukemia (CLL). We investigated the expression of lnc-IRF2-3 and lnc-KIAA1755-4 in peripheral blood mononuclear cells of 112 previously untreated CLL patients by quantitative reverse-transcriptase polymerase chain reaction. Both lncRNAs were found to be overexpressed in CLL samples in comparison to healthy controls, and their high levels were associated with adverse clinico-biological characteristics of patients at diagnosis. High lnc-IRF2-3 expression was associated with high leukocyte and lymphocyte counts, high β2-microglobulin, advanced Binet stage, unfavorable cytogenetics, CD38-positivity and IGHV-unmutated status. Regarding lnc-KIAA1755-4, its high expression was associated with high leukocyte count, lymphocyte count, β2-microglobulin, lactate dehydrogenase and low hemoglobin, as well as with IGHV-unmutated status. In addition, we observed shorter time to first treatment and overall survival of patients expressing high levels of both lncRNAs in comparison to low-expressing patients. In summary, our study showed that high lnc-IRF2-3 and lnc-KIAA1755-4 expression at diagnosis predicts poor survival in CLL. The mechanisms of their upregulation, as well as their specific targets in CLL cells, remain to be elucidated.

BCL-2 inhibitors in hematological malignancies: biomarkers that predict response and management strategies

Apoptosis is an essential characteristic of cancer and its dysregular promotes tumor growth, clonal evolution, and treatment resistance. B-cell lymphoma-2 (BCL-2) protein family members are key to the intrinsic, mitochondrial apoptotic pathway. The inhibition of the BCL-2 family pro-survival proteins, which are frequently overexpressed in B-cell malignancies and pose a fundamental carcinogenic mechanism has been proposed as a promising therapeutic option, with venetoclax (ABT-199) being the first FDA-approved BCL-2 inhibitor. Unfortunately, although BCL-2 inhibition has shown remarkable results in a range of B-cell lymphoid cancers as well as acute myeloid leukemia (AML), the development of resistance significantly reduces response rates in specific tumor subtypes. In this article, we explain the role of BCL-2 family proteins in apoptosis and their mechanism of action that justifies their inhibition as a potential treatment target in B-cell malignancies, including chronic lymphocytic leukemia, multiple myeloma, B-cell lymphomas, but also AML. We further analyze the tumor characteristics that result in the development of intrinsic or inherited resistance to BCL-2 inhibitors. Finally, we focus on the biomarkers that can be used to predict responses to treatment in the name of personalized medicine, with the goal of exploring alternative strategies to overcome resistance.

Exosomal lncRNAs as diagnostic and therapeutic targets in multiple myeloma

Multiple Myeloma (MM) is the second most common malignancy of the hematopoietic system, accounting for approximately 10% of all hematological malignancies, and currently, there is no complete cure. Existing research indicates that exosomal long non-coding RNAs (lncRNAs) play a crucial regulatory role in the initiation and progression of tumors, involving various interactions such as lncRNA-miRNA, lncRNA-mRNA, and lncRNA-RNA binding proteins (RBP). Despite the significant clinical application potential of exosomal lncRNAs, research in this area still faces challenges due to their low abundance and technical limitations. To our knowledge, this review is the first to comprehensively integrate and elucidate the three mechanisms of action of exosomal lncRNAs in MM, and to propose potential therapeutic targets and clinical cases based on these mechanisms. We highlight the latest advancements in the potential of exosomal lncRNAs as biomarkers and therapeutic targets, offering not only a comprehensive analysis of the role of exosomal lncRNAs in MM but also new perspectives and methods for future clinical diagnosis and treatment of multiple myeloma.

Self-assembling nanoparticles for delivery of miR-603 and miR-221 in glioblastoma as a new strategy to overcome resistance to temozolomide

Glioblastoma (GBM) is a highly aggressive brain cancer with poor clinical outcome. Unfortunately, chemotherapy with temozolomide (TMZ) has a limited efficacy due to resistance mainly attributed to O6-methylguanine methyl transferase (MGMT) activity. Recently, miR-603 and miR-221 have been identified to target MGMT, thus improving the efficacy of temozolomide (TMZ) in the treatment of GBM. Previously, self-assembling nanoparticles (SANPs) have been proposed to deliver miRNAs into the brain. Here, SANP co-encapsulating miRNA-603 (miR-603) and miRNA-221 (miR-221) have been developed to enhance the efficacy of TMZ in the treatment of GBM by preventing the occurrence of chemoresistance. Preliminarily, SANPs encapsulating miRNAs were optimized in terms of lipid composition to assure physical stability and no hemolytic activity. Subsequently, SANPs with the lowest cytotoxicity and excellent internalization efficiency of miRNAs were selected through MTT assay and real-time PCR, respectively. To evaluate a potential synergistic effect between TMZ and miRNAs, MTT and clonogenic assays were performed. In our biological model, miRNA delivery via SANPs in combination with TMZ treatment strongly reduced cell viability and tumorigenic potential. Finally, in vivo assays were carried out on orthotopic xenograft mouse models. The treatment with SANPs encapsulating both miRNAs in combination with TMZ greatly decreased tumour growth, and even more significantly increased animal survival. In conclusion, this strategy provides the rationale for the development of new therapeutic approaches based on SANP technology to deliver miRNAs that play a key role in suppressing tumour.

Genome-Wide microRNA Expression Profiling in Human Spermatozoa and Its Relation to Sperm Quality

BACKGROUND

Sperm samples are separated into bad and good quality samples in function of their phenotype, but this does not indicate their genetic quality.

METHODS

Here, we used GeneChip miRNA arrays to analyze microRNA expression in ten semen samples selected based on high-magnification morphology (score 6 vs. score 0) to identify miRNAs linked to sperm phenotype.

RESULTS

We found 86 upregulated and 21 downregulated miRNAs in good-quality sperm (score 6) compared with bad-quality sperm samples (score 0) (fold change > 2 and p-value < 0.05). MiR-34 (FC × 30, p = 8.43 × 10-8), miR-30 (FC × 12, p = 3.75 × 10-6), miR-122 (FC × 8, p = 0.0031), miR-20 (FC × 5.6, p = 0.0223), miR-182 (FC × 4.83, p = 0.0008) and miR-191 (FC × 4, p = 1.61 × 10-6) were among these upregulated miRNAs. In silico prediction algorithms predicted that miRNAs upregulated in good-quality sperm targeted 910 genes involved in key biological functions of spermatozoa, such as cell death and survival, cellular movement, molecular transport, response to stimuli, metabolism, and the regulation of oxidative stress. Genes deregulated in bad-quality sperm were involved in cell growth and proliferation.

CONCLUSIONS

This study reveals that miRNA profiling may provide potential biomarkers of sperm quality.

MYC-dependent MiR-7-5p regulated apoptosis and autophagy in diffuse large B cell lymphoma by targeting AMBRA1

Diffuse large B-cell lymphoma (DLBCL) is the leading cause of mortality from invasive hematological malignancies worldwide. MicroRNA-7-5p (miR-7-5p) has been shown to be a tumor suppressor in several types of tumors. However, its role in DLBCL is not fully understood. This study explored the role of miR-7-5p in the progression of DLBCL and pursued the underlying mechanism. Quantitative real-time PCR and transfection of miRNA mimic and inhibitors were used to assess the effects of miR-7-5p on autophagy and apoptosis in SU-DHL-4 and SU-DHL-10 cells. Dual-luciferase reporter assay was used to identify target genes of miR-7-5p. Immunofluorescence, flow cytometry, and western blotting (WB) were performed to explore the underlying mechanism and downstream pathways of miR-7-5p and AMBRA1 in DLBCL cells. MiR-7-5p was upregulated in DLBCL cells. Luciferase reporter assays implicated AMBRA1 as a downstream target of miR-7-5p in DLBCL. WB and flow cytometry showed that an increase in miR-7-5p level and a decrease in AMBRA1 expression led to a decrease in autophagy and apoptosis-related protein expression. Furthermore, miR-7-5p prevented c-MYC dephosphorylation through AMBRA1 downregulation. On the contrary, c-MYC increased the expression of miR-7-5p, thereby establishing positive feedback on miR-7-5p transcription. The addition of hydroxychloroquine, an autophagy inhibitor, reduced autophagy and increased apoptosis in DLBCL cells. In vivo experiments further proved that the increase of miR-7-5p played a regulatory role in the expression of downstream AMBRA1 and c-MYC. These results demonstrate that c-MYC-dependent MiR-7-5p suppressed autophagy and apoptosis by targeting AMBRA1 in DLBCL cells. MiR-7-5p also suppressed autophagy and apoptosis by targeting AMBRA1 in DLBCL cells. Therefore, these data suggest that targeting miR-7-5p may be a promising strategy in DLBCL therapy.

A Practical Guideline for MicroRNA Sequencing Data Analysis in Chronic Lymphocytic Leukemia

MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression. They have been associated with several diseases and cancers, including chronic lymphocytic leukemia (CLL). CLL is the most common form of adult leukemia, and its pathogenesis is driven by the deletion of miRNAs, such as the miR-15a/16-1 cluster. In addition to initiating the development of CLL, the function of miRNAs in regulating the progression of this tumor remains to be investigated. Here, we present a computational pipeline, from the processing of miRNA sequencing files to functional analysis, including differential gene expression and gene set enrichment analysis.We exemplified the utility of the pipeline by applying it to genome-wide small RNA sequencing data from a cohort of CLL patients. The analysis revealed dysregulated expression profiles of miRNAs in CLL. The target genes of these miRNAs are not only associated with the response of CLL patients to current therapies but also involved in several cancer hallmarks, including the avoidance of cell death, the deregulation of cellular energetics, the activation of invasion and metastasis, and genome instability. The identified miRNA-gene interactions offer valuable insights for developing targeted therapies for CLL. In addition, we underscored the importance of a practical and robust computational pipeline to ensure the reliability and reproducibility of miRNA sequencing data analysis.

Plasma miR-1-3p levels predict severity in hospitalized COVID-19 patients

Background and Purpose:

Accumulating evidence suggests circulating microRNAs (miRNAs) are important regulators of biological processes involved in COVID-19 complications. We sought to assess whether circulating miRNAs are associated with COVID-19 clinical phenotype and outcome.

Experimental Approach:

To discover signatures of circulating miRNAs associated with COVID-19 disease severity and mortality, miRNA quantification was performed on plasma samples collected at hospital admission from a cohort of 106 patients with mild or severe COVID-19. Variable importance projection scoring with partial least squared discriminant analysis and Random Forest Classifier were employed to identify key miRNAs associated with COVID-19 severity. ROC analysis was performed to detect promising miRNA able to discriminate between mild and severe COVID status.

Key Results:

Hsa-miR-1-3p was the most promising miRNA in differentiating COVID-19 patients who developed severe, rather than mild, disease. Hsa-miR-1-3p levels rose with increasing disease severity, and the highest levels were associated with prolonged hospital length of stay and worse survival. Longitudinal miRNA profiling demonstrated that plasma hsa-miR-1-3p expression levels were significantly increased in patients during acute infection compared with those observed 6 months after the disease onset. Specific blockade of miR-1-3p in SARS-CoV-2–infected endothelial cells decreased up-regulation of genes involved in endothelialto-mesenchymal transition, inflammation and thrombosis. Furthermore, miR-1-3p inhibition reversed the impaired angiogenic capacity induced by plasma from patients with severe COVID-19.

Conclusion and Implications:

Our data establish a novel role for miR-1-3p in the pathogenesis of COVID-19 infection and provide a strong rationale for its usefulness as early prognostic biomarkers of severity status and survival.

Association of miRNA and Bone Tumors: Future Therapeutic Inroads

Small endogenous non-coding RNA molecules known as micro-ribonucleic acids (miRNAs) control post-transcriptional gene regulation. A change in miRNA expression is related to various diseases, including bone tumors. Benign bone tumors are categorized based on matrix production and predominant cell type. Osteochondromas and giant cell tumors are among the most common bone tumors. Interestingly, miRNAs can function as either tumor suppressor genes or oncogenes, thereby determining the fate of a tumor. In the present review, we discuss various bone tumors with regard to their prognosis, pathogenesis, and diagnosis. The association between miRNAs and bone tumors, such as osteosarcoma, Ewing's sarcoma, chondrosarcoma, and giant-cell tumors, is also discussed. Moreover, miRNA may play an important role in tumor proliferation, growth, and metastasis. Knowledge of the dysregulation, amplification, and deletion of miRNA can be beneficial for the treatment of various bone cancers. The miRNAs could be beneficial for prognosis, treatment, future drug design, and treatment of resistant cases of bone cancer.

The critical role of miRNA in bacterial zoonosis

The public's health and the financial sustainability of international societies remain threatened by bacterial zoonoses, with limited reliable diagnostic and therapeutic options available for bacterial diseases. Bacterial infections influence mammalian miRNA expression in host-pathogen interactions. In order to counteract bacterial infections, miRNAs participate in gene-specific expression and play important regulatory roles that rely on translational inhibition and target gene degradation by binding to the 3' non-coding region of target genes. Intriguingly, according to current studies, that exogenous miRNAs derived from plants could potentially serve as effective medicinal components sourced from traditional Chinese medicine plants. These exogenous miRNAs exhibit stable functionality in mammals and mimic the regulatory roles of endogenous miRNAs, illuminating the molecular processes behind the therapeutic effects of plants. This review details the immune defense mechanisms of inflammation, apoptosis, autophagy and cell cycle disturbance caused by some typical bacterial infections, summarizes the role of some mammalian miRNAs in regulating these mechanisms, and introduces the cGAS-STING signaling pathway in detail. Evidence suggests that this newly discovered immune defense mechanism in mammalian cells can also be affected by miRNAs. Meanwhile, some examples of transboundary regulation of mammalian mRNA and even bacterial diseases by exogenous miRNAs from plants are also summarized. This viewpoint provides fresh understanding of microbial tactics and host mechanisms in the management of bacterial illnesses.

MicroRNA regulator gene mutations in thyroid follicular nodular disease and thyroid cancer: does it all come down to timing?

In recent years, germline mutations in the microRNA (miRNA) processor genes DICER1 and DGCR8 have been coupled to the development of thyroid follicular nodular disease (TFND), thereby casting new light on the etiology of this enigmatic, benign condition in non-iodine-deficient regions. Moreover, DICER1 and DGCR8 mutations have also been reported in rare subsets of follicular cell-derived thyroid carcinomas. Specifically, truncating germline or missense somatic DICER1 mutations have been reported in small subsets of pediatric and adolescent follicular thyroid carcinoma (FTC) and poorly differentiated thyroid carcinoma (PDTC). Similarly, a recurrent somatic mutation of the DGCR8 gene has been observed in highly aggressive FTCs and in some indolent cases of encapsulated follicular variant of papillary thyroid carcinoma. The reason why identical mutations in the same miRNA processor gene can lead to such a myriad of thyroid conditions, ranging from benign TFND to FTCs and PDTCs, remains unclear. This review highlights key features of miRNA regulator gene mutations in thyroid disease and explores their potential roles as drivers or progression events in tumor development.

Tetra aniline-based polymers ameliorate BPA-induced cardiotoxicity in Sprague Dawley rats, in silico and in vivo analysis

AIMS

Bisphenol A (BPA), xenoestrogen, is an environmental toxicant, that generates oxidative stress leading to cardiotoxicity. The oxidative stress can be neutralized by natural and synthetic antioxidants. The present study elucidates the highly selective antioxidative potential of synthetic tetra aniline polymers Es-37 and L-37 against Bisphenol A-induced cardiac cellular impairments and the role of miRNA-15a-5p in the regulation of different apoptotic proteins.

MATERIALS AND METHODS

The molecular docking of L-37 and Es-37 with three proteins (p53, Cytochrome c, and Bcl-2) were performed. The dose of 1 mg/kg BW of BPA, 1 mg/kg BW Es-37 and L-37 and 50 mg/kg BW N-acetyl cysteine (NAC) was administered to Sprague Dawley rats. The miRNA and target gene expression were confirmed by qRt-PCR and Immunoblotting.

KEY FINDINGS

In our results, BPA administration significantly elevated the reactive oxygen species (ROS), p53, cytochrome c, and particularly miRNA-15a-5p expression; however: these changes were notably reversed by Es-37 and L-37 treatment. Additionally, molecular docking of synthetic polymers validated that L-37 has a greater binding affinity with the target proteins compared to Es-37, with the highest binding values reported for the enzymatic protein cytochrome c.

SIGNIFICANCE

These results suggest that both synthetic polymers Es-37 and L-37 have the potential to scavenge free radicals, boost-up antioxidant enzyme activities, and avert (BPA-induced) toxicity, thus, may serve as cardioprotective agents. Moreover, this study first time proposes that miRNA-15a-5p overexpression is associated with oxidative stress and coincides with BPA induced cardiotoxicity, thus may serve as potential therapeutic target in future.

Molecular Composition and Kinetics of B Cells During Ibrutinib Treatment in Patients with Chronic Lymphocytic Leukemia

Chronic lymphocytic leukemia (CLL) is characterized by the accumulation of B cells due to constitutive B-cell receptor (BCR) signaling, leading to apoptosis resistance and increased proliferation. This study evaluates the effects of the Bruton Tyrosine Kinase (BTK) inhibitor ibrutinib on the molecular composition, clonality, and kinetics of B cells during treatment in CLL patients. Employing a multi-omics approach of up to 3.2 years of follow-up, we analyzed data from 24 CLL patients, specifically focusing on nine patients treated with ibrutinib monotherapy. In this study, clonal stability was observed within the ibrutinib-treated group following an effective initial clinical response, where clonotype frequencies of residual CLL cells remained high and stable, ranging from 74.9% at 1.5 years to 87.7% at approximately 3 years. In contrast, patients treated with the B-cell lymphoma 2 (BCL2) inhibitor venetoclax exhibited substantial reductions in clonal frequencies, approaching molecular eradication. Deep whole-exome sequencing revealed minimal genomic progression in the ibrutinib group, maintaining somatic drivers and variant allele frequencies (VAF) above 0.2 throughout treatment. At the single-cell level, the NF-κB pathway inhibition and apoptotic signals were detected or even augmented during treatment in ibrutinib-treated patients. These findings may corroborate the role of ibrutinib in stabilizing the genomic landscape of CLL cells, preventing significant genomic evolution despite maintaining a high clonal burden within the residual B-cell compartment.

Therapeutic advances in the targeting of ROR1 in hematological cancers

Receptor tyrosine kinases (RTKs) are key cell surface receptors involved in cell communication and signal transduction, with great importance in cell growth, differentiation, survival, and metabolism. Dysregulation of RTKs, such as EGFR, VEGFR, HER2 or ROR, could lead to various diseases, particularly cancers. ROR1 has emerged as a promising target in hematological malignancies. The development of ROR1 targeted therapies is continuously growing leading to remarkable novel therapeutical approaches using mAbs, antibody-drug conjugates, several small molecules or CAR T cells which have shown encouraging preclinical results. In the hematological field, mAbs, small molecules, BiTEs or CAR T cell therapies displayed promising outcomes with the clinical trials data encouraging the use of anti-ROR1 therapies. This paper aims to offer a comprehensive analysis of the current landscape of ROR1-targeted therapies in hematological malignancies marking the innovative approaches with promising preclinical and clinical. Offering a better understanding of structural and functional aspects of ROR1 could lead to new perspectives in targeting a wide spectrum of malignancies.

Apoptosis: A Comprehensive Overview of Signaling Pathways, Morphological Changes, and Physiological Significance and Therapeutic Implications

Cell survival and death are intricately governed by apoptosis, a meticulously controlled programmed cell death. Apoptosis is vital in facilitating embryonic development and maintaining tissue homeostasis and immunological functioning. It is a complex interplay of intrinsic and extrinsic signaling pathways that ultimately converges on executing the apoptotic program. The extrinsic pathway is initiated by the binding of death ligands such as TNF-α and Fas to their respective receptors on the cell surface. In contrast, the intrinsic pathway leads to increased permeability of the outer mitochondrial membrane and the release of apoptogenic factors like cytochrome c, which is regulated by the Bcl-2 family of proteins. Once activated, these pathways lead to a cascade of biochemical events, including caspase activation, DNA fragmentation, and the dismantling of cellular components. Dysregulation of apoptosis is implicated in various disorders, such as cancer, autoimmune diseases, neurodegenerative disorders, and cardiovascular diseases. This article focuses on elucidating the molecular mechanisms underlying apoptosis regulation, to develop targeted therapeutic strategies. Modulating apoptotic pathways holds immense potential in cancer treatment, where promoting apoptosis in malignant cells could lead to tumor regression. This article demonstrates the therapeutic potential of targeting apoptosis, providing options for treating cancer and neurological illnesses. The safety and effectiveness of apoptosis-targeting drugs are being assessed in ongoing preclinical and clinical trials (phase I-III), opening the door for more effective therapeutic approaches and better patient outcomes.

MicroRNAs as Promising Therapeutic Agents Against Prostate Cancer Resistant to Castration-Where Are We Now?

MicroRNAs are a conserved class of small, tissue-specific, non-coding RNAs that regulate gene expression to preserve cellular homeostasis. Proper miRNA expression is crucial for physiological balance because it affects numerous genetic pathways, including cell cycle control, proliferation, and apoptosis, through gene expression targeting. Deregulated miRNA expression has been implicated in several cancer types, including prostate cancer (PC), acting as tumor suppressors or oncogenes. Despite the availability of promising therapies to control tumor growth and progression, effective diagnostic and therapeutic strategies for different types of cancer are still lacking. PC continues to be a significant health challenge, particularly its castration-resistant (CRPC) form, which presents major therapeutic obstacles because of its resistance to conventional androgen deprivation treatments. This review explores miRNAs' critical roles in gene regulation and cancer biology, as well as various miRNA delivery systems, highlighting their potential and the challenges in effectively targeting cancer cells. It aims to provide a comprehensive overview of the status of miRNA research in the fight against CRPC, summarizing miRNA-based therapies' successes and limitations. It also highlights the promise of miRNAs as therapeutic agents for CRPC, underlining the need for further research to overcome existing challenges and move these therapies toward clinical applications.

Novel nanoformulation for enhanced amphotericin B efficacy and sustained release using vetiver root cellulose nanofibers against Candida albicans

The formidable antifungal agent, Amphotericin B, is well-known for its potency; however, its clinical application has been significantly limited due to toxicity and poor solubility. This study aims to address these challenges by developing and evaluating a novel nano-cellulose-based formulation of Amphotericin B to enhance its efficacy. Amphotericin B was encapsulated within cellulose nanofibers at varying ratios to optimize formulation parameters, including drug concentration, particle size, zeta potential, and entrapment efficiency. Notably, a composition ratio of 10:1 of cellulose nanofibers to Amphotericin B achieved an impressive encapsulation efficiency of 96.64%. Subsequent physicochemical characterizations employing techniques such as FTIR, DLS, XRD, and SEM provided insights into structural attributes and interactions within formulation. Controlled and extended-release profiles were observed at various physiological pH levels, with the Korsmeyer-Peppas model showing the highest correlation, indicating predominant drug diffusion. Importantly, nanoformulation demonstrated non-toxicity to A431 cells and human erythrocytes up to a maximum concentration of 20 μg/ml, as corroborated by MTT and hemolysis assays. Furthermore, antimicrobial susceptibility and efficacy assessments, conducted using agar disc diffusion and broth micro-dilution methods, revealed enhanced inhibition of Candida albicans growth. The nanoformulation produced a larger diameter of the inhibition zone (DIZ) of 19.66 mm compared to a DIZ of 16.33 mm for Amphotericin B alone. Impressively, the nanoformulation exhibited a minimum inhibitory concentration (MIC) of 25 μg/ml against Candida albicans, underscoring its heightened efficacy. Additionally, the formulation's ability to improve the targetability and bioavailability of Amphotericin B holds promise for enhancing its antifungal effectiveness while reducing associated toxicity.

Intelligent guide RNA: dual toehold switches for modulating luciferase in the presence of trigger RNA

The CRISPR system finds extensive application in molecular biology, but its continuous activity can yield adverse effects. Leveraging programmable CRISPR/Cas9 function via nano-device mediation effectively mitigates these drawbacks. The integration of RNA-sensing platforms into CRISPR thus empowers it as a potent tool for processing internal cell data and modulating gene activity. Here, an intelligent guide RNA-a cis-repressed gRNA synthetic circuit enabling efficient recognition of specific trigger RNAs-is developed. This platform carries two toehold switches and includes an inhibited CrRNA sequence. In this system, the presence of cognate trigger RNA promotes precise binding to the first toehold site, initiating a cascade that releases CrRNA to target a reporter gene (luciferase) in this study. Decoupling the CrRNA segment from the trigger RNA enhances the potential of this genetic logic circuit to respond to specific cellular circumstances, offering promise as a synthetic biology platform.

Stage-specific modulation of multinucleation, fusion, and resorption by the long non-coding RNA DLEU1 and miR-16 in human primary osteoclasts

Osteoclasts are the only cells able to resorb all the constituents of the bone matrix. While the modulation of osteoclast activity is well established for preventing bone-related diseases, there is an increasing demand for novel classes of anti-resorption agents. Herein, we investigated non-coding RNA molecules and proposed DLEU1 and miR-16 as potential candidates for modulating osteoclast functions. DLEU1 and miR-16 target cell fusion at both the early and late stages of osteoclastogenesis but operate through independent pathways. DLEU1 silencing hinders the fusion process, leading to abrogation of the phagocytic cup fusion modality and a reduction in the fusion events between mononucleated precursors and multinucleated osteoclasts, while miR-16 influences monocyte-to-osteoclast differentiation, impairing osteoclasts formation but not the number of nuclei at early stages. On the other hand, using these non-coding RNAs to engineer mature osteoclasts has implications for bone resorption. Both DLEU1 and miR-16 influence the speed of resorption in pit-forming osteoclasts, without affecting the resorbed area. However, the impact of increasing miR-16 levels extends more broadly, affecting trench-forming osteoclasts as well, leading to a reduction in their percentage, speed, and resorbed area. These findings offer potential new therapeutic targets to ameliorate bone destruction in skeletal diseases.

Decoding the intricacies: a comprehensive analysis of microRNAs in the pathogenesis, diagnosis, prognosis and therapeutic strategies for COVID-19

The pandemic of coronavirus disease-19 (COVID-19), provoked by the appearance of a novel coronavirus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), required a worldwide healthcare emergency. This has elicited an immediate need for accelerated research into its mechanisms of disease, criteria for diagnosis, methods for forecasting outcomes, and treatment approaches. microRNAs (miRNAs), are diminutive RNA molecules, that are non-coding and participate in gene expression regulation post-transcriptionally, having an important participation in regulating immune processes. miRNAs have granted substantial interest in their impact on viral replication, cell proliferation, and modulation of how the host's immune system responds. This narrative review delves into host miRNAs' multifaceted roles within the COVID-19 context, highlighting their involvement in disease progression, diagnostics, and prognostics aspects, given their stability in biological fluids and varied expression profiles when responding to an infection. Additionally, we discuss complicated interactions between SARS-CoV-2 and host cellular machinery facilitated by host miRNAs revealing how dysregulation of host miRNA expression profiles advances viral replication, immune evasion, and inflammatory responses. Furthermore, it investigates the potential of host miRNAs as therapeutic agents, whether synthetic or naturally occurring, which could be harnessed to either mitigate harmful inflammation or enhance antiviral responses. However, searching more deeply is needed to clarify how host's miRNAs are involved in pathogenesis of COVID-19, its diagnosis processes, prognostic assessments, and treatment approaches for patients.

Elucidating gastric cancer mechanisms and therapeutic potential of Adociaquinone A targeting EGFR: A genomic analysis and Computer Aided Drug Design (CADD) approach

Gastric cancer predominantly adenocarcinoma, accounts for over 85% of gastric cancer diagnoses. Current therapeutic options are limited, necessitating the discovery of novel drug targets and effective treatments. The Affymetrix gene expression microarray dataset (GSE64951) was retrieved from NCBI-GEO data normalization and DEGs identification was done by using R-Bioconductor package. Gene Ontology (GO) analysis of DEGs was performed using DAVID. The protein-protein interaction network was constructed by STRING database plugin in Cytoscape. Subclusters/modules of important interacting genes in main network were extracted by using MCODE. The hub genes from in the network were identified by using Cytohubba. The miRNet tool built a hub gene/mRNA-miRNA network and Kaplan-Meier-Plotter conducted survival analysis. AutoDock Vina and GROMACS MD simulations were used for docking and stability analysis of marine compounds against the 5CNN protein. Total 734 DEGs (507 up-regulated and 228 down-regulated) were identified. Differentially expressed genes (DEGs) were enriched in processes like cell-cell adhesion and ATP binding. Eight hub genes (EGFR, HSPA90AA1, MAPK1, HSPA4, PPP2CA, CDKN2A, CDC20, and ATM) were selected for further analysis. A total of 23 miRNAs associated with hub genes were identified, with 12 of them targeting PPP2CA. EGFR displayed the highest expression and hazard rate in survival analyses. The kinase domain of EGFR (PDBID: 5CNN) was chosen as the drug target. Adociaquinone A from Petrosia alfiani, docked with 5CNN, showed the lowest binding energy with stable interactions across a 50 ns MD simulation, highlighting its potential as a lead molecule against EGFR. This study has identified crucial DEGs and hub genes in gastric cancer, proposing novel therapeutic targets. Specifically, Adociaquinone A demonstrates promising potential as a bioactive drug against EGFR in gastric cancer, warranting further investigation. The predicted miRNA against the hub gene/proteins can also be used as potential therapeutic targets.

miR-497 Target Gene Regulatory Network in Angiosarcoma

Angiosarcoma is a vascular sarcoma that is highly aggressive and metastatic. Because of its rarity, treatment options for patients are limited. Therefore, more research is needed to identify possible therapeutic vulnerabilities. We previously found that conditional deletion of Dicer1 drives angiosarcoma development in mice. Given the role of DICER1 in canonical miRNA biogenesis, this suggests that miRNA loss is important in angiosarcoma development. After testing miRNAs previously suggested to have a tumor-suppressive role in angiosarcoma, miRNA-497-5p (miR-497) suppressed cell viability most significantly. We also found that miR-497 overexpression led to significantly reduced cell migration and tumor formation. To understand the mechanism of miR-497 in tumor suppression, we identified clinically relevant target genes using a combination of RNA-sequencing data in an angiosarcoma cell line, expression data from patients with angiosarcoma, and target prediction algorithms. We validated miR-497 direct regulation of cyclin-D2, cyclin-dependent kinase 6, and vesicle amine transport protein 1 (VAT1). One of these genes, VAT1, is an understudied protein that has been suggested to promote cell migration and metastasis in other cancers. Indeed, we find that pharmacologic inhibition of VAT1 with the natural product neocarzilin A reduces angiosarcoma migration. Implications: This work supports the potent tumor-suppressive abilities of miR-497 in angiosarcoma, providing evidence for its potential as a therapeutic agent, and provides insight into the mechanisms of tumor suppression through analysis of the target gene regulatory network of miR-497.

Biomechanic, proteomic and miRNA transcriptional changes in the trabecular meshwork of primates injected with intravitreal triamcinolone

Although biomechanical changes of the trabecular meshwork (TM) are important to the pathogenesis of glucocorticoids-induced ocular hypertension (GC-OHT), there is a knowledge gap in the underlying molecular mechanisms of the development of it. In this study, we performed intravitreal triamcinolone injection (IVTA) in one eye of 3 rhesus macaques. Following IVTA, we assessed TM stiffness using atomic force microscopy and investigated changes in proteomic and miRNA expression profiles. One of 3 macaques developed GC-OHT with a difference in intraocular pressure of 4.2 mmHg and a stiffer TM with a mean increase in elastic moduli of 0.60 kPa versus the non-injected control eye. In the IVTA-treated eyes, proteins associated with extracellular matrix remodeling, cytoskeletal rearrangement, and mitochondrial oxidoreductation were significantly upregulated. The significantly upregulated miR-29b and downregulated miR-335-5p post-IVTA supported the role of oxidative stress and mitophagy in the GC-mediated biomechanical changes in TM, respectively. The significant upregulation of miR-15/16 cluster post-IVTA may indicate a resultant TM cell apoptosis contributing to the increase in outflow resistance. Despite the small sample size, these results expand our knowledge of GC-mediated responses in the TM and furthermore, may help explain steroid responsiveness in clinical settings.

Effect of Crocin and Crocetin Compared to Cyclophosphamide on the Expression Level of miRNA-16-1 in a B Cell Transformed with EBV Virus Cell Line

INTRODUCTION

Crocin and Crocetin are compounds that have shown promising therapeutic potentials in various medical contexts. To date, the effect of crocin and crocetin on the expression level of miRNA-16-1 in Epstein Barr Virus (EBV)-induced lymphoma has not been investigated. This research delved into a comparative analysis of the cytotoxic effects of crocin and crocetin compared to cyclophosphamide, the main drug used in the treatment of lymphoma and PTLD, on B-cell lymphoma infected with EBV (cell line CO 88BV59-1). Additionally, the study examines the changes in miRNA-16-1 expression following these treatments in this cell line.

MATERIALS AND METHODS

CO 88BV59-1 LCL cells were treated with crocin, crocetin (0.2 to 200 μM), and cyclophosphamide (0.05 to 50 μM) for 72 hours. Cell viability and apoptosis were assessed using resazurin and Annexin V/PI techniques, respectively. Additionally, the expression of miRNA-16-1-3p and miRNA-16-1-5p was determined using the Real-Time PCR method. The data were analyzed using one-way analysis of variance (ANOVA) with Tukey's multiple comparisons post-hoc test.

RESULTS

Crocin and crocetin inhibited the proliferation and apoptosis caused by EBV-infected cells in a dose- and time-dependent manner (P<0.05). The expression levels of miRNA-16-1-3p and miRNA-16-1-5p remained unchanged in cells treated with crocin and crocetin.

CONCLUSION

The study found that the cytotoxic effect of Crocin, Crocetin, and Cyclophosphamide on CO 88BV59-1 LCL is independent of the expression level of miRNA-16-1. The results showed a reduction in cell survival and an increase in cell death.

Cognitive Dysfunction and Exercise: From Epigenetic to Genetic Molecular Mechanisms

Maintaining good health is crucial, and exercise plays a vital role in achieving this goal. It offers a range of positive benefits for cognitive function, regardless of age. However, as our population ages and life expectancy increases, cognitive impairment has become a prevalent issue, often coexisting with age-related neurodegenerative conditions. This can result in devastating consequences such as memory loss, difficulty speaking, and confusion, greatly hindering one's ability to lead an ordinary life. In addition, the decrease in mental capacity has a significant effect on an individual's physical and emotional well-being, greatly reducing their overall level of contentment and causing a significant financial burden for communities. While most current approaches aim to slow the decline of cognition, exercise offers a non-pharmacological, safe, and accessible solution. Its effects on cognition are intricate and involve changes in the brain's neural plasticity, mitochondrial stability, and energy metabolism. Moreover, exercise triggers the release of cytokines, playing a significant role in the body-brain connection and its impact on cognition. Additionally, exercise can influence gene expression through epigenetic mechanisms, leading to lasting improvements in brain function and behavior. Herein, we summarized various genetic and epigenetic mechanisms that can be modulated by exercise in cognitive dysfunction.

MicroRNA Profiling as a Predictive Indicator for Time to First Treatment in Chronic Lymphocytic Leukemia: Insights from the O-CLL1 Prospective Study

A "watch and wait" strategy, delaying treatment until active disease manifests, is adopted for most CLL cases; however, prognostic models incorporating biomarkers have shown to be useful to predict treatment requirement. In our prospective O-CLL1 study including 224 patients, we investigated the predictive role of 513 microRNAs (miRNAs) on time to first treatment (TTFT). In the context of this study, six well-established variables (i.e., Rai stage, beta-2-microglobulin levels, IGVH mutational status, del11q, del17p, and NOTCH1 mutations) maintained significant associations with TTFT in a basic multivariable model, collectively yielding a Harrell's C-index of 75% and explaining 45.4% of the variance in the prediction of TTFT. Concerning miRNAs, 73 out of 513 were significantly associated with TTFT in a univariable model; of these, 16 retained an independent relationship with the outcome in a multivariable analysis. For 8 of these (i.e., miR-582-3p, miR-33a-3p, miR-516a-5p, miR-99a-5p, and miR-296-3p, miR-502-5p, miR-625-5p, and miR-29c-3p), a lower expression correlated with a shorter TTFT, whereas in the remaining eight (i.e., miR-150-5p, miR-148a-3p, miR-28-5p, miR-144-5p, miR-671-5p, miR-1-3p, miR-193a-3p, and miR-124-3p), the higher expression was associated with shorter TTFT. Integrating these miRNAs into the basic model significantly enhanced predictive accuracy, raising the Harrell's C-index to 81.1% and the explained variation in TTFT to 63.3%. Moreover, the inclusion of the miRNA scores enhanced the integrated discrimination improvement (IDI) and the net reclassification index (NRI), underscoring the potential of miRNAs to refine CLL prognostic models and providing insights for clinical decision-making. In silico analyses on the differently expressed miRNAs revealed their potential regulatory functions of several pathways, including those involved in the therapeutic responses. To add a biological context to the clinical evidence, an miRNA-mRNA correlation analysis revealed at least one significant negative correlation between 15 of the identified miRNAs and a set of 50 artificial intelligence (AI)-selected genes, previously identified by us as relevant for TTFT prediction in the same cohort of CLL patients. In conclusion, the identification of specific miRNAs as predictors of TTFT holds promise for enhancing risk stratification in CLL to predict therapeutic needs. However, further validation studies and in-depth functional analyses are required to confirm the robustness of these observations and to facilitate their translation into meaningful clinical utility.