Construction of miRNA-target networks using microRNA profiles of CVB3-infected HeLa cells

Molecular Biomarkers of Canine Reproductive Functions

The aim of the current study is to review potential molecular biomarker substances selected so far as useful for assessing the quality of dog semen. Proteins, lipids, carbohydrates, and ions can serve as molecular biomarkers of reproductive functions (BRFs) for evaluating male reproductive health and identifying potential risk factors for infertility or reproductive disorders. Evaluation of BRF levels in semen samples or reproductive tissues may provide insights into the underlying causes of infertility, such as impaired sperm function, abnormal sperm-egg interaction, or dysfunction of the male reproductive tract. Molecular biomarker proteins may be divided into two groups: proteins that are well-studied, such as A-kinase anchoring proteins (AKAPs), albumins (ALBs), alkaline phosphatase (ALPL), clusterin (CLU), canine prostate-specific esterase (CPSE), cysteine-rich secretory protein 2 (CRISP2), lactotransferrin (LTF), metalloproteinases (MMPs), and osteopontin (OPN) and proteins that are not well-studied. Non-protein markers include lipid-based substances (fatty acids, phosphatidylcholine), carbohydrates (glycosaminoglycans), and ions (zinc, calcium). Assessing the levels of BRFs in semen samples may provide valuable information for breeding management and reproductive assessments in dogs. This review systematizes current knowledge that could serve as a starting point for developing practical tests with the use of biomarkers of canine reproductive functions and their predictive value for assisted reproductive technique outcomes and semen preservation.

Age-Dependent Variations in Functional Quality and Proteomic Characteristics of Canine (Canis lupus familiaris) Epididymal Spermatozoa

Increased male age is associated with a significant reduction in semen quality. Little is known about the sperm proteome changes resulting from the aging process. This study aimed to investigate the relationship between the functional quality and proteome of epididymal spermatozoa of dogs that were differing in age. The study was conducted on 30 male dogs that were divided into three age groups. G1—12 to 41 months old, G2—42 to 77 months old, and G3—78 to 132 months old. The sperm samples were assessed using a computer-assisted semen analysis (CASA). The epididymal sperm proteins were analyzed using gel electrophoresis (SDS-PAGE), nano-liquid chromatography coupled to quadrupole time of flight mass spectrometry (NanoUPLC-Q-TOF/MS) and bioinformatic tools. The sperm quality parameters were significantly lower in older dogs. NanoUPLC-Q-TOF/MS identification resulted in 865 proteins that were found in the G1, 472 in G2, and 435 in G3. There were seven proteins that were present in all three age groups, and four of them (ACTB, CE10, NPC2, CRISP2) showed significant changes among the studied groups. Age-dependent variations were detected in the sperm proteome composition and were related to important metabolite pathways, which might suggest that several proteins are implicated in sperm maturation and could be potential aging biomarkers.

DYRK1A inhibitors for disease therapy: Current status and perspectives

Dual-specificity tyrosine phosphorylation-regulated kinase 1 A (DYRK1A) is a conserved protein kinase that plays essential roles in various biological processes. It is located in the region q22.2 of chromosome 21, which is involved in the pathogenesis of Down syndrome (DS). Moreover, DYRK1A has been shown to promote the accumulation of amyloid beta (Aβ) peptides leading to gradual Tau hyperphosphorylation, which contributes to neurodegeneration. Additionally, alterations in the DRK1A expression are also associated with cancer and diabetes. Recent years have witnessed an explosive increase in the development of DYRK1A inhibitors. A variety of novel DYRK1A inhibitors have been reported as potential treatments for human diseases. In this review, the latest therapeutic potential of DYRK1A for different diseases and the novel DYRK1A inhibitors discoveries are summarized, guiding future inhibitor development and structural optimization.

The circRNA circSIAE Inhibits Replication of Coxsackie Virus B3 by Targeting miR-331-3p and Thousand and One Amino-Acid Kinase 2

Coxsackie virus B3 (CVB3), an enterovirus, is the main pathogen causing viral myocarditis, pericarditis, hepatitis and other inflammation-related diseases. Non-coding RNAs with a closed loop molecular structure, called circular RNAs (circRNAs), have been shown to be involved in multiple virus-related processes, but roles and mechanisms in CVB3 infection have not been systematically studied. In this study, when HeLa cells were infected with CVB3, the expression of hsa_circ_0000367 (circSIAE) was significantly decreased as demonstrated by real-time quantitative PCR assays. We found that circSIAE downregulated the expression of miR-331-3p through direct binding and inhibited the replication of CVB3 in HeLa and 293T cells. The analysis of signals downstream of miR-331-3p suggested that miR-331-3p promotes CVB3 replication, viral plaque formation and fluorescent virus cell production through interactions with the gene coding for thousand and one amino-acid kinase 2 (TAOK2). In conclusion, this study found that circSIAE can target TAOK2 through sponge adsorption of miR-331-3p to inhibit the replication and proliferation of CVB3 virus, providing an early molecular target for the diagnosis of CVB3 infection.

Transcriptomic analysis reveals that coxsackievirus B3 Woodruff and GD strains use similar key genes to induce FoxO signaling pathway activation in HeLa cells

Coxsackievirus B3 (CVB3) is a major cause of viral myocarditis in humans. Although there have been studies on CVB3 infection and pathogenesis, the precise disease mechanism is still not clear. In this study, we used RNA-seq technology to compare the transcriptomic profile of virus-infected HeLa cells to that of uninfected cells to identify key genes involved in host-virus interaction. For this, two CVB3 strains, CVB3 Woodruff, an experimental strain, and GD16-69/GD/CHN/2016, a clinical strain, were selected to examine the common mechanisms underlying their infection. Transcriptomic profiles revealed increased expression of the cell cycle genes CCNG2, GADD45B, PIM1, RBM15, KLF10, and RIOK3 and decreased expression of CYBA. The autophagy-related genes ATG12 and YOD1 were found to be upregulated, while the expression of SOD2 and XPO1 increased slightly in infected cells, and only a minor change was observed in GABARAP expression. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed the FoxO signaling pathway to be enriched and showed a close interaction with differentially expressed genes (DEGs) in the protein-protein interaction network. DEGs associated with related pathways such as cell cycle, autophagy, and oxidative stress resistance were also confirmed by qRT-PCR. In summary, the FoxO signaling pathway was activated during infection with both CVB3 strains and was found to have a regulatory role in downstream pathways such as cell cycle, autophagy, oxidative stress resistance, and the antiviral immune response.

Inter-regulatory role of microRNAs in interaction between viruses and stem cells

MicroRNAs (miRNAs) are well known for post-transcriptional regulatory ability over specific mRNA targets. miRNAs exhibit temporal or tissue-specific expression patterns and regulate the cell and tissue developmental pathways. They also have determinative roles in production and differentiation of multiple lineages of stem cells and might have therapeutic advantages. miRNAs are a part of some viruses’ regulatory machinery, not a byproduct. The trace of miRNAs was detected in the genomes of viruses and regulation of cell reprograming and viral pathogenesis. Combination of inter-regulatory systems has been detected for miRNAs during viral infections in stem cells. Contraction between viruses and stem cells may be helpful in therapeutic tactics, pathogenesis, controlling viral infections and defining stem cell developmental strategies that is programmed by miRNAs as a tool. Therefore, in this review we intended to study the inter-regulatory role of miRNAs in the interaction between viruses and stem cells and tried to explain the advantages of miRNA regulatory potentials, which make a new landscape for future studies.

Proteomics analysis of tissue small extracellular vesicles reveals protein panels for the reoccurrence prediction of colorectal cancer

Many stage II/III colorectal cancer (CRC) patients might relapse after routine treatment and there is a great need of reliable biomarkers for predicting its reoccurrence risk. Small extracellular vesicles (sEVs) could regulate many pathophysiological processes of diseases, which are promising source for biomarker discovery. In this study, we implemented a MS-based workflow that utilizes data-dependent acquisition (DDA) for discovery and parallel reaction monitoring (PRM) for validation of high relapse risk related biomarkers. We compared the protein profiling of sEVs from CRC tissues and paired adjacent tissues in relapsed group (n = 5) and non-relapsed group (n = 5). 417 and 1140 proteins were differentially expressed between the tumor tissues and adjacent tissues in relapsed group and non-relapsed group, respectively. Bioinformatics analysis showed that immunity of the relapsed patients (Z-score - 0.69) was relatively poorer than the non-relapsed patients (Z-score 2.59), while chronic inflammatory response was activated (Z-score 3.0), which might enhance the reoccurrence risk. Four proteins (HLA-DPA1, S100P, NUP205, PCNA) showed significant expressions in the adjacent tissues of the relapsed group by PRM validation. ROC analysis of HLA-DPA1 (AUC = 0.96) achieved the best classification accuracy in separating the relapsed group and the non-relapsed group. Our data demonstrate that tissue-derived sEVs harbor prognostic proteomic signatures of CRC. SIGNIFICANCE: In this research, our proteomics analysis of tissue sEVs revealed that poor immunity as well as chronic inflammatory of the CRC relapsed patient likely lead to poor prognosis and high risk of reoccurrence. The significant expression levels of four proteins (HLA-DPA1, S100P, NUP205, PCNA) in the adjacent tissues of the relapsed group might be used to predict the risk of relapse in postoperative follow-ups.

miRGTF-net: Integrative miRNA-gene-TF network analysis reveals key drivers of breast cancer recurrence

Analysis of regulatory networks is a powerful framework for identification and quantification of intracellular interactions. We introduce miRGTF-net, a novel tool for construction of miRNA-gene-TF networks. We consider multiple transcriptional and post-transcriptional interaction types, including regulation of gene and miRNA expression by transcription factors, gene silencing by miRNAs, and co-expression of host genes with their intronic miRNAs. The underlying algorithm uses information on experimentally validated interactions as well as integrative miRNA/mRNA expression profiles in a given set of samples. The latter ensures simultaneous tissue-specificity and biological validity of interactions. We applied miRGTF-net to paired miRNA/mRNA-sequencing data of breast cancer samples from The Cancer Genome Atlas (TCGA). Together with topological analysis of the constructed network we showed that considered players can form reliable prognostic gene signatures for ER-positive breast cancer. A number of signatures demonstrated remarkably high accuracy on transcriptomic data obtained by both microarrays and RNA sequencing from several independent patient cohorts. Furthermore, an essential part of prognostic genes were identified as direct targets of transcription factor E2F1. The putative interplay between estrogen receptor alpha and E2F1 was suggested as a potential recurrence factor in patients treated with tamoxifen. Source codes of miRGTF-net are available at GitHub (https://github.com/s-a-nersisyan/miRGTF-net).

Essential Role of Non-Coding RNAs in Enterovirus Infection: From Basic Mechanisms to Clinical Prospects

Enteroviruses (EVs) are common RNA viruses that can cause various types of human diseases and conditions such as hand, foot, and mouth disease (HFMD), myocarditis, meningitis, sepsis, and respiratory disorders. Although EV infections in most patients are generally mild and self-limiting, a small number of young children can develop serious complications such as encephalitis, acute flaccid paralysis, myocarditis, and cardiorespiratory failure, resulting in fatalities. Established evidence has suggested that certain non-coding RNAs (ncRNAs) such as microRNAs (miRNAs), long ncRNAs (lncRNAs), and circular RNAs (circRNAs) are involved in the occurrence and progression of many human diseases. Recently, the involvement of ncRNAs in the course of EV infection has been reported. Herein, the authors focus on recent advances in the understanding of ncRNAs in EV infection from basic viral pathogenesis to clinical prospects, providing a reference basis and new ideas for disease prevention and research directions.

Circular RNA profiles and the potential involvement of down-expression of hsa_circ_0001360 in cutaneous squamous cell carcinogenesis

Circular RNAs (circRNAs) act as sponges of noncoding RNAs and have been implicated in many pathophysiological processes, including tumor development and progression. However, their roles in cutaneous squamous cell carcinoma (cSCC) are not yet well understood. This study aimed to identify differentially expressed circRNAs and their potential functions in cutaneous squamous cell carcinogenesis. The expression profiles of circRNAs in three paired cSCC and adjacent nontumorous tissues were detected with RNA sequencing and bioinformatics analysis. The candidate circRNAs were validated by PCR, Sanger sequencing and quantitative RT‐PCR in another five matched samples. The biological functions of circRNAs in SCL‐1 cells were assessed using circRNA silencing and overexpression, 3‐(4,5‐dimethylthiazol‐2‐yl)‐5‐(3‐carboxymethoxyphenyl)‐2‐(4‐sulfophenyl)‐2H‐tetrazolium inner salt (MTS), flow cytometry, transwell and colony formation assays. In addition, the circRNA–miRNA–mRNA interaction networks were predicted by bioinformatics. In summary, 1115 circRNAs, including 457 up‐regulated and 658 down‐regulated circRNAs (fold change ≥ 2 and P < 0.05), were differentially expressed in cSCC compared with adjacent nontumorous tissues. Of four selected circRNAs, two circRNAs (hsa_circ_0000932 and hsa_circ_0001360) were confirmed to be significantly decreased in cSCC using PCR, Sanger sequencing and quantitative RT‐PCR. Furthermore, hsa_circ_0001360 silencing was found to result in a significant increase of the proliferation, migration and invasion but a significant decrease of apoptosis in SCL‐1 cells in vitro, whereas hsa_circ_0001360 overexpression showed the opposite regulatory effects. hsa_circ_0001360 was predicted to interact with five miRNAs and their corresponding genes. In conclusion, circRNA dysregulation may play a critical role in carcinogenesis of cSCC, and hsa_circ_0001360 may have potential as a biomarker for cSCC.

LncRNA Snhg8 attenuates microglial inflammation response and blood-brain barrier damage in ischemic stroke through regulating miR-425-5p mediated SIRT1/NF-κB signaling

Increasing studies have indicated that abnormal expressed long noncoding RNAs (lncRNAs) play a vital role in ischemic stroke. Small nucleolar RNA host gene 8 (Snhg8), a member of lncRNAs, has been found to induce neuronal apoptosis in chronic cerebral ischemia models. Here, we aim to explore the function and molecular mechanism of Snhg8 in modulating microglial inflammation as well as brain microvascular endothelial cell (BMEC) damage following ischemic injury. Our data suggested that Snhg8 was low-expressed in the brain tissues of mice that underwent middle cerebral artery occlusion (MCAO) surgery and oxygen-glucose deprivation (OGD)-treated primary microglia and BMECs. Gain- or loss-of function approaches found that Snhg8 upregulation not only attenuated ischemic induced inflammatory response in microglia but also relieved BMECs injury both in vitro and in vivo. Furthermore, we conducted a bioinformatics analysis to explore the underlying mechanism of Snhg8. The results indicated that Snhg8 served as a competitive endogenous RNA by sponging miR-425-5p, which was proved to promote microglial inflammation and BMECs injury by targeting sirtuin1 (SIRT1)-mediated nuclear factor-κB (NF-κB) pathway. Overall, these results revealed that the Snhg8/miR-425-5p/SIRT1/NF-κB axis plays a critical role in the regulation of cerebral ischemia-induced microglial inflammation and brain-blood barrier damage.