An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues

Liquid biopsies in cancer

Cancer ranks among the most lethal diseases worldwide. Tissue biopsy is currently the primary method for the diagnosis and biological analysis of various solid tumors. However, this method has some disadvantages related to insufficient tissue specimen collection and intratumoral heterogeneity. Liquid biopsy is a noninvasive approach for identifying cancer-related biomarkers in peripheral blood, which allows for repetitive sampling across multiple time points. In the field of liquid biopsy, representative biomarkers include circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), and exosomes. Many studies have evaluated the prognostic and predictive roles of CTCs and ctDNA in various solid tumors. Although these studies have limitations, the results of most studies appear to consistently demonstrate the correlations of high CTC counts and ctDNA mutations with lower survival rates in cancer patients. Similarly, a reduction in CTC counts throughout therapy may be a potential prognostic indicator related to treatment response in advanced cancer patients. Moreover, the biochemical characteristics of CTCs and ctDNA can provide information about tumor biology as well as resistance mechanisms against targeted therapy. This review discusses the current clinical applications of liquid biopsy in cancer patients, emphasizing its possible utility in outcome prediction and treatment decision-making.

Mix-and-Read Digital MicroRNA Analysis Based on Flow Cytometric Counting of Target-Clicked Nanobead Dimer

A one-step, enzyme-free, and highly sensitive digital microRNA (miRNA) assay is rationally devised based on flow cytometric counting of target miRNA-clicked nanobead dimers via a facile mix-and-read manner. In this strategy, highly efficient miRNA-sandwiched click chemical ligation of two DNA probes may remarkably stabilize and boost the dimer formation between two kinds of fluorescence-coded nanobeads, and the number of as-produced bead dimers will be target dose-responsive, particularly when the trace number of miRNA is much less than that of employed nanobeads. Finally, each fluorescence-coded bead dimer can be easily identified and digitally counted by a powerful flow cytometer (FCM) and accordingly, the amount of target miRNA can be accurately quantified in a digital way. This new digital miRNA assay can be accomplished with a facile mix-and-read operation just by simply mixing the target miRNA with two kinds of preprepared DNA probe-functionalized nanobeads, which do not require any nucleic acid amplification, purification, and complex operation procedures. In spite of the extremely simple one-step operation, benefiting from the low-background but high target-mediated click ligation efficiency, and the powerfully digital statistical capability of FCM, this strategy achieves high sensitivity with a quite low detection limit of 5.2 fM target miRNA as well as high specificity and good generality for miRNA analysis, pioneering a new direction for fabricating digital bioassays.

Hormonal regulation of miRNA during mammary gland development

The mammary gland is a unique organ as most of its development occurs after birth through stages of proliferation, differentiation and apoptosis that are tightly regulated by circulating hormones and growth factors. Throughout development, hormonal cues induce the regulation of different pathways, ultimately leading to differential transcription and expression of genes involved in this process, but also in the activation or inhibition of post-transcriptional mechanisms of regulation. However, the role of microRNAs (miRNAs) in the different phases of mammary gland remodeling is still poorly understood. The objectives of this study were to analyze the expression of miRNA in key stages of mammary gland development in mice and to determine whether it could be associated with hormonal variation between stages. To do so, miRNAs were isolated from mouse mammary glands at stages of adulthood, pregnancy, lactation and involution, and sequenced. Results showed that 490, 473, 419, and 460 miRNAs are detected in adult, pregnant, lactating and involuting mice, respectively, most of them being common to all four groups, and 58 unique to one stage. Most genes could be divided into six clusters of expression, including two encompassing the highest number of miRNA (clusters 1 and 3) and showing opposite profiles of expression, reaching a peak at adulthood and valley at lactation, or showing the lowest expression at adulthood and peaking at lactation. GO and KEGG analyses suggest that the miRNAs differentially expressed between stages influence the expression of targets associated with mammary gland homeostasis and hormone regulation. To further understand the links between miRNA expression and hormones involved in mammary gland development, miRNAs were then sequenced in breast cells exposed to estradiol, progesterone, prolactin and oxytocin. Four, 38, 24 and 66 miRNAs were associated with progesterone, estradiol, prolactin, and oxytocin exposure, respectively. Finally, when looking at miRNAs modulated by the hormones, differentially expressed during mammary gland development, and having a pattern of expression that could be correlated with the relative levels of hormones known to be found in vivo, 16 miRNAs were identified as likely regulated by circulating hormones. Overall, our study brings a better understanding of the regulation of miRNAs throughout mammary gland development and suggests that there is a relationship between their expression and the main hormones involved in mammary gland development. Future studies will examine this role more in detail.

MiRNAs as potential biomarkers in early breast cancer detection: a systematic review

Breast cancer remains a significant global health challenge, with high incidence and mortality rates. While mammography has contributed to declining mortality, its limitations in sensitivity and specificity for early detection, particularly in distinguishing between pure atypical ductal hyperplasia (ADH), ductal carcinoma in situ (DCIS), and invasive ductal carcinoma (IDC), highlight the need for more precise tools. Even with core needle biopsy (CNB), conclusive diagnoses often require surgical excision. This underscores the urgency for non-invasive biomarkers to improve early detection and differentiation, potentially reducing invasive procedures. Recent research has shifted focus from mRNA to microRNAs (miRNAs) as promising biomarkers for breast cancer screening. These small non-coding RNAs, which exhibit abnormal expression patterns in breast cancer patients' tissue and serum/plasma, play crucial roles in early breast cancer development by modulating proto-oncogenes or tumor suppressor genes at the post-transcriptional level. Notably, miRNAs such as miR-21, miR-155, and miR-200c are key regulators of cell proliferation and apoptosis, with the potential to distinguish between normal tissue and various stages of breast lesions, including ADH, DCIS, and IDC. Additionally, miRNAs in serum and plasma offer a non-invasive method to differentiate breast cancer stages. This review aims to consolidate current knowledge on early breast lesions and explore the potential of miRNAs as biomarkers for early breast cancer detection, which could enhance risk prediction and reduce reliance on invasive diagnostic procedures.

PNA-Functionalized, Silica Nanowires-Filled Glass Microtube for Ultrasensitive and Label-Free Detection of miRNA-21

MicroRNAs (miRNAs) are endogenous and noncoding single-stranded RNA molecules with a length of approximately 18-25 nucleotides, which play an undeniable role in early cancer screening. Therefore, it is very important to develop an ultrasensitive and highly specific method for detecting miRNAs. Here, we present a bottom-up assembly approach for modifying glass microtubes with silica nanowires (SiNWs) and develop a label-free sensing platform for miRNA-21 detection. The three-dimensional (3D) networks formed by SiNWs make them abundant and highly accessible sites for binding with peptide nucleic acid (PNA). As a receptor, PNA has no phosphate groups and exhibits an overall electrically neutral state, resulting in a relatively small repulsion between PNA and RNA, which can improve the hybridization efficiency. The SiNWs-filled glass microtube (SiNWs@GMT) sensor enables ultrasensitive, label-free detection of miRNA-21 with a detection limit as low as 1 aM at a detection range of 1 aM-100 nM. Noteworthy, the sensor can still detect miRNA-21 in the range of 102-108 fM in complex solutions containing 1000-fold homologous interference of miRNAs. The high anti-interference performance of the sensor enables it to specifically recognize target miRNA-21 in the presence of other miRNAs and distinguish 1-, 3-mismatch nucleotide sequences. Significantly, the sensor platform is able to detect miRNA-21 in the lysate of breast cancer cell lines (e.g., MCF-7 cells and MDA-MB-231 cells), indicating that it has good potential in the screening of early breast cancers.

Identification of Gene Expression in Different Stages of Breast Cancer with Machine Learning

Determining the tumor origin in humans is vital in clinical applications of molecular diagnostics. Metastatic cancer is usually a very aggressive disease with limited diagnostic procedures, despite the fact that many protocols have been evaluated for their effectiveness in prognostication. Research has shown that dysregulation in miRNAs (a class of non-coding, regulatory RNAs) is remarkably involved in oncogenic conditions. This research paper aims to develop a machine learning model that processes an array of miRNAs in 1097 metastatic tissue samples from patients who suffered from various stages of breast cancer. The suggested machine learning model is fed with miRNA quantitative read count data taken from The Cancer Genome Atlas Data Repository. Two main feature-selection techniques have been used, mainly Neighborhood Component Analysis and Minimum Redundancy Maximum Relevance, to identify the most discriminant and relevant miRNAs for their up-regulated and down-regulated states. These miRNAs are then validated as biological identifiers for each of the four cancer stages in breast tumors. Both machine learning algorithms yield performance scores that are significantly higher than the traditional fold-change approach, particularly in earlier stages of cancer, with Neighborhood Component Analysis and Minimum Redundancy Maximum Relevance achieving accuracy scores of up to 0.983 and 0.931, respectively, compared to 0.920 for the FC method. This study underscores the potential of advanced feature-selection methods in enhancing the accuracy of cancer stage identification, paving the way for improved diagnostic and therapeutic strategies in oncology.

Association of miR-146a-5p and miR-21-5p with Prognostic Features in Melanomas

BACKGROUND

Cutaneous melanoma (CM) is one of the most lethal tumors among skin cancers and its incidence is rising worldwide. Recent data support the role of microRNAs (miRNAs) in melanoma carcinogenesis and their potential use as disease biomarkers.

METHODS

We quantified the expression of miR-146a-5p and miR-21-5p in 170 formalin-fixed paraffin embedded (FFPE) samples of CM, namely 116 superficial spreading melanoma (SSM), 26 nodular melanoma (NM), and 28 lentigo maligna melanoma (LMM). We correlated miRNA expression with specific histopathologic features including Breslow thickness (BT), histological subtype, ulceration and regression status, and mitotic index.

RESULTS

miR-146a-5p and miR-21-5p were significantly higher in NM compared to SSM and LMM. The positive correlation between miR-146a-5p and miR-21-5p expression and BT was confirmed for both miRNAs in SSM. Considering the ulceration status, we assessed that individual miR-21-5p expression was significantly higher in ulcerated CMs. The increased combined expression of the two miRNAs was strongly associated with ulceration (p = 0.0093) and higher mitotic rate (≥1/mm2) (p = 0.0005). We demonstrated that the combination of two-miRNA expression and prognostic features (BT and ulceration) can better differentiate cutaneous melanoma prognostic groups, considering overall survival and time-to-relapse clinical outcomes. Specifically, miRNA expression can further stratify prognostic groups among patients with BT ≥ 0.8 mm but without ulceration. Our findings provide further insights into the characterization of CM with specific prognostic features. The graphical abstract was created with BioRender.com.

Effect of pre-treatment of melatonin on superovulation response, circulatory hormones, and miRNAs in goats during environmental heat stress conditions

Environmental heat stress has a deleterious impact on farm animal reproductive performance. The purpose of this study was to see how the addition of melatonin affected the efficacy of the superovulation regimen in goats in hot climatic conditions. Sixteen Shiba goats were synchronized and divided into two equal groups (n = 8, each): the melatonin group, which received a single S/C dose of melatonin, and a control group, treated with one ml of corn oil only. Ultrasonographic assessment of ovarian structures (Graafian follicles; GFs and corpus lutea; CLs) morphometry and hemodynamics were performed during the estrous phase of the superovulation (D0) and at day7 after ovulation (D7) of the superovulation regimen. The peripheral reproductive hormones were measured, and microRNAs were characterized. The mean diameter and the total-colored area of GFs during the D0 were significantly (P˂0.05) higher in the melatonin group (5.42 ± 0.11 mm and 1592.20 ± 45.26 pixels, respectively) compared to the control group (4.62 ± 0.12 mm and 1052.55 ± 29.47 pixels, respectively). Concentrations of LH and E2 increased significantly (P˂0.05) in the melatonin group (1.06 ± 0.06 ng/ml and 46.34 ± 2.77 pg/ml, respectively) compared to the control group (0.75 ± 0.12 ng/ml and 29.33 ± 1.89 pg/ml, respectively). At D7, the melatonin-received goats attained greater values in the mean count (6.75 ± 0.33, P˂0.005), diameters (6.08 ± 0.12 mm, P˂0.01), and total-colored area (17137.30 ± 128.53 pixels, P˂0.01) of detected CLs and progesterone concentrations (4.08 ± 0.24 ng/ml) compared to control goats (4.00 ± 0.28, 4.50 ± 0.19 mm, 11156.87 ± 117.90 pixels, and 2.90 ± 0.18 ng/ml respectively). MiRNA expression analysis was identified during both stages denoting several up and downregulated miRNA candidates among the studied groups. In conclusion, incorporating melatonin enhanced the efficiency of the superovulation regimen in goats under hot climatic conditions.

(Eu-MOF)-derived Smart luminescent sensing for Ultrasensitive on-site detection of MiR-892b

MicroRNAs (miRNAs) are important biomacromolecules used as biomarkers for the diagnosis of several diseases. However, current detection strategies are limited by expensive equipment and complicated procedures. Here, we develop a portable, sensitive, and stable (Eu-MOF)-based sensing platform to detect miRNA via smartphone. The Eu-MOF absorbs the carboxyfluorescein (FAM)-tagged probe DNA (pDNA) to generate hybrid pDNA@Eu-MOF, which can efficiently quench the fluorescence of FAM through a photoinduced electron transfer (PET) process. When integrated with a smartphone, the nonemissive pDNA@ Eu-MOF hybrid could be utilized as a portable and sensitive platform to sense miRNA (miR-892b) with a detection limit of 0.32 pM, which could be even distinguished by the naked eye. Moreover, this system demonstrates high selectivity for identifying miRNA family members with single-base mismatches. Furthermore, the expression levels of miRNA in cancer cell samples could be analyzed accurately. Therefore, the proposed method offers a promising guideline for the design of MOF-based sensing strategies and expands their potential applications for diagnostic purposes.

Electrochemiluminescent bioassay based on Ru@Zr-BTC-MOFs nanoparticles for determination of let-7a miRNA using the hybridization chain reaction

Carboxyl-rich tris(4,4'-dicarboxylic acid-2,2'-bipyridyl) ruthenium(II) ([Ru(dcbpy)3]2+) and 1,3,5-phenyl tricarboxylic acid (H3BTC) were used as the organic ligand to synthesize the metal-organic frameworks by a simple one-pot hydrothermal method with ZrCl4 as metal ion source. Subsequently, the excellent electrochemiluminescence (ECL) luminophore (denoted as Ru@Zr-BTC-MOFs) was obtained. The Ru@Zr-BTC-MOFs displayed outstanding ECL properties, and a sensitive ECL bioassay based on Ru@Zr-BTC-MOFs was designed for the detection of let-7a microRNA (miRNA) using hybrid chain reaction (HCR). Under the optimal experimental conditions, the proposed bioassay exhibited a good linear relationship in the range from 50.0 fM to 5.00 × 102 pM with a detection limit of 3.71 fM. Besides, the proposed sensor exhibited satisfactory performance in real samples. The recovery was 91 ~ 108%, and the relative standard deviation was less than 5.6%. It might have potential clinical applications for detecting miRNA in biomedical research and clinical diagnosis. The schematic diagram of the preparation of Ru@Zr-BTC-MOFs (a) and ECL sensor for detecting let -7a (b).

Overexpression of cytochrome P450 and esterase genes involved in permethrin resistance in larvae and adults of Culex quinquefasciatus

Mosquitoes are important vectors of several arthropod-borne diseases, which remain a priority for epidemiological research. Mosquito vector control strategies have traditionally relied on chemical insecticides such as synthetic pyrethroids. However, the indiscriminate use of pesticides has resulted in the development of resistance in many mosquito species. In insects, resistance evolves primarily through the overexpression of one or more gene products from the cytochrome P450, carboxylesterase, and glutathione superfamilies. The current study examined the expression of cytochrome P450 CYP6M2, CYP6AA7, CYP6Z2, CYP9J34, α-Esterase, Esterase B1, and neuroactin genes in larvae and adults of a permethrin-resistant (PerRes) and susceptible (Sus) Culex quinquefasciatus strains. The results showed that the CYP6AA7 gene was overexpressed (10-fold) in larvae and adults with PerRes (p < 0.01) followed by CYPJ34 (9.0-fold) and CYP6Z2 (5.0-fold) compared to the Sus, whereas fewer changes in CYP6M gene expression were observed in PerRes adults (p < 0.05), and no expression was found in larvae. The esterase gene was overexpressed in PerRes larvae (9.0-fold) followed by adults (2.5-fold) compared to the susceptible strain. Based on data, the present study suggests that cytochrome P450, CYP6AA7, CYP6Z2, CYP9J34, α-Esterase, Esterase B1, and neuroactin genes were involved in permethrin resistance in larval and adult Cx. quinquefasciatus.

Comparative transcriptomics analysis of testicular miRNA from indicine and taurine cattle

Numerous studies have shown that several microRNAs (miRNAs) are specifically expressed in testis, play an essential role in regulating testicular spermatogenesis. Hainan and Mongolian cattle are two representative Chinese native cattle breeds representing Bos indicus (indicine cattle) and Bos taurus (taurine cattle), respectively, which are distributed in hot Hainan and cold Inner Mongolia province. To study the functional differences of miRNA in spermatogenesis between indicine and taurine cattle, six mature testes samples from indicine cattle (n = 3) and taurine cattle (n = 3) were collected, respectively. We detected miRNA expression using small RNA sequencing technology following bioinformatic analysis. A total of 578 known miRNAs and 132 novel miRNAs were detected in the six libraries. Among the 710 miRNAs, 564 miRNAs were expressed in both indicine and taurine cattle, 73 miRNAs were found solely in indicine cattle and 73 miRNAs were found solely in taurine cattle. After further analysis, among the miRNAs were identified in both indicine and taurine cattle, 184 miRNAs were differentially expressed (|log2 fold change| ≥ 1 and corrected p-value <0.05). Among the miRNAs that were only expressed in indicine cattle, 10 miRNAs were differentially expressed, whereas, among the miRNAs that were only expressed in taurine cattle, six miRNAs were differentially expressed. The enrichment analysis result showed that predicted target genes of a total of 200 differentially expressed miRNAs were enriched on some testicular spermatogenesis-related Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, especially mitogen-activated protein kinase (MAPK) signaling pathway. These findings identify miRNAs as key factors to regulate spermatogenesis in both indicine and taurine cattle, which may also be helpful for improving cattle reproductive performance in future studies.

microRNA-382 as a tumor suppressor? Roles in tumorigenesis and clinical significance

MicroRNAs (miRNAs) are small single-stranded RNAs belonging to a class of non-coding RNAs with an average length of 18-22 nucleotides. Although not able to encode any protein, miRNAs are vastly studied and found to play role in various human physiologic as well as pathological conditions. A huge number of miRNAs have been identified in human cells whose expression is straightly regulated with crucial biological functions, while this number is constantly increasing. miRNAs are particularly studied in cancers, where they either can act with oncogenic function (oncomiRs) or tumor-suppressors role (referred as tumor-suppressor/oncorepressor miRNAs). miR-382 is a well-studied miRNA, which is revealed to play regulatory roles in physiological processes like osteogenic differentiation, hematopoietic stem cell differentiation and normal hematopoiesis, and liver progenitor cell differentiation. Notably, miR-382 deregulation is reported in pathologic conditions, such as renal fibrosis, muscular dystrophies, Rett syndrome, epidural fibrosis, atrial fibrillation, amelogenesis imperfecta, oxidative stress, human immunodeficiency virus (HIV) replication, and various types of cancers. The majority of oncogenesis studies have claimed miR-382 downregulation in cancers and suppressor impact on malignant phenotype of cancer cells in vitro and in vivo, while a few studies suggest opposite findings. Given the putative role of this miRNA in regulation of oncogenesis, assessment of miR-382 expression is suggested in a several clinical investigations as a prognostic/diagnostic biomarker for cancer patients. In this review, we have an overview to recent studies evaluated the role of miR-382 in oncogenesis as well as its clinical potential.

Concealed for a Long Time on the Marches of Empires: Hepatitis B Virus Genotype I

Genotype I, the penultimate HBV genotype to date, was granted the status of a bona fide genotype only in the XXIst century after some hesitations. The reason for these hesitations was that genotype I is a complex recombinant virus formed with segments from three original genotypes, A, C, and G. It was estimated that genotype I is responsible for only an infinitesimal fraction (<1.0%) of the chronic HBV infection burden worldwide. Furthermore, most probably due to its recent discovery and rarity, the natural history of infection with genotype I is poorly known in comparison with those of genotypes B or C that predominate in their area of circulation. Overall, genotype I is a minor genotype infecting ethnic minorities. It is endemic to the Southeast Asian Massif or Eastern Zomia, a vast mountainous or hilly region of 2.5 million km2 spreading from Eastern India to China, inhabited by a little more than 100 million persons belonging primarily to ethnic minorities speaking various types of languages (Tibeto-Burman, Austroasiatic, and Tai-Kadai) who managed to escape the authority of central states during historical times. Genotype I consists of two subtypes: I1, present in China, Laos, Thailand, and Vietnam; and I2, encountered in India, Laos, and Vietnam.

MicroRNA‑30a‑5p regulates cypermethrin-induced apoptosis of Sertoli cells by targeting KLF9 in vitro

Cypermethrin (CYP) has been identified as one kind of endocrine-disrupting chemicals (EDCs) to induce male reproduction damage. This study aimed to investigate the effects and mechanisms of miR-30a-5p on CYP induced apoptosis of TM4 mouse Sertoli cells in vitro. In the present study, 0 μM, 10 μM, 20 μM, 40 μM and 80 μM CYP were used to treat TM4 cells for 24 h. The apoptosis of TM4 cells, the expression level of miR-30a-5p, the protein expressions and the interaction between miR-30a-5p and KLF9 were detected by flow cytometry, quantitative Real-Time PCR, Western blot and luciferase reporter assays. CYP induced apoptosis of TM4 cells, inhibited expression of miR-30a-5p in TM4 cells, and overexpression of miR-30a-5p partially recovered CYP induced cells apoptosis. Furthermore, KLF9 was a potential downstream target of miR-30a-5p predicted by publicly available databases. KLF9 expression level in TM4 cells was significantly elevated after treatment with CYP, and the induction was inhibited by miR-30a-5p mimics transfection. Meanwhile, dual-luciferase reporter assay demonstrated that miR-30a-5p directly targeted KLF9-3'UTR. Moreover, in the presence of CYP, the apoptosis regulator p53 expression was also increased in TM4 cells. Overexpression miR-30a-5p or down-regulation of KLF9 both attenuated the induction of CYP on p53 expression. Overall, the present study demonstrated that miR-30a-5p regulated CYP induced TM4 cells apoptosis by targeting KLF9/p53 axis.

Human Breast Milk microRNAs, Potential Players in the Regulation of Nervous System

Human milk is the biological fluid with the highest exosome amount and is rich in microRNAs (miRNAs). These are key regulators of gene expression networks in both normal physiologic and disease contexts, miRNAs can influence many biological processes and have also shown promise as biomarkers for disease. One of the key aspects in the regeneration of the nervous system is that there are practically no molecules that can be used as potential drugs. In the first weeks of lactation, we know that human breast milk must contain the mechanisms to transmit molecular and biological information for brain development. For this reason, our objective is to identify new modulators of the nervous system that can be used to investigate neurodevelopmental functions based on miRNAs. To do this, we collected human breast milk samples according to the time of delivery and milk states: mature milk and colostrum at term; moderate and very preterm mature milk and colostrum; and late preterm mature milk. We extracted exosomes and miRNAs and realized the miRNA functional assays and target prediction. Our results demonstrate that miRNAs are abundant in human milk and likely play significant roles in neurodevelopment and normal function. We found 132 different miRNAs were identified across all samples. Sixty-nine miRNAs had significant differential expression after paired group comparison. These miRNAs are implicated in gene regulation of dopaminergic/glutamatergic synapses and neurotransmitter secretion and are related to the biological process that regulates neuron projection morphogenesis and synaptic vesicle transport. We observed differences according to the delivery time and with less clarity according to the milk type. Our data demonstrate that miRNAs are abundant in human milk and likely play significant roles in neurodevelopment and normal function.

miRNAs: Potential as Biomarkers and Therapeutic Targets for Cancer

MicroRNAs (miRNAs) are single-stranded, non-coding RNA molecules that regulate gene expression post-transcriptionally by binding to messenger RNAs. miRNAs are important regulators of gene expression, and their dysregulation is implicated in many human and canine diseases. Most cancers tested to date have been shown to express altered miRNA levels, which indicates their potential importance in the oncogenic process. Based on this evidence, numerous miRNAs have been suggested as potential cancer biomarkers for both diagnosis and prognosis. miRNA-based therapies have also been tested in different cancers and have provided measurable clinical benefits to patients. In addition, understanding miRNA biogenesis and regulatory mechanisms in cancer can provide important knowledge about resistance to chemotherapies, leading to more personalized cancer treatment. In this review, we comprehensively summarized the importance of miRNA in human and canine cancer research. We discussed the current state of development and potential for the miRNA as both a diagnostic marker and a therapeutic target.

The deleted in oral cancer (DOC1 aka CDK2AP1) tumor suppressor gene is downregulated in oral squamous cell carcinoma by multiple microRNAs

Cyclin-dependent kinase 2-associated protein 1 (CDK2AP1; also known as deleted in oral cancer or DOC1) is a tumor suppressor gene known to play functional roles in both cell cycle regulation and in the epigenetic control of embryonic stem cell differentiation, the latter as a core subunit of the nucleosome remodeling and histone deacetylation (NuRD) complex. In the vast majority of oral squamous cell carcinomas (OSCC), expression of the CDK2AP1 protein is reduced or lost. Notwithstanding the latter (and the DOC1 acronym), mutations or deletions in its coding sequence are extremely rare. Accordingly, CDK2AP1 protein-deficient oral cancer cell lines express as much CDK2AP1 mRNA as proficient cell lines. Here, by combining in silico and in vitro approaches, and by taking advantage of patient-derived data and tumor material in the analysis of loss of CDK2AP1 expression, we identified a set of microRNAs, namely miR-21-5p, miR-23b-3p, miR-26b-5p, miR-93-5p, and miR-155-5p, which inhibit its translation in both cell lines and patient-derived OSCCs. Of note, no synergistic effects were observed of the different miRs on the CDK2AP1-3-UTR common target. We also developed a novel approach to the combined ISH/IF tissue microarray analysis to study the expression patterns of miRs and their target genes in the context of tumor architecture. Last, we show that CDK2AP1 loss, as the result of miRNA expression, correlates with overall survival, thus highlighting the clinical relevance of these processes for carcinomas of the oral cavity.

Extracellular vesicle-associated microRNA signatures related to lymphovascular invasion in early-stage lung adenocarcinoma

Lymphovascular invasion (LVI) is a fundamental step toward the spread of cancer. Extracellular vesicles (EVs) promote cellular communication by shuttling cargo, such as microRNAs (miRNAs). However, whether EV-associated miRNAs serve as biomarkers for LVI remains unclear. This study aimed to identify EV-associated miRNAs related to LVI and validate the miRNA levels from patients with early-stage lung adenocarcinoma (LADC). Blood samples were collected from patients undergoing pulmonary resection for stage I LADC before surgery. The patients were classified into three groups according to the presence of LVI and postoperative recurrence. Serum-derived EVs in the derivation cohort were used for small RNA sequencing, while the selected LVI miRNA candidates were validated via real-time quantitative polymerase chain reaction using 44 patient and 16 healthy donor samples as the validation cohorts. Five miRNAs (miR-99b-3p, miR-26a-5p, miR-93-5p, miR-30d-5p, and miR-365b-3p) were assessed, and miR-30d-5p (p = 0.036) levels were significantly downregulated in the LVI-positive group. miR-30d-5p levels in healthy donors were lower than those in LADC patients. Patients with high miR-30d-5p levels had favorable survival compared to those with low miR-30d-5p levels. miR-30d-5p level in EVs may serve as a promising biomarker for detecting LVI in patients with early-stage LADC.

A rapid and simple method for simultaneous determination of three breast cancer related microRNAs based on magnetic nanoparticles modified with S9.6 antibody

Cancer progression is typically associated with the simultaneous changes of multiple microRNA (miR) levels. Therefore, simultaneous determination of multiple miR biomarkers exhibits great promise in early diagnosis of cancers. This research seeks to discuss a simple biosensing method for the ultrasensitive and specific detection of the three miRs related to the breast cancer based on S9.6 antibody coated magnetic beads, titanium phosphate nanospheres, and screen-printed carbon electrode. To prepare signaling probes, three hairpin DNAs (hDNAs) were labeled with three encoding titanium phosphate nanospheres with large quantities of different heavy metal ions (zinc, cadmium, lead), which have been utilized to discriminate the signals of three microRNA targets in relation with the corresponding heavy metal ions. After that, these hairpin structures hybridize with miR-21, miR-155 and miR-10b to form miR-21/hDNA1, miR-155/hDNA2 and miR-10b/hDNA3 complexes, which were captured by S9.6 antibodies (one anti-DNA/RNA antibody) pre-modified on magnetic bead surface. Therefore, the specific preconcentration of targets from complex matrixes can be carried out using magnetic actuation, increasing the sensitivity and specificity of the detection. The biosensor was suitably applied for direct and rapid detection of multiple microRNAs in real sample. It was observed that there were no significant differences between the results obtained by the suggested method and qRT-PCR as a reference method. So, this method makes an ultrasensitive novel platform for miRNAs expression profiling in clinical diagnosis and biomedical research.

MicroRNA-195a-5p Regulates Blood Pressure by Inhibiting NKCC2A

BACKGROUND

Previous studies showed that miR-195a-5p was among the most abundant microRNAs (miRNAs) expressed in the kidney.

METHODS

Lentivirus silencing of tumor necrosis factor-α (TNF) was performed in vivo and in vitro. Luciferase reporter assays confirmed that bumetanide-sensitive Na+-K+-2Cl- cotransporter isoform A (NKCC2A) mRNA is targeted and repressed by miR-195a-5p. Radiotelemetry was used to measure mean arterial pressure.

RESULTS

TNF upregulates mmu-miR-195a-5p, and -203 and downregulates mmu-miR-30c and -100 in the medullary thick ascending limb of male mice. miR-195a-5p was >3-fold higher in the renal outer medulla of mice given an intrarenal injection of murine recombinant TNF, whereas silencing TNF inhibited miR-195a-5p expression by ≈51%. Transient transfection of a miR-195a-5p mimic into medullary thick ascending limb cells suppressed NKCC2A mRNA by ≈83%, whereas transfection with Anti-miR-195a-5p increased NKCC2A mRNA. Silencing TNF in medullary thick ascending limb cells prevented increases in miR-195 induced by 400 mosmol/kg H2O medium, an effect reversed by transfection with a miR-195a-5p mimic. Expression of phosphorylated NKCC2 increased 1.5-fold in medullary thick ascending limb cells transfected with Anti-miR-195a-5p and a miR-195a-5p mimic prevented the increase, which was induced by silencing TNF in cells exposed to 400 mosmol/kg H2O medium after osmolality was increased by adding NaCl. Intrarenal injection of TNF suppressed NKCC2A mRNA, whereas injection of miR-195a-5p prevented the increase of NKCC2A mRNA abundance and phosphorylated NKCC2 expression when TNF was silenced. Intrarenal injection with miR-195a-5p markedly attenuated MAP after renal silencing of TNF in mice given 1% NaCl.

CONCLUSIONS

The study identifies miR-195a-5p as a salt-sensitive and TNF-inducible miRNA that attenuates NaCl-mediated increases in blood pressure by inhibiting NKCC2A.

Quantification of MicroRNAs or Viral RNAs with Microelectrode Sensors Enabled by Electrochemical Signal Amplification

Quantification of circulating microRNAs (miRNAs) or viral RNAs is of great significance because of their broad relevance to human health. Currently, quantitative reverse transcription polymerase chain reaction (qRT-PCR), as well as microarray and gene sequencing, are considered mainstream techniques for miRNA identification and quantitation and the gold standard for SARS-CoV2 detection in the COVID-19 pandemic. However, these laboratory techniques are challenged by the low levels and wide dynamic range (from aM to nM) of miRNAs in a physiological sample, as well as the difficulty in the implementation in point-of-care settings. Here, we describe a one-step label-free electrochemical sensing technique by assembling self-folded multi-stem DNA-redox probe structure on gold microelectrodes and introducing a reductant, tris(2-carboxyethyl) phosphine hydrochloride (TCEP), in the detection buffer solution to achieve ultrasensitive detection with a detection limit of 0.1 fM that can be further improved if needed.

Identification of Circular RNAs of Testis and Caput Epididymis and Prediction of Their Potential Functional Roles in Donkeys

Circular RNAs (circRNAs) are a class of noncoding RNAs with a covalently closed loop. Studies have demonstrated that circRNA can function as microRNA (miRNA) sponges or competing endogenous RNAs. Although circRNA has been explored in some species and tissues, the genetic basis of testis development and spermatogenesis in donkeys remain unknown. We performed RNA-seq to detect circRNA expression profiles of adult donkey testes. Length distribution and other characteristics were shown a total of 1971 circRNAs were differentially expressed and 12,648 and 6261 circRNAs were detected from the testis and caput epididymis, respectively. Among these circRNAs, 1472 circRNAs were downregulated and 499 circRNAs were upregulated in the testis. Moreover, KEGG pathway analyses and Gene Ontology were performed for host genes of circRNAs. A total of 39 upregulated circRNA host genes were annotated in spermatogenesis terms, including PIWIL2, CATSPERD, CATSPERB, SPATA6, and SYCP1. Other host genes were annotated in the focal adhesion, Rap1 signaling pathway. Downregulated expressed circRNA host genes participated in the TGF-β signaling pathway, GnRH signaling pathway, estrogen signaling pathway, and calcium signaling pathway. Our discoveries provide a solid foundation for identifying and characterizing critical circRNAs involved in testis development or spermatogenesis.

MicroRNA-200c Affects Milk Fat Synthesis by Targeting PANK3 in Ovine Mammary Epithelial Cells

Milk fat is the foremost nutrient of milk and a vital indicator in evaluating milk quality. Accumulating evidence suggests that microRNAs (miRNAs) are involved in the synthesis of milk fat. The miR-200c is closely related to lipid metabolism, but little is known about its effect on the synthesis of milk fat in MECs of ewes. Herein, the effect of miR-200c on the proliferation of ovine mammary epithelial cells (MECs) and its target relationship with a predicted target gene were investigated. The regulatory effects of miR-200c on the expression of the target genes and the content of triglycerides in ovine MECs were further analyzed. The results revealed that the expression level of miR-200c was differentially expressed in both eight tissues selected during lactation and in mammary gland tissues at different physiological periods. Overexpression of miR-200c inhibited the viability and proliferation of ovine MECs, while inhibition of miR-200c increased cell viability and promoted the proliferation of ovine MECs. Target gene prediction results indicated that miR-200c would bind the 3'UTR region of pantothenate kinase 3 (PANK3). Overexpression of miR-200c reduced the luciferase activity of PANK3, while inhibition of miR-200c increased its luciferase activity. These findings illustrated that miR-200c could directly interact with the target site of the PANK3. It was further found that overexpression of miR-200c reduced the expression levels of PANK3 and, thus, accelerated the synthesis of triglycerides. In contrary, the inhibitor of miR-200c promoted the expression of PANK3 that, thus, inhibited the synthesis of triglycerides in ovine MECs. Together, these findings revealed that miR-200c promotes the triglycerides synthesis in ovine MECs via increasing the lipid synthesis related genes expression by targeting PANK3.

Updated review of advances in microRNAs and complex diseases: experimental results, databases, webservers and data fusion

MicroRNAs (miRNAs) are gene regulators involved in the pathogenesis of complex diseases such as cancers, and thus serve as potential diagnostic markers and therapeutic targets. The prerequisite for designing effective miRNA therapies is accurate discovery of miRNA-disease associations (MDAs), which has attracted substantial research interests during the last 15 years, as reflected by more than 55 000 related entries available on PubMed. Abundant experimental data gathered from the wealth of literature could effectively support the development of computational models for predicting novel associations. In 2017, Chen et al. published the first-ever comprehensive review on MDA prediction, presenting various relevant databases, 20 representative computational models, and suggestions for building more powerful ones. In the current review, as the continuation of the previous study, we revisit miRNA biogenesis, detection techniques and functions; summarize recent experimental findings related to common miRNA-associated diseases; introduce recent updates of miRNA-relevant databases and novel database releases since 2017, present mainstream webservers and new webserver releases since 2017 and finally elaborate on how fusion of diverse data sources has contributed to accurate MDA prediction.

Identification of pathogenic genes associated with CKD: An integrated bioinformatics approach

Chronic kidney disease (CKD) is defined as a persistent abnormality in the structure and function of kidneys and leads to high morbidity and mortality in individuals across the world. Globally, approximately 8%–16% of the population is affected by CKD. Proper screening, staging, diagnosis, and the appropriate management of CKD by primary care clinicians are essential in preventing the adverse outcomes associated with CKD worldwide. In light of this, the identification of biomarkers for the appropriate management of CKD is urgently required. Growing evidence has suggested the role of mRNAs and microRNAs in CKD, however, the gene expression profile of CKD is presently uncertain. The present study aimed to identify diagnostic biomarkers and therapeutic targets for patients with CKD. The human microarray profile datasets, consisting of normal samples and treated samples were analyzed thoroughly to unveil the differentially expressed genes (DEGs). After selection, the interrelationship among DEGs was carried out to identify the overlapping DEGs, which were visualized using the Cytoscape program. Furthermore, the PPI network was constructed from the String database using the selected DEGs. Then, from the PPI network, significant modules and sub-networks were extracted by applying the different centralities methods (closeness, betweenness, stress, etc.) using MCODE, Cytohubba, and Centiserver. After sub-network analysis we identified six overlapped hub genes (RPS5, RPL37A, RPLP0, CXCL8, HLA-A, and ANXA1). Additionally, the enrichment analysis was undertaken on hub genes to determine their significant functions. Furthermore, these six genes were used to find their associated miRNAs and targeted drugs. Finally, two genes CXCL8 and HLA-A were common for Ribavirin drug (the gene-drug interaction), after docking studies HLA-A was selected for further investigation. To conclude our findings, we can say that the identified hub genes and their related miRNAs can serve as potential diagnostic biomarkers and therapeutic targets for CKD treatment strategies.

Examining micro-ribonucleic acids as diagnostic and therapeutic prospects in autoimmune hepatitis

INTRODUCTION

Micro-ribonucleic acids modulate the immune response by affecting the post-transcriptional expression of genes that influence the proliferation and function of activated immune cells, including regulatory T cells. Individual expressions or patterns in peripheral blood and liver tissue may have diagnostic value, reflect treatment response, or become therapeutic targets. The goals of this review are to present the properties and actions of micro-ribonucleic acids, indicate the key individual expressions in autoimmune hepatitis, and describe prospective clinical applications in diagnosis and management.

AREAS COVERED

Abstracts were identified in PubMed using the search words "microRNAs", "microRNAs in liver disease", and "microRNAs in autoimmune hepatitis". The number of abstracts reviewed exceeded 2000, and the number of full-length articles reviewed was 108.

EXPERT OPINION

Individual micro-ribonucleic acids, miR-21, miR-122, and miR-155, have been associated with biochemical severity, histological grade of inflammation, and pivotal pathogenic mechanisms in autoimmune hepatitis. Antisense oligonucleotides that down-regulate deleterious individual gene expressions, engineered molecules that impair targeting of gene products, and drugs that non-selectively up-regulate the biogenesis of potentially deficient gene regulators are feasible treatment options. Micro-ribonucleic acids constitute an under-evaluated area in autoimmune hepatitis that promises to improve diagnosis, pathogenic concepts, and therapy.

Framework Nucleic Acid-Based Spatial-Confinement Amplifier for miRNA Imaging in Living Cells

Real-time in situ monitoring of miRNAs in living cells is often appealed to signal amplifiers to tackle their low abundance challenges. However, the poor kinetics of amplifiers and potential interferences from the complex intracellular environment hamper its widespread applications in vivo. Herein, we report a framework nucleic acid (FNA)-based nonenzymatic spatial-confinement amplifier for rapid and reliable intracellular miRNA imaging. The amplifier consists of a localized catalytic hairpin assembly (L-CHA) reactor encapsulated in the inner cavity of an FNA (a 20 bp cube). The L-CHA reactor is certainly confined to the internal frame by integrating two probes (H1 and H2) of the L-CHA within a DNA strand and harnessing it to the opposite angles of the cube. We find that the stability of the amplifier is remarkably improved due to the protection of the FNA. More importantly, the spatial-confinement effect of the FNA can endow the confined L-CHA amplifier with enhanced local concentrations of reagents (5000-fold), thereby accelerating the reaction rate and improving the dynamic performance (up to 14.34-fold). With these advantages, the proposed amplifier can enable accurate and effective monitoring of miRNA expression levels in living cells and poses great potential in medical diagnostics and biomedical research.

Experimental MicroRNA Targeting Validation

microRNAs (miRNAs) have recently been recognized as a new dimension of posttranscriptional regulation. It is well defined that most human protein-coding genes are regulated by one or more miRNAs. Therefore, it is crucial to identify genes targeted by the miRNAs to better understand their functions. Although bioinformatics tools have the ability to identify target candidates it is still essential to identify physiological targets by experimental approaches. Currently, the majority of miRNA-target experimental validation approaches assess the changes in target expression in mRNA or protein level upon miRNA upregulation or downregulation. Additionally, finding out direct physical interactions between miRNAs and their targets is also among the experimental techniques. In this chapter we reviewed the existing experimental techniques for miRNA target identification by considering their advantages and potential drawbacks.

Cancer drug resistance related microRNAs: recent advances in detection methods

MiRNAs are related to cancer drug resistance through various mechanisms. The advanced detection methods for the miRNAs are reviewed.

Experimental MicroRNA Detection Methods

MicroRNAs (miRNAs) are considerably small yet highly important riboregulators involved in nearly all cellular processes. Due to their critical roles in posttranscriptional regulation of gene expression, they have the potential to be used as biomarkers in addition to their use as drug targets. Although computational approaches speed up the initial genomewide identification of putative miRNAs, experimental approaches are essential for further validation and functional analyses of differentially expressed miRNAs. Therefore, sensitive, specific, and cost-effective microRNA detection methods are imperative for both individual and multiplex analysis of miRNA expression in different tissues and during different developmental stages. There are a number of well-established miRNA detection methods that can be exploited depending on the comprehensiveness of the study (individual miRNA versus multiplex analysis), the availability of the sample and the location and intracellular concentration of miRNAs. This review aims to highlight not only traditional but also novel strategies that are widely used in experimental identification and quantification of microRNAs.

microRNA-based diagnostic and therapeutic applications in cancer medicine

It has been almost two decades since the first link between microRNAs and cancer was established. In the ensuing years, this abundant class of short noncoding regulatory RNAs has been studied in virtually all cancer types. This tremendously large body of research has generated innovative technological advances for detection of microRNAs in tissue and bodily fluids, identified the diagnostic, prognostic, and/or predictive value of individual microRNAs or microRNA signatures as potential biomarkers for patient management, shed light on regulatory mechanisms of RNA-RNA interactions that modulate gene expression, uncovered cell-autonomous and cell-to-cell communication roles of specific microRNAs, and developed a battery of viral and nonviral delivery approaches for therapeutic intervention. Despite these intense and prolific research efforts in preclinical and clinical settings, there are a limited number of microRNA-based applications that have been incorporated into clinical practice. We review recent literature and ongoing clinical trials that highlight most promising approaches and standing challenges to translate these findings into viable microRNA-based clinical tools for cancer medicine. This article is categorized under: RNA in Disease and Development > RNA in Disease.

Rapid, multiplexed detection of the let-7 miRNA family using γPNA amphiphiles in micelle-tagging electrophoresis

miRNA is a promising class of biomarkers whose levels can be assayed to detect various forms of cancer and other serious diseases. These short, noncoding nucleic acids are difficult to detect due to their low abundance and the marginal stability of their duplexes with DNA probes. In addition, miRNAs within the same family have high sequence homology, and often, related miRNA differ in sequence by only a single base. In this report, we demonstrate an independent detection seven members of the let-7 family of miRNA in a single run. Key to success is the use of mini-PEG-substituted PNA amphiphiles (γPNAA) and highly fluorescent DNA nanotags in micelle tagging electrophoresis (MTE). Multiplexed detection is accomplished in capillary electrophoresis (CE) using oligomeric nanotags of pre-programmed lengths where the presence of a specific miRNA links its nanotag to a micelle drag-tag, which shifts the nanotag elution time to a defined region for detection. We further demonstrate that the peak shape and elution time are unaffected by the presence of up to 10 mg/ml of serum protein in the sample, with a total runtime of less than 4 min and a LOD of 10-100 pM. We discuss efforts to substantially decrease the detection limit using nanotags that are >1000 bp in length.

Prognostic value of miR-1181 in non-small cell lung cancer and its regulatory effect on tumor progression

Non-small cell lung cancer (NSCLC) is one of the most important causes of cancer-related death. miR-1181 has been reported to have roles in various cancer types and its function in the progression of NSCLC was investigated in the present study. A total of 118 patients with NSCLC were recruited and their tumor tissues were collected. The expression of miR-1181 in NSCLC tissues and cells was detected by reverse transcription-quantitative PCR. The prognostic value of miR-1181 was evaluated by Kaplan-Meier and Cox regression analysis and the roles of miR-1181 in cell proliferation, migration and invasion of NSCLC were analyzed by Cell Counting Kit-8 and Transwell assays. miR-1181 was indicated to be upregulated in NSCLC tissues and cell lines, and to be associated with lymph node metastasis and the TNM stage of patients. Patients with high miR-1181 expression had a poorer prognosis than those with low miR-1181 expression. miR-1181 levels and TNM stage were determined to be two independent prognostic factors for NSCLC. In addition, overexpression of miR-1181 exerted enhancing effects on cell proliferation, migration and invasion of NSCLC, while its knockdown inhibited these cellular processes. In conclusion, upregulation of miR-1181 in NSCLC was associated with lymph node metastasis and TNM stage of patients and was indicative of poor prognosis. miR-1181 was indicated to exert promoting effects on cell proliferation, migration and invasion of NSCLC cells and to be involved in tumor progression, providing novel insight for the development of biomarkers and therapies for NSCLC.

MiR-30d Participates in Vincristine-Induced Neuropathic Pain by Down-Regulating GAD67

Vincristine is a common chemotherapeutic agent in cancer treatment, while it often causes chemotherapy-induced peripheral neuropathy(CIPN), which brings patients a great disease burden and associated economic pressure. The mechanism under CIPN remains mostly unknown. The previous study has shown that cell-type-specific spinal synaptic plasticity in the dorsal horn plays a pivotal role in neuropathic pain. Downregulation of GABA transmission, which mainly acts as an inhibitory pathway, has been reported in the growing number of research. Our present study found that GAD67, responsible for > 90% of basal GABA synthesis, is down-regulated, while its relative mRNA remains unchanged in vincristine-induced neuropathy. Considering microRNAs (miRNAs) as a post-transcription modifier by degrading targeted mRNA or repressing mRNA translation, we performed genome-wide miRNA screening and revealed that miR-30d might contribute to GAD67 down-regulation. Further investigation confirmed that miR-30d could affect the fluorescence activity of GAD67 by binding to the 3 'UTR of the GAD67 gene, and intrathecal injection of miR-30d antagomir increased the expression of GAD67, partially rescued vincristine-induced thermal hyperalgesia and mechanical allodynia. In summary, our study revealed the molecule interactions of GAD67 and miR-30d in CIPN, which has not previously been discussed in the literature. The results give more profound insight into understanding the CIPN mechanism and hopefully helps pain control.

Investigation of miRNA dysregulation and association with immune cell profile during malignant transformation of colorectal cells

BACKGROUND

Colorectal cancer (CRC) is one of the most prevalent and life-threatening cancer among the world. Accumulated somatic mutations during malignant transformation process endow cancer cells with increased growth, invasiveness and immunogenicity. These highly immunogenic cancer cells develop multiple strategies to evade immune attack. Through post-transcriptional regulation, microRNAs (miRNAs) not only participate in cancer development and progression but also manipulate anti-cancer immune response. This study aims to identify miRNAs associated with the colorectal cell malignant transformation process and their association with immune cell population using synchronous adjacent normal, polyp and CRC specimens.

METHODS

We conducted a Low Density Array to compare the miRNA expression profile of synchronous colorectal adenoma, adenocarcinoma and adjacent normal colon mucosa collected from 8 patients, in order to identify candidate miRNAs involved in CRC progression. These findings were further validated in 14 additional patients and GEO dataset GSE41655. The relative abundance of dendritic cells, natural killer cells, neutrophil and macrophage was determined and correlated with dysregulated miRNA levels.

RESULTS

MicroRNA microarray identified 39 miRNAs aberrantly expressed during the colorectal cell transformation process. Seven novel miRNAs were shortlisted, and dysregulation of miR-149-3p, miR-192-3p, miR-335-5p and miR-425 were further validated by the qPCR validation experiment and data retrieved from the GEO dataset. Furthermore, these miRNAs demonstrated certain associations with level of dendritic cells, natural killer cells, neutrophil and macrophage within the polyp or CRC specimens.

CONCLUSION

This study revealed miRNA dysregulated during stepwise malignant transformation of colorectal mucosal cells and their association with immune cell population.

Circulating and Intracellular miRNAs as Prognostic and Predictive Factors in HER2-Positive Early Breast Cancer Treated with Neoadjuvant Chemotherapy: A Review of the Literature

MicroRNAs (miRNA) are small noncoding RNAs that can act as both oncogene and tumor suppressors. Deregulated miRNA expression has been detected in human cancers, including breast cancer (BC). Considering their important roles in tumorigenesis, miRNAs have been investigated as potential prognostic and diagnostic biomarkers. Neoadjuvant setting is an optimal model to investigate in vivo the mechanism of treatment resistance. In the management of human epidermal growth factor receptor-2 (HER2)-positive early BC, the anti-HER2-targeted therapies have drastically changed the survival outcomes. Despite this, growing drug resistance due to the pressure of therapy is relatively frequent. In the present review, we focused on the main miRNAs involved in HER2-positive BC tumorigenesis and discussed the recent evidence on their predictive and prognostic value.

Cross-triggered and cascaded recycling amplification system for electrochemical detection of circulating microRNA in human serum

A cross-triggered and cascaded recycling amplification system was developed for electrochemical sensing of microRNA 122 based on the DNAzyme/multicomponent nucleic acid enzyme cleavage technique and a dumbbell-shaped probe. The linear range and detection limit were obtained to be 1 fM-100 pM and 0.34 fM, respectively. Compared with some reported studies, the proposed system can achieve the selective detection of endogenous miRNA in liver injury patients and healthy human serums with the advantages of high sensitivity, low cost, and easy manipulation, which are significant for disease diagnosis as well as the fundamental research of molecular biology.

MicroRNA: A Potential Diagnosis for Male Infertility

Male infertility is one of the major global health problems, in particular, in more than half of the affected men. Genetic factors are important for identifying men with idiopathic infertility along with semen analysis. Valid and useful information can be obtained through non-invasive molecular research. Among these, small single-stranded non-coding RNA molecules of microRNAs (abbreviated miRNAs) are non-invasive biomarkers with a diagnostic value by regulating the post-transcriptional gene silence through repression and prevention of the translation process. The association between various types of male infertility and miRNA regulation changes has been evaluated to understand the biological function of miRNA and gene targets. Accordingly, further study of the function of miRNAs associated with reproductive disorders could lead researchers to further understand the molecular mechanisms of male infertility in order to find effective biomarkers and therapeutic strategies. Therefore, the present review article aimed at scrutinizing those researches investigating the altered miRNA expression in testicles, epididymis, and spermatozoa.

miRNA biomarkers in renal disease

Chronic kidney disease (CKD), which is characterized by the gradual loss of kidney function, is a growing worldwide problem due to CKD-related morbidity and mortality. There are no reliable and early biomarkers enabling the monitoring, the stratification of CKD progression and the estimation of the risk of CKD-related complications, and therefore, the search for such molecules is still going on. Numerous studies have provided evidence that miRNAs are potentially important particles in the CKD field. Studies indicate that some miRNA levels can be increased in patients with CKD stages III–V and hemodialysis and decreased in renal transplant recipients (miR-143, miR-145 and miR-223) as well as elevated in patients with CKD stages III–V, decreased in hemodialysis patients and even more markedly decreased in renal transplant recipients (miR-126 and miR-155). miRNA have great potential of being sensitive and specific biomarkers in kidney diseases as they are tissue specific and stable in various biological materials. Some promising non-invasive miRNA biomarkers have already been recognized in renal disease with the potential to enhance diagnostic accuracy, predict prognosis and monitor the course of disease. However, large-scale clinical trials enrolling heterogeneous patients are required to evaluate the clinical value of miRNAs.

Unraveling the role of microRNA/isomiR network in multiple primary melanoma pathogenesis

Malignant cutaneous melanoma (CM) is a potentially lethal form of skin cancer whose worldwide incidence has been constantly increasing over the past decades. During their lifetime, about 8% of CM patients will develop multiple primary melanomas (MPMs), usually at a young age and within 3 years from the first tumor/diagnosis. With the aim of improving our knowledge on MPM biology and pathogenesis, we explored the miRNome of 24 single and multiple primary melanomas, including multiple tumors from the same patient, using a small RNA-sequencing approach. From a supervised analysis, 22 miRNAs were differentially expressed in MPM compared to single CM, including key miRNAs involved in epithelial-mesenchymal transition. The first and second melanoma from the same patient presented a different miRNA profile. Ten miRNAs, including miR-25-3p, 149-5p, 92b-3p, 211-5p, 125a-5p, 125b-5p, 205-5p, 200b-3p, 21-5p, and 146a-5p, were further validated in 47 single and multiple melanoma samples. Pathway enrichment analysis of miRNA target genes revealed a more differentiated and less invasive status of MPMs compared to CMs. Bioinformatic analyses at the miRNA isoform (isomiR) level detected a panel of highly expressed isomiRs belonging to miRNA families implicated in human tumorigenesis, including miR-200, miR-30, and miR-10 family. Moreover, we identified hsa-miR-125a-5p|0|-2 isoform as tenfold over-represented in melanoma than the canonical form and differentially expressed in MPMs arising in the same patient. Target prediction analysis revealed that the miRNA shortening could change the pattern of target gene regulation, specifically in genes implicated in cell adhesion and neuronal differentiation. Overall, we provided a putative and comprehensive characterization of the miRNA/isomiR regulatory network of MPMs, highlighting mechanisms of tumor development and molecular features differentiating this subtype from single melanomas.

Rheb-mTOR activation rescues Aβ-induced cognitive impairment and memory function by restoring miR-146 activity in glial cells

Deposition of amyloid beta plaques in adult rat or human brain is associated with increased production of proinflammatory cytokines by associated glial cells that are responsible for degeneration of the diseased tissue. The expression of these cytokines is usually under check and is controlled at the post-transcriptional level via several microRNAs. Computational analysis of gene expression profiles of cortical regions of Alzheimer’s disease patients’ brain suggests ineffective target cytokine mRNA suppression by existing micro-ribonucleoproteins (miRNPs) in diseased brain. Exploring the mechanism of amyloid beta-induced cytokine expression, we have identified how the inactivation of the repressive miR-146 miRNPs causes increased production of cytokines in amyloid beta-exposed glial cells. In exploration of the cause of miRNP inactivation, we have noted amyloid beta oligomer-induced sequestration of the mTORC1 complex to early endosomes that results in decreased Ago2 phosphorylation, limited Ago2-miRNA uncoupling, and retarded Ago2-cytokine mRNA interaction in rat astrocytes. Interestingly, constitutive activation of mTORC1 by Rheb activator restricts proinflammatory cytokine production by reactivating miR-146 miRNPs in amyloid beta-exposed glial cells to rescue the disease phenotype in the in vivo rat model of Alzheimer’s disease.

Translational Potential of Epigenetic-Based Markers on Fine-Needle Aspiration Thyroid Specimens

The awareness of epigenetic alterations leading to neoplasia attracted the attention of researchers toward its potential use in the management of cancer, from diagnosis to prognosis and prediction of response to therapies. Our group has focused its attention on the epigenomics of thyroid neoplasms. Although most of the epigenetic studies have been applied on histological samples, the fact is that cytology, through fine-needle aspiration, is a primary diagnostic method for many pathologies, of which thyroid nodules are one of the most paradigmatic examples. This has led to an increasing literature report of epigenetic studies using these biological samples over the past decade. In this review, our group aimed to document recent research of epigenetic alterations and its associated assessment techniques, based on cytology material. Our review covers the main epigenetic categories—DNA methylation, histone modification, and RNA-silencing—whose evidence in thyroid cytology samples may represent solid soil for future prospectively designed studies aiming at validating patterns of epigenetic alterations and their potential use in the clinical management of thyroid neoplasms.

Epigenetics: New Insights into Mammary Gland Biology

The mammary gland undergoes important anatomical and physiological changes from embryogenesis through puberty, pregnancy, lactation and involution. These steps are under the control of a complex network of molecular factors, in which epigenetic mechanisms play a role that is increasingly well described. Recently, studies investigating epigenetic modifications and their impacts on gene expression in the mammary gland have been performed at different physiological stages and in different mammary cell types. This has led to the establishment of a role for epigenetic marks in milk component biosynthesis. This review aims to summarize the available knowledge regarding the involvement of the four main molecular mechanisms in epigenetics: DNA methylation, histone modifications, polycomb protein activity and non-coding RNA functions.

Advances in multiplexed techniques for the detection and quantification of microRNAs

MicroRNA detection is currently a crucial analytical chemistry challenge: almost 2000 papers were referenced in PubMed in 2018 and 2019 for the keywords "miRNA detection method". MicroRNAs are potential biomarkers for multiple diseases including cancers, neurodegenerative and cardiovascular diseases. Since miRNAs are stably released in bodily fluids, they are of prime interest for the development of non-invasive diagnosis methods, such as liquid biopsies. Their detection is however challenging, as high levels of sensitivity, specificity and robustness are required. The analysis also needs to be quantitative, since the aim is to detect miRNA concentration changes. Moreover, a high multiplexing capability is also of crucial importance, since the clinical potential of miRNAs probably lays in our ability to perform parallel mapping of multiple miRNA concentrations and recognize typical disease signature from this profile. A plethora of biochemical innovative detection methods have been reported recently and some of them provide new solutions to the problem of sensitive multiplex detection. In this review, we propose to analyze in particular the new developments in multiplexed approaches to miRNA detection. The main aspects of these methods (including sensitivity and specificity) will be analyzed, with a particular focus on the demonstrated multiplexing capability and potential of each of these methods.

Bringing MicroRNAs to Light: Methods for MicroRNA Quantification and Visualization in Live Cells

MiRNAs are small non-coding RNAs that interact with their target mRNAs for posttranscriptional gene regulation. Finely controlled miRNA biogenesis, target recognition and degradation indicate that maintaining miRNA homeostasis is essential for regulating cell proliferation, growth, differentiation and apoptosis. Increasingly, miRNAs have been recognized as a potential biomarker for disease diagnosis. MiRNAs can be found in blood, plasma, and tissues, and miRNA expression and activity differ in developmental stages, tissues and in response to external stimuli. MiRNA transcripts are matured from pri-miRNA over pre-miRNA to mature miRNA, a process that includes multiple steps and enzymes. Many tools are available to identify and quantify specific miRNAs, ranging from measuring total miRNA, specific miRNA activity, miRNA arrays and miRNA localization. The various miRNA assays differ in accuracy, cost, efficiency and convenience of monitoring miRNA dynamics. To acknowledge the significance and increasing research interest in miRNAs, we summarize the traditional as well as novel methods of miRNA quantification with strengths and limitations of various techniques in biochemical and medical research.

Elevated serum miR-3129-5p contributes to the progression of coronary heart disease via targeting mTOR

The current study aims to explore the miRNA changes that occur in the serum of patients with coronary heart disease (CHD) and healthy controls using a microarray technique, thereby exploring the potential biomarkers in the diagnosis of CHD and the underlying mechanism. Clinical data were reviewed, and venous blood samples were collected from 66 cases of CHD and 58 cases of healthy controls. MicroRNA-wide expression profiling identified 16 miRNAs that were aberrantly decreased by ~2-fold in the serum of patients with CHD compared to that of healthy controls. RT-PCR analysis indicated that the expression of miR-3129-5p was increased the most in patients with CHD compared with that of controls. Moreover, serum miR-3129-5p was found to be highest in the severe stenosis group, followed by the moderate stenosis group and mild stenosis group. ROC analysis showed that serum miR-3129-5p could differentiate patients with CHD from controls. Further study showed that mTOR was a target gene of miR-3129-5p. Western blot assays demonstrated that miR-3129-5p significantly suppressed the phosphorylation of S6 but increased LC3II/LC3I and Beclin1 levels. Consistently, GFP-LC3 and TEM assays indicated that miR-3129 increased autophagy puncta in H9C2 cells. More importantly, silencing mTOR significantly decreased the expression of p-S6 but increased LC3II/LC3I and Beclin expression even in H9C2 cells transfected with miR-3129-5p inhibitor, indicating that miR-3129-5p-induced cell autophagy was mediated via mTOR in H9C2 cells. In summary, elevated serum miR-3129-5p contributes to CHD by targeting mTOR signaling and may be a therapeutic target in the treatment of CHD.

microRNAs Biogenesis, Functions and Role in Tumor Angiogenesis

microRNAs (miRNAs) are small non-coding RNA molecules, evolutionary conserved. They target more than one mRNAs, thus influencing multiple molecular pathways, but also mRNAs may bind to a variety of miRNAs, either simultaneously or in a context-dependent manner. miRNAs biogenesis, including miRNA transcription, processing by Drosha and Dicer, transportation, RISC biding, and miRNA decay, are finely controlled in space and time. miRNAs are critical regulators in various biological processes, such as differentiation, proliferation, apoptosis, and development in both health and disease. Their dysregulation is involved in tumor initiation and progression. In tumors, they can act as onco-miRNAs or oncosuppressor-miRNA participating in distinct cellular pathways, and the same miRNA can perform both activities depending on the context. In tumor progression, the angiogenic switch is fundamental. miRNAs derived from tumor cells, endothelial cells, and cells of the surrounding microenvironment regulate tumor angiogenesis, acting as pro-angiomiR or anti-angiomiR. In this review, we described miRNA biogenesis and function, and we update the non-classical aspects of them. The most recent role in the nucleus, as transcriptional gene regulators and the different mechanisms by which they could be dysregulated, in tumor initiation and progression, are treated. In particular, we describe the role of miRNAs in sprouting angiogenesis, vessel co-option, and vasculogenic mimicry. The role of miRNAs in lymphoma angiogenesis is also discussed despite the scarcity of data. The information presented in this review reveals the need to do much more to discover the complete miRNA network regulating angiogenesis, not only using high-throughput computational analysis approaches but also morphological ones.