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Even at low levels, exposure to ionising radiation can lead to eye damage. However, the underlying molecular mechanisms are not yet fullyunderstood. We aimed to address this gap with a comprehensive in silico approach to the issue. For this purpose we relied on the ComparativeToxicogenomics Database (CTD), ToppGene Suite, Cytoscape, GeneMANIA, and Metascape to identify six key regulator genes associatedwith radiation-induced eye damage (ATM, CRYAB, SIRT1, TGFB1, TREX1, and YAP1), all of which have physical interactions. Someof the identified molecular functions revolve around DNA repair mechanisms, while others are involved in protein binding, enzymaticactivities, metabolic processes, and post-translational protein modifications. The biological processes are mostly centred on response toDNA damage, the p53 signalling pathway in particular. We identified a significant role of several miRNAs, such as hsa-miR-183 and hsamiR-589, in the mechanisms behind ionising radiation-induced eye injuries. Our study offers a valuable method for gaining deeper insightsinto the adverse effects of radiation exposure., Izloženost ionizirajućem zračenju čak i pri niskim razinama može pridonijeti nastanku oštećenja oka. Međutim, osnovni molekulskimehanizmi i dalje nisu potpuno razjašnjeni. Cilj našega istraživanja bio je ispuniti tu nedostajuću kariku primjenom sveobuhvatnog in silicopristupa problemu. U tu svrhu, pomoću genomskih baza podataka, portala i poslužitelja (Comparative Toxicogenomics Database, ToppGeneSuite portal, Cytoscape, GeneMANIA i Metascape), identificirano je šest ključnih regulacijskih gena koji su povezani s oštećenjem okaprouzročenog ionizirajućim zračenjem (ATM, CRYAB, SIRT1, TGFB1, TREX1 i YAP1) i koji su svi bili u fizičkoj interakciji. Neke odidentificiranih molekulskih funkcija odnosile su se na mehanizme popravka oštećenja DNA, a druge su bile uključene u vezanje proteina,enzimsku aktivnost, metaboličke procese i posttranslacijske modifikacije proteina. Biološki procesi uglavnom su bili povezani s odgovoromna oštećenje DNA, pogotovo sa signalnim putem p53. Uočena je i značajna uloga nekoliko miRNA, poput hsa-miR-183 i hsa-miR-589,u mehanizmima povezanima s oštećenjem oka prouzročenog ionizirajućim zračenjem. Osim toga, u ovom je istraživanju opisana korisnametoda za ispitivanje štetnih učinaka izloženosti zračenju.

Environmental pollution with heavy metals such as copper (Cu) severely hinders optimal plant growth and development. Silicon (Si) is a plant nutrient that can improve plant health through diverse mechanisms. microRNAs (miRNAs) are recognized as effective regulators of various processes in plants, including stress responses, however, their involvement in Si-protective effect remains unrevealed. To clarify the molecular pathways involved in the protective effect of Si, small RNA-seq analyses (Illumina Sequencing SE50) was performed on cucumber plants treated with silicon (Si) alone or with a high concentration of Cu (Cu+Si). The small RNA tags were mapped to the reference sequence by Bowtie tool, following no-mismatch or one mismatch criterion, to analyze their expression and distribution. Identification of known miRNAs among the mapped small RNA tags was accomplished by miRBase22.0 database. miREvo and mirdeep2 were exploited to predict novel miRNAs by analyzing the secondary structure, Dicer cleavage site, and minimum free energy of the small RNA tags unannotated in the previous steps. The prediction of the target gene of miRNA was performed by psRobot. Differential expression analysis of two treatments was done using edgeR, with the default threshold qvalue < 0.05 and |log2(fold change)| > 1. A total of 71 miRNAs were identified in cucumber plants. Twenty miRNAs that were significantly differentially expressed, including seven novel miRNAs were clustered to find similar expression patterns. miR398 and miR408, which are known to target Cu-proteins important for Cu metabolism and transport, were significantly downregulated in Cu+Si treatment. In contrast, miR156, miR164, mir167, miR394, and miR477 were upregulated in Cu+Si. Additionally, two novel miRNAs (Novel_15 and Novel_19) were highly expressed and specific to Cu+Si, while, the Novel_12 miRNA was specific to Si treatment. The putative target genes of the differentially expressed miRNAs were subjected to Gene Ont

The insertion between tendons and bones is called enthesis. Injuries at the enthesis account for a significant proportion of all sport-related injuries. Additionally, sedentarism, obesity, and ageing are risk factors for enthesis injuries. The enthesis does not heal properly, and the regeneration of the native morphology of this tissue after injury constitutes an unmet challenge for tissue engineers. This thesis is focused on researching potential tissue engineering approaches to aid the process of enthesis healing by exploring the use of biomimetic biomaterials and novel molecular tools to enhance the quality of healing upon injury. This thesis describes the use of biomimetic silk-fibroin scaffolds with an enthesis-like morphology to yield better enthesis healing upon injury in a rodent animal model. Additionally, this thesis investigated the patterns of expression of an interesting class of molecules known as miRNAs during the early stages of enthesis healing. miRNAs have the potential to regulate the process of healing and fibrosis. A set of at least 13 miRNAs were hereby identified as relevant for enthesis healing. Moreover, miRNA-16-5p was evaluated in vitro for its potential therapeutic use to regulate the occurrence of fibrosis and scar tissue.

This work has been in part financed by benefactors, through the crowdfunding project “Match point against breast cancer” (PRECIPITA PR242, 2019; FECYT; Spanish Ministry of Science and Innovation, MICINN, led by MS‑R), and donations to Asociación Española contra el Cáncer (AECC). We are extremely thankful to all our donors. The work has been also funded by the Spanish Ministry of Science and Innovation and the Ministry of Economy and Competitiveness (supported with European Regional Development funds): PID2021‑128726 to MM, CNS2022‑135364 to MS‑R, PI20/00590 to CS, as well as by Comunidad de Madrid (Y2020/BIO‑6519 and S2022/BMD‑7437) to MM. MS‑R was supported by AECC (AIOA120833SALA and INVES18005SALA), a Juan de la Cierva incorporación and a Ramón y Cajal contract (RYC2020028929‑I, from the MICINN, FSE/ Agencia Estatal de Investigación). NGM‑I was supported by AECC (PRDMA19003GARC)., A hallmark of many malignant tumors is dedifferentiated (immature) cells bearing slight or no resemblance to the normal cells from which the cancer originated. Tumor dedifferentiated cells exhibit a higher capacity to survive to chemo and radiotherapies and have the ability to incite tumor relapse. Inducing cancer cell differentiation would abolish their self-renewal and invasive capacity and could be combined with the current standard of care, especially in poorly differentiated and aggressive tumors (with worst prognosis). However, differentiation therapy is still in its early stages and the intrinsic complexity of solid tumor heterogeneity demands innovative approaches in order to be efficiently translated into the clinic. We demonstrate here that microRNA 203, a potent driver of differentiation in pluripotent stem cells (ESCs and iPSCs), promotes the differentiation of mammary gland tumor cells. Combining mouse in vivo approaches and both mouse and human-derived tridimensional organoid cultures, we report that miR-203 influences the self-renewal capacity, plasticity and differentiation potential of breast cancer cells and prevents tumor cell growth in vivo. Our work sheds light on differentiation-based antitumor therapies and offers miR-203 as a promising tool for directly confronting the tumor-maintaining and regeneration capability of cancer cells., Ministerio de Ciencia e Innvoación, Depto. de Bioquímica y Biología Molecular, Fac. de Ciencias Biológicas, TRUE, pub

Skeletal muscle regeneration entails a multifaceted process marked by distinct phases, encompassing inflammation, regeneration, and remodeling. The coordination of these phases hinges upon precise intercellular communication orchestrated by diverse cell types and signaling molecules. Recent focus has turned towards extracellular vesicles (EVs), particularly small EVs, as pivotal mediators facilitating intercellular communication throughout muscle regeneration. Notably, injured muscle provokes the release of EVs originating from myofibers and various cell types, including mesenchymal stem cells, satellite cells, and immune cells such as M2 macrophages, which exhibit anti-inflammatory and promyogenic properties. EVs harbor a specific cargo comprising functional proteins, lipids, and nucleic acids, including microRNAs (miRNAs), which intricately regulate gene expression in target cells and activate downstream pathways crucial for skeletal muscle homeostasis and repair. Furthermore, EVs foster angiogenesis, muscle reinnervation, and extracellular matrix remodeling, thereby modulating the tissue microenvironment and promoting effective tissue regeneration. This review consolidates the current understanding on EVs released by cells and damaged tissues throughout various phases of muscle regeneration with a focus on EV cargo, providing new insights on potential therapeutic interventions to mitigate muscle-related pathologies.

Alzheimer's disease (AD) diagnosis relies on clinical symptoms complemented with biological biomarkers, the Amyloid Tau Neurodegeneration (ATN) framework. Small non-coding RNA (sncRNA) in the blood have emerged as potential predictors of AD. We identified sncRNA signatures specific to ATN and AD, and evaluated both their contribution to improving AD conversion prediction beyond ATN alone.This nested case-control study was conducted within the ACE cohort and included MCI patients matched by sex. Patients free of type 2 diabetes underwent cerebrospinal fluid (CSF) and plasma collection and were followed-up for a median of 2.45-years. Plasma sncRNAs were profiled using small RNA-sequencing. Conditional logistic and Cox regression analyses with elastic net penalties were performed to identify sncRNA signatures for A+(T|N)+ and AD. Weighted scores were computed using cross-validation, and the association of these scores with AD risk was assessed using multivariable Cox regression models. Gene ontology (GO) and Kyoto encyclopaedia of genes and genomes (KEGG) enrichment analysis of the identified signatures were performed.The study sample consisted of 192 patients, including 96 A+(T|N)+ and 96 A-T-N- patients. We constructed a classification model based on a 6-miRNAs signature for ATN. The model could classify MCI patients into A-T-N- and A+(T|N)+ groups with an area under the curve of 0.7335 (95% CI, 0.7327 to 0.7342). However, the addition of the model to conventional risk factors did not improve the prediction of AD beyond the conventional model plus ATN status (C-statistic: 0.805 [95% CI, 0.758 to 0.852] compared to 0.829 [95% CI, 0.786, 0.872]). The AD-related 15-sncRNAs signature exhibited better predictive performance than the conventional model plus ATN status (C-stati

Atherosclerosis and non-alcoholic fatty liver disease (NAFLD) are pathologies related to ectopic fat accumulation, both of which are continuously increasing in prevalence. These threats are prompting researchers to develop effective therapies for their clinical management. One of the common pathophysiological alterations that underlies both diseases is oxidative stress (OxS), which appears as a result of lipid deposition in affected tissues. However, the molecular mechanisms that lead to OxS generation are different in each disease. Non-coding RNAs (ncRNAs) are RNA transcripts that do not encode proteins and function by regulating gene expression. In recent years, the involvement of ncRNAs in OxS modulation has become more recognized. This review summarizes the most recent advances regarding ncRNA-mediated regulation of OxS in atherosclerosis and NAFLD. In both diseases, ncRNAs can exert pro-oxidant or antioxidant functions by regulating gene targets and even other ncRNAs, positioning them as potential therapeutic targets. Interestingly, both diseases have common altered ncRNAs, suggesting that the same molecule can be targeted simultaneously when both diseases coexist. Finally, since some ncRNAs have already been used as therapeutic agents, their roles as potential drugs for the clinical management of atherosclerosis and NAFLD are analyzed., Ministerio de Ciencia e Innovación (España), Depto. de Bioquímica y Biología Molecular, Fac. de Farmacia, TRUE, pub, Descuento UCM

Tesis por compendio, [ES] El cáncer constituye la segunda causa de muerte en España. El tromboembolismo venoso (TEV), una complicación del cáncer, conlleva gran gasto del presupuesto sanitario y representa la segunda causa de muerte en estos pacientes. Sin embargo, las herramientas actuales disponibles para la identificación de pacientes oncológicos con elevado riesgo trombótico son limitadas. Adicionalmente, no existen métodos simples, mínimamente invasivos y económicos de diagnóstico de cáncer vesical. Por este motivo, se utilizan técnicas dañinas como la tomografía computarizada la cual implica una elevada dosis de exposición a radiación y procedimientos invasivos como la cistoscopia. Además, un estado hipercoagulable parece tener una relación directa con una mayor carga tumoral y un peor pronóstico. El objetivo principal de la presente Tesis Doctoral es explorar la utilidad clínica de nuevos métodos diagnósticos y pronósticos para el cáncer y sus complicaciones trombóticas. En la primera parte de la Tesis, nos hemos centrado en el papel de miRNAs en orina como biomarcadores de cáncer vesical. Hemos identificado al miR-29c-3p como el miRNA más estable por lo que fue utilizado como normalizador. Hemos ajustado un modelo de regresión logística ordinal para el diagnóstico y estratificación de cáncer vesical utilizando la expresión de miRNAs en orina de pacientes y controles. Este modelo incluyó la expresión de 7 miRNAs: miR-221-3p, miR-93-5p, miR-362-3p, miR-191-5p, miR-200c-3p, miR-192-5p y miR-21-5p. En la segunda parte de la Tesis, nos centramos en el estudio de nuevos biomarcadores para la trombosis asociada a cáncer. Analizamos el potencial predictivo de los miRNAs y de marcadores de activación de neutrófilos en pacientes con cáncer pancreático y pacientes con glioma y meningioma. En cáncer pancreático, obtuvimos un perfil de 7 miRNAs (miR-486-5p, miR-106b-5p, let-7i-5p, let-7g-5p, miR-144-3p, miR-19a-3p y miR-103a-3p) capaz de estimar el riesgo de TEV al diagnóstico con dianas inc, [CA] El càncer constitueix la segona causa de mort a Espanya. El tromboembolisme venós (TEV), una complicació del càncer, representa la segona causa de mort en aquests pacients i comporta una gran despesa sanitària. No obstant això, les eines disponibles actualment per a la identificació de pacients oncològics amb elevat risc trombòtic són limitades. Actualment, no existeixen mètodes diagnòstics per al càncer de bufeta senzills, mínimament invasius i econòmics. Per aquest motiu, s'utilitzen tècniques nocives com la tomografia computada la qual implica una elevada dosi d'exposició a radiació i procediments invasius com la cistoscòpia. A més, un estat hipercoagulable sembla tindre una relació directa amb una major càrrega tumoral i un pitjor pronòstic. L'objectiu principal de la present Tesi Doctoral fou explorar la utilitat clínica de nous mètodes diagnòstics i pronòstics per al càncer i les seues complicacions trombòtiques. En la primera part de la Tesi, ens hem centrat en el paper dels microRNAs (miRNAs) en orina com biomarcadors de càncer de bufeta. Hem identificat al miR-29c-3p com el miRNA més estable per la qual cosa va ser utilitzat com a normalitzador. Hem ajustat un model de regressió logística ordinal per al diagnòstic i estratificació de càncer de bufeta utilitzant l'expressió de miRNAs en orina de pacients i controls. Aquest model va incloure l'expressió de 7 miRNAs: miR-221-3p, miR-93-5p, miR-362-3p, miR-191-5p, miR-200c-3p, miR-192-5p i miR-21-5p. En la segona part de la Tesi, ens centràrem en l'estudi de nous biomarcadors per a la trombosi associada a càncer. Analitzàrem el potencial predictiu dels miRNAs i de marcadors d'activació de neutròfils en pacients amb càncer pancreàtic i pacients amb glioma i meningioma. En càncer pancreàtic, vàrem obtindre un perfil de 7 miRNAs (miR-486-5p, miR-106b-5p, let-7i-5p, let-7g-5p, miR-144-3p, miR-19a-3p i miR-103a-3p) capaç d'estimar el risc de TEV al diagnostic dels pacients els quals tenen dianes incloses en les, [EN] Cancer is the second leading cause of death in Spain. Collaterally, venous thromboembolism (VTE), as a complication of cancer, consumes a great part of its healthcare budget and, more importantly, it is the second cause of death in these patients. However, limited tools are available to identify high risk patients. Additionally, a simple, minimally invasive and economical diagnostic methods for bladder cancer are also lacking. For that aim, harmful techniques are used like CT scan with high radiation exposure and invasive procedures like cystoscopy. Moreover, a hypercoagulable state seems directly related to a large tumor burden and poor prognosis. The overall aim of this Doctoral Thesis is to explore the clinical utility of novel diagnostic and prognostic methods for cancer and its thrombotic complications. In the first part of this Doctoral Thesis, we focused on the role of urine miRNAs as bladder cancer biomarkers. We identified miR-29c-3p as the most stable miRNA and was therefore used as normalizer. We adjusted an ordinal logistic regression model for the diagnosis and stratification of BC using the urine miRNA expression levels of patients and controls. This model included 7 miRNAs: miR-221-3p, miR-93-5p, miR-362-3p, miR-191-5p, miR-200c-3p, miR-192-5p and miR-21-5p. In the second part of this Doctoral Thesis, we focused on the study of novel biomarkers for cancer-associated thrombosis. We analyzed the predictive potential of miRNAs and neutrophil activation markers of thrombotic events in patients with pancreatic cancer and patients with glioma and meningioma. In pancreatic cancer, we obtained a profile of 7 miRNAs (miR-486-5p, miR-106b-5p, let-7i-5p, let-7g-5p, miR-144-3p, miR-19a-3p and miR-103a-3p) able to estimate the risk of potential VTE at diagnosis with targets involved in the pancreatic cancer and complement and coagulation cascades pathways. In the study of the neutrophil activation makers, we obtained a new predictive model of VTE with calprot

Tesis por compendio, [ES] El cáncer constituye la segunda causa de muerte en España. El tromboembolismo venoso (TEV), una complicación del cáncer, conlleva gran gasto del presupuesto sanitario y representa la segunda causa de muerte en estos pacientes. Sin embargo, las herramientas actuales disponibles para la identificación de pacientes oncológicos con elevado riesgo trombótico son limitadas. Adicionalmente, no existen métodos simples, mínimamente invasivos y económicos de diagnóstico de cáncer vesical. Por este motivo, se utilizan técnicas dañinas como la tomografía computarizada la cual implica una elevada dosis de exposición a radiación y procedimientos invasivos como la cistoscopia. Además, un estado hipercoagulable parece tener una relación directa con una mayor carga tumoral y un peor pronóstico. El objetivo principal de la presente Tesis Doctoral es explorar la utilidad clínica de nuevos métodos diagnósticos y pronósticos para el cáncer y sus complicaciones trombóticas. En la primera parte de la Tesis, nos hemos centrado en el papel de miRNAs en orina como biomarcadores de cáncer vesical. Hemos identificado al miR-29c-3p como el miRNA más estable por lo que fue utilizado como normalizador. Hemos ajustado un modelo de regresión logística ordinal para el diagnóstico y estratificación de cáncer vesical utilizando la expresión de miRNAs en orina de pacientes y controles. Este modelo incluyó la expresión de 7 miRNAs: miR-221-3p, miR-93-5p, miR-362-3p, miR-191-5p, miR-200c-3p, miR-192-5p y miR-21-5p. En la segunda parte de la Tesis, nos centramos en el estudio de nuevos biomarcadores para la trombosis asociada a cáncer. Analizamos el potencial predictivo de los miRNAs y de marcadores de activación de neutrófilos en pacientes con cáncer pancreático y pacientes con glioma y meningioma. En cáncer pancreático, obtuvimos un perfil de 7 miRNAs (miR-486-5p, miR-106b-5p, let-7i-5p, let-7g-5p, miR-144-3p, miR-19a-3p y miR-103a-3p) capaz de estimar el riesgo de TEV al diagnóstico con dianas inc, [CA] El càncer constitueix la segona causa de mort a Espanya. El tromboembolisme venós (TEV), una complicació del càncer, representa la segona causa de mort en aquests pacients i comporta una gran despesa sanitària. No obstant això, les eines disponibles actualment per a la identificació de pacients oncològics amb elevat risc trombòtic són limitades. Actualment, no existeixen mètodes diagnòstics per al càncer de bufeta senzills, mínimament invasius i econòmics. Per aquest motiu, s'utilitzen tècniques nocives com la tomografia computada la qual implica una elevada dosi d'exposició a radiació i procediments invasius com la cistoscòpia. A més, un estat hipercoagulable sembla tindre una relació directa amb una major càrrega tumoral i un pitjor pronòstic. L'objectiu principal de la present Tesi Doctoral fou explorar la utilitat clínica de nous mètodes diagnòstics i pronòstics per al càncer i les seues complicacions trombòtiques. En la primera part de la Tesi, ens hem centrat en el paper dels microRNAs (miRNAs) en orina com biomarcadors de càncer de bufeta. Hem identificat al miR-29c-3p com el miRNA més estable per la qual cosa va ser utilitzat com a normalitzador. Hem ajustat un model de regressió logística ordinal per al diagnòstic i estratificació de càncer de bufeta utilitzant l'expressió de miRNAs en orina de pacients i controls. Aquest model va incloure l'expressió de 7 miRNAs: miR-221-3p, miR-93-5p, miR-362-3p, miR-191-5p, miR-200c-3p, miR-192-5p i miR-21-5p. En la segona part de la Tesi, ens centràrem en l'estudi de nous biomarcadors per a la trombosi associada a càncer. Analitzàrem el potencial predictiu dels miRNAs i de marcadors d'activació de neutròfils en pacients amb càncer pancreàtic i pacients amb glioma i meningioma. En càncer pancreàtic, vàrem obtindre un perfil de 7 miRNAs (miR-486-5p, miR-106b-5p, let-7i-5p, let-7g-5p, miR-144-3p, miR-19a-3p i miR-103a-3p) capaç d'estimar el risc de TEV al diagnostic dels pacients els quals tenen dianes incloses en les, [EN] Cancer is the second leading cause of death in Spain. Collaterally, venous thromboembolism (VTE), as a complication of cancer, consumes a great part of its healthcare budget and, more importantly, it is the second cause of death in these patients. However, limited tools are available to identify high risk patients. Additionally, a simple, minimally invasive and economical diagnostic methods for bladder cancer are also lacking. For that aim, harmful techniques are used like CT scan with high radiation exposure and invasive procedures like cystoscopy. Moreover, a hypercoagulable state seems directly related to a large tumor burden and poor prognosis. The overall aim of this Doctoral Thesis is to explore the clinical utility of novel diagnostic and prognostic methods for cancer and its thrombotic complications. In the first part of this Doctoral Thesis, we focused on the role of urine miRNAs as bladder cancer biomarkers. We identified miR-29c-3p as the most stable miRNA and was therefore used as normalizer. We adjusted an ordinal logistic regression model for the diagnosis and stratification of BC using the urine miRNA expression levels of patients and controls. This model included 7 miRNAs: miR-221-3p, miR-93-5p, miR-362-3p, miR-191-5p, miR-200c-3p, miR-192-5p and miR-21-5p. In the second part of this Doctoral Thesis, we focused on the study of novel biomarkers for cancer-associated thrombosis. We analyzed the predictive potential of miRNAs and neutrophil activation markers of thrombotic events in patients with pancreatic cancer and patients with glioma and meningioma. In pancreatic cancer, we obtained a profile of 7 miRNAs (miR-486-5p, miR-106b-5p, let-7i-5p, let-7g-5p, miR-144-3p, miR-19a-3p and miR-103a-3p) able to estimate the risk of potential VTE at diagnosis with targets involved in the pancreatic cancer and complement and coagulation cascades pathways. In the study of the neutrophil activation makers, we obtained a new predictive model of VTE with calprot

MicroRNAs (miRNAs) constitute a new category of biomarkers. Studies on miRNAs in non-mammalian species have drastically increased in the last few years. Here, we explored the use of miRNAs as potential, poorly invasive markers, to identify sex and characterize acute stress in fish. The European seabass (Dicentrarchus labrax) was chosen as a model because of its rapid response to stress and its specific sex determination system, devoid of sexual chromosomes. We performed a small RNA-sequencing analysis in the blood plasma of male and female European seabass (mature and immature) as well as in the blood plasma of juveniles submitted to an acute stress and sampled throughout the recovery period (at 0 h, 0.5 h, 1.5 h and 6 h). In immature individuals, both miR-1388-3p and miR-7132a-5p were up-regulated in females, while miR-499a-5p was more abundant in males. However, no miRNAs were found to be differentially expressed between sexes in the blood plasma of mature individuals. For the acute stress analysis, five miRNAs (miR-155-5p, miR-200a-3p, miR-205-1-5p, miR-143-3p, and miR-223-3p) followed cortisol production over time. All miRNAs identified were tested and validated by RT-qPCR on sequenced samples. A complementary analysis on the 3′UTR sequences of the European seabass allowed to predict potential mRNA targets, some of them being particularly relevant regarding stress regulation, e.g., the glucocorticoid receptor 1 and the mineralocorticoid receptor. The present study provides new avenues and recommendations on the use of miRNAs as biomarkers of sex or stress of the European seabass, with potential application on other fish species.

Introduction. Albuminuria greater than 300mg/dL/24h (A1-300mg/g) is a characteristic of diabetic nephropathy (DN), which can trigger the development of advanced chronic kidney disease (ACKD). Objective. Identify genes regulated by miRNAs that are associated with DN through an in-silico analysis. Material and methods. Through the use of microarrays and bioinformatic analysis, potential miRNA target genes were identified: hsa-miR-126-3p, miR-320a-3p, and miR-1288-3p. These genes were subjected to signaling pathway analysis to identify processes associated with DN pathogenesis. Results. 57 target genes were identified from the analyzed miRNAs, which were associated with 14 genetic ontologies and 7 KEGG signaling pathways. These results allowed the generation of an in-silico model showing an interaction network between target genes regulated by miRNAs whose alteration can lead to the development of ND. Conclusions. In the in-silico model, the network of interactions found between target genes regulated by miRNAs could contribute to the understanding of the DN mechanism, opening the panorama for new research on genes and miRNAs that could be evaluated as markers in the early detection of DN., Introducción. Albuminuria superior a 300 mg/dL/24h (A1-300mg/g) es una característica de la nefropatía diabética (ND), lo que puede desencadenar en el desarrollo de enfermedad renal crónica avanzada (ERCA). Objetivo. Identificar genes regulados por miRNAs asociados con ND a través de un análisis in sílico. Material y Métodos. A través del uso de microarreglos y análisis bioinformáticos se identificaron potenciales genes blancos de los miRNAs; hsa-miR-126-3p, miR-320a-3p y miR-1288-3p. Estos genes fueron sometidos a un análisis de vías de señalización para identificar procesos asociados con la patogénesis de la ND. Resultados. Se identificaron 57 genes blanco de los miRNAs analizados, los cuales fueron asociados con 14 ontologías genéticas y 7 vías de señalización KEGG. Estos resultados permitieron generar un modelo in sílico en el que se muestra una red de interacción entre genes blanco regulados por miRNAs cuya alteración puede conducir al desarrollo de la ND. Conclusiones. En el modelo in sílico la red de interacciones encontradas entre genes blancoregulados por miRNAs podrían contribuir a la comprensión del mecanismo de la ND abriendo el panorama para realizar nuevas investigaciones sobre genes y miRNAs que podrían ser evaluados como marcadores en la detección temprana de la ND

Micro RNAs (miRNAs) are known regulators of various processes in plants, including growth, development and stress responses. They achieve this through mRNA cleavage or translational inhibition, in a process called RNA interference. Herein, their role in chilling stress response in young maize seedlings (Zea mays L.) is examined, using high-throughput sequencing methods. Bringing light to all aspects of chilling stress response in maize is necessary since earlier sowing, during colder periods, is one of the most promising strategies of avoiding maize yield loss due to effects of climate change in these areas. Sterilized seeds of two maize genotypes (tolerant - T and sensitive - S to low temperatures) were germinated in the dark for five days (optimal conditions), after which the 5-d old seedlings were exposed to chilling conditions for 6h (10° C). Samples for RNA isolation and cDNA library preparation were taken after the treatment ended, and single-end 50 bp sequencing was performed (Illumina® Novaseq 6000). The miRNAs were then filtered, mapped, identified and quantified using adequate bioinformatics tools; and the differential expression analysis was carried out using the DEGseq R package. The analysis was performed on 859 miRNAs, after previously executed TPM normalization using the MA-plot-based method with random sampling model (MARS). The threshold for significantly differential expression was set as the Bayesian adjusted p-value, or q-value < 0.01 and log2 fold change > 1. A total of 612 were expressed differentially, but only 55 miRNAs were common for both genotypes and at the same time differentially expressed between control and treatment conditions – 40 novel and 15 known. Half of the common miRNAs showed the same expression patterns in both genotypes, while the other half did not. Among them, seven known miRNAs showed opposing expression patterns between the genotypes (zma-miR167b-3p zma-miR167e-3p, zma-miR159c-5p, zma-miR164g-3p, zma-miR166a-5p, zma-miR

Epigenetic changes may be biomarkers of health. Epigenetic age acceleration (EAA), the discrepancy between epigenetic age measured via epigenetic clocks and chronological age, is associated with morbidity and mortality. However, the intersection of epigenetic clocks with microRNAs (miRNAs) and corresponding miRNA-based health implications have not been evaluated. We analyzed DNA methylation and miRNA profiles from blood sampled among 332 individuals enrolled across 2 U.S.-based firefighter occupational studies (2015-2018 and 2018-2020). We considered 7 measures of EAA in leukocytes (PhenoAge, GrimAge, Horvath, skin-blood, and Hannum epigenetic clocks, and extrinsic and intrinsic epigenetic age acceleration). We identified miRNAs associated with EAA using individual linear regression models, adjusted for sex, race/ethnicity, chronological age, and cell type estimates, and investigated downstream effects of associated miRNAs with miRNA enrichment analyses and genomic annotations. On average, participants were 38 years old, 88% male, and 75% non-Hispanic white. We identified 183 of 798 miRNAs associated with EAA (FDR q < 0.05); 126 with PhenoAge, 59 with GrimAge, 1 with Horvath, and 1 with the skin-blood clock. Among miRNAs associated with Horvath and GrimAge, there were 61 significantly enriched disease annotations including age-related metabolic and cardiovascular conditions and several cancers. Enriched pathways included those related to proteins and protein modification. We identified miRNAs associated with EAA of multiple epigenetic clocks. PhenoAge had more associations with individual miRNAs, but GrimAge and Horvath had greater implications for miRNA-associated pathways. Understanding the relationship between these epigenetic markers could contribute to our understanding of the molecular underpinnings of aging and aging-related diseases.

Systemic lupus erythematosus (SLE) is a chronic immune-inflammatory disease characterized by multiorgan affectation and lowered self-tolerance. Additionally, epigenetic changes have been described as playing a pivotal role in SLE. This work aims to assess the effects of oleacein (OLA), one of the main extra virgin olive oil secoiridoids, when used to supplement the diet of a murine pristane-induced SLE model. In the study, 12-week-old female BALB/c mice were injected with pristane and fed with an OLA-enriched diet (0.01 % (w/w)) for 24 weeks. The presence of immune complexes was evaluated by immunohistochemistry and immunofluorescence. Endothelial dysfunction was studied in thoracic aortas. Signaling pathways and oxidative-inflammatory-related mediators were evaluated by Western blotting. Moreover, we studied epigenetic changes such as DNA methyltransferase (DNMT-1) and micro(mi)RNAs expression in renal tissue. Nutritional treatment with OLA reduced the deposition of immune complexes, ameliorating kidney damage. These protective effects could be related to the modulation of mitogen-activated protein kinases, the Janus kinase/signal transducer and transcription activator of transcription, nuclear factor kappa, nuclear-factor-erythroid-2-related factor 2, inflammasome signaling pathways, and the regulation of miRNAs (miRNA-126, miRNA-146a, miRNA-24-3p, and miRNA-123) and DNMT-1 expression. Moreover, the OLA-enriched diet normalized endothelial nitric oxide synthase and nicotinamide adenine dinucleotide phosphate (NADPH) oxidase-1 overexpression. These preliminary results suggest that an OLA-supplemented diet could constitute a new alternative nutraceutical therapy in the management of SLE, supporting this compound as a novel epigenetic modulator of the immunoinflammatory response.

In this study, novel Trojan particles were engineered for direct delivery of doxorubicin (DOX) and miR-34a as model drugs to the lungs to raise local drug concentration, decrease pulmonary clearance, increase lung drug deposition, reduce systemic side effects, and overcome multi-drug resistance. For this purpose, targeted polyelectrolyte nanoparticles (tPENs) developed with layer-by-layer polymers (i.e., chitosan, dextran sulfate, and mannose-g-polyethyleneimine) were spray dried into a multiple-excipient (i.e., chitosan, leucine, and mannitol). The resulting nanoparticles were first characterized in terms of size, morphology, in vitro DOX release, cellular internalization, and in vitro cytotoxicity. tPENs showed comparable cellular uptake levels to PENs in A549 cells and no significant cytotoxicity on their metabolic activity. Co-loaded DOX/miR-34a showed a greater cytotoxicity effect than DOX-loaded tPENs and free drugs, which was confirmed by Actin staining. Thereafter, nano-in-microparticles were studied through size, morphology, aerosolization efficiency, residual moisture content, and in vitro DOX release. It was demonstrated that tPENs were successfully incorporated into microspheres with adequate emitted dose and fine particle fraction but low mass median aerodynamic diameter for deposition into the deep lung. The dry powder formulations also demonstrated a sustained DOX release at both pH values of 6.8 and 7.4.

Systemic lupus erythematosus (SLE) is a chronic immune-inflammatory disease characterized by multiorgan affectation and lowered self-tolerance. Additionally, epigenetic changes have been described as playing a pivotal role in SLE. This work aims to assess the effects of oleacein (OLA), one of the main extra virgin olive oil secoiridoids, when used to supplement the diet of a murine pristane-induced SLE model. In the study, 12-week-old female BALB/c mice were injected with pristane and fed with an OLA-enriched diet (0.01 % (w/w)) for 24 weeks. The presence of immune complexes was evaluated by immunohistochemistry and immunofluorescence. Endothelial dysfunction was studied in thoracic aortas. Signaling pathways and oxidative-inflammatory-related mediators were evaluated by Western blotting. Moreover, we studied epigenetic changes such as DNA methyltransferase (DNMT-1) and micro(mi)RNAs expression in renal tissue. Nutritional treatment with OLA reduced the deposition of immune complexes, ameliorating kidney damage. These protective effects could be related to the modulation of mitogen-activated protein kinases, the Janus kinase/signal transducer and transcription activator of transcription, nuclear factor kappa, nuclear-factor-erythroid-2-related factor 2, inflammasome signaling pathways, and the regulation of miRNAs (miRNA-126, miRNA-146a, miRNA-24-3p, and miRNA-123) and DNMT-1 expression. Moreover, the OLA-enriched diet normalized endothelial nitric oxide synthase and nicotinamide adenine dinucleotide phosphate (NADPH) oxidase-1 overexpression. These preliminary results suggest that an OLA-supplemented diet could constitute a new alternative nutraceutical therapy in the management of SLE, supporting this compound as a novel epigenetic modulator of the immunoinflammatory response.

Systemic lupus erythematosus (SLE) is a chronic immune-inflammatory disease characterized by multiorgan affectation and lowered self-tolerance. Additionally, epigenetic changes have been described as playing a pivotal role in SLE. This work aims to assess the effects of oleacein (OLA), one of the main extra virgin olive oil secoiridoids, when used to supplement the diet of a murine pristane-induced SLE model. In the study, 12-week-old female BALB/c mice were injected with pristane and fed with an OLA-enriched diet (0.01 % (w/w)) for 24 weeks. The presence of immune complexes was evaluated by immunohistochemistry and immunofluorescence. Endothelial dysfunction was studied in thoracic aortas. Signaling pathways and oxidative-inflammatory-related mediators were evaluated by Western blotting. Moreover, we studied epigenetic changes such as DNA methyltransferase (DNMT-1) and micro(mi)RNAs expression in renal tissue. Nutritional treatment with OLA reduced the deposition of immune complexes, ameliorating kidney damage. These protective effects could be related to the modulation of mitogen-activated protein kinases, the Janus kinase/signal transducer and transcription activator of transcription, nuclear factor kappa, nuclear-factor-erythroid-2-related factor 2, inflammasome signaling pathways, and the regulation of miRNAs (miRNA-126, miRNA-146a, miRNA-24-3p, and miRNA-123) and DNMT-1 expression. Moreover, the OLA-enriched diet normalized endothelial nitric oxide synthase and nicotinamide adenine dinucleotide phosphate (NADPH) oxidase-1 overexpression. These preliminary results suggest that an OLA-supplemented diet could constitute a new alternative nutraceutical therapy in the management of SLE, supporting this compound as a novel epigenetic modulator of the immunoinflammatory response.

Systemic lupus erythematosus (SLE) is a chronic immune-inflammatory disease characterized by multiorgan affectation and lowered self-tolerance. Additionally, epigenetic changes have been described as playing a pivotal role in SLE. This work aims to assess the effects of oleacein (OLA), one of the main extra virgin olive oil secoiridoids, when used to supplement the diet of a murine pristane-induced SLE model. In the study, 12-week-old female BALB/c mice were injected with pristane and fed with an OLA-enriched diet (0.01 % (w/w)) for 24 weeks. The presence of immune complexes was evaluated by immunohistochemistry and immunofluorescence. Endothelial dysfunction was studied in thoracic aortas. Signaling pathways and oxidative-inflammatory-related mediators were evaluated by Western blotting. Moreover, we studied epigenetic changes such as DNA methyltransferase (DNMT-1) and micro(mi)RNAs expression in renal tissue. Nutritional treatment with OLA reduced the deposition of immune complexes, ameliorating kidney damage. These protective effects could be related to the modulation of mitogen-activated protein kinases, the Janus kinase/signal transducer and transcription activator of transcription, nuclear factor kappa, nuclear-factor-erythroid-2-related factor 2, inflammasome signaling pathways, and the regulation of miRNAs (miRNA-126, miRNA-146a, miRNA-24-3p, and miRNA-123) and DNMT-1 expression. Moreover, the OLA-enriched diet normalized endothelial nitric oxide synthase and nicotinamide adenine dinucleotide phosphate (NADPH) oxidase-1 overexpression. These preliminary results suggest that an OLA-supplemented diet could constitute a new alternative nutraceutical therapy in the management of SLE, supporting this compound as a novel epigenetic modulator of the immunoinflammatory response.

MicroRNAs (miRNAs) constitute a new category of biomarkers. Studies on miRNAs in non-mammalian species have drastically increased in the last few years. Here, we explored the use of miRNAs as potential, poorly invasive markers, to identify sex and characterize acute stress in fish. The European seabass (Dicentrarchus labrax) was chosen as a model because of its rapid response to stress and its specific sex determination system, devoid of sexual chromosomes. We performed a small RNA-sequencing analysis in the blood plasma of male and female European seabass (mature and immature) as well as in the blood plasma of juveniles submitted to an acute stress and sampled throughout the recovery period (at 0 h, 0.5 h, 1.5 h and 6 h). In immature individuals, both miR-1388-3p and miR-7132a-5p were up-regulated in females, while miR-499a-5p was more abundant in males. However, no miRNAs were found to be differentially expressed between sexes in the blood plasma of mature individuals. For the acute stress analysis, five miRNAs (miR-155-5p, miR-200a-3p, miR-205-1-5p, miR-143-3p, and miR-223-3p) followed cortisol production over time. All miRNAs identified were tested and validated by RT-qPCR on sequenced samples. A complementary analysis on the 3′UTR sequences of the European seabass allowed to predict potential mRNA targets, some of them being particularly relevant regarding stress regulation, e.g., the glucocorticoid receptor 1 and the mineralocorticoid receptor. The present study provides new avenues and recommendations on the use of miRNAs as biomarkers of sex or stress of the European seabass, with potential application on other fish species.

Microprocessor (MP), DROSHA-DGCR8, processes primary miRNA transcripts (pri-miRNAs) to initiate miRNA biogenesis. The canonical cleavage mechanism of MP has been extensively investigated and comprehensively validated for two decades. However, this canonical mechanism cannot account for the processing of certain pri-miRNAs in animals. In this study, by conducting high-throughput pri-miRNA cleavage assays for approximately 260,000 pri-miRNA sequences, we discovered and comprehensively characterized a noncanonical cleavage mechanism of MP. This noncanonical mechanism does not need several RNA and protein elements essential for the canonical mechanism; instead, it utilizes previously unrecognized DROSHA dsRNA recognition sites (DRESs). Interestingly, the noncanonical mechanism is conserved across animals and plays a particularly significant role in C. elegans. Our established noncanonical mechanism elucidates MP cleavage in numerous RNA substrates unaccounted for by the canonical mechanism in animals. This study suggests a broader substrate repertoire of animal MPs and an expanded regulatory landscape for miRNA biogenesis.

5S rRNA is highly transcribed in fish oocytes and this transcription levels can be used to identify the presence of oocytes in the intersex testes of fish exposed to xenoestrogens. Similar to 5S rRNA, tRNAs are transcribed by RNA polymerase III (Pol-III) in eukaryotes, so this study focuses in the analysis of the levels of expression of tRNAs in the gonads (ovaries and testes) of eight teleost species as a possible new oocyte molecular marker. Total RNA extracted from gonads of six commercial teleost species in the Biscay Bay, from the pollution sentinel species thicklip grey mullet (Chelon labrosus) known present intersex testes in response to xenoestrogens in Gernika estuary and from the laboratory model species Danio rerio were analysed through capillary electrophoresis. Bioanalyzer electropherograms were used to quantify the concentrations of tRNAs, 5S and 5.8S rRNA. All studied ovaries expressed significantly higher levels of tRNAs and 5S rRNA than testes. A tRNA to 5.8S rRNA index was calculated which differentiates ovaries from testes, and identifies some intersex testes in between testes and ovaries in mullets. The tRNA/5.8S ratio was highest in ovaries in previtellogenic stage, decreasing towards maturity. Thus, strong oocyte expression of tRNAs is an additional proof of high activity levels of Pol-III during early stages of oocyte development in teleost ovaries. Incidentally, we observed that miRNA concentrations were always higher in testes than ovaries. The indexing approach developed in the present study could have multiple applications in teleost reproduction research and in the development of early molecular markers of intersex condition.

Metabolic diseases such as obesity, diabetes, dyslipidemia, and insulin resistance are characterized by glucose and lipid metabolism alterations and represent a global health problem. Many studies have established the crucial role of micro-ribonucleic acids (miRNAs) in controlling metabolic processes in various tissues. miRNAs are single-stranded, highly conserved non-coding RNAs containing 20-24 oligonucleotides that are expressed in a tissue-specific manner. miRNAs mainly interact through base pairing with 3' untranslated regions of target gene mRNAs to promote inhibition of their translation. miRNAs regulate the expression of as many as 30% of the human genes and have a role in crucial physiological processes such as human growth and development, cell proliferation, apoptosis, and metabolism. The number of miRNA molecules with a confirmed role in the pathogenesis of metabolic diseases is quickly expanding due to the availability of high-throughput methodologies for their identification. In this review, we present recent findings regarding the role of miRNAs as endocrine signaling molecules involved in the regulation of insulin production and fat metabolism. We discuss the potential of extracellular miRNAs present in biological fluids miRNAs as biomarkers for the prediction of diabetes and MetS. We also give an updated overview of therapeutic interventions based on antisense oligonucleotides and the CRISPR/Cas9 editing platform for manipulating levels of miRNAs involved in metabolic disorders. © 2023 Bentham Science Publishers.

In this course, we will investigate the diverse types and functions of different RNA species, with a focus on "non-coding RNAs," i.e. those that do not directly encode proteins. The course will convey both the exciting discoveries in and frontiers of RNA research that are propelling our understanding of cell biology as well as the intellectual and experimental approaches responsible.The molecular biology revolution firmly established the role of DNA as the primary carrier of genetic information and proteins as the primary effector molecules of the cell. The intermediate between DNA and proteins is RNA, which initially was regarded as the "molecule in the middle" of the central dogma. This view has been transformed over the past two decades, as RNA has become recognized as a critical regulator of cellular processes. &nbsp

In this course, we will investigate the diverse types and functions of different RNA species, with a focus on "non-coding RNAs," i.e. those that do not directly encode proteins. The course will convey both the exciting discoveries in and frontiers of RNA research that are propelling our understanding of cell biology as well as the intellectual and experimental approaches responsible.The molecular biology revolution firmly established the role of DNA as the primary carrier of genetic information and proteins as the primary effector molecules of the cell. The intermediate between DNA and proteins is RNA, which initially was regarded as the "molecule in the middle" of the central dogma. This view has been transformed over the past two decades, as RNA has become recognized as a critical regulator of cellular processes. &nbsp

In this study, novel Trojan particles were engineered for direct delivery of doxorubicin (DOX) and miR-34a as model drugs to the lungs to raise local drug concentration, decrease pulmonary clearance, increase lung drug deposition, reduce systemic side effects, and overcome multi-drug resistance. For this purpose, targeted polyelectrolyte nanoparticles (tPENs) developed with layer-by-layer polymers (i.e., chitosan, dextran sulfate, and mannose-g-polyethyleneimine) were spray dried into a multiple-excipient (i.e., chitosan, leucine, and mannitol). The resulting nanoparticles were first characterized in terms of size, morphology, in vitro DOX release, cellular internalization, and in vitro cytotoxicity. tPENs showed comparable cellular uptake levels to PENs in A549 cells and no significant cytotoxicity on their metabolic activity. Co-loaded DOX/miR-34a showed a greater cytotoxicity effect than DOX-loaded tPENs and free drugs, which was confirmed by Actin staining. Thereafter, nano-in-microparticles were studied through size, morphology, aerosolization efficiency, residual moisture content, and in vitro DOX release. It was demonstrated that tPENs were successfully incorporated into microspheres with adequate emitted dose and fine particle fraction but low mass median aerodynamic diameter for deposition into the deep lung. The dry powder formulations also demonstrated a sustained DOX release at both pH values of 6.8 and 7.4.

[Background and Aims]: The molecular mechanisms driving non-alcoholic fatty liver disease (NAFLD) are poorly understood; however, microRNAs might play a key role in these processes. We hypothesize that let-7d- 5p could contribute to the pathophysiol-ogy of NAFLD and serve as a potential diagnostic biomarker., [Methods]: We evaluated let-7d- 5p levels and its targets in liver biopsies from a cross- sectional study including patients with NAFLD and healthy donors, and from a mouse model of NAFLD. Moreover, the induction of let-7d- 5p expression by fatty acids was evaluated in vitro. Further, we overexpressed let-7d- 5p in vitro to corroborate the results observed in vivo. Circulating let-7d- 5p and its potential as a NAFLD biomarker was determined in isolated extracellular vesicles from human plasma by RT-qPCR., [Results]: Our results demonstrate that hepatic let-7d-5p was significantly up-regulated in patients with steatosis, and this increase correlated with obesity and a decreased expression of AKT serine/threonine kinase (AKT), insulin-like growth factor 1 (IGF1), IGF-I receptor (IGF1R) and insulin receptor (INSR). These alterations were corroborated in a NAFLD mouse model. In vitro, fatty acids increased let-7d-5p expression, and its overexpression decreased AKT, IGF-IR and IR protein expression. Furthermore, let-7d-5p hindered AKT phosphorylation in vitro after insulin stimulation. Finally, circulating let-7d-5p significantly decreased in steatosis patients and receiver operating characteristic (ROC) analyses confirmed its utility as a diagnostic biomarker., [Conclusions]: Our results highlight the emerging role of let-7d-5p as a potential therapeutic target for NAFLD since its overexpression impairs hepatic insulin signalling, and also, as a novel non-invasive biomarker for NAFLD diagnosis.

Systemic lupus erythematosus (SLE) is a chronic immune-inflammatory disease characterized by multiorgan affectation and lowered self-tolerance. Additionally, epigenetic changes have been described as playing a pivotal role in SLE. This work aims to assess the effects of oleacein (OLA), one of the main extra virgin olive oil secoiridoids, when used to supplement the diet of a murine pristane-induced SLE model. In the study, 12-week-old female BALB/c mice were injected with pristane and fed with an OLA-enriched diet (0.01 % (w/w)) for 24 weeks. The presence of immune complexes was evaluated by immunohistochemistry and immunofluorescence. Endothelial dysfunction was studied in thoracic aortas. Signaling pathways and oxidative-inflammatory-related mediators were evaluated by Western blotting. Moreover, we studied epigenetic changes such as DNA methyltransferase (DNMT-1) and micro(mi)RNAs expression in renal tissue. Nutritional treatment with OLA reduced the deposition of immune complexes, ameliorating kidney damage. These protective effects could be related to the modulation of mitogen-activated protein kinases, the Janus kinase/signal transducer and transcription activator of transcription, nuclear factor kappa, nuclear-factor-erythroid-2-related factor 2, inflammasome signaling pathways, and the regulation of miRNAs (miRNA-126, miRNA-146a, miRNA-24-3p, and miRNA-123) and DNMT-1 expression. Moreover, the OLA-enriched diet normalized endothelial nitric oxide synthase and nicotinamide adenine dinucleotide phosphate (NADPH) oxidase-1 overexpression. These preliminary results suggest that an OLA-supplemented diet could constitute a new alternative nutraceutical therapy in the management of SLE, supporting this compound as a novel epigenetic modulator of the immunoinflammatory response.

Cell-to-cell communication strategies include extracellular vesicles (EVs) in plants and animals. The bioactive molecules in a diet rich in vegetables and fruits are associated with disease-preventive effects. Plant-derived EVs (PDEVs) are biogenetically and morphologically comparable to mammalian EVs and transport bioactive molecules, including miRNAs. However, the biological functions of PDEVs are not fully understood, and standard isolation protocols are lacking. Here, PDEVs were isolated from four foods with a combination of ultracentrifugation and size exclusion chromatography, and evaluated as vehicles for enhanced transport of synthetic miRNAs. In addition, the role of food-derived EVs as carriers of dietary (poly)phenols and other secondary metabolites was investigated. EVs from broccoli, pomegranate, apple, and orange were efficiently isolated and characterized. In all four sources, 4 miRNA families were present in tissues and EVs. miRNAs present in broccoli and fruit-derived EVs showed a reduced RNase degradation and were ferried inside exposed cells. EVs transfected with a combination of ath-miR159a, ath-miR162a-3p, ath-miR166b-3p, and ath-miR396b-5p showed toxic effects on human cells, as did natural broccoli EVs alone. PDEVs transport trace amounts of phytochemicals, including flavonoids, anthocyanidins, phenolic acids, or glucosinolates. Thus, PDEVs can act as nanocarriers for functional miRNAs that could be used in RNA-based therapy

Colorectal cancer (CRC) is one of the main tumor pathologies in our society considering its incidence and mortality. Various authors have linked the development of CRC with overweight and obesity. However, no molecular markers have been defined to connect both pathologies and that can be assessed in serum for diagnostic and/or prognostic purposes. The main objective of this work is to analyze and correlate the expression levels of four miRNAs previously associated with cancer and/or obesity in patients affected by CRC, as well as in a control group without cancer, considering the body mass index (BMI) of subjects. The main novelty of this study consists in the variety of samples investigated: adipose tissues, omental and subcutaneous; serum; and tumor and non-tumor tissues in the case of CRC patients. Results conclude about the utility mainly of hsa-miR-143-3p and hsa-miR-181a-5p in the clinical management of CRC., Carlos III Institute of Health (Ministerio de Economía y Competitividad), Spain, European Union through the European Regional Development Fund (ERDF) ‘A way to make Europe’, Depto. de Bioquímica y Biología Molecular, Depto. de Medicina, Depto. de Cirugía, Fac. de Farmacia, Fac. de Medicina, TRUE, pub

MicroRNAs (miRNAs) are small, single-stranded, non-coding RNA molecules of 22-24 nucleotides that regulate gene expression. In the last decade, miRNAs have been described in sperm of several mammals, including cattle. It is known that miRNAs can act as key gene regulators of early embryogenesis in mice and humans; however, little is known about the content, expression, and function of sperm-borne miRNAs in early bovine embryo. In this study, total sperm RNA was isolated from 29 cryopreserved sperm samples (each coming from a separate bull) using a RNeasy kit and treatment with DNase I. RNA concentration and purity were determined through an Epoch spectrophotometer and an Agilent Bioanalyzer. The expression of 10 candidate miRNAs in bovine sperm (bta-miR-10a, bta-miR-10b, bta-miR-138, bta-miR-146b, bta-miR-19b, bta-miR-26a, bta-miR-34a, bta-miR-449a, bta-miR-495 and bta-miR-7), previously identified in testis and/or epididymis, was evaluated with RT-qPCR. The cel-miR-39-3p was used as a spike-in exogenous control. Nonparametric Mann-Whitney tests were run to evaluate which miRNAs were differentially expressed between bulls with high fertility [HF; non-return rates (NRR) ranging from 39.5 to 43.5] and those with subfertility (SF; NRR ranging from 33.3 to 39.3). Several sperm functionality parameters (e.g., viability, membrane stability or oxygen consumption, among others) were measured by multiplexing flow cytometry and oxygen sensing technologies.RNA concentration and purity (260/280 nm ratio) (mean ± SD) from the 29 samples were 99.3 ± 84.6 ng/µL and 1.97 ± 0.72, respectively. Bioanalyzer results confirmed the lack of RNA from somatic cells. In terms of the presence or absence of miRNAs, and after applying the Livak method, 8 out of 10 miRNAs (bta-miR-10b, -138, -146b

Extracellular vesicles (EVs) and their cargo microRNAs (miRNAs) are important regulators of embryo development to the blastocyst stage and beyond. Before implantation can take place, hatching of blastocysts from their zona pellucida is required. However, underlying mechanisms by which blastocyst formation and hatching are initiated remain largely unknown. Here, we provide evidence that embryonic EVs containing bta-miR-378a-3p play a crucial role in blastocyst hatching, using a bovine model. A customized procedure was used to isolate EV-miRNAs from culture droplets conditioned by individual bovine embryos that either developed to the blastocyst stage or did not (nonblastocyst). RNA sequencing identified 69 differentially expressed miRNAs between EVs derived from blastocyst conditioned medium (CM) and nonblastocyst CM. Among the miRNAs up-regulated in blastocyst CM, we selected bta-miR-378a-3p for further validation by functionality testing on developing in vitro embryos by means of mimics and inhibitors. Supplementing the embryo culture medium with miR-378a-3p mimic significantly improved blastocyst quality, with higher cell numbers and reduced apoptosis, and improved hatching, while the opposite was found after supplementation with miR-378a-3p inhibitor (P < 0.01). Transcriptomic analysis of embryos treated with miR-378 mimic/inhibitor showed differential expression (P < 0.01) of genes associated with embryo development and implantation, including RAP1GAP, ARFGEF2, SLC7A6, CENPA, SP1, LDLR, PYCR1, MYD88, TPP1, and NCOA3. In conclusion, miR-378a-3p is up-regulated in EVs secreted by embryos that develop to the blastocyst stage, and this EV-derived miR-378a-3p increases blastocyst quality and regulates embryo hatching, which is essential for embryo implantation.

Cell reprogramming is a groundbreaking technology that, in few decades, generated a new paradigm in biomedical science. To date we can use cell reprogramming to potentially generate every cell type by converting somatic cells and suitably modulating the expression of key transcription factors. This approach can be used to convert skin fibroblasts into pluripotent stem cells as well as into a variety of differentiated and medically relevant cell types, including cardiomyocytes and neural cells. The molecular mechanisms underlying such striking cell phenotypes are still largely unknown, but in the last decade it has been proven that cell reprogramming approaches are significantly influenced by non-coding RNAs. Specifically, this review will focus on the role of microRNAs in the reprogramming processes that lead to the generation of pluripotent stem cells, neurons, and cardiomyocytes. As highlighted here, non-coding RNA-forced expression can be sufficient to support some cell reprogramming processes, and, therefore, we will also discuss how these molecular determinants could be used in the future for biomedical purposes.

[ES] La presente tesis doctoral, titulada "papel del miR-99a-5p en cáncer de mama: transformando hallazgos moleculares en herramientas clínicas" está centrada en el estudio del microRNA miR-99a-5p en cáncer de mama y en la determinación de su potencial como diana terapéutica y biomarcador para el diagnóstico de dicha enfermedad. En el primer capítulo, se lleva a cabo una revisión general del cáncer de mama y los microRNAs. A continuación, en el segundo capítulo se presentan los objetivos. En el tercer capítulo se compararon los perfiles de expresión de microRNAs de una línea celular de cáncer de mama resistente a doxorrubicina frente a la línea celular parental, dando lugar a la identificación del microRNA miR-99a-5p como el más desregulado entre ambas. A continuación, se confirmó que el miR-99a-5p aumenta la sensibilidad a doxorrubicina mediante la inhibición directa de la expresión de COX-2, que conlleva la inhibición de la expresión de la proteína ABCG2, ampliamente descrita por su papel en resistencia a fármacos. En base a los resultados obtenidos, se diseñaron nanodispositivos basados en nanopartículas mesoporosas de sílice para la liberación de miR-99a-5p y doxorrubicina en los tumores. Se confirmó la eficacia de las nanopartículas para reducir el crecimiento tumoral así como los efectos adversos asociados a la doxorrubicina libre en un modelo ortotópico murino de cáncer de mama. En el cuarto capítulo, se evaluó el potencial del miR-99a-5p como biomarcador para el diagnóstico del cáncer de mama. Se determinó la expresión del microRNA en tumores primarios de cáncer de mama y en tejidos sanos. Los resultados mostraron que el miR-99a-5p se encuentra infraexpresado en los tejidos cancerosos. A continuación, con el objeto de determinar el potencial del miR-99a-5p como biomarcador mínimamente invasivo, se determinaron los niveles de expresión en plasma de pacientes de cáncer de mama y de donantes sanos. Se encontró que el miR-99a-5p se encuentra a mayor concentració, [CA] La present tesis doctoral, titulada "paper del miR-99a-5p en càncer de mama: transformant descobriments moleculars en eines clíniques" està centrada en l'estudi del microRNA miR-99a-5p en càncer de mama i en la determinació del seu potencial com a diana terapèutica i biomarcador per al diagnòstic d'aquesta malaltia. En el primer capítol, es du a terme una revisió general del càncer de mama i els microRNAs. A continuació, en el segon capítol es presenten els objectius. En el tercer capítol es van comparar els perfils d'expressió de microRNAs d'una línia cel·lular de càncer de mama resistent a doxorrubicina amb la seua línia parental, donant lloc a la identificació del microRNA miR-99a-5p com el més desregulat entre ambdues. A continuació, es va confirmar que el miR-99a-5p augmenta la sensibilitat al fàrmac mijançant la inhibició directa de l'expressió de COX-2 de forma directa, que comporta la inhibició de l'expressió de la proteïna ABCG2 que està àmpliament descrita pel seu paper en resistència a fàrmacs. Basant-se en els resultats obtinguts, es van dissenyar nanodispositius basats en nanopartícules mesoporoses de sílice per a l'alliberament d'una combinació de miR-99a-5p i doxorrubicina en els tumors. L'eficacia dels sistemes per a reduir el creixement tumoral així com els efectes adversos associats a la doxorrubicina lliure es va confirmar en un model ortotòpic murí de càncer de mama. En el quart capítol, es va avaluar el potencial del miR-99a-5p com a biomarcador per al diagnòstic del càncer de mama. Es va determinar l'expressió del microRNA en tumors primaris de càncer de mama i en teixits sans. Els resultats van mostrar que el miR-99a-5p es troba infraexpressat en els teixits cancerosos. A continuació, amb l'objectiu de determinar el potencial del miR-99a-5p com a biomarcador mínimament invasiu, es van determinar els nivells d'expressió en plasma de pacients de càncer de mama i de donants sans. Es va trobar que el miR-99a-5p es troba a major concentració e, [EN] This PhD thesis, entitled "Role of miR-99a-5p in breast cancer: translating molecular findings into clinical tools" is focused on the study of the microRNA miR-99a-5p in breast cancer and in determining its potential as a therapeutic target and biomarker for the diagnosis of this disease. In the first chapter, a general review of breast cancer is carried out and microRNAs are also introduced. Next, in the second chapter, the objectives are detailed. In the third chapter, the microRNA expression profile of a doxorubicin-resistant breast cancer cell line was compared with its parental cell line, leading to the identification of the microRNA miR-99a-5p as the most deregulated between the two of them. Subsequently, it was confirmed that miR-99a-5p increases drug sensitivity through directly targeting COX-2, which leads to the inhibition of the expression of the ABCG2 protein, widely described to be involved in drug resistance. Based on the obtained results, nanodevices based on mesoporous silica nanoparticles were designed for the combined release of miR-99a-5p and doxorubicin in tumors. The ability of the systems to specifically target the CD44 receptor, which is overexpressed in breast cancer tumors, as well as to release the cargo specifically after internalization, were tested in vitro. Furthermore, the efficacy of the nanoparticles to reduce tumor growth and the adverse effects associated with free doxorubicin was confirmed in a murine orthotopic model of breast cancer. In the fourth chapter, the potential of miR-99a-5p as a biomarker for the diagnosis of breast cancer was evaluated. First, microRNA expression was determined in primary breast cancer tumors and compared with healthy tissues. The results showed that miR-99a-5p is downregulated in breast cancer tissues. Next, to determine the potential of the microRNA as a minimally invasive biomarker, the expression levels of miR-99a-5p in plasma of breast cancer patients and healthy donors were determined. In t

[ES] La presente tesis doctoral, titulada "papel del miR-99a-5p en cáncer de mama: transformando hallazgos moleculares en herramientas clínicas" está centrada en el estudio del microRNA miR-99a-5p en cáncer de mama y en la determinación de su potencial como diana terapéutica y biomarcador para el diagnóstico de dicha enfermedad. En el primer capítulo, se lleva a cabo una revisión general del cáncer de mama y los microRNAs. A continuación, en el segundo capítulo se presentan los objetivos. En el tercer capítulo se compararon los perfiles de expresión de microRNAs de una línea celular de cáncer de mama resistente a doxorrubicina frente a la línea celular parental, dando lugar a la identificación del microRNA miR-99a-5p como el más desregulado entre ambas. A continuación, se confirmó que el miR-99a-5p aumenta la sensibilidad a doxorrubicina mediante la inhibición directa de la expresión de COX-2, que conlleva la inhibición de la expresión de la proteína ABCG2, ampliamente descrita por su papel en resistencia a fármacos. En base a los resultados obtenidos, se diseñaron nanodispositivos basados en nanopartículas mesoporosas de sílice para la liberación de miR-99a-5p y doxorrubicina en los tumores. Se confirmó la eficacia de las nanopartículas para reducir el crecimiento tumoral así como los efectos adversos asociados a la doxorrubicina libre en un modelo ortotópico murino de cáncer de mama. En el cuarto capítulo, se evaluó el potencial del miR-99a-5p como biomarcador para el diagnóstico del cáncer de mama. Se determinó la expresión del microRNA en tumores primarios de cáncer de mama y en tejidos sanos. Los resultados mostraron que el miR-99a-5p se encuentra infraexpresado en los tejidos cancerosos. A continuación, con el objeto de determinar el potencial del miR-99a-5p como biomarcador mínimamente invasivo, se determinaron los niveles de expresión en plasma de pacientes de cáncer de mama y de donantes sanos. Se encontró que el miR-99a-5p se encuentra a mayor concentració, [CA] La present tesis doctoral, titulada "paper del miR-99a-5p en càncer de mama: transformant descobriments moleculars en eines clíniques" està centrada en l'estudi del microRNA miR-99a-5p en càncer de mama i en la determinació del seu potencial com a diana terapèutica i biomarcador per al diagnòstic d'aquesta malaltia. En el primer capítol, es du a terme una revisió general del càncer de mama i els microRNAs. A continuació, en el segon capítol es presenten els objectius. En el tercer capítol es van comparar els perfils d'expressió de microRNAs d'una línia cel·lular de càncer de mama resistent a doxorrubicina amb la seua línia parental, donant lloc a la identificació del microRNA miR-99a-5p com el més desregulat entre ambdues. A continuació, es va confirmar que el miR-99a-5p augmenta la sensibilitat al fàrmac mijançant la inhibició directa de l'expressió de COX-2 de forma directa, que comporta la inhibició de l'expressió de la proteïna ABCG2 que està àmpliament descrita pel seu paper en resistència a fàrmacs. Basant-se en els resultats obtinguts, es van dissenyar nanodispositius basats en nanopartícules mesoporoses de sílice per a l'alliberament d'una combinació de miR-99a-5p i doxorrubicina en els tumors. L'eficacia dels sistemes per a reduir el creixement tumoral així com els efectes adversos associats a la doxorrubicina lliure es va confirmar en un model ortotòpic murí de càncer de mama. En el quart capítol, es va avaluar el potencial del miR-99a-5p com a biomarcador per al diagnòstic del càncer de mama. Es va determinar l'expressió del microRNA en tumors primaris de càncer de mama i en teixits sans. Els resultats van mostrar que el miR-99a-5p es troba infraexpressat en els teixits cancerosos. A continuació, amb l'objectiu de determinar el potencial del miR-99a-5p com a biomarcador mínimament invasiu, es van determinar els nivells d'expressió en plasma de pacients de càncer de mama i de donants sans. Es va trobar que el miR-99a-5p es troba a major concentració e, [EN] This PhD thesis, entitled "Role of miR-99a-5p in breast cancer: translating molecular findings into clinical tools" is focused on the study of the microRNA miR-99a-5p in breast cancer and in determining its potential as a therapeutic target and biomarker for the diagnosis of this disease. In the first chapter, a general review of breast cancer is carried out and microRNAs are also introduced. Next, in the second chapter, the objectives are detailed. In the third chapter, the microRNA expression profile of a doxorubicin-resistant breast cancer cell line was compared with its parental cell line, leading to the identification of the microRNA miR-99a-5p as the most deregulated between the two of them. Subsequently, it was confirmed that miR-99a-5p increases drug sensitivity through directly targeting COX-2, which leads to the inhibition of the expression of the ABCG2 protein, widely described to be involved in drug resistance. Based on the obtained results, nanodevices based on mesoporous silica nanoparticles were designed for the combined release of miR-99a-5p and doxorubicin in tumors. The ability of the systems to specifically target the CD44 receptor, which is overexpressed in breast cancer tumors, as well as to release the cargo specifically after internalization, were tested in vitro. Furthermore, the efficacy of the nanoparticles to reduce tumor growth and the adverse effects associated with free doxorubicin was confirmed in a murine orthotopic model of breast cancer. In the fourth chapter, the potential of miR-99a-5p as a biomarker for the diagnosis of breast cancer was evaluated. First, microRNA expression was determined in primary breast cancer tumors and compared with healthy tissues. The results showed that miR-99a-5p is downregulated in breast cancer tissues. Next, to determine the potential of the microRNA as a minimally invasive biomarker, the expression levels of miR-99a-5p in plasma of breast cancer patients and healthy donors were determined. In t

Exogenous RNA polymerase III (pol III) promoters are commonly used to express short hairpin RNA (shRNA). Previous studies have indicated that expression of shRNAs using standard pol III promoters can cause toxicity in vivo due to saturation of the native miRNA pathway. A potential way of mitigating shRNA-associated toxicity is by utilising native miRNA processing enzymes to attain tolerable shRNA expression levels. Here, we examined parallel processing of exogenous shRNAs by harnessing the natural miRNA processing enzymes and positioning a shRNA adjacent to microRNA107 (miR107), located in the intron 5 of the Pantothenate Kinase 1 (PANK1) gene. We developed a vector encoding the PANK1 intron containing miR107 and examined the expression of a single shRNA or multiple shRNAs. Using qRT-PCR analysis and luciferase assay-based knockdown assay, we confirmed that miR30-structured shRNAs have resulted in the highest expression and subsequent transcript knockdown. Next, we injected Hamburger and Hamilton stage 14–15 chicken embryos with a vector encoding multiple shRNAs and confirmed that the parallel processing was not toxic. Taken together, this data provides a novel strategy to harness the native miRNA processing pathways for shRNA expression. This enables new opportunities for RNAi based applications in animal species such as chickens.

Hematopoietic stem cells (HSCs) possess two important properties such as self-renewal and differentiation. These properties of HSCs are maintained through hematopoiesis. This process gives rise to two subpopulations, long-term and short-term HSCs, which have become a popular convention for treating various hematological disorders. The clinical application of HSCs is bone marrow transplant in patients with aplastic anemia, congenital neutropenia, sickle cell anemia, thalassemia, or replacement of damaged bone marrow in case of chemotherapy. The self-renewal attribute of HSCs ensures long-term hematopoiesis post-transplantation. However, HSCs need to be infused in large numbers to reach their target site and meet the demands since they lose their self-renewal capacity after a few passages. Therefore, a more in-depth understanding of ex vivo HSCs expansion needs to be developed to delineate ways to enhance the self-renewability of isolated HSCs. The multifaceted self-renewal process is regulated by factors, including transcription factors, miRNAs, and the bone marrow niche. A developed classical hierarchical model that outlines the hematopoiesis in a lineage-specific manner through in vivo fate mapping, barcoding, and determination of self-renewal regulatory factors are still to be explored in more detail. Thus, an in-depth study of the self-renewal property of HSCs is essentially required to be utilized for ex vivo expansion. This review primarily focuses on the Hematopoietic stem cell self-renewal pathway and evaluates the regulatory molecular factors involved in considering a targeted clinical approach in numerous malignancies and outlining gaps in the current knowledge.

BackgroundDysfunction or loss of limbal stem cells can result in limbal stem cell deficiency (LSCD), a disease that cause corneal opacity, pain, and loss of vision. Cultivated limbal epithelial transplantation (CLET) can be used to restore stem cell niche homeostasis and replenish the progenitor pool. Transplantation has been reported with high success rate, but there is an unmet need of prognostic markers that correlate with clinical outcomes. To date, the progenitor content in the graft is the only parameter that has been retrospectively linked to success.MethodsIn this study, we investigate extracellular micro RNAs (miRNAs) associated with stem/progenitor cells in cultivated limbal epithelial cells (cLECs). Using micro RNA sequencing and linear regression modelling, we identify a miRNA signature in cultures containing high proportion of stem/progenitor cells. We then develop a robust RNA extraction workflow from culture media to confirm a positive miRNA correlation with stem/progenitor cell proportion.ResultsmiR-6723-5p is associated with cultures containing high proportion of stem/progenitor cells, and is detected in the basal layer of corneal epithelium.ConclusionsThese results indicate that miR-6723-5p could potentially serve as a stem/progenitor cell marker in cLECs.

Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory disease commonly induced by cigarette smoke. The expression of miRNAs can be altered in patients with COPD and could be used as a biomarker. We aimed to identify a panel of miRNAs in bron-choalveolar lavage (BAL) to differentiate COPD patients from smokers and non-smokers with normal lung function. Accordingly, forty-five subjects classified as COPD, smokers, and non-smokers (n = 15 per group) underwent clinical, functional characterization and bronchoscopy with BAL. The mean age of the studied population was 61.61 ± 12.95 years, BMI 25.72 ± 3.82 Kg/m2, FEV1/FVC 68.37 ± 12.00%, and FEV1 80.07 ± 23.63% predicted. According to microarray analysis, three miRNAs of the most upregulated were chosen: miR-320c, miR-200c-3p, and miR-449c-5p. These miRNAs were validated by qPCR and were shown to be differently expressed in COPD patients. ROC analysis showed that these three miRNAs together had an area under the curve of 0.89 in differentiating COPD from controls. Moreover, in silico analysis of candidate miRNAs by DIANA-miRPath showed potential involvement in the EGFR and Hippo pathways. These results suggest a specific 3-miRNA signature that could be potentially used as a biomarker to distinguish COPD patients from smokers and non-smoker subjects.

Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory disease commonly induced by cigarette smoke. The expression of miRNAs can be altered in patients with COPD and could be used as a biomarker. We aimed to identify a panel of miRNAs in bron-choalveolar lavage (BAL) to differentiate COPD patients from smokers and non-smokers with normal lung function. Accordingly, forty-five subjects classified as COPD, smokers, and non-smokers (n = 15 per group) underwent clinical, functional characterization and bronchoscopy with BAL. The mean age of the studied population was 61.61 ± 12.95 years, BMI 25.72 ± 3.82 Kg/m2, FEV1/FVC 68.37 ± 12.00%, and FEV1 80.07 ± 23.63% predicted. According to microarray analysis, three miRNAs of the most upregulated were chosen: miR-320c, miR-200c-3p, and miR-449c-5p. These miRNAs were validated by qPCR and were shown to be differently expressed in COPD patients. ROC analysis showed that these three miRNAs together had an area under the curve of 0.89 in differentiating COPD from controls. Moreover, in silico analysis of candidate miRNAs by DIANA-miRPath showed potential involvement in the EGFR and Hippo pathways. These results suggest a specific 3-miRNA signature that could be potentially used as a biomarker to distinguish COPD patients from smokers and non-smoker subjects.

BackgroundDysfunction or loss of limbal stem cells can result in limbal stem cell deficiency (LSCD), a disease that cause corneal opacity, pain, and loss of vision. Cultivated limbal epithelial transplantation (CLET) can be used to restore stem cell niche homeostasis and replenish the progenitor pool. Transplantation has been reported with high success rate, but there is an unmet need of prognostic markers that correlate with clinical outcomes. To date, the progenitor content in the graft is the only parameter that has been retrospectively linked to success.MethodsIn this study, we investigate extracellular micro RNAs (miRNAs) associated with stem/progenitor cells in cultivated limbal epithelial cells (cLECs). Using micro RNA sequencing and linear regression modelling, we identify a miRNA signature in cultures containing high proportion of stem/progenitor cells. We then develop a robust RNA extraction workflow from culture media to confirm a positive miRNA correlation with stem/progenitor cell proportion.ResultsmiR-6723-5p is associated with cultures containing high proportion of stem/progenitor cells, and is detected in the basal layer of corneal epithelium.ConclusionsThese results indicate that miR-6723-5p could potentially serve as a stem/progenitor cell marker in cLECs.

Hematopoietic stem cells (HSCs) possess two important properties such as self-renewal and differentiation. These properties of HSCs are maintained through hematopoiesis. This process gives rise to two subpopulations, long-term and short-term HSCs, which have become a popular convention for treating various hematological disorders. The clinical application of HSCs is bone marrow transplant in patients with aplastic anemia, congenital neutropenia, sickle cell anemia, thalassemia, or replacement of damaged bone marrow in case of chemotherapy. The self-renewal attribute of HSCs ensures long-term hematopoiesis post-transplantation. However, HSCs need to be infused in large numbers to reach their target site and meet the demands since they lose their self-renewal capacity after a few passages. Therefore, a more in-depth understanding of ex vivo HSCs expansion needs to be developed to delineate ways to enhance the self-renewability of isolated HSCs. The multifaceted self-renewal process is regulated by factors, including transcription factors, miRNAs, and the bone marrow niche. A developed classical hierarchical model that outlines the hematopoiesis in a lineage-specific manner through in vivo fate mapping, barcoding, and determination of self-renewal regulatory factors are still to be explored in more detail. Thus, an in-depth study of the self-renewal property of HSCs is essentially required to be utilized for ex vivo expansion. This review primarily focuses on the Hematopoietic stem cell self-renewal pathway and evaluates the regulatory molecular factors involved in considering a targeted clinical approach in numerous malignancies and outlining gaps in the current knowledge.

FOXO1 transcription factor not only limits the cell cycle progression but also promotes cell death as a tumor suppressor protein. Though the expression of FOXO1 is largely examined in breast cancer, the regulation of FOXO1 by miRNA is yet to be explored. In the current study, self-assembled branched DNA (bDNA) nanostructures containing oncogenic miRNAs were designed and transfected to the MCF7 cell line to decipher the FOXO1 expression. bDNA containing oncogenic miRNAs 27a, 96, and 182 synergistically downregulate the expression of FOXO1 in MCF7 cells. The down-regulation is evident both in mRNA and protein levels suggesting that bDNA having miRNA sequences can selectively bind to mRNA and inhibit translation. Secondly, the downstream gene expression of p21 and p27 was also significantly downregulated in presence of miR-bDNA nanostructures. The cell proliferation activity was progressively increased in presence of miR-bDNA nanostructures which confirms the reduced tumor suppression activity of FOXO1 and the downstream gene expression. This finding can be explored to design novel bDNA structures which can downregulate the tumor suppressor proteins in normal cells and induce cell proliferation activity to identify early-phase markers of cancer.

FOXO1 transcription factor not only limits the cell cycle progression but also promotes cell death as a tumor suppressor protein. Though the expression of FOXO1 is largely examined in breast cancer, the regulation of FOXO1 by miRNA is yet to be explored. In the current study, self-assembled branched DNA (bDNA) nanostructures containing oncogenic miRNAs were designed and transfected to the MCF7 cell line to decipher the FOXO1 expression. bDNA containing oncogenic miRNAs 27a, 96, and 182 synergistically downregulate the expression of FOXO1 in MCF7 cells. The down-regulation is evident both in mRNA and protein levels suggesting that bDNA having miRNA sequences can selectively bind to mRNA and inhibit translation. Secondly, the downstream gene expression of p21 and p27 was also significantly downregulated in presence of miR-bDNA nanostructures. The cell proliferation activity was progressively increased in presence of miR-bDNA nanostructures which confirms the reduced tumor suppression activity of FOXO1 and the downstream gene expression. This finding can be explored to design novel bDNA structures which can downregulate the tumor suppressor proteins in normal cells and induce cell proliferation activity to identify early-phase markers of cancer.

FOXO1 transcription factor not only limits the cell cycle progression but also promotes cell death as a tumor suppressor protein. Though the expression of FOXO1 is largely examined in breast cancer, the regulation of FOXO1 by miRNA is yet to be explored. In the current study, self-assembled branched DNA (bDNA) nanostructures containing oncogenic miRNAs were designed and transfected to the MCF7 cell line to decipher the FOXO1 expression. bDNA containing oncogenic miRNAs 27a, 96, and 182 synergistically downregulate the expression of FOXO1 in MCF7 cells. The down-regulation is evident both in mRNA and protein levels suggesting that bDNA having miRNA sequences can selectively bind to mRNA and inhibit translation. Secondly, the downstream gene expression of p21 and p27 was also significantly downregulated in presence of miR-bDNA nanostructures. The cell proliferation activity was progressively increased in presence of miR-bDNA nanostructures which confirms the reduced tumor suppression activity of FOXO1 and the downstream gene expression. This finding can be explored to design novel bDNA structures which can downregulate the tumor suppressor proteins in normal cells and induce cell proliferation activity to identify early-phase markers of cancer.

Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory disease commonly induced by cigarette smoke. The expression of miRNAs can be altered in patients with COPD and could be used as a biomarker. We aimed to identify a panel of miRNAs in bron-choalveolar lavage (BAL) to differentiate COPD patients from smokers and non-smokers with normal lung function. Accordingly, forty-five subjects classified as COPD, smokers, and non-smokers (n = 15 per group) underwent clinical, functional characterization and bronchoscopy with BAL. The mean age of the studied population was 61.61 ± 12.95 years, BMI 25.72 ± 3.82 Kg/m2, FEV1/FVC 68.37 ± 12.00%, and FEV1 80.07 ± 23.63% predicted. According to microarray analysis, three miRNAs of the most upregulated were chosen: miR-320c, miR-200c-3p, and miR-449c-5p. These miRNAs were validated by qPCR and were shown to be differently expressed in COPD patients. ROC analysis showed that these three miRNAs together had an area under the curve of 0.89 in differentiating COPD from controls. Moreover, in silico analysis of candidate miRNAs by DIANA-miRPath showed potential involvement in the EGFR and Hippo pathways. These results suggest a specific 3-miRNA signature that could be potentially used as a biomarker to distinguish COPD patients from smokers and non-smoker subjects.

FOXO1 transcription factor not only limits the cell cycle progression but also promotes cell death as a tumor suppressor protein. Though the expression of FOXO1 is largely examined in breast cancer, the regulation of FOXO1 by miRNA is yet to be explored. In the current study, self-assembled branched DNA (bDNA) nanostructures containing oncogenic miRNAs were designed and transfected to the MCF7 cell line to decipher the FOXO1 expression. bDNA containing oncogenic miRNAs 27a, 96, and 182 synergistically downregulate the expression of FOXO1 in MCF7 cells. The down-regulation is evident both in mRNA and protein levels suggesting that bDNA having miRNA sequences can selectively bind to mRNA and inhibit translation. Secondly, the downstream gene expression of p21 and p27 was also significantly downregulated in presence of miR-bDNA nanostructures. The cell proliferation activity was progressively increased in presence of miR-bDNA nanostructures which confirms the reduced tumor suppression activity of FOXO1 and the downstream gene expression. This finding can be explored to design novel bDNA structures which can downregulate the tumor suppressor proteins in normal cells and induce cell proliferation activity to identify early-phase markers of cancer.

Background: In vitro production of bovine embryos is a well-established technology, but the in vitro culture (IVC) system still warrants improvements, especially regarding embryo quality. This study aimed to evaluate the effect of extracellular vesicles (EVs) isolated from oviductal (OF) and uterine fluid (UF) in sequential IVC on the development and quality of bovine embryos. Zygotes were cultured in SOF supplemented with either BSA or EVs-depleted fetal calf serum (dFCS) in the presence (BSA-EV and dFCS-EV) or absence of EVs from OF (D1 to D4) and UF (D5 to D8), mimicking in vivo conditions. EVs from oviducts (early luteal phase) and uterine horns (mid-luteal phase) from slaughtered heifers were isolated by size exclusion chromatography. Blastocyst rate was recorded on days 7–8 and their quality was assessed based on lipid contents, mitochondrial activity and total cell numbers, as well as survival rate after vitrification. Relative mRNA abundance for lipid metabolism-related transcripts and levels of phosphorylated hormone-sensitive lipase (pHSL) proteins were also determined. Additionally, the expression levels of 383 miRNA in OF- and UF-EVs were assessed by qRT-PCR. Results: Blastocyst yield was lower (P < 0.05) in BSA treatments compared with dFCS treatments. Survival rates after vitrification/warming were improved in dFCS-EVs (P < 0.05). EVs increased (P < 0.05) blastocysts total cell number in dFCS-EV and BSA-EV compared with respective controls (dFCS and BSA), while lipid content was decreased in dFCS-EV (P < 0.05) and mitochondrial activity did not change (P > 0.05). Lipid metabolism transcripts were affected by EVs and showed interaction with type of protein source in medium (PPARGC1B, LDLR, CD36, FASN and PNPLA2, P < 0.05). Levels of pHSL were lower in dFCS (P < 0.05). Twenty miRNA were differentially expressed between OF- and UF-EVs and only bta-miR-148b was increased in OF-EVs (P < 0.05). Conclusions: Mimicking physiological conditions using EVs from O

In vitro production of bovine embryos is a well-established technology, but the in vitro culture (IVC) system still warrants improvements, especially regarding embryo quality. This study aimed to evaluate the effect of extracellular vesicles (EVs) isolated from oviductal (OF) and uterine fluid (UF) in sequential IVC on the development and quality of bovine embryos. Zygotes were cultured in SOF supplemented with either BSA or EVs-depleted fetal calf serum (dFCS) in the presence (BSA-EV and dFCS-EV) or absence of EVs from OF (D1 to D4) and UF (D5 to D8), mimicking in vivo conditions. EVs from oviducts (early luteal phase) and uterine horns (mid-luteal phase) from slaughtered heifers were isolated by size exclusion chromatography. Blastocyst rate was recorded on days 7-8 and their quality was assessed based on lipid contents, mitochondrial activity and total cell numbers, as well as survival rate after vitrification. Relative mRNA abundance for lipid metabolism-related transcripts and levels of phosphorylated hormone-sensitive lipase (pHSL) proteins were also determined. Additionally, the expression levels of 383 miRNA in OF- and UF-EVs were assessed by qRT-PCR.

FOXO1 transcription factor not only limits the cell cycle progression but also promotes cell death as a tumor suppressor protein. Though the expression of FOXO1 is largely examined in breast cancer, the regulation of FOXO1 by miRNA is yet to be explored. In the current study, self-assembled branched DNA (bDNA) nanostructures containing oncogenic miRNAs were designed and transfected to the MCF7 cell line to decipher the FOXO1 expression. bDNA containing oncogenic miRNAs 27a, 96, and 182 synergistically downregulate the expression of FOXO1 in MCF7 cells. The down-regulation is evident both in mRNA and protein levels suggesting that bDNA having miRNA sequences can selectively bind to mRNA and inhibit translation. Secondly, the downstream gene expression of p21 and p27 was also significantly downregulated in presence of miR-bDNA nanostructures. The cell proliferation activity was progressively increased in presence of miR-bDNA nanostructures which confirms the reduced tumor suppression activity of FOXO1 and the downstream gene expression. This finding can be explored to design novel bDNA structures which can downregulate the tumor suppressor proteins in normal cells and induce cell proliferation activity to identify early-phase markers of cancer.

Although genomes from many edible mushrooms are sequenced, studies on fungal micro RNAs (miRNAs) are scarce. Most of the bioinformatic tools are designed for plants or animals, but the processing and expression of fungal miRNAs share similarities and differences with both kingdoms. Moreover, since mushroom species such as Agaricus bisporus (A. bisporus, white button mushroom) are frequently consumed as food, controversial discussions are still evaluating whether their miRNAs might or might not be assimilated, perhaps within extracellular vesicles (i.e., exosomes). Therefore, the A. bisporus RNA-seq was studied in order to identify potential de novo miRNA-like small RNAs (milRNAs) that might allow their later detection in diet. Results pointed to 1 already known and 37 de novo milRNAs. Three milRNAs were selected for RT-qPCR experiments. Precursors and mature milRNAs were found in the edible parts (caps and stipes), validating the predictions carried out in silico. When their potential gene targets were investigated, results pointed that most were involved in primary and secondary metabolic regulation. However, when the human transcriptome is used as the target, the results suggest that they might interfere with important biological processes related with cancer, infection and neurodegenerative diseases.