MicroRNA expression in HTLV-1 infection and pathogenesis

Our laboratory is examining the profiles of microRNA expression in ATLL cells and infected T-cell lines using microarrays and small RNA libraries. Microarray analysis of ATLL samples revealed 6 upregulated and 21 downregulated microRNAs in ATLL cells compared to CD4+ T-cell controls. Potential targets for deregulated microRNAs were identified by integrating microRNA and mRNA expression profiles. Current experiments are aimed at verifying these predicted microRNA-target interactions

Impact of Host Genes and Strand Selection on miRNA and miRNA* Expression

Dysregulation of miRNAs expression plays a critical role in the pathogenesis of genetic, multifactorial disorders and in human cancers. We exploited sequence, genomic and expression information to investigate two main aspects of post-transcriptional regulation in miRNA biogenesis, namely strand selection regulation and expression relationships between intragenic miRNAs and host genes. We considered miRNAs expression profiles, measured in five sizeable microarray datasets, including samples from different normal cell types and tissues, as well as different tumours and disease states. First, the study of expression profiles of “sister” miRNA pairs (miRNA/miRNA*, 5′ and 3′ strands of the same hairpin precursor) showed that the strand selection is highly regulated since it shows tissue-/cell-/condition-specific modulation. We used information about the direction and the strength of the strand selection bias to perform an unsupervised cluster analysis for the sample classification evidencing that is able to distinguish among different tissues, and sometimes between normal and malignant cells. Then, considering a minimum expression threshold, in few miRNA pairs only one mature miRNA is always present in all considered cell types, whereas the majority of pairs were concurrently expressed in some cell types and alternatively in others. In a significant fraction of concurrently expressed pairs, the major and the minor forms found at comparable levels may contribute to post-transcriptional gene silencing, possibly in a coordinate way. In the second part of the study, the behaved tendency to co-expression of intragenic miRNAs and their “host” mRNA genes was confuted by expression profiles examination, suggesting that the expression profile of a given host gene can hardly be a good estimator of co-transcribed miRNA(s) for post-transcriptional regulatory networks inference. Our results point out the regulatory importance of post-transcriptional phases of miRNAs biogenesis, reinforcing the role of such layer of miRNA biogenesis in miRNA-based regulation of cell activities

MicroRNAs: from biogenesis to post-transcriptional regulatory networks

The discovery of microRNA-based post-transcriptional regulation of gene expression added a novel level of genetic regulation to a wide range of biological processes. Dysregulation of miRNAs expression plays a critical role in the pathogenesis of genetic and multifactorial disorders and of most human cancers. To bypass limitations of computational predictions of miRNA–target relationships, we developed a method for integrated analysis of miRNA and gene expression profiles in combination with target prediction, allowing the identification and study of post-transcriptional regulatory networks in specific biological contexts. This methodology was also implemented in a web tool, MAGIA, that allows integrating target predictions and miRNA and gene expression profiles for the miRNA–mRNA bipartite networks reconstruction, gene functional enrichment and pathway annotations for results browsing. Network analysis has been applied to highlight the importance of some regulatory elements in the regulatory network reconstructed calculating the drop of network efficiency caused by node deactivation. Biologically relevant results, obtained by bioinfomatic analyses in the frame of different projects, were the starting point for further experimental studies, which identified key miRNA-target relations in cancerogenesis. miRNAs biogenesis is not still completely understood. Thus with the integration of genomic information with sequence and expression data we studied the strand selection bias and the expression behavior of intragenic miRNAs and host genes. In contrast with classical biogenesis model, these analyses highlighted that 5’ and 3’ miRNA strands, the “major” and the “minor” forms, deriving from the same hairpin precursor may co-coordinately contribute to silencing of different sets of target genes. Indeed, the behaved tendency to co-expression of intragenic miRNAs and their “host” mRNA genes was confuted by expression profiles examination, suggesting that the expression profile of a given host gene can hardly be a good estimator of co-transcribed miRNA(s) for post-transcriptional regulatory networks inference. In the last year, short RNAs massive sequencing was exploited for a miRNOme analysis of myeloproliferative neoplasms (MPN). This analysis allowed the characterization of short RNAs (known and novel miRNAs, isomiRs and moRNAs) expressed by SET2 cells, a JAK2-mutated cell line model for MPN. moRNAs (microRNA-offset RNA) derived from extended hairpin stem sequences, probably by alternative nuclear and/or cytoplasmic processing. They seem to be conserved across species and the conservation extent correlates with expression level. This evidence suggests that moRNAs might be miRNA co-products, representing a distinct functional class of miRNA-related agents. In conclusion, our analyses were addressed to shed light on the complexity of microRNA-mediated gene regulation, pointing out the regulatory importance of post-transcriptional phases of miRNAs biogenesis, reinforcing the role of such layer of miRNA biogenesis in miRNA-based regulation of cell activities in physiology and in different disease.La scoperta della regolazione post-trascrizionale dei miRNA ha aggiunto un nuovo livello alla regolazione genetica in numerosi processi biologici. Alterazioni nell’espressione dei miRNA possono giocare un importante ruolo nell’insorgenza di svariate patologie ed in particolare in molte neoplasie. Per ovviare alle limitazioni presenti nelle relazioni miRNA-mRNA degli algoritmi di predizione computazionali, è stata sviluppata una metodologia per l’integrazione dei profili d’espressione di miRNA e mRNA con le predizioni dei bersagli biologici dei miRNA, che ha permesso l’identificazione di reti regolative post-trascrizionali in diversi contesti biologici. Questa metodologia è stata inoltre implementata in un “web-tool”, soprannominato MAGIA. Per evidenziare l’importanza di alcuni elementi regolativi presenti nei circuiti biologici è stata applicata la teoria delle reti per l’identificazione di geni critici attraverso la loro de-attivazione nella rete. I frutti di queste analisi bioinformatiche, svolte nell’ambito di numerosi progetti, hanno rappresentato il punto di partenza per successivi studi sperimentali che hanno portato alla scoperta di rilevanti relazioni miRNA-target in specifici tumori. La biogenesi dei miRNA non è stata ancora completamente chiarita, perciò, integrando informazioni derivanti dalle sequenze genomiche e da dati d’espressione, sono stati approfonditi alcuni loro aspetti, quali la teoria di generazione dei miRNA maturi per selezione del filamento e la co-espressione dei miRNA intragenici e dei loro geni ospiti. Le suddette analisi hanno evidenziato che i miRNA generati dal 5’ ed il 3’, derivanti dallo stesso miRNA precursore, supportano solo parzialmente il modello classico della biogenesi dei miRNA, secondo il quale uno dei due miRNA maturi è scelto in modo deterministico e degradato. Entrambe le forme “major” e “minor”, infatti, possono contribuire insieme al silenziamento di gruppi diversi di geni bersaglio. La tendenza alla co-espressione tra i miRNA intragenici e i loro geni ospiti, inoltre, è stata confutata dall’analisi dei loro profili d’espressione, dimostrando che i profili d’espressione dei geni ospite non possono essere usati come stimatori dell’espressione dei miRNA per l’inferenza di reti regolative post-trascrizionali. Nell’ultimo anno, il sequenziamento massivo di brevi RNA è stato sfruttato per l’analisi approfondita di miRNA nelle neoplasie mieloproliferative. Attraverso questo approccio è stato possibile scoprire e caratterizzare numerosi brevi RNA, quali miRNA noti e nuovi, isomiRNA e i moRNA, che sono espressi nelle cellule SET2, linee cellulari con mutazione del gene JAK2. I moRNA (microRNA-offset RNA) derivano dalle sequenze dei precursori dei miRNA, probabilmente da un processo alternativo del nucleo e/o citoplasmatico, e sembrano essere conservati in varie specie. Il loro grado di conservazione è correlato con i livelli d’espressione e si potrebbe dedurre che siano prodotti insieme ai miRNA, ma rappresentando una classe funzionale distinta da essi. In conclusione, le nostre analisi sono state indirizzate a far luce sulla complessità della regolazione dei geni da parte dei miRNA, in particolare sull’importanza delle fasi post-trascrizionali della biogenesi dei miRNA ed il loro ruolo nella regolazione delle attività cellulari fisiologiche ed in diverse patologie

microRNA-offset RNAs (moRNAs): by-product spectators or functional players?

Recent studies have exponentially increased the number of known noncoding RNA categories, including microRNA (miRNA), small interfering RNA (siRNA), PIWI element-interacting RNA and various classes of long noncoding RNA (ncRNA), that fulfill key roles as transcriptional and post-transcriptional regulators and guides of chromatin-modifying complexes [1]. Among these short RNAs, miRNAs are post-transcriptional regulators of gene expression in a wide range of biological processes and diseases [2]. miRNAs are considered as prominent tumour markers, relevant targets for therapy and therapeutic agents [3]. Here, we discuss the discovery of a novel type of miRNA-related small RNA, miRNA\u2013offset RNA (moRNA), whose function is currently unknown

Evaluating field-goal shooting effectiveness in wheelchair basketball players across a competitive season: a preliminary study

Background Information about non-elite wheelchair basketball (WB) players across national competitive seasons are still missing. This study aimed at identifying which situational-related variables were associated with shooting effectiveness in non-elite WB players. Methods All the matches played by one WB team across one national competitive season were video-recorded and analysed; 333 shooting attempts from high-point players and several situational-related variables were considered. Results Pearson’s Chi-square test showed that increased shooting effectiveness under the following conditions: playing on home ground, during won matches, while taking shots with the wheelchair in motion, and when no opposing player raised their arm in defence. Results of the multivariable logistic regression analysis showed a statistically significant influence of match location (p-value = 0.001), shot-clock remaining (p-value = 0.015) and modality of press (p-value < 0.001). The highest attack effectiveness was achieved when teams played at home (odds ratio [OR] = 2.49), while the shooting effectiveness decreased when the shot occurred during the last seconds of the action (OR = 0.36), or the opponents defended with the arm raised (OR = 0.19). These results suggest that coaches should include exercises aimed at shooting under conditions of increased pressure in their programmes in order to create specific situations during the training sessions to prepare their high-point athletes for shots under specific match constraints

SerpinB3 administration protects liver against ischemia-reperfusion injury

We have investigated the change in SerpinB3 during hepatic ischemia and the potential role of its antiprotease activity in cell protection by the administration of wild-type SerpinB3 (SerpinB3-WT) or active loop-deleted recombinant SerpinB3 protein (SerpinB3-D) in a rat model of ischemia (60 min)/reperfusion (60 min) (I/R). A time-dependent increase of SerpinB3, both at transcription and protein level, was found in ischemic livers after 60, 120 and 180 min. SerpinB3-WT decreased polymorphonuclear cell infiltration and serum enzymes, and increased ATP when compared with I/R group. These events were not obtained using SerpinB3-D. No signifi-cant changes in both liver SerpinB3 mRNA and protein were found in all I/R groups considered. The present data show that the administration of SerpinB3-WT reduced the I/R injury and this effect appears to be depen-dent on its anti-protease activity

Human miRNome profiling in colorectal cancer and liver metastasis development

Qualitative alterations or abnormal expression of microRNAs (miRNAs) in colorectal cancer has mainly been demonstrated in primary tumors. The miRNA expression profiles in 78 samples from 46 patients were analyzed to identify changes in miRNA expression level among normal colon mucosa, primary tumor and liver metastasis samples. Using this dataset, we describe the interplay of miRNA groups in regulating pathways that are important for tumor development. Here we describe in details the contents and quality controls for the miRNA expression and clinical data associated with the study published by Pizzini and colleagues in the BMC Genomics in 2013 (Pizzini et al., 2013). Data are deposited in GEO database as GSE35834 series