Mg/Zn mixed-metal borohydride for hydrogen storage:<i>ab initio</i>periodic computational study of the phase stability and decomposition

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Lipid-induced hepatocyte-derived extracellular vesicles regulate hepatic stellate cell via microRNAs targeting PPAR-γ.

Background&amp;aimsHepatic stellate cells (HSCs) play a key role in liver fibrosis in various chronic liver disorders including nonalcoholic fatty liver disease (NAFLD). The development of liver fibrosis requires a phenotypic switch from quiescent to activated HSCs. The triggers for HSCs activation in NAFLD remain poorly understood. We investigated the role and molecular mechanism of extracellular vesicles (EVs) released by hepatocytes during lipotoxicity in modulation of HSC phenotype.MethodsEVs were isolated from fat-laden hepatocytes by differential centrifugation and incubated with HSCs. EV internalization and HSCs activation, migration and proliferation were assessed. Loss- and gain-of-functions studies were performed to explore the potential role of PPAR-γ-targeting miRNAs carried by EVs into HSC.ResultsHepatocyte-derived EVs released during lipotoxicity are efficiently internalized by HSCs resulting in their activation, as shown by marked up-regulation of pro-fibrogenic genes (Collagen-I, α-SMA and TIMP-2), proliferation, chemotaxis and wound healing responses. These changes were associated with miRNAs shuttled by EVs and suppression of PPAR-γ expression in HSC. Hepatocyte-derived EVs miRNA content included various miRNAs that are known inhibitors of PPAR-γ expression with miR-128-3p being the most effectively transferred. Furthermore loss- and gain-of-function studies identified miR-128-3p as a central modulator of the effects of EVs on PPAR-γ inhibition and HSC activation.ConclusionOur findings demonstrate a link between fat-laden hepatocyte-derived EVs and liver fibrosis and have potential implications for the development of novel anti-fibrotic targets for NAFLD and other fibrotic diseases

Interplay between non-coding rna transcription, stringent/relaxed phenotype and antibiotic production in streptomyces ambofaciens

While in recent years the key role of non-coding RNAs (ncRNAs) in the regulation of gene expression has become increasingly evident, their interaction with the global regulatory circuits is still obscure. Here we analyzed the structure and organization of the transcriptome of Streptomyces ambofaciens, the producer of spiramycin. We identified ncRNAs including 45 small-RNAs (sRNAs) and 119 antisense-RNAs (asRNAs I) that appear transcribed from dedicated promoters. Some sRNAs and asRNAs are unprecedented in Streptomyces and were predicted to target mRNAs encoding proteins involved in transcription, translation, ribosomal structure and biogenesis, and regulation of morphological and biochemical differentiation. We then compared ncRNA expression in three strains: (i) the wild-type strain; (ii) an isogenic pirA-defective mutant with central carbon metabolism imbalance, “relaxed” phenotype, and repression of antibiotic production; and (iii) a pirA-derivative strain harboring a “stringent” RNA polymerase that suppresses pirA-associated phenotypes. Data indicated that the expression of most ncRNAs was correlated to the stringent/relaxed phenotype suggesting novel effector mechanisms of the stringent response

Expression profiling of microRNAs and isomiRs in conventional central chondrosarcoma

Conventional central chondrosarcoma (CCC) is a malignant bone tumor that is characterized by the production of chondroid tissue. Since radiation therapy and chemotherapy have limited effects on CCC, treatment of most patients depends on surgical resection. This study aimed to identify the expression profiles of microRNAs (miRNAs) and isomiRs in CCC tissues to highlight their possible participation to the regulation of pathways critical for the formation and growth of this type of tumor. Our study analyzed miRNAs and isomiRs from Grade I (GI), Grade II (GII), and Grade III (GIII) histologically validated CCC tissue samples. While the different histological grades shared a similar expression profile for the top abundant miRNAs, we found several microRNAs and isomiRs showing a strong different modulation in GII + GIII vs GI grade samples and their involvement in tumor biology could be consistently hypothesized. We then in silico validated these differently expressed miRNAs in a larger chondrosarcoma public dataset and confirmed the expression trend for 17 out of 34 miRNAs. Our results clearly suggests that the contribution of miRNA deregulation, and their targeted pathways, to the progression of CCC could be relevant and strongly indicates that when studying miRNA deregulation in tumors, not only the canonical miRNAs, but the whole set of corresponding isomiRs should be taken in account. Improving understanding of the precise roles of miRNAs and isomiRs over the course of central chondrosarcoma progression could help identifying possible targets for precision medicine therapeutic intervention

A compendium of DIS3 mutations and associated transcriptional signatures in plasma cell dyscrasias

DIS3 is a catalytic subunit of the human exosome complex, containing exonucleolytic (RNB) and endonucleolytic (PIN) domains, recently found mutated in multiple myeloma (MM), a clinically and genetically heterogeneous form of plasma cell (PC) dyscrasia. We analyzed by next-generation sequencing (NGS) the DIS3 PIN and RNB domains in purified bone marrow PCs from 164 representative patients, including 130 cases with MM, 24 with primary PC leukemia and 10 with secondary PC leukemia. DIS3 mutations were found respectively in 18.5%, 25% and 30% of cases. Identified variants were predominantly missense mutations localized in the RNB domain, and were often detected at low allele frequency. DIS3 mutations were preferentially carried by IGH-translocated/nonhyperdiploid patients. Sequential analysis at diagnosis and relapse in a subset of cases highlighted some instances of increasing DIS3 mutation burden during disease progression. NGS also revealed that the majority of DIS3 variants in mutated cases were comparably detectable at transcriptional level. Furthermore, gene expression profiling analysis in DIS3-mutated patients identified a transcriptional signature suggestive for impaired RNA exosome function. In conclusion, these data further support the pathological relevance of DIS3 mutations in plasma cell dyscrasias and suggest that DIS3 may represent a potential tumor suppressor gene in such disorders

Analisi del numero di copie e sequenza del DNA in campioni sequenziali di melanoma alla diagnosi e recidiva=DNA copy number and whole-exome sequencing analyses in sequential myeloma samples at diagnosis and relapse

Introduction. Multiple myeloma (MM) is a plasma cell (PC) malignancy characterized by a marked genetic heterogeneity at onset, followed by further genomic complexity acquired during disease progression and particularly after treatment. To gain insight into the molecular evolution associated with MM progression, we investigated sequential samples of 7 MMs and 1 primary PC leukemia (pPCL) by genome-wide DNA copy number analysis and whole-exome sequencing (WES). Methods. Highly purified PC samples obtained at diagnosis and relapse after first line therapy (7 symptomatic MMs and 1 pPCL) were subjected to genome-wide DNA profiling (all cases) and WES (1 MM and 1 pPCL samples, with matched negative controls). Copy number data were generated on Affymetrix CytoScan HD Array, using the Chromosome Analysis Suite software. Single sample analysis was performed with default parameters and setting the Reference Model. WES was carried out on Illumina GAIIx platform and variant calling was performed using Mutect algorithm, by separately comparing primary and progression samples to its matched normal control. Results. Concerning regions of prognostic importance, 1p loss was identified as a novel lesion or evolving from a sub-clone in 3 relapsed samples, whereas 1q gain or 17p loss were respectively acquired in two cases. Notably, some alterations, present at diagnosis only in sub-clones, were detected in the majority of tumor cells in at least one of 5 relapsed MMs. Such lesions involved single or combined gains or losses of whole chromosomes (chr) 3, 8, 9, 18, 20, aberrations of short/long arms of chrs 11, 13, 14, 15, 18, 21 or smaller altered regions on chrs 4, 10, 12, 16, 17, 19. Interestingly, deletions involving chr 5q (3/8 relapsed MMs) or 8q (2/8 relapsed MMs) were detected as de novo acquired lesions. Furthermore, we investigated by WES two cases, a MM progressed to secondary PCL (sPCL) and a pPCL patient at diagnosis and relapse. Each patient showed a dynamic mutational pattern, involving both the acquisition and the loss of a large number of point mutations. Specifically, 19 genes were exclusively mutated in MM at diagnosis and 66 only in sPCL phase, whereas 12 genes were mutated in both conditions; in pPCL patient, 138 genes were evidenced at diagnosis and 166 at relapse, while 78 were commonly altered. Genes acquiring mutations in disease course were mostly involved in DNA repair, histone methylation, protein metabolism, regulation of NF-kB cascade, focal adhesion and MAPK signaling pathways. Concerning genes frequently altered in MM, it is worth reporting mutations of TP53 and CYLD at relapse, in sPCL and pPCL, respectively. Conclusions. Our data highlight the importance of using high-throughput approaches to provide insights into the definition of genetic alterations potentially related to mechanisms of drug resistance and MM progression

Influence of fruit maturation process on the sensory quality of virgin olive oils from Picual, Hojiblanca and Picudo cultivars

La calidad sensorial del aceite de oliva virgen (AOV) está estrechamente relacionada con la variedad y el grado de maduración de la aceituna. El objetivo del presente trabajo fue investigar la influencia del grado de maduración sobre el perfil sensorial de aceites de oliva virgen monovarietales con el fin de establecer el momento óptimo de recolección. Los frutos de tres variedades diferentes, Picual, Picudo y Hojiblanca fueron recolectados en nueve etapas de maduración diferentes. Los parámetros de calidad fueron evaluados y las características organolépticas se determinaron por un panel de cata. Los resultados muestran que los parámetros analíticos disminuyeron ligeramente en todas las variedades. Para cada variedad se describe la evolución de las características organolépticas de los aceites de oliva virgen así como sus flavores típicos. En todas las variedades estudiadas, los atributos «frutado» (afrutado) y «amargo» disminuyeron durante la maduración, por el contrario el atributo «dulce» se incrementó. Los resultados mostrados pueden ser de gran utilidad para proveer información sobre la evolución de la calidad sensorial de los aceites de oliva virgen durante la maduración para obtener aceites basados en las preferencias del mercado.The sensory quality of virgin olive oil is closely correlated with the cultivar and the degree of ripening of the olive fruit. The aim of the present work was to investigate the influence of ripening degree on sensory profile of monovarietal virgin olive oils (VOO) in order to establish an optimum harvesting time. Fruit obtained from three different cultivars, Picual, Picudo and Hojiblanca were picked at nine different stages of ripeness. The quality parameters were evaluated and the sensory characteristics were determinate by a sensor panel. The analytical parameters decrease slightly in all cultivars. The evolution of the organoleptic characteristics of the virgin olive oil is reported and typical flavors are described for each cultivar. In all studied cultivar, “fruity” and “bitter” attributes decreased during the ripening and conversely “sweet” attribute increased. The results showed in this work could be considered useful for providing information about the evolution of sensory quality of virgin olive oils during ripening to obtain those based on market preferences

Whole-exome sequencing of primary plasma cell leukemia discloses heterogeneous mutational patterns

Primary plasma cell leukemia (pPCL) is a rare and aggressive form of plasma cell dyscrasia and may represent a valid model for high-risk multiple myeloma (MM). To provide novel information concerning the mutational profile of this disease, we performed the whole-exome sequencing of a prospective series of 12 pPCL cases included in a Phase II multicenter clinical trial and previously characterized at clinical and molecular levels. We identified 1, 928 coding somatic non-silent variants on 1, 643 genes, with a mean of 166 variants per sample, and only few variants and genes recurrent in two or more samples. An excess of C > T transitions and the presence of two main mutational signatures (related to APOBEC over-activity and aging) occurring in different translocation groups were observed. We identified 14 candidate cancer driver genes, mainly involved in cell-matrix adhesion, cell cycle, genome stability, RNA metabolism and protein folding. Furthermore, integration of mutation data with copy number alteration profiles evidenced biallelically disrupted genes with potential tumor suppressor functions. Globally, cadherin/Wnt signaling, extracellular matrix and cell cycle checkpoint resulted the most affected functional pathways. Sequencing results were finally combined with gene expression data to better elucidate the biological relevance of mutated genes. This study represents the first whole-exome sequencing screen of pPCL and evidenced a remarkable genetic heterogeneity of mutational patterns. This may provide a contribution to the comprehension of the pathogenetic mechanisms associated with this aggressive form of PC dyscrasia and potentially with high-risk MM

The apobec mutational activity in multiple myeloma: from diagnosis to cell lines

Next generation sequencing (NGS) studies have highlighted the role of aberrant activity of APOBEC DNA deaminases in generating the mu- tational repertoire of multiple myeloma (MM). However, the contribu- tion of this mutational process across the landscape of plasma cell dyscrasias, or its prognostic role, has never been investigated in detail. To answer these unexplored aspects of MM biology, we used published NGS data from our own work as well as others, including the large CoMMpass trial for a total of 1153 whole-exomes of MM. Furthermore, we investigated 5 MGUS, 6 primary plasma cell leukemias (pPCL) and 18 MM cell lines (MMCL). Overall, we identified signatures of two mu- tational processes, one related to spontaneous deamination of methy- lated cytosines (30% of variants, range 0-100%) and one attributed to aberrant APOBEC activity (70% of variants, range 0-100%). APOBEC contribution was extremely heterogeneous among MM patients, but was correlated with a higher mutational burden (r=0.71, p=<0.0001) and with MAF gene translocations t(14;16) and t(14;20). The activity of APOBEC increased from MGUS to MM to pPCL, both in terms of ab- solute number of mutations and as percentage contribution. In MMCL we instead observed a bi-modal distribution whereby 8 cell lines showed the highest numbers of mutations caused by APOBEC (5/8 car- ried MAF translocations), while 10 where virtually devoid of APOBEC mutations (0/10 carried MAF translocations). The contribution of APOBEC to the total mutational repertoire in MM had a clear prognos- tic impact. MM patients with APOBEC mutations in the lowest quartile had a survival advantage over patients with APOBEC mutations in the highest quartile both in terms of progression-free survival (3-y PFS 46% vs 67% months, p=<0.0001) and overall survival (3-y OS 52% vs 83%, p=0.0084). This association was retained in a multivariate model that included age, gender, cytogenetic class, ISS, and quartiles of mutational load both in PFS [p=0.02, HR 2.06 (95IC 1.11-3.81] and OS [p=0.02, HR 2.88 (95IC 1.17-7.09)]. Interestingly we found that APOBEC mutations in the 4th quartile retained its independent prognostic respect to high mutational load and presence of MAF translocations. Overall, our data suggest that APOBEC-mediated mutagenesis is strongly involved in MM pathogenesis and its activity persists during different phases of evolution, playing a critical role in MM genomic complexity, and im- pacting prognosis of the patients