Liver transcriptome profile in pigs with extreme phenotypes of intramuscular fatty acid composition

Abstract Background New advances in high-throughput technologies have allowed for the massive analysis of genomic data, providing new opportunities for the characterization of the transcriptome architectures. Recent studies in pigs have employed RNA-Seq to explore the transcriptome of different tissues in a reduced number of animals. The main goal of this study was the identification of differentially-expressed genes in the liver of Iberian x Landrace crossbred pigs showing extreme phenotypes for intramuscular fatty acid composition using RNA-Seq. Results The liver transcriptomes of two female groups (H and L) with phenotypically extreme intramuscular fatty acid composition were sequenced using RNA-Seq. A total of 146 and 180 unannotated protein-coding genes were identified in intergenic regions for the L and H groups, respectively. In addition, a range of 5.8 to 7.3% of repetitive elements was found, with SINEs being the most abundant elements. The expression in liver of 186 (L) and 270 (H) lncRNAs was also detected. The higher reproducibility of the RNA-Seq data was validated by RT-qPCR and porcine expression microarrays, therefore showing a strong correlation between RT-qPCR and RNA-Seq data (ranking from 0.79 to 0.96), as well as between microarrays and RNA-Seq (r=0.72). A differential expression analysis between H and L animals identified 55 genes differentially-expressed between groups. Pathways analysis revealed that these genes belong to biological functions, canonical pathways and three gene networks related to lipid and fatty acid metabolism. In concordance with the phenotypic classification, the pathways analysis inferred that linolenic and arachidonic acids metabolism was altered between extreme individuals. In addition, a connection was observed among the top three networks, hence suggesting that these genes are interconnected and play an important role in lipid and fatty acid metabolism. Conclusions In the present study RNA-Seq was used as a tool to explore the liver transcriptome of pigs with extreme phenotypes for intramuscular fatty acid composition. The differential gene expression analysis showed potential gene networks which affect lipid and fatty acid metabolism. These results may help in the design of selection strategies to improve the sensorial and nutritional quality of pork meat.This work was funded by MICINN projects AGL2008-04818-C03/GAN and AGL2011-29821-C02 (Ministerio de Economía y Competitividad), and by the Innovation Consolider-Ingenio 2010 Program (CSD2007-00036, Centre for Research in Agrigenomics). Y. Ramayo-Caldas was funded by a FPU PhD grant from the Spanish Ministerio de Educación (AP2008-01450), J. Corominas was funded by a FPI PhD grant from the Spanish Ministerio de Educación (BES-2009-018223), A. Esteve-Codina is recipient of a FPI PhD fellowship from the Ministerio de Educación (BES-2008-005772), Spain.Peer Reviewe

Assessing sleep health in a European population: results of the catalan health survey 2015

Objective To describe the overall sleep health of the Catalan population using data from the 2015 Catalan Health Survey and to compare the performance of two sleep health indicators: sleep duration and a 5-dimension sleep scale (SATED). Methods Multistage probability sampling representative of the non-institutionalized population aged 15 or more years, stratified by age, gender and municipality size, was used, excluding nightshift-workers. A total of 4385 surveys were included in the analyses. Associations between sleep health and the number of reported chronic diseases were assessed using non-parametric smoothed splines. Differences in the predictive ability of age-adjusted logistic regression models of self-rated health status were assessed. Multinomial logistic regression models were used to assess SATED determinants. Results Overall mean (SD) sleep duration was 7.18 (1.16) hours; and SATED score 7.91 (2.17) (range 0–10), lower (worse) scores were associated with increasing age and female sex. Alertness and efficiency were the most frequently impaired dimensions across age groups. SATED performed better than sleep duration when assessing self-rated health status (area under the curve = 0.856 vs. 0.798; p-value <0.001), and had a linear relationship with the number of reported chronic diseases, while the sleep duration relationship was u-shaped. Conclusions Sleep health in Catalonia is associated with age and gender. SATED has some advantaged compared to sleep duration assessment, as it relates linearly to health indicators, has a stronger association with self-rated health status, and provides a more comprehensive assessment of sleep health. Therefore, the inclusion of multi-dimensional sleep health assessment tools in national surveys should be considered.This work was cofunded by Ministerio de Economía y Competitividad [COFUND2014-51501]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

A comparison of RNA-Seq results from paired formalin-fixed paraffin-embedded and fresh-frozen glioblastoma tissue samples.

The molecular classification of glioblastoma (GBM) based on gene expression might better explain outcome and response to treatment than clinical factors. Whole transcriptome sequencing using next-generation sequencing platforms is rapidly becoming accepted as a tool for measuring gene expression for both research and clinical use. Fresh frozen (FF) tissue specimens of GBM are difficult to obtain since tumor tissue obtained at surgery is often scarce and necrotic and diagnosis is prioritized over freezing. After diagnosis, leftover tissue is usually stored as formalin-fixed paraffin-embedded (FFPE) tissue. However, RNA from FFPE tissues is usually degraded, which could hamper gene expression analysis. We compared RNA-Seq data obtained from matched pairs of FF and FFPE GBM specimens. Only three FFPE out of eleven FFPE-FF matched samples yielded informative results. Several quality-control measurements showed that RNA from FFPE samples was highly degraded but maintained transcriptomic similarities to RNA from FF samples. Certain issues regarding mutation analysis and subtype prediction were detected. Nevertheless, our results suggest that RNA-Seq of FFPE GBM specimens provides reliable gene expression data that can be used in molecular studies of GBM if the RNA is sufficiently preserved

Developmental RNA-Seq transcriptomics of haploid germ cells and spermatozoa uncovers novel pathways associated with teleost spermiogenesis

In non-mammalian vertebrates, the molecular mechanisms involved in the transformation of haploid germ cells (HGCs) into spermatozoa (spermiogenesis) are largely unknown. Here, we investigated this process in the marine teleost gilthead seabream (Sparus aurata) through the examination of the changes in the transcriptome between cell-sorted HGCs and ejaculated sperm (SPZEJ). Samples were collected under strict quality controls employing immunofluorescence microscopy as well as by determining the sperm motion kinematic parameters by computer-assisted sperm analysis. Deep sequencing by RNA-seq identified a total of 7286 differentially expressed genes (DEGs) (p-value < 0.01) between both cell types, of which nearly half were upregulated in SPZEJ compared to HCGs. In addition, approximately 9000 long non-coding RNAs (lncRNAs) were found, of which 56% were accumulated or emerged de novo in SPZEJ. The upregulated transcripts are involved in transcriptional and translational regulation, chromatin and cytoskeleton organization, metabolic processes such as glycolysis and oxidative phosphorylation, and also include a number of ion and water channels, exchangers, transporters and receptors. Pathway analysis conducted on DEGs identified 37 different signaling pathways enriched in SPZEJ, including 13 receptor pathways, from which the most predominant correspond to the chemokine and cytokine, gonadotropin-releasing hormone receptor and platelet derived growth factor signaling pathways. Our data provide new insight into the mRNA and lncRNA cargos of teleost spermatozoa and uncover the possible involvement of novel endocrine mechanisms during the differentiation and maturation of spermatozoa.info:eu-repo/semantics/publishedVersio

The pluripotency state of human embryonic stem cells derived from single blastomeres of eight-cell embryos

Human embryonic stem cells (hESCs) derived from blastocyst stage embryos present a primed state of pluripotency, whereas mouse ESCs (mESCs) display na & iuml;ve pluripotency. Their unique characteristics make na & iuml;ve hESCs more suitable for particular applications in biomedical research. This work aimed to derive hESCs from single blastomeres and determine their pluripotency state, which is currently unclear. We derived hESC lines from single blastomeres of 8-cell embryos and from whole blastocysts, and analysed several na & iuml;ve pluripotency indicators, their transcriptomic profile and their trilineage differentiation potential. No significant differences were observed between blastomere-derived hESCs (bm-hESCs) and blastocyst-derived hESCs (bc-hESCs) for most na & iuml;ve pluripotency indicators, including TFE3 localization, mitochondrial activity, and global DNA methylation and hydroxymethylation, nor for their trilineage differentiation potential. Nevertheless, bm-hESCs showed an increased single-cell clonogenicity and a higher expression of na & iuml;ve pluripotency markers at early passages than bc-hESCs. Furthermore, RNA-seq revealed that bc-hESCs overexpressed a set of genes related to the postimplantational epiblast. Altogether, these results suggest that bm-hESCs, although displaying primed pluripotency, would be slightly closer to the na & iuml;ve end of the pluripotency continuum than bc-hESCs

Polystyrene nanoplastics target lysosomes interfering with lipid metabolism through the PPAR system and affecting macrophage functionalization

Altres ajuts: acords transformatius de la UABNanoplastics (NPs) are currently a main concern for environmental, animal and human health due to their potential to accumulate in different environmental compartments and provoke effects in living organisms. Nevertheless, neither these effects nor the interaction of NPs with the cellular machinery are well characterized, and only scattered information is available. In the present work, we focused on the interaction between NPs and fish cells, both intestinal cells and macrophages, in order to understand which cell organelles are targeted by polystyrene (PS)-NPs and how this could impact cell function. PS-NPs can pass through phospholipid membranes, entering cells via endocytosis, phagocytosis or passive transport. Once internalized, we found that PS-NPs co-localize with lysosomes but not with mitochondria. Moreover, using two types of fluorescent probe (HDCFDA and DHE) we demonstrated that NPs did not trigger the production of reactive oxygen species (ROS), which was corroborated by the fact that neither the oxidative consumption ratio (OCR) nor the extracellular acidification rate (ECAR) in mitochondrial respiration were altered. RNASeq data revealed clear interference by PS-NPs with lipid metabolism, peroxisomes and PPAR signaling. The M1/M2 balance critically determines tissue homeostasis when exposed to exogenous agents such as microorganisms or pollutants. Thus, the expression of different genes (il1β, tnfα, il6, il10, il12, cox2, mmp9, ppar a, b and g) was further assessed to characterize the macrophage phenotype M1 or M2, induced by PS-NPs. Overall, in this study we demonstrate that PS-NPs co-localize within lysosomes, both in macrophages and in intestinal cells of rainbow trout, but do not trigger ROS production nor alter mitochondrial respiration. In macrophages, PS-NPs modulate polarization towards the M2-like phenotype

Developmental RNA-Seq transcriptomics of haploid germ cells and spermatozoa uncovers novel pathways associated with teleost spermiogenesis

In non-mammalian vertebrates, the molecular mechanisms involved in the transformation of haploid germ cells (HGCs) into spermatozoa (spermiogenesis) are largely unknown. Here, we investigated this process in the marine teleost gilthead seabream (Sparus aurata) through the examination of the changes in the transcriptome between cell-sorted HGCs and ejaculated sperm (SPZ). Samples were collected under strict quality controls employing immunofluorescence microscopy as well as by determining the sperm motion kinematic parameters by computer-assisted sperm analysis. Deep sequencing by RNA-seq identified a total of 7286 differentially expressed genes (DEGs) (p-value < 0.01) between both cell types, of which nearly half were upregulated in SPZ compared to HCGs. In addition, approximately 9000 long non-coding RNAs (lncRNAs) were found, of which 56% were accumulated or emerged de novo in SPZ. The upregulated transcripts are involved in transcriptional and translational regulation, chromatin and cytoskeleton organization, metabolic processes such as glycolysis and oxidative phosphorylation, and also include a number of ion and water channels, exchangers, transporters and receptors. Pathway analysis conducted on DEGs identified 37 different signaling pathways enriched in SPZ, including 13 receptor pathways, from which the most predominant correspond to the chemokine and cytokine, gonadotropin-releasing hormone receptor and platelet derived growth factor signaling pathways. Our data provide new insight into the mRNA and lncRNA cargos of teleost spermatozoa and uncover the possible involvement of novel endocrine mechanisms during the differentiation and maturation of spermatozoa

Alteration in the Culex pipiens transcriptome reveals diverse mechanisms of the mosquito immune system implicated upon Rift Valley fever phlebovirus exposure

Rift Valley fever phlebovirus (RVFV) causes an emerging zoonotic disease and is mainly transmitted by Culex and Aedes mosquitoes. While Aedes aegypti-dengue virus (DENV) is the most studied model, less is known about the genes involved in infection-responses in other mosquito-arboviruses pairing. The main objective was to investigate the molecular responses of Cx. pipiens to RVFV exposure focusing mainly on genes implicated in innate immune responses. Mosquitoes were fed with blood spiked with RVFV. The fully-engorged females were pooled at 3 different time points: 2 hours post-exposure (hpe), 3- and 14-days post-exposure (dpe). Pools of mosquitoes fed with non-infected blood were also collected for comparisons. Total RNA from each mosquito pool was subjected to RNA-seq analysis and a de novo transcriptome was constructed. A total of 451 differentially expressed genes (DEG) were identified. Most of the transcriptomic alterations were found at an early infection stage after RVFV exposure. Forty-eight DEG related to immune infection-response were characterized. Most of them were related with the RNAi system, Toll and IMD pathways, ubiquitination pathway and apoptosis. Our findings provide for the first time a comprehensive view on Cx. pipiens-RVFV interactions at the molecular level. The early depletion of RNAi pathway genes at the onset of the RVFV infection would allow viral replication in mosquitoes. While genes from the Toll and IMD immune pathways were altered in response to RVFV none of the DEG were related to the JAK/STAT pathway. The fact that most of the DEG involved in the Ubiquitin-proteasome pathway (UPP) or apoptosis were found at an early stage of infection would suggest that apoptosis plays a regulatory role in infected Cx. pipiens midguts. This study provides a number of target genes that could be used to identify new molecular targets for vector control.info:eu-repo/semantics/publishedVersio

Schlafen 12 restricts HIV-1 latency reversal by a codon-usage dependent post-transcriptional block in CD4+ T cells

HIV infections; Restriction factorsInfecciones por VIH; Factores de restricciónInfeccions pel VIH; Factors de restriccióLatency is a major barrier towards virus elimination in HIV-1-infected individuals. Yet, the mechanisms that contribute to the maintenance of HIV-1 latency are incompletely understood. Here we describe the Schlafen 12 protein (SLFN12) as an HIV-1 restriction factor that establishes a post-transcriptional block in HIV-1-infected cells and thereby inhibits HIV-1 replication and virus reactivation from latently infected cells. The inhibitory activity is dependent on the HIV-1 codon usage and on the SLFN12 RNase active sites. Within HIV-1-infected individuals, SLFN12 expression in PBMCs correlated with HIV-1 plasma viral loads and proviral loads suggesting a link with the general activation of the immune system. Using an RNA FISH-Flow HIV-1 reactivation assay, we demonstrate that SLFN12 expression is enriched in infected cells positive for HIV-1 transcripts but negative for HIV-1 proteins. Thus, codon-usage dependent translation inhibition of HIV-1 proteins participates in HIV-1 latency and can restrict the amount of virus release after latency reversal.This work was supported by following grants: M.K.I., JSPS Oversea Research Fellowship and Takeda Science Foundation; A.E.C., PT17/0009/0019 (ISCIII/MINECO and FEDER); M.J.B., RTI2018-101082-B-I00 and PID2021-123321OB-I00 [MINECO/FEDER]), and the Miguel Servet program by ISCIII (CP17/00179 and CPII22/00005); C.B., M.R.R., C.D.C., European Union’s Horizon 2020 research and innovation program under grant agreement 681137-EAVI2020 and NIH grant P01-AI131568; J.D., the Spanish Ministry of Science and Innovation (PID2019106959RB-I00/AEI/10.13039/501100011033); A.M., the Spanish Ministry of Science and Innovation (PID2019-106323RB-I00 AEI//10.13039/501100011033) and the institutional “María de Maeztu” Programme for Units of Excellence in R&D (CEX2018-000792-M)