De novo Transcriptome Assembly and Comprehensive Annotation of Two Tree Tomato Cultivars (Solanum betaceum Cav.) with Different Fruit Color

[EN] The tree tomato (Solanum betaceum Cav.) is an underutilized fruit crop native to the Andean region and phylogenetically related to the tomato and potato. Tree tomato fruits have a high amount of nutrients and bioactive compounds. However, so far there are no studies at the genome or transcriptome level for this species. We performed a de novo assembly and transcriptome annotation for purple-fruited (A21) and an orange-fruited (A23) accessions. A total of 174,252 (A21) and 194,417 (A23) transcripts were assembled with an average length of 851 and 849 bp. A total of 34,636 (A21) and 36,224 (A23) transcripts showed a significant similarity to known proteins. Among the annotated unigenes, 22,096 (A21) and 23,095 (A23) were assigned to the Gene Ontology (GO) term and 14,035 (A21) and 14,540 (A23) were found to have Clusters of Orthologous Group (COG) term classifications. Furthermore, 22,096 (A21) and 23,095 (A23) transcripts were assigned to 155 and 161 (A23) KEGG pathways. The carotenoid biosynthetic process GO terms were significantly enriched in the purple-fruited accession A21. Finally, 68,647 intraspecific single-nucleotide variations (SNVs) and almost 2 million interspecific SNVs were identified. The results of this study provide a wealth of genomic data for the genetic improvement of the tree tomato.Pietro Gramazio is grateful to the Spanish Ministerio de Ciencia e Innovacion for a Juan de laCierva-Formacion post-doctoral grant FJC2019-038921-I funded by MCIN/AEI/10.13039/501100011033)Pacheco, J.; Vilanova Navarro, S.; Grillo-Risco, R.; García-García, F.; Prohens Tomás, J.; Gramazio, P. (2021). De novo Transcriptome Assembly and Comprehensive Annotation of Two Tree Tomato Cultivars (Solanum betaceum Cav.) with Different Fruit Color. Horticulturae. 7(11):1-18. https://doi.org/10.3390/horticulturae7110431S11871

Ptpn1 deletion protects oval vells against lipoapotosis by favoring lipid droplet formation and dynamics

Trabajo presentado en el The international liver congress, celebrado en Londres (Inglaterra) del 22 al 26 de junio de 2022.[Background and aims]: Activation of oval cells has been related to hepatocyte injury during chronic liver diseases including nonalcoholic fatty liver disease (NAFLD). However, oval cells plasticity can be affected by the pathological environment. We previously found a protection against hepatocyte cell death by inhibiting protein tyrosine phosphatase 1B (PTP1B). Herein, we investigated the molecular and cellular processes involved in the lipotoxic susceptibility in oval cells expressing or not PTP1B. [Method]: Palmitic acid (PA) induced apoptotic cell death in wild-type (Ptpn1+/+) oval cells in parallel to oxidative stress and impaired autophagy. This lipotoxic effect was attenuated in oval cells lacking Ptpn1 that showed up-regulated antioxidant defences, increased unfolded protein response (UPR) signaling, higher endoplasmic reticulum (ER) content and elevated stearoyl CoA desaturase (Scd1) expression and activity. [Results]: These effects in Ptpn1−/− oval cells concurred with an active autophagy, higher mitochondrial efficiency and a molecular signature of starvation, favoring lipid droplet (LD) formation and dynamics. Autophagy blockade in Ptpn1−/− oval cells reduced Scd1 expression, mitochondrial fitness, LD formation and restored lipoapoptosis, an effect also recapitulated by Scd1 silencing. Importantly, oval cells with LDs were found in livers from Ptpn1−/− mice with NAFLD. [Conclusion]: Ptpn1 deficiency restrained lipoapoptosis in oval cells through a metabolic rewiring towards a “starvation-like” fate, favoring autophagy, mitochondrial fitness and LD formation. Dynamic LD-lysosomal interations likely ensured lipid recycling and, overall, these adaptations protect against lipotoxicity. The identification of LDs in oval cells from Ptpn1−/− mice with NAFLD opens new therapeutic perspectives to ensure oval cells viability and plasticity under lipotoxic liver damage

Deciphering the sex bias in housekeeping gene expression in adipose tissue: a comprehensive meta-analysis of transcriptomic studies

Abstract Background As the housekeeping genes (HKG) generally involved in maintaining essential cell functions are typically assumed to exhibit constant expression levels across cell types, they are commonly employed as internal controls in gene expression studies. Nevertheless, HKG may vary gene expression profile according to different variables introducing systematic errors into experimental results. Sex bias can indeed affect expression display, however, up to date, sex has not been typically considered as a biological variable. Methods In this study, we evaluate the expression profiles of six classical housekeeping genes (four metabolic: GAPDH, HPRT, PPIA, and UBC, and two ribosomal: 18S and RPL19) to determine expression stability in adipose tissues (AT) of Homo sapiens and Mus musculus and check sex bias and their overall suitability as internal controls. We also assess the expression stability of all genes included in distinct whole-transcriptome microarrays available from the Gene Expression Omnibus database to identify sex-unbiased housekeeping genes (suHKG) suitable for use as internal controls. We perform a novel computational strategy based on meta-analysis techniques to identify any sexual dimorphisms in mRNA expression stability in AT and to properly validate potential candidates. Results Just above half of the considered studies informed properly about the sex of the human samples, however, not enough female mouse samples were found to be included in this analysis. We found differences in the HKG expression stability in humans between female and male samples, with females presenting greater instability. We propose a suHKG signature including experimentally validated classical HKG like PPIA and RPL19 and novel potential markers for human AT and discarding others like the extensively used 18S gene due to a sex-based variability display in adipose tissue. Orthologs have also been assayed and proposed for mouse WAT suHKG signature. All results generated during this study are readily available by accessing an open web resource ( https://bioinfo.cipf.es/metafun-HKG ) for consultation and reuse in further studies. Conclusions This sex-based research proves that certain classical housekeeping genes fail to function adequately as controls when analyzing human adipose tissue considering sex as a variable. We confirm RPL19 and PPIA suitability as sex-unbiased human and mouse housekeeping genes derived from sex-specific expression profiles, and propose new ones such as RPS8 and UBB

Molecular and functional atlas of sex-differences in multiple sclerosis subtypes analising single cell and single nucleus transcriptomic data

Multiple sclerosis (MS) is the commonest cause of non-traumatic disability among young adults. MS hallmark underlies myelin damage induced by defective autoimmune responses, leading to the neurodegeneration of the central nervous system. Sex differences in MS have been reported at several epidemiological and clinical levels as prevalence, progression and response to treatment. However, the molecular mechanisms underneath those differences remain poorly understood.  To exhaustively characterise sex bias in MS by cell type, we performed an in silico analysis of scRNA-seq and snRNA-seq data using R programming language. Firstly, we performed a systematic review implementing PRISMA guidelines [PMID:33780438] in public repositories. Then, we processed each selected dataset through quality control filtering, normalisation, high variable genes selection, dimensionality reduction, clustering and cell type annotation. Finally, we characterise each cell type by differential gene expression and functional profiling analyses, evaluating for the latter biological functions from the Gene Ontology [PMID:10802651] and pathways from the KEGG [PMID:10592173] databases. Three datasets, each representing a different subtype of MS, were spotted. Nervous tissue dataset (n=1) stored astrocytes, microglia, neurons, oligodendrocytes, and oligodendrocyte precursor cells, whilst blood datasets (n=2) included diverse types of lymphocytes, dendritic cells and monocytes. We found significant sex-differential and sex-specific gene expression patterns, biological functions, and pathways for almost all cell types in each dataset. Some significant features were shared among cell types with similar or opposite patterns, whilst others were cell type exclusive. Therefore, this atlas enhances personalised medicine by unveiling molecular and functional sex-dependent prospective biomarkers.</p

Ptpn1 deletion protects oval cells against lipoapoptosis by favoring lipid droplet formation and dynamics

Activation of oval cells (OCs) has been related to hepatocyte injury during chronic liver diseases including non-alcoholic fatty liver disease (NAFLD). However, OCs plasticity can be affected under pathological environments. We previously found protection against hepatocyte cell death by inhibiting protein tyrosine phosphatase 1B (PTP1B). Herein, we investigated the molecular and cellular processes involved in the lipotoxic susceptibility in OCs expressing or not PTP1B. Palmitic acid (PA) induced apoptotic cell death in wild-type (Ptpn1+/+) OCs in parallel to oxidative stress and impaired autophagy. This lipotoxic effect was attenuated in OCs lacking Ptpn1 that showed upregulated antioxidant defences, increased unfolded protein response (UPR) signaling, higher endoplasmic reticulum (ER) content and elevated stearoyl CoA desaturase (Scd1) expression and activity. These effects in Ptpn1−/− OCs concurred with an active autophagy, higher mitochondrial efficiency and a molecular signature of starvation, favoring lipid droplet (LD) formation and dynamics. Autophagy blockade in Ptpn1−/− OCs reduced Scd1 expression, mitochondrial fitness, LD formation and restored lipoapoptosis, an effect also recapitulated by Scd1 silencing. PTP1B immunostaining was detected in OCs from mouse liver and, importantly, LDs were found in OCs from Ptpn1−/− mice with NAFLD. In conclusion, we demonstrated that Ptpn1 deficiency restrains lipoapoptosis in OCs through a metabolic rewiring towards a “starvation-like” fate, favoring autophagy, mitochondrial fitness and LD formation. Dynamic LD-lysosomal interations likely ensure lipid recycling and, overall, these adaptations protect against lipotoxicity. The identification of LDs in OCs from Ptpn1−/− mice with NAFLD opens therapeutic perspectives to ensure OC viability and plasticity under lipotoxic liver damage.This work was funded by grants RTI2018-094052-B-100 (MICINN/AEI/FEDER, EU), S2017/BMD-3684 (Comunidad de Madrid, Spain) and Fundación Ramón Areces (Spain) to AMV, grant PID2019-105989RB-I00 (MICINN/AEI/FEDER, EU) to JB, grants SAF2017-83813-C3-1-R (MICINN/AEI/FEDER, EU, cofunded by the ERDF) and CB06/03/0001 (CIBEROBN, ISCIII, Spain) to LH and DS, grants PID2019-106982RB-I00 (MICINN/AEI/FEDER, EU) and CB12/03/30002 (CIBERobn, ISCIII, Spain) to MJM-A, grant PI20/00837 (ISCIII/FEDER, Spain) to CG-M, grant PI19/00123 (ISCIII/FEDER, Spain) to AG-R. We acknowledge support from CIBERDEM (ISCII) to JB, AMV, and MPV (grant DEM21 PI01/2021). MCS-V is a recipient of the Ajut de Personal Investigador Predoctoral en Formació (APIF) fellowship from the University of Barcelona.Peer reviewe

Contemporary use of cefazolin for MSSA infective endocarditis: analysis of a national prospective cohort

Objectives: This study aimed to assess the real use of cefazolin for methicillin-susceptible Staphylococcus aureus (MSSA) infective endocarditis (IE) in the Spanish National Endocarditis Database (GAMES) and to compare it with antistaphylococcal penicillin (ASP). Methods: Prospective cohort study with retrospective analysis of a cohort of MSSA IE treated with cloxacillin and/or cefazolin. Outcomes assessed were relapse; intra-hospital, overall, and endocarditis-related mortality; and adverse events. Risk of renal toxicity with each treatment was evaluated separately. Results: We included 631 IE episodes caused by MSSA treated with cloxacillin and/or cefazolin. Antibiotic treatment was cloxacillin, cefazolin, or both in 537 (85%), 57 (9%), and 37 (6%) episodes, respectively. Patients treated with cefazolin had significantly higher rates of comorbidities (median Charlson Index 7, P <0.01) and previous renal failure (57.9%, P <0.01). Patients treated with cloxacillin presented higher rates of septic shock (25%, P = 0.033) and new-onset or worsening renal failure (47.3%, P = 0.024) with significantly higher rates of in-hospital mortality (38.5%, P = 0.017). One-year IE-related mortality and rate of relapses were similar between treatment groups. None of the treatments were identified as risk or protective factors. Conclusion: Our results suggest that cefazolin is a valuable option for the treatment of MSSA IE, without differences in 1-year mortality or relapses compared with cloxacillin, and might be considered equally effective