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Nitrate and ammonium are the main nitrogen sources in agricultural soils. In the last decade, ammonium (NH4+), a double-sided metabolite, has attracted considerable attention by researchers. Its ubiquitous presence in plant metabolism and its metabolic energy economy for being assimilated contrast with its toxicity when present in high amounts in the external medium. Plant species can adopt different strategies to maintain NH4+ homeostasis, as the maximization of its compartmentalization and assimilation in organic compounds, primarily as amino acids and proteins. In the present study, we report an integrative metabolic response to ammonium nutrition of seven plant species, belonging to four different families: Gramineae (ryegrass, wheat, Brachypodium distachyon), Leguminosae (clover), Solanaceae (tomato), and Brassicaceae (oilseed rape, Arabidopsis thaliana). We use principal component analysis (PCA) and correlations among metabolic and biochemical data from 40 experimental conditions to understand the whole-plant response. The nature of main amino acids is analyzed among species, under the hypothesis that those Asn-accumulating species will show a better response to ammonium nutrition. Given the provision of carbon (C) skeletons is crucial for promotion of the nitrogen assimilation, the role of different anaplerotic enzymes is discussed in relation to ammonium nutrition at a whole-plant level. Among these enzymes, isocitrate dehydrogenase (ICDH) shows to be a good candidate to increase nitrogen assimilation in plants. Overall, metabolic adaptation of different carbon anaplerotic activities is linked with the preference to synthesize Asn or Gln in their organs. Lastly, glutamate dehydrogenase (GDH) reveals as an important enzyme to surpass C limitation during ammonium assimilation in roots, with a disparate collaboration of glutamine synthetase (GS). The design of the study, analysis, and interpretation of data and writing of the manuscript was supported by the Basque Government [IT932-16] or GIC15/179, the Spanish Ministry of Economy and Competitiveness [AGL2015-64582-C3-2-R] and [BIO2017-84035-R]. IVM held a postdoctoral grant from the Basque Government (conv. 2018) and MDLP held a PhD grant by COLCIENCIAS (conv. 672).

mRNA stability influences gene expression and translation in almost all living organisms, and the levels of mRNA molecules in the cell are determined by a balance between production and decay. Maintaining an accurate balance is crucial for the correct function of a wide variety of biological processes and to maintain an appropriate cellular homeostasis. Long non-coding RNAs (lncRNAs) have been shown to participate in the regulation of gene expression through different molecular mechanisms, including mRNA stabilization. In this review we provide an overview on the molecular mechanisms by which lncRNAs modulate mRNA stability and decay. We focus on how lncRNAs interact with RNA binding proteins and microRNAs to avoid mRNA degradation, and also on how lncRNAs modulate epitranscriptomic marks that directly impact on mRNA stability. LncRNA work in author’s laboratory is supported by European Foundation for the Study of Diabetes (EFSD)-EFSD/JDRF/Lilly Programme on Type 1 Diabetes Research and the Spanish Ministry of Science, Innovation and Universities (PID2019-104475GA-I00) to I.S; and Spanish Ministry of Science, Innovation and Universities (SAF2017-91873-EXP and PGC2018-097573-A-I00) to ACR. M.S.D. and I.G.M. are supported by a Predoctoral Fellowship Grant from the UPV/EHU (Universidad del País Vasco/Euskal Herriko Unibertsitatea) and A.O.G. is supported by a Predoctoral Fellowship Grant from the Education Department of Basque Government.

Type 1 diabetes (T1D) is a complex autoimmune disease in which genetic factors interact with environmental changes (e.g. viral infections) to trigger an autoimmune assault against insulin producing pancreatic β-cells. The majority of T1D-associated single nucleotide polymorphisms (SNPs) lay into non-coding regions of the human genome and many have been predicted to affect the expression, secondary structure and function of long non-coding RNAs (lncRNAs). However, the molecular mechanisms by which these non-coding molecules contribute to T1D pathogenesis remain to be clarified. Lnc10 is a lncRNA harboring a T1D-associated SNP that has been described to control Ebi2 expression in immune cells. Ebi2 is a trans-eQTL that regulates the IRF7-driven inflammatory network (iDIN), an antiviral gene network which is enriched with T1D-associated genes. Taking into account that the T1D-associated SNP is located in Lnc10, our hypothesis is that Lnc10 might be dysregulated in T1D patients, influencing the regulation of the iDIN network at the pancreatic β-cell level and provoking an exacerbated antiviral response, and eventually, β-cell destruction. Preliminary results of our group have demonstrated that diabetogenic stimuli, such as pro-inflammatory cytokines and viral infections, upregulate Lnc10 expression in pancreatic β-cells. Lnc10 is located in the nuclei of β-cells, both in basal and stimulated conditions, suggesting a potential role in transcriptional regulation. Lnc10 overexpression in combination with polyinosinic:polycytidylic acid (PIC) transfection to mimic a viral infection, increased the expression of several antiviral genes of the iDIN pathway, including key genes in type I IFN signaling and antiviral response (STAT1, CXCL1, GBP1, SP110, TAP2, IFITM1, DYNLT1, MAP3K7, CCL2 and ERAP1). Interestingly, the type I IFN signaling has been shown to play a crucial role in the initial stages of T1D pathogenesis in pancreatic β-cells. In conclusion, our results show that Lnc10 is upregulated after a viral infection in pancreatic β-cells. Upregulation of Lnc10 in combination with a viral infection exacerbates the expression of several antiviral genes from the iDIN pathway. Further studies are required to elucidate the molecular mechanisms by which this lncRNA regulates the expression of iDIN genes and to determine its impact in virus-induced β-cell dysfunction and T1D development in genetically susceptible individuals.

The SARS-CoV-2 pandemic has evolved far more aggressively in countries lacking a robust testing strategy to identify infected individuals. Given the global demand for fast and reliable diagnosis to determine the carrier individuals, a stock-out scenario for a number of essential reagents/kits used along the diagnostic process has been foreseen by many organizations. Having identified the RNA extraction step as one of the key bottlenecks, we tested several alternatives that avoid the use of commercial kits for this step. The analysis showed that 2-propanol precipitation of the viral RNA, followed by one-step RT-qPCR results in a sensitivity and specificity comparable to that provided currently by automatized systems such as the COBAS 6800 system. Therefore, this simple protocol allows SARS-CoV-2 testing independently of commercial kit providers in a time and cost-effective manner. It can be readily implemented in research and/or diagnostic laboratories worldwide, provided that patient confidentiality and researcher safety are ensured. Scaling up the testing capabilities of hospitals and research facilities will identify larger numbers of infected individuals to paint a clear picture of the COVID-19 prevalence, a pre-requisite for informed policy decision making.

The vast majority of type 1 diabetes (T1D) genetic association signals lie in noncoding regions of the human genome. Many have been predicted to affect the expression and secondary structure of long noncoding RNAs (lncRNAs), but the contribution of these lncRNAs to the pathogenesis of T1D remains to be clarified. Here, we performed a complete functional characterization of a lncRNA that harbors a single nucleotide polymorphism (SNP) associated with T1D, namely, Lnc13. Human pancreatic islets harboring the T1D-associated SNP risk genotype in Lnc13 (rs917997*CC) showed higher STAT1 expression than islets harboring the heterozygous genotype (rs917997*CT). Up-regulation of Lnc13 in pancreatic β-cells increased activation of the proinflammatory STAT1 pathway, which correlated with increased production of chemokines in an allele-specific manner. In a mirror image, Lnc13 gene disruption in β-cells partially counteracts polyinosinic-polycytidylic acid (PIC)-induced STAT1 and proinflammatory chemokine expression. Furthermore, we observed that PIC, a viral mimetic, induces Lnc13translocation from the nucleus to the cytoplasm promoting the interaction of STAT1 mRNA with (poly[rC] binding protein 2) (PCBP2). Interestingly, Lnc13-PCBP2 interaction regulates the stability of the STAT1 mRNA, sustaining inflammation in β-cells in an allele-specific manner. Our results show that the T1D-associated Lnc13 may contribute to the pathogenesis of T1D by increasing pancreatic β-cell inflammation. These findings provide information on the molecular mechanisms by which disease-associated SNPs in lncRNAs influence disease pathogenesis and open the door to the development of diagnostic and therapeutic approaches based on lncRNA targeting.

The vast majority of type 1 diabetes (T1D) genetic association signals lie in noncoding regions of the human genome. Many have been predicted to affect the expression and secondary structure of long noncoding RNAs (lncRNAs), but the contribution of these lncRNAs to the pathogenesis of T1D remains to be clarified. Here, we performed a complete functional characterization of a lncRNA that harbors a single nucleotide polymorphism (SNP) associated with T1D, namely, Lnc13. Human pancreatic islets harboring the T1D-associated SNP risk genotype in Lnc13 (rs917997*CC) showed higher STAT1 expression than islets harboring the heterozygous genotype (rs917997*CT). Up-regulation of Lnc13 in pancreatic β-cells increased activation of the proinflammatory STAT1 pathway, which correlated with increased production of chemokines in an allele-specific manner. In a mirror image, Lnc13 gene disruption in β-cells partially counteracts polyinosinic-polycytidylic acid (PIC)-induced STAT1 and proinflammatory chemokine expression. Furthermore, we observed that PIC, a viral mimetic, induces Lnc13 translocation from the nucleus to the cytoplasm promoting the interaction of STAT1 mRNA with (poly[rC] binding protein 2) (PCBP2). Interestingly, Lnc13-PCBP2 interaction regulates the stability of the STAT1 mRNA, sustaining inflammation in β-cells in an allele-specific manner. Our results show that the T1D-associated Lnc13 may contribute to the pathogenesis of T1D by increasing pancreatic β-cell inflammation. These findings provide information on the molecular mechanisms by which disease-associated SNPs in lncRNAs influence disease pathogenesis and open the door to the development of diagnostic and therapeutic approaches based on lncRNA targeting., This work was supported by a Research Project Grant from the Basque Department of Health (2015111068) and a Research Grant from Fundación de la Sociedad Española de Diabetes (FSED) to I.S. I.G.-M. and A.O.-G. were supported by Predoctoral Fellowship Grants from the UPV/EHU (Universidad del Pais Vasco/Euskal Herriko Unibertsitatea) and the Basque Department of Education, respectively. A.C.-R. was funded by a Grant from the Spanish Ministry of Science, Innovation and Universities (PGC2018-097573-A-I00). D.L.E. received support from the Fonds National de la Recherche 420 Scientifique (FNRS), Welbio Grant CR-2015A-06. B.R.G. was funded by the Spanish Ministry of Science, Innovation and Universities; the European Fund for Regional Development (FEDER) (Grant BFU2017-83588-P); and the Juvenile Diabetes Research Foundation (Grants 17-2013-372 and 2-SRA-2019-837-S-B).