Biology subjects

Mari, A.

Publications and source records attributed to Mari, A..

6 recordsLinked to original sources

bioRxiv2025

5'tRNA-derived fragments modulate β-cell homeostasis and islet macrophage activation in type 2 diabetes

During obesity and type 2 diabetes, pancreatic {beta}-cells face chronic environmental stress, while islet-resident macrophages (iMACs) undergo metabolic reprogramming that exacerbates {beta}-cell dysfunction. Stress-induced cleavage of transfer RNAs (tRNAs) generates tRNA-derived fragments (tRFs), whose role in this context is not fully understood. We identify elevated levels of 5tRFGlu(CTC) and 5tRFGly(GCC) in {beta}-cells and iMACs from db/db mice and in islets from type 2 diabetic patients. Notably, 5tRFGlu(CTC) is also induced under prediabetic conditions and inversely correlates with insulin secretion. Lipotoxic stress triggers their production via Angiogenin-mediated cleavage. Blocking 5tRFGlu(CTC) in islets protects against {beta}-cell apoptosis and restores insulin secretion under palmitate stress. Using a {beta}-cell/macrophage co-culture system, we show that {beta}-cell contact shapes a unique macrophage phenotype (iMAC-like) that shifts upon palmitate exposure--recapitulating in vivo observations. Inhibiting 5tRFGlu(CTC) in iMAC-like cells prevents this activation switch, reduces {beta}-cell stress, and improves insulin secretion. Mechanistically, 5tRFGlu(CTC) interacts with RNA-binding proteins to regulate transcriptional and post-transcriptional pathways linked to immune activation, extracellular matrex remodeling, neurogenesis, and oxidative stress. Our study identifies 5tRFs as key mediators of islet microenvironment remodeling in diabetes, offering new insights into intercellular stress signaling in metabolic disease.

cell biology↗

bioRxiv2023

Comprehensive IsomiR sequencing profile of human pancreatic islets and EndoC-βH1 beta-cells

Aims/HypothesisMiRNAs play a crucial role in regulating the islet transcriptome, influencing beta cell functions and pathways. Emerging evidence suggests that during biogenesis a single miRNA locus can generate various sequences, known as isomiRNAs (isomiRs). However, a comprehensive profiling analysis of isomiRs in human pancreatic islets and beta cells is still lacking. This study aims to unveil the isomiRs expression profile in Laser Capture Microdissected (LCM) human pancreatic islets (HI) from non-diabetic donors and in the human beta cell line EndoC-{beta}H1, in order to shed light on novel molecular mechanisms governing beta cell function. MethodsRNA was extracted from LCM HI deriving from n=19 non-diabetic donors and from EndoC-{beta}H1 beta cells. Small RNA-seq was performed. Data were processed with the sRNAbench online pipeline for miRNAs/isomiRs quantification. Results were further validated using an external miRNA-seq database (isomiRdb). ResultsIn both HI and EndoC-{beta}H1, isomiRs accounted for a substantial proportion of total miRNA reads (HI: 59.4+/-1.9%; EndoC-{beta}H1: 43.8+/-0.6%). Among isomiRs, the most prevalent types were 3-end modifications, including trimming (HI=71.8+/-2.8%; EndoC-{beta}H1=55.8+/-1.0%) and extension (HI: 12.1+/-1.9%; EndoC-{beta}H1: 17.4+/-0.9%), followed by non-templated addition (HI: 9.8+/-0.9%; EndoC-{beta}H1: 14.0+/-1.2%). The analysis of the composition of the n=10 most expressed miRNAs highlighted a significant contribution of reads assigned to isomiRs. For instance, the most abundant miRNA, miR-375-3p, resulted from 59.7+/-2.4% of canonical and 40.3+/-2.4% of isomiRs in EndoC-{beta}H1 and from 45.3+/-2.0% of canonical and 54.7+/-2.0% of isomiR reads in HI. Interestingly, miR-7-5p, a beta cell-specific miRNA, was predominantly expressed as an isomiR both in EndoC-{beta}H1 (65.3+/-2.7%) and in HI (82.4+/-1.4%). To identify a reliable beta cell isomiR signature, common sequences detected in HI and EndoC-{beta}H1 were filtered based on their contribution to total miRNA expression, ultimately resulting in a set of 46 isomiRs. The expression of the isomiR signature in beta cells was further evaluated using an external database, isomiRdb, which contains small-RNA sequencing data from 99 different human cell types. This analysis revealed a significant enrichment of 11 out of the 46 isomiRs in beta cells compared to other cell types. The signature was functionally characterized through regression analysis with clinical and metabolic parameters related to beta cell function in non-diabetic individuals, demonstrating a significant negative correlation between basal insulin secretion and isomiR-411-5p, but not with its corresponding canonical miRNA. Conclusion/InterpretationThis study provides a comprehensive profile of isomiR expression in pancreatic islets and beta cells, highlighting the potential significance of isomiRs as novel regulators of beta cell function. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC="FIGDIR/small/566223v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@145f36borg.highwire.dtl.DTLVardef@1701433org.highwire.dtl.DTLVardef@13e5866org.highwire.dtl.DTLVardef@1dbe50_HPS_FORMAT_FIGEXP M_FIG C_FIG Research in ContextO_ST_ABSWhat is already know about this subject?C_ST_ABS- isomiRs are sequence variants of microRNAs (miRNAs) and may have distinct functional role respect to the canonical sequence. - isomiRs show cell/tissue specificity and are involved in multiple disease contexts. What is the key question?- What is the profile of isomiRs in human pancreatic islets (HI) and in beta cells? - Do isomiRs have a functional role in beta cells? What are the new findings?- IsomiRs represent a relevant fraction of total miRNAs in HI and beta cells. - 3end miRNA sequence modifications are the major fraction of isomiRs in beta cells. - A set of n=11 isomiRs, more expressed than their canonical miRNAs, are enriched in beta cells compared to the other human cell types. - Specific isomiRs are associated with beta cell glucose sensitivity and basal insulin secretion. How might this impact on clinical practice in the foreseeable future?- A comprehensive profile of isomiRs in beta cells may improve our understanding of molecular mechanisms driving beta cell function and dysfunction. - A highly detailed and granular view of miRNAs sequence variants and their expression levels may help in the design of novel therapeutic RNA-based strategies.

molecular biology↗

bioRxiv2021

Life on leaves : uncovering temporal dynamics in Arabidopsis' leaf microbiota

Leaves are primarily responsible for the plants photosynthetic activity. Thus, changes in the phyllosphere microbiota, which includes deleterious and beneficial microbes, can have far reaching effects on plant fitness and productivity. In this context, identifying the processes and microorganisms that drive the changes in the leaf microbiota over a plants lifetime is crucial. In this study we analyzed the temporal dynamics in the leaf microbiota of Arabidopsis thaliana, integrating both compositional changes and changes in microbe-microbe interactions via the study of microbial networks. Field-grown Arabidopsis were used to follow leaf bacterial, fungal and oomycete communities, throughout the plants growing season (extending from November to March), over three consecutive years. Our results revealed the existence of conserved time patterns, with microbial communities and networks going through a stabilization phase (decreasing diversity and variability) at the beginning of the plants growing season. Despite a high turnover in these communities, we identified 19 core taxa persisting in Arabidopsis leaves across time and plant generations. With the hypothesis these microbes could be playing key roles in the structuring of leaf microbial communities, we conducted a time-informed microbial network analysis which showed core taxa are not necessarily highly connected network hubs and hubs alternate with time. Our study shows that leaf microbial communities exhibit reproducible dynamics and patterns, suggesting it could be possible to predict and drive these microbial communities to desired states.

microbiology↗

bioRxiv2020

Obtaining deeper insights into microbiome diversity using a simple method to block host and non-targets in amplicon sequencing

Microbiome profiling is revolutionizing our understanding of biological mechanisms such as metaorganismal (host+microbiome) assembly, functions and adaptation. Amplicon sequencing of multiple conserved, phylogenetically informative loci is an instrumental tool for characterization of the highly diverse microbiomes of natural systems. Investigations in many study systems are hindered by loss of essential sequencing depth due to amplification of non-target DNA from hosts or overabundant microorganisms. This issue requires urgent attention to address ecologically relevant problems using high throughput, high resolution microbial profiling. Here, we introduce a simple, low cost and highly flexible method using standard oligonucleotides ("blocking oligos") to block amplification of non-targets and an R package to aid in their design. They can be dropped into practically any two-step amplicon sequencing library preparation pipeline. We apply them in leaves, a system presenting exceptional challenges with host and non-target microbial amplification. Blocking oligos designed for use in eight target loci reduce undesirable amplification of host and non-target microbial DNA by up to 90%. In addition, 16S and 18S "universal" plant blocking oligos efficiently block most plant hosts, leading to increased microbial alpha diversity discovery without biasing beta diversity measurements. By blocking only chloroplast 16S amplification, we show that blocking oligos do not compromise quantitative microbial load information inherent to plant-associated amplicon sequencing data. Using these tools, we generated a near-complete survey of the Arabidopsis thaliana leaf microbiome based on diversity data from eight loci and discuss complementarity of commonly used amplicon sequencing regions for describing leaf microbiota. The blocking oligo approach has potential to make new questions in a variety of study systems more tractable by making amplicon sequencing more targeted, leading to deeper, systems-based insights into microbial discovery.

microbiology↗

bioRxiv2019

A novel phyllosphere resident Protomyces species that interacts with the Arabidopsis immune system.

We describe the genome contents of six Protomyces spp. that are pathogenic within the typical host range of the genus and a novel Protomyces strain (SC29) that was previously isolated from the phylloplane of wild Arabidopsis thaliana (Arabidopsis), an atypical or possible alternate host. Genome-wide phylogenetic analysis defined SC29 as a distinct Protomyces sp. Analysis of gene family expansions, gene retention, and gene loss patterns among these Protomyces spp. lead us to hypothesize that SC29 may have undergone a host jump. The role of phyllosphere residency in the lifecycle of Protomyces spp. was previously unknown. Genomic changes in SC29 and all other Protomyces spp. were consistent with adaptations to the plant phylloplane. As predicted by our analysis of its mating locus, SC29 did not cause disease on Arabidopsis as a single strain, but could persist in its phylloplane, while the closely related P. inouyei does not. SC29 treated Arabidopsis exhibited enhanced immunity against Botrytis cinerea infection, associated with activation of MAPK3/6, camalexin, and SA-signalling pathways. We conclude that SC29 is a novel Protomyces sp. able to survive in the Arabidopsis phylloplane and that phylloplane residency is an important element in the lifecycle of Protomyces spp.

microbiology↗

bioRxiv2018

Discovery of biomarkers for glycaemic deterioration before and after the onset of type 2 diabetes: an overview of the data from the epidemiological studies within the IMI DIRECT Consortium

Abstract/SummaryO_ST_ABSBackground and aimsC_ST_ABSUnderstanding the aetiology, clinical presentation and prognosis of type 2 diabetes (T2D) and optimizing its treatment might be facilitated by biomarkers that help predict a persons susceptibility to the risk factors that cause diabetes or its complications, or response to treatment. The IMI DIRECT (Diabetes Research on Patient Stratification) Study is a European Union (EU) Innovative Medicines Initiative (IMI) project that seeks to test these hypotheses in two recently established epidemiological cohorts. Here, we describe the characteristics of these cohorts at baseline and at the first main follow-up examination (18-months).\n\nMaterials and methodsFrom a sampling-frame of 24,682 European-ancestry adults in whom detailed health information was available, participants at varying risk of glycaemic deterioration were identified using a risk prediction algorithm and enrolled into a prospective cohort study (n=2127) undertaken at four study centres across Europe (Cohort 1: prediabetes). We also recruited people from clinical registries with recently diagnosed T2D (n=789) into a second cohort study (Cohort 2: diabetes). The two cohorts were studied in parallel with matched protocols. Endogenous insulin secretion and insulin sensitivity were modelled from frequently sampled 75g oral glucose tolerance (OGTT) in Cohort 1 and with mixed-meal tolerance tests (MMTT) in Cohort 2. Additional metabolic biochemistry was determined using blood samples taken when fasted and during the tolerance tests. Body composition was assessed using MRI and lifestyle measures through self-report and objective methods.\n\nResultsUsing ADA-2011 glycaemic categories, 33% (n=693) of Cohort 1 (prediabetes) had normal glucose regulation (NGR), and 67% (n=1419) had impaired glucose regulation (IGR). 76% of the cohort was male, age=62(6.2) years; BMI=27.9(4.0) kg/m2; fasting glucose=5.7(0.6) mmol/l; 2-hr glucose=5.9(1.6) mmol/l [mean(SD)]. At follow-up, 18.6(1.4) months after baseline, fasting glucose=5.8(0.6) mmol/l; 2-hr OGTT glucose=6.1(1.7) mmol/l [mean(SD)]. In Cohort 2 (diabetes): 65% (n=508) were lifestyle treated (LS) and 35% (n=271) were lifestyle + metformin treated (LS+MET). 58% of the cohort was male, age=62(8.1) years; BMI=30.5(5.0) kg/m2; fasting glucose=7.2(1.4)mmol/l; 2-hr glucose=8.6(2.8) mmol/l [mean(SD)]. At follow-up, 18.2(0.6) months after baseline, fasting glucose=7.8(1.8) mmol/l; 2-hr MMTT glucose=9.5(3.3) mmol/l [mean(SD)].\n\nConclusionThe epidemiological IMI DIRECT cohorts are the most intensely characterised prospective studies of glycaemic deterioration to date. Data from these cohorts help illustrate the heterogeneous characteristics of people at risk of or with T2D, highlighting the rationale for biomarker stratification of the disease - the primary objective of the IMI DIRECT consortium.\n\nAbbreviations

epidemiology↗