Biology subjects

Donini, L.

Publications and source records attributed to Donini, L..

4 recordsLinked to original sources

bioRxiv2025

Empowering multiplexed ultra-throughout ribosome profiling with RiboWich

Ribosome profiling (RiboSeq) improved the understanding of mRNA translation, enabling the precise mapping of ribosome positioning along transcripts at single-nucleotide resolution. Although various library preparation protocols overcome the need for high input material, their technical complexity and limited efficiency hinder robust profiling, preventing them from keeping pace with other sequencing techniques and applications. To move towards high-throughput and single-cell RiboSeq technologies, we developed RiboWich (Ribosome sandWich). By directly ligating adaptors to ribosome-embedded RNA fragments, RiboWich eliminates the need for ribosome purification and size-selecting ribosome footprints and tackles two major bottlenecks, expanding RiboSeq for more advanced technologies. RiboWich offers robustness in profiling and excels in detecting upstream translons in immortalized and primary cells alike. By exploiting a dual-step multiplexing strategy, RiboWich enables the simultaneous profiling of at least 96 samples while retaining sensitivity and capturing condition-specific differences in translation. By enabling scalable, low-input translatome profiling, this advancement empowers proteogenomic approaches and AI/ML-driven data analysis to uncover regulatory dynamics, neoantigens, functional small translons, and drug-responsive signatures across diverse biological contexts and users. Altogether, RiboWich represents a straightforward, versatile, and scalable ribosome profiling conceptual platform that combines accessibility, sensitivity, and throughput potential, laying the foundation for advanced single-cell RiboSeq applications.

molecular biology↗

bioRxiv2025

Model-independent reorganization of translation in TDP-43 Amyotrophic Lateral Sclerosis

The RNA-binding protein TDP-43 is a major contributor and a pathological hallmark of Amyotrophic Lateral Sclerosis (ALS), yet how TDP-43 dysregulation mechanistically alters protein synthesis across neuronal compartments and disease models remains unclear. Here, we dissected TDP-43-driven translational alterations in both in vitro and in vivo TDP-43 models of ALS. Through ribosome and polysome profiling, computational, and biochemical analyses, we observed robust TDP-43-associated translational remodelling at cellular and subcellular resolution. Our findings reveal a conserved mechanism across models, characterized by enhanced ribosome recruitment on polysomes, elongation impairment, axonal downregulation and instability of TDP-43 target mRNAs and redistribution toward non-target transcripts. Notably, TDP-43 dysregulation alters ribosome dynamics and selectively impairs translation of TDP-43 target mRNAs, whilst favouring the translation of other transcripts. This process reflects a compensatory but maladaptive response to TDP-43-induced mRNA destabilization. Together, these data demonstrate that alterations in TDP-43 disrupts neuronal proteostasis through ribosome reorganization and loss of mRNA homeostasis, providing a unifying mechanistic framework for translational imbalance in ALS and revealing early molecular events that may underlie motor neuron vulnerability.

molecular biology↗

bioRxiv2021

Defective linear and circular RNAs biogenesis in Huntington's disease: CAG repeat expansion hijacks neuronal splicing

Alternative splicing (AS) appears to be altered in Huntingtons disease (HD), but its significance for early, pre-symptomatic disease stages has not been inspected. Here, taking advantage of Htt CAG knock-in mouse in vitro and in vivo models, we demonstrate a strong correlation between Htt CAG repeat length and increased aberrant linear AS, specifically affecting neural progenitors and, in vivo, the striatum prior to overt behavioral phenotypes stages. Remarkably, expanded Htt CAG repeats reflect on a previously neglected, global impairment of back-splicing, leading to decreased circular RNAs production in neural progenitors. Though the mechanisms of this dysregulation remain uncertain, our study unveils network of transcriptionally altered micro-RNAs and RNA-binding proteins (CELF, hnRNPS, PTBP, SRSF) which, in turn, might influence the AS machinery, primarily in neural cells. We suggest that this unbalanced expression of linear and circular RNAs might result in altered neural fitness, contributing to HD striatal vulnerability.

genetics↗

bioRxiv2018

Metabolomic signature of angiopoietin-like protein 3 deficiency in fasting and postprandial state

ObjectiveLoss-of-function variants in the angiopoietin-like 3 gene (ANGPTL3) have been associated with low levels of plasma lipoproteins and decreased coronary artery disease risk. We aimed to determine detailed metabolic effects of genetically-induced ANGPTL3 deficiency in fasting and postprandial state.\n\nApproach and ResultsWe studied individuals carrying S17X loss-of-function mutation in ANGPTL3 (6 homozygous and 32 heterozygous carriers) and 38 noncarriers. Nuclear magnetic resonance metabolomics was used to quantify 225 circulating metabolic measures. We compared metabolic differences between loss-of-function carriers and noncarriers in fasting state and after a high fat meal. In fasting, ANGPTL3 deficiency was characterized by similar extent of reductions in low-density lipoprotein cholesterol (0.74 SD-units lower concentration per loss-of-function allele [95%CI 0.42-1.06]) as observed for many triglyceride-rich lipoprotein measures, including very-low-density lipoprotein cholesterol (0.75 [0.45-1.05]). Within most lipoprotein subclasses, absolute levels of cholesterol were decreased more than triglycerides, resulting in the relative proportion of cholesterol being reduced within triglyceride-rich lipoproteins and their remnants. Further, beta-hydroxybutyrate was elevated (0.55 [0.21-0.89]). Homozygous ANGPTL3 loss-of-function carriers showed essentially no postprandial increase in triglyceride-rich lipoproteins and fatty acids, without evidence for adverse compensatory metabolic effects.\n\nConclusionsIn addition to overall triglyceride and low-density lipoprotein cholesterol lowering effects, ANGPTL3 deficiency results in reduction of cholesterol proportion within triglyceride-rich lipoproteins and their remnants. Further, ANGPTL3 loss-of-function carriers had elevated ketone body production, suggesting enhanced hepatic fatty acid beta-oxidation. The detailed metabolic profile in human knockouts of ANGPTL3 reinforces inactivation of ANGPTL3 as a promising therapeutic target for decreasing cardiovascular risk.\n\nHIGHLIGHTSO_LIANGPTL3 deficiency results in similar reductions in LDL cholesterol and many triglyceride-rich lipoprotein lipids measures, such as VLDL cholesterol, with no evidence of substantial adverse effects on the comprehensive panel of circulating metabolite biomarkers tested here.\nC_LIO_LIIn particular, ANGPTL3 deficiency results in reduction of cholesterol content in triglyceride-rich lipoproteins and their remnants, which have been highlighted as risk factor for cardiovascular disease independently of LDL levels.\nC_LIO_LIHomozygous ANGPTL3 loss-of-function carriers show essentially no postprandial increase in triglyceride-rich lipoproteins and fatty acids in response to a fat challenge, and display consistently elevated postprandial levels of ketone bodies and lactate when compared to noncarriers, suggesting enhanced hepatic fatty acid beta-oxidation.\nC_LI

genetics↗