Biology subjects

Cotrufo, T.

Publications and source records attributed to Cotrufo, T..

3 recordsLinked to original sources

bioRxiv2024

Accurate Predictions of Phase Separating Proteins at Single Amino Acid Resolution

Liquid-liquid phase separation (LLPS) is a molecular mechanism that leads to the formation of membraneless organelles inside the cell. Despite recent advances in the experimental probing and computational prediction of proteins involved in this process, the identification of the protein regions driving LLPS and the prediction of the effect of mutations on LLPS are lagging behind. Here, we introduce catGRANULE 2.0 ROBOT (R - Ribonucleoprotein, O - Organization, in B - Biocondensates, O - Organelle, T - Types), an advanced algorithm for predicting protein LLPS at single amino acid resolution. Integrating physico-chemical properties of the proteins and structural features derived from AlphaFold models, catGRANULE 2.0 ROBOT significantly surpasses traditional sequence-based and state-of-the-art structure-based methods in performance, achieving an Area Under the Receiver Operating Characteristic Curve (AUROC) of 0.76 or higher. We present a comprehensive evaluation of the algorithm across multiple organisms and cellular components, demonstrating its effectiveness in predicting LLPS propensities at the single amino acid level and the impacts of mutations on LLPS. Our results are robustly supported by experimental validations, including immunofluorescence microscopy images from the Human Protein Atlas. catGRANULE 2.0 ROBOTs potential in protein design and mutation control can improve our understanding of proteins propensity to form subcellular compartments and help develop strategies to influence biological processes through LLPS. catGRANULE 2.0 ROBOT is freely available at https://tools.tartaglialab. com/catgranule2.

biochemistry↗

bioRxiv2023

miR-519a-3p, found to regulate cellular prion protein during Alzheimer's disease pathogenesis, as a biomarker of asymptomatic stages

MiRNAs induce post-transcriptional gene silencing by binding to the 3-UTR of complementary messenger RNAs and causing either degradation or inhibition of translation. The clinical relevance of miRNAs as biomarkers is growing due to their stability and detection in biofluids. In this sense, diagnosis at asymptomatic stages of Alzheimers disease (AD) remains a challenge since it can only be made at autopsy according to Braak NFT staging. Achieving the objective of detecting AD at early stages would allow possible therapies to be addressed before the onset of cognitive impairment. Many studies have determined that the expression pattern of some miRNAs is deregulated in AD patients, but to date, none has been correlated with downregulated expression of cellular prion protein (PrPC) during disease progression. That is why, by means of cross studies of miRNAs up-regulated in AD with in silico identification of potential miRNAs-binding to 3UTR of human PRNP gene, we selected miR-519a-3p for our study. Other family members of miR-519 have been shown to bind to the 3UTR region of PRNP in vitro and presumably degrade PRNP mRNA. In addition, up-regulation of some of them has been reported in various tissues from AD patients, including cerebrospinal fluid, plasma, and blood serum. In fact, miR-519d-3p is marked as a bridge regulator between mild cognitive impairment and severe AD. However, none of the studies address the prodromal stages of the disease or the expression profile of miR-519 in other neurodegenerative diseases that also may present dementia. Therefore, in this study we analyzed miR-519a-3p expression in cerebral samples of AD at different stages of evolution as well as other neurodegenerative diseases such as other tauopathies and synucleinopathies. Our results show the specific and early upregulation of miR-519a-3p starting from Braak stage I of AD, suggesting its potential use as a biomarker of preclinical stages of the disease.

neuroscience↗

bioRxiv2021

Syntaxin-1 is necessary for UNC5/Netrin-1-dependent macropinocytosis and chemorepulsion

Brain connectivity requires correct axonal guidance to drive axons to their appropriate targets. This process is orchestrated by guidance cues that exert attraction or repulsion to developing axons. However, the intricacies of the cellular machinery responsible for the correct response of growth cones are just being unveiled. Netrin-1 is a bifunctional molecule involved in axon pathfinding and cell migration that induces repulsion during postnatal cerebellar development. This process is mediated by Uncoordinated locomotion 5 (UNC5) receptors located on external granule layer (EGL) tracts. Here, we demonstrate that this response is characterized by enhanced membrane internalization through macropinocytosis, but not clathrin-mediated endocytosis. We show that UNC5 receptors form a protein complex with the t-SNARE syntaxin-1 (Stx1). By combining botulinum neurotoxins, a shRNA knock-down strategy and Stx1 knock-out mice, we demonstrate that this SNARE protein is required for Netrin-1-induced macropinocytosis and chemorepulsion, suggesting that Stx1 is crucial in regulating Netrin-1-mediated axonal guidance.

neuroscience↗