ACADEMIC PROFILES
SOCIAL
REPOSITORIES
CONTACTS
+39 049 827 6260
+39 049 827 6269
Journal Articles
2026
1.
Begue S C; Leonardi E; Minervini G; Tosatto S C E
Exploring proteins and protein–ligand complexes through residue interaction networks Journal Article
In: Nature Protocols, 2026, (Cited by: 0).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:105033505349,
title = {Exploring proteins and protein–ligand complexes through residue interaction networks},
author = {Sol C. Begue and Emanuela Leonardi and Giovanni Minervini and Silvio C. E. Tosatto},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-105033505349&origin=inward},
doi = {10.1038/s41596-026-01334-0},
year = {2026},
date = {2026-01-01},
journal = {Nature Protocols},
publisher = {Springer Nature},
abstract = {© Springer Nature Limited 2026.Protein structures provide a wealth of information regarding biological functions and underlying mechanisms. The growing availability of high-quality structure predictions and extended molecular simulations has further expanded the potential to leverage these data in a myriad of different ways. Yet, an abundance of data can obscure important information, making it difficult to focus on biologically relevant features. Residue interaction networks (RINs) address this challenge by condensing structural data into subsets of well-defined noncovalent molecular interactions. In this Protocol, we explore how the RIN generator (RING) software can be used to gain biological insights by constructing detailed RINs for proteins and protein–ligand complexes. We provide a step-by-step guide to performing both single- and multi-state protein analyses using the RING web server and a stand-alone software package. In addition, we include a dedicated procedure for sequential multi-file analysis, which can be performed exclusively through the command-line interface. All potential inputs and outputs are explained in detail, along with strategies for downstream data processing. Designed for researchers in biology and related fields with minimal or no programming experience, the entire workflow can be completed in <45 min.},
note = {Cited by: 0},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
© Springer Nature Limited 2026.Protein structures provide a wealth of information regarding biological functions and underlying mechanisms. The growing availability of high-quality structure predictions and extended molecular simulations has further expanded the potential to leverage these data in a myriad of different ways. Yet, an abundance of data can obscure important information, making it difficult to focus on biologically relevant features. Residue interaction networks (RINs) address this challenge by condensing structural data into subsets of well-defined noncovalent molecular interactions. In this Protocol, we explore how the RIN generator (RING) software can be used to gain biological insights by constructing detailed RINs for proteins and protein–ligand complexes. We provide a step-by-step guide to performing both single- and multi-state protein analyses using the RING web server and a stand-alone software package. In addition, we include a dedicated procedure for sequential multi-file analysis, which can be performed exclusively through the command-line interface. All potential inputs and outputs are explained in detail, along with strategies for downstream data processing. Designed for researchers in biology and related fields with minimal or no programming experience, the entire workflow can be completed in <45 min.
2.
Guazzo A; Vanaja I P; Bona A D; Bariani R; Disalvo M C; Albiero M; Kuperwasser N; David P; Celeghin R; Mauro V D; Scalco A; López-Moreno M; Cason M; Gaspari M D; Barbera M D; Rizzo S; Ventura L; Corrado D; Bauce B; Zanotti G; Thiene G; Pilichou K; Minervini G; Pomares J M P; Pende M; Basso C; Mongillo M; Zaglia T
Desmoplakin Cardiomyopathy: Gene Dose-Dependent Myocardial Remodeling, Arrhythmias, and Premature Death Journal Article
In: JACC: Clinical Electrophysiology, 2026, (Cited by: 1; Open Access).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:105027149057,
title = {Desmoplakin Cardiomyopathy: Gene Dose-Dependent Myocardial Remodeling, Arrhythmias, and Premature Death},
author = {Anna Guazzo and Induja Perumal Vanaja and Anna Di Bona and Riccardo Bariani and Maria C. Disalvo and Mattia Albiero and Nicolas Kuperwasser and Pierre David and Rudy Celeghin and Vittoria Di Mauro and Arianna Scalco and María López-Moreno and Marco Cason and Monica De Gaspari and Mila Della Barbera and Stefania Rizzo and Laura Ventura and Domenico Corrado and Barbara Bauce and Giuseppe Zanotti and Gaetano Thiene and Kalliopi Pilichou and Giovanni Minervini and José Maria Perez Pomares and Mario Pende and Cristina Basso and Marco Mongillo and Tania Zaglia},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-105027149057&origin=inward},
doi = {10.1016/j.jacep.2025.10.031},
year = {2026},
date = {2026-01-01},
journal = {JACC: Clinical Electrophysiology},
publisher = {Elsevier Inc.},
abstract = {© 2025 The AuthorsBackground: Pathogenic variants in DSP cause arrhythmogenic cardiomyopathies with variable inheritance pattern. Recessive mutations underlie syndromic forms such as Carvajal syndrome, whereas dominant variants cause DSP cardiomyopathy, a left-dominant arrhythmogenic cardiomyopathy characterized by early electrical instability, inflammation, and fibrosis. The mechanisms driving these phenotypes remain poorly defined. Objectives: The authors sought to create a clinically relevant platform to investigate disease mechanisms in Desmoplakin Cardiomyopathy. Methods: We generated a knock-in mouse carrying the DspS311A mutation, orthologous to the human pathogenic hotspot S299R. Heterozygous and homozygous mice (n ≥6/group) were longitudinally phenotyped by echocardiography, electrocardiographic telemetry, histology, and ultrastructural and molecular analyses. Moderate treadmill exercise was used as a physiological stressor. Outcomes included cardiac function, arrhythmias, fibrosis, apoptosis, inflammation, and desmosomal integrity. Results: Homozygous DspS311A/S311A mice developed early biventricular dysfunction with subepicardial necrosis, replacement fibrosis, myocardial inflammation, spontaneous arrhythmias, and cutaneous defects, recapitulating Carvajal syndrome. Heterozygous DspWT/S311A mice exhibited hallmarks of dominant DSP cardiomyopathy: patchy left ventricular fibrosis, apoptosis, inflammation, and electrical instability preceding systolic impairment. Desmosomal remodeling occurred in both genotypes, with connexin-43 mislocalization evident from 1 month, whereas β-catenin nuclear translocation and reduced DSP/DSG2 protein were restricted to homozygotes. Of note, spontaneous arrhythmias and electrical instability were already present in both genotypes, temporally preceding structural remodeling. Exercise accelerated apoptosis, fibrosis, arrhythmias, and premature death. Conclusions: This DspS311A knock-in model captures key aspects of recessive and dominant DSP cardiomyopathies, uniquely combining spontaneous arrhythmias, inflammation, and extracardiac features. This model provides a unique in vivo platform to dissect DSP-related arrhythmogenic mechanisms and to test therapies aimed at preventing sudden cardiac death.},
note = {Cited by: 1; Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
© 2025 The AuthorsBackground: Pathogenic variants in DSP cause arrhythmogenic cardiomyopathies with variable inheritance pattern. Recessive mutations underlie syndromic forms such as Carvajal syndrome, whereas dominant variants cause DSP cardiomyopathy, a left-dominant arrhythmogenic cardiomyopathy characterized by early electrical instability, inflammation, and fibrosis. The mechanisms driving these phenotypes remain poorly defined. Objectives: The authors sought to create a clinically relevant platform to investigate disease mechanisms in Desmoplakin Cardiomyopathy. Methods: We generated a knock-in mouse carrying the DspS311A mutation, orthologous to the human pathogenic hotspot S299R. Heterozygous and homozygous mice (n ≥6/group) were longitudinally phenotyped by echocardiography, electrocardiographic telemetry, histology, and ultrastructural and molecular analyses. Moderate treadmill exercise was used as a physiological stressor. Outcomes included cardiac function, arrhythmias, fibrosis, apoptosis, inflammation, and desmosomal integrity. Results: Homozygous DspS311A/S311A mice developed early biventricular dysfunction with subepicardial necrosis, replacement fibrosis, myocardial inflammation, spontaneous arrhythmias, and cutaneous defects, recapitulating Carvajal syndrome. Heterozygous DspWT/S311A mice exhibited hallmarks of dominant DSP cardiomyopathy: patchy left ventricular fibrosis, apoptosis, inflammation, and electrical instability preceding systolic impairment. Desmosomal remodeling occurred in both genotypes, with connexin-43 mislocalization evident from 1 month, whereas β-catenin nuclear translocation and reduced DSP/DSG2 protein were restricted to homozygotes. Of note, spontaneous arrhythmias and electrical instability were already present in both genotypes, temporally preceding structural remodeling. Exercise accelerated apoptosis, fibrosis, arrhythmias, and premature death. Conclusions: This DspS311A knock-in model captures key aspects of recessive and dominant DSP cardiomyopathies, uniquely combining spontaneous arrhythmias, inflammation, and extracardiac features. This model provides a unique in vivo platform to dissect DSP-related arrhythmogenic mechanisms and to test therapies aimed at preventing sudden cardiac death.
2025
3.
Inciardi I; Rizzotto E; Gregoris F; Fongaro B; Sosic A; Minervini G; Laureto P P
Catechol-induced covalent modifications modulate the aggregation tendency of α-synuclein: An in-solution and in-silico study Journal Article
In: BioFactors, vol. 51, no. 1, 2025, (Cited by: 3; Open Access).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:85194767977,
title = {Catechol-induced covalent modifications modulate the aggregation tendency of α-synuclein: An in-solution and in-silico study},
author = {Ilenia Inciardi and Elena Rizzotto and Francesco Gregoris and Benedetta Fongaro and Alice Sosic and Giovanni Minervini and Patrizia Polverino Laureto},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-85194767977&origin=inward},
doi = {10.1002/biof.2086},
year = {2025},
date = {2025-01-01},
journal = {BioFactors},
volume = {51},
number = {1},
publisher = {John Wiley and Sons Inc},
abstract = {© 2024 International Union of Biochemistry and Molecular Biology.Parkinson's disease (PD) stands as a challenging neurodegenerative condition characterized by the emergence of Lewy Bodies (LBs), intracellular inclusions within dopaminergic neurons. These LBs harbor various proteins, prominently including α-Synuclein (Syn) aggregates, implicated in disease pathology. A promising avenue in PD treatment involves targeting Syn aggregation. Recent findings from our research have shown that 3,4-dihydroxyphenylacetic acid (DOPAC) and 3,4-dihydroxyphenylethanol (DOPET) possess the ability to impede the formation of Syn fibrils by disrupting the aggregation process. Notably, these compounds primarily engage in noncovalent interactions with the protein, leading to the formation of off-pathway oligomers that deter fibril growth. Through proteolysis studies and mass spectrometry (MS) analysis, we have identified potential covalent modifications of Syn in the presence of DOPAC, although the exact site remains elusive. Employing molecular dynamics simulations, we delved into how DOPAC-induced covalent alterations might affect the mechanism of Syn aggregation. Our findings indicate that the addition of a covalent adduct on certain residues enhances fibril flexibility without compromising its secondary structure stability. Furthermore, in the monomeric state, the modified residue fosters novel bonding interactions, thereby influencing long-range interactions between the N- and C-termini of the protein.},
note = {Cited by: 3; Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
© 2024 International Union of Biochemistry and Molecular Biology.Parkinson’s disease (PD) stands as a challenging neurodegenerative condition characterized by the emergence of Lewy Bodies (LBs), intracellular inclusions within dopaminergic neurons. These LBs harbor various proteins, prominently including α-Synuclein (Syn) aggregates, implicated in disease pathology. A promising avenue in PD treatment involves targeting Syn aggregation. Recent findings from our research have shown that 3,4-dihydroxyphenylacetic acid (DOPAC) and 3,4-dihydroxyphenylethanol (DOPET) possess the ability to impede the formation of Syn fibrils by disrupting the aggregation process. Notably, these compounds primarily engage in noncovalent interactions with the protein, leading to the formation of off-pathway oligomers that deter fibril growth. Through proteolysis studies and mass spectrometry (MS) analysis, we have identified potential covalent modifications of Syn in the presence of DOPAC, although the exact site remains elusive. Employing molecular dynamics simulations, we delved into how DOPAC-induced covalent alterations might affect the mechanism of Syn aggregation. Our findings indicate that the addition of a covalent adduct on certain residues enhances fibril flexibility without compromising its secondary structure stability. Furthermore, in the monomeric state, the modified residue fosters novel bonding interactions, thereby influencing long-range interactions between the N- and C-termini of the protein.
4.
Sabbatini D; Gorgoglione D; Minervini G; Fusto A; Suman M; Romualdi C; Vianello S; Capece G; Sorarù G; Marchioretti C; Pennuto M; Vedovelli L; Szabadkai G; Bello L; Pegoraro E
RYR1-Related Myopathies Involve More than Calcium Dysregulation: Insights from Transcriptomic Profiling Journal Article
In: Biomolecules, vol. 15, no. 11, 2025, (Cited by: 0; Open Access).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:105023126850,
title = {RYR1-Related Myopathies Involve More than Calcium Dysregulation: Insights from Transcriptomic Profiling},
author = {Daniele Sabbatini and Domenico Gorgoglione and Giovanni Minervini and Aurora Fusto and Matteo Suman and Chiara Romualdi and Sara Vianello and Giuliana Capece and Gianni Sorarù and Caterina Marchioretti and Maria Pennuto and Luca Vedovelli and Gyorgy Szabadkai and Luca Bello and Elena Pegoraro},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-105023126850&origin=inward},
doi = {10.3390/biom15111599},
year = {2025},
date = {2025-01-01},
journal = {Biomolecules},
volume = {15},
number = {11},
publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},
abstract = {© 2025 by the authors.Ryanodine receptor 1-related myopathies (RYR1-RM) are caused by RYR1 gene variants and comprise a wide spectrum of histopathological manifestations. Here, we focus on patients carrying RYR1 variants and muscle histopathology consistent with central core disease (CCD) or multi-minicore disease (MmD). RNA-sequencing analyses of skeletal muscle biopsies obtained from both CCD and MmD patients and from healthy controls were performed to better understand the molecular pathways activated by RYR1 variants. Our analyses revealed that, beyond the well-established role of RYR1 in calcium homeostasis, broader cellular pathways are implicated. In CCD, differentially expressed genes were enriched for pathways related to oxidative stress response, SMAD signalling, and apoptosis, consistent with the role of intracellular calcium dysregulation in promoting mitochondrial dysfunction and cell death. In contrast, MmD patients exhibited enrichment of pathways related to immune activation. This was corroborated by the upregulation of GTPase-regulating genes and the down-regulation of transcriptional repressors such as ZFP36 and ATN1. When considering all RYR1-RM patients collectively, Wnt signalling, immune-related pathways, and oxidative phosphorylation emerged as shared enriched pathways, indicating possible convergent mechanisms across histopathological phenotypes. Our study suggests that complex gene regulation driven by RYR1 variants may be a unifying feature in CCD and MmD, offering new insight into potential therapeutic targets.},
note = {Cited by: 0; Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
© 2025 by the authors.Ryanodine receptor 1-related myopathies (RYR1-RM) are caused by RYR1 gene variants and comprise a wide spectrum of histopathological manifestations. Here, we focus on patients carrying RYR1 variants and muscle histopathology consistent with central core disease (CCD) or multi-minicore disease (MmD). RNA-sequencing analyses of skeletal muscle biopsies obtained from both CCD and MmD patients and from healthy controls were performed to better understand the molecular pathways activated by RYR1 variants. Our analyses revealed that, beyond the well-established role of RYR1 in calcium homeostasis, broader cellular pathways are implicated. In CCD, differentially expressed genes were enriched for pathways related to oxidative stress response, SMAD signalling, and apoptosis, consistent with the role of intracellular calcium dysregulation in promoting mitochondrial dysfunction and cell death. In contrast, MmD patients exhibited enrichment of pathways related to immune activation. This was corroborated by the upregulation of GTPase-regulating genes and the down-regulation of transcriptional repressors such as ZFP36 and ATN1. When considering all RYR1-RM patients collectively, Wnt signalling, immune-related pathways, and oxidative phosphorylation emerged as shared enriched pathways, indicating possible convergent mechanisms across histopathological phenotypes. Our study suggests that complex gene regulation driven by RYR1 variants may be a unifying feature in CCD and MmD, offering new insight into potential therapeutic targets.
5.
Gasparotto D; Zanon A; Bonaldo V; Marchiori E; Casagranda M; Domenico E D; Copat L; Asquini T F; Rigoli M; Feltrin S V; Lorenzo N L; Lolli G; Pennuto M; Requena J R; Stabelli O R; Minervini G; Micheletti C; Spagnolli G; Faccioli P; Biasini E
Mapping cryptic phosphorylation sites in the human proteome Journal Article
In: EMBO Journal, vol. 44, no. 22, pp. 6704-6731, 2025, (Cited by: 1; Open Access).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:105017879475,
title = {Mapping cryptic phosphorylation sites in the human proteome},
author = {Dino Gasparotto and Annarita Zanon and Valerio Bonaldo and Elisa Marchiori and Massimo Casagranda and Erika Di Domenico and Laura Copat and Tommaso Fortunato Asquini and Marta Rigoli and Sirio Vittorio Feltrin and Nuria Lopez Lorenzo and Graziano Lolli and Maria Pennuto and Jesùs R Requena and Omar Rota Stabelli and Giovanni Minervini and Cristian Micheletti and Giovanni Spagnolli and Pietro Faccioli and Emiliano Biasini},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-105017879475&origin=inward},
doi = {10.1038/s44318-025-00567-1},
year = {2025},
date = {2025-01-01},
journal = {EMBO Journal},
volume = {44},
number = {22},
pages = {6704-6731},
publisher = {Springer Science and Business Media Deutschland GmbH},
abstract = {© The Author(s) 2025.Advances in computational and experimental methods have revealed the existence of transient, non-native protein folding intermediates that could play roles in disparate biological processes, from regulation of protein expression to disease-relevant misfolding mechanisms. Here, we tested the possibility that specific post-translational modifications may involve residues exposed during the folding process by assessing the solvent accessibility of 87,138 post-translationally modified amino acids in the human proteome. Unexpectedly, we found that one-third of phosphorylated proteins present at least one phosphosite completely buried within the protein’s inner core. Computational and experimental analyses suggest that these cryptic phosphosites may become exposed during the folding process, where their modification could destabilize native structures and trigger protein degradation. Phylogenetic investigation also reveals that cryptic phosphosites are more conserved than surface-exposed phosphorylated residues. Finally, cross-referencing with cancer mutation databases suggests that phosphomimetic mutations in cryptic phosphosites can increase tumor fitness by inactivating specific onco-suppressors. These findings define a novel role for co-translational phosphorylation in shaping protein folding and expression, laying the groundwork for exploring the implications of cryptic phosphorylation in health and disease.},
note = {Cited by: 1; Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
© The Author(s) 2025.Advances in computational and experimental methods have revealed the existence of transient, non-native protein folding intermediates that could play roles in disparate biological processes, from regulation of protein expression to disease-relevant misfolding mechanisms. Here, we tested the possibility that specific post-translational modifications may involve residues exposed during the folding process by assessing the solvent accessibility of 87,138 post-translationally modified amino acids in the human proteome. Unexpectedly, we found that one-third of phosphorylated proteins present at least one phosphosite completely buried within the protein’s inner core. Computational and experimental analyses suggest that these cryptic phosphosites may become exposed during the folding process, where their modification could destabilize native structures and trigger protein degradation. Phylogenetic investigation also reveals that cryptic phosphosites are more conserved than surface-exposed phosphorylated residues. Finally, cross-referencing with cancer mutation databases suggests that phosphomimetic mutations in cryptic phosphosites can increase tumor fitness by inactivating specific onco-suppressors. These findings define a novel role for co-translational phosphorylation in shaping protein folding and expression, laying the groundwork for exploring the implications of cryptic phosphorylation in health and disease.
6.
Pradelli F; Minervini G; Venkatesh P; Azad S; Gomez H; Tosatto S C E
Mathematical modeling and simulation of tumor-induced angiogenesis in retinal hemangioblastoma Journal Article
In: PLOS Computational Biology, vol. 21, no. 9, 2025, (Cited by: 1; Open Access).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:105018034228,
title = {Mathematical modeling and simulation of tumor-induced angiogenesis in retinal hemangioblastoma},
author = {Franco Pradelli and Giovanni Minervini and Pradeep Venkatesh and Shorya Azad and Hector Gomez and Silvio C. E. Tosatto},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-105018034228&origin=inward},
doi = {10.1371/journal.pcbi.1012799},
year = {2025},
date = {2025-01-01},
journal = {PLOS Computational Biology},
volume = {21},
number = {9},
publisher = {Public Library of Science},
abstract = {Copyright: © 2025 Pradelli et al. This is an open access article distributed under the terms of the Creative Commons Attribution LicenseRetinal Hemangioblastoma (RH) is the most frequent manifestation of the von Hippel-Lindau syndrome (VHL), a rare disease associated with the germline mutation of the von Hippel-Lindau protein (pVHL). An emblematic feature of RH is the high vascularity, which is explained by the overexpression of angiogenic factors (AFs) arising from the pVHL impairment. The introduction of Optical Coherence Tomography Angiography (OCTA) allowed observing this feature with exceptional detail. Here, we combine OCTA images and a mechanistic model to investigate tumor growth and vascular development in a patient-specific way. We derived our model from the agreed pathology for RH and focused on the earliest stages of tumor-induced angiogenesis. Our simulations closely resemble the medical images, supporting the capability of our model to simulate vascular patterning in actual patients. Our results also suggest that angiogenesis in RH occurs upon reaching a critical dimension (around 200 μm), followed by the rapid formation of stable vascular networks. These findings open a new perspective on the crucial role of time in antiangiogenic therapy in RH, which has resulted in ineffective control. Indeed, it might be that when RH is diagnosed, angiogenesis is already too advanced to be effectively targeted with any effective means. Moreover, our simulations suggest that vascularization in RH is not a continuous process but an inconstant development with long, stable phases and rapid episodes of vascular sprouting.},
note = {Cited by: 1; Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Copyright: © 2025 Pradelli et al. This is an open access article distributed under the terms of the Creative Commons Attribution LicenseRetinal Hemangioblastoma (RH) is the most frequent manifestation of the von Hippel-Lindau syndrome (VHL), a rare disease associated with the germline mutation of the von Hippel-Lindau protein (pVHL). An emblematic feature of RH is the high vascularity, which is explained by the overexpression of angiogenic factors (AFs) arising from the pVHL impairment. The introduction of Optical Coherence Tomography Angiography (OCTA) allowed observing this feature with exceptional detail. Here, we combine OCTA images and a mechanistic model to investigate tumor growth and vascular development in a patient-specific way. We derived our model from the agreed pathology for RH and focused on the earliest stages of tumor-induced angiogenesis. Our simulations closely resemble the medical images, supporting the capability of our model to simulate vascular patterning in actual patients. Our results also suggest that angiogenesis in RH occurs upon reaching a critical dimension (around 200 μm), followed by the rapid formation of stable vascular networks. These findings open a new perspective on the crucial role of time in antiangiogenic therapy in RH, which has resulted in ineffective control. Indeed, it might be that when RH is diagnosed, angiogenesis is already too advanced to be effectively targeted with any effective means. Moreover, our simulations suggest that vascularization in RH is not a continuous process but an inconstant development with long, stable phases and rapid episodes of vascular sprouting.
7.
Damulewicz M; Gregoris F; Colaianni D; Cendron F; Biscontin A; Minervini G; Mazzotta G M
Cryptochrome interaction networks across different tissues in Drosophila melanogaster Journal Article
In: Biology Direct, vol. 20, no. 1, 2025, (Cited by: 0; Open Access).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:105023334728,
title = {Cryptochrome interaction networks across different tissues in Drosophila melanogaster},
author = {Milena Damulewicz and Francesco Gregoris and Davide Colaianni and Filippo Cendron and Alberto Biscontin and Giovanni Minervini and Gabriella M. Mazzotta},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-105023334728&origin=inward},
doi = {10.1186/s13062-025-00696-x},
year = {2025},
date = {2025-01-01},
journal = {Biology Direct},
volume = {20},
number = {1},
publisher = {BioMed Central Ltd},
abstract = {© The Author(s) 2025.Background: Drosophila CRYPTOCHROME (dCRY) is a blue light-sensitive protein involved in various biological processes, including photoreception, circadian rhythm regulation, synaptic plasticity, and magnetoreception. Its circadian function is strictly connected with light: upon light exposure, dCRY undergoes a conformational change, becoming active and binding to various proteins. However, it can also form complexes in the absence of light, with its function varying depending on the cell type in which it is expressed. Results: Here, we use an experimental approach based on co-immunoprecipitation followed by mass spectrometry analysis, obtaining the in vivo interactome of dCRY in two distinct cell populations - retina photoreceptors and glial cells - at two specific time points: just before lights-on (ZT0) and one hour after lights-on (ZT1). To gain deeper insights into the functional dynamics of dCRY, we constructed reliable protein-protein interaction networks in both cell types and across the two experimental conditions, revealing a complex landscape of interactions. Additionally, we explored the biological pathways associated with the identified dCRY interactors, highlighting several tissue- and time-specific enrichments. We focused on RNA-related pathways, indicating that dCRY and its interactors are involved in regulating RNA metabolism in photoreceptors at ZT0 and in glial cells at ZT1. Finally, as a case study, we further investigated the functions of the RNA-binding protein SQUID, found to interact with dCRY in both tissues. Notably, the impaired circadian locomotor behavior exhibited by Squid mutant flies accounts for the involvement of this hnRNP in the generation of the circadian rhythmicity. Conclusions: In conclusion, our work provides the first tissue- and time-specific dCRY interactome, offering valuable insights into previously unrecognized biological processes in which it may be involved. Specifically, its potential role in the regulation of RNA metabolism contributes crucial evidence concerning the relationship between the circadian clock and RNA metabolism, thereby laying the groundwork for future research in this area.},
note = {Cited by: 0; Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
© The Author(s) 2025.Background: Drosophila CRYPTOCHROME (dCRY) is a blue light-sensitive protein involved in various biological processes, including photoreception, circadian rhythm regulation, synaptic plasticity, and magnetoreception. Its circadian function is strictly connected with light: upon light exposure, dCRY undergoes a conformational change, becoming active and binding to various proteins. However, it can also form complexes in the absence of light, with its function varying depending on the cell type in which it is expressed. Results: Here, we use an experimental approach based on co-immunoprecipitation followed by mass spectrometry analysis, obtaining the in vivo interactome of dCRY in two distinct cell populations – retina photoreceptors and glial cells – at two specific time points: just before lights-on (ZT0) and one hour after lights-on (ZT1). To gain deeper insights into the functional dynamics of dCRY, we constructed reliable protein-protein interaction networks in both cell types and across the two experimental conditions, revealing a complex landscape of interactions. Additionally, we explored the biological pathways associated with the identified dCRY interactors, highlighting several tissue- and time-specific enrichments. We focused on RNA-related pathways, indicating that dCRY and its interactors are involved in regulating RNA metabolism in photoreceptors at ZT0 and in glial cells at ZT1. Finally, as a case study, we further investigated the functions of the RNA-binding protein SQUID, found to interact with dCRY in both tissues. Notably, the impaired circadian locomotor behavior exhibited by Squid mutant flies accounts for the involvement of this hnRNP in the generation of the circadian rhythmicity. Conclusions: In conclusion, our work provides the first tissue- and time-specific dCRY interactome, offering valuable insights into previously unrecognized biological processes in which it may be involved. Specifically, its potential role in the regulation of RNA metabolism contributes crucial evidence concerning the relationship between the circadian clock and RNA metabolism, thereby laying the groundwork for future research in this area.
2024
8.
Gregoris F; Minervini G; Tosatto S C E
In Silico Exploration of AHR-HIF Pathway Interplay: Implications for Therapeutic Targeting in ccRCC Journal Article
In: Genes, vol. 15, no. 9, 2024, (Cited by: 4; Open Access).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:85205114282,
title = {In Silico Exploration of AHR-HIF Pathway Interplay: Implications for Therapeutic Targeting in ccRCC},
author = {Francesco Gregoris and Giovanni Minervini and Silvio C. E. Tosatto},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-85205114282&origin=inward},
doi = {10.3390/genes15091167},
year = {2024},
date = {2024-01-01},
journal = {Genes},
volume = {15},
number = {9},
publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},
abstract = {© 2024 by the authors.The oxygen-sensing pathway is a crucial regulatory circuit that defines cellular conditions and is extensively exploited in cancer development. Pathogenic mutations in the von Hippel–Lindau (VHL) tumour suppressor impair its role as a master regulator of hypoxia-inducible factors (HIFs), leading to constitutive HIF activation and uncontrolled angiogenesis, increasing the risk of developing clear cell renal cell carcinoma (ccRCC). HIF hyperactivation can sequester HIF-1β, preventing the aryl hydrocarbon receptor (AHR) from correctly activating gene expression in response to endogenous and exogenous ligands such as TCDD (dioxins). In this study, we used protein–protein interaction networks and gene expression profiling to characterize the impact of VHL loss on AHR activity. Our findings reveal specific expression patterns of AHR interactors following exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and in ccRCC. We identified several AHR interactors significantly associated with poor survival rates in ccRCC patients. Notably, the upregulation of the androgen receptor (AR) and retinoblastoma-associated protein (RB1) by TCDD, coupled with their respective downregulation in ccRCC and association with poor survival rates, suggests novel therapeutic targets. The strategic activation of the AHR via selective AHR modulators (SAhRMs) could stimulate its anticancer activity, specifically targeting RB1 and AR to reduce cell cycle progression and metastasis formation in ccRCC. Our study provides comprehensive insights into the complex interplay between the AHR and HIF pathways in ccRCC pathogenesis, offering novel strategies for targeted therapeutic interventions.},
note = {Cited by: 4; Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
© 2024 by the authors.The oxygen-sensing pathway is a crucial regulatory circuit that defines cellular conditions and is extensively exploited in cancer development. Pathogenic mutations in the von Hippel–Lindau (VHL) tumour suppressor impair its role as a master regulator of hypoxia-inducible factors (HIFs), leading to constitutive HIF activation and uncontrolled angiogenesis, increasing the risk of developing clear cell renal cell carcinoma (ccRCC). HIF hyperactivation can sequester HIF-1β, preventing the aryl hydrocarbon receptor (AHR) from correctly activating gene expression in response to endogenous and exogenous ligands such as TCDD (dioxins). In this study, we used protein–protein interaction networks and gene expression profiling to characterize the impact of VHL loss on AHR activity. Our findings reveal specific expression patterns of AHR interactors following exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and in ccRCC. We identified several AHR interactors significantly associated with poor survival rates in ccRCC patients. Notably, the upregulation of the androgen receptor (AR) and retinoblastoma-associated protein (RB1) by TCDD, coupled with their respective downregulation in ccRCC and association with poor survival rates, suggests novel therapeutic targets. The strategic activation of the AHR via selective AHR modulators (SAhRMs) could stimulate its anticancer activity, specifically targeting RB1 and AR to reduce cell cycle progression and metastasis formation in ccRCC. Our study provides comprehensive insights into the complex interplay between the AHR and HIF pathways in ccRCC pathogenesis, offering novel strategies for targeted therapeutic interventions.
9.
Conte A D; Camagni G F; Clementel D; Minervini G; Monzon A M; Ferrari C; Piovesan D; Tosatto S C E
RING 4.0: Faster residue interaction networks with novel interaction types across over 35,000 different chemical structures Journal Article
In: Nucleic Acids Research, vol. 52, no. W1, pp. W306-W312, 2024, (Cited by: 75; Open Access).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:85197788039,
title = {RING 4.0: Faster residue interaction networks with novel interaction types across over 35,000 different chemical structures},
author = {Alessio Del Conte and Giorgia F Camagni and Damiano Clementel and Giovanni Minervini and Alexander Miguel Monzon and Carlo Ferrari and Damiano Piovesan and Silvio C. E Tosatto},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-85197788039&origin=inward},
doi = {10.1093/nar/gkae337},
year = {2024},
date = {2024-01-01},
journal = {Nucleic Acids Research},
volume = {52},
number = {W1},
pages = {W306-W312},
publisher = {Oxford University Press},
abstract = {© 2024 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.Residue interaction networks (RINs) are a valuable approach for representing contacts in protein structures. RINs have been widely used in various research areas, including the analysis of mutation effects, domain-domain communication, catalytic activity, and molecular dynamics simulations. The RING server is a powerful tool to calculate non-covalent molecular interactions based on geometrical parameters, providing high-quality and reliable results. Here, we introduce RING 4.0, which includes significant enhancements for identifying both covalent and non-covalent bonds in protein structures. It now encompasses seven different interaction types, with the addition of π-hydrogen, halogen bonds and metal ion coordination sites. The definitions of all available bond types have also been refined and RING can now process the complete PDB chemical component dictionary (over 35000 different molecules) which provides atom names and covalent connectivity information for all known ligands. Optimization of the software has improved execution time by an order of magnitude. The RING web server has been redesigned to provide a more engaging and interactive user experience, incorporating new visualization tools. Users can now visualize all types of interactions simultaneously in the structure viewer and network component. The web server, including extensive help and tutorials, is available from URL: https://ring.biocomputingup.it/.},
note = {Cited by: 75; Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
© 2024 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.Residue interaction networks (RINs) are a valuable approach for representing contacts in protein structures. RINs have been widely used in various research areas, including the analysis of mutation effects, domain-domain communication, catalytic activity, and molecular dynamics simulations. The RING server is a powerful tool to calculate non-covalent molecular interactions based on geometrical parameters, providing high-quality and reliable results. Here, we introduce RING 4.0, which includes significant enhancements for identifying both covalent and non-covalent bonds in protein structures. It now encompasses seven different interaction types, with the addition of π-hydrogen, halogen bonds and metal ion coordination sites. The definitions of all available bond types have also been refined and RING can now process the complete PDB chemical component dictionary (over 35000 different molecules) which provides atom names and covalent connectivity information for all known ligands. Optimization of the software has improved execution time by an order of magnitude. The RING web server has been redesigned to provide a more engaging and interactive user experience, incorporating new visualization tools. Users can now visualize all types of interactions simultaneously in the structure viewer and network component. The web server, including extensive help and tutorials, is available from URL: https://ring.biocomputingup.it/.
10.
Bellanda M; Damulewicz M; Zambelli B; Costanzi E; Gregoris F; Mammi S; Tosatto S C E; Costa R; Minervini G; Mazzotta G M
A PDZ scaffolding/CaM-mediated pathway in Cryptochrome signaling Journal Article
In: Protein Science, vol. 33, no. 3, 2024, (Cited by: 3; Open Access).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:85185346556,
title = {A PDZ scaffolding/CaM-mediated pathway in Cryptochrome signaling},
author = {Massimo Bellanda and Milena Damulewicz and Barbara Zambelli and Elisa Costanzi and Francesco Gregoris and Stefano Mammi and Silvio C. E. Tosatto and Rodolfo Costa and Giovanni Minervini and Gabriella M. Mazzotta},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-85185346556&origin=inward},
doi = {10.1002/pro.4914},
year = {2024},
date = {2024-01-01},
journal = {Protein Science},
volume = {33},
number = {3},
publisher = {John Wiley and Sons Inc},
abstract = {© 2024 The Protein Society.Cryptochromes are cardinal constituents of the circadian clock, which orchestrates daily physiological rhythms in living organisms. A growing body of evidence points to their participation in pathways that have not traditionally been associated with circadian clock regulation, implying that cryptochromes may be subject to modulation by multiple signaling mechanisms. In this study, we demonstrate that human CRY2 (hCRY2) forms a complex with the large, modular scaffolding protein known as Multi-PDZ Domain Protein 1 (MUPP1). This interaction is facilitated by the calcium-binding protein Calmodulin (CaM) in a calcium-dependent manner. Our findings suggest a novel cooperative mechanism for the regulation of mammalian cryptochromes, mediated by calcium ions (Ca2+) and CaM. We propose that this Ca2+/CaM-mediated signaling pathway may be an evolutionarily conserved mechanism that has been maintained from Drosophila to mammals, most likely in relation to its potential role in the broader context of cryptochrome function and regulation. Further, the understanding of cryptochrome interactions with other proteins and signaling pathways could lead to a better definition of its role within the intricate network of molecular interactions that govern circadian rhythms.},
note = {Cited by: 3; Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
© 2024 The Protein Society.Cryptochromes are cardinal constituents of the circadian clock, which orchestrates daily physiological rhythms in living organisms. A growing body of evidence points to their participation in pathways that have not traditionally been associated with circadian clock regulation, implying that cryptochromes may be subject to modulation by multiple signaling mechanisms. In this study, we demonstrate that human CRY2 (hCRY2) forms a complex with the large, modular scaffolding protein known as Multi-PDZ Domain Protein 1 (MUPP1). This interaction is facilitated by the calcium-binding protein Calmodulin (CaM) in a calcium-dependent manner. Our findings suggest a novel cooperative mechanism for the regulation of mammalian cryptochromes, mediated by calcium ions (Ca2+) and CaM. We propose that this Ca2+/CaM-mediated signaling pathway may be an evolutionarily conserved mechanism that has been maintained from Drosophila to mammals, most likely in relation to its potential role in the broader context of cryptochrome function and regulation. Further, the understanding of cryptochrome interactions with other proteins and signaling pathways could lead to a better definition of its role within the intricate network of molecular interactions that govern circadian rhythms.
